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RJR: Recommended Bibliography 19 Feb 2025 at 01:46 Created:
Ecological Informatics
Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are the National Science Foundation's Datanet , DataONE and Data Conservancy projects.
Created with PubMed® Query: ( "ecology OR ecological" AND ("data management" OR informatics) NOT "assays for monitoring autophagy" ) NOT pmcbook NOT ispreviousversion
Citations The Papers (from PubMed®)
RevDate: 2025-02-18
CmpDate: 2025-02-18
DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.
Ecology, 106(2):e4519.
Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.
Additional Links: PMID-39963945
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PubMed:
Citation:
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@article {pmid39963945,
year = {2025},
author = {Giglio, VJ and Adelir-Alves, J and Balzaretti Merino, N and Bravo-Olivas, ML and Camp, EF and Casoli, E and Chávez-Dagostino, RM and Ferretti, E and Fraser, D and Grillo, AC and Jiménez-Guiérrez, S and Leite, KL and Lucrezi, S and Luiz, OJ and Luna-Pérez, B and McBride, J and Milanese, M and Moity, N and Pinheiro, JV and Renfro, B and Roche, R and Saliba, BM and Sara, A and Schiavetti, A and Toso, Y and Valle-Pérez, C and Ferreira, CEL},
title = {DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.},
journal = {Ecology},
volume = {106},
number = {2},
pages = {e4519},
doi = {10.1002/ecy.4519},
pmid = {39963945},
issn = {1939-9170},
support = {17/22273-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 111.210/2014//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Diving/physiology ; *Coral Reefs ; *Databases, Factual ; *Recreation ; Animals ; Humans ; Male ; Female ; Time Factors ; },
abstract = {Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Diving/physiology
*Coral Reefs
*Databases, Factual
*Recreation
Animals
Humans
Male
Female
Time Factors
RevDate: 2025-02-18
A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.
Molecular ecology resources [Epub ahead of print].
Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.
Additional Links: PMID-39963041
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PubMed:
Citation:
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@article {pmid39963041,
year = {2025},
author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE},
title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14088},
doi = {10.1111/1755-0998.14088},
pmid = {39963041},
issn = {1755-0998},
support = {INV-009416/GATES/Bill & Melinda Gates Foundation/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; },
abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.
Journal of visualized experiments : JoVE.
Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.
Additional Links: PMID-39960184
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PubMed:
Citation:
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@article {pmid39960184,
year = {2025},
author = {Ferdousee, S and Alam, MS and Hwangbo, M and Kim, J},
title = {Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {215},
pages = {},
doi = {10.3791/67715},
pmid = {39960184},
issn = {1940-087X},
mesh = {*Wetlands ; *Methane/metabolism ; Texas ; Geographic Information Systems ; },
abstract = {Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Wetlands
*Methane/metabolism
Texas
Geographic Information Systems
RevDate: 2025-02-17
Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).
Biology open pii:366992 [Epub ahead of print].
Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g., substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.
Additional Links: PMID-39957502
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PubMed:
Citation:
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@article {pmid39957502,
year = {2025},
author = {Latini, L and Burini, G and Mazza, V and Grignani, G and De Donno, R and Bello, E and Tricarico, E and Malavasi, S and Nascetti, G and Canestrelli, D and Carere, C},
title = {Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.061901},
pmid = {39957502},
issn = {2046-6390},
support = {//Universite degli Studi della Tuscia/ ; //Universite degli Studi di Firenze/ ; //Universite Ca' Foscari Venezia/ ; },
abstract = {Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g., substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.},
}
RevDate: 2025-02-15
Pollution control mechanism of national water network with water quality differences based on differential game and case study.
Scientific reports, 15(1):5588.
The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.
Additional Links: PMID-39955351
PubMed:
Citation:
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@article {pmid39955351,
year = {2025},
author = {Yang, Y and Yang, Y and Yang, S and Zhang, J},
title = {Pollution control mechanism of national water network with water quality differences based on differential game and case study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5588},
pmid = {39955351},
issn = {2045-2322},
support = {51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; },
abstract = {The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.},
}
RevDate: 2025-02-14
The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.
Insect molecular biology [Epub ahead of print].
Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.
Additional Links: PMID-39952648
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PubMed:
Citation:
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@article {pmid39952648,
year = {2025},
author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G},
title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12983},
pmid = {39952648},
issn = {1365-2583},
support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; },
abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.},
}
RevDate: 2025-02-14
The rapid diagnosis of intraamniotic infection with nanopore sequencing.
American journal of obstetrics and gynecology pii:S0002-9378(25)00091-2 [Epub ahead of print].
BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction. However, both methods take time, and results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.
OBJECTIVES: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation; and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.
STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin-6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin-6 <2.6 ng/mL and no microorganisms in the amniotic cavity determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin-6 ≥2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin-6 ≥2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a midtrimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.
RESULTS: 1) 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% CI, 4.8-75.4), negative likelihood ratio of 0.1 (95% CI, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection [prevalence, 17% (9/52)]; 2) the microbial load determined by 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin-6 concentration; Spearman's correlation 0.9; p = 0.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.
CONCLUSION: 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.
Additional Links: PMID-39952543
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PubMed:
Citation:
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@article {pmid39952543,
year = {2025},
author = {Chaemsaithong, P and Romero, R and Pongchaikul, P and Warintaksa, P and Mongkolsuk, P and Bhuwapathanapun, M and Kotchompoo, K and Nimsamer, P and Kruasuwan, W and Amnuaykiatlert, O and Vivithanaporn, P and Meyyazhagan, A and Awonuga, A and Settacomkul, R and Singhsnaeh, A and Laolerd, W and Santanirand, P and Thaipisuttikul, I and Wongsurawat, T and Jenjaroenpun, P},
title = {The rapid diagnosis of intraamniotic infection with nanopore sequencing.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.02.011},
pmid = {39952543},
issn = {1097-6868},
abstract = {BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction. However, both methods take time, and results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.
OBJECTIVES: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation; and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.
STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin-6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin-6 <2.6 ng/mL and no microorganisms in the amniotic cavity determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin-6 ≥2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin-6 ≥2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a midtrimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.
RESULTS: 1) 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% CI, 4.8-75.4), negative likelihood ratio of 0.1 (95% CI, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection [prevalence, 17% (9/52)]; 2) the microbial load determined by 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin-6 concentration; Spearman's correlation 0.9; p = 0.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.
CONCLUSION: 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.},
}
RevDate: 2025-02-14
Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.
Environmental research pii:S0013-9351(25)00371-8 [Epub ahead of print].
Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.
Additional Links: PMID-39952461
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PubMed:
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@article {pmid39952461,
year = {2025},
author = {Shi, W and Lu, P and Yang, H and Han, J and Wang, Q},
title = {Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121120},
doi = {10.1016/j.envres.2025.121120},
pmid = {39952461},
issn = {1096-0953},
abstract = {Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.
Ecotoxicology and environmental safety, 290:117731.
Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.
Additional Links: PMID-39823671
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PubMed:
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@article {pmid39823671,
year = {2025},
author = {Liu, T and Wang, M and Wang, M and Xiong, Q and Jia, L and Ma, W and Sui, S and Wu, W and Guo, X},
title = {Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117731},
doi = {10.1016/j.ecoenv.2025.117731},
pmid = {39823671},
issn = {1090-2414},
mesh = {*Soil Pollutants/analysis ; *Metals, Heavy/analysis ; China ; *Environmental Monitoring/methods ; *Algorithms ; Geographic Information Systems ; Soil/chemistry ; Risk Assessment ; Environmental Pollution/analysis/statistics & numerical data ; Monte Carlo Method ; Principal Component Analysis ; Random Forest ; },
abstract = {Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Soil Pollutants/analysis
*Metals, Heavy/analysis
China
*Environmental Monitoring/methods
*Algorithms
Geographic Information Systems
Soil/chemistry
Risk Assessment
Environmental Pollution/analysis/statistics & numerical data
Monte Carlo Method
Principal Component Analysis
Random Forest
RevDate: 2025-02-15
CmpDate: 2025-02-15
Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.
Ecotoxicology and environmental safety, 290:117635.
Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.
Additional Links: PMID-39742640
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PubMed:
Citation:
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@article {pmid39742640,
year = {2025},
author = {Zhang, H and Dong, S and Shan, H and Yang, C and Wang, F},
title = {Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117635},
doi = {10.1016/j.ecoenv.2024.117635},
pmid = {39742640},
issn = {1090-2414},
mesh = {Animals ; *Brachyura/physiology/drug effects/growth & development/genetics ; *Salinity ; *Aquaculture ; Life History Traits ; Reproduction/drug effects ; Fresh Water ; Female ; Oxidative Stress ; Water Pollutants, Chemical/toxicity ; Osmoregulation ; Multiomics ; },
abstract = {Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Brachyura/physiology/drug effects/growth & development/genetics
*Salinity
*Aquaculture
Life History Traits
Reproduction/drug effects
Fresh Water
Female
Oxidative Stress
Water Pollutants, Chemical/toxicity
Osmoregulation
Multiomics
RevDate: 2025-02-14
CmpDate: 2025-02-14
Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.
Genome research, 35(2):368-378 pii:gr.279825.124.
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.
Additional Links: PMID-39730187
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PubMed:
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@article {pmid39730187,
year = {2025},
author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z},
title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.},
journal = {Genome research},
volume = {35},
number = {2},
pages = {368-378},
doi = {10.1101/gr.279825.124},
pmid = {39730187},
issn = {1549-5469},
mesh = {Animals ; *Ruminants/microbiology ; *Deep Learning ; *Fungi/genetics/classification ; Rumen/microbiology/parasitology ; Databases, Protein ; Metagenome ; Metagenomics/methods ; Eukaryota/genetics/classification ; Gastrointestinal Microbiome ; Computational Biology/methods ; },
abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Ruminants/microbiology
*Deep Learning
*Fungi/genetics/classification
Rumen/microbiology/parasitology
Databases, Protein
Metagenome
Metagenomics/methods
Eukaryota/genetics/classification
Gastrointestinal Microbiome
Computational Biology/methods
RevDate: 2025-02-14
CmpDate: 2025-02-14
DNAdesign: feature-aware in silico design of synthetic DNA through mutation.
Bioinformatics (Oxford, England), 41(2):.
MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.
RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.
The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.
Additional Links: PMID-39891349
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PubMed:
Citation:
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@article {pmid39891349,
year = {2025},
author = {Wang, Y and Li, J and Chiu, TP and Gompel, N and Rohs, R},
title = {DNAdesign: feature-aware in silico design of synthetic DNA through mutation.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {2},
pages = {},
doi = {10.1093/bioinformatics/btaf052},
pmid = {39891349},
issn = {1367-4811},
support = {RGP0021/2018//Human Frontier Science Program/ ; },
mesh = {*DNA/chemistry/genetics ; *Mutation ; *Software ; Nucleic Acid Conformation ; Binding Sites ; Computer Simulation ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; },
abstract = {MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.
RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.
The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*DNA/chemistry/genetics
*Mutation
*Software
Nucleic Acid Conformation
Binding Sites
Computer Simulation
Sequence Analysis, DNA/methods
Computational Biology/methods
RevDate: 2025-02-14
CmpDate: 2025-02-14
The Hidden Global Diversity of the Yeast Genus Carlosrosaea: A Biodiversity Databases Perspective.
Yeast (Chichester, England), 41(11-12):658-667.
Biodiversity gaps in microorganisms, such as yeasts, blur our understanding of microbial diversity, introducing biases in their biogeography, ecology, and taxonomy. The genus Carlosrosaea is a potential plant growth booster, yet it is still a little-known yeast group. Considering that databases like GBIF and GenBank are powerful tools for exploring biodiversity data, we aimed to map the geographic distribution, ecological patterns, and taxonomic potential of the genus Carlosrosaea. We found 176 records of the genus, with about 70% associated with plant material, mostly leaves. Furthermore, 55% of the records pertained to the tropical region and only 12% to the temperate. The data indicates the existence of more than a dozen possible new species of the genus, cataloged yet undescribed. This study advances our understanding of the geographic, ecological, and taxonomic aspects of Carlosrosaea. It also highlights how public databases and literature reviews provide accessible ways to analyze information about microbial groups with limited data.
Additional Links: PMID-39623597
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PubMed:
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@article {pmid39623597,
year = {2024},
author = {Félix, CR and Navarro, HMC and Landell, MF},
title = {The Hidden Global Diversity of the Yeast Genus Carlosrosaea: A Biodiversity Databases Perspective.},
journal = {Yeast (Chichester, England)},
volume = {41},
number = {11-12},
pages = {658-667},
doi = {10.1002/yea.3986},
pmid = {39623597},
issn = {1097-0061},
support = {//This work was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, number of grants 475378/2013-0, 312889/2021-6 and 311553/2018-4), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de amparo a Pesquisa de Alagoas (FAPEAL). This work is also part of the project "INCT Yeasts: Biodiversity, preservation and biotechnological innovation", funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant #406564/2022-1./ ; },
mesh = {*Biodiversity ; Phylogeny ; Saccharomycetales/classification/genetics/isolation & purification ; Databases, Factual ; },
abstract = {Biodiversity gaps in microorganisms, such as yeasts, blur our understanding of microbial diversity, introducing biases in their biogeography, ecology, and taxonomy. The genus Carlosrosaea is a potential plant growth booster, yet it is still a little-known yeast group. Considering that databases like GBIF and GenBank are powerful tools for exploring biodiversity data, we aimed to map the geographic distribution, ecological patterns, and taxonomic potential of the genus Carlosrosaea. We found 176 records of the genus, with about 70% associated with plant material, mostly leaves. Furthermore, 55% of the records pertained to the tropical region and only 12% to the temperate. The data indicates the existence of more than a dozen possible new species of the genus, cataloged yet undescribed. This study advances our understanding of the geographic, ecological, and taxonomic aspects of Carlosrosaea. It also highlights how public databases and literature reviews provide accessible ways to analyze information about microbial groups with limited data.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Biodiversity
Phylogeny
Saccharomycetales/classification/genetics/isolation & purification
Databases, Factual
RevDate: 2025-02-14
The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).
Wellcome open research, 8:72.
We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.
Additional Links: PMID-39949385
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@article {pmid39949385,
year = {2023},
author = {Lohse, K and , and , and , and Vila, R and , },
title = {The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {72},
pmid = {39949385},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.},
}
RevDate: 2025-02-13
Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.
BMC psychiatry, 25(1):122.
People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.
Additional Links: PMID-39948527
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@article {pmid39948527,
year = {2025},
author = {Rakshasa-Loots, AM and Steyn, C and Swiffen, D and Marwick, KFM and Semple, RK and Reynolds, RM and Burgess, K and Lawrie, SM and Lightman, SL and Luz, S and Smith, DJ},
title = {Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {122},
pmid = {39948527},
issn = {1471-244X},
support = {MR/Z503563/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
The population genetics of convergent adaptation in maize and teosinte is not locally restricted.
eLife, 12: pii:92405.
What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.
Additional Links: PMID-39945053
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@article {pmid39945053,
year = {2025},
author = {Tittes, S and Lorant, A and McGinty, SP and Holland, JB and de Jesus Sánchez-González, J and Seetharam, A and Tenaillon, M and Ross-Ibarra, J},
title = {The population genetics of convergent adaptation in maize and teosinte is not locally restricted.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.92405},
pmid = {39945053},
issn = {2050-084X},
support = {1822330//National Science Foundation/ ; 1238014//National Science Foundation/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture/ ; },
mesh = {*Zea mays/genetics/physiology ; *Adaptation, Physiological/genetics ; *Genetics, Population ; Genetic Variation ; Selection, Genetic ; },
abstract = {What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Zea mays/genetics/physiology
*Adaptation, Physiological/genetics
*Genetics, Population
Genetic Variation
Selection, Genetic
RevDate: 2025-02-13
CmpDate: 2025-02-13
Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.
Sensors (Basel, Switzerland), 25(3): pii:s25030937.
Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.
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@article {pmid39943576,
year = {2025},
author = {Cleveland, P and Morrison, A},
title = {Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {3},
pages = {},
doi = {10.3390/s25030937},
pmid = {39943576},
issn = {1424-8220},
support = {2023//Annual Award, School of Future Environments, Auckland University of Techolology/ ; },
mesh = {*Plastics ; *Rivers/chemistry ; *Environmental Monitoring/methods ; Vietnam ; Water Pollutants, Chemical/analysis ; Water Pollution/analysis ; Geographic Information Systems ; Ecosystem ; },
abstract = {Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Plastics
*Rivers/chemistry
*Environmental Monitoring/methods
Vietnam
Water Pollutants, Chemical/analysis
Water Pollution/analysis
Geographic Information Systems
Ecosystem
RevDate: 2025-02-12
CmpDate: 2025-02-13
Environmental impact on the genome shaping of putative new Streptomyces species.
BMC microbiology, 25(1):72.
BACKGROUND: The bacterial evolution and the emergence of new species are likely influenced by multiple forces, including long-term environmental pressure such as living in extreme conditions. In this study, the genomes of two potentially new Streptomyces species isolated from a former mine heap in Tarnowskie Góry in Poland, were analyzed.
RESULTS: A bioinformatic approach revealed notable phylogenetic and metabolic differences between the studied Streptomyces strains, despite originating from the same environment. While both strains are characterized by genetic features common to actinomycetes, additional unique biosynthetic gene clusters were also predicted in their genomes. The comparative genomic analysis with other Streptomyces spp. revealed a high conservation in heavy metal adaptive mechanisms, indicating a preadaptation to extreme conditions. The difference observed in the cad and mer operons could be attributed to the specific adaptations to heavy metal contamination. The high metal tolerance of examined strains was also confirmed by an agar dilution assay in the presence of several heavy metals. The confirmed siderophore production represents an additional mechanism allowing streptomycetes to survive in extreme conditions. On the other hand, both of studied genomes show significant differences in energy acquisition processes and the production of putative novel secondary metabolites. The isolates showed these differences not only among themselves but also compared to other Streptomyces species, indicating their uniqueness.
CONCLUSIONS: Our results demonstrate that extreme environmental conditions can lead to the development of various adaptation mechanisms in the Streptomyces spp. Furthermore, the results indicate that diverse Streptomyces species have developed conserved adaptation mechanisms against the heavy metals under extreme conditions, indicating the emergence of preadaptations that allow bacteria to respond rapidly to polluted environments and evolve their genomes accordingly up to the evolution of new species.
Additional Links: PMID-39939924
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@article {pmid39939924,
year = {2025},
author = {Lorková, Z and Cimermanová, M and Piknová, M and Adhvaryu, S and Pristaš, P and Kisková, J},
title = {Environmental impact on the genome shaping of putative new Streptomyces species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {72},
pmid = {39939924},
issn = {1471-2180},
support = {VEGA 1/0779/21//Grant Agency of the Ministry of Education, Science, Research and Sport, Slovak Republic and the Slovak Academy of Sciences/ ; },
mesh = {*Streptomyces/genetics/classification/metabolism/isolation & purification ; *Genome, Bacterial/genetics ; *Phylogeny ; *Metals, Heavy/metabolism ; Siderophores/metabolism ; Multigene Family ; Poland ; Secondary Metabolism/genetics ; Adaptation, Physiological/genetics ; Mining ; Computational Biology/methods ; },
abstract = {BACKGROUND: The bacterial evolution and the emergence of new species are likely influenced by multiple forces, including long-term environmental pressure such as living in extreme conditions. In this study, the genomes of two potentially new Streptomyces species isolated from a former mine heap in Tarnowskie Góry in Poland, were analyzed.
RESULTS: A bioinformatic approach revealed notable phylogenetic and metabolic differences between the studied Streptomyces strains, despite originating from the same environment. While both strains are characterized by genetic features common to actinomycetes, additional unique biosynthetic gene clusters were also predicted in their genomes. The comparative genomic analysis with other Streptomyces spp. revealed a high conservation in heavy metal adaptive mechanisms, indicating a preadaptation to extreme conditions. The difference observed in the cad and mer operons could be attributed to the specific adaptations to heavy metal contamination. The high metal tolerance of examined strains was also confirmed by an agar dilution assay in the presence of several heavy metals. The confirmed siderophore production represents an additional mechanism allowing streptomycetes to survive in extreme conditions. On the other hand, both of studied genomes show significant differences in energy acquisition processes and the production of putative novel secondary metabolites. The isolates showed these differences not only among themselves but also compared to other Streptomyces species, indicating their uniqueness.
CONCLUSIONS: Our results demonstrate that extreme environmental conditions can lead to the development of various adaptation mechanisms in the Streptomyces spp. Furthermore, the results indicate that diverse Streptomyces species have developed conserved adaptation mechanisms against the heavy metals under extreme conditions, indicating the emergence of preadaptations that allow bacteria to respond rapidly to polluted environments and evolve their genomes accordingly up to the evolution of new species.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Streptomyces/genetics/classification/metabolism/isolation & purification
*Genome, Bacterial/genetics
*Phylogeny
*Metals, Heavy/metabolism
Siderophores/metabolism
Multigene Family
Poland
Secondary Metabolism/genetics
Adaptation, Physiological/genetics
Mining
Computational Biology/methods
RevDate: 2025-02-13
CmpDate: 2025-02-13
Mobile Applications to Support Multiple Sclerosis Communities: The Post-COVID-19 Scenario.
Telemedicine journal and e-health : the official journal of the American Telemedicine Association, 30(6):e1615-e1628.
Introduction: The increase in the use of mobile apps since the COVID-19 pandemic, even among people with multiple sclerosis (PwMS) and health care providers (HCPs), has enabled access to reliable information, symptoms monitoring and management, and social connections. The pandemic has undoubtedly contributed to the acceleration of the "digital revolution." But how far has it progressed for the MS communities? Methods: Italian Google Play and App Store were queried, selecting MS-specific apps in English or Italian language and usable by a wide public. Results: Fifty-four (n = 54) MS-specific apps were identified; most were PwMS-oriented (83%), free of charge (94%), and in English language (76%). The 45 PwMS-oriented apps focused on increasing MS knowledge (71%), tracking symptoms (33%), and promoting networking with peers or HCPs (38%). The 13 HCPs-oriented tools addressed education and updates on MS (62%), disease assessment and management (54%), and research (15%). Google Search tool was also queried to find non-MS-specific apps to fulfill some unmet domains (as sleep, pain, sexual or mental health). Twenty-four additional apps were listed to provide a valuable contribution. Conclusion: The "digital revolution" led to increasingly customized tools for PwMS, especially as m-health or social-networking apps. However, apps to support other specific MS-relevant domains, appealing HCPs-oriented apps, and specific mobile tools for MS caregivers are still lacking. The absence of data assessing the usability and quality of MS apps in ecologically contexts leads to not reliable conclusions about potential benefits. A strong dialogue between MS communities and the digital industry is encouraged to fill this gap.
Additional Links: PMID-38452336
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@article {pmid38452336,
year = {2024},
author = {Vacchi, L and Zirone, E and Strina, V and Cavaletti, G and Ferrarese, C},
title = {Mobile Applications to Support Multiple Sclerosis Communities: The Post-COVID-19 Scenario.},
journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association},
volume = {30},
number = {6},
pages = {e1615-e1628},
doi = {10.1089/tmj.2023.0515},
pmid = {38452336},
issn = {1556-3669},
mesh = {Humans ; Access to Information ; COVID-19/epidemiology/prevention & control ; *Digital Health/trends ; Health Knowledge, Attitudes, Practice ; Italy/epidemiology ; *Mobile Applications/trends ; *Multiple Sclerosis/diagnosis/therapy ; Social Networking ; *Telemedicine/trends ; },
abstract = {Introduction: The increase in the use of mobile apps since the COVID-19 pandemic, even among people with multiple sclerosis (PwMS) and health care providers (HCPs), has enabled access to reliable information, symptoms monitoring and management, and social connections. The pandemic has undoubtedly contributed to the acceleration of the "digital revolution." But how far has it progressed for the MS communities? Methods: Italian Google Play and App Store were queried, selecting MS-specific apps in English or Italian language and usable by a wide public. Results: Fifty-four (n = 54) MS-specific apps were identified; most were PwMS-oriented (83%), free of charge (94%), and in English language (76%). The 45 PwMS-oriented apps focused on increasing MS knowledge (71%), tracking symptoms (33%), and promoting networking with peers or HCPs (38%). The 13 HCPs-oriented tools addressed education and updates on MS (62%), disease assessment and management (54%), and research (15%). Google Search tool was also queried to find non-MS-specific apps to fulfill some unmet domains (as sleep, pain, sexual or mental health). Twenty-four additional apps were listed to provide a valuable contribution. Conclusion: The "digital revolution" led to increasingly customized tools for PwMS, especially as m-health or social-networking apps. However, apps to support other specific MS-relevant domains, appealing HCPs-oriented apps, and specific mobile tools for MS caregivers are still lacking. The absence of data assessing the usability and quality of MS apps in ecologically contexts leads to not reliable conclusions about potential benefits. A strong dialogue between MS communities and the digital industry is encouraged to fill this gap.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Access to Information
COVID-19/epidemiology/prevention & control
*Digital Health/trends
Health Knowledge, Attitudes, Practice
Italy/epidemiology
*Mobile Applications/trends
*Multiple Sclerosis/diagnosis/therapy
Social Networking
*Telemedicine/trends
RevDate: 2025-02-12
Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.
Journal of environmental management, 376:124505 pii:S0301-4797(25)00481-5 [Epub ahead of print].
The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.
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@article {pmid39938295,
year = {2025},
author = {Zhuo, W and Wu, N and Shi, R and Cui, Y and Zhang, C and Liu, S and Zhu, F and Zhang, B and Liu, P},
title = {Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124505},
doi = {10.1016/j.jenvman.2025.124505},
pmid = {39938295},
issn = {1095-8630},
abstract = {The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.},
}
RevDate: 2025-02-12
Digital health equity frameworks and key concepts: a scoping review.
Journal of the American Medical Informatics Association : JAMIA pii:8010284 [Epub ahead of print].
OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.
MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.
RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.
DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.
CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.
Additional Links: PMID-39936843
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@article {pmid39936843,
year = {2025},
author = {Kim, KK and Backonja, U},
title = {Digital health equity frameworks and key concepts: a scoping review.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {},
number = {},
pages = {},
doi = {10.1093/jamia/ocaf017},
pmid = {39936843},
issn = {1527-974X},
support = {//The MITRE Innovation Program/ ; //MITRE Corporation/ ; },
abstract = {OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.
MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.
RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.
DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.
CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.},
}
RevDate: 2025-02-12
CmpDate: 2025-02-12
[Reformulations in the national mental health policy: analysis of assistance data in the period from 2012 to 2022].
Ciencia & saude coletiva, 30(2):e13372023.
This article aims to analyze data on care in the field of public mental healthcare in Brazil from 2012 to 2022, corresponding to the years before and after the implementation of the New Mental Health Policy. For this purpose, quantitative methodology, of the longitudinal ecological study type, was used. Data was extracted for the period from 2012 to 2022. The sources used were Health Information Systems. The data was compiled into time series and analyzed using descriptive statistical techniques. The results pointed to the enhancement of outpatient services and a decrease in the expansion of Psychosocial Care Centers and Primary Care facilities after 2017, indicating compliance with the New Policy guidelines to deprioritize territorial and community-based services. The number of psychiatric hospitals showed little variation for the entire period, indicating not only alignment with the strengthening of hospital institutions indicated in the New Policy, but also weaknesses in the deinstitutionalization policy of the period prior to 2017. This study concludes that the effects of the changes in national policies on the organization, management and execution of the health system can be seen, but at the same time there is continuity in various aspects.
Additional Links: PMID-39936690
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@article {pmid39936690,
year = {2025},
author = {Krefer, LT and Oliveira, WF},
title = {[Reformulations in the national mental health policy: analysis of assistance data in the period from 2012 to 2022].},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {2},
pages = {e13372023},
doi = {10.1590/1413-81232025302.13372023},
pmid = {39936690},
issn = {1678-4561},
mesh = {Brazil ; Humans ; *Health Policy ; *Mental Health Services/organization & administration ; *Hospitals, Psychiatric/organization & administration/statistics & numerical data ; Longitudinal Studies ; *Deinstitutionalization/trends ; Primary Health Care/organization & administration ; Mental Health ; Ambulatory Care/statistics & numerical data ; Health Care Reform ; Health Information Systems/organization & administration ; },
abstract = {This article aims to analyze data on care in the field of public mental healthcare in Brazil from 2012 to 2022, corresponding to the years before and after the implementation of the New Mental Health Policy. For this purpose, quantitative methodology, of the longitudinal ecological study type, was used. Data was extracted for the period from 2012 to 2022. The sources used were Health Information Systems. The data was compiled into time series and analyzed using descriptive statistical techniques. The results pointed to the enhancement of outpatient services and a decrease in the expansion of Psychosocial Care Centers and Primary Care facilities after 2017, indicating compliance with the New Policy guidelines to deprioritize territorial and community-based services. The number of psychiatric hospitals showed little variation for the entire period, indicating not only alignment with the strengthening of hospital institutions indicated in the New Policy, but also weaknesses in the deinstitutionalization policy of the period prior to 2017. This study concludes that the effects of the changes in national policies on the organization, management and execution of the health system can be seen, but at the same time there is continuity in various aspects.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Brazil
Humans
*Health Policy
*Mental Health Services/organization & administration
*Hospitals, Psychiatric/organization & administration/statistics & numerical data
Longitudinal Studies
*Deinstitutionalization/trends
Primary Health Care/organization & administration
Mental Health
Ambulatory Care/statistics & numerical data
Health Care Reform
Health Information Systems/organization & administration
RevDate: 2025-02-12
CmpDate: 2025-02-12
Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.
Journal of environmental management, 375:124292.
Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.
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@article {pmid39889433,
year = {2025},
author = {Shukla, S and Khan, R and Chrzanowski, Ł and Vagliasindi, FGA and Roccaro, P},
title = {Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124292},
doi = {10.1016/j.jenvman.2025.124292},
pmid = {39889433},
issn = {1095-8630},
mesh = {*Agriculture/methods ; Soil/chemistry ; Wastewater/chemistry ; Multiomics ; },
abstract = {Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.},
}
MeSH Terms:
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*Agriculture/methods
Soil/chemistry
Wastewater/chemistry
Multiomics
RevDate: 2025-02-12
CmpDate: 2025-02-12
Assessing riparian functioning condition for improved ecosystem services: A case study of the Back Creek watershed (Virginia, USA).
Journal of environmental management, 375:124154.
Riparian functioning condition refers to a rating and description of the current ecological status of a reach of a riparian ecosystem in consideration of its potential hydrology, vegetation, and geomorphology. Reach rating options are Proper Functioning Condition (PFC), Functional-At-Risk (FAR), Non-Functional, and apparent or monitored trends. We assessed the functioning condition of flowing riverbank areas of Back Creek located in Virginia (USA) following a PFC protocol developed by the U.S. Department of the Interior and the U.S. Department of Agriculture. The PFC protocol involves 17 qualitative assessment items that address three categories of attributes (hydrology, vegetation, and geomorphology); each is answered as "yes", "no," or "not applicable" with an explanation. We discussed key PFC items driving stream water quality contextualizing the previously modeled riparian buffer zones and ecosystem services tradeoffs in the Back Creek watershed published by U.S. Environmental Protection Agency. Using the remote sensing data in the Geographic Information System, we delineated and characterized 26 Back Creek reaches of 41.1 km length. We also analyzed the 38-year (1981-2018) daily datasets of the precipitation, surface runoff, temperature, soil moisture pattern, and vegetation types for the watershed. Then, we conducted the PFC assessments using field reconnaissance of 10 reaches, 19.3 km of the Back Creek. The field assessments concluded that 52% of the assessed length of Back Creek was in PFC, attributed to diverse vegetation, maintained channel characteristics, floodplain accessibility (where appropriate), and balanced water and sediment loading supplied by individual headwater streams to the Back Creek. 48% of the assessed length was in FAR condition due to land use changes and urban road network. This study provides an exemplar of nonpoint source (diffused pollution generated by land runoff) methodology for identifying key riparian functioning issues and assessing effectiveness of the non-point source best management practice programs.
Additional Links: PMID-39854904
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@article {pmid39854904,
year = {2025},
author = {Ghimire, SR and Schumacher, B and Swanson, S and Hall, R and Hall, ES and Zambrana, J and Johnston, JM},
title = {Assessing riparian functioning condition for improved ecosystem services: A case study of the Back Creek watershed (Virginia, USA).},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124154},
doi = {10.1016/j.jenvman.2025.124154},
pmid = {39854904},
issn = {1095-8630},
mesh = {*Ecosystem ; *Rivers ; Virginia ; *Environmental Monitoring/methods ; Water Quality ; Conservation of Natural Resources ; Hydrology ; Geographic Information Systems ; },
abstract = {Riparian functioning condition refers to a rating and description of the current ecological status of a reach of a riparian ecosystem in consideration of its potential hydrology, vegetation, and geomorphology. Reach rating options are Proper Functioning Condition (PFC), Functional-At-Risk (FAR), Non-Functional, and apparent or monitored trends. We assessed the functioning condition of flowing riverbank areas of Back Creek located in Virginia (USA) following a PFC protocol developed by the U.S. Department of the Interior and the U.S. Department of Agriculture. The PFC protocol involves 17 qualitative assessment items that address three categories of attributes (hydrology, vegetation, and geomorphology); each is answered as "yes", "no," or "not applicable" with an explanation. We discussed key PFC items driving stream water quality contextualizing the previously modeled riparian buffer zones and ecosystem services tradeoffs in the Back Creek watershed published by U.S. Environmental Protection Agency. Using the remote sensing data in the Geographic Information System, we delineated and characterized 26 Back Creek reaches of 41.1 km length. We also analyzed the 38-year (1981-2018) daily datasets of the precipitation, surface runoff, temperature, soil moisture pattern, and vegetation types for the watershed. Then, we conducted the PFC assessments using field reconnaissance of 10 reaches, 19.3 km of the Back Creek. The field assessments concluded that 52% of the assessed length of Back Creek was in PFC, attributed to diverse vegetation, maintained channel characteristics, floodplain accessibility (where appropriate), and balanced water and sediment loading supplied by individual headwater streams to the Back Creek. 48% of the assessed length was in FAR condition due to land use changes and urban road network. This study provides an exemplar of nonpoint source (diffused pollution generated by land runoff) methodology for identifying key riparian functioning issues and assessing effectiveness of the non-point source best management practice programs.},
}
MeSH Terms:
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*Ecosystem
*Rivers
Virginia
*Environmental Monitoring/methods
Water Quality
Conservation of Natural Resources
Hydrology
Geographic Information Systems
RevDate: 2025-02-12
CmpDate: 2025-02-12
Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.
Journal of environmental management, 375:124182.
The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.
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@article {pmid39848196,
year = {2025},
author = {Wang, S and Liping, Y and Arif, M},
title = {Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124182},
doi = {10.1016/j.jenvman.2025.124182},
pmid = {39848196},
issn = {1095-8630},
mesh = {China ; *Tourism ; Humans ; Conservation of Natural Resources ; Geographic Information Systems ; Ecology ; },
abstract = {The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.},
}
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China
*Tourism
Humans
Conservation of Natural Resources
Geographic Information Systems
Ecology
RevDate: 2025-02-12
CmpDate: 2025-02-12
Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.
World journal of microbiology & biotechnology, 40(10):325.
Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.
Additional Links: PMID-39294488
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@article {pmid39294488,
year = {2024},
author = {Zhang, WH and Gao, JW and Lau, CC and Jiang, ZF and Yeong, YS and Mok, WJ and Zhou, W},
title = {Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {325},
pmid = {39294488},
issn = {1573-0972},
support = {22zxbtsn00020//Tianjin Municipal Science and Technology Bureau/ ; },
mesh = {*Euglena gracilis/genetics/growth & development/metabolism/ultrastructure ; *Gene Expression Profiling ; *Amino Acids/metabolism ; *Fatty Acids/metabolism ; *Pigments, Biological/metabolism ; Biomass ; Gene Ontology ; Gene Expression Regulation, Developmental ; Heterotrophic Processes ; },
abstract = {Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.},
}
MeSH Terms:
show MeSH Terms
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*Euglena gracilis/genetics/growth & development/metabolism/ultrastructure
*Gene Expression Profiling
*Amino Acids/metabolism
*Fatty Acids/metabolism
*Pigments, Biological/metabolism
Biomass
Gene Ontology
Gene Expression Regulation, Developmental
Heterotrophic Processes
RevDate: 2025-02-11
PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.
Microbiome, 13(1):50.
BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.
RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.
CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.
Additional Links: PMID-39934908
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@article {pmid39934908,
year = {2025},
author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L},
title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {50},
pmid = {39934908},
issn = {2049-2618},
support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.
RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.
CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.},
}
RevDate: 2025-02-11
The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).
Wellcome open research, 9:618.
We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.
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@article {pmid39931107,
year = {2024},
author = {Boyes, D and Murray, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {618},
pmid = {39931107},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.},
}
RevDate: 2025-02-11
CmpDate: 2025-02-11
Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.
PLoS computational biology, 21(2):e1012753 pii:PCOMPBIOL-D-23-01766.
Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.
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@article {pmid39899595,
year = {2025},
author = {McKenzie-Smith, GC and Wolf, SW and Ayroles, JF and Shaevitz, JW},
title = {Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012753},
doi = {10.1371/journal.pcbi.1012753},
pmid = {39899595},
issn = {1553-7358},
mesh = {Animals ; *Drosophila melanogaster/physiology ; *Behavior, Animal/physiology ; *Locomotion/physiology ; *Circadian Rhythm/physiology ; *Posture/physiology ; Computational Biology ; Deep Learning ; Grooming/physiology ; Female ; Male ; },
abstract = {Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.},
}
MeSH Terms:
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Animals
*Drosophila melanogaster/physiology
*Behavior, Animal/physiology
*Locomotion/physiology
*Circadian Rhythm/physiology
*Posture/physiology
Computational Biology
Deep Learning
Grooming/physiology
Female
Male
RevDate: 2025-02-11
CmpDate: 2025-02-11
Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.
Environmental pollution (Barking, Essex : 1987), 367:125656.
Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.
Additional Links: PMID-39793648
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@article {pmid39793648,
year = {2025},
author = {Ji, G and Wang, Y and Lu, Z and Long, G and Xu, C},
title = {Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125656},
doi = {10.1016/j.envpol.2025.125656},
pmid = {39793648},
issn = {1873-6424},
mesh = {*Benzene ; Humans ; United Kingdom ; Male ; *Stroke/epidemiology/chemically induced ; Middle Aged ; Female ; *Environmental Exposure/statistics & numerical data ; *Air Pollutants/analysis ; Aged ; *Aging ; *Biological Specimen Banks ; Adult ; Cohort Studies ; Risk Factors ; UK Biobank ; },
abstract = {Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.},
}
MeSH Terms:
show MeSH Terms
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*Benzene
Humans
United Kingdom
Male
*Stroke/epidemiology/chemically induced
Middle Aged
Female
*Environmental Exposure/statistics & numerical data
*Air Pollutants/analysis
Aged
*Aging
*Biological Specimen Banks
Adult
Cohort Studies
Risk Factors
UK Biobank
RevDate: 2025-02-10
The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.
Social science & medicine (1982), 368:117817 pii:S0277-9536(25)00146-7 [Epub ahead of print].
While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.
Additional Links: PMID-39929026
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@article {pmid39929026,
year = {2025},
author = {Song, J and Zhou, S and Kwan, MP and Song, G and Long, J and Song, W},
title = {The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.},
journal = {Social science & medicine (1982)},
volume = {368},
number = {},
pages = {117817},
doi = {10.1016/j.socscimed.2025.117817},
pmid = {39929026},
issn = {1873-5347},
abstract = {While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.},
}
RevDate: 2025-02-10
Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.
International journal of biometeorology [Epub ahead of print].
To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.
Additional Links: PMID-39928107
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@article {pmid39928107,
year = {2025},
author = {Güneri, FD and Karaarslan, F and Özen, H and Odabaşi, E},
title = {Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.},
journal = {International journal of biometeorology},
volume = {},
number = {},
pages = {},
pmid = {39928107},
issn = {1432-1254},
abstract = {To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.},
}
RevDate: 2025-02-10
CmpDate: 2025-02-10
RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.
PLoS computational biology, 21(2):e1012777 pii:PCOMPBIOL-D-24-00337.
Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.
Additional Links: PMID-39899643
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@article {pmid39899643,
year = {2025},
author = {Hozé, N and Pons-Salort, M and Metcalf, CJE and White, M and Salje, H and Cauchemez, S},
title = {RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012777},
doi = {10.1371/journal.pcbi.1012777},
pmid = {39899643},
issn = {1553-7358},
mesh = {Seroepidemiologic Studies ; Humans ; *Software ; *Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Disease Outbreaks/statistics & numerical data ; Communicable Diseases/epidemiology/transmission ; },
abstract = {Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Seroepidemiologic Studies
Humans
*Software
*Bayes Theorem
Computational Biology/methods
Computer Simulation
Disease Outbreaks/statistics & numerical data
Communicable Diseases/epidemiology/transmission
RevDate: 2025-02-10
CmpDate: 2025-02-10
Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.
FEMS microbiology letters, 371:.
Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.
Additional Links: PMID-38866716
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@article {pmid38866716,
year = {2024},
author = {Brock, MT and Morrison, HG and Maignien, L and Weinig, C},
title = {Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae044},
pmid = {38866716},
issn = {1574-6968},
support = {IOS-1444571//NSF/ ; },
mesh = {*Specimen Handling ; *Soil Microbiology ; *Microbiota ; *Preservation, Biological ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Data Curation ; Phylogeny ; Biodiversity ; Principal Component Analysis ; },
abstract = {Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Specimen Handling
*Soil Microbiology
*Microbiota
*Preservation, Biological
RNA, Ribosomal, 16S/genetics
Sequence Analysis, RNA
Data Curation
Phylogeny
Biodiversity
Principal Component Analysis
RevDate: 2025-02-09
Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.
The Science of the total environment, 966:178600 pii:S0048-9697(25)00234-7 [Epub ahead of print].
Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.
Additional Links: PMID-39923474
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PubMed:
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@article {pmid39923474,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.},
journal = {The Science of the total environment},
volume = {966},
number = {},
pages = {178600},
doi = {10.1016/j.scitotenv.2025.178600},
pmid = {39923474},
issn = {1879-1026},
abstract = {Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.},
}
RevDate: 2025-02-09
Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).
Cancer epidemiology, 95:102766 pii:S1877-7821(25)00025-6 [Epub ahead of print].
BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.
METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.
RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92 %), ≥ 65 years old (233,059; 58.89 %), diagnosed with malignant neoplasm of the colon (212,277; 53.63 %), with 1-7 years of education (157.564; 39.81 %), married (192.276; 48.58 %), hospital as place of death (331.393; 83.73 %) and white (212.666; 65.07 %). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p < 0.05), men (APC: 1.5; p < 0.05) and 45-64 years old (APC: 1.2; p < 0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.
CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.
Additional Links: PMID-39923291
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PubMed:
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@article {pmid39923291,
year = {2025},
author = {de Melo, LRS and Dos Santos Pereira, J and Melo, MS and Andrade, LA and Bezerra-Santos, M and Lima, CA and Dos Santos, AD},
title = {Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).},
journal = {Cancer epidemiology},
volume = {95},
number = {},
pages = {102766},
doi = {10.1016/j.canep.2025.102766},
pmid = {39923291},
issn = {1877-783X},
abstract = {BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.
METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.
RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92 %), ≥ 65 years old (233,059; 58.89 %), diagnosed with malignant neoplasm of the colon (212,277; 53.63 %), with 1-7 years of education (157.564; 39.81 %), married (192.276; 48.58 %), hospital as place of death (331.393; 83.73 %) and white (212.666; 65.07 %). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p < 0.05), men (APC: 1.5; p < 0.05) and 45-64 years old (APC: 1.2; p < 0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.
CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.},
}
RevDate: 2025-02-08
CmpDate: 2025-02-08
Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.
Cognitive research: principles and implications, 10(1):5.
It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.
Additional Links: PMID-39921816
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@article {pmid39921816,
year = {2025},
author = {Asuako, PAG and Stojan, R and Bock, O and Mack, M and Voelcker-Rehage, C},
title = {Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {5},
pmid = {39921816},
issn = {2365-7464},
support = {SPP 1772//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; Female ; Young Adult ; Male ; Adult ; *Automobile Driving ; Adolescent ; *Psychomotor Performance/physiology ; *Multitasking Behavior/physiology ; *Executive Function/physiology ; Reaction Time/physiology ; Attention/physiology ; },
abstract = {It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Female
Young Adult
Male
Adult
*Automobile Driving
Adolescent
*Psychomotor Performance/physiology
*Multitasking Behavior/physiology
*Executive Function/physiology
Reaction Time/physiology
Attention/physiology
RevDate: 2025-02-08
CmpDate: 2025-02-08
Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.
Marine environmental research, 204:106873.
Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.
Additional Links: PMID-39615103
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@article {pmid39615103,
year = {2025},
author = {Sha, J and Liu, X and Wang, H and Song, X and Bao, M and Yu, Q and Wen, G and Wei, M},
title = {Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106873},
doi = {10.1016/j.marenvres.2024.106873},
pmid = {39615103},
issn = {1879-0291},
mesh = {*Ecosystem ; China ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; Oceans and Seas ; Geographic Information Systems ; },
abstract = {Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.},
}
MeSH Terms:
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*Ecosystem
China
*Environmental Monitoring/methods
*Conservation of Natural Resources
Oceans and Seas
Geographic Information Systems
RevDate: 2025-02-07
A framework for quantifying the multisectoral burden of animal disease to support decision making.
Frontiers in veterinary science, 12:1476505.
Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.
Additional Links: PMID-39917311
PubMed:
Citation:
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@article {pmid39917311,
year = {2025},
author = {Lysholm, S and Chaters, GL and Di Bari, C and Hughes, EC and Huntington, B and Rushton, J and Thomas, L},
title = {A framework for quantifying the multisectoral burden of animal disease to support decision making.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1476505},
pmid = {39917311},
issn = {2297-1769},
abstract = {Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.},
}
RevDate: 2025-02-07
CmpDate: 2024-12-23
A functional microbiome catalogue crowdsourced from North American rivers.
Nature, 637(8044):103-112.
Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.
Additional Links: PMID-39567690
PubMed:
Citation:
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@article {pmid39567690,
year = {2025},
author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC},
title = {A functional microbiome catalogue crowdsourced from North American rivers.},
journal = {Nature},
volume = {637},
number = {8044},
pages = {103-112},
pmid = {39567690},
issn = {1476-4687},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; },
mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; },
abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Crowdsourcing
*Microbiota/genetics
*Rivers/microbiology
United States
Water Microbiology
Transcriptome
Carbon Cycle
Metagenome
Databases, Factual
RevDate: 2025-02-06
Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.
BMC biology, 23(1):35.
Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.
Additional Links: PMID-39915771
PubMed:
Citation:
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@article {pmid39915771,
year = {2025},
author = {Gould, E and Fraser, HS and Parker, TH and Nakagawa, S and Griffith, SC and Vesk, PA and Fidler, F and Hamilton, DG and Abbey-Lee, RN and Abbott, JK and Aguirre, LA and Alcaraz, C and Aloni, I and Altschul, D and Arekar, K and Atkins, JW and Atkinson, J and Baker, CM and Barrett, M and Bell, K and Bello, SK and Beltrán, I and Berauer, BJ and Bertram, MG and Billman, PD and Blake, CK and Blake, S and Bliard, L and Bonisoli-Alquati, A and Bonnet, T and Bordes, CNM and Bose, APH and Botterill-James, T and Boyd, MA and Boyle, SA and Bradfer-Lawrence, T and Bradham, J and Brand, JA and Brengdahl, MI and Bulla, M and Bussière, L and Camerlenghi, E and Campbell, SE and Campos, LLF and Caravaggi, A and Cardoso, P and Carroll, CJW and Catanach, TA and Chen, X and Chik, HYJ and Choy, ES and Christie, AP and Chuang, A and Chunco, AJ and Clark, BL and Contina, A and Covernton, GA and Cox, MP and Cressman, KA and Crotti, M and Crouch, CD and D'Amelio, PB and de Sousa, AA and Döbert, TF and Dobler, R and Dobson, AJ and Doherty, TS and Drobniak, SM and Duffy, AG and Duncan, AB and Dunn, RP and Dunning, J and Dutta, T and Eberhart-Hertel, L and Elmore, JA and Elsherif, MM and English, HM and Ensminger, DC and Ernst, UR and Ferguson, SM and Fernandez-Juricic, E and Ferreira-Arruda, T and Fieberg, J and Finch, EA and Fiorenza, EA and Fisher, DN and Fontaine, A and Forstmeier, W and Fourcade, Y and Frank, GS and Freund, CA and Fuentes-Lillo, E and Gandy, SL and Gannon, DG and García-Cervigón, AI and Garretson, AC and Ge, X and Geary, WL and Géron, C and Gilles, M and Girndt, A and Gliksman, D and Goldspiel, HB and Gomes, DGE and Good, MK and Goslee, SC and Gosnell, JS and Grames, EM and Gratton, P and Grebe, NM and Greenler, SM and Griffioen, M and Griffith, DM and Griffith, FJ and Grossman, JJ and Güncan, A and Haesen, S and Hagan, JG and Hager, HA and Harris, JP and Harrison, ND and Hasnain, SS and Havird, JC and Heaton, AJ and Herrera-Chaustre, ML and Howard, TJ and Hsu, BY and Iannarilli, F and Iranzo, EC and Iverson, ENK and Jimoh, SO and Johnson, DH and Johnsson, M and Jorna, J and Jucker, T and Jung, M and Kačergytė, I and Kaltz, O and Ke, A and Kelly, CD and Keogan, K and Keppeler, FW and Killion, AK and Kim, D and Kochan, DP and Korsten, P and Kothari, S and Kuppler, J and Kusch, JM and Lagisz, M and Lalla, KM and Larkin, DJ and Larson, CL and Lauck, KS and Lauterbur, ME and Law, A and Léandri-Breton, DJ and Lembrechts, JJ and L'Herpiniere, K and Lievens, EJP and de Lima, DO and Lindsay, S and Luquet, M and MacLeod, R and Macphie, KH and Magellan, K and Mair, MM and Malm, LE and Mammola, S and Mandeville, CP and Manhart, M and Manrique-Garzon, LM and Mäntylä, E and Marchand, P and Marshall, BM and Martin, CA and Martin, DA and Martin, JM and Martinig, AR and McCallum, ES and McCauley, M and McNew, SM and Meiners, SJ and Merkling, T and Michelangeli, M and Moiron, M and Moreira, B and Mortensen, J and Mos, B and Muraina, TO and Murphy, PW and Nelli, L and Niemelä, P and Nightingale, J and Nilsonne, G and Nolazco, S and Nooten, SS and Novotny, JL and Olin, AB and Organ, CL and Ostevik, KL and Palacio, FX and Paquet, M and Parker, DJ and Pascall, DJ and Pasquarella, VJ and Paterson, JH and Payo-Payo, A and Pedersen, KM and Perez, G and Perry, KI and Pottier, P and Proulx, MJ and Proulx, R and Pruett, JL and Ramananjato, V and Randimbiarison, FT and Razafindratsima, OH and Rennison, DJ and Riva, F and Riyahi, S and Roast, MJ and Rocha, FP and Roche, DG and Román-Palacios, C and Rosenberg, MS and Ross, J and Rowland, FE and Rugemalila, D and Russell, AL and Ruuskanen, S and Saccone, P and Sadeh, A and Salazar, SM and Sales, K and Salmón, P and Sánchez-Tójar, A and Santos, LP and Santostefano, F and Schilling, HT and Schmidt, M and Schmoll, T and Schneider, AC and Schrock, AE and Schroeder, J and Schtickzelle, N and Schultz, NL and Scott, DA and Scroggie, MP and Shapiro, JT and Sharma, N and Shearer, CL and Simón, D and Sitvarin, MI and Skupien, FL and Slinn, HL and Smith, GP and Smith, JA and Sollmann, R and Whitney, KS and Still, SM and Stuber, EF and Sutton, GF and Swallow, B and Taff, CC and Takola, E and Tanentzap, AJ and Tarjuelo, R and Telford, RJ and Thawley, CJ and Thierry, H and Thomson, J and Tidau, S and Tompkins, EM and Tortorelli, CM and Trlica, A and Turnell, BR and Urban, L and Van de Vondel, S and van der Wal, JEM and Van Eeckhoven, J and van Oordt, F and Vanderwel, KM and Vanderwel, MC and Vanderwolf, KJ and Vélez, J and Vergara-Florez, DC and Verrelli, BC and Vieira, MV and Villamil, N and Vitali, V and Vollering, J and Walker, J and Walker, XJ and Walter, JA and Waryszak, P and Weaver, RJ and Wedegärtner, REM and Weller, DL and Whelan, S and White, RL and Wolfson, DW and Wood, A and Yanco, SW and Yen, JDL and Youngflesh, C and Zilio, G and Zimmer, C and Zimmerman, GM and Zitomer, RA},
title = {Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {35},
pmid = {39915771},
issn = {1741-7007},
abstract = {Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.},
}
RevDate: 2025-02-05
Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.
BMC public health, 25(1):469.
BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.
METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.
RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.
CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.
Additional Links: PMID-39910401
PubMed:
Citation:
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@article {pmid39910401,
year = {2025},
author = {Fatima, M and Butt, I and MohammadEbrahimi, S and Kiani, B and Gruebner, O},
title = {Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {469},
pmid = {39910401},
issn = {1471-2458},
abstract = {BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.
METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.
RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.
CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.},
}
RevDate: 2025-02-05
Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis.
Molecular biology and evolution pii:8002229 [Epub ahead of print].
Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.
Additional Links: PMID-39907430
Publisher:
PubMed:
Citation:
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@article {pmid39907430,
year = {2025},
author = {Hebert, JD and Tang, YJ and Szamecz, M and Andrejka, L and Lopez, SS and Petrov, DA and Boross, G and Winslow, MM},
title = {Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf023},
pmid = {39907430},
issn = {1537-1719},
abstract = {Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.},
}
RevDate: 2025-02-05
Expression-based machine learning models for predicting plant tissue identity.
Applications in plant sciences, 13(1):e11621.
PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.
METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.
RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.
DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.
Additional Links: PMID-39906497
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Citation:
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@article {pmid39906497,
year = {2025},
author = {Palande, S and Arsenault, J and Basurto-Lozada, P and Bleich, A and Brown, BNI and Buysse, SF and Connors, NA and Das Adhikari, S and Dobson, KC and Guerra-Castillo, FX and Guerrero-Carrillo, MF and Harlow, S and Herrera-Orozco, H and Hightower, AT and Izquierdo, P and Jacobs, M and Johnson, NA and Leuenberger, W and Lopez-Hernandez, A and Luckie-Duque, A and Martínez-Avila, C and Mendoza-Galindo, EJ and Plancarte, DC and Schuster, JM and Shomer, H and Sitar, SC and Steensma, AK and Thomson, JE and Villaseñor-Amador, D and Waterman, R and Webster, BM and Whyte, M and Zorilla-Azcué, S and Montgomery, BL and Husbands, AY and Krishnan, A and Percival, S and Munch, E and VanBuren, R and Chitwood, DH and Rougon-Cardoso, A},
title = {Expression-based machine learning models for predicting plant tissue identity.},
journal = {Applications in plant sciences},
volume = {13},
number = {1},
pages = {e11621},
pmid = {39906497},
issn = {2168-0450},
abstract = {PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.
METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.
RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.
DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.},
}
RevDate: 2025-02-05
CmpDate: 2025-02-05
A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.
G3 (Bethesda, Md.), 15(2):.
Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.
Additional Links: PMID-39611775
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@article {pmid39611775,
year = {2025},
author = {Andorf, CM and Ross-Ibarra, J and Seetharam, AS and Hufford, MB and Woodhouse, MR},
title = {A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {2},
pages = {},
pmid = {39611775},
issn = {2160-1836},
support = {5030-21000-072-00-D//US. Department of Agriculture, Agricultural Research Service/ ; //Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; //Iowa State University/ ; //SCINet/ ; 0201-88888-003-000D//AI Center of Excellence of the USDA Agricultural Research Service/ ; CA-D-PLS-2066-H//USDA/ ; },
mesh = {*Zea mays/genetics ; *Genome, Plant ; *Polymorphism, Single Nucleotide ; *Genomics/methods ; *Databases, Genetic ; Software ; Molecular Sequence Annotation ; Linkage Disequilibrium ; Genotype ; Genetic Variation ; },
abstract = {Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Zea mays/genetics
*Genome, Plant
*Polymorphism, Single Nucleotide
*Genomics/methods
*Databases, Genetic
Software
Molecular Sequence Annotation
Linkage Disequilibrium
Genotype
Genetic Variation
RevDate: 2025-02-04
CmpDate: 2025-02-04
Systematic shifts in the variation among host individuals must be considered in climate-disease theory.
Proceedings. Biological sciences, 292(2040):20242515.
To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.
Additional Links: PMID-39904391
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PubMed:
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@article {pmid39904391,
year = {2025},
author = {Mihaljevic, JR and Páez, DJ},
title = {Systematic shifts in the variation among host individuals must be considered in climate-disease theory.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2040},
pages = {20242515},
doi = {10.1098/rspb.2024.2515},
pmid = {39904391},
issn = {1471-2954},
support = {//Exxon Valdez Oil Spill Trustee Council/ ; //Division of Environmental Biology/ ; },
mesh = {*Climate Change ; Animals ; *Host-Pathogen Interactions ; Temperature ; Population Dynamics ; Models, Biological ; Disease Susceptibility ; },
abstract = {To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.},
}
MeSH Terms:
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*Climate Change
Animals
*Host-Pathogen Interactions
Temperature
Population Dynamics
Models, Biological
Disease Susceptibility
RevDate: 2025-02-04
The genomic landscape, causes, and consequences of extensive phylogenomic discordance in murine rodents.
Genome biology and evolution pii:7998737 [Epub ahead of print].
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents - a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
Additional Links: PMID-39903560
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@article {pmid39903560,
year = {2025},
author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM},
title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in murine rodents.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf017},
pmid = {39903560},
issn = {1759-6653},
abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents - a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.},
}
RevDate: 2025-02-04
CmpDate: 2025-02-04
Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.
Microbiology spectrum, 13(2):e0106624.
Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.
Additional Links: PMID-39745426
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@article {pmid39745426,
year = {2025},
author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A},
title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0106624},
pmid = {39745426},
issn = {2165-0497},
mesh = {*Prophages/genetics/isolation & purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation & purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; },
abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.},
}
MeSH Terms:
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hide MeSH Terms
*Prophages/genetics/isolation & purification
*Retroelements
Humans
*Metagenomics
Genome, Viral/genetics
Gastrointestinal Microbiome
Computational Biology/methods
Host Specificity
Bacteriophages/genetics/classification/isolation & purification/physiology
Genome, Bacterial/genetics
Phylogeny
Genetic Variation
RevDate: 2025-02-03
CmpDate: 2025-02-03
The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.
Scientific data, 12(1):201.
Mytella strigata, a potentially invasive species native to South America, is rapidly spreading across various aquatic ecosystems around the globe, posing a threat to native mussels. This study presents the first comprehensive de novo transcriptome assembly of M. strigata. We generated 254 million reads, which were processed and assembled using the Trinity assembler, resulting in 60362 transcripts with an N50 of 1,578 bp and over 93-98% completeness, as confirmed by BUSCO analysis with multiple ortho-datasets. A number of databases were used for functional annotation, including UniProt, KEGG, Reactome, InterPro, and eggNOG. Gene Ontology and pathway analyses identified transcripts associated with key biological processes, including those associated with cell signalling, metabolism, stress responses, cancer pathways, and immune regulation. This dataset enriches the bivalve database by advancing the understanding of the adaptive success and evolutionary resilience of this invasive species. The present study provides a fundamental framework for future research on the ecological and evolutionary impacts of this invasive species.
Additional Links: PMID-39900973
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@article {pmid39900973,
year = {2025},
author = {Vysakh, VG and Sukumaran, S and Sebastian, W and Gopalakrishnan, A},
title = {The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {201},
pmid = {39900973},
issn = {2052-4463},
mesh = {*Introduced Species ; Animals ; *Transcriptome ; Mytilidae/genetics ; South America ; Gene Ontology ; Molecular Sequence Annotation ; },
abstract = {Mytella strigata, a potentially invasive species native to South America, is rapidly spreading across various aquatic ecosystems around the globe, posing a threat to native mussels. This study presents the first comprehensive de novo transcriptome assembly of M. strigata. We generated 254 million reads, which were processed and assembled using the Trinity assembler, resulting in 60362 transcripts with an N50 of 1,578 bp and over 93-98% completeness, as confirmed by BUSCO analysis with multiple ortho-datasets. A number of databases were used for functional annotation, including UniProt, KEGG, Reactome, InterPro, and eggNOG. Gene Ontology and pathway analyses identified transcripts associated with key biological processes, including those associated with cell signalling, metabolism, stress responses, cancer pathways, and immune regulation. This dataset enriches the bivalve database by advancing the understanding of the adaptive success and evolutionary resilience of this invasive species. The present study provides a fundamental framework for future research on the ecological and evolutionary impacts of this invasive species.},
}
MeSH Terms:
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*Introduced Species
Animals
*Transcriptome
Mytilidae/genetics
South America
Gene Ontology
Molecular Sequence Annotation
RevDate: 2025-02-03
CmpDate: 2025-02-03
Design of field trials for the evaluation of transmissible vaccines in animal populations.
PLoS computational biology, 21(2):e1012779 pii:PCOMPBIOL-D-23-01443.
Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.
Additional Links: PMID-39899630
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PubMed:
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@article {pmid39899630,
year = {2025},
author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE},
title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012779},
doi = {10.1371/journal.pcbi.1012779},
pmid = {39899630},
issn = {1553-7358},
mesh = {Animals ; *Vaccines/immunology ; Vaccination/methods ; Computational Biology ; Sample Size ; Research Design ; },
abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.},
}
MeSH Terms:
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hide MeSH Terms
Animals
*Vaccines/immunology
Vaccination/methods
Computational Biology
Sample Size
Research Design
RevDate: 2025-02-03
Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.
Heliyon, 11(2):e42038.
Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.
Additional Links: PMID-39897903
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Citation:
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@article {pmid39897903,
year = {2025},
author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B},
title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e42038},
pmid = {39897903},
issn = {2405-8440},
abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.},
}
RevDate: 2025-02-03
Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.
Heliyon, 11(2):e41845.
This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.
Additional Links: PMID-39897842
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@article {pmid39897842,
year = {2025},
author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A},
title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41845},
pmid = {39897842},
issn = {2405-8440},
abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.},
}
RevDate: 2025-02-03
Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.
Heliyon, 11(2):e41656.
Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.
Additional Links: PMID-39897809
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@article {pmid39897809,
year = {2025},
author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A},
title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41656},
pmid = {39897809},
issn = {2405-8440},
abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.},
}
RevDate: 2025-02-03
CmpDate: 2025-02-03
Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.
PeerJ, 13:e18853.
AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.
INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.
MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.
Additional Links: PMID-39897501
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@article {pmid39897501,
year = {2025},
author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D},
title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18853},
pmid = {39897501},
issn = {2167-8359},
mesh = {*Biodiversity ; *Databases, Factual ; Feasibility Studies ; Information Storage and Retrieval/methods ; Algorithms ; Quebec ; Conservation of Natural Resources/methods ; },
abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.
INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.
MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Biodiversity
*Databases, Factual
Feasibility Studies
Information Storage and Retrieval/methods
Algorithms
Quebec
Conservation of Natural Resources/methods
RevDate: 2025-02-03
CmpDate: 2025-02-03
Optimal control of agent-based models via surrogate modeling.
PLoS computational biology, 21(1):e1012138.
This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.
Additional Links: PMID-39808665
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@article {pmid39808665,
year = {2025},
author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC},
title = {Optimal control of agent-based models via surrogate modeling.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012138},
pmid = {39808665},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; Humans ; Computer Simulation ; Systems Analysis ; Models, Biological ; },
abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Algorithms
*Computational Biology/methods
Humans
Computer Simulation
Systems Analysis
Models, Biological
RevDate: 2025-01-31
Racial disparities in intrapartum care experiences and birth hospital characteristics.
Social science & medicine (1982), 367:117720 pii:S0277-9536(25)00049-8 [Epub ahead of print].
Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.
Additional Links: PMID-39889380
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PubMed:
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@article {pmid39889380,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.},
journal = {Social science & medicine (1982)},
volume = {367},
number = {},
pages = {117720},
doi = {10.1016/j.socscimed.2025.117720},
pmid = {39889380},
issn = {1873-5347},
abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.},
}
RevDate: 2025-01-31
Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.
Molecular ecology resources [Epub ahead of print].
Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.
Additional Links: PMID-39888239
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PubMed:
Citation:
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@article {pmid39888239,
year = {2025},
author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P},
title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14075},
doi = {10.1111/1755-0998.14075},
pmid = {39888239},
issn = {1755-0998},
support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; },
abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.},
}
RevDate: 2025-01-31
CmpDate: 2025-01-31
Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.
PLoS computational biology, 21(1):e1012740 pii:PCOMPBIOL-D-24-00073.
Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.
Additional Links: PMID-39854567
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@article {pmid39854567,
year = {2025},
author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ},
title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012740},
doi = {10.1371/journal.pcbi.1012740},
pmid = {39854567},
issn = {1553-7358},
mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; Birds/physiology ; Computational Biology ; Social Behavior ; Behavior, Animal/physiology ; Sexual Behavior, Animal/physiology ; },
abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
Female
Male
*Aggression/physiology
*Territoriality
Birds/physiology
Computational Biology
Social Behavior
Behavior, Animal/physiology
Sexual Behavior, Animal/physiology
RevDate: 2025-01-31
CmpDate: 2025-01-31
Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches.
Journal of biomolecular structure & dynamics, 43(4):1788-1803.
Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.
Additional Links: PMID-38112302
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PubMed:
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@article {pmid38112302,
year = {2025},
author = {Marques, PH and Rodrigues, TCV and Santos, EH and Bleicher, L and Aburjaile, FF and Martins, FS and Oliveira, CJF and Azevedo, V and Tiwari, S and Soares, S},
title = {Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches.},
journal = {Journal of biomolecular structure & dynamics},
volume = {43},
number = {4},
pages = {1788-1803},
doi = {10.1080/07391102.2023.2293256},
pmid = {38112302},
issn = {1538-0254},
mesh = {*Cholera/prevention & control/immunology ; *Computational Biology/methods ; Humans ; *Cholera Vaccines/immunology ; *Vaccinology/methods ; Epitopes, T-Lymphocyte/immunology/chemistry ; Epitopes/immunology/chemistry ; Epitopes, B-Lymphocyte/immunology/chemistry ; Vibrio Infections/prevention & control/immunology ; Molecular Docking Simulation ; Immunoinformatics ; },
abstract = {Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Cholera/prevention & control/immunology
*Computational Biology/methods
Humans
*Cholera Vaccines/immunology
*Vaccinology/methods
Epitopes, T-Lymphocyte/immunology/chemistry
Epitopes/immunology/chemistry
Epitopes, B-Lymphocyte/immunology/chemistry
Vibrio Infections/prevention & control/immunology
Molecular Docking Simulation
Immunoinformatics
RevDate: 2025-01-29
CmpDate: 2025-01-29
Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.
Journal of agricultural and food chemistry, 73(4):2678-2695.
Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.
Additional Links: PMID-39834325
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PubMed:
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@article {pmid39834325,
year = {2025},
author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G},
title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {4},
pages = {2678-2695},
doi = {10.1021/acs.jafc.4c09001},
pmid = {39834325},
issn = {1520-5118},
mesh = {*Oryza/metabolism/growth & development/drug effects/genetics/chemistry ; *Enrofloxacin/metabolism ; *Hormesis/drug effects ; *Metabolic Networks and Pathways/drug effects ; Anti-Bacterial Agents/pharmacology ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; },
abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Oryza/metabolism/growth & development/drug effects/genetics/chemistry
*Enrofloxacin/metabolism
*Hormesis/drug effects
*Metabolic Networks and Pathways/drug effects
Anti-Bacterial Agents/pharmacology
Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant/drug effects
Multiomics
RevDate: 2025-01-28
CmpDate: 2025-01-28
Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.
Journal of medical Internet research, 27:e51689 pii:v27i1e51689.
BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.
OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.
METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre Jülich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.
RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.
CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.
Additional Links: PMID-39874571
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PubMed:
Citation:
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@article {pmid39874571,
year = {2025},
author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J},
title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e51689},
doi = {10.2196/51689},
pmid = {39874571},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Mobile Applications ; Smartphone ; },
abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.
OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.
METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre Jülich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.
RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.
CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.},
}
MeSH Terms:
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Humans
*Ecological Momentary Assessment
*Mobile Applications
Smartphone
RevDate: 2025-01-28
CmpDate: 2025-01-28
Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.
Journal of environmental management, 374:124130.
Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.
Additional Links: PMID-39813804
Publisher:
PubMed:
Citation:
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@article {pmid39813804,
year = {2025},
author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H},
title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {124130},
doi = {10.1016/j.jenvman.2025.124130},
pmid = {39813804},
issn = {1095-8630},
mesh = {*Floods ; *Cities ; Geographic Information Systems ; Climate Change ; Risk Management/methods ; Urbanization ; Risk Assessment ; },
abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Floods
*Cities
Geographic Information Systems
Climate Change
Risk Management/methods
Urbanization
Risk Assessment
RevDate: 2025-01-28
CmpDate: 2025-01-28
Diabetes in China: epidemiology, pathophysiology and multi-omics.
Nature metabolism, 7(1):16-34.
Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.
Additional Links: PMID-39809974
PubMed:
Citation:
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@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {7},
number = {1},
pages = {16-34},
pmid = {39809974},
issn = {2522-5812},
mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; },
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}
MeSH Terms:
show MeSH Terms
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Humans
China/epidemiology
*Diabetes Mellitus/epidemiology
Risk Factors
Prevalence
Metabolomics
Multiomics
RevDate: 2025-01-28
CmpDate: 2025-01-28
In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.
Environmental science & technology, 59(3):1673-1682.
While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.
Additional Links: PMID-39648557
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PubMed:
Citation:
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@article {pmid39648557,
year = {2025},
author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X},
title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.},
journal = {Environmental science & technology},
volume = {59},
number = {3},
pages = {1673-1682},
doi = {10.1021/acs.est.4c06186},
pmid = {39648557},
issn = {1520-5851},
mesh = {*Lung/drug effects/pathology ; Animals ; *Metal Nanoparticles/toxicity ; Mice ; *Oxides/toxicity ; Data Mining ; Humans ; },
abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Lung/drug effects/pathology
Animals
*Metal Nanoparticles/toxicity
Mice
*Oxides/toxicity
Data Mining
Humans
RevDate: 2025-01-27
Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.
Obesity surgery [Epub ahead of print].
BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.
METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10 GB. Evaluations before (0 M) and 6 months (6 M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16 s rRNA next-generation sequencing approach. Statistical significance was set to a p value < 0.05 with an FDR < 0.1.
RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6 M showed near significant differences (p = 0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.
CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.
Additional Links: PMID-39870942
PubMed:
Citation:
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@article {pmid39870942,
year = {2025},
author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H},
title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39870942},
issn = {1708-0428},
abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.
METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10 GB. Evaluations before (0 M) and 6 months (6 M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16 s rRNA next-generation sequencing approach. Statistical significance was set to a p value < 0.05 with an FDR < 0.1.
RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6 M showed near significant differences (p = 0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.
CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.},
}
RevDate: 2025-01-27
CmpDate: 2025-01-27
A quantitative prediction method utilizing whole omics data for biosensing.
Scientific reports, 15(1):1928.
Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.
Additional Links: PMID-39870652
PubMed:
Citation:
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@article {pmid39870652,
year = {2025},
author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y},
title = {A quantitative prediction method utilizing whole omics data for biosensing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1928},
pmid = {39870652},
issn = {2045-2322},
support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; },
mesh = {*Biosensing Techniques/methods ; *Biomarkers ; Transcriptome ; Humans ; Metabolomics/methods ; Gene Regulatory Networks ; Genomics/methods ; Computational Biology/methods ; Metabolome ; Microbiota/genetics ; Gene Expression Profiling/methods ; },
abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Biosensing Techniques/methods
*Biomarkers
Transcriptome
Humans
Metabolomics/methods
Gene Regulatory Networks
Genomics/methods
Computational Biology/methods
Metabolome
Microbiota/genetics
Gene Expression Profiling/methods
RevDate: 2025-01-27
The biodiversity of ice-free Antarctica database.
Ecology, 106(1):e70000.
Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).
Additional Links: PMID-39871100
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PubMed:
Citation:
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@article {pmid39871100,
year = {2025},
author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL},
title = {The biodiversity of ice-free Antarctica database.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e70000},
doi = {10.1002/ecy.70000},
pmid = {39871100},
issn = {1939-9170},
support = {n°FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n°RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; },
abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).},
}
RevDate: 2025-01-27
CmpDate: 2025-01-27
A global dataset of freshwater fish trophic interactions.
Scientific data, 12(1):160.
Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines. Our project, TroPhish, builds upon FishBase by digitizing over 100 years of data from the fish predation literature. Data from 1,106 published papers, theses, dissertations, and government reports were filtered, scanned in through third-party software (Able2Extract), reorganized, and consolidated with FishBase to form a unified dataset. This dataset contains 54,750 observations of data on 4,571 unique dietary samples, representing 9% (982) of all freshwater fish species and 43% (111) of all freshwater fish families. Fish species and family representation varied by continent, ranging from 3-32% and 34-75%, respectively. Users are encouraged to submit errors or additional data through GitHub's fork and pull model.
Additional Links: PMID-39870651
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Citation:
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@article {pmid39870651,
year = {2025},
author = {Ridgway, J and Wesner, J},
title = {A global dataset of freshwater fish trophic interactions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {160},
pmid = {39870651},
issn = {2052-4463},
mesh = {Animals ; *Fishes ; *Fresh Water ; Food Chain ; Diet/veterinary ; Predatory Behavior ; Databases, Factual ; },
abstract = {Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines. Our project, TroPhish, builds upon FishBase by digitizing over 100 years of data from the fish predation literature. Data from 1,106 published papers, theses, dissertations, and government reports were filtered, scanned in through third-party software (Able2Extract), reorganized, and consolidated with FishBase to form a unified dataset. This dataset contains 54,750 observations of data on 4,571 unique dietary samples, representing 9% (982) of all freshwater fish species and 43% (111) of all freshwater fish families. Fish species and family representation varied by continent, ranging from 3-32% and 34-75%, respectively. Users are encouraged to submit errors or additional data through GitHub's fork and pull model.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Fishes
*Fresh Water
Food Chain
Diet/veterinary
Predatory Behavior
Databases, Factual
RevDate: 2025-01-27
CmpDate: 2025-01-27
Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.
JMIR mental health, 12:e67478 pii:v12i1e67478.
BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.
OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.
METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.
RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P≤.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.
CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.
TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.
Additional Links: PMID-39869900
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PubMed:
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@article {pmid39869900,
year = {2025},
author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH},
title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.},
journal = {JMIR mental health},
volume = {12},
number = {},
pages = {e67478},
doi = {10.2196/67478},
pmid = {39869900},
issn = {2368-7959},
mesh = {Humans ; Middle Aged ; Male ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Female ; Adult ; *Severity of Illness Index ; Aged ; Cohort Studies ; *Wearable Electronic Devices ; Young Adult ; Ecological Momentary Assessment ; Sleep/physiology ; Exercise/psychology/physiology ; Self Report ; },
abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.
OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.
METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.
RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P≤.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.
CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.
TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Middle Aged
Male
*Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis
Female
Adult
*Severity of Illness Index
Aged
Cohort Studies
*Wearable Electronic Devices
Young Adult
Ecological Momentary Assessment
Sleep/physiology
Exercise/psychology/physiology
Self Report
RevDate: 2025-01-27
Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.
Emerging microbes & infections [Epub ahead of print].
Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1,122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12,8% (SUEP) and 13% (HAP) respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.
Additional Links: PMID-39868965
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PubMed:
Citation:
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@article {pmid39868965,
year = {2025},
author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S},
title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2459137},
doi = {10.1080/22221751.2025.2459137},
pmid = {39868965},
issn = {2222-1751},
abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1,122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12,8% (SUEP) and 13% (HAP) respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.},
}
RevDate: 2025-01-27
Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.
ArXiv.
In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.
Additional Links: PMID-39830079
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Citation:
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@article {pmid39830079,
year = {2024},
author = {Couch, J and Arnaout, R and Arnaout, R},
title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39830079},
issn = {2331-8422},
support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; },
abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.},
}
RevDate: 2025-01-27
CmpDate: 2025-01-27
TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.
Acta clinica Croatica, 62(4):605-614.
The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.
Additional Links: PMID-39866757
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@article {pmid39866757,
year = {2023},
author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J},
title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.},
journal = {Acta clinica Croatica},
volume = {62},
number = {4},
pages = {605-614},
pmid = {39866757},
issn = {1333-9451},
mesh = {Humans ; Male ; Serbia/epidemiology ; Female ; Adult ; *Obesity/epidemiology ; *Overweight/epidemiology ; Prevalence ; Middle Aged ; *Body Mass Index ; Cross-Sectional Studies ; Health Surveys ; Young Adult ; Aged ; },
abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Male
Serbia/epidemiology
Female
Adult
*Obesity/epidemiology
*Overweight/epidemiology
Prevalence
Middle Aged
*Body Mass Index
Cross-Sectional Studies
Health Surveys
Young Adult
Aged
RevDate: 2025-01-26
CmpDate: 2025-01-26
The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.
Biochemistry. Biokhimiia, 89(12):2274-2286.
Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.
Additional Links: PMID-39865039
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PubMed:
Citation:
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@article {pmid39865039,
year = {2024},
author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA},
title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {12},
pages = {2274-2286},
doi = {10.1134/S0006297924120150},
pmid = {39865039},
issn = {1608-3040},
mesh = {Humans ; *Trace Elements/metabolism/analysis ; Minerals/metabolism ; Sequence Analysis, RNA ; Neoplasms/genetics/metabolism ; Male ; Colorectal Neoplasms/genetics/metabolism ; Female ; Gene Expression Profiling ; Multiomics ; },
abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Trace Elements/metabolism/analysis
Minerals/metabolism
Sequence Analysis, RNA
Neoplasms/genetics/metabolism
Male
Colorectal Neoplasms/genetics/metabolism
Female
Gene Expression Profiling
Multiomics
RevDate: 2025-01-25
CmpDate: 2025-01-25
Elephant Sound Classification Using Deep Learning Optimization.
Sensors (Basel, Switzerland), 25(2): pii:s25020352.
Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.
Additional Links: PMID-39860723
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PubMed:
Citation:
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@article {pmid39860723,
year = {2025},
author = {Dewmini, H and Meedeniya, D and Perera, C},
title = {Elephant Sound Classification Using Deep Learning Optimization.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {2},
pages = {},
doi = {10.3390/s25020352},
pmid = {39860723},
issn = {1424-8220},
mesh = {*Elephants/physiology ; *Deep Learning ; Animals ; *Vocalization, Animal/physiology ; *Bayes Theorem ; Sound Spectrography/methods ; Sound ; Algorithms ; },
abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Elephants/physiology
*Deep Learning
Animals
*Vocalization, Animal/physiology
*Bayes Theorem
Sound Spectrography/methods
Sound
Algorithms
RevDate: 2025-01-24
Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.
Scientific reports, 15(1):3037.
This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.
Additional Links: PMID-39856257
PubMed:
Citation:
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@article {pmid39856257,
year = {2025},
author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T},
title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3037},
pmid = {39856257},
issn = {2045-2322},
support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; },
abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.},
}
RevDate: 2025-01-24
CmpDate: 2025-01-24
Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.
PloS one, 20(1):e0316255 pii:PONE-D-24-36597.
Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.
Additional Links: PMID-39854555
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PubMed:
Citation:
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@article {pmid39854555,
year = {2025},
author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F},
title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316255},
doi = {10.1371/journal.pone.0316255},
pmid = {39854555},
issn = {1932-6203},
mesh = {China ; *Rivers ; *Conservation of Natural Resources/methods ; *Carbon/metabolism/analysis ; Models, Theoretical ; Carbon Sequestration ; Ecosystem ; Spatio-Temporal Analysis ; Computer Simulation ; Humans ; Agriculture/methods ; },
abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
China
*Rivers
*Conservation of Natural Resources/methods
*Carbon/metabolism/analysis
Models, Theoretical
Carbon Sequestration
Ecosystem
Spatio-Temporal Analysis
Computer Simulation
Humans
Agriculture/methods
RevDate: 2025-01-24
CmpDate: 2025-01-24
Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.
PloS one, 20(1):e0292418 pii:PONE-D-23-28302.
Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.
Additional Links: PMID-39854538
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@article {pmid39854538,
year = {2025},
author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K},
title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0292418},
doi = {10.1371/journal.pone.0292418},
pmid = {39854538},
issn = {1932-6203},
mesh = {*Fertilizers/analysis ; Animals ; *Insecta ; Models, Theoretical ; Agriculture/methods ; Computer Simulation ; },
abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.},
}
MeSH Terms:
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*Fertilizers/analysis
Animals
*Insecta
Models, Theoretical
Agriculture/methods
Computer Simulation
RevDate: 2025-01-24
Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.
The New phytologist [Epub ahead of print].
A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.
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@article {pmid39853577,
year = {2025},
author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K},
title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20405},
pmid = {39853577},
issn = {1469-8137},
support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; },
abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.},
}
RevDate: 2025-01-22
CmpDate: 2025-01-22
Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.
Scientific reports, 15(1):2778.
Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.
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@article {pmid39843543,
year = {2025},
author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C},
title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2778},
pmid = {39843543},
issn = {2045-2322},
support = {GJC22071//Cariplo Telethon Alliance/ ; },
mesh = {*Rett Syndrome/genetics ; Humans ; Animals ; *Alternative Splicing ; Mice ; *Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Computational Biology/methods ; Mutation ; },
abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.},
}
MeSH Terms:
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hide MeSH Terms
*Rett Syndrome/genetics
Humans
Animals
*Alternative Splicing
Mice
*Disease Models, Animal
*Methyl-CpG-Binding Protein 2/genetics/metabolism
Gene Expression Profiling
Gene Expression Regulation
Computational Biology/methods
Mutation
RevDate: 2025-01-22
CmpDate: 2025-01-22
Asthma-related deaths in Brazil: data from an ecological study.
Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia, 50(6):e20240296 pii:S1806-37132024000600608.
OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.
METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.
RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 ± 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.
CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.
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@article {pmid39841777,
year = {2025},
author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF},
title = {Asthma-related deaths in Brazil: data from an ecological study.},
journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia},
volume = {50},
number = {6},
pages = {e20240296},
doi = {10.36416/1806-3756/e20240296},
pmid = {39841777},
issn = {1806-3756},
mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Hospitalization/statistics & numerical data ; Young Adult ; Adolescent ; Child ; Sex Distribution ; Age Distribution ; Child, Preschool ; Aged ; Infant ; Sex Factors ; Age Factors ; Cause of Death ; Time Factors ; },
abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.
METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.
RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 ± 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.
CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Brazil/epidemiology
*Asthma/mortality/epidemiology
Male
Female
Middle Aged
Adult
*Hospitalization/statistics & numerical data
Young Adult
Adolescent
Child
Sex Distribution
Age Distribution
Child, Preschool
Aged
Infant
Sex Factors
Age Factors
Cause of Death
Time Factors
RevDate: 2025-01-22
Recent advances in deep learning and language models for studying the microbiome.
Frontiers in genetics, 15:1494474.
Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.
Additional Links: PMID-39840283
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@article {pmid39840283,
year = {2024},
author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S},
title = {Recent advances in deep learning and language models for studying the microbiome.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1494474},
pmid = {39840283},
issn = {1664-8021},
abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.},
}
RevDate: 2025-01-22
CmpDate: 2025-01-22
GOPhage: protein function annotation for bacteriophages by integrating the genomic context.
Briefings in bioinformatics, 26(1):.
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.
Additional Links: PMID-39838963
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PubMed:
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@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
MeSH Terms:
show MeSH Terms
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*Bacteriophages/genetics
*Genome, Viral
*Molecular Sequence Annotation
*Viral Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods
Software
RevDate: 2025-01-21
CmpDate: 2025-01-21
The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.
Molecular ecology, 34(1):e17591.
Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.
Additional Links: PMID-39558756
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@article {pmid39558756,
year = {2025},
author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR},
title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.},
journal = {Molecular ecology},
volume = {34},
number = {1},
pages = {e17591},
pmid = {39558756},
issn = {1365-294X},
support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; },
mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; },
abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Genome
*Transcription, Genetic/drug effects
*Adaptation, Physiological/drug effects/genetics
*Rivers
*Water Pollutants, Chemical/toxicity
*Salmon/genetics/physiology
Gene Expression Profiling
Gene Expression Regulation/drug effects
*Metals/toxicity
United Kingdom
Genetic Loci
Gene Library
Metagenomics
Organ Specificity/drug effects
Gene Ontology
Animals
RevDate: 2025-01-20
CmpDate: 2025-01-21
Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.
Journal of epidemiology and global health, 15(1):2.
BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.
METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.
RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group > = 15 years compared to < 15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.
CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.
Additional Links: PMID-39833495
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Citation:
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@article {pmid39833495,
year = {2025},
author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S},
title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {2},
pmid = {39833495},
issn = {2210-6014},
mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology ; Male ; Female ; Adolescent ; Retrospective Studies ; Adult ; Middle Aged ; Young Adult ; Child ; Child, Preschool ; Infant ; Climate ; Disease Outbreaks/statistics & numerical data ; Yellow fever virus ; Risk Factors ; Socioeconomic Factors ; Sociodemographic Factors ; Population Surveillance/methods ; },
abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.
METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.
RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group > = 15 years compared to < 15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.
CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Nigeria/epidemiology
*Yellow Fever/epidemiology
Male
Female
Adolescent
Retrospective Studies
Adult
Middle Aged
Young Adult
Child
Child, Preschool
Infant
Climate
Disease Outbreaks/statistics & numerical data
Yellow fever virus
Risk Factors
Socioeconomic Factors
Sociodemographic Factors
Population Surveillance/methods
RevDate: 2025-01-20
CmpDate: 2025-01-20
PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.
Briefings in bioinformatics, 26(1):.
Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.
Additional Links: PMID-39833104
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@article {pmid39833104,
year = {2024},
author = {Liu, F and Zhao, Z and Liu, Y},
title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf017},
pmid = {39833104},
issn = {1477-4054},
support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; },
mesh = {*Bacteriophages/genetics ; Algorithms ; Software ; Computational Biology/methods ; Host-Pathogen Interactions/genetics ; Bacteria/virology/genetics ; Phage Therapy ; },
abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.},
}
MeSH Terms:
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*Bacteriophages/genetics
Algorithms
Software
Computational Biology/methods
Host-Pathogen Interactions/genetics
Bacteria/virology/genetics
Phage Therapy
RevDate: 2025-01-20
CmpDate: 2025-01-20
Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.
BMJ open, 15(1):e089521 pii:bmjopen-2024-089521.
OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.
DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.
SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.
PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.
DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.
RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100 000 women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).
CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.
Additional Links: PMID-39832988
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@article {pmid39832988,
year = {2025},
author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG},
title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089521},
doi = {10.1136/bmjopen-2024-089521},
pmid = {39832988},
issn = {2044-6055},
mesh = {Humans ; Ethiopia/epidemiology ; *Uterine Cervical Neoplasms/epidemiology/prevention & control ; Female ; Incidence ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Young Adult ; Bayes Theorem ; Aged ; Geographic Information Systems ; Adolescent ; Papillomavirus Vaccines ; },
abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.
DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.
SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.
PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.
DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.
RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100 000 women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).
CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Ethiopia/epidemiology
*Uterine Cervical Neoplasms/epidemiology/prevention & control
Female
Incidence
Adult
Middle Aged
*Spatio-Temporal Analysis
Young Adult
Bayes Theorem
Aged
Geographic Information Systems
Adolescent
Papillomavirus Vaccines
RevDate: 2025-01-20
CmpDate: 2025-01-20
Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.
Central European journal of public health, 32(Supplement):18-24.
OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.
METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.
RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 ± 4.13) and depression in the HADS-D subscale (9.09 ± 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.
CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.
Additional Links: PMID-39832144
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@article {pmid39832144,
year = {2024},
author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K},
title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.},
journal = {Central European journal of public health},
volume = {32},
number = {Supplement},
pages = {18-24},
pmid = {39832144},
issn = {1210-7778},
mesh = {Humans ; Female ; Male ; Middle Aged ; Aged ; Slovakia/epidemiology ; Aged, 80 and over ; *Stroke/epidemiology/psychology ; Anxiety/epidemiology ; Depressive Disorder/epidemiology ; Surveys and Questionnaires ; Depression/epidemiology ; Anxiety Disorders/epidemiology ; },
abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.
METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.
RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 ± 4.13) and depression in the HADS-D subscale (9.09 ± 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.
CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Female
Male
Middle Aged
Aged
Slovakia/epidemiology
Aged, 80 and over
*Stroke/epidemiology/psychology
Anxiety/epidemiology
Depressive Disorder/epidemiology
Surveys and Questionnaires
Depression/epidemiology
Anxiety Disorders/epidemiology
RevDate: 2025-01-20
Sesterterpenoids: sources, structural diversity, biological activity, and data management.
Natural product reports [Epub ahead of print].
Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.
Additional Links: PMID-39832137
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PubMed:
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@article {pmid39832137,
year = {2025},
author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A},
title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00041b},
pmid = {39832137},
issn = {1460-4752},
abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.},
}
RevDate: 2025-01-20
A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.
Communications earth & environment, 6(1):21.
Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.
Additional Links: PMID-39830898
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@article {pmid39830898,
year = {2025},
author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T},
title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.},
journal = {Communications earth & environment},
volume = {6},
number = {1},
pages = {21},
doi = {10.1038/s43247-024-01883-w},
pmid = {39830898},
issn = {2662-4435},
abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.},
}
RevDate: 2025-01-18
Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.
International journal of biological macromolecules pii:S0141-8130(25)00529-X [Epub ahead of print].
Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.
Additional Links: PMID-39826720
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PubMed:
Citation:
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@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}
RevDate: 2025-01-20
The long way from raw data to NAM-based information: Overview on data layers and processing steps.
ALTEX, 42(1):167-180.
Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, processing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the development and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxicological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.
Additional Links: PMID-39817434
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PubMed:
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@article {pmid39817434,
year = {2025},
author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M},
title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.},
journal = {ALTEX},
volume = {42},
number = {1},
pages = {167-180},
doi = {10.14573/altex.2412171},
pmid = {39817434},
issn = {1868-8551},
abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, processing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the development and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxicological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.},
}
RevDate: 2025-01-20
CmpDate: 2025-01-20
Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.
Annals of internal medicine, 178(1):1-10.
BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.
OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.
DESIGN: Cohort study.
SETTING: United Kingdom.
PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.
MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.
RESULTS: In 388 224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P < 0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P < 0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.
LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.
CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.
PRIMARY FUNDING SOURCE: National Human Genome Research Institute.
Additional Links: PMID-39652873
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PubMed:
Citation:
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@article {pmid39652873,
year = {2025},
author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ},
title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.},
journal = {Annals of internal medicine},
volume = {178},
number = {1},
pages = {1-10},
doi = {10.7326/ANNALS-24-00716},
pmid = {39652873},
issn = {1539-3704},
mesh = {Humans ; Male ; United Kingdom/epidemiology ; Middle Aged ; *Coronary Disease/epidemiology ; Female ; Prospective Studies ; Risk Assessment ; *Life Style ; Risk Factors ; Incidence ; Social Determinants of Health ; Machine Learning ; UK Biobank ; },
abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.
OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.
DESIGN: Cohort study.
SETTING: United Kingdom.
PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.
MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.
RESULTS: In 388 224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P < 0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P < 0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.
LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.
CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.
PRIMARY FUNDING SOURCE: National Human Genome Research Institute.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Male
United Kingdom/epidemiology
Middle Aged
*Coronary Disease/epidemiology
Female
Prospective Studies
Risk Assessment
*Life Style
Risk Factors
Incidence
Social Determinants of Health
Machine Learning
UK Biobank
RevDate: 2025-01-20
The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).
Wellcome open research, 8:375.
We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.
Additional Links: PMID-39830091
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@article {pmid39830091,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {375},
doi = {10.12688/wellcomeopenres.19840.1},
pmid = {39830091},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.},
}
RevDate: 2025-01-17
CmpDate: 2025-01-17
First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.
Parasites & vectors, 18(1):14.
BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.
METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.
RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).
CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.
Additional Links: PMID-39825388
PubMed:
Citation:
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@article {pmid39825388,
year = {2025},
author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM},
title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {14},
pmid = {39825388},
issn = {1756-3305},
support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; },
mesh = {Animals ; Female ; *Encephalitis Viruses, Tick-Borne/physiology/isolation & purification/genetics ; *Kyasanur Forest Disease/transmission/virology ; India/epidemiology ; *Larva/virology ; *Rhipicephalus/virology ; *Ixodidae/virology ; Arachnid Vectors/virology ; },
abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.
METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.
RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).
CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
Female
*Encephalitis Viruses, Tick-Borne/physiology/isolation & purification/genetics
*Kyasanur Forest Disease/transmission/virology
India/epidemiology
*Larva/virology
*Rhipicephalus/virology
*Ixodidae/virology
Arachnid Vectors/virology
RevDate: 2025-01-17
CmpDate: 2025-01-17
Evaluating the performance of multi-omics integration: a thyroid toxicity case study.
Archives of toxicology, 99(1):309-332.
Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.
Additional Links: PMID-39441382
PubMed:
Citation:
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@article {pmid39441382,
year = {2025},
author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J},
title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.},
journal = {Archives of toxicology},
volume = {99},
number = {1},
pages = {309-332},
pmid = {39441382},
issn = {1432-0738},
support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; },
mesh = {Animals ; *Thyroid Gland/drug effects/pathology ; *Propylthiouracil/toxicity ; Rats ; Metabolomics ; Proteomics ; Transcriptome/drug effects ; Male ; Genomics ; Risk Assessment ; Female ; Antithyroid Agents/toxicity ; Rats, Sprague-Dawley ; Proteome/metabolism ; Multiomics ; },
abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Thyroid Gland/drug effects/pathology
*Propylthiouracil/toxicity
Rats
Metabolomics
Proteomics
Transcriptome/drug effects
Male
Genomics
Risk Assessment
Female
Antithyroid Agents/toxicity
Rats, Sprague-Dawley
Proteome/metabolism
Multiomics
RevDate: 2025-01-17
The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis & Schiffermüller, 1775).
Wellcome open research, 9:696.
We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.
Additional Links: PMID-39822595
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PubMed:
Citation:
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@article {pmid39822595,
year = {2024},
author = {Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {696},
doi = {10.12688/wellcomeopenres.23371.1},
pmid = {39822595},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.},
}
RevDate: 2025-01-17
Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.
Biodiversity data journal, 13:e138257 pii:138257.
BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.
NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.
Additional Links: PMID-39822261
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Citation:
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@article {pmid39822261,
year = {2025},
author = {Proença Neto, MA and De Sousa, MPA},
title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e138257},
doi = {10.3897/BDJ.13.e138257},
pmid = {39822261},
issn = {1314-2828},
abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.
NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.},
}
RevDate: 2025-01-17
CmpDate: 2025-01-17
A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.
Drug development research, 86(1):e70045.
Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.
Additional Links: PMID-39821365
Publisher:
PubMed:
Citation:
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@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics & numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Famotidine/adverse effects
*Adverse Drug Reaction Reporting Systems/statistics & numerical data
United States/epidemiology
*Histamine H2 Antagonists/adverse effects
*Pharmacovigilance
*United States Food and Drug Administration
Female
Male
Adult
Middle Aged
Aged
Adolescent
Young Adult
Child
Child, Preschool
Drug-Related Side Effects and Adverse Reactions/epidemiology
Databases, Factual
Infant
RevDate: 2025-01-17
CmpDate: 2025-01-17
BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.
ACS synthetic biology, 14(1):285-289.
Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.
Additional Links: PMID-39423319
Publisher:
PubMed:
Citation:
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@article {pmid39423319,
year = {2025},
author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN},
title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.},
journal = {ACS synthetic biology},
volume = {14},
number = {1},
pages = {285-289},
doi = {10.1021/acssynbio.4c00347},
pmid = {39423319},
issn = {2161-5063},
mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; Databases, Factual ; Software ; Computational Biology/methods ; },
abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Synthetic Biology/methods
*Knowledge Bases
Databases, Factual
Software
Computational Biology/methods
RevDate: 2025-01-17
CmpDate: 2025-01-17
Quality assessment of gene repertoire annotations with OMArk.
Nature biotechnology, 43(1):124-133.
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.
Additional Links: PMID-38383603
PubMed:
Citation:
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@article {pmid38383603,
year = {2025},
author = {Nevers, Y and Warwick Vesztrocy, A and Rossier, V and Train, CM and Altenhoff, A and Dessimoz, C and Glover, NM},
title = {Quality assessment of gene repertoire annotations with OMArk.},
journal = {Nature biotechnology},
volume = {43},
number = {1},
pages = {124-133},
pmid = {38383603},
issn = {1546-1696},
mesh = {*Software ; *Molecular Sequence Annotation ; *Proteome/genetics ; Animals ; Databases, Protein ; Genomics/methods ; },
abstract = {In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Software
*Molecular Sequence Annotation
*Proteome/genetics
Animals
Databases, Protein
Genomics/methods
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RJR Experience and Expertise
Researcher
Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.
Educator
Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.
Administrator
Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.
Technologist
Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.
Publisher
While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.
Speaker
Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.
Facilitator
Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.
Designer
Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.
RJR Picks from Around the Web (updated 11 MAY 2018 )
Old Science
Weird Science
Treating Disease with Fecal Transplantation
Fossils of miniature humans (hobbits) discovered in Indonesia
Paleontology
Dinosaur tail, complete with feathers, found preserved in amber.
Astronomy
Mysterious fast radio burst (FRB) detected in the distant universe.
Big Data & Informatics
Big Data: Buzzword or Big Deal?
Hacking the genome: Identifying anonymized human subjects using publicly available data.