@article {pmid40841825,
year = {2025},
author = {De Rovere, F and Mastropierro, M and Jungclaus, JH and Khodri, M and Rubino, A and Zanchettin, D},
title = {Future Atlantification of the European Arctic limited under sustained global warming.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30802},
pmid = {40841825},
issn = {2045-2322},
support = {2022CCRN7R, "ATTRACTION - ATlantificaTion dRiven by polAr-subpolar ConnecTIONs", CUP: H53D23001550006//Next-GenerationEU - PNRR - M.4 C.2, INVESTIMENTO 1.1 - PRIN22/ ; },
abstract = {Atlantification is an ongoing oceanic phenomenon characterised by the expansion of the typical Atlantic domain towards the Arctic, driving rapid oceanic and ecological changes in the European Arctic. Using reanalyses and a multi-model ensemble of unperturbed and transient preindustrial, historical and future-scenario simulations, this study shows that modern Atlantification possibly initiated in the late nineteenth century, preceded by several "Arctification" episodes in the preindustrial millennium. In the historical period, Atlantification and pan-Arctic warming superposed constructively to drive upper-ocean warming and salinification in the Barents Sea. Modern Atlantification is projected to continue in the next few decades, fully revealing its exceptional character in the context of the past millennium. However, Atlantification halts during the second half of the twenty-first century, decoupling from pan-Arctic warming. The northward expansion of the Atlantic domain is hindered by the onset of a damping mechanism where the Atlantic-Arctic density gradient increases progressively, which sustains a countercurrent by baroclinic adjustment pushing the Arctic polar front southward. As the evolution of this density gradient is intertwined with the retreat of the sea-ice edge, a late-summer ice-free Barents Sea may mark the end of modern Atlantification.},
}

@article {pmid40841201,
year = {2025},
author = {Sena, AVDS and Telles, L and Melo, PHM and Salomão, SL and Uzeda, TS and Pereira Lima, BL and Kratky, L and Mooney, DP and Bustorff-Silva, J},
title = {The management of cryptorchidism in Brazil: An ecological overview.},
journal = {Journal of pediatric urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jpurol.2025.07.025},
pmid = {40841201},
issn = {1873-4898},
abstract = {INTRODUCTION: Cryptorchidism refers to the extra-scrotal location of the testicle and is the most common male genital anomaly. Although the recommended age ranges for both hormonal and surgical treatments are well-established, within the Brazilian Unified Health System (SUS), children with cryptorchidism undergo surgery at varying ages across the country. As a time-sensitive procedure, delayed orchidopexy has consequences such as an increased risk of infertility or even testicular cancer. Correlating data on cryptorchidism treatment in SUS with geographic and socioeconomic indicators may help to understand how a population's profile influences the public healthcare system. This study explores the potential relationship between the age at which orchiopexy is performed and the quality of public healthcare services in Brazil while also assessing the impact of the COVID-19 pandemic on this surgery's backlog.

METHODS: To achieve this, we collected data from the Department of Informatics of the Brazilian Public Health System (DATASUS) and indicators provided by the Brazilian Institute of Geography (IBGE) and the Institute for Applied Economic Research (IPEA). We cataloged and compiled the data for comprehensive analysis.

RESULTS: Between 2008 and 2022, 94,237 orchiopexies were performed in SUS in patients aged 0-15. Nationwide, this represents only 47.6 % of the expected procedures, ranging from 22.75 % in the North to 68.18 % in the South. The proportion of surgeries performed before age 2 was very low, ranging from 12 % in the North and Northeast to 24 % in the South. Most orchiopexies in Brazil were performed after the age of five. The COVID-19 pandemic significantly worsened this situation, causing a 44.45 % decline in surgeries in 2020 compared to 2019, disproportionately affecting all age groups and exacerbating the backlog of surgeries.

CONCLUSION: Our study indicates that many children with cryptorchidism remain undiagnosed or receive delayed treatment. The COVID-19 pandemic further worsened this scenario, temporarily reducing the number of operations. These findings underscore the urgent need for comprehensive public policies to improve healthcare access and prevent complications associated with untreated cryptorchism.},
}

@article {pmid40838167,
year = {2025},
author = {Boyes, D and Fletcher, C and Phillips, D and Sivess, L and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {189},
pmid = {40838167},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Archips podanus (Tortix moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 549.00 megabases. Most of the assembly (99.72%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.45 kilobases.},
}

@article {pmid40829560,
year = {2025},
author = {McKnight, JC and Solms, B and Jensen, M and Turnbull, J and Balfour, S and Laagland, M and Bronkhorst, M and Lee, HJ and Kang, G and Lee, JY and Bell, A and Hastie, G and Ilardo, M},
title = {Diving behaviour and physiology of the Korean Haenyeo.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R797-R798},
doi = {10.1016/j.cub.2025.06.066},
pmid = {40829560},
issn = {1879-0445},
mesh = {*Diving/physiology ; Humans ; Female ; Adult ; Republic of Korea ; },
abstract = {There is a long history of breath-hold diving cultures in East Asia, with references in Japanese chronicles as early as the third century BC. Given evidence of genetic adaptations for phenotypes associated with enhanced diving capacity within such populations[1], it is likely they hold the most prodigious human diving abilities - abilities that may be akin to semi-aquatic mammals, and even some marine mammals. Yet, a dearth of fine-scale information exists on the combined natural diving behaviour and physiological responses within these diving populations. One such extraordinary population is the all-female Haenyeo. Here, we assess the fine-scale diving behaviours and physiological responses of these women during natural harvest diving. Our results show that Haenyeo divers demonstrate the highest proportions of time underwater of any humans, also exceeding those of semi-aquatic mammals and being comparable with some marine mammals. Additionally, they do not exhibit an overt cardiovascular depression, or 'dive response', classically associated with consummate diving mammals.},
}

*Diving/physiology
Humans
Female
Adult
Republic of Korea

@article {pmid40827702,
year = {2025},
author = {Chung, J and Moloney, ME and Seixas, AA and Jackson, CL},
title = {The Environment Around the Sleeper is Changing: A Perspective.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsaf235},
pmid = {40827702},
issn = {1550-9109},
abstract = {Sleep is shaped by a complex interplay of biological, behavioral, and environmental factors. While substantial attention has been paid to the first two factors, the role of environmental exposures, particularly weather patterns, ambient temperature variability, and other dynamic atmospheric conditions, remains relatively underexplored in sleep research. This gap is notable given the increasing availability of high-resolution environmental data and growing evidence that ambient conditions can influence circadian regulation, thermal comfort, and sleep continuity. This perspective paper reviews emerging evidence linking environmental factors to sleep patterns, highlighting both direct effects (e.g., thermal disruptions) and indirect pathways (e.g., displacement or stress from extreme weather events). Recent advances in environmental sensing, geospatial data, and real-time monitoring offer new opportunities to capture high-resolution environmental data relevant to sleep. This perspective highlights the need for data infrastructure capable of integrating these dynamic environmental inputs with sleep metrics from, for instance, wearables, surveys, and clinical records. We also examine the methodological and informatics challenges of integrating environmental data with sleep measures and suggest directions for future research. As environmental conditions evolve, understanding their influence on sleep holds promise for advancing both scientific knowledge and public health relevance, particularly in identifying affected populations, designing responsive interventions, and contextualizing sleep within broader ecological systems.},
}

@article {pmid40825407,
year = {2025},
author = {Tarandek, A and Boštjančić, LL and Francesconi, C and Bonassin, L and Schardt, L and Jussila, J and Kokko, H and Schwenk, K and Hudina, S and Lecompte, O and Theissinger, K},
title = {Characterisation of the noble crayfish immune response to oomycete-derived immunostimulants.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110666},
doi = {10.1016/j.fsi.2025.110666},
pmid = {40825407},
issn = {1095-9947},
abstract = {The invasive oomycete pathogen Aphanomyces astaci significantly threatens native European crayfish populations, prompting investigations towards the effects of protective immunostimulation on the immune response of the vulnerable noble crayfish (Astacus astacus). Here, we evaluate the effect of three oomycete-derived immunostimulant treatments: laminarin (β-1,3-glucan found within the Ap. astaci cell wall), inactivated Ap. astaci spores and Ap. astaci hyphal homogenate. Our findings reveal immediate changes in the noble crayfish total haemocyte count (THC), differential haemocyte count (DHC), and gene expression. A short-term increase in the THC was observed in all treatments, with a gradual return to normal values eight hours post immunostimulation. Granular haemocytes seem to be involved in response to immunostimulation with inactivated Ap. astaci spores, while the number of semi-granular and hyaline haemocytes increased in response to laminarin and Ap. astaci hyphal homogenate. Analysis of the differentially expressed genes showed that the prophenoloxidase pathway genes and Toll pathway genes are involved in the response to oomycete-derived immunostimulants. Prolonged effects of immunostimulation were reflected in the decreased C/EBP and Kr-h1 gene expression in the hyphal homogenate group as well as decreased Kr-h1 expression in the spore group. Taken together, our results indicate that immunostimulation causes a dynamic change in the noble crayfish immune system response, with similarities in the gene expression patterns between immunostimulated and Ap. astaci infected noble crayfish. As a future research focus, we highlight the importance of molecular characterisation of the genes involved in the anti-oomycete response which could provide valuable insights into pathogen resistance in freshwater crayfish. In the context of the Ap. astaci mediated downfall of the noble crayfish stocks across Europe, further exploration is needed regarding the benefits of the oomycete-derived immunostimulation that can potentially support conservation and aquacultural efforts.},
}

@article {pmid40818234,
year = {2025},
author = {Poudel, B and Xie, J and Guo, C and Watt, OE and Pulster, EL and Patel, RJ and Steevens, JA and Xu, D},
title = {Real-time oil spill concentration assessment through fluorescence imaging and deep learning.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139374},
doi = {10.1016/j.jhazmat.2025.139374},
pmid = {40818234},
issn = {1873-3336},
abstract = {Oil spills may pose severe ecological and socioeconomic threats, necessitating rapid and accurate environmental assessment. Traditional assessment methods used to determine the extent of a spill including gas chromatography-mass spectrometry, satellite imaging, and visual surveys, are often time-consuming, expensive, and limited by weather conditions or sampling constraints. Furthermore, these methods frequently struggle to provide real-time data crucial for prompt decision-making during spill emergencies. This study addresses these limitations by combining fluorescence imaging, deep learning, a mobile application, and a data management system for automated and real-time oil spill assessment. Our approach leverages a convolutional neural network architecture for feature extraction coupled with a custom regression model, trained and evaluated on a self-curated comprehensive dataset of 1530 fluorescence images from two distinct oil types, a napthalenic crude oil and an aromatic-napthalenic crude oil, at concentrations ranging from 0 to 500 mg/L. The proposed approach demonstrates superior performance compared to both traditional machine learning models and more complex deep learning architectures, achieving an R[2] score of 0.9958 and RMSE of 9.28. The application enables rapid, cost-effective field measurements with robust data tracking and analysis capabilities. This research advances oil spill monitoring technology with a scalable solution that balances accuracy, speed, and accessibility for real-time environmental assessment and emergency response.},
}

@article {pmid39981105,
year = {2025},
author = {Plaitano, EG and McNeish, D and Bartels, SM and Bell, K and Dallery, J and Grabinski, M and Kiernan, M and Lavoie, HA and Lemley, SM and Lowe, MR and MacKinnon, DP and Metcalf, SA and Onken, L and Prochaska, JJ and Sand, CL and Scherer, EA and Stoeckel, LE and Xie, H and Marsch, LA},
title = {Adherence to a digital therapeutic mediates the relationship between momentary self-regulation and health risk behaviors.},
journal = {Frontiers in digital health},
volume = {7},
number = {},
pages = {1467772},
pmid = {39981105},
issn = {2673-253X},
support = {P30 DA029926/DA/NIDA NIH HHS/United States ; R37 DA009757/DA/NIDA NIH HHS/United States ; T32 DA037202/DA/NIDA NIH HHS/United States ; UH3 DA041713/DA/NIDA NIH HHS/United States ; },
abstract = {INTRODUCTION: Smoking, obesity, and insufficient physical activity are modifiable health risk behaviors. Self-regulation is one fundamental behavior change mechanism often incorporated within digital therapeutics as it varies momentarily across time and contexts and may play a causal role in improving these health behaviors. However, the role of momentary self-regulation in achieving behavior change has been infrequently examined. Using a novel momentary self-regulation scale, this study examined how targeting self-regulation through a digital therapeutic impacts adherence to the therapeutic and two different health risk behavioral outcomes.

METHODS: This prospective interventional study included momentary data for 28 days from 50 participants with obesity and binge eating disorder and 50 participants who smoked regularly. An evidence-based digital therapeutic, called Laddr™, provided self-regulation behavior change tools. Participants reported on their momentary self-regulation via ecological momentary assessments and health risk behaviors were measured as steps taken from a physical activity tracker and breathalyzed carbon monoxide. Medical regimen adherence was assessed as daily Laddr usage. Bayesian dynamic mediation models were used to examine moment-to-moment mediation effects between momentary self-regulation subscales, medical regimen adherence, and behavioral outcomes.

RESULTS: In the binge eating disorder sample, the perseverance [β 1 = 0.17, 95% CI = (0.06, 0.45)] and emotion regulation [β 1 = 0.12, 95% CI = (0.03, 0.27)] targets of momentary self-regulation positively predicted Laddr adherence on the following day, and higher Laddr adherence was subsequently a positive predictor of steps taken the same day for both perseverance [β 2 = 0.335, 95% CI = (0.030, 0.717)] and emotion regulation [β 2 = 0.389, 95% CI = (0.080, 0.738)]. In the smoking sample, the perseverance target of momentary self-regulation positively predicted Laddr adherence on the following day [β = 0.91, 95% CI = (0.60, 1.24)]. However, higher Laddr adherence was not a predictor of CO values on the same day [β 2 = -0.09, 95% CI = (-0.24, 0.09)].

CONCLUSIONS: This study provides evidence that a digital therapeutic targeting self-regulation can modify the relationships between momentary self-regulation, medical regimen adherence, and behavioral health outcomes. Together, this work demonstrated the ability to digitally assess the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and pro-health behavioral outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier (NCT03774433).},
}

@article {pmid38416313,
year = {2024},
author = {Vigna-Taglianti, FD and Martorana, M and Viola, E and Renna, M and Vadrucci, S and Sciutto, A and Andrà, C and Mehanović, E and Ginechesi, M and Vullo, C and Ceccano, A and Casella, P and Faggiano, F and , },
title = {Evaluation of Effectiveness of the Unplugged Program on Gambling Behaviours among Adolescents: Study Protocol of the Experimental Controlled Study "GAPUnplugged".},
journal = {Journal of prevention (2022)},
volume = {45},
number = {3},
pages = {405-429},
pmid = {38416313},
issn = {2731-5541},
support = {0005406//ASLRoma1/ ; },
mesh = {Humans ; *Gambling/prevention & control/psychology ; Adolescent ; Female ; Male ; Surveys and Questionnaires ; Adolescent Behavior/psychology ; Program Evaluation ; Risk-Taking ; Students/psychology ; Italy ; },
abstract = {Gambling risk behaviour is an emerging problem among adolescents. "Unplugged" is an effective Social Influence curriculum for preventing substance use among students. This study aims to develop and test a new component focused on gambling added to the Unplugged program. Schools of Piedmont region and Rome city were invited to participate in the study. A self-completed anonymous questionnaire including questions on socio-demographic characteristics, addictive behaviours, beliefs, attitudes and risk perceptions about gambling, normative perceptions, parental practices, school climate, refusal skills, impulsiveness, self-esteem, antisocial behaviours and sensation seeking was prepared for baseline and follow-up surveys. The protocol of the study was submitted and approved by the Novara Ethical Committee and registered in ClinicalTrials.gov (NCT05630157, Protocol ID: 080.742, 11/17/2022). Twenty-nine schools accepted to participate in the study. Sixty-three classes (1325 students) satisfied the eligibility criteria for intervention and were allocated to the intervention arm, and the other 61 (1269 students) were allocated to the control arm. Because of drop-out, absentees, refusals, and invalid questionnaires, data on 1874 students (998 in the intervention and 876 in the control arm), were available for the analysis at baseline. Data management of follow-up questionnaires is in progress. Results of the present study will be useful to clarify the effectiveness of prevention interventions in reducing gambling behaviours among adolescents. Moreover, this will be the first experience of evaluating a new component focused on a different risk behaviour, added to a curriculum previously shown as effective on other risk behaviours.},
}

Humans
*Gambling/prevention & control/psychology
Adolescent
Female
Male
Surveys and Questionnaires
Adolescent Behavior/psychology
Program Evaluation
Risk-Taking
Students/psychology
Italy

@article {pmid35373179,
year = {2022},
author = {Scherer, EA and Metcalf, SA and Whicker, CL and Bartels, SM and Grabinski, M and Kim, SJ and Sweeney, MA and Lemley, SM and Lavoie, H and Xie, H and Bissett, PG and Dallery, J and Kiernan, M and Lowe, MR and Onken, L and Prochaska, JJ and Stoeckel, LE and Poldrack, RA and MacKinnon, DP and Marsch, LA},
title = {Momentary Influences on Self-Regulation in Two Populations With Health Risk Behaviors: Adults Who Smoke and Adults Who Are Overweight and Have Binge-Eating Disorder.},
journal = {Frontiers in digital health},
volume = {4},
number = {},
pages = {798895},
pmid = {35373179},
issn = {2673-253X},
support = {P30 DA029926/DA/NIDA NIH HHS/United States ; UH2 DA041713/DA/NIDA NIH HHS/United States ; UH3 DA041713/DA/NIDA NIH HHS/United States ; },
abstract = {INTRODUCTION: Self-regulation has been implicated in health risk behaviors and is a target of many health behavior interventions. Despite most prior research focusing on self-regulation as an individual-level trait, we hypothesize that self-regulation is a time-varying mechanism of health and risk behavior that may be influenced by momentary contexts to a substantial degree. Because most health behaviors (e.g., eating, drinking, smoking) occur in the context of everyday activities, digital technologies may help us better understand and influence these behaviors in real time. Using a momentary self-regulation measure, the current study (which was part of a larger multi-year research project on the science of behavior change) used ecological momentary assessment (EMA) to assess if self-regulation can be engaged and manipulated on a momentary basis in naturalistic, non-laboratory settings.

METHODS: This one-arm, open-label exploratory study prospectively collected momentary data for 14 days from 104 participants who smoked regularly and 81 participants who were overweight and had binge-eating disorder. Four times per day, participants were queried about momentary self-regulation, emotional state, and social and environmental context; recent smoking and exposure to smoking cues (smoking sample only); and recent eating, binge eating, and exposure to binge-eating cues (binge-eating sample only). This study used a novel, momentary self-regulation measure comprised of four subscales: momentary perseverance, momentary sensation seeking, momentary self-judgment, and momentary mindfulness. Participants were also instructed to engage with Laddr, a mobile application that provides evidence-based health behavior change tools via an integrated platform. The association between momentary context and momentary self-regulation was explored via mixed-effects models. Exploratory assessments of whether recent Laddr use (defined as use within 12 h of momentary responses) modified the association between momentary context and momentary self-regulation were performed via mixed-effects models.

RESULTS: Participants (mean age 35.2; 78% female) in the smoking and binge-eating samples contributed a total of 3,233 and 3,481 momentary questionnaires, respectively. Momentary self-regulation subscales were associated with several momentary contexts, in the combined as well as smoking and binge-eating samples. For example, in the combined sample momentary perseverance was associated with location, positively associated with positive affect, and negatively associated with negative affect, stress, and tiredness. In the smoking sample, momentary perseverance was positively associated with momentary difficulty in accessing cigarettes, caffeine intake, and momentary restraint in smoking, and negatively associated with temptation and urge to smoke. In the binge-eating sample, momentary perseverance was positively associated with difficulty in accessing food and restraint in eating, and negatively associated with urge to binge eat. While recent Laddr use was not associated directly with momentary self-regulation subscales, it did modify several of the contextual associations, including challenging contexts.

CONCLUSIONS: Overall, this study provides preliminary evidence that momentary self-regulation may vary in response to differing momentary contexts in samples from two exemplar populations with risk behaviors. In addition, the Laddr application may modify some of these relationships. These findings demonstrate the possibility of measuring momentary self-regulation in a trans-diagnostic way and assessing the effects of momentary, mobile interventions in context. Health behavior change interventions may consider measuring and targeting momentary self-regulation in addition to trait-level self-regulation to better understand and improve health risk behaviors. This work will be used to inform a later stage of research focused on assessing the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and health outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, Identifier: NCT03352713.},
}

@article {pmid34100767,
year = {2021},
author = {Mascheroni, A and Choe, EK and Luo, Y and Marazza, M and Ferlito, C and Caverzasio, S and Mezzanotte, F and Kaelin-Lang, A and Faraci, F and Puiatti, A and Ratti, PL},
title = {The SleepFit Tablet Application for Home-Based Clinical Data Collection in Parkinson Disease: User-Centric Development and Usability Study.},
journal = {JMIR mHealth and uHealth},
volume = {9},
number = {6},
pages = {e16304},
pmid = {34100767},
issn = {2291-5222},
mesh = {*COVID-19 ; Data Collection ; Humans ; Pandemics ; *Parkinson Disease/drug therapy ; Quality of Life ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Parkinson disease (PD) is a common, multifaceted neurodegenerative disorder profoundly impacting patients' autonomy and quality of life. Assessment in real-life conditions of subjective symptoms and objective metrics of mobility and nonmotor symptoms such as sleep disturbance is strongly advocated. This information would critically guide the adaptation of antiparkinsonian medications and nonpharmacological interventions. Moreover, since the spread of the COVID-19 pandemic, health care practices are being reshaped toward a more home-based care. New technologies could play a pivotal role in this new approach to clinical care. Nevertheless, devices and information technology tools might be unhandy for PD patients, thus dramatically limiting their widespread employment.

OBJECTIVE: The goals of the research were development and usability evaluation of an application, SleepFit, for ecological momentary assessment of objective and subjective clinical metrics at PD patients' homes, and as a remote tool for researchers to monitor patients and integrate and manage data.

METHODS: An iterative and user-centric strategy was employed for the development of SleepFit. The core structure of SleepFit consists of (1) an electronic finger-tapping test; (2) motor, sleepiness, and emotional subjective scales; and (3) a sleep diary. Applicable design, ergonomic, and navigation principles have been applied while tailoring the application to the specific patient population. Three progressively enhanced versions of the application (alpha, v1.0, v2.0) were tested by a total of 56 patients with PD who were asked to perform multiple home assessments 4 times per day for 2 weeks. Patient compliance was calculated as the proportion of completed tasks out of the total number of expected tasks. Satisfaction on the latest version (v2.0) was evaluated as potential willingness to use SleepFit again after the end of the study.

RESULTS: From alpha to v1.0, SleepFit was improved in graphics, ergonomics, and navigation, with automated flows guiding the patients in performing tasks throughout the 24 hours, and real-time data collection and consultation were made possible thanks to a remote web portal. In v2.0, the kiosk-mode feature restricts the use of the tablet to the SleepFit application only, thus preventing users from accidentally exiting the application. A total of 52 (4 dropouts) patients were included in the analyses. Overall compliance (all versions) was 88.89% (5707/6420). SleepFit was progressively enhanced and compliance increased from 87.86% (2070/2356) to 89.92% (2899/3224; P=.04). Among the patients who used v2.0, 96% (25/26) declared they would use SleepFit again.

CONCLUSIONS: SleepFit can be considered a state-of-the-art home-based system that increases compliance in PD patients, ensures high-quality data collection, and works as a handy tool for remote monitoring and data management in clinical research. Thanks to its user-friendliness and modular structure, it could be employed in other clinical studies with minimum adaptation efforts.

TRIAL REGISTRATION: ClinicalTrials.gov NCT02723396; https://clinicaltrials.gov/ct2/show/NCT02723396.},
}

*COVID-19
Data Collection
Humans
Pandemics
*Parkinson Disease/drug therapy
Quality of Life
SARS-CoV-2

@article {pmid22851645,
year = {2012},
author = {Wang, C and Schroeder, KB and Rosenberg, NA},
title = {A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes.},
journal = {Genetics},
volume = {192},
number = {2},
pages = {651-669},
pmid = {22851645},
issn = {1943-2631},
support = {R01 GM081441/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01-HG005855/HG/NHGRI NIH HHS/United States ; R01 HG005855/HG/NHGRI NIH HHS/United States ; R01-GM081441/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Alleles ; Computer Simulation ; Data Interpretation, Statistical ; *Genetics, Population ; Genotype ; Heterozygote ; Humans ; Inbreeding ; Indians, North American ; *Likelihood Functions ; Microsatellite Repeats/*genetics ; *Models, Theoretical ; },
abstract = {Allelic dropout is a commonly observed source of missing data in microsatellite genotypes, in which one or both allelic copies at a locus fail to be amplified by the polymerase chain reaction. Especially for samples with poor DNA quality, this problem causes a downward bias in estimates of observed heterozygosity and an upward bias in estimates of inbreeding, owing to mistaken classifications of heterozygotes as homozygotes when one of the two copies drops out. One general approach for avoiding allelic dropout involves repeated genotyping of homozygous loci to minimize the effects of experimental error. Existing computational alternatives often require replicate genotyping as well. These approaches, however, are costly and are suitable only when enough DNA is available for repeated genotyping. In this study, we propose a maximum-likelihood approach together with an expectation-maximization algorithm to jointly estimate allelic dropout rates and allele frequencies when only one set of nonreplicated genotypes is available. Our method considers estimates of allelic dropout caused by both sample-specific factors and locus-specific factors, and it allows for deviation from Hardy-Weinberg equilibrium owing to inbreeding. Using the estimated parameters, we correct the bias in the estimation of observed heterozygosity through the use of multiple imputations of alleles in cases where dropout might have occurred. With simulated data, we show that our method can (1) effectively reproduce patterns of missing data and heterozygosity observed in real data; (2) correctly estimate model parameters, including sample-specific dropout rates, locus-specific dropout rates, and the inbreeding coefficient; and (3) successfully correct the downward bias in estimating the observed heterozygosity. We find that our method is fairly robust to violations of model assumptions caused by population structure and by genotyping errors from sources other than allelic dropout. Because the data sets imputed under our model can be investigated in additional subsequent analyses, our method will be useful for preparing data for applications in diverse contexts in population genetics and molecular ecology.},
}

Algorithms
Alleles
Computer Simulation
Data Interpretation, Statistical
*Genetics, Population
Genotype
Heterozygote
Humans
Inbreeding
Indians, North American
*Likelihood Functions
Microsatellite Repeats/*genetics
*Models, Theoretical

@article {pmid40822726,
year = {2025},
author = {Piršelová, B and Jakubčinová, J},
title = {Plant cyanogenic glycosides: from structure to properties and potential applications.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1612132},
doi = {10.3389/fpls.2025.1612132},
pmid = {40822726},
issn = {1664-462X},
abstract = {Cyanogenic glycosides (CGs) represent an important group of secondary metabolites predominantly of plant origin, characterized by their ability to release hydrogen cyanide upon enzymatic hydrolysis. These compounds are widely distributed across the plant kingdom, where they play a crucial role in defense against herbivores and pathogens. In recent years, advanced analytical tools have greatly expanded our knowledge of CGs by enabling the identification of less abundant forms. Based on the latest data from published scientific studies, this review presents a comprehensive overview of CGs, with a focus on their structural variability, biosynthetic pathways, ecological functions, and inherent toxicity. Special attention is given to the quantity and distribution of significant CGs in plants, as the available data is often heterogeneous, fragmented, and dispersed across the literature. Furthermore, the review explores emerging evidence regarding the biomedical relevance of selected CGs, including their putative anticancer properties and broader therapeutic potential. The findings presented in this review may be applied in fields such as pharmacology, toxicology, food safety, and plant biotechnology - either to enhance CG content for crop protection or, conversely, to eliminate such content in order to improve food safety.},
}

@article {pmid40821442,
year = {2025},
author = {Motlagh, SH and Momtazi, F and Saeedi, H},
title = {Senckenberg dogger bank long-term monitoring: First dataset on amphipods.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111931},
doi = {10.1016/j.dib.2025.111931},
pmid = {40821442},
issn = {2352-3409},
abstract = {This dataset includes unique occurrence records of amphipod specimens collected during the 2024 annual Senckenberg Long-Term Monitoring Project in Dogger Bank (a shallow sand bank in the central North Sea), Cruise DOG24. This cruise was part of an ongoing effort to monitor biodiversity, which has occurred annually from 1991 to 2024 by the Marine Zoology Department at the Senckenberg Research Institute and Natural History Museum. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank's stable sandy substrate. A total of 8444 specimens of ten species belonging to 13 families and 14 genera were identified using morphological methods with Leica M60 and DM750 microscopes. This study presents the first species-level identification of benthic amphipods in the Dagger Bank, providing a taxonomically resolved dataset that serves as a reliable identification key for future monitoring efforts in the area. Data were structured and published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) following the Darwin Core (DwC) standard. This dataset is the first-hand data ever published open-access from the Senckenberg Long Term Monitoring Project since 1991. This dataset also supports a broader research project aimed at (i) revealing the distribution pattern of amphipods in the North Sea, (ii) identifying environmental drivers of species distribution and diversity, and (iii) evaluating the response of the amphipod community to ecosystem changes.},
}

@article {pmid40817347,
year = {2025},
author = {Rajpal, H and Stengel, CV and Mediano, PAM and Rosas, FE and Viegas, E and Marquet, PA and Jensen, HJ},
title = {Information dynamics and the emergence of high-order individuality in ecosystems.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1231},
pmid = {40817347},
issn = {2399-3642},
support = {EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/X03870X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W007142/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; ES/T005319/2//RCUK | Economic and Social Research Council (ESRC)/ ; },
abstract = {At what level does natural selection occur? When considering the reproductive dynamics of interacting and mutating agents, it has long been debated whether selection is better understood by focusing on the individual or if hierarchical selection emerges as a consequence of joint adaptation. Despite longstanding efforts in theoretical ecology, there is still no consensus on this fundamental issue, most likely due to the difficulty in obtaining adequate data spanning a sufficient number of generations and the lack of adequate tools to quantify the effect of hierarchical selection. Here, we capitalise on recent advances in information-theoretic data analysis to advance this state of affairs by investigating the emergence of high-order structures- such as groups of species- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that evolutionary dynamics can lead to clusters of species that act as a self-perpetuating group that exhibits greater information-theoretic agency than a single species for a broad range of stable mutation rates. However, this higher-order organization breaks down for mutation rates close to the error threshold, where increased information processing is observed at the level of a single species. For mutation rates higher than the error threshold, no stable population of species are observed in time, and all individuality is lost in the ecosystem. Overall, our findings provide quantitative evidence supporting the emergence of higher-order structures in evolutionary ecology from relatively simple processes of adaptation and reproduction.},
}

@article {pmid40816181,
year = {2025},
author = {Xu, Z and Xu, D and Ma, J and Wang, J and Yan, S and Fu, R and Cui, Y},
title = {The risk assessment for metal(loid)s in soil-slag mixing systems: Coupling sequential extraction, leaching tests, and in vitro bioaccessibility assays.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139544},
doi = {10.1016/j.jhazmat.2025.139544},
pmid = {40816181},
issn = {1873-3336},
abstract = {The metals and metalloids (metal[loid]s) in the newly formed soil-slag mixing systems (SSMS), formed by the invasion of smelting slag into contaminated soils, may pose potential risks to environment and residents near the smelter sites. In this study, sequential extraction, leaching tests and in vitro bioaccessibility assays were conducted to assess the ecological and human health risk of metal(loid)s in SSMS. The results indicated that the contaminated soils and smelting slags were composed of more than 80 % silicate and oxide minerals, which served as the host phases for metal(loid)s in SSMS. Cd exhibited high mobility and availability, with its exchangeable fraction ranging from 0.15 % to 69.23 %. Leaching tests revealed high leachability and bioavailability of Cd, Mn and Zn. Moreover, metal(loid)s bioaccessibility varied amongst samples: 2.78-46.63 % of As, 11.87-95.25 % of Cd, 37.35-93.88 % of Mn, 1.97-87.84 % of Pb and 0-57.98 % of Zn. Risk assessment calculation results indicated potentially ecological risks posed by Cd, Mn, Pb, and Zn, and unfavorable carcinogenic risks associated with As and Cd, suggesting that remediation efforts were warranted. Overall, this study highlighted how the invasion of smelting slags can affect the accuracy of risk assessments, providing new guidance for risk control and environmental management at slag dumping sites.},
}

@article {pmid40814786,
year = {2025},
author = {Misono, S and Nguyen-Feng, VN and Lei, X and Feddema, E and Tella, A and Stockness, A and Frazier, PA and Kummerfeld, E and Lim, KO},
title = {Ecological Momentary Assessment of Voice & Psychological Factors: Group & Individual Mechanisms.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.70049},
pmid = {40814786},
issn = {1531-4995},
support = {K23DC016335/DC/NIDCD NIH HHS/United States ; //American College of Surgeons, Triological Society: Clinical Scientist Development Award/ ; KL2TR000113/TR/NCATS NIH HHS/United States ; UL1TR002494/TR/NCATS NIH HHS/United States ; },
abstract = {OBJECTIVES: Cross-sectional associations between voice and psychological factors are known, but changes over time offer opportunities to refine our understanding of their interactions and consider customized treatment options. Study objectives were to measure relationships between voice and psychological factors using ecological momentary assessment and applying (1) group-level time series analysis and (2) group and (3) individual causal modeling to identify key psychological factors relevant for voice outcomes.

METHODS: Adults (N = 32) with primary muscle tension dysphonia completed multiple assessments daily for 10 days. Measures included items from the Voice Handicap Index-10, voice-adapted perceived present control scale, items from NIH PROMIS and the NIH Toolkit to assess distress, and the Positive and Negative Affect Scale. Group-level time series analysis was conducted using dynamic structural equation modeling; causal analysis utilized the Greedy Fast Causal Inference algorithm.

RESULTS: In group-level time series analyses, neither perceived control nor distress predicted subsequent timepoint voice handicap scores. In group-level causal modeling, anxiety was causal for voice handicap, but perceived control was not. Individual-level analyses identified various causal factors for voice handicap including perceived control and negative affect, and to a lesser extent, serenity, anxiety, somatic arousal, and stress.

CONCLUSIONS: Group-level analyses may obscure important heterogeneity that is identifiable using individual-level causal analyses. For example, perceived control was not identified as predictive or causal for voice handicap at the group level; but was a salient causal factor for voice handicap in some individuals. Causal modeling using intensive longitudinal datasets offers a potential avenue for individualized treatment approaches.},
}

@article {pmid40812171,
year = {2025},
author = {Lundberg, DS and Bergelson, J and Roux, F and Weigel, D and Karasov, TL},
title = {Lab to field: Challenges and opportunities for plant biology.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1212-1216},
doi = {10.1016/j.chom.2025.05.027},
pmid = {40812171},
issn = {1934-6069},
abstract = {Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between laboratory studies, offering control and repeatability, versus field experiments, revealing ecological relevance and environmental effects, should not be seen as failure but motivate further inquiry and allow complementary discovery.},
}

@article {pmid40811794,
year = {2025},
author = {Shen, S and Qi, W and Zeng, J and Li, S and Liu, X and Zhu, X and Dong, C and Wang, B and Shi, Y and Yao, J and Wang, B and Lou, X and Gu, S and Li, P and Wang, J and Jiang, G and Cao, S},
title = {Passive Sensing for Mental Health Monitoring Using Machine Learning With Wearables and Smartphones: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e77066},
doi = {10.2196/77066},
pmid = {40811794},
issn = {1438-8871},
abstract = {BACKGROUND: Mental health issues have become a significant global public health challenge. Traditional assessments rely on subjective methods with limited ecological validity. Passive sensing via wearable devices and smartphones, combined with machine learning (ML), enables objective, continuous, and noninvasive mental health monitoring.

OBJECTIVE: This study aimed to provide a comprehensive review of the current state of passive sensing-based and ML technologies for mental health monitoring. We summarized the technical approaches, revealed the association patterns between behavioral features and mental disorders, and explored potential directions for future advancements.

METHODS: This scoping review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines and was prospectively registered on the Open Science Framework. We systematically searched 7 databases (Web of Science, PubMed, IEEE Xplore, Embase, PsycINFO, Scopus, and ACM Digital Library) for studies published between January 2015 and February 2025. We included 42 peer-reviewed studies that used passive sensing from wearables or smartphones with ML to monitor clinically diagnosed mental disorders, such as depression and anxiety. Data were synthesized across technical dimensions (data collection, preprocessing, feature engineering, and ML models) and clinical associations, with behavioral features categorized into 8 domains.

RESULTS: The 42 included studies were predominantly cohort designs (23/42, 55%), with a median sample size of 60.5 (IQR 54-99). Most studies focused on depression (23/42, 55%) and anxiety (9/42, 21%) using primarily wrist-worn devices (32/42, 76%) collecting heart rate (28/42, 67%), movement index (25/42, 60%), and step count (17/42, 40%) as key biomarkers. Deep learning models (eg, convolutional neural networks and long short-term memory) showed high accuracy, while traditional ML (eg, random forest) remained prevalent due to better interpretability. We identified critical limitations, including small samples (32/42, 76% with N<100), short monitoring periods (19/42, 45% <7 days), scarce external validation (1/42, 2%), and limited reporting on data anonymization (6/42, 14%).

CONCLUSIONS: While passive sensing and ML demonstrate promising accuracy (eg, convolutional neural network-long short-term memory achieving 92.16% in anxiety detection), the evidence remains constrained by three key limitations: (1) methodological heterogeneity (32/42, 76% single-device studies; 19/42, 45% with <7-day monitoring), (2) high risk of bias from small samples (median 60.5, IQR 54-99 participants) and scarce external validation (1/42, 2%), and (3) ethical gaps (only 6/42, 14% addressing anonymization). These findings underscore the technology's potential to transform mental health care through objective, continuous monitoring-particularly for depression (heart rate and step count biomarkers) and anxiety (sleep and social interaction patterns). However, clinical translation requires standardized protocols, larger longitudinal studies (≥3 months), and ethical frameworks for data privacy. Future work should prioritize multimodal sensor fusion and explainable artificial intelligence to bridge the gap between technical performance and clinical deployability.},
}

@article {pmid40805736,
year = {2025},
author = {Lu, F and Yi, B and Ma, JX and Wang, SN and Feng, YJ and Qin, K and Tu, Q and Bu, ZJ},
title = {Drought and Shrub Encroachment Accelerate Peatland Carbon Loss Under Climate Warming.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805736},
issn = {2223-7747},
support = {U23A2003//The National Nature Science Foundation of China/ ; 42407354//The National Nature Science Foundation of China/ ; 42371050//The National Nature Science Foundation of China/ ; 20230203002SF and 20210402032GH//Jilin Provincial Science and Technology Development Project/ ; 2024QN1081//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands store substantial amounts of carbon (C) in the form of peat, but are increasingly threatened by drought and shrub encroachment under climate warming. However, how peat decomposition and its temperature sensitivity (Q10) vary with depth and plant litter input under these stressors remains poorly understood. We incubated peat from two depths with different degrees of decomposition, either alone or incubated with Sphagnum divinum shoots or Betula ovalifolia leaves, under five temperature levels and two moisture conditions in growth chambers. We found that drought and Betula addition increased CO2 emissions in both peat layers, while Sphagnum affected only shallow peat. Deep peat alone or with Betula exhibited higher Q10 than pure shallow peat. Drought increased the Q10 of both depths' peat, but this effect disappeared with fresh litter addition. The CO2 production rate showed a positive but marginal correlation with microbial biomass carbon, and it displayed a rather similar responsive trend to warming as the microbial metabolism quotient. These results indicate that both deep and dry peat are more sensitive to warming, highlighting the importance of keeping deep peat buried and waterlogged to conserve existing carbon storage. Additionally, they further emphasize the necessity of Sphagnum moss recovery following vascular plant encroachment in restoring carbon sink function in peatlands.},
}

@article {pmid40803399,
year = {2025},
author = {Jin, L and Lu, Y and Huang, J and Liu, J and Wei, X and Ma, G and Yu, H},
title = {Metabolism exploration of disinfection byproducts halonitromethanes (HNMs) by cytochrome P450 enzymes and toxicity evaluation.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122575},
doi = {10.1016/j.envres.2025.122575},
pmid = {40803399},
issn = {1096-0953},
abstract = {The nitrogen-contained disinfection by-products, halonitromethanes (HNMs), are known for their high cytotoxicity and genotoxicity. Although HNMs can be metabolized by cytochrome P450 enzymes (P450s), the specific mechanism has remained unclear. To shed light on this, density functional theory (DFT) calculations were performed to elucidate the potential oxidative P450-catalytic activation of the nine HNMs. Our findings reveal that active species of P450s (Cpd I) predominantly react with halogen-substituted nitromethanes via hydrogen abstraction and bromine atom abstraction, rather than chlorosylation. As a result of these reactions, oxidized HNMs are produced and can undergo further hydrolysis, leading to nitro-formaldehyde, nitro formyl halogen, halogen hydride, hypobromous acid, and nitroformic acid. To experimentally validate the computational predictions, in vitro experiments were conducted on five typical nitromethanes using human liver microsomes and the results reveal that DCNM, BCNM and DBCNM form nitroformyl chlorine (NO2CClO), while BCNM, DBNM and TBNM are transferred into nitroformyl bromide (NO2CBrO). Nitroformic acid is also identified as a metabolite in the TBNM metabolism reaction. Toxicity assessment reveals that metabolic transformation leads to an overall reduction in the ecological toxicity. However, metabolites showed similar toxicity to Fathead minnow and even higher acute toxicity to rat, as well as larger probability of hERG inhibition effects than HNMs, underscoring the need for caution in health risk assessment. By integrating in silico and in vitro approaches, this work has provided a comprehensive understanding of the metabolism of HNMs and offered potential toxicity data basis of these compounds.},
}

@article {pmid40798830,
year = {2025},
author = {Abraham, AJ and Clauss, M and Bailey, MA and Duvall, ES},
title = {Body Mass Scaling of Sodium Regulation in Mammals.},
journal = {Acta physiologica (Oxford, England)},
volume = {241},
number = {9},
pages = {e70090},
doi = {10.1111/apha.70090},
pmid = {40798830},
issn = {1748-1716},
}

@article {pmid40797121,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {9},
pages = {257},
pmid = {40797121},
issn = {1554-3528},
support = {UL1TR002378/NH/NIH HHS/United States ; },
abstract = {This article reports on the validation of Fabla, a researcher-developed and university-hosted smartphone app that facilitates naturalistic and secure collection of participants' spoken responses to researcher questions. Fabla was developed to meet the need for tools that (a) collect longitudinal qualitative data and (b) capture speech biomarkers from participants' natural environments. This study put Fabla to its first empirical test using a repeated-measures experimental design in which participants (n = 87) completed a 1-week voice daily diary via the Fabla app, and an identical 1-week text-entry daily diary administered via Qualtrics, with diary method order counterbalanced and randomized. A preregistered analysis plan investigated (1) adherence, usability, and acceptability of Fabla, (2) concurrent validity of voice diaries (vs. text-entry diaries) by comparing linguistic features obtained via each diary method, and (3) differences in the strength of the association between linguistic features and their known psychological correlates when assessed by voice versus text-entry diary. Voice diaries yielded more than double the mean daily language volume (word count) compared to text-entry diaries and received high usability and acceptability ratings. Linguistic markers consistently associated with depression in prior research were significantly associated with depression symptoms when assessed via voice but not text-entry diaries, and the difference in correlation magnitude was significant. Word-count-adjusted linguistic patterns were highly correlated between diary methods, with statistically significant mean differences observed for some linguistic dimensions in the presence of these associations. Fabla is a promising tool for collecting high-quality speech data from participants' naturalistic environments, overcoming multiple limitations of text-entry responding.},
}

@article {pmid40796553,
year = {2025},
author = {Arehart, CH and Lin, M and Gibson, RA and , and Raghavan, S and Gignoux, CR and Stanislawski, MA and Grotzinger, AD and Evans, LM},
title = {Modeling the genomic architecture of adiposity and anthropometrics across the lifespan.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7494},
pmid = {40796553},
issn = {2041-1723},
support = {R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; RF1 AG073593/AG/NIA NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 MH120219/MH/NIMH NIH HHS/United States ; },
abstract = {Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic influences, longitudinal variation, heterogeneity between sexes, and differing health risks based on adipose distribution. Here, we construct a 4-factor genomic structural equation model using 18 measures, unveiling shared and distinct genetic architectures underlying birth size, abdominal size, adipose distribution, and adiposity. Multivariate genome-wide associations reveal the adiposity factor is enriched specifically in neural tissues and pathways, while adipose distribution is enriched more broadly across physiological systems. In addition, polygenic scores for the adiposity factor predict many adverse health outcomes, while those for body size and composition predict a more limited subset. Finally, we characterize the factors' genetic correlations with obesity-related traits and examine the druggable genome by constructing a bipartite drug-gene network to identify potential therapeutic targets.},
}

@article {pmid40794746,
year = {2025},
author = {Alkhatib, SA and Arya, S and Islayem, D and Nyadzayo, RM and Mohamed, S and Yousef, AF and Hernandez, HH and Pappa, AM},
title = {Revealing bioremediation potential of novel indigenous bacteria from oil-contaminated sites in the UAE: A combined bioinformatics and experimental validation.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329515},
pmid = {40794746},
issn = {1932-6203},
mesh = {*Biodegradation, Environmental ; *Computational Biology/methods ; United Arab Emirates ; Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteria/metabolism/genetics/isolation & purification ; Phenols/metabolism ; *Soil Pollutants/metabolism ; },
abstract = {Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.},
}

*Biodegradation, Environmental
*Computational Biology/methods
United Arab Emirates
Polycyclic Aromatic Hydrocarbons/metabolism
*Bacteria/metabolism/genetics/isolation & purification
Phenols/metabolism
*Soil Pollutants/metabolism

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40786600,
year = {2025},
author = {Boyes, D and Gardiner, A and , and , and , and , and , and , and , and , },
title = {The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {197},
pmid = {40786600},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Chloroclystis v-ata (V-Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 275.35 megabases. Most of the assembly (99.95%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.49 kilobases.},
}

@article {pmid40781446,
year = {2025},
author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK},
title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {305},
pmid = {40781446},
issn = {1573-0972},
support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; },
mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; },
abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.},
}

*Desulfovibrio/genetics/metabolism/classification
*Genome, Bacterial
*Sulfates/metabolism
Phylogeny
Multigene Family
Gene Regulatory Networks
Genes, Bacterial
Gene Ontology

@article {pmid40781089,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1385},
doi = {10.1038/s41597-025-05752-9},
pmid = {40781089},
issn = {2052-4463},
}

@article {pmid40778113,
year = {2025},
author = {Sprint, G and Schmitter-Edgecombe, M and Weaver, R and Wiese, L and Cook, DJ},
title = {CogProg: Utilizing Large Language Models to Forecast In-the-moment Health Assessment.},
journal = {ACM transactions on computing for healthcare},
volume = {6},
number = {2},
pages = {},
pmid = {40778113},
issn = {2637-8051},
support = {R01 AG066748/AG/NIA NIH HHS/United States ; R25 AG046114/AG/NIA NIH HHS/United States ; R01 AG065218/AG/NIA NIH HHS/United States ; R35 AG071451/AG/NIA NIH HHS/United States ; R01 EB009675/EB/NIBIB NIH HHS/United States ; },
abstract = {Forecasting future health status is beneficial for understanding health patterns and providing anticipatory support for cognitive and physical health difficulties. In recent years, generative large language models (LLMs) have shown promise as forecasters. Though not traditionally considered strong candidates for numeric tasks, LLMs demonstrate emerging abilities to address various forecasting problems. They also provide the ability to incorporate unstructured information and explain their reasoning process. In this paper, we explore whether LLMs can effectively forecast future self-reported health state. To do this, we utilized in-the-moment assessments of mental sharpness, fatigue, and stress from multiple studies, utilizing daily responses (N=106 participants) and responses that are accompanied by text descriptions of activities (N=32 participants). With these data, we constructed prompt/response pairs to predict a participant's next answer. We fine-tuned several LLMs and applied chain-of-thought prompting evaluating forecasting accuracy and prediction explainability. Notably, we found that LLMs achieved the lowest mean absolute error (MAE) overall (0.851), while gradient boosting achieved the lowest overall root mean squared error (RMSE) (1.356). When additional text context was provided, LLM forecasts achieved the lowest MAE for predicting mental sharpness (0.862), fatigue (1.000), and stress (0.414). These multimodal LLMs further outperformed the numeric baselines in terms of RMSE when predicting stress (0.947), although numeric algorithms achieved the best RMSE results for mental sharpness (1.246) and fatigue (1.587). This study offers valuable insights for future applications of LLMs in health-based forecasting. The findings suggest that LLMs, when supplemented with additional text information, can be effective tools for improving health forecasting accuracy.},
}

@article {pmid40777262,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777262},
issn = {2692-8205},
support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.},
}

@article {pmid40776104,
year = {2025},
author = {Bauberg, H and Tachnai, N and Hanan, G and Nehama, D and Tamburis, O and Darmoni, S and Grosjean, J and Benis, A},
title = {Automated Elicitation of Human and Ecological Health Indicators: An LLM-Based Practical Implementation for One Digital Health.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1488-1492},
doi = {10.3233/SHTI251086},
pmid = {40776104},
issn = {1879-8365},
mesh = {Humans ; *One Health ; *Health Status Indicators ; *Environmental Health/methods ; Digital Health ; },
abstract = {This paper presents a new method for automating the identification of human and ecological health indicators using the One Digital Health framework, which combines One Health and Digital Health principles. By applying mainly Large Language Models, we conduct a systematic literature review on urban freshwater environments. This automation streamlines the process of finding and analyzing relevant research, allowing us to extract vital health indicators related to urban aquatic ecosystems and human wellness. The findings support the OneAquaHealth project's goals, enhancing environmental monitoring and linking human, animal, and environmental health in a digital context.},
}

Humans
*One Health
*Health Status Indicators
*Environmental Health/methods
Digital Health

@article {pmid40774918,
year = {2025},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santsch, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Corrigendum to "Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050" [Mar. Pollut. Bull. 206 (2024) 116664].},
journal = {Marine pollution bulletin},
volume = {},
number = {},
pages = {118543},
doi = {10.1016/j.marpolbul.2025.118543},
pmid = {40774918},
issn = {1879-3363},
}

@article {pmid40774560,
year = {2025},
author = {Guo, J and Lei, W and Liang, X and Wang, H and Qi, W and Huang, S and Chen, X and He, S},
title = {Three-dimensional distribution and key drivers of neonicotinoid residues in hilly agricultural areas.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122524},
doi = {10.1016/j.envres.2025.122524},
pmid = {40774560},
issn = {1096-0953},
abstract = {Neonicotinoids (NNIs) raise global concern due to their substantial soil residues and potential health risks to animal and human health. High water solubility and low soil adsorption enhanced vertical and horizontal migration of NNIs. However, understanding of NNIs' three-dimensional distribution in soils and influencing factors remains limited, limiting accurate risk assessment and remediation strategies for agriculture ecosystems. This study selected typical mountainous farmland soil to investigate the three-dimensional distribution of NNIs contents and composition. The findings indicated that the average detection rate of imidacloprid (IMI) in the 0-20 cm layer was 33% higher than that in the 30-40 cm layer, whereas clothianidin (CLO) detection rates remained consistent across 0-40 cm layer. The contents of eight NNIs (∑8NNIs) in the study area ranged from 0.09 to 37.08 ng/g, with the 6.58±8.65 ng/g in the 0-10 cm and 2.60±7.78 ng/g in the 30-40 cm layer. The contents of ∑8NNIs, IMI, and CLO decreased by 60%, 62%, and 75%, respectively, with increasing depth. The proportion of IMI and CLO to ∑8NNIs decreased and increased by 35% and 12%, respectively, in the 0-40 cm soil, leading to IMI predominance in the topsoil (60%) and CLO in the deeper soil (29%). Correlation analysis revealed that soil particle size, slope, and elevation were significantly associated with both the ∑8NNIs and the proportions of IMI and CLO. These results highlighted the substantial influence of topography and soil structure on the vertical distribution of NNIs. Additionally, the ∑8NNIs content in stem mustard soil was higher than sweet potato, rice, corn, and forest. Overall, the study found very low health risks to humans (hazard index, HI<1) and no overall potential ecological risk in the study area, though localized sublethal risks to non-target organisms were identified. Furthermore, the spatial correlation between IMI and CLO health risk regions identified overlapping high-risk areas.},
}

@article {pmid40774342,
year = {2025},
author = {Cao, W and Cao, X and Sutherland, AD},
title = {Planning for the Unexpected and Unintended Effects of mHealth Interventions: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e68909},
pmid = {40774342},
issn = {1438-8871},
mesh = {*Telemedicine ; Humans ; },
abstract = {BACKGROUND: Mobile health (mHealth) interventions can produce both intended and unintended effects. Examining these unintended effects helps create a more complete and objective understanding of mHealth interventions and can reduce potential harm to participants. Existing studies on the unintended effects, which were published several years ago, tend to have either a general focus on health IT or a specific focus on health care providers, thereby excluding other key stakeholders (eg, patients and community health workers). Additionally, these studies did not systematically outline the causes of the unintended effects or strategies for their prevention.

OBJECTIVE: To address this gap, this systematic review, guided by the ecological framework, aims to systematically identify the unintended effects of mHealth interventions, create a typology for them, investigate the reasons for their occurrence, describe how they were detected, and propose ways to prevent or lessen them.

METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to examine the unintended effects of health interventions that use mobile technology.

RESULTS: A total of 15 papers were included in the review. An ecological typology of mHealth intervention unintended effects (mHUE) was developed, which includes 26 distinct effects (eg, silencing and boomerang). The majority of these unintended effects (n=20) occur at the individual level and span physical or behavioral (n=7), psychological (n=8), cognitive (n=4), and financial (n=1) domains. Three effects occur at the interpersonal level and another 3 at the community or institutional level. Most of the identified effects (n=22) were negative. Potential causes for these effects include the improper use of mHealth technology, poorly designed interventions, the application of unsuitable intervention mechanisms, or a misalignment between the intended outcomes and the sociocultural context. Strategies and recommendations (eg, considering the context such as cultural norms) were suggested to help prevent or reduce the unintended effects.

CONCLUSIONS: The unintended effects detailed in the mHUE typology were heterogenous and context-dependent. These effects can influence individuals across different domains and also affect unintended people within the ecological system. As most of the unintended effects are negative, if they are not monitored, mHealth interventions designed to empower participants could paradoxically disempower them (eg, decreasing self-efficacy for disease management, undermining patient control, and engagement). The mHUE typology, together with the proposed recommendations and strategies, can be used as a guide to enhance the planning, design, implementation, and postimplementation evaluation on mHealth interventions. Future research should concentrate on understanding the specific mechanisms behind these unintended effects.},
}

*Telemedicine
Humans

@article {pmid40772610,
year = {2025},
author = {Tsuji, S and Kunimatsu, S and Watanabe, K},
title = {Environmental DNA Comparative Phylogeography: Simultaneous Estimation of Population Structures Within a Species-Rich Group of Freshwater Gobies.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70059},
doi = {10.1111/mec.70059},
pmid = {40772610},
issn = {1365-294X},
support = {23K13967//Japan Society for the Promotion of Science/ ; //ESPEC Foundation for Global Environment Research and Technology/ ; },
abstract = {Comparative phylogeography provides crucial insights into evolutionary processes shaping biodiversity patterns by analysing spatial genetic variations across multiple species. However, conventional capture-based methods are often labour-intensive, particularly for multi-species analyses. Environmental DNA (eDNA) analysis has significant advantages in comparative phylogeography, including simplified field surveys requiring only water collection and the potential to simultaneously analyse multiple species from a single sample. To further expand the eDNA application and demonstrate its utility in comparative phylogeographic studies, this study employed eDNA analysis to simultaneously analyse the phylogeographic patterns in a species-rich freshwater goby group (Rhinogobius) in the Japanese Archipelago. DNA amplification was performed on eDNA samples collected from 573 sites across the archipelago using newly designed group-specific primers targeting the mitochondrial cytochrome b region of Rhinogobius. High-throughput sequencing detected haplotypes of all nine known species (or species groups) occurring in this region, followed by phylogenetic and network analyses. The eDNA analysis successfully revealed the genetic population structures across multiple species. A landlocked species, R. flumineus, exhibited fine-scale population differentiation shaped by geomorphological barriers, while amphidromous species showed broader genetic patterns likely influenced by ocean currents and their ecological traits. The phylogenetic and phylogeographic patterns reconstructed by the eDNA analysis were almost completely concordant with previously identified patterns of limited groups based on conventional methods, demonstrating the reliability of eDNA-based comparative phylogeography. This study highlights the potential of eDNA to complement and partially replace conventional methods, facilitating large-scale comparative phylogeographic research to gain new insights into spatial patterns and evolutionary processes of biodiversity.},
}

@article {pmid40770961,
year = {2025},
author = {Lopes-Araujo, HF and Guimarães, RL and Carvalho-Silva, WHV},
title = {Correlations between new HIV infections and hospital admissions for non-Hodgkin lymphoma in Brazil.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70076},
pmid = {40770961},
issn = {1097-0215},
abstract = {Despite advancements in antiretroviral therapy, human immunodeficiency virus (HIV) infections remain a significant global health challenge. With increasing life expectancy among people living with HIV, the emergence of HIV-related malignancies, notably non-Hodgkin lymphoma (NHL), has become a prominent concern. This study aims to investigate the correlation between new HIV infections and NHL hospitalizations in Brazil from 2010 to 2022. Using an ecological time series design, data from authoritative sources, including the Notifiable Diseases Information System and the Department of Unified Health System Informatics, were analyzed. The study cohort comprised individuals admitted to the Brazilian Unified Health System, categorized by geographical region, sex, and age cohorts. Pearson's and Spearman's correlation coefficients were utilized to examine the correlation between new HIV infections and NHL hospitalizations. Our analysis revealed a strong positive and statistically significant correlation between the incidence of new HIV cases and NHL hospitalizations in Brazil (r = 0.8901; p = .0001) and in most regions (r > 0.80; p < .001). Moreover, our findings indicate that this correlation becomes evident from the age of 15 onward, with a discernible tendency to escalate with advancing age from moderate to very strong (r > 0.62; p < .02). Regarding sex, the observed correlations were strong positive for male (r = 0.8681; p = .0003) and female (r = 0.7912; p = .0020). These results underscore the importance of vigilant monitoring for individuals living with HIV. Furthermore, we emphasize the importance of rigorous screening practices and adherence to antiretroviral therapy, which may hold promising implications for managing neoplastic conditions.},
}

@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}

Humans
*Aging
*Biometry/methods
*Deep Learning
*Gastrointestinal Microbiome
*Principal Component Analysis/methods
*Skin Microbiome
Software Validation

@article {pmid40764303,
year = {2025},
author = {Xu, Y and Gkoutos, GV},
title = {A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {87},
pmid = {40764303},
issn = {2056-7189},
support = {101095480//HYPERMARKER/ ; 101095480//HYPERMARKER/ ; 731032//Nanocommons H2020-EU/ ; 965286//MAESTRIA/ ; 101057014//PARC/ ; HDRUK/CFC/01//MRC Heath Data Research UK/ ; },
mesh = {Animals ; *Computational Biology/methods ; Mice ; Humans ; *Microbiota ; Computer Simulation ; Machine Learning ; Gastrointestinal Microbiome ; *Ecology/methods ; Ecosystem ; Clostridioides difficile ; Clostridium Infections/microbiology ; Models, Biological ; Microbial Interactions ; },
abstract = {We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem modeling by coupling a modified generalized Lotka-Volterra formulation with machine learning optimization. Unlike traditional methods that rely on gradient matching, MBPert leverages numerical solutions of differential equations and iterative parameter estimation to robustly capture microbial dynamics. The framework is assessed within the context of two experimental scenarios: (i) paired before-and-after measurements under targeted perturbations, and (ii) longitudinal time-series data with time-dependent perturbations. Extensive simulation studies, benchmarking on standardized MTIST datasets, and application to Clostridium difficile infection in mice and repeated antibiotic perturbations of human gut micribiota, demonstrate that MBPert accurately recapitulates species interactions and predicts system dynamics. Our results highlight MBPert as a powerful and flexible tool for mechanistic insight into microbiota ecology, with broad potential applicability to other complex dynamical systems.},
}

Animals
*Computational Biology/methods
Mice
Humans
*Microbiota
Computer Simulation
Machine Learning
Gastrointestinal Microbiome
*Ecology/methods
Ecosystem
Clostridioides difficile
Clostridium Infections/microbiology
Models, Biological
Microbial Interactions

@article {pmid40763572,
year = {2025},
author = {Sagawa, N and Ichikawa, K and Furukawa, K and Morita, H and Takahara, A and Hinata, H},
title = {Time-resolved fragmentation pathways of expanded polystyrene microplastics: Intrinsic pathway modulated by sand morphology and degradation state.},
journal = {The Science of the total environment},
volume = {997},
number = {},
pages = {180172},
doi = {10.1016/j.scitotenv.2025.180172},
pmid = {40763572},
issn = {1879-1026},
abstract = {Microplastic fragmentation, driven by ultraviolet exposure, mechanical forces, and sand properties, remains poorly understood in natural settings despite its ecological significance. This study investigates temporal variation (6-240 h) in the shape, size, and number of EPS fragments (size distribution) and their dependence on sand morphology and parent microplastic degradation state based on pot mill experiments. Two experimental setups were employed: Time-Resolved Fragmentation (TRF) experiments using virgin EPS (∼5000 μm) with beach sand (TRF-VB), and virgin or degraded EPS with river sand (TRF-VR/DR). In the TRF-VB, two dominant size classes were identified: size class 1 (5-100 μm), appearing early (6-12 h), and size class 2 (200-1000 μm), emerging at 48-72 h and plateauing at 120 h due to hardened surface layer exfoliation of the parent EPS. The steep slopes of the size distributions (<-3) are explained by a combination of continuous-cascading and leap-cascading fragmentation mechanisms. In the TRF-VR experiment, only size class 1 persisted, whereas in the TRF-DR experiment, degraded EPS produced both classes by 120 h. The fragmentation pathway was influenced by both sand morphology and the parent degradation state. Volume balance analysis revealed the dominance of fine fragments (<5 μm) in both experiments, indicating their environmental relevance. These findings provide a conceptual framework for modeling EPS fragmentation and highlight the ecological risks associated with the rapid generation of fine microplastics. In the future, the continued integration of experimental, numerical, and theoretical approaches will be essential for advancing our understanding of plastic fragmentation processes.},
}

@article {pmid40763003,
year = {2025},
author = {Chen, AT and Wang, LC and Pike, KC and Conway, M and Glass, JE},
title = {Comparing the Use Experiences, Contextual Factors, and Recovery Strategies Associated with Different Substances: An Analysis of Social Media Narratives.},
journal = {Substance use & misuse},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10826084.2025.2540938},
pmid = {40763003},
issn = {1532-2491},
abstract = {BACKGROUND: Research on use experience and recovery has often focused on a single substance or polysubstance use. However, there can be substance-specific differences; understanding these can be critical to developing targeted interventions. We examined social media relating to alcohol, cannabis, and/or opioids to: 1) construct use profiles highlighting salient settings, actors, and contextual factors; and 2) characterize differences in recovery strategies depending on readiness to change.

METHODS: We constructed a dataset of Reddit posts from subreddits pertaining to alcohol, cannabis, and opioids, authored between January 2013 and December 2019. We leveraged computational techniques to sample posts containing stigma, logistic regression to compare substance use experiences, and content analysis to identify stages of change and recovery strategies.

RESULTS: We examined 748 posts (alcohol, n = 316; cannabis, n = 335; opioids, n = 135). Regression models indicated leisure settings, coworkers, health, and legal consequences were associated with alcohol versus other substances. Posts involving cannabis were more likely to include school, and heightened self-awareness, demonstrated through curiosity, disgust, and realization. Posts involving opioids were more likely to include anticipated stigma, anger, healthcare, medications, financial, and religious content; they were less likely to include home and leisure. With respect to recovery strategies, social support seeking and awareness of substance use consequences were more common in earlier stages of readiness. In the action and maintenance stages, there was greater use of recovery strategies overall.

CONCLUSIONS: Substance-specific use profiles highlighted salient settings, actors, and contextual factors. Recovery strategies were also differentiated across stages of change, affording opportunities for treatment and intervention.},
}

@article {pmid40757428,
year = {2025},
author = {Callaway, RM and Pal, RW and Schaar, A and Hooper, D and Auge, H and Hensen, I and Kožić, K and Lekberg, Y and Nagy, DU and Selke, JA and Thoma, AE and Träger, S and Rosche, C},
title = {Exotic Invasive Plant Species Increase Primary Productivity, but Not in Their Native Ranges.},
journal = {Ecology letters},
volume = {28},
number = {8},
pages = {e70187},
doi = {10.1111/ele.70187},
pmid = {40757428},
issn = {1461-0248},
support = {//German Research Foundation/ ; //federal state of Saxony-Anhalt/ ; //German Academic Exchange Service London/ ; },
mesh = {*Introduced Species ; *Biomass ; *Ecosystem ; *Plants ; },
abstract = {Ecosystem net primary productivity is thought to occur near the maximum that abiotic constraints allow; but exotic invasive plants often correlate with increased productivity. However, field patterns and experimental evidence for this come only from the non-native ranges of exotic species. Thus, we do not know if this pattern is caused by exotic invasions per se or whether successful exotic species are disproportionately productive or colonise more productive microsites. We measured aboveground biomass in the field and in common gardens with five plant species in their native and non-native ranges. For all species combined, exotic invaders increased total plot productivity in their non-native ranges by 91% in the field, and by 107% in the common garden, but had much smaller or no such effects in their native ranges. Thus, exotic invaders appear to be a driver of increased productivity, not simply a passenger, but only in their non-native ranges.},
}

*Introduced Species
*Biomass
*Ecosystem
*Plants

@article {pmid40753432,
year = {2025},
author = {Sigrist, C and Bechdolf, A and Bertsch, K and Bullenkamp, R and Busse, M and Darrelmann, UG and Dempfle, A and Driessen, M and Frodl, T and Kersting, JM and Kesik, J and Matzke, B and Neukel, C and Niessen, E and Nückel, S and Oertel, V and Padberg, F and Philipsen, A and Pink, D and Reif, A and Reinhard, M and Steuwe, C and Wolkenstein, L and Herpertz, SC and Consortium, TM},
title = {A mechanism-based group psychotherapy approach to aggressive behavior (MAAP) in borderline personality disorder: a multicenter randomized controlled clinical trial.},
journal = {Trials},
volume = {26},
number = {1},
pages = {265},
pmid = {40753432},
issn = {1745-6215},
support = {462340798//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Borderline Personality Disorder/therapy/psychology/diagnosis ; *Aggression/psychology ; Treatment Outcome ; *Psychotherapy, Group/methods ; Germany ; Adult ; Multicenter Studies as Topic ; Female ; Male ; Randomized Controlled Trials as Topic ; Young Adult ; Time Factors ; },
abstract = {BACKGROUND: High levels of trait anger and aggressive behavior are common and problematic phenomena in patients with borderline personality disorder (BPD). In BPD, patterns of reactive aggression often lead to functional impairment affecting important areas of life. Despite the high burden on individuals and their social environment, there are no specific, cost-effective treatments to reduce aggression in BPD. In previous studies, we and others have been able to infer specific biobehavioral mechanisms underlying patterns of reactive aggression in BPD that can be used as potential treatment targets. To address this, we developed a mechanism-based anti-aggression psychotherapy (MAAP) for the group setting that specifically targets the biobehavioral mechanisms underlying outward-directed aggression in BPD. A previously conducted proof-of-concept study had suggested beneficial effects for this neglected group of patients.

METHODS: In this multicenter, confirmatory, randomized-controlled-clinical-trial, MAAP, which consists of multifaceted, evidence-based treatment elements adapted from other sophisticated treatment programs such as Dialectical Behavior Therapy and Mentalization-Based Treatment, is tested for efficacy against a non-specific supportive psychotherapy (NSSP) program focusing on non-specific general factors of psychotherapy at seven different sites in Germany. Both treatment arms, based on one individual and 13 group therapeutic sessions (1.5 h per session, twice a week), are delivered over a period of 7-10 weeks. A total of N = 186 patients will be recruited, half of whom will be cluster-randomized to MAAP. Outcomes are assessed at baseline, immediately, and 4, 12, 20, and 24 weeks post-treatment using ecological momentary assessment, clinical interviews, questionnaires, and online tasks.

DISCUSSION: If proven superior, MAAP can be incorporated into standard psychiatric care, filling a critical gap in the current therapeutic landscape by offering a structured, cost-effective, and evidence-based treatment that directly targets the biobehavioral mechanisms underlying reactive aggression in BPD. By potentially improving clinical outcomes and reducing the burden of reactive aggression in BPD, MAAP could be beneficial for both individuals and their social environments. The study's large, multicenter design enhances the generalizability of the results, making them more relevant for broader clinical applications.

TRIAL REGISTRATION: This study was registered in the German Clinical Trials Register DRKS (DRKS00031608) on 31.10.2023 (https://drks.de/search/de/trial/DRKS00031608).},
}

Humans
*Borderline Personality Disorder/therapy/psychology/diagnosis
*Aggression/psychology
Treatment Outcome
*Psychotherapy, Group/methods
Germany
Adult
Multicenter Studies as Topic
Female
Male
Randomized Controlled Trials as Topic
Young Adult
Time Factors

@article {pmid40744438,
year = {2025},
author = {Posthuma, L and Price, T and Viljanen, M},
title = {Improving the Ecotoxicological Hazard Assessment of Chemicals by Pairwise Learning.},
journal = {Environmental science & technology},
volume = {59},
number = {31},
pages = {16250-16260},
pmid = {40744438},
issn = {1520-5851},
mesh = {*Ecotoxicology ; *Machine Learning ; Animals ; Risk Assessment ; Environmental Pollutants ; },
abstract = {This study demonstrates how machine learning techniques can bridge data gaps in the ecotoxicological hazard assessment of chemical pollutants and illustrates how the results can be used in practice. The innovation herein consists of the prediction of the sensitivity of all species that were tested for at least one chemical for all chemicals based on all available data. As proof of concept, pairwise learning was applied to 3295 × 1267 (chemical,species) pairs of Observed LC50 data, where only 0.5% of the pairs have experimental data. This yielded more than four million Predicted LC50s for separate exposure durations. These were used to create (1) a novel Hazard Heatmap of Predicted LC50s, (2) Species Sensitivity Distributions (SSD) for all chemicals based on 1267 species each, as well as (3) for taxonomic groups separately, and (4) newly defined Chemical Hazard Distributions (CHD) for all species based on 3295 chemicals each. Validation results and graphical examples illustrate the utility of the results and highlight species and compound selection biases in the input data. The results are broadly applicable, ranging from Safe and Sustainable by Design (SSbD) assessments and setting protective standards to Life Cycle Assessment of products and assessing and mitigating impacts of chemical pollution on biodiversity.},
}

*Ecotoxicology
*Machine Learning
Animals
Risk Assessment
Environmental Pollutants

@article {pmid40743301,
year = {2025},
author = {Lu, Z and Chen, Z and Zhou, M and Lei, D and Chen, Y},
title = {Spatiotemporal patterns of water and vegetation in Poyang Lake from 2013 to 2021 using remote sensing data.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327579},
pmid = {40743301},
issn = {1932-6203},
mesh = {*Lakes ; *Remote Sensing Technology ; China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Support Vector Machine ; *Plants ; Water ; },
abstract = {Continuous monitoring and research on Poyang Lake is essential to understand its ecological dynamics and promote sustainable development. Spatial and temporal dynamic monitoring and analyses of vegetation changes in the water body of Poyang Lake are still limited. This study fills this gap by using remote sensing and GIS techniques for dynamic monitoring and analysing the changes of water bodies and vegetation in Poyang Lake from 2013 to 2021. We used a combination of Maximum Likelihood Classification (MLC) and Support Vector Machine (SVM) to preprocess and classify 42 Landsat 8 OLI images. The results showed that the stability of the water body and vegetation varied greatly, with the water body showing the obvious change pattern of water rises, vegetation recedes and water recedes, vegetation grows, and the high-frequency inundation area was concentrated in the northeastern part of the lake (accounting for 60% of the total inundation area). Vegetation frequency distribution showed a pattern of sparse in the north and dense in the south, with the middle frequency area being the most, accounting for 19.88%, and the low frequency area being the least, accounting for 16.09%. The results show that the spatial and temporal distribution characteristics of water body and vegetation in Poyang Lake show low stability, which is a highly dynamic ecosystem. This study relatively makes up for the missing analysis of the stability change of water body and vegetation in the cycle of Poyang Lake, and provides a solid scientific basis for the protection and sustainable management work.},
}

*Lakes
*Remote Sensing Technology
China
*Environmental Monitoring/methods
Spatio-Temporal Analysis
Ecosystem
Geographic Information Systems
Support Vector Machine
*Plants
Water

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40733364,
year = {2025},
author = {Onyeagoziri, CA and Minoarivelo, HO and Hui, C},
title = {Mutualism and Dispersal Heterogeneity Shape Stability, Biodiversity, and Structure of Theoretical Plant-Pollinator Meta-Networks.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40733364},
issn = {2223-7747},
support = {89967//National Research Foundation/ ; //PhD bursary of the Southern African Systems Analysis Centre (SASAC), with partial funding from the German Academic Exchange Service (DAAD - Deutscher Akademischer Austauschdienst)/ ; },
abstract = {Mutualistic interactions are crucial to the structure and functioning of ecological communities, playing a vital role in maintaining biodiversity amidst environmental perturbations. In studies of meta-networks, which are groups of local networks connected by dispersal, most research has focused on the effect of dispersal on interaction networks of competition and predation, without much attention given to mutualistic interactions. Consequently, the role of different dispersal rates (between local networks and across species) in stability and network structures is not well understood. We present a competition-mutualism model for meta-networks where mutualistic interactions follow a type II functional response, to investigate stability and species abundance dynamics under varying dispersal scenarios. We specifically assess the impact of mutualism and dispersal heterogeneity, both between local networks and across species, on the structure and stability of meta-networks. We find that mutualistic meta-networks exhibit greater stability, higher total abundance, lower species unevenness, and greater nestedness compared to meta-networks with only competition interactions. Although dispersal heterogeneity across species exerts some influence, dispersal heterogeneity between local networks mainly drives the patterns observed: it reduces total abundance, increases unevenness, and diminishes compositional similarity across the meta-network. These results highlight the pivotal role of both mutualism and spatial dispersal structure in shaping ecological networks. Our work advances understanding of how mutualistic interactions and dispersal dynamics interact to influence biodiversity and stability in complex ecosystems.},
}

@article {pmid40732512,
year = {2025},
author = {Adlou, B and Wilburn, C and Weimar, W},
title = {Motion Capture Technologies for Athletic Performance Enhancement and Injury Risk Assessment: A Review for Multi-Sport Organizations.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {14},
pages = {},
pmid = {40732512},
issn = {1424-8220},
mesh = {Humans ; *Athletic Performance/physiology ; Risk Assessment ; *Athletic Injuries/prevention & control ; *Sports ; Geographic Information Systems ; Movement/physiology ; Motion Capture ; },
abstract = {Background: Motion capture (MoCap) technologies have transformed athlete monitoring, yet athletic departments face complex decisions when selecting systems for multiple sports. Methods: We conducted a narrative review of peer-reviewed studies (2015-2025) examining optical marker-based, inertial measurement unit (IMU) systems, including Global Navigation Satellite System (GNSS)-integrated systems, and markerless computer vision systems. Studies were evaluated for validated accuracy metrics across indoor court, aquatic, and outdoor field environments. Results: Optical systems maintain sub-millimeter accuracy in controlled environments but face field limitations. IMU systems demonstrate an angular accuracy of 2-8° depending on movement complexity. Markerless systems show variable accuracy (sagittal: 3-15°, transverse: 3-57°). Environmental factors substantially impact system performance, with aquatic settings introducing an additional orientation error of 2° versus terrestrial applications. Outdoor environments challenge GNSS-based tracking (±0.3-3 m positional accuracy). Critical gaps include limited gender-specific validation and insufficient long-term reliability data. Conclusions: This review proposes a tiered implementation framework combining foundation-level team monitoring with specialized assessment tools. This evidence-based approach guides the selection of technology aligned with organizational priorities, sport-specific requirements, and resource constraints.},
}

Humans
*Athletic Performance/physiology
Risk Assessment
*Athletic Injuries/prevention & control
*Sports
Geographic Information Systems
Movement/physiology
Motion Capture

@article {pmid40732191,
year = {2025},
author = {Eaton, WD and Hamilton, DA and Lemenze, A and Soteropoulos, P},
title = {Initial Analysis of Plant Soil for Evidence of Pathogens Associated with a Disease of Seedling Ocotea monteverdensis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732191},
issn = {2076-2607},
support = {no number//Fundacion Conservacionista Costarricense Fundacion/ ; 2022-10//Fondation Franklinia/ ; no number//Pace University Dyson College Deans Office/ ; no number//Pace University Dyson College Faculty Research Grant Committee/ ; no number//Pace University Provost Office for Research and Support/ ; },
abstract = {Seedlings of the ecologically important, critically endangered tree Ocotea monteverdensisis experience high mortality in the Monteverde, Costa Rica, cloud forests at the onset of the wet season, yet there are no studies suggesting the disease etiology. Here, healthy and diseased plant root and bulk soils were analyzed for various carbon and nitrogen (N) metrics and respiration levels, and DNA sequence-based bacterial and fungal community compositions. All nitrogen metric levels were greater in diseased vs. healthy plant root soils, which could enhance pathogen growth and pathogenic mechanisms. Greater DNA percentages from several potential pathogens were found in diseased vs. healthy plant root soils, suggesting this disease may be associated with a root pathogen. The DNA of the fungus Mycosphaerella was at greater levels in diseased vs. healthy plant root soils than other potential pathogens. Mycosphaerella causes similar diseases in other plants, including coffee, after onset of the wet season. The O. monteverdensis disease also occurs in seedlings planted within or near former coffee plantations at wet season onset. Distance-based linear model analyses indicated that NO3[-] levels best predicted the pattern of fungal pathogens in the soils, and Mycosphaerella and Tremella best predicted the patterns of the different N metrics in the soils, supporting their possible roles in this disease.},
}

@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@article {pmid40730013,
year = {2025},
author = {Chen, CF and Zhou, Z and Li, C and Liu, W},
title = {Ecological compensation and breakthrough innovation: Evidence from heavily polluting firms.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126682},
doi = {10.1016/j.jenvman.2025.126682},
pmid = {40730013},
issn = {1095-8630},
abstract = {The continuous deepening of the concept of green development and the increasing pressure of environmental governance leads great theoretical significance and practical value to explore the impact of the ecological compensation (eco-compensation) policy on the innovation behavior of enterprises. Taking the implementation of China's ecological compensation policy as an exogenous shock, this paper adopts a multi-period difference-in-differences (DID) model to systematically assess the impact of eco-compensation on corporate breakthrough innovation based on the data of A-share listed companies in the heavy pollution industry from 2014 to 2023. The findings indicate that eco-compensation significantly promotes breakthrough innovation activities of heavy polluting firms. Mechanism analysis further reveals that the policy indirectly drives the enhancement of firms' breakthrough innovation capability mainly by improving the level of data asset disclosure, reducing innovation risk and enhancing R&D activity. The heterogeneity analysis reveals that the eco-compensation policy promotes breakthrough innovation more significantly in firms located in regions where big data management institutions remain unreformed, data factor utilization is low, or industry-university-research collaboration is absent. This study theoretically expands the understanding of the impact mechanism of environmental regulation on enterprises' green innovation and enriches the research framework of incentives for breakthrough innovation; in practice, it provides policy references for optimizing the design of eco-compensation policies and guiding heavily polluting enterprises to achieve green transformation and high-quality development.},
}

@article {pmid40728939,
year = {2025},
author = {Franco, ME and Araújo, CVM and Cerveny, D and Koubová, A and Danneels, B and Goksøyr, A and Bertram, MG},
title = {The extended chemical defensome: emphasizing mechanisms of defense as key research avenues to tackle priority questions in environmental toxicology.},
journal = {Environmental toxicology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/etojnl/vgaf190},
pmid = {40728939},
issn = {1552-8618},
abstract = {Chemical pollution threatens organismal integrity, affecting growth, reproduction, behavior, and overall fitness, ultimately leading to shifts in biodiversity and the provisioning of ecosystem services. In response to chemical exposure, organisms use specific regions of their genome coding for different defense mechanisms-this collection of genes is termed the "chemical defensome". Specifically, genes associated with efflux transporters, transcription factors, antioxidant systems, and biotransformation pathways, among others, are expressed to reduce toxicity. These sub-individual processes are, for the most part, widely conserved across taxa and play a critical role in enabling organisms to cope with polluted environments. Additionally, we argue that behavioral responses-particularly spatial avoidance-should be recognized as an individual-level defense mechanism and incorporated into an extended chemical defensome framework. Expanding and reinforcing the concept of the chemical defensome beyond traditional studies at the genome level, as well as developing strategies to synthesize existing data, offers a valuable opportunity to link gene composition to physiological and behavioral responses, thereby addressing key research needs in environmental toxicology. These include: estimating the impact of chemical mixtures across different exposure scenarios, identifying the main drivers of intra- and interspecific sensitivity to pollution, and assessing large-scale ecological processes, such as biodiversity losses, in polluted habitats in a more integrated manner. In ecotoxicology and environmental risk assessment, understanding not only how chemical pollutants exert toxicity but also how organisms counteract these effects is essential. Indeed, investigating chemical-induced shifts in defense mechanisms can improve predictions of adverse outcomes at higher levels of biological organization and can inform more effective chemical management and regulatory strategies.},
}

@article {pmid40724857,
year = {2025},
author = {Piotrowski, M and Pawlaczyk, A and Szynkowska-Jóźwik, MI and Maras, P and Kozicki, M},
title = {Radiation-Sensitive Nano-, Micro-, and Macro-Gels and Polymer Capsules for Use in Radiotherapy Dosimetry.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724857},
issn = {1422-0067},
mesh = {*Polymers/chemistry ; *Radiometry/methods ; Alginates/chemistry ; Capsules/chemistry ; *Hydrogels/chemistry ; Humans ; Iron/chemistry ; *Radiotherapy/methods ; Gels/chemistry ; Radiation, Ionizing ; },
abstract = {This work introduces an original approach to the manufacturing of ionizing radiation-sensitive systems for radiotherapy applications-dosimetry. They are based on the Fricke dosimetric solution and the formation of macro-gels and capsules, and nano- and micro-gels. The reaction of ionic polymers, such as sodium alginate, with Fe and Ca metal ions is employed. Critical polymer concentration (c*) is taken as the criterion. Reaction of ionic polymers with metal ions leads to products related to c*. Well below c*, nano- and micro-gels may form. Above c*, macro-gels and capsules can be prepared. Nano- and micro-gels containing Fe in the composition can be used for infusion of a physical gel matrix to prepare 2D or 3D dosimeters. In turn, macro-gels can be formed with Fe ions crosslinking polymer chains to obtain radiation-sensitive hydrogels, so-called from wall-to-wall, serving as 3D dosimeters. The encapsulation process can lead to capsules with Fe ions serving as 1D dosimeters. This work presents the concept of manufacturing various gel structures, their main features and manufacturing challenges. It proposes new directions of research towards novel dosimeters.},
}

*Polymers/chemistry
*Radiometry/methods
Alginates/chemistry
Capsules/chemistry
*Hydrogels/chemistry
Humans
Iron/chemistry
*Radiotherapy/methods
Gels/chemistry
Radiation, Ionizing

@article {pmid40724441,
year = {2025},
author = {Hunyadi, ID and Cismaș, C},
title = {Mining Complex Ecological Patterns in Protected Areas: An FP-Growth Approach to Conservation Rule Discovery.},
journal = {Entropy (Basel, Switzerland)},
volume = {27},
number = {7},
pages = {},
pmid = {40724441},
issn = {1099-4300},
support = {LBUS-IRG-10-2024//Lucian Blaga University of Sibiu/ ; },
abstract = {This study introduces a data-driven framework for enhancing the sustainable management of fish species in Romania's Natura 2000 protected areas through ecosystem modeling and association rule mining (ARM). Drawing on seven years of ecological monitoring data for 13 fish species of ecological and socio-economic importance, we apply the FP-Growth algorithm to extract high-confidence co-occurrence patterns among 19 codified conservation measures. By encoding expert habitat assessments into binary transactions, the analysis revealed 44 robust association rules, highlighting interdependent management actions that collectively improve species resilience and habitat conditions. These results provide actionable insights for integrated, evidence-based conservation planning. The approach demonstrates the interpretability, scalability, and practical relevance of ARM in biodiversity management, offering a replicable method for supporting adaptive ecological decision making across complex protected area networks.},
}

@article {pmid40715537,
year = {2025},
author = {Zhang, F and Guo, A and Hu, Z and Liang, Y},
title = {A novel image fusion method based on UAV and Sentinel-2 for environmental monitoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27256},
pmid = {40715537},
issn = {2045-2322},
support = {2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; 2018SMHKJ-A-J-03//the Research and Demonstration of Key Technology for Water Resources Protection and Utilization and Ecological Reconstruction in Coal Mining area of Northern Shaanxi/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; N25XQD015//Funding for Basic Research Operations in Higher Education/ ; },
abstract = {In recent years, with the rapid development of remote sensing technology, environmental monitoring in mining areas using remote sensing imagery has gained increasing attention. Due to the small scale of mining areas, the resolution of satellite remote sensing imagery is insufficient for detailed monitoring needs. UAV remote sensing imagery provides high resolution, but its monitoring range is limited and lacks access to historical data. Furthermore, effectively fusing multi-source data with disparate spatial-temporal characteristics to accurately capture the complex dynamic changes in mining areas remains a key methodological challenge.To address this, this study, utilizing UAV remote sensing imagery and Sentinel-2 satellite imagery acquired on September 5, 2023, from the Erlintu mining area, proposes a novel fusion method aimed at achieving small-scale, long-term environmental monitoring in mining areas.First, the spatial resolution of both UAV and Sentinel-2 imagery is resampled to 0.1 m. Second, a two-layer preprocessing approach is applied to enhance data quality. Third, a stacked inversion model based on an ensemble learning framework is developed. Finally, using high-resolution UAV imagery as the reference, and original, resampled, and model-inverted Sentinel-2 imagery as experimental values, accuracy is assessed and analyzed with Mean Absolute Percentage Error (MAPE) as the metric. Results demonstrate that the stacked learning model, combined with cubic convolution resampling, reduces the MAPE of NDVI values between Sentinel-2 and UAV imagery from 54.31 to 10.01%, markedly improving accuracy. This study further uncovers the synergistic effect of resampling techniques and model architecture, offering reliable data support for small-scale, long-term environmental monitoring in mining areas.},
}

@article {pmid40715152,
year = {2025},
author = {Aubouin, L and Genoud, D and Givord-Coupeau, B and Tercerie, S and Gargominy, O and Geslin, B and Schatz, B},
title = {BeeFunc, a comprehensive trait database for French bees.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1302},
pmid = {40715152},
issn = {2052-4463},
mesh = {Bees/classification/anatomy & histology ; Animals ; France ; *Databases, Factual ; },
abstract = {Given pollinator's reported decline, it is of utmost importance to better understand the vulnerability of wild bees to human pressures. One way to achieve this goal is to explore how their traits are associated with exposure to anthropogenic perturbations. To date, there is no database synthesizing traits of bees at the species level in France, limiting the functional interpretation of inventories. We present BeeFunc 1.0, the first database on traits for the entire fauna of French wild bees. Based on extensive literature research and expert knowledge, the database is structured according to the French taxonomic register (TAXREF) and its associated knowledge base. The base gathers 26,176 trait information from 483 sources, describing 932 species for 20 features related to morphology, ecology, biogeography, and conservation. BeeFunc is intended to be collaborative and regularly updated. Bees can finally be better considered from a functional perspective. We expect this database to be widely used by researchers, conservationists, naturalists, and stakeholders, stimulating future research on wild bees.},
}

Bees/classification/anatomy & histology
Animals
France
*Databases, Factual

@article {pmid40713811,
year = {2025},
author = {Sun, B and Yuan, J and Zhang, X and Ma, X and Hao, Z and Wang, L and Li, Y and Zhang, L and Li, L},
title = {Metaproteomics Reveals Community Coalescence Outcomes in Co-Cultured Human Gut Microbiota.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70009},
doi = {10.1002/pmic.70009},
pmid = {40713811},
issn = {1615-9861},
support = {32370050//National Natural Science Foundation of China/ ; 82371559//National Natural Science Foundation of China/ ; },
abstract = {The human gut microbiome exhibits characteristics of complex ecosystems, including the ability to resist and compete with exogenous species or communities. Understanding the microbiome response that emerges from such competitive interactions is crucial, particularly for applications like fecal microbiota transplantation (FMT), where the success of treatment largely depends on the outcome of these microbial competitions. During these processes, microbial communities undergo coalescence, a phenomenon where distinct microbial communities combine and interact, leading to complex ecological outcomes that are still being uncovered. In this study, we examined the coalescent dynamics of 10 different pairs of human gut microbiota by co-culturing the plateau-phase communities of individual samples in vitro, and highlighted the critical role of metaproteomics in elucidating the competitive dynamics of co-cultured human fecal samples. Results showed that microbiome changes observed after coalescent co-culture were not straightforwardly an approximate average of the initial taxonomic or functional compositions of the two samples. Instead, both coalescent microbiotas behaved as cohesive structures, influencing the competitive outcome toward one of them. Although co-cultured communities usually exhibited high degrees of taxonomic similarities to one of its parental samples, we found that 23% of the observed proteins still showed differential expression or abundance at the metaproteomic level. Interestingly, and somewhat counterintuitively, no specific microbial ecological characteristic could linearly determine which of the two initial microbiotas would act as the driving microbiota. Instead, we observed that the outcomes of the microbial co-cultures resembled a "rock-paper-scissors"-like dynamic. Through an analysis of co-colonizing species in such "rock-paper-scissors"-like triangle, we discovered that co-colonizing species that contributed to winning each between-community competition differed from one community pair to another. This suggests that no single species or function consistently dominates across all situations; instead, this involves more complex mechanisms, which require further in-depth investigation in future studies. Our findings demonstrate that the complex competitive interactions between microbial communities make predicting success through a single parameter challenging, whereas pre-co-culturing shows promise as an effective method for predicting outcomes in ecological therapies such as FMT. SUMMARY: This study underscores the critical importance of integrating metaproteomics with microbial systems ecology to gain a functional understanding of microbial coalescence. By addressing the ecological question of how two communities compete when they are brought into contact, we investigated the metaproteomic responses of pairs of coalescent co-cultured human gut microbiotas. Our results revealed significant insights: post-co-culture microbiota changes were not merely a simple average of the initial compositions but instead exhibited distinct shifts toward one of the original samples. Notably, due to the observed rock-paper-scissors-like cycle of winning, we argue that no single microbial ecological characteristic could straightforwardly predict which of the two samples would dominate as the driving microbiota. Overall, our findings suggest that during coalescence, microbial communities behave as cohesive structures both taxonomically and functionally, influencing competitive dynamics and ecosystem complexity, indicating that an in vitro coalescence pretest may help predict the success of therapies like FMT.},
}

@article {pmid40705801,
year = {2025},
author = {Solowiej-Wedderburn, J and Pentz, JT and Lizana, L and Schroeder, BO and Lind, PA and Libby, E},
title = {Competition and cooperation: The plasticity of bacterial interactions across environments.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013213},
pmid = {40705801},
issn = {1553-7358},
mesh = {*Microbial Interactions/physiology ; *Models, Biological ; *Bacteria/genetics/metabolism ; Computational Biology ; Computer Simulation ; *Bacterial Physiological Phenomena ; Metabolic Networks and Pathways/genetics ; Ecosystem ; Environment ; },
abstract = {Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.},
}

*Microbial Interactions/physiology
*Models, Biological
*Bacteria/genetics/metabolism
Computational Biology
Computer Simulation
*Bacterial Physiological Phenomena
Metabolic Networks and Pathways/genetics
Ecosystem
Environment

@article {pmid40705402,
year = {2025},
author = {Oba, T and Takano, K and Sugawara, D and Kimura, K},
title = {Just-in-Time Delivery of Cognitive Behavioral Therapy-Based Exercises: Single-Case Experimental Design With Random Multiple Baselines.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e69556},
pmid = {40705402},
issn = {2561-326X},
mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Female ; Adult ; Male ; Middle Aged ; *Stress, Psychological/therapy/psychology ; *Mobile Applications ; Smartphone ; Single-Case Studies as Topic ; Feasibility Studies ; Japan ; },
abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) are a promising approach in mental health care given the potential scalability (ie, interventions are offered automatically and remotely) and preciseness (ie, the right interventions are offered at the right moments). Typically, a smartphone app is programmed to assess users' psychological states in daily life; when a particular state is detected, the app prompts users to engage in specific behaviors. Conceptually, JITAIs hold significant potential for precision health, although there is currently limited evidence in the literature.

OBJECTIVE: We implemented this scheme as a smartphone intervention for daily stress management, based on cognitive behavioral therapy (CBT), and evaluated its feasibility and efficacy using a single-case experimental design.

METHODS: A total of 8 Japanese adults (community sample: 4 women; mean 37.6, SD 13.1 y) were recruited. An AB phase design with multiple random baselines was used, where "A" represents the baseline phase and "B" represents the intervention phase. Throughout the study period (28 d), participants were prompted to indicate their momentary levels of stress (range 0-100) using a smartphone thrice a day. The baseline phase duration was randomly varied among participants, lasting between 7 and 14 days. The remaining period was used as the intervention phase (14-21 d), where 6 CBT-based exercises (ie, breath control, mindfulness, relaxation, self-talk, cognitive defusion, and cognitive restructuring) were offered depending on the reported levels of stress.

RESULTS: Approximately 70% (6/8) of the participants perceived the intervention to be useful and helpful. A randomization test detected a statistically significant decrease in reported stress levels after the intervention began (P=.005), though this effect was less pronounced when analyzed individually for each participant. Multilevel model analysis detected a significant acute reduction in the momentary level of stress right after completing a CBT-based exercise (pre-exercise: mean 47.98, SD 21.65; post exercise: mean 42.13, SD 19.88; P=.03; Cohen dz=0.58). Also, a significant reduction in depressive rumination was observed in the postintervention assessment (preintervention: mean 13.00, SD 3.21; post intervention: mean 9.25, SD 2.60; P=.01, Cohen dz=1.17).

CONCLUSIONS: The intervention was feasible and effective in reducing subjective stress (and rumination) in the study sample. The small sample size and the nonclinical nature of the sample may limit the generalizability and implications of the study findings for clinical practice. More evidence should be collected to draw solid conclusions for technical and technological as well as clinical aspects of mobile interventions. Accumulating exemplars with different implementations will clarify how a JITAI can be designed and developed on a mobile platform and how the program can be delivered in the prevention and treatment of mental ill health.},
}

Humans
*Cognitive Behavioral Therapy/methods
Female
Adult
Male
Middle Aged
*Stress, Psychological/therapy/psychology
*Mobile Applications
Smartphone
Single-Case Studies as Topic
Feasibility Studies
Japan

@article {pmid40703330,
year = {2025},
author = {Boyes, D and Crowley, LM and Adewumi, T and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Dotted Buff moth, Photedes minima Haworth, 1809.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {299},
pmid = {40703330},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Photedes minima (Small Dotted Buff; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 694.66 megabases. Most of the assembly (99.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.38 kilobases.},
}

@article {pmid40702785,
year = {2025},
author = {Lee, TY and Chen, CH and Liu, CM and Chen, IM and Chen, HC and Wu, SI and Hsiao, CK and Kuo, PH},
title = {Fourier Transform Analysis of GPS-Derived Mobility Patterns for Diagnosis and Mood Monitoring of Bipolar and Major Depressive Disorders: Prospective Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71658},
pmid = {40702785},
issn = {1438-8871},
mesh = {Humans ; *Depressive Disorder, Major/diagnosis ; *Bipolar Disorder/diagnosis ; *Geographic Information Systems ; Female ; Male ; Adult ; Prospective Studies ; *Fourier Analysis ; Middle Aged ; Affect ; },
abstract = {BACKGROUND: Mood disorders, including bipolar disorder (BP) and major depressive disorder (MDD), are characterized by significant psychological and behavioral fluctuations, with mobility patterns serving as potential markers of emotional states.

OBJECTIVE: This study explores the diagnostic and monitoring capabilities of Fourier transform, a frequency-domain analysis method, in mood disorders by leveraging GPS data as an objective measure.

METHODS: A total of 62 participants (BP: n=20, MDD: n=27, and healthy controls: n=15) contributed 5177 person-days of data over observation periods ranging from 5 days to 6 months. Key GPS indicators-location variance (LV), transition time (TT), and entropy-were identified as reflective of mood fluctuations and diagnostic differences between BP and MDD.

RESULTS: Fourier transform analysis revealed that the maximum power spectra of LV and entropy differed significantly between BP and MDD groups, with patients with BP exhibiting greater periodicity and intensity in mobility patterns. Notably, participants with BP demonstrated consistent periodic waves (eg, 1-d, 4-d, and 9-d cycles), while such patterns were absent in those with MDD. In addition, after adjusting for age, gender, and employment status, only the power spectrum of LV remained a significant predictor of depressed mood (odds ratio [OR] 0.9976, 95% CI 0.9956-0.9996; P=.02). Daily GPS data showed stronger correlations with ecological momentary assessment (EMA)-reported mood states compared to weekly or monthly aggregations, emphasizing the importance of day-to-day monitoring. Depressive states were associated with reduced LV (OR 0.975, 95% CI 0.957-0.993; P=.008) and TT (OR 0.048, 95% CI 0.012-0.200; P<.001) on weekdays, and lower entropy (OR 0.662, 95% CI 0.520-0.842; P=.001) on weekends, indicating that mobility features vary with social and temporal contexts.

CONCLUSIONS: This study underscores the potential of GPS-derived mobility data, analyzed through Fourier transform, as a noninvasive and real-time diagnostic and monitoring tool for mood disorders. The findings suggest that the intensity of mobility patterns, rather than their frequency, may better differentiate BP from MDD. Integrating GPS data with EMAs could enhance the precision of clinical assessments, provide early warnings for mood episodes, and support personalized interventions, ultimately improving mental health outcomes. This approach represents a promising step toward digital phenotyping and advanced mental health monitoring strategies.},
}

Humans
*Depressive Disorder, Major/diagnosis
*Bipolar Disorder/diagnosis
*Geographic Information Systems
Female
Male
Adult
Prospective Studies
*Fourier Analysis
Middle Aged
Affect

@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}

*Genome, Viral
*RNA Viruses/genetics
Animals
*Computational Biology/methods
Metagenomics/methods
*Software
RNA, Viral/genetics

@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
pmid = {40700599},
issn = {1367-4811},
mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}

*Phylogeny
*Models, Biological
*Microbiota
*Metagenomics/methods
*Computational Biology/methods
Computer Simulation

@article {pmid40699651,
year = {2025},
author = {Wang, H and Zhou, H and Yao, X},
title = {Different Species of Bats: Genomics, Transcriptome, and Immune Repertoire.},
journal = {Current issues in molecular biology},
volume = {47},
number = {4},
pages = {},
pmid = {40699651},
issn = {1467-3045},
support = {82160279//National Natural Science Foundation of China/ ; No. (2018)5637//Guizhou Provincial Hundred level Talent Fund/ ; },
abstract = {Bats are the only mammals with the ability to fly and are the second largest order after rodents, with 20 families and 1213 species (over 3000 subspecies) and are widely distributed in regions around the world except for Antarctica. What makes bats unique are their biological traits: a tolerance to zoonotic infections without getting clinical symptoms, long lifespans, a low incidence of tumors, and a high metabolism. As a result, they are receiving increasing attention in the field of life sciences, particularly in medical research. The rapid advancements in sequencing technology have made it feasible to comprehensively analyze the diverse biological characteristics of bats. This review comprehensively discusses the following: (1) The assembly and annotation overview of 77 assemblies from 54 species across 11 families and the transcriptome sequencing overview of 42 species from 7 families, focused on a comparative analysis of genomic architecture, sensory adaptations (auditory, visual, and olfactory), and immune functions. Key findings encompass marked interspecies divergence in genome size, lineage-specific expansions/contractions of immune-related gene families (APOBEC, IFN, and PYHIN), and sensory gene adaptations linked to ecological niches. Notably, echolocating bats exhibited convergent evolution in auditory genes (SLC26A5 and FOXP2), while fruit-eating bats displayed a degeneration of vision-associated genes (RHO), reflecting trade-offs between sensory specialization and ecological demands. (2) The annotation of the V (variable), D (diversity), J (joining), and C (constant) gene families in the TR and IG loci of 12 species from five families, with a focus on a comparative analysis of the differences in TR and IG genes and CDR3 repertoires between different bats and between bats and other mammals, provides us with a deeper understanding of the development and function of the immune system in organisms. Integrated genomic, transcriptomic, and immune repertoire analyses reveal that bats employ distinct antiviral strategies, primarily mediated by enhanced immune tolerance and suppressed inflammatory responses. This review provides foundational information, collaboration directions, and new perspectives for various laboratories conducting basic and applied research on the vast array of bat biology.},
}

@article {pmid40698863,
year = {2025},
author = {Woo, H and Eyun, SI},
title = {Applications and techniques of single-cell RNA sequencing across diverse species.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40698863},
issn = {1477-4054},
support = {RS-2022-KS221676//Korea Institute of Marine Science & Technology Promotion/ ; RS-2025-02215227//Korea Institute of Marine Science & Technology Promotion/ ; 2022R1A2C4002058//National Research Foundation of Korea/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Sequence Analysis, RNA/methods ; Animals ; Gene Expression Profiling/methods ; Transcriptome ; Computational Biology/methods ; },
abstract = {Single-cell ribonucleic acid sequencing (scRNA-seq) is an important tool in molecular biology, allowing transcriptomic profiling at the single-cell level. This transformative technology has provided unprecedented insights into cellular heterogeneity, lineage differentiation, and cell-type-specific gene expression patterns, significantly advancing our understanding of complex biological systems. scRNA-seq is broadly applied across various fields, including oncology, where it sheds light on intratumoral heterogeneity and precision medicine strategies, and developmental biology, where it uncovers cellular trajectories in both model and non-model organisms. Additionally, scRNA-seq has been instrumental in ecological genomics, which can help elucidate cellular responses to environmental perturbations and species interactions. Despite these advancements, several challenges remain, particularly technical and financial barriers, limiting its application to non-model organisms and tissues with complex cellular compositions. Addressing these issues will require continued innovation in single-cell isolation methods, cost-effective sequencing technologies, and sophisticated bioinformatics tools. As scRNA-seq advances, it can deepen our understanding of biological systems, with broad implications for personalized medicine, evolutionary biology, and ecological research.},
}

*Single-Cell Analysis/methods
Humans
*Sequence Analysis, RNA/methods
Animals
Gene Expression Profiling/methods
Transcriptome
Computational Biology/methods

@article {pmid40697421,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dark Umber moth, Philereme transversata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {300},
pmid = {40697421},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Philereme transversata (Dark Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 591.75 megabases. Most of the assembly (99.1%) is scaffolded into 20 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.07 kilobases. Gene annotation of this assembly on Ensembl identified 12,207 protein-coding genes.},
}

@article {pmid40694591,
year = {2025},
author = {Gong, R and Feng, Z and Zhang, Y},
title = {Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013301},
pmid = {40694591},
issn = {1553-7358},
mesh = {Animals ; *Influenza in Birds/virology/epidemiology ; *Reassortant Viruses/genetics ; *Influenza A virus/genetics ; Birds/virology ; Computational Biology ; Poultry/virology ; Phylogeny ; },
abstract = {The resurgence of H5Nx reassortment has caused multiple epidemics resulting in severe disease even death in wild birds and poultry. Assessing H5Nx reassortment risk is crucial for designing targeted interventions and enhancing preparedness efforts to manage H5Nx outbreaks effectively. However, the complexity in H5Nx reassortment, driven by the diversity of influenza A viruses (IAVs) and wide range of hosts, has hindered the effective quantification of reassortment risk. In this study, we utilized a network approach to explore the reassortment history using a large-scale dataset. By inferring genomic homogeneity among IAVs, we constructed an IAVs homologous network with reassortment history embedded within it. We estimated the communities within the IAVs homologous network to represent the reassortment risk of various viruses, revealing diverse reassortment risks across different H5Nx viruses. Our analysis also identified the primary hosts contributing to reassortment: domestic poultry in China, and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a framework for quantifying and ranking H5Nx reassortment risk, contributing to enhanced preparedness and prevention efforts.},
}

Animals
*Influenza in Birds/virology/epidemiology
*Reassortant Viruses/genetics
*Influenza A virus/genetics
Birds/virology
Computational Biology
Poultry/virology
Phylogeny

@article {pmid40691457,
year = {2025},
author = {Steckler, MR and Kumar, J and Breen, AL and Zhang, T and Hoffman, FM and Hargrove, WW and Walker, DA and Wells, AF and Droghini, A and Nawrocki, TW and Wullschleger, SD and Macander, MJ and Frost, GV and Salmon, VG and Barnett, DT and Iversen, CM},
title = {PAVC: The foundation for a Pan-Arctic Vegetation Cover database.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1271},
pmid = {40691457},
issn = {2052-4463},
mesh = {Arctic Regions ; *Plants/classification ; *Databases, Factual ; Remote Sensing Technology ; Ecosystem ; Trees ; },
abstract = {Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and "other" vegetation, as well as absolute cover for litter and top cover for water and bare ground.},
}

Arctic Regions
*Plants/classification
*Databases, Factual
Remote Sensing Technology
Ecosystem
Trees

@article {pmid40688383,
year = {2025},
author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S},
title = {Analysis of metagenomic data.},
journal = {Nature reviews. Methods primers},
volume = {5},
number = {},
pages = {},
pmid = {40688383},
issn = {2662-8449},
support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.},
}

@article {pmid40687154,
year = {2025},
author = {Filippova, NV and Zvyagina, EA and Bolshakov, SY and Arefyev, SP and Bulyonkova, TM and Filippov, IV and Rebriev, YA and Shiryaev, AG and Stavishenko, IV and Svetasheva, TY},
title = {Occurrence dataset of protected fungal species for the Red Data Book in Yugra Region, Western Siberia.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e155657},
pmid = {40687154},
issn = {1314-2828},
abstract = {BACKGROUND: The data paper describes a dataset of occurrences of fungal species listed in the Red Data Book of Yugra Region (Western Siberia, Russia). The dataset is based on all digitised records of fungal occurrences in the region. The authors conducted an assessment of the conservation status of fungal species for the revised third edition of the Red Data Book of Yugra. The third edition of the Red Data Book of Yugra includes a total of 61 fungal species (excluding lichens). Of these, nine species are listed on the IUCN Red List and six are included in the Red Data Book of Russia. At the time of publication, the dataset comprises 1180 records of protected species, including human observations, preserved specimens and material citations from literature.

NEW INFORMATION: The paper provides the first overview of the history of fungal conservation in Yugra (Khanty-Mansi Autonomous Okrug-Yugra, KhMAO-Yugra). For the first time, open-source data are used for the assessment of the occurrence of rare species and evaluation of their conservation status for the revised third edition of the Red Data Book of Yugra. An integrated occurrence dataset for the species included in the new edition of the Red Data Book is presented.},
}

@article {pmid40683291,
year = {2025},
author = {Winkler, AS and Brux, CM and Carabin, H and das Neves, CG and Häsler, B and Zinsstag, J and Fèvre, EM and Okello, A and Laing, G and Harrison, WE and Pöntinen, AK and Huber, A and Ruckert, A and Natterson-Horowitz, B and Abela, B and Aenishaenslin, C and Heymann, DL and Rødland, EK and Berthe, FCJ and Capua, I and Sejvar, J and Lubroth, J and Corander, J and May, J and Roth, LF and Thomas, LF and Blumberg, L and Lapinski, MK and Stone, M and Agbogbatey, MK and Xiao, N and Hassan, OA and Dar, O and Daszak, P and Guinto, RR and Senturk, S and Sahay, S and Samuels, TA and Wasteson, Y and Amuasi, JH},
title = {The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems.},
journal = {Lancet (London, England)},
volume = {406},
number = {10502},
pages = {501-570},
doi = {10.1016/S0140-6736(25)00627-0},
pmid = {40683291},
issn = {1474-547X},
}

@article {pmid40681316,
year = {2025},
author = {Nekrakalaya, B and Kotimoole, CN and Arefian, M and Prasad, TSK and Palliyath, GK and Veerappa Hanumanthappa, P and Pandian Ramasubramania, TP and Bangalore Jayaseelan, NK and Muddumadiah, C and Santhappan, P and Muliyar Krishna, R},
title = {A Gel-Free Genome Annotation Provides Insights into the Proteome of the Oomycete Phytophthora meadii, a Disease-Causing Pathogen in Economically Important Crops.},
journal = {Omics : a journal of integrative biology},
volume = {29},
number = {8},
pages = {384-393},
doi = {10.1177/15578100251359566},
pmid = {40681316},
issn = {1557-8100},
mesh = {*Phytophthora/genetics/metabolism/pathogenicity ; *Proteome/genetics/metabolism ; *Plant Diseases/microbiology/parasitology ; Molecular Sequence Annotation ; *Crops, Agricultural/microbiology/parasitology ; Proteomics/methods ; Computational Biology/methods ; Tandem Mass Spectrometry ; Gene Ontology ; Chromatography, Liquid ; },
abstract = {Phytophthora meadii is a polyphagous oomycete causing fatal diseases in economically important cash crops such as rubber, arecanut, cardamom, and other crops and plants of economic significance. Although information on the proteogenomic and proteomic analysis is available for several Phytophthora species, no information on the proteome repertoire of P. meadii is available. In the present study, a gel-free protein annotation was performed using liquid chromatography with tandem mass spectrometry analysis of the P. meadii hyphae, followed by bioinformatics analysis. The results were compared with a global Phytophthora proteome database-based search and an in-house P. meadii genome database, along with RefSeq proteome databases of other selected species of Phytophthora. A total of 7725 and 3979 proteins were exclusively matched with global and in-house databases, respectively. Basic Local Alignment Search Tool analysis showed 209 unique peptide sequences belonging to 85 proteins of P. meadii. Gene Ontology-based functional analysis of the P. meadii mycelial proteome categorized the proteins based on their role in cellular components, molecular functions, and biological processes. Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein network analysis further revealed the role of these proteins in growth and development functions. In addition, proteins potentially involved in virulence, infections in the host system, and several signaling mechanisms were deduced. The current study is the first report on the P. meadii mycelial proteins under optimum growth conditions. These omics data also have socioeconomic implications since Phytophthora causes disease in a wide range of economically noteworthy crops and forest ecosystems.},
}

*Phytophthora/genetics/metabolism/pathogenicity
*Proteome/genetics/metabolism
*Plant Diseases/microbiology/parasitology
Molecular Sequence Annotation
*Crops, Agricultural/microbiology/parasitology
Proteomics/methods
Computational Biology/methods
Tandem Mass Spectrometry
Gene Ontology
Chromatography, Liquid

@article {pmid40680476,
year = {2025},
author = {Roel Lesur, M and Longo, MR and Tajadura-Jiménez, A},
title = {Linking spatial metaphors to body size perception: Different roles of top-down associations and multisensory contributions when mapping auditory cues to finger length.},
journal = {Cortex; a journal devoted to the study of the nervous system and behavior},
volume = {190},
number = {},
pages = {178-191},
doi = {10.1016/j.cortex.2025.06.014},
pmid = {40680476},
issn = {1973-8102},
abstract = {Temporospatial and semantic multisensory aspects contribute to bodily and spatial perception. An informative paradigm to study this is the Auditory Pinocchio Illusion, in which participants perceive an elongation of their finger upon vertically pulling their finger and hearing a concurrent upward pitch glissando. This arguably relies on anchoring (i.e., associating) the ecologically unrelated upward pitch glissando to the finger and allows to separately assess the role of semantic and multisensory contributions. However, what is needed for this anchoring to occur is unknown. In a first Experiment, we manipulated top-down attention to the finger upon which either an ascending or descending sound would be produced. In a second experiment, we compared how different bottom-up multisensory cues (arising from actions performed on the finger) concurrent to the ascending or descending pitch affected finger length perception. Participants either pulled, touched or stretched their finger. Through a perceptual judgment task of finger landmark localization and questionnaire ratings, we measured participants' perceived finger length in both studies and separately assessed their sensory imagery skills. Our results show that attention alters finger length perception according to questionnaire ratings but not perceptual judgements, while concurrent multisensory signals similarly affect both measures. No relationship between these effects and participants' sensory imagery was found. We suggest that while top-down associations between pitch and verticality are necessary and affect questionnaire ratings, they are not sufficient to affect perceptual judgements. Bottom-up somatosensory cues seem to be additionally needed to impact such judgements in this illusion.},
}

@article {pmid40680084,
year = {2025},
author = {Laplane, L and Lamoureux, A and Richker, HI and Marquez Alcaraz, G and Fortunato, A and Shaffer, Z and Aktipis, A and Mischel, PS and Plutynski, A and Townsend, JP and Maley, CC},
title = {Applying multilevel selection to understand cancer evolution and progression.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003290},
pmid = {40680084},
issn = {1545-7885},
support = {OT2 CA278688/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Biological Evolution ; Cell Proliferation ; Disease Progression ; *Neoplasms/genetics/pathology ; *Selection, Genetic ; },
abstract = {Natural selection occurs at multiple levels of organization in cancer. At an organismal level, natural selection has led to the evolution of diverse tumor suppression mechanisms, while at a cellular level, it favors traits that promote cellular proliferation, survival and cancer. Natural selection also occurs at a subcellular level, among collections of cells and even among collections of organisms; selection at these levels could influence the evolution of cancer and cancer suppression mechanisms, affecting cancer risk and treatment strategies. There may also be cancer-like processes happening at different levels of organization, in which uncontrolled proliferation at lower levels may disrupt a higher level of organization. This Essay examines how selection operates across levels, highlighting how we might leverage this understanding to improve cancer research, prevention and treatment.},
}

Animals
Humans
Biological Evolution
Cell Proliferation
Disease Progression
*Neoplasms/genetics/pathology
*Selection, Genetic

@article {pmid40678991,
year = {2025},
author = {Miller-Ter Kuile, A and Bui, A and Apigo, A and Lamm, S and Swan, M and Sanderlin, JS and Ogle, K},
title = {If You're Rare, Should I Care? How Imperfect Detection Changes Relationships Between Biodiversity and Global Change Drivers.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70362},
doi = {10.1111/gcb.70362},
pmid = {40678991},
issn = {1365-2486},
support = {Challenge Cost Share 21-CS-11221635-194//Rocky Mountain Research Station/ ; },
mesh = {*Biodiversity ; Animals ; Birds ; Plants ; Insecta ; *Climate Change ; Uncertainty ; Conservation of Natural Resources ; },
abstract = {Across ecosystems and biomes, most species in biological communities are rare. Many studies discount rare species when examining biodiversity patterns, assuming that common species are most influential for ecosystem functioning. There is growing evidence, however, that rare species contribute unique functions in many ecosystems; thus, discounting them produces misleading conclusions about how biodiversity is changing in the face of natural and anthropogenic forces. Rare species are more likely to be missed by multi-species sampling designs and are thus particularly vulnerable to detection error. Best practice in biodiversity assessments should include rare species and account for error in the detection process. We outline a general approach that accounts for detection error in sampling designs using multi-species occupancy and abundance models (MSOM/MSAM). We then show how uncertainty in detection can be propagated from MSOM/MSAM results to derive more accurate estimates of alpha and beta diversity metrics. Finally, we show how uncertainty in these diversity metrics can be accounted for in follow-up regression models to evaluate relationships between biodiversity and global change covariates. Using three case studies across diverse taxa (birds, insects, and plants), we demonstrate how accounting for the detection process alters the relationships between biodiversity and global change drivers in ways that are important for understanding and predicting ongoing change in these communities. Our generalizable analysis approach can aid in accounting for rare species in studies of global biodiversity.},
}

*Biodiversity
Animals
Birds
Plants
Insecta
*Climate Change
Uncertainty
Conservation of Natural Resources

@article {pmid40677746,
year = {2025},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19674},
pmid = {40677746},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; },
abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods/standards
Pacific Ocean
Animals
*Aquatic Organisms/genetics/classification
Biodiversity
Electron Transport Complex IV/genetics
*Databases, Nucleic Acid/standards
*Databases, Genetic

@article {pmid40674907,
year = {2025},
author = {Fan, Q and Hu, Y and Huang, S and Guo, Y and Guo, J and Liu, F and Qi, W and Liu, H and Qu, J},
title = {Anti-epidemic pharmaceuticals predominantly contributed to PPCPs flux in the Yangtze River during 2020.},
journal = {Water research},
volume = {286},
number = {},
pages = {124228},
doi = {10.1016/j.watres.2025.124228},
pmid = {40674907},
issn = {1879-2448},
abstract = {The COVID-19 pandemic triggered a surge in pharmaceutical consumption, yet its impact on large-scale riverine systems remains poorly quantified. This study investigated the spatiotemporal distribution, sources and transport flux of 58 pharmaceuticals and personal care products (PPCPs) across the Yangtze River Basin (3400 km mainstream and 8 tributaries) during 2020. The mean concentration of PPCPs was 200.2 ± 205.7 ng/L in 2020, with caffeine (28.2 %), carbamazepine (13.2 %), and metronidazole (9.2 %) as dominant compounds. It was estimated that 449.8 tons of PPCPs were discharged into the sea via the Yangtze River in 2020, of which 48 % (216.0 tons) originated from COVID-19-related pharmaceuticals (e.g., metronidazole, diclofenac). Compared to pre-pandemic levels (2018), the river experienced additional pollution pressure from 209.6 tons of COVID-19 related pharmaceutical emissions. Source apportionment identified post-consumer anthropogenic activities (domestic discharges, clinical effluent outflows, and veterinary applications) as primary contributors (p < 0.05), while industrial sources associated with pharmaceutical production contributed little. Low ecological risks were observed in the study area, likely attributable to high wastewater treatment rates (>90 % in most cities) and the high efficacy of centralized wastewater management. This study provided the first basin-scale quantitative evidence of pandemic-driven PPCP pollution, offering critical insights for balancing public health emergencies with sustainable water resource governance.},
}

@article {pmid40670386,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1195},
pmid = {40670386},
issn = {2052-4463},
support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2OD034190//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HG011274//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; OT2 OD034190/OD/NIH HHS/United States ; 60NANB20D166//United States Department of Commerce | National Institute of Standards and Technology (NIST)/ ; P01 CA272295/CA/NCI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35GM133747//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1936791//National Science Foundation (NSF)/ ; U01CA253405//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54 AG089334/AG/NIA NIH HHS/United States ; R01 CA266279/CA/NCI NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; 1919691//National Science Foundation (NSF)/ ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24HG011853//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
mesh = {Humans ; Whole Genome Sequencing ; *Genome, Human ; *Pancreatic Neoplasms/genetics ; *Carcinoma, Pancreatic Ductal/genetics ; Cell Line, Tumor ; },
abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.},
}

Humans
Whole Genome Sequencing
*Genome, Human
*Pancreatic Neoplasms/genetics
*Carcinoma, Pancreatic Ductal/genetics
Cell Line, Tumor

@article {pmid40669920,
year = {2025},
author = {Piedboeuf-Potyka, K and Hering, R and Schulz, M and Mackowiak, M and Brinks, R and Kuß, O and Hoyer, A and Tönnies, T},
title = {Incidence of type 2 diabetes by socioeconomic deprivation in Germany between 2014 and 2019: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e094824},
pmid = {40669920},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; Adult ; *Social Deprivation ; Socioeconomic Factors ; },
abstract = {OBJECTIVE: To estimate type 2 diabetes incidence trends by sex and socioeconomic position (SEP) and evaluate trends in SEP-related inequalities in incidence.

DESIGN: Ecological study using ambulatory claims data and regression-based modelling.

SETTING: All 401 counties in Germany, covering the entire country.

PARTICIPANTS: All individuals with statutory health insurance (~85% of the population). Incident cases of type 2 diabetes were identified annually from 2014 to 2019 using the International Statistical Classification of Diseases and Related Health Problems, 10th revision codes.

Incident type 2 diabetes at the county level, adjusted for age and modelled using a mixed negative binomial regression. SEP was measured using the German Index of Socioeconomic Deprivation, and a random intercept accounted for county-level heterogeneity.

RESULTS: The incidence of type 2 diabetes decreased between 2014 and 2017 and plateaued thereafter. Trends were similar between sexes and deprivation levels. The greatest difference was observed between high and low deprivation, with an incidence rate ratio of 1.20 (95% CI: 1.14 to 1.27) among men and 1.21 (95% CI: 1.14 to 1.27) among women in 2014.

CONCLUSIONS: There was a positive trend in the decline in age-adjusted type 2 diabetes incidence between 2014 and 2019. However, social inequality persisted with deprived groups at higher risk of type 2 diabetes. The level of inequality was comparable between men and women. Continued monitoring is essential to assess whether these short-term trends persist over time.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology
Germany/epidemiology
Female
Male
Incidence
Middle Aged
Aged
Adult
*Social Deprivation
Socioeconomic Factors

@article {pmid40664368,
year = {2025},
author = {Li, P and Zhu, B and Fu, J and Liu, X and Huang, K and Pan, W and Xue, Q and Zhang, H and Zhang, A and Fu, J and Jiang, G},
title = {Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {14842-14852},
doi = {10.1021/acs.est.4c13225},
pmid = {40664368},
issn = {1520-5851},
mesh = {Risk Assessment ; *Environmental Pollutants ; *Big Data ; *Toxicology ; },
abstract = {Synthetic chemicals are intensively utilized in modern societies, and their mixtures pose significant health and ecological threats. Nontarget screening (NTS) analysis allows for the simultaneous chemical identification and quantitative reporting of tens of thousands of chemicals in complex environmental matrices, whereas the computational toxicology (CT) serves as another high-throughput means of rapidly and comprehensively screening chemicals for toxicity. To date, there has been a lack of guidance on how to combine NTS experiments and CT for the risk assessment of chemical mixtures and the prioritization of pollutants. In this perspective, the combination of two "big data" approaches in field studies is systematically proposed. The basic principles of performing NTS and CT in environmental studies are briefly outlined. The "top-down" and "bottom-up" strategies are proposed to summarize the two technologies during the experimental design stage, in accordance with research objectives and available information and tools. Following this, a universal framework combining NTS and CT is thoroughly explored. Six recommendations for future research are highlighted to enhance the utilization of this paradigm, involving multistep combination, multidisciplinary database, application platform, multilayered functionality, effect validation, and standardization.},
}

Risk Assessment
*Environmental Pollutants
*Big Data
*Toxicology

@article {pmid40663905,
year = {2025},
author = {Errea, P and Lasanta, T and Zabalza-Martínez, J and Cortijos-López, M and Nadal-Romero, E},
title = {Rethinking extensive livestock grazing to revive Mediterranean mountain landscapes.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126541},
doi = {10.1016/j.jenvman.2025.126541},
pmid = {40663905},
issn = {1095-8630},
mesh = {Mediterranean Region ; Altitude ; *Herbivory ; Ecosystem ; *Livestock ; Anthropogenic Effects ; *Animal Husbandry/methods ; Conservation of Natural Resources ; Geographic Information Systems ; Public Policy ; Agroecology/methods ; Climate ; Animals ; Animal Migration ; },
abstract = {Extensive livestock grazing is vital for the socio-economic resilience of Mediterranean mountains, providing key environmental benefits. Grazing patterns result from complex interactions between topographical, environmental, and anthropogenic factors, requiring an understanding of these dynamics to optimise land management. This study analyses spatio-temporal patterns of extensive livestock grazing in the Iberian System (north-eastern Spain), a representative Mediterranean mountain with a history of agricultural abandonment. Using GPS tracking, spatial analysis, and statistical modelling, this research evaluates how land use and land cover, environmental variables, public policy, and human infrastructure affect livestock movement. Three hypotheses are tested: (1) grazing distribution is influenced by both environmental and anthropogenic factors; (2) silvopastoral systems are key components of grazing; and (3) shrub cleared areas display heterogeneous levels of use. Results reveal diurnal and seasonal patterns, with peak grazing during early morning and late afternoon, and a decline in cattle presence during autumn and winter. Approximately 81 % of grazing occurs on land subsidised by the Common Agricultural Policy (CAP), whereas sheep dominate silvopastoral areas (non-subsidised). Shrub pastures and pastures are most frequently grazed, though wooded pastures exhibited the highest intensity. Species-specific preferences were evident: sheep prefer higher altitudes and steeper terrains, while cattle favour areas with higher NDVI values. Multiple regression analysis reveals that proximity to water, salt, and feed points and livestock sheds are key predictors of grazing distribution. Shrub clearing enhances grazing activity. These findings highlight the need for targeted grazing management strategies to improve the ecological and economic sustainability of Mediterranean mountains.},
}

Mediterranean Region
Altitude
*Herbivory
Ecosystem
*Livestock
Anthropogenic Effects
*Animal Husbandry/methods
Conservation of Natural Resources
Geographic Information Systems
Public Policy
Agroecology/methods
Climate
Animals
Animal Migration

@article {pmid40661153,
year = {2025},
author = {Castoe, TA and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, S and Macrander, J and Mehr, S and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M},
title = {A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {7},
number = {1},
pages = {obaf026},
pmid = {40661153},
issn = {2517-4843},
abstract = {Venoms are complex bioactive mixtures that have independently evolved across diverse animal lineages, including snails, insects, sea anemones, spiders, scorpions, and snakes. Despite the growing interest in venom research, data is fragmented across disparate databases which lack standardization and interoperability. A vision for the proposed VenomsBase platform presented here seeks to address these challenges by using the best practices approach in creating a centralized, open-access platform adhering to FAIR principles (Findable, Accessible, Interoperable, and Reproducible). VenomsBase will unify venom datasets, standardize terminology, and enable comparative analyses across species, facilitating novel toxin discovery and functional annotation. Key features of VenomsBase include user-friendly data submission modules with built-in validation, advanced cross-species analysis tools, and integration of multidisciplinary datasets spanning genomics, transcriptomics, proteomics, functional assays, and ecological metadata. A modular, cloud-based design will ensure scalability, while heuristic scoring systems will guide users toward high-confidence data entries. To promote accessibility, the envisioned VenomsBase will provide tutorials, regular training sessions, case studies, and feedback loops, supporting researchers at all levels. By harmonizing venom research and addressing the limitations of outdated or nonstandardized methods, VenomsBase aims to revolutionize the field, while being continuously improved and refined by venom experts. This initiative will unlock venoms' potential to make groundbreaking discoveries, address global health challenges, and foster collaboration and innovation across the scientific community.},
}

@article {pmid40660705,
year = {2025},
author = {Fernando Devasahayam, BR and Uthe, H and Poeschl, Y and Deising, HB},
title = {Confrontations of the Pathogenic Fungus Colletotrichum graminicola With a Biocontrol Bacterium or a Ubiquitous Fungus Trigger Synthesis of Secondary Metabolites With Lead Structures of Synthetic Fungicides.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70145},
pmid = {40660705},
issn = {1462-2920},
support = {//Deutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-Leipzig/ ; },
mesh = {*Colletotrichum/metabolism/genetics/physiology ; *Fungicides, Industrial/metabolism/chemistry ; Secondary Metabolism ; *Aspergillus nidulans/metabolism/genetics/physiology ; *Bacillus amyloliquefaciens/metabolism/physiology/genetics ; Zea mays/microbiology ; Plant Diseases/microbiology ; Biological Control Agents ; Multigene Family ; },
abstract = {Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant-colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de-regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de-regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de-regulated, respectively. Correspondingly, non-targeted high-resolution LC-MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus-bacterium and fungus-fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.},
}

*Colletotrichum/metabolism/genetics/physiology
*Fungicides, Industrial/metabolism/chemistry
Secondary Metabolism
*Aspergillus nidulans/metabolism/genetics/physiology
*Bacillus amyloliquefaciens/metabolism/physiology/genetics
Zea mays/microbiology
Plant Diseases/microbiology
Biological Control Agents
Multigene Family

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40659395,
year = {2025},
author = {Ka, MM and Gaye, ND and Tukakira, J and Kyem, D and Gary-Webb, T and Sattler, L and Jobe, M and Gaye, B},
title = {Trends over time in age-standardised prevalence of cardiometabolic risk factors in Senegal between 1975 and 2021 by sex: an ecological study from the WHO Inequality Data Repository.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e101323},
pmid = {40659395},
issn = {2044-6055},
mesh = {Humans ; Senegal/epidemiology ; Male ; Female ; Prevalence ; Middle Aged ; *Diabetes Mellitus/epidemiology ; Adult ; *Hypertension/epidemiology ; *Obesity/epidemiology ; *Cardiometabolic Risk Factors ; Sex Factors ; World Health Organization ; Aged ; *Cardiovascular Diseases/epidemiology ; *Tobacco Use/epidemiology/trends ; Young Adult ; Overweight/epidemiology ; Risk Factors ; Adolescent ; Sex Distribution ; },
abstract = {OBJECTIVE: We aimed to analyse the time trends of cardiometabolic risk factors in Senegal from 1975 to 2021.

DESIGN: Ecological study of publicly available data from the WHO Health Inequality Data Repository.

SETTING: Disaggregated datasets from publicly available sources.

PRIMARY OUTCOME: Trends of age-standardised prevalence rates, stratified by sex for tobacco use, obesity, diabetes and hypertension, were analysed for significance.

PARTICIPANTS: Only data from Senegal were included in this study.

RESULTS: Tobacco use decreased in both sexes between 2000 and 2021, from 1.7% to 0.7% (p value 0.04) in females and from 28.1% to 12.8% (p value 0.04) in males. Obesity and overweight increased in both sexes between 1975 and 2016, from 14.2% to 35.9% (p value <0.001) in females and from 7.2% to 19.5% (p value<0.001) in males. Diabetes increased in both sexes between 1980 and 2014, from 4% to 7.3% (p value <0.001) in females and from 3.6% to 7.5% (p value <0.001) in males. Between 1990 and 2019, hypertension increased in females from 39.1% to 42.9% (p value <0.001). The prevalence of hypertension in males first rose from 37.5% to 40.0% (p value <0.001), then decreased to 37.3% (p value 0.013).

CONCLUSION: Our findings highlight changes in cardiometabolic risk factors in Senegal between 1975 and 2020 by sex. While tobacco use declined, rates of obesity, diabetes and hypertension increased. These findings underscore the need for strategies to mitigate this increase in cardiometabolic risk factors and a consequential rise in non-communicable diseases.},
}

Humans
Senegal/epidemiology
Male
Female
Prevalence
Middle Aged
*Diabetes Mellitus/epidemiology
Adult
*Hypertension/epidemiology
*Obesity/epidemiology
*Cardiometabolic Risk Factors
Sex Factors
World Health Organization
Aged
*Cardiovascular Diseases/epidemiology
*Tobacco Use/epidemiology/trends
Young Adult
Overweight/epidemiology
Risk Factors
Adolescent
Sex Distribution

@article {pmid40658737,
year = {2025},
author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and , and Weigel, D},
title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003237},
pmid = {40658737},
issn = {1545-7885},
mesh = {*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Plant Diseases/microbiology/genetics/immunology ; Plant Leaves/microbiology/growth & development/genetics/metabolism ; Salicylic Acid/metabolism ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; Alleles ; Microbiota ; },
abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.},
}

*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism
*Arabidopsis Proteins/genetics/metabolism
Plant Diseases/microbiology/genetics/immunology
Plant Leaves/microbiology/growth & development/genetics/metabolism
Salicylic Acid/metabolism
Gene Expression Regulation, Plant
Disease Resistance/genetics
Alleles
Microbiota

@article {pmid40656455,
year = {2025},
author = {Komosar, M and Tamburro, G and Graichen, U and Comani, S and Haueisen, J},
title = {Combination of spatial and temporal de-noising and artifact reduction techniques in multi-channel dry EEG.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1576954},
pmid = {40656455},
issn = {1662-4548},
abstract = {INTRODUCTION: Dry electroencephalography (EEG) allows for recording cortical activity in ecological scenarios with a high channel count, but it is often more prone to artifacts as compared to gel-based EEG. Spatial harmonic analysis (SPHARA) and ICA-based methods (Fingerprint and ARCI) have been separately used in previous studies for dry EEG de-noising and physiological artifact reduction. Here, we investigate if the combination of these techniques further improves EEG signal quality. For this purpose, we also introduced an improved version of SPHARA.

METHODS: Dry 64-channel EEG was recorded from 11 healthy volunteers during a motor performance paradigm (left and right hand, feet, and tongue movements). EEG signals were denoised separately using Fingerprint + ARCI, SPHARA, a combination of these two methods, and a combination of these two methods including an improved SPHARA version. The improved version of SPHARA includes an additional zeroing of artifactual jumps in single channels before application of SPHARA. The EEG signal quality after application of each denoising method was calculated by means of standard deviation (SD), signal to noise ratio (SNR), and root mean square deviation (RMSD), and a generalized linear mixed effects (GLME) model was used to identify significant changes of these parameters and quantify the changes in the EEG signal quality.

RESULTS: The grand average values of SD improved from 9.76 (reference preprocessed EEG) to 8.28, 7.91, 6.72, and 6.15 μV for Fingerprint + ARCI, SPHARA, Fingerprint + ARCI + SPHARA, and Fingerprint + ARCI + improved SPHARA, respectively. Similarly, the RMSD values improved from 4.65 to 4.82, 6.32, and 6.90 μV, and the SNR values changed from 2.31 to 1.55, 4.08, and 5.56 dB.

DISCUSSION: Our results demonstrate the different performance aspects of Fingerprint + ARCI and SPHARA, artifact reduction and de-noising techniques that complement each other. We also demonstrated that a combination of these techniques yields superior performance in the reduction of artifacts and noise in dry EEG recordings, which can be extended to infant EEG and adult MEG applications.},
}

@article {pmid40651964,
year = {2025},
author = {Onofri, S and Moeller, R and Billi, D and Balsamo, M and Becker, A and Benvenuto, E and Cassaro, A and Catanzaro, I and Cockell, CS and Desiderio, A and Ellis, T and Gonzáles-Pastor, JE and Hahn, C and Leys, N and Leo, P and Maurel, MC and Pacelli, C and Pavletic, B and Ripa, C and Rothschild, LJ and Surdo, L},
title = {Synthetic biology for space exploration.},
journal = {NPJ microgravity},
volume = {11},
number = {1},
pages = {41},
pmid = {40651964},
issn = {2373-8065},
support = {4000132667/20/NL/CLR/pt//European Space Agency (ESA)/ ; },
abstract = {Human space exploration faces different challenges. Topics like Bioregenerative Life Support Systems, In Situ Resource Utilization, and radiation protection, still require for more suitable solutions to be applied in long-term space exploration. Synthetic biology could be a powerful tool for enabling human exploration of space and planets. This paper explores key topics including resource utilization, life support systems, radiation protection, and human health, providing recommendations for short-, mid-, and long-term advancements in space exploration.},
}

@article {pmid40650501,
year = {2025},
author = {Davies, H and Smyth, S and Pinchbeck, G and Pirmohamed, M and Savory, R and Noble, PJ and Killick, D},
title = {An e-Reporting Tool for Facilitating Submission of Veterinary Adverse Drug Reaction Reports.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {4},
pages = {e70173},
pmid = {40650501},
issn = {1939-1676},
support = {204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; VM0541//Veterinary Medicines Directorate/ ; },
mesh = {Animals ; *Adverse Drug Reaction Reporting Systems ; Electronic Health Records ; United Kingdom ; *Veterinary Drugs/adverse effects ; *Veterinary Medicine ; },
abstract = {BACKGROUND: Adverse events (AEs) are under-reported in veterinary medicine. The ability to report AEs directly from the practice management system (PMS) has been suggested to facilitate reporting. The Small Animal Veterinary Surveillance Network (SAVSNET) informatics system provides an opportunity to integrate reporting into the workflow such that reports can be submitted directly to the National Competent Authority, the Veterinary Medicines Directorate (VMD).

OBJECTIVES: Develop an AE reporting form linked to the PMS allowing for pre-population of some fields from the electronic health record (EHR). Analyze the quality of submitted reports.

ANIMALS: Animals attending United Kingdom (UK) first-opinion veterinary practices participating in SAVSNET.

METHODS: An AE "reporting button" was developed and available in the normal clinical workflow for SAVSNET enrolled practices using the Robovet PMS. The button facilitated capture of pertinent information relating to AEs, including the ability to append clinical notes from the associated EHR. After submission, reports were automatically submitted daily to the VMD. Report quality was assessed using an adapted version of the vigiGrade scoring system, which was used to compare the quality of reports submitted to the VMD via standard routes to those submitted via SAVSNET. Assessment of reports submitted via SAVSNET, was conducted twice. First, considering only information contained in the report and second, considering information contained in both the report and associated clinical notes.

RESULTS: Sixty reports were submitted during the first 18 months by 42 different veterinary practices. The quality of SAVSNET reports was significantly improved by information contained within the clinical notes. These reports were more likely to be well-documented than those submitted via standard routes.

Adverse event reports populated using EHR data are well documented and can support efficient reporting of AEs in veterinary medicine.},
}

Animals
*Adverse Drug Reaction Reporting Systems
Electronic Health Records
United Kingdom
*Veterinary Drugs/adverse effects
*Veterinary Medicine

@article {pmid40648098,
year = {2025},
author = {Quisbert-Trujillo, E and Vuillerme, N},
title = {Towards the Operationalization of Health Technology Sustainability Assessment and the Early Eco Design of the Internet of Medical Things.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {13},
pages = {},
pmid = {40648098},
issn = {1424-8220},
support = {ANR-23-IACL-0006//National Research Agency (ANR), France/ ; ANR-10-AIRT-05//Investissements d'avenir, French program/ ; ANR-15-IDEX-02//Investissements d'avenir, French program/ ; },
mesh = {*Digital Health/economics/ethics ; *Sustainable Development/economics ; Humans ; *Internet of Things/economics/ethics ; },
abstract = {An increasing number of scholars are raising concerns about the sustainability of digital health, calling for action to prevent its harmful effects on the environment. At this point, however, the comprehensive appraisal of emerging technology in the health sector remains theoretically challenging, and highly difficult to implement in practice and in ecological design. Indeed, background factors such as the rapid evolution of technology or effectiveness-efficiency tradeoffs complicate the task of distinguishing the benefits of digital health from its drawbacks, rendering early Health Technology Sustainability Assessment (HTSA) extremely complex. Within this context, the aim of this article is to draw attention to the pragmatism that should be adopted when anticipating the sustainability of technological innovation in the medical field, while simultaneously proposing an assessment framework grounded in a structural and conceptual dissection of the fundamental purpose of smart technologies and the Internet of Medical Things (IoMT). Building on this, we demonstrate how our framework can be strategically applied through a rapid back-of-the-envelope assessment of the economic and ecological balance when introducing IoMT prototypes for treating a specific condition, based on a preliminary simulation of a defined clinical outcome. In this manner, the article presents evidence that challenges two primary hypotheses, and also encourages reflection on the central role of information and its interpretation when addressing key barriers in the HTSA of digital health. Thereby, it contributes to advancing cost-benefit and cost-effectiveness evaluation tools that support eco design strategies and guide informed decision-making regarding the integration of sustainable IoMT systems into healthcare.},
}

*Digital Health/economics/ethics
*Sustainable Development/economics
Humans
*Internet of Things/economics/ethics

@article {pmid40646719,
year = {2025},
author = {Tong, X and Kobayashi, Y and Ikeda, M and Wen, H and Akimoto, S-i and Shigenobu, S},
title = {Draft genome sequences of Buchnera aphidicola from three aphid species (Hemiptera: Aphididae: Eriosomatinae) associated with gall formation on elm trees.},
journal = {Microbiology resource announcements},
volume = {14},
number = {7},
pages = {e0033625},
pmid = {40646719},
issn = {2576-098X},
support = {Special Postdoctoral Researcher Fellowship//RIKEN/ ; 22K20588//Japan Society for the Promotion of Science/ ; 24-IMS-C279//National Institute for Basic Biology/ ; },
abstract = {The Buchnera aphidicola genomes from eriosomatine gall-forming aphids Tetraneura sorini, Tetraneura akinire, and Eriosoma harunire were sequenced, with genome sizes of 533,871, 530,863, and 627,315 bp, respectively. These genomes shed light on Buchnera's role in aphid symbiosis and adaptation.},
}

@article {pmid40646401,
year = {2025},
author = {Cobos, ME and Dunnum, JL and Armién, B and González, P and Juárez, E and Salazar, JR and Cook, JA and Colella, JP},
title = {Selecting Sites for Strategic Surveillance of Zoonotic Pathogens: A Case Study in Panamá.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40646401},
issn = {1612-9210},
support = {ftd06-089//PICANTE (Pathogen Informatics Center for Analysis, Networking, Translation, and Education, US National Science Foundation)/ ; 347998861//Climate Change Capacity Building Program: Research and Public Health Action Award from the Centers for Infectious Diseases/ ; 111130150.501.274//Ministry of Economy and Finance of Panama/ ; FPI-MEF-056//Ministry of Economy and Finance of Panama/ ; PHoEZyTV I-II//Ministry of Economy and Finance of Panama/ ; ftd06-089//Gorgas Memorial Institute of Studies of Health, Secretaria Nacional de Ciencia y Tecnología/ ; },
abstract = {Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography; however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panamá sampled available environments and propose a multistep approach to selecting survey localities in the future. We use > 8000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identify a few key environmental sampling gaps. To refine surveillance strategies, we select a series of "core" historically sampled localities for continued surveillance, supplemented with additional environmentally distinct sites to more completely represent available environments in Panamá. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling of wildlife for zoonotic pathogen surveillance.},
}

@article {pmid40646315,
year = {2025},
author = {Tsimpida, D and Piroddi, R and Daras, K and Melis, G},
title = {Assessing hearing health inequalities using routine health information systems.},
journal = {Journal of public health policy},
volume = {46},
number = {3},
pages = {630-644},
pmid = {40646315},
issn = {1745-655X},
support = {MHF106//National Institute for Health and Care Research/ ; NIHR200182//National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care North West Coast/ ; 177946//Research England/ ; },
mesh = {Humans ; *Hearing Loss/epidemiology ; England/epidemiology ; Male ; Middle Aged ; Female ; *Health Status Disparities ; Adult ; Aged ; *Health Information Systems/statistics & numerical data ; Prevalence ; Adolescent ; Young Adult ; Primary Health Care/statistics & numerical data ; Socioeconomic Factors ; Child ; },
abstract = {Hearing loss is a significant public health challenge, with prevalence estimates based on projected age demographics rather than actual public health needs. This study aimed to quantify hearing loss using real-world data from primary care and explore local patterns and trends from 2013 to 2022 in Cheshire and Merseyside counties of Northwest England. Annual hearing loss prevalence was measured using an ecological space-time analysis of 2.7 million primary care records from Cheshire and Merseyside Integrated Care System. We applied cluster and outlier analysis with geographically weighted regression to examine local deprivation effects. We detected spatial clusters of high prevalence of hearing loss in Cheshire and an increasing trend in hearing loss prevalence in Halton. Deprivation accounted for up to 35% of hearing loss variance in 2020. Monitoring spatial patterns of hearing loss is crucial for addressing health inequalities and guiding targeted prevention and intervention strategies.},
}

Humans
*Hearing Loss/epidemiology
England/epidemiology
Male
Middle Aged
Female
*Health Status Disparities
Adult
Aged
*Health Information Systems/statistics & numerical data
Prevalence
Adolescent
Young Adult
Primary Health Care/statistics & numerical data
Socioeconomic Factors
Child

@article {pmid40642517,
year = {2025},
author = {Zapata-Bedoya, S and Velandia-González, M and Contreras, M and Ortiz, C and Neira, Y and La Torre, L and García, S and Salas, D and Carrizales, CJ and Echazú Torres, CD and Ojeda Ocampo, JR and Cox, A and Villalta Coro, MG and Hernándes Rocha, TA},
title = {[Validation of satellite estimates for health interventions: use of microcensus data in Bolivia, 2024Validação de estimativas por satélite para intervenções de saúde: o uso de microcensos na Bolívia, 2024].},
journal = {Revista panamericana de salud publica = Pan American journal of public health},
volume = {49},
number = {},
pages = {e71},
pmid = {40642517},
issn = {1680-5348},
abstract = {OBJECTIVE: To provide more accurate population estimates to support the operation of Bolivia's immunization program.

METHODS: This cross-sectional ecological study calculated population estimates using geospatial covariates extracted from Meta Data for Good and WorldPop satellite imagery, and validated them with the results of a microcensus conducted in five Bolivian municipalities.

RESULTS: Of the 6077 buildings identified in satellite images, 4505 residential buildings were found to be occupied. Of these, 3087 (68.52%) agreed to participate in the survey. A total of 17 617 people were expected and 13 397 were enumerated. Field enumeration identified fewer people under 30 years of age and more people over 60 years of age than expected. The Meta images provided excellent matches when analyzing population estimates by sex. Meta matched best with enumeration in rural areas, and WorldPop matched best with enumeration in urban areas.

CONCLUSIONS: This study demonstrates that combining geospatial analysis with microcensus validation can significantly improve health planning, enabling equitable resource distribution and more effective immunization coverage.},
}

@article {pmid40642052,
year = {2025},
author = {Temmerman, M and Peeters, E and Delacroix, C and Arunda, M and Khalid, S and Hanson, C and Ojong, SA},
title = {The impact of implementing the women's reproductive rights agenda on climate change.},
journal = {Frontiers in global women's health},
volume = {6},
number = {},
pages = {1594066},
pmid = {40642052},
issn = {2673-5059},
abstract = {The 1994 International Conference on Population and Development (ICPD) established sexual and reproductive health and rights (SRHR) as foundational to sustainable development. Thirty years later, advancing women's reproductive rights (WRR), encompassing agency, decision-making autonomy, and universal access to family planning-remains critical not only for health and gender equity but also for mitigating environmental degradation. By reducing unintended pregnancies and empowering women to align childbearing with personal and ecological capacity, WRR alleviates ecological stressors such as deforestation while enhancing health resilience in climate-vulnerable communities. Yet, despite well-documented linkages between population dynamics and environmental change, contemporary climate policies and funding mechanisms persistently exclude WRR. This oversight undermines the potential of reproductive justice to enhance climate resilience. Additionally, claims that integrating WRR into climate agendas covertly promotes population control or represses women in low- and middle-income countries are fundamentally misleading. Crucially, research is needed to quantify the specific environmental impacts of WRR, underscoring the urgent need for robust global models to predict and validate these co-benefits. Strengthening this evidence base is imperative to inform policies that integrate WRR indicators into climate financing frameworks, ensuring gender-responsive programming. Bridging this gap requires interdisciplinary collaboration to develop metrics that capture WRR's role in reducing resource consumption and enhancing adaptive capacity. Embedding WRR within climate agendas would harmonize reproductive justice with environmental action, unlocking synergies between gender equity, health resilience, and sustainability. Fulfilling the ICPD's vision demands centering WRR in global climate strategies, thereby advancing a just and livable future for all.},
}

@article {pmid40641609,
year = {2025},
author = {O'Connor, L and Behar, S and Tarrant, S and Stamegna, P and Pretz, C and Wang, B and Savage, B and Scornavacca, T and Shirshac, J and Wilkie, T and Hyder, M and Zai, A and Toomey, S and Mullen, M and Fisher, K and Tigas, E and Wong, S and McManus, DD and Alper, E and Lindenauer, PK and Dickson, E and Broach, JP and Kheterpal, V and Soni, A},
title = {Healthy at Home for COPD: An Integrated Digital Monitoring, Treatment, and Pulmonary Rehabilitation Intervention.},
journal = {BMC digital health},
volume = {3},
number = {},
pages = {},
pmid = {40641609},
issn = {2731-684X},
support = {KL2 TR001455/TR/NCATS NIH HHS/United States ; TL1 TR000145/TR/NCATS NIH HHS/United States ; U54 HL143541/HL/NHLBI NIH HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality in the United States. Frequent exacerbations result in higher use of emergency services and hospitalizations, leading to poor patient outcomes and high costs. The objective of this study is to demonstrate the feasibility of a multimodal, community-based intervention in treating acute COPD exacerbations.

RESULTS: Over 18 months, 1,333 patients were approached and 100 (7.5%) were enrolled (mean age 66, 52% female). Ninety-six participants (96%) remained in the study for the full enrollment period. Fifty-five (55%) participated in tele-pulmonary-rehabilitation. Participants wore the smartwatch for a median of 114 days (IQR 30-210) and 18.9 hours/day (IQR16-20) resulting in a median of 1034 minutes/day (IQR 939-1133). The rate at which participants completed scheduled survey instruments ranged from 78-93%. Nearly all participants (85%) performed COPD ecological momentary assessment at least once with a median of 4.85 recordings during study participation. On average, a 2.48-point improvement (p=0.03) in COPD Assessment Test Score was observed from baseline to study completion. The adherence and symptom improvement metrics were not associated with baseline patient activation measures.

CONCLUSIONS: A multimodal intervention combining preventative care, symptom and biometric monitoring, and MIH services was feasible in adults living with COPD. Participants demonstrated high protocol fidelity and engagement and reported improved quality of life.},
}

@article {pmid40641182,
year = {2025},
author = {Sung, HM and Kim, SH and Kwon, EJ and Jeong, SH and Lee, HM and Kim, YH and Oh, CK},
title = {Single-Cell Transcriptomic Analysis Reveals Hair Cell-Specific Molecular Responses to Polystyrene Nanoplastics in a Zebrafish Embryo Model.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70028},
pmid = {40641182},
issn = {1470-8744},
support = {RS-2023-00301938//NRF/ ; 30-2023003//Pusan National University Yangsan Hospital/ ; },
abstract = {Polystyrene nanoplastics (PSNPs) have emerged as pervasive environmental pollutants with potential toxicological effects on aquatic ecosystems. Their small size, hydrophobicity, and structural stability enable penetration into biological tissues, inducing diverse toxic responses. This study investigates the physiological and molecular impacts of PSNPs on zebrafish embryos using single-cell RNA sequencing and phenotypic analyses. While PS-NP exposure at environmentally relevant concentrations caused no significant changes in survival or overt phenotypes, it led to alterations in cell type proportions and gene expression. Differentially expressed gene (DEG) analysis revealed the upregulation of genes such as col1a1a, fgfbp2b, cytl1, and fstl1a, which were validated in vivo. These genes are associated with extracellular matrix remodeling, immune regulation, and tissue repair, suggesting that PSNPs activate defensive and reparative mechanisms in response to environmental stress. These findings highlight the molecular and cellular responses to PSNP exposure in zebrafish embryos and underscore the importance of evaluating the ecological risks posed by nanoplastics.},
}

@article {pmid40640514,
year = {2025},
author = {Jaman, T and Bhaskar, S and Saikhom, V and Gogoi, RB and Sarma, KK and Aggarwal, SP},
title = {GeoAI-based soil erosion risk assessment in the Brahmaputra River Basin: a synergistic approach using RUSLE and advanced machine learning.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {901},
doi = {10.1007/s10661-025-14314-w},
pmid = {40640514},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Machine Learning ; Rivers ; Risk Assessment ; Geographic Information Systems ; *Soil Erosion/statistics & numerical data ; Remote Sensing Technology ; Soil/chemistry ; India ; },
abstract = {Soil erosion is a critical environmental issue in the Brahmaputra River Basin, threatening agricultural productivity, water resources, and ecological balance. This study employs the revised universal soil loss equation (RUSLE) alongside remote sensing, geographic information systems (GIS), and advanced machine learning models like random forest (RF) and gradient boosting (GB) to analyze soil erosion patterns from 2005 to 2024. The analysis revealed that average annual soil loss increased from 15.8 tons/ha/year in 2005 to 25.4 tons/ha/year in 2024, marking a 60.76% rise over two decades. Peak erosion rates were observed in 2020, with localized hotspots recording up to 32,130 tons/ha/year. Spatial analysis from 2005 to 2024 indicated substantial variability, with soil loss values ranging from - 7.024 to 9034 tons/ha in 2005. Topographic influence, quantified using the LS factor, revealed that 47.2% of the basin area has slopes steeper than 16°, significantly contributing to elevated erosion risk. The rainfall erosivity (R-factor) fluctuated throughout the period, peaking at 2305.73 MJ mm/ha h year in 2015 but declining to 799.21 MJ mm/ha h year by 2024, indicating a temporal shift in rainfall patterns. Vegetation cover improvements during this time reduced the mean C-factor from 0.52 to 0.34, though 13.8% of the basin (approximately 3.05 million ha) still falls under high to very high erosion risk zones. RF model predictions achieved an R[2] of 0.915 and RMSE of 4.82, while GB attained an R[2] of 0.952 with RMSE of 3.97, indicating superior predictive performance. These findings underscore the urgent need for targeted soil conservation measures, afforestation programs, and sustainable watershed management. The integration of AI-driven modeling with remote sensing and GIS provides a robust framework for long-term soil erosion monitoring, enabling informed decision-making for climate adaptation in the region.},
}

*Environmental Monitoring/methods
*Machine Learning
Rivers
Risk Assessment
Geographic Information Systems
*Soil Erosion/statistics & numerical data
Remote Sensing Technology
Soil/chemistry
India

@article {pmid40638618,
year = {2025},
author = {Nagel, CL and Chen, S and Allore, HG and Botoseneanu, A and Newsom, JT and Bishop, N and Dorr, DA and Kaye, J and Quiñones, AR},
title = {Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326309},
pmid = {40638618},
issn = {1932-6203},
mesh = {Humans ; Aged ; Female ; Male ; *Dementia/epidemiology/etiology ; *Multimorbidity ; Longitudinal Studies ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/complications ; Cluster Analysis ; },
abstract = {BACKGROUND: Patterns of development of cardiometabolic multimorbidity (CMM) and the impact of specific cardiometabolic disease combinations on cognitive function are not well understood. This study utilizes sequence analysis to describe the ordering and timing of cardiometabolic disease accumulation over a five-year period and to assess both sociodemographic predictors and cognitive outcomes of typical cardiometabolic disease sequences.

METHODS: We analyzed data from the National Health and Aging Trends Study (2011-2022), including respondents aged ≥65 years without CMM or cognitive impairment at baseline (N = 4956). We used sequence analysis with optimal matching and hierarchical cluster analysis to describe temporal patterns of cardiometabolic disease accumulation and to construct a typology by clustering similar sequences. Sociodemographic predictors of CMM cluster membership were assessed using multinomial logistic regression and discrete time survival analysis was used to examine the association of CMM clusters with subsequent dementia development.

RESULTS: 11.8% of respondents developed CMM within 5-years. From a total of 366 distinct cardiometabolic disease sequences, we identified eight cardiometabolic sequence clusters. The first five clusters, "No Cardiometabolic Disease" (N = 2283, 46.1%); "Diabetes Only" (N=642, 13.0%); Heart Disease Only" (N = 297, 6.0%); "MI Only" (N = 145, 2.9%); "Stroke Only" (N = 132, 2.7%), were composed of persons who did not develop CMM over the observation period. The sixth cluster, "Incident CVD with Multimorbidity" (N = 656, 13.2%), was largely composed of persons with no conditions at baseline who developed incident cardiometabolic disease and/or CMM during the observation period (N = 477, 72.7%) and the seventh cluster, "Diabetes Multimorbidity" (N = 333, 6.7%), primarily consisted of persons with diabetes who developed incident CMM. Finally, the eight cluster (N = 468, 9.4%) was characterized by mortality early in the observation period with minimal CMM development during the observation period. Black and Hispanic race/ethnicity, lower wealth, and obesity were associated with increased likelihood of membership in one or both of the clusters characterized by CMM development. We observed increased dementia risk among persons in the Incident CVD with Multimorbidity cluster (HR = 1.32, 95% CI = 1.04-1.67) and the Diabetes MM cluster (HR = 1.88, 95% CI = 1.44,2.44).

CONCLUSIONS: Development of cardiometabolic multimorbidity is more likely among minoritized and/or low-income older adults and is associated with increased risk of subsequent dementia. Targeted approaches to cardiometabolic disease prevention and risk reduction may be an effective means of slowing or preventing the onset of cognitive decline among these groups.},
}

Humans
Aged
Female
Male
*Dementia/epidemiology/etiology
*Multimorbidity
Longitudinal Studies
Aged, 80 and over
*Cardiovascular Diseases/epidemiology/complications
Cluster Analysis

@article {pmid40638150,
year = {2025},
author = {Fujioka, E and Yoshimura, K and Ujino, T and Yoda, K and Fukui, D and Hiryu, S},
title = {High-Resolution GPS Tracking of Perch-Hunting Bats, Rhinolophus nippon, during Nightly Foraging Behavior.},
journal = {Zoological science},
volume = {42},
number = {3},
pages = {249-259},
doi = {10.2108/zs240033},
pmid = {40638150},
issn = {0289-0003},
mesh = {Animals ; *Chiroptera/physiology ; *Feeding Behavior/physiology ; *Geographic Information Systems ; Echolocation ; Flight, Animal ; Male ; },
abstract = {While the echolocation behavior and specialized adaptive auditory system of the greater horseshoe bat (Rhinolophus ferrumequinum) are well documented, comprehensive insights into its wild ecology, especially its detailed nocturnal movements for foraging behavior, remain scarce. Therefore, our objective was to obtain information on the spatiotemporal features of the movements of the Japanese greater horseshoe bat (Rhinolophus nippon), a close relative of R. ferrumequinum, during foraging. Hence, we investigated the nightly flight paths of R. nippon using high-resolution GPS data loggers. Initially, hidden Markov modeling analysis classified bat flight paths into two behavioral patterns: commuting and area-restricted behavior, the latter primarily corresponding to foraging activities. Focusing on foraging behavior along their trajectory, we observed that R. nippon repeatedly foraged with brief stops lasting only a few minutes and an average distance of approximately 300 m between any two foraging sites. Notably, one individual covered a considerable distance (23.6 km) from its roost, possibly because of irregular social behavior during the mating season. Furthermore, for commuting, bats occasionally used forest roads, which were located along the middle of relatively steep slopes. In cases of echolocations with limited detection distances, echoes from the ground and adjacent tree lines offered crucial navigation cues, underscoring the significance of forest roads as nightly movement routes for echolocating bats. Overall, our findings highlight the importance and urgency of ongoing research on bat movement ecology in Japan.},
}

Animals
*Chiroptera/physiology
*Feeding Behavior/physiology
*Geographic Information Systems
Echolocation
Flight, Animal
Male