@article {pmid38464619,
year = {2024},
author = {Scognamiglio, C and Sorge, A and Borrelli, G and Perrella, R and Saita, E},
title = {Exploring the connection between childhood trauma, dissociation, and borderline personality disorder in forensic psychiatry: a comprehensive case study.},
journal = {Frontiers in psychology},
volume = {15},
number = {},
pages = {1332914},
pmid = {38464619},
issn = {1664-1078},
abstract = {This case study examines the complex relationship between childhood trauma, dissociation, and Borderline Personality Disorder (BPD) within the context of forensic psychiatry. It focuses on a young murder defendant named "Paul," who has experienced various traumatic events, including childhood maltreatment and domestic violence. These experiences have led to dissociative states marked by high emotional intensity, particularly of an aggressive nature, and impaired impulse control, resulting in violent behavior during dissociative episodes. The study employs advanced assessment tools like Raven's Standard Progressive Matrices (SPM), the Millon Clinical Multiaxial Inventory-III (MCMI-III), and the Level of Service/Case Management Inventory (LS/CMI) to gain a comprehensive understanding of Paul's psychopathological condition, risk factors, and rehabilitation needs. The LS/CMI assessment highlights a high risk of recidivism, mainly influenced by family relationships, educational challenges, interpersonal connections, and aggressive tendencies. To address the multifaceted needs of individuals like Paul, the study emphasizes the importance of using transdiagnostic models for trauma and dissociation. This approach informs tailored treatment programs that include processing past traumatic experiences, improving self-identity, nurturing healthy relational patterns, and enhancing emotional regulation. Although this study is based on a single case, it serves as a model for integrating assessment tools and theoretical-clinical models in the field of forensic psychiatry. Understanding the intricate dynamics of childhood trauma, dissociation, and BPD is crucial for making informed decisions, conducting risk assessments, and developing rehabilitation programs within the justice system. Future research should expand the scope of cases and further validate assessment tools to advance our understanding of this complex relationship.},
}

@article {pmid38391697,
year = {2024},
author = {de Chiusole, D and Spinoso, M and Anselmi, P and Bacherini, A and Balboni, G and Mazzoni, N and Brancaccio, A and Epifania, OM and Orsoni, M and Giovagnoli, S and Garofalo, S and Benassi, M and Robusto, E and Stefanutti, L and Pierluigi, I},
title = {PsycAssist: A Web-Based Artificial Intelligence System Designed for Adaptive Neuropsychological Assessment and Training.},
journal = {Brain sciences},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/brainsci14020122},
pmid = {38391697},
issn = {2076-3425},
support = {PRIN: Progetti di Ricerca di Rilevante Interesse Nazionale - Bando 2020, Protocol n. 20209WKCLL, Project title: Computerized, adaptive and personalized assessment of executive functions and fluid intelligence//Italian Ministry of Research and University/ ; },
abstract = {Assessing executive functions in individuals with disorders or clinical conditions can be challenging, as they may lack the abilities needed for conventional test formats. The use of more personalized test versions, such as adaptive assessments, might be helpful in evaluating individuals with specific needs. This paper introduces PsycAssist, a web-based artificial intelligence system designed for neuropsychological adaptive assessment and training. PsycAssist is a highly flexible and scalable system based on procedural knowledge space theory and may be used potentially with many types of tests. We present the architecture and adaptive assessment engine of PsycAssist and the two currently available tests: Adap-ToL, an adaptive version of the Tower of London-like test to assess planning skills, and MatriKS, a Raven-like test to evaluate fluid intelligence. Finally, we describe the results of an investigation of the usability of Adap-ToL and MatriKS: the evaluators perceived these tools as appropriate and well-suited for their intended purposes, and the test-takers perceived the assessment as a positive experience. To sum up, PsycAssist represents an innovative and promising tool to tailor evaluation and training to the specific characteristics of the individual, useful for clinical practice.},
}

@article {pmid38363314,
year = {2024},
author = {Zahid, N and Enam, SA and Mårtensson, T and Azam, I and Mushtaq, N and Moochhala, M and Javed, F and Kausar, F and Hasan, A and Rehman, L and Mughal, MN and Altaf, S and Kirmani, S and Brown, N},
title = {Predictors of neurocognition outcomes in children and young people with primary brain tumor presenting to tertiary care hospitals of Karachi, Pakistan: a prospective cohort study.},
journal = {Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery},
volume = {},
number = {},
pages = {},
pmid = {38363314},
issn = {1433-0350},
abstract = {INTRODUCTION: Primary brain tumors are a common cause of morbidity and mortality in children and young people (CYP) globally. Impaired neurocognitive function is a potential severe consequence in primary brain tumor (PBT) survivors. There are no in-depth studies from low- and middle-income countries (LMICs) to inform management and follow-up. The research questions of this study were as follows: Are the sociodemographic factors (lower age of CYP, female gender, low socioeconomic status, low parental education), disease-related factors (high grade of tumor, presence of seizures, presence of hydrocephalous), and treatment-related factors (adjuvant therapy, no surgical intervention, post-treatment seizures, placement of shunts) associated with decline in neurcognition outcomes 12 months post-treatment in CYP with PBTs?

METHODS: A prospective cohort study was conducted from November 2020 to July 2023 at the Aga Khan University Hospital and Jinnah Postgraduate Medical Centre, tertiary care hospitals in Karachi, Pakistan. All CYP aged 5 to 21 years with a newly diagnosed PBTs were eligible. The neurocognition assessment was undertaken by a psychologist at two points, i.e., pre-treatment and at 12 months post-treatment using validated tools. The verbal intelligence was assessed by Slosson Intelligence tool, revised 3rd edition (SIT-R3), perceptual reasoning by Raven's Progressive Matrices (RPM), and the Processing Speed Index by Wechsler Intelligence Scale (WISC V) and Wechsler Adult Intelligence Scale (WAIS-IV). The data were analyzed by STATA version 12 software. Generalized estimating equation (GEE) was used to determine the factors associated with the mean change in 12 months post-treatment verbal and non-verbal neurocognition scores. Unadjusted and adjusted beta coefficients with their 95% confidence intervals were reported.

RESULTS: A total of 48 CYPs with PBTs were enrolled, 23 (48%) of them were lost to follow-up and 10 (21%) died. The remaining 25 (52%) were reassessed 12 months after treatment. On multivariable analysis, a significant decline in verbal intelligence scores at 12 months was predicted by post-treatment seizures beta =  - 20.8 (95% CI, - 38.2, - 3.4), mothers having no formal educational status and lower household monthly income. Similarly, a significant decline in perceptual reasoning scores was also predicted by post-treatment seizures beta =  - 10.7 (95% CI, - 20.6, - 0.8), mothers having no formal education and having lower household monthly income. Worsening of processing speed scores at 12 months post-treatment were predicted by tumor histology, post-treatment seizures beta =  - 33.9 (95% CI, - 47.7, - 20.0), lower educational status of the mother, and having lower household monthly. However, an improvement was seen in processing speed scores after surgical tumor resection.

CONCLUSION: In this novel study, the post-treatment mean change in verbal and non-verbal neurocognition scores was associated with sociodemographic, tumor, and treatment factors. These findings may have potential implications for targeted early psychological screening of higher risk CYP with PBTs. Identification of these predictors may serve as a foundation for developing more cost-effective treatment thereby alleviating the burden of neurocognitive morbidity. However to establish generalizability, future research should prioritize larger-scale, multicountry studies. (Trial registration: ClinicalTrials.gov Identifier: NCT05709522).},
}

@article {pmid38279165,
year = {2024},
author = {Ziegler, S and Srivastava, S and Parmar, D and Basu, S and Jain, N and De Allegri, M},
title = {A step closer towards achieving universal health coverage: the role of gender in enrolment in health insurance in India.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {141},
pmid = {38279165},
issn = {1472-6963},
abstract = {BACKGROUND: There is limited understanding of how universal health coverage (UHC) schemes such as publicly-funded health insurance (PFHI) benefit women as compared to men. Many of these schemes are gender-neutral in design but given the existing gender inequalities in many societies, their benefits may not be similar for women and men. We contribute to the evidence by conducting a gender analysis of the enrolment of individuals and households in India's national PFHI scheme, Rashtriya Swasthya Bima Yojana (RSBY).

METHODS: We used data from a cross-sectional household survey on RSBY eligible families across eight Indian states and studied different outcome variables at both the individual and household levels to compare enrolment among women and men. We applied multivariate logistic regressions and controlled for several demographic and socio-economic characteristics.

RESULTS: At the individual level, the analysis revealed no substantial differences in enrolment between men and women. Only in one state were women more likely to be enrolled in RSBY than men (AOR: 2.66, 95% CI: 1.32-5.38), and this pattern was linked to their status in the household. At the household level, analyses revealed that female-headed households had a higher likelihood to be enrolled (AOR: 1.36, 95% CI: 1.14-1.62), but not necessarily to have all household members enrolled.

CONCLUSION: Findings are surprising in light of India's well-documented gender bias, permeating different aspects of society, and are most likely an indication of success in designing a policy that did not favour participation by men above women, by mandating spouse enrolment and securing enrolment of up to five family members. Higher enrolment rates among female-headed households are also an indication of women's preferences for investments in health, in the context of a conducive policy environment. Further analyses are needed to examine if once enrolled, women also make use of the scheme benefits to the same extent as men do. India is called upon to capitalise on the achievements of RSBY and apply them to newer schemes such as PM-JAY.},
}

@article {pmid38244996,
year = {2024},
author = {Williams, ME and Corn, EA and Martinez Ransanz, S and Berl, MM and Andringa-Seed, R and Mulkey, SB},
title = {Neurodevelopmental assessments used to measure preschoolers' cognitive development in Latin America: a systematic review.},
journal = {Journal of pediatric psychology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpepsy/jsad089},
pmid = {38244996},
issn = {1465-735X},
support = {R01HD102445/NH/NIH HHS/United States ; },
abstract = {OBJECTIVE: The objective of this study was to systematically review the standardized neurodevelopmental assessments used to study preschool-aged children's cognitive development in Spanish-speaking Latin America.

METHODS: The authors systematically searched PubMed, PsycINFO, and ERIC databases for peer-reviewed articles from Spanish-speaking Latin American countries. Articles were included if they measured cognitive development among children aged 2-6 years using at least one standardized assessment tool; 97 articles were included and reviewed in accordance with PRISMA guidelines to assess their use of these tools.

RESULTS: Ninety-seven studies across 13 countries used a total of 41 assessments to measure cognitive development; most widely used were the Wechsler intelligence scales (n = 46/97), particularly the Wechsler Preschool and Primary Scale of Intelligence and Wechsler Intelligence Scale for Children (n = 23 and 29, respectively). Other common assessments included the McCarthy Scales of Children's Abilities (n = 9), Raven's Progressive Matrices (n = 9), Child Neuropsychological Assessment (n = 8), and Peabody Picture Vocabulary Test (n = 7). In regions where normative data for a given assessment were unpublished, authors commonly used norms from the United States, Mexico, or Spain or did not report standard scores in their analyses.

CONCLUSIONS: The wide range of tools used in these studies presents a challenge for generalizing results when measuring the neurodevelopment of Latin American preschool-aged children. The low availability of normative data for specific regions reveals concerns if some tools are culturally and linguistically appropriate even when Spanish is a common language, particularly in low-resource settings. Future work to forge greater consistency in the use of validated measures, clarity in reporting research methods, and publication of regional normative data would benefit the field.},
}

@article {pmid38232729,
year = {2024},
author = {Wang, X and Kostrzewa, C and Reiner, A and Shen, R and Begg, C},
title = {Adaptation of a mutual exclusivity framework to identify driver mutations within oncogenic pathways.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2023.12.009},
pmid = {38232729},
issn = {1537-6605},
abstract = {Distinguishing genomic alterations in cancer-associated genes that have functional impact on tumor growth and disease progression from the ones that are passengers and confer no fitness advantage have important clinical implications. Evidence-based methods for nominating drivers are limited by existing knowledge on the oncogenic effects and therapeutic benefits of specific variants from clinical trials or experimental settings. As clinical sequencing becomes a mainstay of patient care, applying computational methods to mine the rapidly growing clinical genomic data holds promise in uncovering functional candidates beyond the existing knowledge base and expanding the patient population that could potentially benefit from genetically targeted therapies. We propose a statistical and computational method (MAGPIE) that builds on a likelihood approach leveraging the mutual exclusivity pattern within an oncogenic pathway for identifying probabilistically both the specific genes within a pathway and the individual mutations within such genes that are truly the drivers. Alterations in a cancer-associated gene are assumed to be a mixture of driver and passenger mutations with the passenger rates modeled in relationship to tumor mutational burden. We use simulations to study the operating characteristics of the method and assess false-positive and false-negative rates in driver nomination. When applied to a large study of primary melanomas, the method accurately identifies the known driver genes within the RTK-RAS pathway and nominates several rare variants as prime candidates for functional validation. A comprehensive evaluation of MAGPIE against existing tools has also been conducted leveraging the Cancer Genome Atlas data.},
}

@article {pmid38000912,
year = {2022},
author = {Cosma, BM and Shirali Hossein Zade, R and Jordan, EN and van Lent, P and Peng, C and Pillay, S and Abeel, T},
title = {Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
doi = {10.1093/gigascience/giad100},
pmid = {38000912},
issn = {2047-217X},
abstract = {BACKGROUND: Assembly algorithm choice should be a deliberate, well-justified decision when researchers create genome assemblies for eukaryotic organisms from third-generation sequencing technologies. While third-generation sequencing by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) has overcome the disadvantages of short read lengths specific to next-generation sequencing (NGS), third-generation sequencers are known to produce more error-prone reads, thereby generating a new set of challenges for assembly algorithms and pipelines. However, the introduction of HiFi reads, which offer substantially reduced error rates, has provided a promising solution for more accurate assembly outcomes. Since the introduction of third-generation sequencing technologies, many tools have been developed that aim to take advantage of the longer reads, and researchers need to choose the correct assembler for their projects.

RESULTS: We benchmarked state-of-the-art long-read de novo assemblers to help readers make a balanced choice for the assembly of eukaryotes. To this end, we used 12 real and 64 simulated datasets from different eukaryotic genomes, with different read length distributions, imitating PacBio continuous long-read (CLR), PacBio high-fidelity (HiFi), and ONT sequencing to evaluate the assemblers. We include 5 commonly used long-read assemblers in our benchmark: Canu, Flye, Miniasm, Raven, and wtdbg2 for ONT and PacBio CLR reads. For PacBio HiFi reads , we include 5 state-of-the-art HiFi assemblers: HiCanu, Flye, Hifiasm, LJA, and MBG. Evaluation categories address the following metrics: reference-based metrics, assembly statistics, misassembly count, BUSCO completeness, runtime, and RAM usage. Additionally, we investigated the effect of increased read length on the quality of the assemblies and report that read length can, but does not always, positively impact assembly quality.

CONCLUSIONS: Our benchmark concludes that there is no assembler that performs the best in all the evaluation categories. However, our results show that overall Flye is the best-performing assembler for PacBio CLR and ONT reads, both on real and simulated data. Meanwhile, best-performing PacBio HiFi assemblers are Hifiasm and LJA. Next, the benchmarking using longer reads shows that the increased read length improves assembly quality, but the extent to which that can be achieved depends on the size and complexity of the reference genome.},
}

@article {pmid37989310,
year = {2023},
author = {Harrington, KJ and Folkertsma, R and Auersperg, AMI and Biondi, L and Lambert, ML},
title = {Innovative problem solving by wild falcons.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.10.061},
pmid = {37989310},
issn = {1879-0445},
abstract = {Innovation (i.e., a new solution to a familiar problem, or applying an existing behavior to a novel problem[1][,][2]) plays a fundamental role in species' ecology and evolution. It can be a useful measure for cross-group comparisons of behavioral and cognitive flexibility and a proxy for general intelligence.[3][,][4][,][5] Among birds, experimental studies of innovation (and cognition more generally) are largely from captive corvids and parrots,[6][,][7][,][8][,][9][,][10][,][11][,][12] though we lack serious models for avian technical intelligence outside these taxa. Striated caracaras (Phalcoboenus australis) are Falconiformes, sister clade to parrots and passerines,[13][,][14][,][15] and those endemic to the Falkland Islands (Malvinas) show curiosity and neophilia similar to notoriously neophilic kea parrots[16][,][17] and face similar socio-ecological pressures to corvids and parrots.[18][,][19] We tested wild striated caracaras as a new avian model for technical cognition and innovation using a field-applicable 8-task comparative paradigm (adapted from Rössler et al.[20] and Auersperg et al.[21]). The setup allowed us to assess behavior, rate, and flexibility of problem solving over repeated exposure in a natural setting. Like other generalist species with low neophobia,[21][,][22] we predicted caracaras to demonstrate a haptic approach to solving tasks, flexibly switching to new, unsolved problems and improving their performance over time. Striated caracaras performed comparably to tool-using parrots,[20] nearly reaching ceiling levels of innovation in few trials, repeatedly and flexibly solving tasks, and rapidly learning. We attribute our findings to the birds' ecology, including geographic restriction, resource unpredictability, and opportunistic generalism,[23][,][24][,][25] and encourage future work investigating their cognitive abilities in the wild.},
}

@article {pmid37863938,
year = {2023},
author = {Pendergraft, LT and Marzluff, JM and Cross, DJ and Shimizu, T and Templeton, CN},
title = {American crows that excel at tool use activate neural circuits distinct from less talented individuals.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {6539},
pmid = {37863938},
issn = {2041-1723},
abstract = {Tools enable animals to exploit and command new resources. However, the neural circuits underpinning tool use and how neural activity varies with an animal's tool proficiency, are only known for humans and some other primates. We use 18F-fluorodeoxyglucose positron emission tomography to image the brain activity of naïve vs trained American crows (Corvus brachyrhynchos) when presented with a task requiring the use of stone tools. As in humans, talent affects the neural circuits activated by crows as they prepare to execute the task. Naïve and less proficient crows use neural circuits associated with sensory- and higher-order processing centers (the mesopallium and nidopallium), while highly proficient individuals increase activity in circuits associated with motor learning and tactile control (hippocampus, tegmentum, nucleus basorostralis, and cerebellum). Greater proficiency is found primarily in adult female crows and may reflect their need to use more cognitively complex strategies, like tool use, to obtain food.},
}

@article {pmid37164878,
year = {2023},
author = {Basak, S and Bhattacharyya, B},
title = {Optimal scheduling in demand-side management based grid-connected microgrid system by hybrid optimization approach considering diverse wind profiles.},
journal = {ISA transactions},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.isatra.2023.04.027},
pmid = {37164878},
issn = {1879-2022},
abstract = {Demand side management (DSM) is one of the trending economic strategies which shifts the elastic demand to the off-peak hours from the peak hours so as to reduce the overall generation cost of the system. The work done in this paper can be categorized in three phases. In the first phase, various wind speed to power conversion mathematical models available in literature are analysed to find out the one with maximum level of wind penetration. For second phase, an economic DSM strategy is implemented to restructure the forecasted load demand model for various participation levels. In the final phase the cost-effective optimization of two microgrid distribution systems are percolated. As an optimization tool, novel hybrid CSAJAYA has been used to carry on the study. Different types of grid participating and pricing strategies along with valve point loading effect and wind energy uncertainty are considered to amplify the complexity and practicality of the study. The generation costs reduced from 3 to 5% when the forecasted demand was reformed with 20% DSM participation for both the test systems. A detailed comparison with the results from various optimization tools studied confirms the effectiveness of the proposed hybrid approach. The hybrid optimization tool presented in this paper performs better in terms of central tendencies, nonparametric statistical analysis, and algorithm execution time.},
}

@article {pmid36720748,
year = {2023},
author = {Hunt, GR and Villard, P},
title = {Oscillatory extraction behaviour suggests functional attributes of crows' hooked-stick tools.},
journal = {Animal cognition},
volume = {26},
number = {3},
pages = {1091-1095},
pmid = {36720748},
issn = {1435-9456},
mesh = {Animals ; *Tool Use Behavior ; *Crows ; Feeding Behavior ; },
abstract = {New Caledonian crows are the only nonhuman animals known to craft hooked-sticks for use in foraging. Since their first description over 25 years ago, researchers have been unable to provide a detailed account of how these complex tools function in natural probe sites. Using close-up video footage, we document how a New Caledonian crow operated a hooked-stick to extract a large tree weta from a chamber in a tree trunk. The extraction technique had two distinct, separate components: (1) simultaneous oscillating head rotation and reciprocating bill action, and (2) measured pulling with the tool. Analysis of this first detailed field observation of hooked-stick use suggests a link between hooked-stick tool characteristics, functionality and skilled manipulation in natural prey extraction by these technological birds. Our findings also provide a rare, if not novel, example of tool-associated oscillatory manipulation in nonhuman animals.},
}

Animals
*Tool Use Behavior
*Crows
Feeding Behavior

@article {pmid36498712,
year = {2022},
author = {Faber, D and Grosse, GM and Klietz, M and Petri, S and Schwenkenbecher, P and Sühs, KW and Kopp, B},
title = {Towards the Validation of Executive Functioning Assessments: A Clinical Study.},
journal = {Journal of clinical medicine},
volume = {11},
number = {23},
pages = {},
pmid = {36498712},
issn = {2077-0383},
abstract = {Neuropsychological assessment needs a more profound grounding in psychometric theory. Specifically, psychometrically reliable and valid tools are required, both in patient care and in scientific research. The present study examined convergent and discriminant validity of some of the most popular indicators of executive functioning (EF). A sample of 96 neurological inpatients (aged 18-68 years) completed a battery of standardized cognitive tests (Raven's matrices, vocabulary test, Wisconsin Card Sorting Test, verbal fluency test, figural fluency test). Convergent validity of indicators of intelligence (Raven's matrices, vocabulary test) and of indicators of EF (Wisconsin Card Sorting Test, verbal fluency test, figural fluency) were calculated. Discriminant validity of indicators of EF against indicators of intelligence was also calculated. Convergent validity of indicators of intelligence (Raven's matrices, vocabulary test) was good (rxtyt = 0.727; R[2] = 0.53). Convergent validity of fluency indicators of EF against executive cognition as indicated by performance on the Wisconsin Card Sorting Test was poor (0.087 ≤ rxtyt ≤ 0.304; 0.008 ≤ R[2] ≤ 0.092). Discriminant validity of indicators of EF against indicators of intelligence was good (0.106 ≤ rxtyt ≤ 0.548; 0.011 ≤ R[2] ≤ 0.300). Our conclusions from these data are clear-cut: apparently dissimilar indicators of intelligence converge on general intellectual ability. Apparently dissimilar indicators of EF (mental fluency, executive cognition) do not converge on general executive ability. Executive abilities, although non-unitary, can be reasonably well distinguished from intellectual ability. The present data contribute to the hitherto meager evidence base regarding the validity of popular indicators of EF.},
}

@article {pmid36371445,
year = {2022},
author = {Chang, X and Zhao, W and Kang, J and Xiang, S and Xie, C and Corona-Hernández, H and Palaniyappan, L and Feng, J},
title = {Language abnormalities in schizophrenia: binding core symptoms through contemporary empirical evidence.},
journal = {Schizophrenia (Heidelberg, Germany)},
volume = {8},
number = {1},
pages = {95},
pmid = {36371445},
issn = {2754-6993},
support = {2018SHZDZX01//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; 21YF1402400//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; 82102138//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Both the ability to speak and to infer complex linguistic messages from sounds have been claimed as uniquely human phenomena. In schizophrenia, formal thought disorder (FTD) and auditory verbal hallucinations (AVHs) are manifestations respectively relating to concrete disruptions of those abilities. From an evolutionary perspective, Crow (1997) proposed that "schizophrenia is the price that Homo sapiens pays for the faculty of language". Epidemiological and experimental evidence points to an overlap between FTD and AVHs, yet a thorough investigation examining their shared neural mechanism in schizophrenia is lacking. In this review, we synthesize observations from three key domains. First, neuroanatomical evidence indicates substantial shared abnormalities in language-processing regions between FTD and AVHs, even in the early phases of schizophrenia. Second, neurochemical studies point to a glutamate-related dysfunction in these language-processing brain regions, contributing to verbal production deficits. Third, genetic findings further show how genes that overlap between schizophrenia and language disorders influence neurodevelopment and neurotransmission. We argue that these observations converge into the possibility that a glutamatergic dysfunction in language-processing brain regions might be a shared neural basis of both FTD and AVHs. Investigations of language pathology in schizophrenia could facilitate the development of diagnostic tools and treatments, so we call for multilevel confirmatory analyses focused on modulations of the language network as a therapeutic goal in schizophrenia.},
}

@article {pmid36262611,
year = {2022},
author = {Wang, Y and Song, J and Teng, Z},
title = {An Improved New Caledonian Crow Learning Algorithm for Global Function Optimization.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {9248771},
pmid = {36262611},
issn = {1687-5273},
mesh = {Animals ; Humans ; *Crows ; Algorithms ; },
abstract = {The New Caledonian crow learning algorithm (NCCLA) is a novel metaheuristic algorithm inspired by the learning behavior of New Caledonian crows learning to make tools to obtain food. However, it suffers from the problems of easily falling into local optima and insufficient convergence accuracy and convergence precision. To further improve the convergence performance of NCCLA, an improved New Caledonian crow learning algorithm (INCCLA) is proposed in this paper. By determining the parent individuals based on the cosine similarity, the juveniles are guided to search toward different ranges to maintain the population diversity; a novel hybrid mechanism of complete and incomplete learning is proposed to balance the exploration and exploitation capabilities of the algorithm; the update strategy of juveniles and parent individuals is improved to enhance the convergence speed and precision of the algorithm. The test results of the CEC2013 and CEC2020 test suites show that, compared with the original NCCLA algorithm and four of the best metaheuristics to date, INCCLA has significant advantages in terms of convergence speed, convergence precision, and stability.},
}

Animals
Humans
*Crows
Algorithms

@article {pmid35833319,
year = {2022},
author = {Mack, C and Uomini, N},
title = {Modulation of behavioural laterality in wild New Caledonian crows (Corvus moneduloides): Vocalization, age and function.},
journal = {Laterality},
volume = {27},
number = {4},
pages = {379-405},
doi = {10.1080/1357650X.2022.2098969},
pmid = {35833319},
issn = {1464-0678},
mesh = {Animals ; Functional Laterality ; *Crows ; *Tool Use Behavior ; },
abstract = {The New Caledonian crow (Corvus moneduloides) is known for displaying a unique set of tool-related behaviours, with the bird's bill acting as an individually consistently lateralized effector. However, we still fail to understand how such laterality develops, is modulated or even if its expression is consistent across other behavioural categories. Creating the first ethogram for this species allowed us to examine laterality and vocalisations in a population of wild, free-flying New Caledonian crows using detailed analyses of close-up video footage. We revealed the existence of an overall strong left-sided bias during object manipulation only and which was driven by the adult crows of our focal population, the stabilization of individual preferences occurring during the birds' juvenile years. Individually, at least one crow showed consistent side biases to the right and left within different behavioural categories. Our findings highlight previously unknown variability in behavioural laterality in this species, thus advocating for further investigation. Specifically, we argue that a better understanding of the New Caledonian crow's biology and ecology is required if one wishes to pursue the promising comparative road that laterality could be connected to the evolution of tool-making.},
}

Animals
Functional Laterality
*Crows
*Tool Use Behavior

@article {pmid35799015,
year = {2022},
author = {Domjanović, J and Matetic, A and Baković Kramarić, D and Domjanović Škopinić, T and Borić Škaro, D and Delić, N and Runjić, F and Jeličić, I},
title = {Association of the novel CROW-65 risk score and mortality in hospitalized kidney transplant recipients with COVID-19 : A retrospective observational study.},
journal = {Wiener klinische Wochenschrift},
volume = {134},
number = {23-24},
pages = {842-849},
pmid = {35799015},
issn = {1613-7671},
mesh = {Adult ; Animals ; Humans ; *COVID-19/etiology ; Retrospective Studies ; *Crows ; *Kidney Transplantation/adverse effects ; Aftercare ; Patient Discharge ; Risk Factors ; },
abstract = {BACKGROUND: Kidney transplant recipients (KTR) are a group of patients with heterogeneous risks for adverse outcomes with COVID-19, but risk stratification tools in this patient group are lacking.

METHODS AND PARTICIPANTS: This retrospective observational, hypothesis-generating study included 49 hospitalized adult KTR patients with COVID-19 at the University Hospital of Split (August 2020 to October 2021) and evaluated the performance of novel risk score CROW-65 (age, Charlson Comorbidity Index [CCI] lactate dehydrogenase to white blood cell [LDH:WBC] ratio, and respiratory rate oxygenation [ROX index]). The primary outcome of the study was 30-day postdischarge all-cause mortality.

RESULTS: A total of 8 fatal events (16.3%) occurred during the study follow-up. When comparing CROW-65 by survival status, it was significantly increased in patients with fatal event (P < 0.001). Using the Cox proportional hazards regression analysis, the CROW-65 risk score showed statistically significant association with mortality (HR 1.11, 95% CI 1.01-1.23, P = 0.027), while receiving operator characteristics (ROC) showed significant discrimination of all-cause mortality with an AUC of 0.85 (95% CI 0.72-0.94, P < 0.001), and satisfactory calibration (χ[2] 4.91, P = 0.555 and Harrell's C 0.835). Finally, survival Kaplan-Meier analysis confirmed significantly higher cumulative incidence of mortality with increasing risk score tertiles and curve separation after 13 days (P = 0.009).

CONCLUSION: A novel risk score CROW-65 showed significant association with all-cause mortality in KTR yielding important hypothesis-generating findings. Further powered studies should reassess the performance of CROW-65 risk score in this population, including predictability, calibration and discrimination.},
}

Adult
Animals
Humans
*COVID-19/etiology
Retrospective Studies
*Crows
*Kidney Transplantation/adverse effects
Aftercare
Patient Discharge
Risk Factors

@article {pmid35350387,
year = {2021},
author = {Lorenc, ZP and Jones, D and Kim, J and Gwak, HM and Batham, S and Vachon, G},
title = {Validating a Series of Photonumeric Rating Scales for Use in Facial Aesthetics Using Statistical Analysis of Intra- and Inter-rater Reliability.},
journal = {Aesthetic surgery journal. Open forum},
volume = {3},
number = {4},
pages = {ojab039},
pmid = {35350387},
issn = {2631-4797},
abstract = {BACKGROUND: Growing demand for minimally invasive aesthetic procedures to correct age-related facial changes and optimize facial proportions has been met with innovation but has created an unmet need for objective assessment tools to evaluate results empirically.

OBJECTIVES: The purpose of this study is to establish the intra- and inter-rater reliability of ordinal, photonumeric, 4-, or 5-point rating scales for clinical use to assess facial aesthetics.

METHODS: Board-certified plastic surgeons and dermatologists (3 raters) performed live validation of jawline contour, temple volume, chin retrusion, nasolabial folds, vertical perioral lip lines, midface volume loss, lip fullness, and crow's feet dynamic- and at rest-rating scales over 2 rounds, 2 weeks apart. Subjects selected for live validation represented the range of scores and included 54 to 83 subjects for each scale. Test-retest reliability was quantitated through intra- and inter-rater reliability, determined from the mean weighted kappa and round 2 intraclass correlation coefficients, respectively. The clinical significance of a 1-grade difference was assessed through rater comparison of 31 pairs of side-by-side photographs of subjects with the same grade or a different grade on the developed scales.

RESULTS: The study demonstrated substantial to near-perfect intra- and inter-rater reliability of all scales when utilized by trained raters to assess a diverse group of live subjects. Furthermore, the clinical significance of a 1-point difference on all the developed scales was established.

CONCLUSIONS: The high test-retest reliability and intuitive layout of these scales provide an objective approach with standardized ratings for clinical assessment of various facial features.},
}

@article {pmid35287378,
year = {2022},
author = {Dida, H and Charif, F and Benchabane, A},
title = {Registration of computed tomography images of a lung infected with COVID-19 based in the new meta-heuristic algorithm HPSGWO.},
journal = {Multimedia tools and applications},
volume = {81},
number = {13},
pages = {18955-18976},
pmid = {35287378},
issn = {1380-7501},
abstract = {Computed tomography (CT) helps the radiologist in the rapid and correct detection of a person infected with the coronavirus disease 2019 (COVID-19), and this by showing the presence of the ground-glass opacity in the lung of with the virus. Tracking the evolution of the spread of the ground-glass opacity (GGO) in the lung of the person infected with the virus needs to study more than one image in different times. The various CT images must be registration to identify the evolution of the ground glass in the lung and to facilitate the study and identification of the virus. Due to the process of registration images is essentially an improvement problem, we present in this paper a new HPSGWO algorithm for registration CT images of a lung infected with the COVID-19. This algorithm is a hybridization of the two algorithms Particle swarm optimization (PSO) and Grey wolf optimizer (GWO). The simulation results obtained after applying the algorithm to the test images show that the proposed approach achieved high-precision and robust registration compared to other methods such as GWO, PSO, Firefly Algorithm (FA), and Crow Searcha Algorithms (CSA).},
}

@article {pmid34997433,
year = {2022},
author = {LaFave, SE and Suen, JJ and Seau, Q and Bergman, A and Fisher, MC and Thorpe, RJ and Szanton, SL},
title = {Racism and Older Black Americans' Health: a Systematic Review.},
journal = {Journal of urban health : bulletin of the New York Academy of Medicine},
volume = {99},
number = {1},
pages = {28-54},
pmid = {34997433},
issn = {1468-2869},
support = {F31 NR019211/NR/NINR NIH HHS/United States ; TL1 TR003100/TR/NCATS NIH HHS/United States ; T32 AG066576/AG/NIA NIH HHS/United States ; DP1 AG069874/AG/NIA NIH HHS/United States ; F31 AG071353/AG/NIA NIH HHS/United States ; },
mesh = {Black or African American/psychology ; Aged ; Black People ; Humans ; Middle Aged ; *Racism/psychology ; *Social Segregation ; Systemic Racism ; },
abstract = {We reviewed research that examines racism as an independent variable and one or more health outcomes as dependent variables in Black American adults aged 50 years and older in the USA. Of the 43 studies we reviewed, most measured perceived interpersonal racism, perceived institutional racism, or residential segregation. The only two measures of structural racism were birth and residence in a "Jim Crow state." Fourteen studies found associations between racism and mental health outcomes, five with cardiovascular outcomes, seven with cognition, two with physical function, two with telomere length, and five with general health/other health outcomes. Ten studies found no significant associations in older Black adults. All but six of the studies were cross-sectional. Research to understand the extent of structural and multilevel racism as a social determinant of health and the impact on older adults specifically is needed. Improved measurement tools could help address this gap in science.},
}

Black or African American/psychology
Aged
Black People
Humans
Middle Aged
*Racism/psychology
*Social Segregation
Systemic Racism

@article {pmid34930523,
year = {2021},
author = {Klump, BC and St Clair, JJ and Rutz, C},
title = {New Caledonian crows keep 'valuable' hooked tools safer than basic non-hooked tools.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34930523},
issn = {2050-084X},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S018484/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G023913/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Crows ; Female ; Male ; *Tool Use Behavior ; },
abstract = {The temporary storage and re-use of tools can significantly enhance foraging efficiency. New Caledonian crows in one of our study populations use two types of stick tools - hooked and non-hooked - which differ in raw material, manufacture costs, and foraging performance. Using a large sample of wild-caught, temporarily captive New Caledonian crows, we investigated experimentally whether individuals prefer one tool type over the other when given a choice and whether they take better care of their preferred tools between successive episodes of use, safely storing them underfoot or in nearby holes. Crows strongly preferred hooked stick tools made from Desmanthus virgatus stems over non-hooked stick tools. Importantly, this preference was also reflected in subsequent tool-handling behaviour, with subjects keeping hooked stick tools safe more often than non-hooked stick tools sourced from leaf litter. These results suggest that crows 'value' hooked stick tools, which are both costlier to procure and more efficient to use, more than non-hooked stick tools. Results from a series of control treatments suggested that crows altered their tool 'safekeeping' behaviour in response to a combination of factors, including tool type and raw material. To our knowledge, our study is the first to use safekeeping behaviour as a proxy for assessing how non-human animals value different tool types, establishing a novel paradigm for productive cross-taxonomic comparisons.},
}

Animals
*Crows
Female
Male
*Tool Use Behavior

@article {pmid34865301,
year = {2022},
author = {Pavicic, T and Pooth, R and Prinz, V and Cajkovsky, M and Green, JB and Hernandez, CA and Mueller, DS and Sattler, S and Klepetko, H and Day, D and Kerscher, M and Suwanchinda, A and Cotofana, S and Frank, K and Fabi, SG},
title = {Validated 5-point photonumeric scales for the assessment of the periorbital region.},
journal = {Journal of cosmetic dermatology},
volume = {21},
number = {1},
pages = {158-166},
doi = {10.1111/jocd.14643},
pmid = {34865301},
issn = {1473-2165},
support = {//Croma Pharma GmbH/ ; },
mesh = {Face ; Humans ; Reproducibility of Results ; *Skin Aging ; },
abstract = {OBJECTIVE: The objective of this investigation was to create and validate 5-point photonumeric scales for the assessment of dynamic crow's feet, static crow's feet, and infraorbital hollows.

MATERIAL AND METHODS: Three novel 5-point photonumeric scales were created by a medical team. A total of 12 raters from all over the world performed a digital validation, and a total of 5 raters a live validation of the created scale.

RESULTS: The statistical analysis revealed almost perfect intra-rater and inter-rater reliability in the digital validation of the scales for the assessment of static and dynamic crow's feet as well as infraorbital hollows. In the live validation, both crow's feet scales showed almost perfect intra-rater reliability, while the Croma Infraorbital Hollow Assessment Scale showed substantial intra-rater reliability. Inter-rater reliability was substantial for all three scales in the live validation. All three scales, the Croma Dynamic Crow's Feet Assessment Scale, Croma Static Crow's Feet Assessment Scale, and Croma Infraorbital Hollow Assessment Scale, were validated digitally and in a live setting.

CONCLUSION: The created scales to assess infraorbital hollowing, dynamic and static crow's feet have been shown to provide substantial to almost perfect agreement in the digital and live validation and can thus be considered as helpful tools in the clinical and research setting. While technical methods and appliances to assess the degrees of severity of age-dependent features are advancing, validated scales are of great importance due to their ease of use and, as shown by the validations, reliability, and reproducibility.},
}

Face
Humans
Reproducibility of Results
*Skin Aging

@article {pmid34465241,
year = {2021},
author = {Boeckle, M and Schiestl, M and Frohnwieser, A and Gruber, R and Miller, R and Suddendorf, T and Gray, RD and Taylor, AH and Clayton, NS},
title = {New Caledonian crows' planning behaviour: a reply to de Mahy et al.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1958},
pages = {20211271},
pmid = {34465241},
issn = {1471-2954},
mesh = {Animals ; Biological Evolution ; *Crows ; *Tool Use Behavior ; },
}

Animals
Biological Evolution
*Crows
*Tool Use Behavior

@article {pmid34465238,
year = {2021},
author = {de Mahy, D and Esteve, NA and Santariello, A},
title = {New test, old problems: comment on 'New Caledonian crows plan for specific future tool use'.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1958},
pages = {20210186},
pmid = {34465238},
issn = {1471-2954},
mesh = {Animals ; Cognition ; *Crows ; *Tool Use Behavior ; },
}

Animals
Cognition
*Crows
*Tool Use Behavior

@article {pmid34256579,
year = {2021},
author = {Breen, AJ},
title = {Animal culture research should include avian nest construction.},
journal = {Biology letters},
volume = {17},
number = {7},
pages = {20210327},
pmid = {34256579},
issn = {1744-957X},
mesh = {Animals ; *Finches ; *Nesting Behavior ; },
abstract = {Material culture-that is, group-shared and socially learned object-related behaviour(s)-is a widespread and diverse phenomenon in humans. For decades, researchers have sought to confirm the existence of material culture in non-human animals; however, the main study systems of interest-namely, tool making and/or using non-human primates and corvids-cannot provide such confirmatory evidence: because long-standing ethical and logistical constraints handicap the collection of necessary experimental data. Synthesizing evidence across decades and disciplines, here, I present a novel framework for (mechanistic, developmental, behavioural, and comparative) study on animal material culture: avian nest construction.},
}

Animals
*Finches
*Nesting Behavior

@article {pmid34253607,
year = {2021},
author = {Steele, MP and Neaves, LE and Klump, BC and St Clair, JJH and Fernandes, JRSM and Hequet, V and Shaw, P and Hollingsworth, PM and Rutz, C},
title = {DNA barcoding identifies cryptic animal tool materials.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {29},
pages = {},
pmid = {34253607},
issn = {1091-6490},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G023913/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RPG-2015-273/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Crows ; *DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; Nesting Behavior/physiology ; Phylogeny ; Plant Structures/anatomy & histology/classification/genetics ; Tool Use Behavior/*physiology ; },
abstract = {Some animals fashion tools or constructions out of plant materials to aid foraging, reproduction, self-maintenance, or protection. Their choice of raw materials can affect the structure and properties of the resulting artifacts, with considerable fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behavior is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (Corvus moneduloides) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using an array of conventional approaches-including targeted observations, camera traps, radio-tracking, bird-mounted video cameras, and behavioral experiments with wild and temporarily captive subjects-had failed. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviors, helping to unlock significant research potential across a wide range of study systems.},
}

Animals
Crows
*DNA Barcoding, Taxonomic
DNA, Plant/genetics
Nesting Behavior/physiology
Phylogeny
Plant Structures/anatomy & histology/classification/genetics
Tool Use Behavior/*physiology

@article {pmid34185776,
year = {2021},
author = {Laumer, IB and Massen, JJM and Boehm, PM and Boehm, A and Geisler, A and Auersperg, AMI},
title = {Individual Goffin´s cockatoos (Cacatua goffiniana) show flexible targeted helping in a tool transfer task.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0253416},
pmid = {34185776},
issn = {1932-6203},
mesh = {Animals ; Cockatoos/*physiology ; *Creativity ; Female ; Learning/*physiology ; Male ; *Reward ; },
abstract = {Flexible targeted helping is considered an advanced form of prosocial behavior in hominoids, as it requires the actor to assess different situations that a conspecific may be in, and to subsequently flexibly satisfy different needs of that partner depending on the nature of those situations. So far, apart from humans such behaviour has only been experimentally shown in chimpanzees and in Eurasian jays. Recent studies highlight the prosocial tendencies of several bird species, yet flexible targeted helping remained untested, largely due to methodological issues as such tasks are generally designed around tool-use, and very few bird species are capable of tool-use. Here, we tested Goffin's cockatoos, which proved to be skilled tool innovators in captivity, in a tool transfer task in which an actor had access to four different objects/tools and a partner to one of two different apparatuses that each required one of these tools to retrieve a reward. As expected from this species, we recorded playful object transfers across all conditions. Yet, importantly and similar to apes, three out of eight birds transferred the correct tool more often in the test condition than in a condition that also featured an apparatus but no partner. Furthermore, one of these birds transferred that correct tool first more often before transferring any other object in the test condition than in the no-partner condition, while the other two cockatoos were marginally non-significantly more likely to do so. Additionally, there was no difference in the likelihood of the correct tool being transferred first for either of the two apparatuses, suggesting that these birds flexibly adjusted what to transfer based on their partner´s need. Future studies should focus on explanations for the intra-specific variation of this behaviour, and should test other parrots and other large-brained birds to see how this can be generalized across the class and to investigate the evolutionary history of this trait.},
}

Animals
Cockatoos/*physiology
*Creativity
Female
Learning/*physiology
Male
*Reward

@article {pmid34090340,
year = {2021},
author = {Guiglielmoni, N and Houtain, A and Derzelle, A and Van Doninck, K and Flot, JF},
title = {Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {303},
pmid = {34090340},
issn = {1471-2105},
support = {764840//H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {Genome ; *Genomics ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking.

RESULTS: We tested different assembly strategies on the genome of the rotifer Adineta vaga, a non-model organism for which high coverages of both PacBio and Nanopore reads were available. The assemblers we tested (Canu, Flye, NextDenovo, Ra, Raven, Shasta and wtdbg2) exhibited strikingly different behaviors when dealing with highly heterozygous regions, resulting in variable amounts of uncollapsed haplotypes. Filtering reads generally improved haploid assemblies, and we also benchmarked three post-processing tools aimed at detecting and purging uncollapsed haplotypes in long-read assemblies: HaploMerger2, purge_haplotigs and purge_dups.

CONCLUSIONS: We provide a thorough evaluation of popular assemblers on a non-model eukaryote genome with variable levels of heterozygosity. Our study highlights several strategies using pre and post-processing approaches to generate haploid assemblies with high continuity and completeness. This benchmark will help users to improve haploid assemblies of non-model organisms, and evaluate the quality of their own assemblies.},
}

Genome
*Genomics
Haplotypes
*High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA

@article {pmid34061249,
year = {2021},
author = {Layton-Matthews, K and Griesser, M and Coste, CFD and Ozgul, A},
title = {Forest management affects seasonal source-sink dynamics in a territorial, group-living bird.},
journal = {Oecologia},
volume = {196},
number = {2},
pages = {399-412},
pmid = {34061249},
issn = {1432-1939},
support = {PPOOP3_123520; PPOOP3_123520//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; 31BD30_172465//ERA-NET BiodivERsA/ ; 665778//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Conservation of Natural Resources ; *Ecosystem ; Forestry ; Forests ; Humans ; *Passeriformes ; Population Dynamics ; Seasons ; },
abstract = {The persistence of wildlife populations is under threat as a consequence of human activities, which are degrading natural ecosystems. Commercial forestry is the greatest threat to biodiversity in boreal forests. Forestry practices have degraded most available habitat, threatening the persistence of natural populations. Understanding population responses is, therefore, critical for their conservation. Population viability analyses are effective tools to predict population persistence under forestry management. However, quantifying the mechanisms driving population responses is complex as population dynamics vary temporally and spatially. Metapopulation dynamics are governed by local dynamics and spatial factors, potentially mediating the impacts of forestry e.g., through dispersal. Here, we performed a seasonal, spatially explicit population viability analysis, using long-term data from a group-living territorial bird (Siberian jay, Perisoreus infaustus). We quantified the effects of forest management on metapopulation dynamics, via forest type-specific demography and spatially explicit dispersal, and how forestry impacted the stability of metapopulation dynamics. Forestry reduced metapopulation growth and stability, through negative effects on reproduction and survival. Territories in higher quality natural forest contributed more to metapopulation dynamics than managed forests, largely through demographic processes rather than dispersal. Metapopulation dynamics in managed forest were also less resilient to disturbances and consequently, may be more vulnerable to environmental change. Seasonal differences in source-sink dynamics observed in managed forest, but not natural forests, were caused by associated seasonal differences in dispersal. As shown here, capturing seasonal source-sink dynamics allows us to predict population persistence under human disturbance and to provide targeted conservation recommendations.},
}

Animals
Conservation of Natural Resources
*Ecosystem
Forestry
Forests
Humans
*Passeriformes
Population Dynamics
Seasons

@article {pmid33735945,
year = {2021},
author = {Johnston, S and Tutticci, N and Theobald, K and Ramsbotham, J},
title = {Comparison of simulation observer tools on engagement and maximising learning: a pilot study.},
journal = {International journal of nursing education scholarship},
volume = {18},
number = {1},
pages = {},
pmid = {33735945},
issn = {1548-923X},
mesh = {Clinical Competence ; Computer Simulation ; Humans ; Pilot Projects ; Problem-Based Learning ; *Simulation Training ; *Students, Nursing ; },
abstract = {OBJECTIVES: This pilot study examined if the Clinical Reasoning Observer Worksheet (CROW) compared to a standard observer worksheet used during simulation, would enhance nursing students active learning behaviours and perceptions of clinical reasoning ability.

METHODS: This pilot study was undertaken to test the design and processes for a future larger study and reports on preliminary evidence of efficacy of recruitment procedures and instrumentation in addition to student's learning outcomes.

RESULTS: There was little overall difference in outcomes between groups who used either simulation observer worksheet. Overall, participants who used either worksheet perceived their ability to apply clinical reasoning to an episode of patient care increased.

CONCLUSIONS: Modifications were identified as necessary for a larger study including changes to instrumentation, method of survey delivery and training of simulation facilitators. A more definitive evaluation will be achievable with a larger group of students in a main study with the suggested modifications.},
}

Clinical Competence
Computer Simulation
Humans
Pilot Projects
Problem-Based Learning
*Simulation Training
*Students, Nursing

@article {pmid33305388,
year = {2021},
author = {Dussex, N and Kutschera, VE and Wiberg, RAW and Parker, DJ and Hunt, GR and Gray, RD and Rutherford, K and Abe, H and Fleischer, RC and Ritchie, MG and Rutz, C and Wolf, JBW and Gemmell, NJ},
title = {A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows.},
journal = {Molecular ecology},
volume = {30},
number = {4},
pages = {973-986},
doi = {10.1111/mec.15775},
pmid = {33305388},
issn = {1365-294X},
support = {BB/G023913/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Crows/genetics ; Hawaii ; *Life History Traits ; *Tool Use Behavior ; },
abstract = {Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.},
}

Animals
*Crows/genetics
Hawaii
*Life History Traits
*Tool Use Behavior

@article {pmid33143583,
year = {2020},
author = {Boeckle, M and Schiestl, M and Frohnwieser, A and Gruber, R and Miller, R and Suddendorf, T and Gray, RD and Taylor, AH and Clayton, NS},
title = {New Caledonian crows plan for specific future tool use.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1938},
pages = {20201490},
pmid = {33143583},
issn = {1471-2954},
mesh = {Animals ; *Crows ; New Caledonia ; *Tool Use Behavior ; },
abstract = {The ability to plan for future events is one of the defining features of human intelligence. Whether non-human animals can plan for specific future situations remains contentious: despite a sustained research effort over the last two decades, there is still no consensus on this question. Here, we show that New Caledonian crows can use tools to plan for specific future events. Crows learned a temporal sequence where they were (a) shown a baited apparatus, (b) 5 min later given a choice of five objects and (c) 10 min later given access to the apparatus. At test, these crows were presented with one of two tool-apparatus combinations. For each combination, the crows chose the right tool for the right future task, while ignoring previously useful tools and a low-value food item. This study establishes that planning for specific future tool use can evolve via convergent evolution, given that corvids and humans shared a common ancestor over 300 million years ago, and offers a route to mapping the planning capacities of animals.},
}

Animals
*Crows
New Caledonia
*Tool Use Behavior

@article {pmid33117228,
year = {2020},
author = {Cabrera-Álvarez, MJ and Clayton, NS},
title = {Neural Processes Underlying Tool Use in Humans, Macaques, and Corvids.},
journal = {Frontiers in psychology},
volume = {11},
number = {},
pages = {560669},
pmid = {33117228},
issn = {1664-1078},
abstract = {It was thought that tool use in animals is an adaptive specialization. Recent studies, however, have shown that some non-tool-users, such as rooks and jays, can use and manufacture tools in laboratory settings. Despite the abundant evidence of tool use in corvids, little is known about the neural mechanisms underlying tool use in this family of birds. This review summarizes the current knowledge on the neural processes underlying tool use in humans, macaques and corvids. We suggest a possible neural network for tool use in macaques and hope this might inspire research to discover a similar brain network in corvids. We hope to establish a framework to elucidate the neural mechanisms that supported the convergent evolution of tool use in birds and mammals.},
}

@article {pmid33113033,
year = {2021},
author = {Laumer, IB and Jelbert, SA and Taylor, AH and Rössler, T and Auersperg, AMI},
title = {Object manufacture based on a memorized template: Goffin's cockatoos attend to different model features.},
journal = {Animal cognition},
volume = {24},
number = {3},
pages = {457-470},
pmid = {33113033},
issn = {1435-9456},
support = {P 29075/FWF_/Austrian Science Fund FWF/Austria ; P29075//FWF/ ; CS 18-023//WWTF/ ; },
mesh = {Animals ; *Cockatoos ; Learning ; Memory ; *Parrots ; Reward ; },
abstract = {Although several nonhuman animals have the ability to recognize and match templates in computerized tasks, we know little about their ability to recall and then physically manufacture specific features of mental templates. Across three experiments, Goffin cockatoos (Cacatua goffiniana), a species that can use tools in captivity, were exposed to two pre-made template objects, varying in either colour, size (long or short) or shape (I or L-shaped), where only one template was rewarded. Birds were then given the opportunity to manufacture versions of these objects themselves. We found that all birds carved paper strips from the same colour material as the rewarded template, and half were also able to match the size of a template (long and short). This occurred despite the template being absent at test and birds being rewarded at random. However, we found no evidence that cockatoos could carve L-shaped pieces after learning that L-shaped templates were rewarded, though their manufactured strips were wider than in previous tests. Overall, our results show that Goffin cockatoos possess the ability to physically adjust at least the size dimension of manufactured objects relative to a mental template. This ability has previously only been shown in New Caledonian crows, where template matching was suggested as a potential mechanism allowing for the cumulative cultural transmission of tool designs. Our results show that within avian tool users, the ability to recreate a physical template from memory does not seem to be restricted to species that have cumulative tool cultures.},
}

Animals
*Cockatoos
Learning
Memory
*Parrots
Reward

@article {pmid33003545,
year = {2020},
author = {Lin, Y and Zhang, X and Huang, Q and Lv, L and Huang, A and Li, A and Wu, K and Huang, Y},
title = {The Prevalence of Dyslexia in Primary School Children and Their Chinese Literacy Assessment in Shantou, China.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {19},
pages = {},
pmid = {33003545},
issn = {1660-4601},
mesh = {Asian People/*statistics & numerical data ; Child ; China ; Dyslexia/*epidemiology ; Female ; Humans ; Language Tests ; *Literacy ; Male ; Prevalence ; *Reading ; Schools ; },
abstract = {The epidemiological studies of Chinese developmental dyslexia (DD) in China are still limited. In addition, literacy assessment has seldom been performed for children with dyslexia, due to lack of uniform assessment tools. This study was aimed at investigating the prevalence rate of children with dyslexia, and to evaluate their Chinese reading ability. A total of 2955 students aged 7-12 years were enrolled by randomized cluster sampling. The study was divided into three stages. In stage I, all participating students were asked to finish the Combined Raven Test (CRT) and Chinese Vocabulary Test and Assessment Scale. In stage II, the Chinese teachers and parents of the children with suspected dyslexia were interviewed by psychiatrists, and finished the Dyslexia Checklist for Chinese Children (DCCC). In stage III, these children were evaluated by child psychiatrists for the diagnosis with or without dyslexia, according to the fifth edition of Diagnostic and Statistical Manual of Mental Disorders (DSM-5), and their Chinese literacy was further evaluated by using the Chinese Reading Ability Test (CRAT). The prevalence rate of children with dyslexia was 5.4% in Shantou city, 8.4% in boys and 2.3% in girls, with a gender ratio of 3.7:1.0. Children with dyslexia scored lower in all the five subscales of the CRAT tests. including phonological awareness, morphological awareness, rapid automatized naming, orthographic awareness, and reading ability than the control group (all p < 0.001). This study suggested that the prevalence rate of Chinese dyslexia in Shantou city is roughly equivalent to that previously reported in China. Children with dyslexia have a relatively lower Chinese reading ability in all assessments.},
}

Asian People/*statistics & numerical data
Child
China
Dyslexia/*epidemiology
Female
Humans
Language Tests
*Literacy
Male
Prevalence
*Reading
Schools

@article {pmid32968948,
year = {2021},
author = {Hunt, GR},
title = {New Caledonian crows' basic tool procurement is guided by heuristics, not matching or tracking probe site characteristics.},
journal = {Animal cognition},
volume = {24},
number = {1},
pages = {177-191},
pmid = {32968948},
issn = {1435-9456},
support = {UOA1208//Marsden Fund/ ; },
mesh = {Animals ; Comprehension ; *Crows ; Heuristics ; *Tool Use Behavior ; },
abstract = {Contrasting findings made it unclear what cognitive processes New Caledonian crows use to procure suitable tools to solve tool tasks. Most previous studies suggested that their tool procurement is achieved by either trial and error or a simple heuristic. The latter provides a fast and cognitively efficient method for stable, routinized behaviour based on past experience with little or no deliberate decision-making. However, early papers by Chappell and Kacelnik reported that two New Caledonian crows procured tools after closely assessing the tool characteristics required for the task, thus using deliberate decision-making, or a 'customized strategy'. Here, I tested eight New Caledonian crows to determine their default behaviour in basic tool procurement tasks as a check on whether or not they use customized strategies. I used two rigorous experiments closely based on Chappell and Kacelnik's experiments. The crows did not use a customized strategy in either experiment, but their behaviour was clearly consistent with tool procurement predominantly guided by a familiarity heuristic. I discuss potential methodological issues that may have led to different conclusions in Chappell and Kacelnik's studies. Heuristic-guided, routinized behaviour in tool procurement has potential implications for understanding how standardization occurs in the early evolution of complex tool manufacture, both in New Caledonian crows and early humans.},
}

Animals
Comprehension
*Crows
Heuristics
*Tool Use Behavior

@article {pmid32788623,
year = {2020},
author = {Latorre-Pérez, A and Villalba-Bermell, P and Pascual, J and Vilanova, C},
title = {Assembly methods for nanopore-based metagenomic sequencing: a comparative study.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {13588},
pmid = {32788623},
issn = {2045-2322},
mesh = {Genome, Bacterial/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Nanopore Sequencing/*methods ; *Nanopores ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.},
}

Genome, Bacterial/genetics
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Metagenome/*genetics
Metagenomics/*methods
Microbiota/genetics
Nanopore Sequencing/*methods
*Nanopores
Reproducibility of Results
Sequence Analysis, DNA/methods

@article {pmid32772986,
year = {2020},
author = {Taylor, AH and Jelbert, S},
title = {The crow in the room: New Caledonian crows offer insight into the necessary and sufficient conditions for cumulative cultural evolution.},
journal = {The Behavioral and brain sciences},
volume = {43},
number = {},
pages = {e178},
doi = {10.1017/S0140525X20000102},
pmid = {32772986},
issn = {1469-1825},
mesh = {Animals ; *Crows ; *Cultural Evolution ; Humans ; Technology ; *Tool Use Behavior ; },
abstract = {New Caledonian (NC) crow populations have developed complex tools that show suggestive evidence of cumulative change. These tool designs, therefore, appear to be the product of cumulative technological culture (CTC). We suggest that tool-using NC crows offer highly useful data for current debates over the necessary and sufficient conditions for the emergence of CTC.},
}

Animals
*Crows
*Cultural Evolution
Humans
Technology
*Tool Use Behavior

@article {pmid32772983,
year = {2020},
author = {Rutz, C and Hunt, GR},
title = {New Caledonian crows afford invaluable comparative insights into human cumulative technological culture.},
journal = {The Behavioral and brain sciences},
volume = {43},
number = {},
pages = {e177},
doi = {10.1017/S0140525X20000187},
pmid = {32772983},
issn = {1469-1825},
mesh = {Animals ; *Crows ; Humans ; Problem Solving ; Technology ; *Tool Use Behavior ; },
abstract = {The New Caledonian crow may be the only non-primate species exhibiting cumulative technological culture. Its foraging tools show clear signs of diversification and progressive refinement, and it seems likely that at least some tool-related information is passed across generations via social learning. Here, we explain how these remarkable birds can help us uncover the basic biological processes driving technological progress.},
}

Animals
*Crows
Humans
Problem Solving
Technology
*Tool Use Behavior

@article {pmid32384646,
year = {2020},
author = {Partchev, I},
title = {Diagnosing a 12-Item Dataset of Raven Matrices: With Dexter.},
journal = {Journal of Intelligence},
volume = {8},
number = {2},
pages = {},
pmid = {32384646},
issn = {2079-3200},
abstract = {We analyze a 12-item version of Raven's Standard Progressive Matrices test, traditionally scored with the sum score. We discuss some important differences between assessment in practice and psychometric modelling. We demonstrate some advanced diagnostic tools in the freely available R package, dexter. We find that the first item in the test functions badly-at a guess, because the subjects were not given exercise items before the live test.},
}

@article {pmid32160191,
year = {2020},
author = {Miller, R and Gruber, R and Frohnwieser, A and Schiestl, M and Jelbert, SA and Gray, RD and Boeckle, M and Taylor, AH and Clayton, NS},
title = {Decision-making flexibility in New Caledonian crows, young children and adult humans in a multi-dimensional tool-use task.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0219874},
pmid = {32160191},
issn = {1932-6203},
mesh = {Adult ; Animals ; Child, Preschool ; Cockatoos/physiology ; Crows/*physiology ; *Decision Making ; Female ; Humans ; Male ; Pongo/physiology ; *Task Performance and Analysis ; *Tool Use Behavior ; },
abstract = {The ability to make profitable decisions in natural foraging contexts may be influenced by an additional requirement of tool-use, due to increased levels of relational complexity and additional work-effort imposed by tool-use, compared with simply choosing between an immediate and delayed food item. We examined the flexibility for making the most profitable decisions in a multi-dimensional tool-use task, involving different apparatuses, tools and rewards of varying quality, in 3-5-year-old children, adult humans and tool-making New Caledonian crows (Corvus moneduloides). We also compared our results to previous studies on habitually tool-making orangutans (Pongo abelii) and non-tool-making Goffin's cockatoos (Cacatua goffiniana). Adult humans, cockatoos and crows, but not children and orangutans, did not select a tool when it was not necessary, which was the more profitable choice in this situation. Adult humans, orangutans and cockatoos, but not crows and children, were able to refrain from selecting non-functional tools. By contrast, the birds, but not the primates tested, struggled to attend to multiple variables-where two apparatuses, two tools and two reward qualities were presented simultaneously-without extended experience. These findings indicate: (1) in a similar manner to humans and orangutans, New Caledonian crows and Goffin's cockatoos can flexibly make profitable decisions in some decision-making tool-use tasks, though the birds may struggle when tasks become more complex; (2) children and orangutans may have a bias to use tools in situations where adults and other tool-making species do not.},
}

Adult
Animals
Child, Preschool
Cockatoos/physiology
Crows/*physiology
*Decision Making
Female
Humans
Male
Pongo/physiology
*Task Performance and Analysis
*Tool Use Behavior

@article {pmid32155318,
year = {2020},
author = {Moradifard, S and Saghiri, R and Ehsani, P and Mirkhani, F and Ebrahimi-Rad, M},
title = {A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.},
journal = {Molecular genetics & genomic medicine},
volume = {8},
number = {5},
pages = {e1219},
pmid = {32155318},
issn = {2324-9269},
mesh = {Collagen Type I/genetics/metabolism ; Collagen Type I, alpha 1 Chain ; Humans ; Mannose-Binding Lectin/genetics/metabolism ; Nitric Oxide Synthase Type II/genetics/metabolism ; Nucleotide Motifs ; *Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Protein Binding ; Sequence Analysis, DNA/*methods ; Software/*standards ; Transcription Factors/genetics/*metabolism ; },
abstract = {BACKGROUND: In the human genome, the transcription factors (TFs) and transcription factor-binding sites (TFBSs) network has a great regulatory function in the biological pathways. Such crosstalk might be affected by the single-nucleotide polymorphisms (SNPs), which could create or disrupt a TFBS, leading to either a disease or a phenotypic defect. Many computational resources have been introduced to predict the TFs binding variations due to SNPs inside TFBSs, sTRAP being one of them.

METHODS: A literature review was performed and the experimental data for 18 TFBSs located in 12 genes was provided. The sequences of TFBS motifs were extracted using two different strategies; in the size similar with synthetic target sites used in the experimental techniques, and with 60 bp upstream and downstream of the SNPs. The sTRAP (http://trap.molgen.mpg.de/cgi-bin/trap_two_seq_form.cgi) was applied to compute the binding affinity scores of their cognate TFs in the context of reference and mutant sequences of TFBSs. The alternative bioinformatics model used in this study was regulatory analysis of variation in enhancers (RAVEN; http://www.cisreg.ca/cgi-bin/RAVEN/a). The bioinformatics outputs of our study were compared with experimental data, electrophoretic mobility shift assay (EMSA).

RESULTS: In 6 out of 18 TFBSs in the following genes COL1A1, Hb ḉᴪ, TF, FIX, MBL2, NOS2A, the outputs of sTRAP were inconsistent with the results of EMSA. Furthermore, no p value of the difference between the two scores of binding affinity under the wild and mutant conditions of TFBSs was presented. Nor, were any criteria for preference or selection of any of the measurements of different matrices used for the same analysis.

CONCLUSION: Our preliminary study indicated some paradoxical results between sTRAP and experimental data. However, to link the data of sTRAP to the biological functions, its optimization via experimental procedures with the integration of expanded data and applying several other bioinformatics tools might be required.},
}

Collagen Type I/genetics/metabolism
Collagen Type I, alpha 1 Chain
Humans
Mannose-Binding Lectin/genetics/metabolism
Nitric Oxide Synthase Type II/genetics/metabolism
Nucleotide Motifs
*Polymorphism, Single Nucleotide
*Promoter Regions, Genetic
Protein Binding
Sequence Analysis, DNA/*methods
Software/*standards
Transcription Factors/genetics/*metabolism

@article {pmid32128152,
year = {2020},
author = {Klein, J and Haverkamp, PJ and Lindberg, E and Griesser, M and Eggers, S},
title = {Remotely sensed forest understory density and nest predator occurrence interact to predict suitable breeding habitat and the occurrence of a resident boreal bird species.},
journal = {Ecology and evolution},
volume = {10},
number = {4},
pages = {2238-2252},
pmid = {32128152},
issn = {2045-7758},
abstract = {Habitat suitability models (HSM) based on remotely sensed data are useful tools in conservation work. However, they typically use species occurrence data rather than robust demographic variables, and their predictive power is rarely evaluated. These shortcomings can result in misleading guidance for conservation. Here, we develop and evaluate a HSM based on correlates of long-term breeding success of an open nest building boreal forest bird, the Siberian jay. In our study site in northern Sweden, nest failure of this permanent resident species is driven mainly by visually hunting corvids that are associated with human settlements. Parents rely on understory nesting cover as protection against these predators. Accordingly, our HSM includes a light detection and ranging (LiDAR) based metric of understory density around the nest and the distance of the nest to the closest human settlement to predict breeding success. It reveals that a high understory density 15-80 m around nests is associated with increased breeding success in territories close to settlements (<1.5 km). Farther away from human settlements breeding success is highest at nest sites with a more open understory providing a favorable warmer microclimate. We validated this HSM by comparing the predicted breeding success with landscape-wide census data on Siberian jay occurrence. The correlation between breeding success and occurrence was strong up to 40 km around the study site. However, the HSM appears to overestimate breeding success in regions with a milder climate and therefore higher corvid numbers. Our findings suggest that maintaining patches of small diameter trees may provide a cost-effective way to restore the breeding habitat for Siberian jays up to 1.5 km from human settlements. This distance is expected to increase in the warmer, southern, and coastal range of the Siberian jay where the presence of other corvids is to a lesser extent restricted to settlements.},
}

@article {pmid32050797,
year = {2020},
author = {Stockbridge, MD and Newman, RS and Zukowski, A and Slawson, KK and Doran, A and Ratner, NB},
title = {Language profiles in children with concussion.},
journal = {Brain injury},
volume = {34},
number = {4},
pages = {567-574},
doi = {10.1080/02699052.2020.1725836},
pmid = {32050797},
issn = {1362-301X},
mesh = {Attention ; *Brain Concussion/complications/diagnosis ; Child ; Humans ; *Language ; Memory, Short-Term ; },
abstract = {Primary Objective: Inform the production of a screening tool for language in children with concussion. The authors predicted that children with a recent concussion would perform the cognitive-linguistic tasks more poorly, but some tasks may be more sensitive to concussion than others.Methods & Procedures: 22 elementary school aged children within 30 days of a concussion and age-matched peers with no history of concussion were assessed on a battery of novel language and cognitive-linguistic tasks. They also completed an auditory attention task and the Raven's Colored Progressive Matrices.Main Outcomes & Results: Children with a recent concussion scored significantly more poorly in novel tasks targeting category identification, grammaticality judgments, and recognizing target words presented in a short story than their age-matched peers with no such injury history. All observed effects had moderate sizes. Inclusion of these three tasks significantly improved prediction of concussion status over symptom score when controlling for the age of participants.Conclusions: The finding supports continued investigation of targeted linguistic tasks in children following concussion, particularly in the domains of semantic and syntactic access and verbal working memory. Future work developing brief language assessments specifically targeting children in this age range may provide a valuable addition to the existing tools for identifying the effects of concussion.},
}

Attention
*Brain Concussion/complications/diagnosis
Child
Humans
*Language
Memory, Short-Term

@article {pmid32034818,
year = {2020},
author = {Slager, DL and Epperly, KL and Ha, RR and Rohwer, S and Wood, C and Van Hemert, C and Klicka, J},
title = {Cryptic and extensive hybridization between ancient lineages of American crows.},
journal = {Molecular ecology},
volume = {29},
number = {5},
pages = {956-969},
doi = {10.1111/mec.15377},
pmid = {32034818},
issn = {1365-294X},
mesh = {Animals ; British Columbia ; Cell Nucleus/genetics ; Crows/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Flow ; *Genetics, Population ; Haplotypes ; *Hybridization, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Washington ; },
abstract = {Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the degree of genetic differentiation between these crows and the extent to which they may hybridize. Our results indicate that American and Northwestern crows have distinct evolutionary histories, supported by two nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the late Pleistocene, when glacial advances may have isolated crow populations in separate refugia. We document extensive hybridization, with geographic overlap of mtDNA clades and admixture of nuDNA across >900 km of western Washington and western British Columbia. This broad hybrid zone consists of late-generation hybrids and backcrosses, but not recent (e.g., F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were both centred in southwestern British Columbia, farther north than previously postulated. Overall, our results suggest a history of reticulate evolution in American and Northwestern crows, perhaps due to recurring neutral expansion(s) from Pleistocene glacial refugia followed by lineage fusion(s). However, we do not rule out a contributing role for more recent potential drivers of hybridization, such as expansion into human-modified habitats.},
}

Animals
British Columbia
Cell Nucleus/genetics
Crows/*genetics
DNA, Mitochondrial/genetics
Evolution, Molecular
Gene Flow
*Genetics, Population
Haplotypes
*Hybridization, Genetic
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Washington

@article {pmid31912522,
year = {2020},
author = {Spanoudis, CG and Andreadis, SS and Bray, DP and Savopoulou-Soultani, M and Ignell, R},
title = {Behavioural response of the house mosquitoes Culex quinquefasciatus and Culex pipiens molestus to avian odours and its reliance on carbon dioxide.},
journal = {Medical and veterinary entomology},
volume = {34},
number = {2},
pages = {129-137},
doi = {10.1111/mve.12429},
pmid = {31912522},
issn = {1365-2915},
mesh = {Animals ; Carbon Dioxide/*metabolism ; *Chemotaxis ; Chickens/metabolism ; Columbidae/metabolism ; Culex/*physiology ; Feeding Behavior ; Female ; Male ; Odorants/*analysis ; Songbirds/metabolism ; Species Specificity ; },
abstract = {How Culex (Diptera: Culicidae) mosquitoes select and discriminate between potential avian hosts is critical for understanding the epidemiology of West Nile virus. Therefore, the present authors studied the behavioural responses of Culex quinquefasciatus (Say) and Culex pipiens molestus (Forsskål) to headspace volatiles of three avian species [chicken and pigeon (sexes analysed separately), and magpie], presented either alone or in combination with 600 p.p.m. carbon dioxide (CO2). The attraction of Cx. quinquefasciatus to the headspace volatiles of both sexes of chicken, and of female pigeon, in combination with CO2 was significantly higher than that achieved by the CO2 and solvent control. Although Cx. p. molestus was attracted to headspace volatiles of chickens and magpies, it was repelled by those of female pigeons when combined with CO2 . An increased effect between the avian volatiles and CO2 was observed for Cx. quinquefasciatus, whereas the addition of CO2 had no effect on the attraction of Cx. p. molestus females. The results of this study demonstrate that Cx. quinquefasciatus and Cx. p. molestus are attracted to the odour of potential avian hosts. Future studies aimed at identifying the bioactive volatile compounds in the headspace of chickens may contribute to the potential development of effective surveillance and control tools against Culex species.},
}

Animals
Carbon Dioxide/*metabolism
*Chemotaxis
Chickens/metabolism
Columbidae/metabolism
Culex/*physiology
Feeding Behavior
Female
Male
Odorants/*analysis
Songbirds/metabolism
Species Specificity

@article {pmid31984131,
year = {2019},
author = {Wick, RR and Holt, KE},
title = {Benchmarking of long-read assemblers for prokaryote whole genome sequencing.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {2138},
pmid = {31984131},
issn = {2046-1402},
mesh = {Benchmarking ; *Genomics ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled - one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye, Miniasm/Minipolish, NECAT, NextDenovo/NextPolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v2.1 produced reliable assemblies and was good with plasmids, but it performed poorly with circularisation and had the longest runtimes of all assemblers tested. Flye v2.8 was also reliable and made the smallest sequence errors, though it used the most RAM. Miniasm/Minipolish v0.3/v0.1.3 was the most likely to produce clean contig circularisation. NECAT v20200803 was reliable and good at circularisation but tended to make larger sequence errors. NextDenovo/NextPolish v2.3.1/v1.3.1 was reliable with chromosome assembly but bad with plasmid assembly. Raven v1.3.0 was reliable for chromosome assembly, though it did not perform well on small plasmids and had circularisation issues. Redbean v2.5 and Shasta v0.7.0 were computationally efficient but more likely to produce incomplete assemblies. Conclusions: Of the assemblers tested, Flye, Miniasm/Minipolish, NextDenovo/NextPolish and Raven performed best overall. However, no single tool performed well on all metrics, highlighting the need for continued development on long-read assembly algorithms.},
}

Benchmarking
*Genomics
*High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Whole Genome Sequencing

@article {pmid31753993,
year = {2019},
author = {Klump, BC},
title = {Of crows and tools.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6468},
pages = {965},
doi = {10.1126/science.aaz7775},
pmid = {31753993},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Crows ; Feeding Behavior ; Hawaii ; New Caledonia ; *Tool Use Behavior ; },
}

Animals
Biological Evolution
*Crows
Feeding Behavior
Hawaii
New Caledonia
*Tool Use Behavior

@article {pmid31515097,
year = {2020},
author = {Shekhawat, S and Saxena, A},
title = {Development and applications of an intelligent crow search algorithm based on opposition based learning.},
journal = {ISA transactions},
volume = {99},
number = {},
pages = {210-230},
doi = {10.1016/j.isatra.2019.09.004},
pmid = {31515097},
issn = {1879-2022},
abstract = {Metaheuristics are proven beneficial tools for solving complex, hard optimization problems. Recently, a plethora of work has been reported on bio inspired optimization algorithms. These algorithms are mimicry of behavior of animals, plants and processes into mathematical paradigms. With these developments, a new entrant in this group is Crow Search Algorithm (CSA). CSA is based on the strategic behavior of crows while searching food, thievery and chasing behavior. This algorithm sometimes suffers with local minima stagnation and unbalance exploration and exploitation phases. To overcome this problem, a cosine function is proposed first, to accelerate the exploration and retard the exploitation process with due course of the iterative process. Secondly the opposition based learning concept is incorporated for enhancing the exploration virtue of CSA. The evolved variant with the inculcation of these two concepts is named as Intelligent Crow Search Algorithm (ICSA). The algorithm is benchmarked on two benchmark function sets, one is the set of 23 standard test functions and another is set of latest benchmark function CEC-2017. Further, the applicability of this variant is tested over structural design problem, frequency wave synthesis problem and Model Order Reduction (MOR). Results reveal that ICSA exhibits competitive performance on benchmarks and real applications when compared with some contemporary optimizers.},
}

@article {pmid31490161,
year = {2019},
author = {Story, SM and Vila, FD and Kas, JJ and Raniga, KB and Pemmaraju, CD and Rehr, JJ},
title = {Corvus: a framework for interfacing scientific software for spectroscopic and materials science applications.},
journal = {Journal of synchrotron radiation},
volume = {26},
number = {Pt 5},
pages = {1694-1704},
doi = {10.1107/S1600577519007495},
pmid = {31490161},
issn = {1600-5775},
support = {DE-AC02-76SF00515//US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering/ ; DE-AC02-05CH11231//US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering/ ; },
abstract = {Corvus, a Python-based package designed for managing workflows of physical simulations that utilize multiple scientific software packages, is presented. Corvus can be run as an executable script with an input file and automatically generated or custom workflows, or interactively, in order to build custom workflows with a set of Corvus-specific tools. Several prototypical examples are presented that link density functional, vibrational and X-ray spectroscopy software packages and are of interest to the synchrotron community. These examples highlight the simplification of complex spectroscopy calculations that were previously limited to expert users, and demonstrate the flexibility of the Corvus infrastructure to tackle more general problems in other research areas.},
}

@article {pmid31378612,
year = {2019},
author = {McCoy, DE and Schiestl, M and Neilands, P and Hassall, R and Gray, RD and Taylor, AH},
title = {New Caledonian Crows Behave Optimistically after Using Tools.},
journal = {Current biology : CB},
volume = {29},
number = {16},
pages = {2737-2742.e3},
doi = {10.1016/j.cub.2019.06.080},
pmid = {31378612},
issn = {1879-0445},
mesh = {Animals ; *Crows ; Motivation ; Optimism ; *Tool Use Behavior ; },
abstract = {Are complex, species-specific behaviors in animals reinforced by material reward alone or do they also induce positive emotions? Many adaptive human behaviors are intrinsically motivated: they not only improve our material outcomes, but improve our affect as well [1-8]. Work to date on animal optimism, as an indicator of positive affect, has generally focused on how animals react to change in their circumstances, such as when their environment is enriched [9-14] or they are manipulated by humans [15-23], rather than whether complex actions improve emotional state. Here, we show that wild New Caledonian crows are optimistic after tool use, a complex, species-specific behavior. We further demonstrate that this finding cannot be explained by the crows needing to put more effort into gaining food. Our findings therefore raise the possibility that intrinsic motivation (enjoyment) may be a fundamental proximate cause in the evolution of tool use and other complex behaviors. VIDEO ABSTRACT.},
}

Animals
*Crows
Motivation
Optimism
*Tool Use Behavior

@article {pmid31270682,
year = {2020},
author = {Vonk, J},
title = {Sticks and stones: Associative learning alone?.},
journal = {Learning & behavior},
volume = {48},
number = {3},
pages = {277-278},
doi = {10.3758/s13420-019-00387-4},
pmid = {31270682},
issn = {1543-4508},
mesh = {Animals ; *Crows ; Learning ; *Tool Use Behavior ; },
abstract = {Gruber et al. (Current Biology, 29, 686-692, 2019) report that New Caledonian crows engage in mental representation to solve a problem involving a tool. Although the crows' success is impressive, an associative account of their behavior calls into question the extent to which the data reflect representation of future states.},
}

Animals
*Crows
Learning
*Tool Use Behavior

@article {pmid30958132,
year = {2019},
author = {Klump, BC and Cantat, M and Rutz, C},
title = {Raw-material selectivity in hook-tool-crafting New Caledonian crows.},
journal = {Biology letters},
volume = {15},
number = {2},
pages = {20180836},
pmid = {30958132},
issn = {1744-957X},
support = {BB/G023913/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Crows ; Feeding Behavior ; Plant Leaves ; *Tool Use Behavior ; },
abstract = {Animals that manufacture foraging tools face the challenge of identifying suitable raw materials among a multitude of options. New Caledonian crows exhibit strong population-specific material preferences for the manufacture of hooked stick tools, but it is unknown how they identify their favourite plants. We investigated experimentally whether crows pay attention to the stems of plants (from which the tools are made) and/or their leaves (which are usually discarded during manufacture but may enable rapid and reliable species identification at a distance). Subjects were highly selective in choice trials with multiple plant species. Two additional treatments with experimental leaf-stem combinations revealed that birds can identify their preferred plant species by its stems alone, and possibly also its leaves. These findings encourage future experiments that investigate whether New Caledonian crows attend to features of the stem that are required for the production of efficient hooked stick tools. Our study provides one of the most detailed assessments to date of how non-human animals identify raw materials for tool manufacture.},
}

Animals
*Crows
Feeding Behavior
Plant Leaves
*Tool Use Behavior

@article {pmid30889388,
year = {2019},
author = {Bugnyar, T},
title = {Tool Use: New Caledonian Crows Engage in Mental Planning.},
journal = {Current biology : CB},
volume = {29},
number = {6},
pages = {R200-R202},
doi = {10.1016/j.cub.2019.01.059},
pmid = {30889388},
issn = {1879-0445},
mesh = {Food ; Humans ; *Tool Use Behavior ; },
abstract = {New Caledonian crows are able to flexibly use different tools in a sequence to retrieve food, whereby each step is out-of-sight of the others. Mental planning is thus not a human-specific trait.},
}

Food
Humans
*Tool Use Behavior

@article {pmid30744978,
year = {2019},
author = {Gruber, R and Schiestl, M and Boeckle, M and Frohnwieser, A and Miller, R and Gray, RD and Clayton, NS and Taylor, AH},
title = {New Caledonian Crows Use Mental Representations to Solve Metatool Problems.},
journal = {Current biology : CB},
volume = {29},
number = {4},
pages = {686-692.e3},
pmid = {30744978},
issn = {1879-0445},
mesh = {Animals ; *Cognition ; Crows/*physiology ; *Imagination ; *Problem Solving ; *Tool Use Behavior ; },
abstract = {One of the mysteries of animal problem-solving is the extent to which animals mentally represent problems in their minds. Humans can imagine both the solution to a problem and the stages along the way [1-3], such as when we plan one or two moves ahead in chess. The extent to which other animals can do the same is far less clear [4-25]. Here, we presented New Caledonian crows with a series of metatool problems where each stage was out of sight of the others and the crows had to avoid either a distractor apparatus containing a non-functional tool or a non-functional apparatus containing a functional tool. Crows were able to mentally represent the sub-goals and goals of metatool problems: crows kept in mind the location and identities of out-of-sight tools and apparatuses while planning and performing a sequence of tool behaviors. This provides the first conclusive evidence that birds can plan several moves ahead while using tools.},
}

Animals
*Cognition
Crows/*physiology
*Imagination
*Problem Solving
*Tool Use Behavior

@article {pmid30564390,
year = {2018},
author = {Lind, J},
title = {What can associative learning do for planning?.},
journal = {Royal Society open science},
volume = {5},
number = {11},
pages = {180778},
pmid = {30564390},
issn = {2054-5703},
abstract = {There is a new associative learning paradox. The power of associative learning for producing flexible behaviour in non-human animals is downplayed or ignored by researchers in animal cognition, whereas artificial intelligence research shows that associative learning models can beat humans in chess. One phenomenon in which associative learning often is ruled out as an explanation for animal behaviour is flexible planning. However, planning studies have been criticized and questions have been raised regarding both methodological validity and interpretations of results. Due to the power of associative learning and the uncertainty of what causes planning behaviour in non-human animals, I explored what associative learning can do for planning. A previously published sequence learning model which combines Pavlovian and instrumental conditioning was used to simulate two planning studies, namely Mulcahy & Call 2006 'Apes save tools for future use.' Science 312, 1038-1040 and Kabadayi & Osvath 2017 'Ravens parallel great apes in flexible planning for tool-use and bartering.' Science 357, 202-204. Simulations show that behaviour matching current definitions of flexible planning can emerge through associative learning. Through conditioned reinforcement, the learning model gives rise to planning behaviour by learning that a behaviour towards a current stimulus will produce high value food at a later stage; it can make decisions about future states not within current sensory scope. The simulations tracked key patterns both between and within studies. It is concluded that one cannot rule out that these studies of flexible planning in apes and corvids can be completely accounted for by associative learning. Future empirical studies of flexible planning in non-human animals can benefit from theoretical developments within artificial intelligence and animal learning.},
}

@article {pmid30534343,
year = {2018},
author = {Klump, BC and Masuda, BM and St Clair, JJH and Rutz, C},
title = {Preliminary observations of tool-processing behaviour in Hawaiian crows Corvus hawaiiensis.},
journal = {Communicative & integrative biology},
volume = {11},
number = {4},
pages = {e1509637},
pmid = {30534343},
issn = {1942-0889},
abstract = {Very few animal species habitually make and use foraging tools. We recently discovered that the Hawaiian crow is a highly skilled, natural tool user. Most captive adults in our experiment spontaneously used sticks to access out-of-reach food from a range of extraction tasks, exhibiting a surprising degree of dexterity. Moreover, many birds modified tools before or during deployment, and some even manufactured tools from raw materials. In this invited addendum article, we describe and discuss these observations in more detail. Our preliminary data, and comparisons with the better-studied New Caledonian crow, suggest that the Hawaiian crow has extensive tool-modification and manufacture abilities. To chart the full extent of the species' natural tool-making repertoire, we have started conducting dedicated experiments where subjects are given access to suitable raw materials for tool manufacture, but not ready-to-use tools.},
}

@article {pmid30410111,
year = {2018},
author = {Laumer, IB and Call, J and Bugnyar, T and Auersperg, AMI},
title = {Spontaneous innovation of hook-bending and unbending in orangutans (Pongo abelii).},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16518},
pmid = {30410111},
issn = {2045-2322},
support = {P 29075/FWF_/Austrian Science Fund FWF/Austria ; P 29084/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; Feeding Behavior/physiology ; Female ; Locomotion ; Male ; Pongo abelii/*physiology ; Stereotyped Behavior/*physiology ; Tool Use Behavior/*physiology ; },
abstract = {Betty the crow astonished the scientific world as she spontaneously crafted hook-tools from straight wire in order to lift a basket out of vertical tubes. Recently it was suggested that this species' solution was strongly influenced by predispositions from behavioural routines from habitual hook-tool manufacture. Nevertheless, the task became a paradigm to investigate tool innovation. Considering that young humans had surprising difficulties with the task, it was yet unclear whether the innovation of a hooked tool would be feasible to primates that lacked habitual hook making. We thus tested five captive orangutans in a hook bending and unbending task. Orangutans are habitually tool-using primates that have been reported to use but not craft hooked tools for locomotion in the wild. Two orangutans spontaneously innovated hook tools and four unbent the wire from their first trial on. Pre-experience with ready-made hooks had some effect but did not lead to continuous success. Further subjects improved the hook-design feature when the task required the subjects to bent the hook at a steeper angle. Our results indicate that the ability to represent and manufacture tools according to a current need does not require stereotyped behavioural routines, but can indeed arise innovatively. Furthermore, the present study shows that the capacity for hook tool innovation is not limited to large brained birds within non-human animals.},
}

Animals
Feeding Behavior/physiology
Female
Locomotion
Male
Pongo abelii/*physiology
Stereotyped Behavior/*physiology
Tool Use Behavior/*physiology

@article {pmid30356096,
year = {2018},
author = {Bayern, AMPV and Danel, S and Auersperg, AMI and Mioduszewska, B and Kacelnik, A},
title = {Compound tool construction by New Caledonian crows.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15676},
pmid = {30356096},
issn = {2045-2322},
mesh = {Animals ; *Behavior, Animal ; Cognition ; Crows/*physiology ; Decision Making ; Executive Function ; Female ; Food ; Inventions ; Male ; *Problem Solving ; Reward ; *Tool Use Behavior ; },
abstract = {The construction of novel compound tools through assemblage of otherwise non-functional elements involves anticipation of the affordances of the tools to be built. Except for few observations in captive great apes, compound tool construction is unknown outside humans, and tool innovation appears late in human ontogeny. We report that habitually tool-using New Caledonian crows (Corvus moneduloides) can combine objects to construct novel compound tools. We presented 8 naïve crows with combinable elements too short to retrieve food targets. Four crows spontaneously combined elements to make functional tools, and did so conditionally on the position of food. One of them made 3- and 4-piece tools when required. In humans, individual innovation in compound tool construction is often claimed to be evolutionarily and mechanistically related to planning, complex task coordination, executive control, and even language. Our results are not accountable by direct reinforcement learning but corroborate that these crows possess highly flexible abilities that allow them to solve novel problems rapidly. The underlying cognitive processes however remain opaque for now. They probably include the species' typical propensity to use tools, their ability to judge affordances that make some objects usable as tools, and an ability to innovate perhaps through virtual, cognitive simulations.},
}

Animals
*Behavior, Animal
Cognition
Crows/*physiology
Decision Making
Executive Function
Female
Food
Inventions
Male
*Problem Solving
Reward
*Tool Use Behavior

@article {pmid30253153,
year = {2018},
author = {Rutz, C and Hunt, GR and St Clair, JJH},
title = {Corvid Technologies: How Do New Caledonian Crows Get Their Tool Designs?.},
journal = {Current biology : CB},
volume = {28},
number = {18},
pages = {R1109-R1111},
doi = {10.1016/j.cub.2018.08.031},
pmid = {30253153},
issn = {1879-0445},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Tool Use Behavior ; },
abstract = {Recent research shows that New Caledonian crows can incorporate information from researcher-made objects into objects they subsequently manufacture. This 'mental template matching' is one of several possible - mutually compatible - mechanisms for the cultural transmission of tool designs among wild crows.},
}

*Tool Use Behavior

@article {pmid30141148,
year = {2018},
author = {Aharoni, T and Goldbourt, A},
title = {Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of fd-y21m bacteriophage using solid state NMR.},
journal = {Journal of biomolecular NMR},
volume = {72},
number = {1-2},
pages = {55-67},
pmid = {30141148},
issn = {1573-5001},
support = {847/17//Israel Science Foundation/ ; },
mesh = {*Anisotropy ; Bacteriophage M13/*chemistry ; Carbon Isotopes ; Molecular Dynamics Simulation ; Motion ; Nuclear Magnetic Resonance, Biomolecular/*methods ; Protein Conformation ; Proteins/*chemistry ; Software ; Time Factors ; },
abstract = {Determination of chemical shift anisotropy (CSA) in immobilized proteins and protein assemblies is one of several tools to determine protein dynamics on the timescales of microseconds and faster. The large CSA values of C=O groups in the rigid limit makes them in particular attractive for measurements of large amplitude motions, or their absence. In this study, we implement a 3D R-symmetry-based sequence that recouples the second spatial component of the [13]C CSA with the corresponding isotropic [13]C'-[13]C cross-peaks in order to probe backbone and sidechain dynamics in an intact fd-y21m filamentous phage viral capsid. The assignment of the isotropic cross-peaks and the analysis were conducted automatically using a new software named 'Raven'. The software can be utilized to auto-assign any 2D [13]C-[13]C or [15]N-[13]C spectrum given a previously-determined assignment table and generates simultaneously all intensity curves acquired in the third dimension. Here, all CSA spectra were automatically generated, and subsequently matched against a simulated set of CSA curves to yield their values. For the multi-copy, 50-residue-long protein capsid of fd-y21m, the backbone of the helical region is rigid, with reduced CSA values of ~ 12.5 kHz (~ 83 ppm). The N-terminus shows motionally-averaged CSA lineshapes and the carboxylic sidechain groups of four residues indicate large amplitude motions for D4, D5, D12 and E20. The current results further strengthen our previous studies of [15]N CSA values and are in agreement with qualitative analysis of [13]C-[13]C dipolar build-up curves, which were automatically obtained using our software. Our automated analysis technique is general and can be applied to study protein structure and dynamics, with data resulting from experiments that probe different variables such as relaxation rates and scaled anisotropic interactions.},
}

*Anisotropy
Bacteriophage M13/*chemistry
Carbon Isotopes
Molecular Dynamics Simulation
Motion
Nuclear Magnetic Resonance, Biomolecular/*methods
Protein Conformation
Proteins/*chemistry
Software
Time Factors

@article {pmid30132156,
year = {2018},
author = {Hennefield, L and Hwang, HG and Weston, SJ and Povinelli, DJ},
title = {Meta-analytic techniques reveal that corvid causal reasoning in the Aesop's Fable paradigm is driven by trial-and-error learning.},
journal = {Animal cognition},
volume = {21},
number = {6},
pages = {735-748},
pmid = {30132156},
issn = {1435-9456},
support = {F32 HD093273/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Cognition ; Crows/*physiology ; *Learning ; *Problem Solving ; Tool Use Behavior ; },
abstract = {The classic Aesop's fable, Crow and the Pitcher, has inspired a major line of research in comparative cognition. Over the past several years, five articles (over 32 experiments) have examined the ability of corvids (e.g., rooks, crows, and jays) to complete lab-based analogs of this fable, by requiring them to drop stones and other objects into tubes of water to retrieve a floating worm (Bird and Emery in Curr Biol 19:1-5, 2009b; Cheke et al. in Anim Cogn 14:441-455, 2011; Jelbert et al. in PLoS One 3:e92895, 2014; Logan et al. in PLoS One 7:e103049, 2014; Taylor et al. in Gray R D 12:e26887, 2011). These researchers have stressed the unique potential of this paradigm for understanding causal reasoning in corvids. Ghirlanda and Lind (Anim Behav 123:239-247, 2017) re-evaluated trial-level data from these studies and concluded that initial preferences for functional objects, combined with trial-and-error learning, may account for subjects' performance on key variants of the paradigm. In the present paper, we use meta-analytic techniques to provide more precise information about the rate and mode of learning that occurs within and across tasks. Within tasks, subjects learned from successful (but not unsuccessful) actions, indicating that higher-order reasoning about phenomena such as mass, volume, and displacement is unlikely to be involved. Furthermore, subjects did not transfer information learned in one task to subsequent tasks, suggesting that corvids do not engage with these tasks as variants of the same problem (i.e., how to generate water displacement to retrieve a floating worm). Our methodological analysis and empirical findings raise the question: Can Aesop's fable studies distinguish between trial-and-error learning and/or higher-order causal reasoning? We conclude they cannot.},
}

Animals
Cognition
Crows/*physiology
*Learning
*Problem Solving
Tool Use Behavior

@article {pmid30105075,
year = {2018},
author = {Morales, D and Ramirez, G and Herrera-Arellano, A and Tortoriello, J and Zavala, M and Zamilpa, A},
title = {Identification of Digestive Enzyme Inhibitors from Ludwigia octovalvis (Jacq.) P.H.Raven.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2018},
number = {},
pages = {8781352},
pmid = {30105075},
issn = {1741-427X},
abstract = {Current antiobesity and antidiabetic tools have been insufficient to curb these diseases and frequently cause side effects; therefore, new pancreatic lipase and α-glucosidase inhibitors could be excellent aids for the prevention and treatment of these diseases. The aim of this study was to identify, quantify, and characterize the chemical compounds with the highest degree of inhibitory activity of these enzymes, contained in a Ludwigia octovalvis hydroalcoholic extract. Chemical purification was performed by liquid-liquid separation and column chromatography. Inhibitory activities were measured in vitro, employing acarbose, orlistat, and a Camellia sinensis hydroalcoholic extract as references. For structural elucidation, Nuclear Magnetic Resonance was carried out, and High Performance Liquid Chromatography was used to quantify the compounds. For α-glucosidases, L. octovalvis hydroalcoholic extract and its ethyl acetate fraction showed half-maximal Inhibitory Concentration (IC50) values of 700 and 250 μg/mL, for lipase, 480 and 718 μg/mL, while C. sinensis showed 260 and 587 μg/mL. The most active compounds were identified as ethyl gallate (1, IC50 832 μM) and gallic acid (2, IC50 969 μM); both displayed competitive inhibition of α-glucosidases and isoorientin (3, IC50 201 μM), which displayed uncompetitive inhibition of lipase. These data could be useful in the development of a novel phytopharmaceutical drug.},
}

@article {pmid30071683,
year = {2018},
author = {Sutton, JT and Helmkampf, M and Steiner, CC and Bellinger, MR and Korlach, J and Hall, R and Baybayan, P and Muehling, J and Gu, J and Kingan, S and Masuda, BM and Ryder, OA},
title = {A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species.},
journal = {Genes},
volume = {9},
number = {8},
pages = {},
pmid = {30071683},
issn = {2073-4425},
abstract = {Abstract: Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world's most endangered bird species, the 'Alalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawai'i, the 'Alalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the 'Alalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications.},
}

@article {pmid30065105,
year = {2018},
author = {Faria, JP and Rocha, M and Rocha, I and Henry, CS},
title = {Methods for automated genome-scale metabolic model reconstruction.},
journal = {Biochemical Society transactions},
volume = {46},
number = {4},
pages = {931-936},
doi = {10.1042/BST20170246},
pmid = {30065105},
issn = {1470-8752},
mesh = {Automation ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; Humans ; Metabolic Networks and Pathways ; *Metagenome ; Microbiota ; *Models, Biological ; Software Design ; },
abstract = {In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. Here, we are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.},
}

Automation
Databases, Genetic
High-Throughput Nucleotide Sequencing
Humans
Metabolic Networks and Pathways
*Metagenome
Microbiota
*Models, Biological
Software Design

@article {pmid29975360,
year = {2018},
author = {Wójciak, P and Rybakowski, J},
title = {Clinical picture, pathogenesis and psychometric assessment of negative symptoms of schizophrenia.},
journal = {Psychiatria polska},
volume = {52},
number = {2},
pages = {185-197},
doi = {10.12740/PP/70610},
pmid = {29975360},
issn = {2391-5854},
mesh = {Emotions ; Humans ; Interview, Psychological/*standards ; Psychiatric Status Rating Scales ; Psychological Tests/standards ; Psychotic Disorders/diagnosis ; Schizophrenia/*diagnosis ; *Schizophrenic Psychology ; Social Behavior ; Symptom Assessment/*standards ; },
abstract = {Negative symptoms of schizophrenia constitute a serious diagnostic and therapeutic problem. They substantially account for the impairment of health, social functioning and quality of life whereas treatment is difficult. In this paper the development of the concept of schizophrenia and negative symptoms is presented. The models of positive and negative symptoms, introduced in the 1980's by Timothy Crow and Nancy Andreasen, and William Carpenter's concept of so-called deficit syndrome with the criteria of the division of negative symptoms into the primary and secondary, are discussed. Current views on the pathogenesis of negative symptoms are shown with reference to neuroimaging studies, neurotransmitter alterations, neuropsychological deficits, genetic, immunological and epidemiological studies. A subsection is devoted to the diagnostics tools for negative symptoms. Chronologically, they are divided into scales of the 1st and 2nd generation. The first generation includes: the Brief Psychiatric Rating Scale (BPRS), the Scale for the Assessment of Negative Symptoms (SANS), the Positive and Negative Syndrome Scale (PANSS), the Schedule for the Deficit Syndrome (SDS), and the Proxy for Deficit Syndrome. The second generation scales, developed as a result of the recommendation by American experts in 2006, include: the Brief Negative Syndrome Scale (BNSS) and the Clinical Assessment Interview for Negative Symptoms (CAINS), also the self-assessment scales: the Motivation and Pleasure Scale - Self Report (MAP-SR) and the Self-assessment of Negative Symptoms (SNS). The BNSS and the SNS scales, whose Polish versions were elaborated in the Department of Adult Psychiatry of Poznan University of Medical Sciences, are discussed in-depth.},
}

Emotions
Humans
Interview, Psychological/*standards
Psychiatric Status Rating Scales
Psychological Tests/standards
Psychotic Disorders/diagnosis
Schizophrenia/*diagnosis
*Schizophrenic Psychology
Social Behavior
Symptom Assessment/*standards

@article {pmid29955154,
year = {2018},
author = {Jelbert, SA and Hosking, RJ and Taylor, AH and Gray, RD},
title = {Mental template matching is a potential cultural transmission mechanism for New Caledonian crow tool manufacturing traditions.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8956},
pmid = {29955154},
issn = {2045-2322},
mesh = {Animals ; Biological Evolution ; Cognition/physiology ; Crows/*physiology ; Female ; Food Dispensers, Automatic ; Imitative Behavior/physiology ; Intelligence Tests ; Male ; Memory, Short-Term/*physiology ; Reward ; Statistics, Nonparametric ; Tool Use Behavior/*physiology ; },
abstract = {Cumulative cultural evolution occurs when social traditions accumulate improvements over time. In humans cumulative cultural evolution is thought to depend on a unique suite of cognitive abilities, including teaching, language and imitation. Tool-making New Caledonian crows show some hallmarks of cumulative culture; but this claim is contentious, in part because these birds do not appear to imitate. One alternative hypothesis is that crows' tool designs could be culturally transmitted through a process of mental template matching. That is, individuals could use or observe conspecifics' tools, form a mental template of a particular tool design, and then reproduce this in their own manufacture - a process analogous to birdsong learning. Here, we provide the first evidence supporting this hypothesis, by demonstrating that New Caledonian crows have the cognitive capacity for mental template matching. Using a novel manufacture paradigm, crows were first trained to drop paper into a vending machine to retrieve rewards. They later learnt that only items of a particular size (large or small templates) were rewarded. At test, despite being rewarded at random, and with no physical templates present, crows manufactured items that were more similar in size to previously rewarded, than unrewarded, templates. Our results provide the first evidence that this cognitive ability may underpin the transmission of New Caledonian crows' natural tool designs.},
}

Animals
Biological Evolution
Cognition/physiology
Crows/*physiology
Female
Food Dispensers, Automatic
Imitative Behavior/physiology
Intelligence Tests
Male
Memory, Short-Term/*physiology
Reward
Statistics, Nonparametric
Tool Use Behavior/*physiology

@article {pmid29358606,
year = {2018},
author = {St Clair, JJH and Klump, BC and Sugasawa, S and Higgott, CG and Colegrave, N and Rutz, C},
title = {Hook innovation boosts foraging efficiency in tool-using crows.},
journal = {Nature ecology & evolution},
volume = {2},
number = {3},
pages = {441-444},
doi = {10.1038/s41559-017-0429-7},
pmid = {29358606},
issn = {2397-334X},
mesh = {Animals ; Crows/*physiology ; *Feeding Behavior ; Female ; Male ; *Tool Use Behavior ; },
abstract = {The New Caledonian crow is the only non-human animal known to craft hooked tools in the wild, but the ecological benefit of these relatively complex tools remains unknown. Here, we show that crows acquire food several times faster when using hooked rather than non-hooked tools, regardless of tool material, prey type and extraction context. This implies that small changes to tool shape can strongly affect energy-intake rates, highlighting a powerful driver for technological advancement.},
}

Animals
Crows/*physiology
*Feeding Behavior
Female
Male
*Tool Use Behavior

@article {pmid29257965,
year = {2017},
author = {van Casteren, A},
title = {Tool Use: Crows Craft the Right Tool for the Job.},
journal = {Current biology : CB},
volume = {27},
number = {24},
pages = {R1314-R1316},
doi = {10.1016/j.cub.2017.10.022},
pmid = {29257965},
issn = {1879-0445},
mesh = {Animals ; *Crows ; Language ; *Tool Use Behavior ; },
abstract = {New research into tool crafting in New Caledonian crows has uncovered factors that influence tool shape and the foraging advantages that these characteristics confer.},
}

Animals
*Crows
Language
*Tool Use Behavior

@article {pmid29225028,
year = {2017},
author = {Sugasawa, S and Klump, BC and St Clair, JJH and Rutz, C},
title = {Causes and Consequences of Tool Shape Variation in New Caledonian Crows.},
journal = {Current biology : CB},
volume = {27},
number = {24},
pages = {3885-3890.e4},
doi = {10.1016/j.cub.2017.11.028},
pmid = {29225028},
issn = {1879-0445},
mesh = {Age Factors ; Animals ; Crows/*physiology ; Feeding Behavior ; Female ; Male ; *Tool Use Behavior ; },
abstract = {Hominins have been making tools for over three million years [1], yet the earliest known hooked tools appeared as recently as 90,000 years ago [2]. Hook innovation is likely to have boosted our ancestors' hunting and fishing efficiency [3], marking a major transition in human technological evolution. The New Caledonian crow is the only non-human animal known to craft hooks in the wild [4, 5]. Crows manufacture hooked stick tools in a multi-stage process, involving the detachment of a branch from suitable vegetation; "sculpting" of a terminal hook from the nodal joint; and often additional adjustments, such as length trimming, shaft bending, and bark stripping [4, 6, 7]. Although tools made by a given population share key design features [4, 6, 8], they vary appreciably in overall shape and hook dimensions. Using wild-caught, temporarily captive crows, we experimentally investigated causes and consequences of variation in hook-tool morphology. We found that bird age, manufacture method, and raw-material properties influenced tool morphology, and that hook geometry in turn affected crows' foraging efficiency. Specifically, hook depth varied with both detachment technique and plant rigidity, and deeper hooks enabled faster prey extraction in the provided tasks. Older crows manufactured tools of distinctive shape, with pronounced shaft curvature and hooks of intermediate depth. Future work should explore the interactive effects of extrinsic and intrinsic factors on tool production and deployment. Our study provides a quantitative assessment of the drivers and functional significance of tool shape variation in a non-human animal, affording valuable comparative insights into early hominin tool crafting [9].},
}

Age Factors
Animals
Crows/*physiology
Feeding Behavior
Female
Male
*Tool Use Behavior

@article {pmid29213080,
year = {2017},
author = {Danel, S and Osiurak, F and von Bayern, AMP},
title = {From the Age of 5 Humans Decide Economically, Whereas Crows Exhibit Individual Preferences.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {17043},
pmid = {29213080},
issn = {2045-2322},
mesh = {Adult ; Animals ; Child, Preschool ; Crows/*physiology ; Female ; Humans ; Male ; Problem Solving ; *Tool Use Behavior ; },
abstract = {Human societies greatly depend on tools, which spare us considerable time and effort. Humans might have evolved a bias to employ tools, using them even when they are unnecessary. This study aimed to investigate whether adult humans and a distantly related habitually tool-using vertebrate species, the New Caledonian crow (Corvus moneduloides), use tools depending on their necessity. In addition, children aged 3 to 5 years were examined to investigate the developmental pattern. The task involved choosing between using a body part (i.e. crows: beak; humans: hand) or a tool for retrieving a reward from a box. All subjects were tested in two conditions. In the Body+/Tool- condition, using the body was more efficient than using the tool, and conversely in the Body-/Tool+ condition. Our results suggest that the capacity to employ tools economically develops late in humans. Crows, however, failed to choose economically. At the individual level, some subjects exhibited striking individual preferences for either using a tool or their beak throughout the task. Whether such biases depend on individual experience or whether they are genetically determined remains to be investigated. Our findings provide new insights about tool use and its cognitive implementation in two outstanding tool-using taxa.},
}

Adult
Animals
Child, Preschool
Crows/*physiology
Female
Humans
Male
Problem Solving
*Tool Use Behavior

@article {pmid28989768,
year = {2017},
author = {Lambert, ML and Schiestl, M and Schwing, R and Taylor, AH and Gajdon, GK and Slocombe, KE and Seed, AM},
title = {Function and flexibility of object exploration in kea and New Caledonian crows.},
journal = {Royal Society open science},
volume = {4},
number = {9},
pages = {170652},
pmid = {28989768},
issn = {2054-5703},
abstract = {A range of non-human animals frequently manipulate and explore objects in their environment, which may enable them to learn about physical properties and potentially form more abstract concepts of properties such as weight and rigidity. Whether animals can apply the information learned during their exploration to solve novel problems, however, and whether they actually change their exploratory behaviour to seek functional information about objects have not been fully explored. We allowed kea (Nestor notabilis) and New Caledonian crows (Corvus moneduloides) to explore sets of novel objects both before and after encountering a task in which some of the objects could function as tools. Following this, subjects were given test trials in which they could choose among the objects they had explored to solve a tool-use task. Several individuals from both species performed above chance on these test trials, and only did so after exploring the objects, compared with a control experiment with no prior exploration phase. These results suggest that selection of functional tools may be guided by information acquired during exploration. Neither kea nor crows changed the duration or quality of their exploration after learning that the objects had a functional relevance, suggesting that birds do not adjust their behaviour to explicitly seek this information.},
}

@article {pmid28963599,
year = {2017},
author = {Stanton, L and Davis, E and Johnson, S and Gilbert, A and Benson-Amram, S},
title = {Adaptation of the Aesop's Fable paradigm for use with raccoons (Procyon lotor): considerations for future application in non-avian and non-primate species.},
journal = {Animal cognition},
volume = {20},
number = {6},
pages = {1147-1152},
doi = {10.1007/s10071-017-1129-z},
pmid = {28963599},
issn = {1435-9456},
mesh = {Animals ; *Cognition ; Female ; Male ; *Problem Solving ; Raccoons/*psychology ; Reward ; *Tool Use Behavior ; },
abstract = {To gain a better understanding of the evolution of animal cognition, it is necessary to test and compare the cognitive abilities of a broad array of taxa. Meaningful inter-species comparisons are best achieved by employing universal paradigms that standardize testing among species. Many cognitive paradigms, however, have been tested in only a few taxa, mostly birds and primates. One such example, known as the Aesop's Fable paradigm, is designed to assess causal understanding in animals using water displacement. To evaluate the universal effectiveness of the Aesop's Fable paradigm, we applied this paradigm to a previously untested taxon, the raccoon (Procyon lotor). We first trained captive raccoons to drop stones into a tube of water to retrieve a floating food reward. Next, we presented successful raccoons with objects that differed in the amount of water they displaced to determine whether raccoons could select the most functional option. Raccoons performed differently than corvids and human children did in previous studies of Aesop's Fable, and we found raccoons to be innovative in many aspects of this task. We suggest that raccoon performance in this paradigm reflected differences in tangential factors, such as behavior, morphology, and testing procedures, rather than cognitive deficiencies. We also present insight into previously undocumented challenges that should better inform future Aesop's Fable studies incorporating more diverse taxa.},
}

Animals
*Cognition
Female
Male
*Problem Solving
Raccoons/*psychology
Reward
*Tool Use Behavior

@article {pmid28878059,
year = {2017},
author = {Laumer, IB and Bugnyar, T and Reber, SA and Auersperg, AMI},
title = {Can hook-bending be let off the hook? Bending/unbending of pliant tools by cockatoos.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1862},
pages = {},
pmid = {28878059},
issn = {1471-2954},
support = {P 29075/FWF_/Austrian Science Fund FWF/Austria ; P 29084/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Animals ; *Cockatoos ; *Learning ; *Tool Use Behavior ; },
abstract = {The spontaneous crafting of hook-tools from bendable material to lift a basket out of a vertical tube in corvids has widely been used as one of the prime examples of animal tool innovation. However, it was recently suggested that the animals' solution was hardly innovative but strongly influenced by predispositions from habitual tool use and nest building. We tested Goffin's cockatoo, which is neither a specialized tool user nor a nest builder, on a similar task set-up. Three birds individually learned to bend hook tools from straight wire to retrieve food from vertical tubes and four subjects unbent wire to retrieve food from horizontal tubes. Pre-experience with ready-made hooks had some effect but was not necessary for success. Our results indicate that the ability to represent and manufacture tools according to a current need does not require genetically hardwired behavioural routines, but can indeed arise innovatively from domain general cognitive processing.},
}

Animals
*Cockatoos
*Learning
*Tool Use Behavior

@article {pmid28706072,
year = {2017},
author = {Kabadayi, C and Osvath, M},
title = {Ravens parallel great apes in flexible planning for tool-use and bartering.},
journal = {Science (New York, N.Y.)},
volume = {357},
number = {6347},
pages = {202-204},
doi = {10.1126/science.aam8138},
pmid = {28706072},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Crows ; Female ; Hominidae/*psychology ; Male ; *Tool Use Behavior ; },
abstract = {The ability to flexibly plan for events outside of the current sensory scope is at the core of being human and is crucial to our everyday lives and society. Studies on apes have shaped a belief that this ability evolved within the hominid lineage. Corvids, however, have shown evidence of planning their food hoarding, although this has been suggested to reflect a specific caching adaptation rather than domain-general planning. Here, we show that ravens plan for events unrelated to caching-tool-use and bartering-with delays of up to 17 hours, exert self-control, and consider temporal distance to future events. Their performance parallels that seen in apes and suggests that planning evolved independently in corvids, which opens new avenues for the study of cognitive evolution.},
}

Animals
Biological Evolution
*Crows
Female
Hominidae/*psychology
Male
*Tool Use Behavior

@article {pmid28706023,
year = {2017},
author = {Boeckle, M and Clayton, NS},
title = {A raven's memories are for the future.},
journal = {Science (New York, N.Y.)},
volume = {357},
number = {6347},
pages = {126-127},
doi = {10.1126/science.aan8802},
pmid = {28706023},
issn = {1095-9203},
mesh = {Animals ; *Crows ; *Memory ; *Tool Use Behavior ; },
}

Animals
*Crows
*Memory
*Tool Use Behavior

@article {pmid28499128,
year = {2017},
author = {Zarrintab, M and Mirzaei, R},
title = {Stress induced by heavy metals on breeding of magpie (Pica pica) from central Iran.},
journal = {Ecotoxicology and environmental safety},
volume = {143},
number = {},
pages = {28-37},
doi = {10.1016/j.ecoenv.2017.04.047},
pmid = {28499128},
issn = {1090-2414},
mesh = {Animals ; Clutch Size/drug effects ; Ecosystem ; Egg Shell/chemistry ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis/*toxicity ; Feathers/chemistry ; Iran ; Metals, Heavy/analysis/*toxicity ; Ovum/chemistry ; Passeriformes/*metabolism/physiology ; Pica ; Random Allocation ; Reproduction/*drug effects ; Stress, Physiological/*drug effects ; },
abstract = {The aim of this study was to address the impacts of some heavy metals (Cd, Pb, Zn, Ni and Cu) contamination on laying behavior, egg quality and breeding performance of Pica pica in north of Isfahan Province, Iran. During the breeding season of 2013, magpie's egg content and eggshell as well as nestling excrements and feathers were collected and total concentrations of heavy metals were measured by ICP-OES. Except for Zn in nestling feathers, the significantly higher concentrations of heavy metals were observed in nestling excrements than other samples. Also, comparison of heavy metals concentrations in egg content and eggshell showed that egg content had significantly higher concentrations of Zn and Pb, instead eggshell had significantly higher amount of Cu and Cd. Except for Cu, all heavy metals concentrations in eggshell had a negative relationship with morphological characters; and also concentration of Cu in egg content showed a significantly negative correlation with egg weight and volume. The most of heavy metals in nestling feathers and excrements had strongly positive correlations with each other. Also all heavy metals levels in eggshell and egg content had significantly positive correlations (except for Cu). Unhatched eggs had significantly lower weight but also greater levels of Zn, Cd, and Pb, than randomly collected eggs. No significant differences were observed for morphometric measurements of eggs between different sites, however, a decreased gradient was observed in egg volume toward the brick kiln site. Samples collected in brick kiln site accumulated higher concentrations of heavy metals than other sites. Although numbers of clutch size in brick kiln site were significantly higher than other sites, however, other breeding variable were lower than other sites. It can be suggested that ecosystem contamination may be caused to decrease the reproduction rate of Pica pica in brick kiln, probably by laying more poor quality eggs per clutch and nestling mortality.},
}

Animals
Clutch Size/drug effects
Ecosystem
Egg Shell/chemistry
Environmental Monitoring/*methods
Environmental Pollutants/analysis/*toxicity
Feathers/chemistry
Iran
Metals, Heavy/analysis/*toxicity
Ovum/chemistry
Passeriformes/*metabolism/physiology
Pica
Random Allocation
Reproduction/*drug effects
Stress, Physiological/*drug effects

@article {pmid28494226,
year = {2017},
author = {Whalley, CL and Cutting, N and Beck, SR},
title = {The effect of prior experience on children's tool innovation.},
journal = {Journal of experimental child psychology},
volume = {161},
number = {},
pages = {81-94},
doi = {10.1016/j.jecp.2017.03.009},
pmid = {28494226},
issn = {1096-0457},
mesh = {Child ; Child Development ; Child, Preschool ; *Cognition ; Female ; Humans ; Male ; *Problem Solving ; },
abstract = {Spontaneous tool innovation to solve physical problems is difficult for young children. In three studies, we explored the effect of prior experience with tools on tool innovation in children aged 4-7years (N=299). We also gave children an experience more consistent with that experienced by corvids in similar studies to enable fairer cross-species comparisons. Children who had the opportunity to use a premade target tool in the task context during a warm-up phase were significantly more likely to innovate a tool to solve the problem on the test trial compared with children who had no such warm-up experience. Older children benefited from either using or merely seeing a premade target tool prior to a test trial requiring innovation. Younger children were helped by using a premade target tool. Seeing the tool helped younger children in some conditions. We conclude that spontaneous innovation of tools to solve physical problems is difficult for children. However, children from 4years of age can innovate the means to solve the problem when they have had experience with the solution (visual or haptic exploration). Directions for future research are discussed.},
}

Child
Child Development
Child, Preschool
*Cognition
Female
Humans
Male
*Problem Solving

@article {pmid28386435,
year = {2017},
author = {Matsui, H and Izawa, EI},
title = {Flexible motor adjustment of pecking with an artificially extended bill in crows but not in pigeons.},
journal = {Royal Society open science},
volume = {4},
number = {2},
pages = {160796},
pmid = {28386435},
issn = {2054-5703},
abstract = {The dextrous foraging skills of primates, including humans, are underpinned by flexible vision-guided control of the arms/hands and even tools as body-part extensions. This capacity involves a visuomotor conversion process that transfers the locations of the hands/arms and a target in retinal coordinates into body coordinates to generate a reaching/grasping movement and to correct online. Similar capacities have evolved in birds, such as tool use in corvids and finches, which represents the flexible motor control of extended body parts. However, the flexibility of avian head-reaching and bill-grasping with body-part extensions remains poorly understood. This study comparatively investigated the flexibility of pecking with an artificially extended bill in crows and pigeons. Pecking performance and kinematics were examined when the bill extension was attached, and after its removal. The bill extension deteriorated pecking in pigeons in both performance and kinematics over 10 days. After the bill removal, pigeons started bill-grasping earlier, indicating motor adaptation to the bill extension. Contrastingly, pecking in crows was deteriorated transiently with the bill extension, but was recovered by adjusting pecking at closer distances, suggesting a quick adjustment to the bill extension. These results indicate flexible visuomotor control to extended body parts in crows but not in pigeons.},
}

@article {pmid28364366,
year = {2017},
author = {Uomini, N and Hunt, G},
title = {A new tool-using bird to crow about.},
journal = {Learning & behavior},
volume = {45},
number = {3},
pages = {205-206},
pmid = {28364366},
issn = {1543-4508},
mesh = {Animals ; Cognition ; *Crows ; *Tool Use Behavior ; },
abstract = {The Hawaiian crow has been revealed as a skilled tool user, confirmed by testing the last members of this endangered species that survive in captivity. The finding suggests its behavior is tantalizingly similar to that of the famous tool-using New Caledonian crow and has implications for the evolution of tool use and intelligence in birds.},
}

Animals
Cognition
*Crows
*Tool Use Behavior

@article {pmid27973610,
year = {2016},
author = {Neilands, PD and Jelbert, SA and Breen, AJ and Schiestl, M and Taylor, AH},
title = {How Insightful Is 'Insight'? New Caledonian Crows Do Not Attend to Object Weight during Spontaneous Stone Dropping.},
journal = {PloS one},
volume = {11},
number = {12},
pages = {e0167419},
pmid = {27973610},
issn = {1932-6203},
mesh = {Animals ; Crows/*physiology ; Tool Use Behavior/physiology ; },
abstract = {It is highly difficult to pinpoint what is going through an animal's mind when it appears to solve a problem by 'insight'. Here, we searched for an information processing error during the emergence of seemingly insightful stone dropping in New Caledonian crows. We presented these birds with the platform apparatus, where a heavy object needs to be dropped down a tube and onto a platform in order to trigger the release of food. Our results show New Caledonian crows exhibit a weight inattention error: they do not attend to the weight of an object when innovating stone dropping. This suggests that these crows do not use an understanding of force when solving the platform task in a seemingly insightful manner. Our findings showcase the power of the signature-testing approach, where experiments search for information processing biases, errors and limits, in order to make strong inferences about the functioning of animal minds.},
}

Animals
Crows/*physiology
Tool Use Behavior/physiology

@article {pmid27867222,
year = {2016},
author = {St Clair, JJ and Klump, BC and van der Wal, JE and Sugasawa, S and Rutz, C},
title = {Strong between-site variation in New Caledonian crows' use of hook-tool-making materials.},
journal = {Biological journal of the Linnean Society. Linnean Society of London},
volume = {118},
number = {2},
pages = {226-232},
pmid = {27867222},
issn = {0024-4066},
abstract = {Functional tool use requires the selection of appropriate raw materials. New Caledonian crows Corvus moneduloides are known for their extraordinary tool-making behaviour, including the crafting of hooked stick tools from branched vegetation. We describe a surprisingly strong between-site difference in the plant materials used by wild crows to manufacture these tools: crows at one study site use branches of the non-native shrub Desmanthus virgatus, whereas only approximately 7 km away, birds apparently ignore this material in favour of the terminal twigs of an as-yet-unidentified tree species. Although it is likely that differences in local plant communities drive this striking pattern, it remains to be determined how and why crows develop such strong site-specific preferences for certain raw materials.},
}

@article {pmid27853622,
year = {2016},
author = {Rutz, C and Sugasawa, S and van der Wal, JE and Klump, BC and St Clair, JJ},
title = {Tool bending in New Caledonian crows.},
journal = {Royal Society open science},
volume = {3},
number = {8},
pages = {160439},
pmid = {27853622},
issn = {2054-5703},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {'Betty' the New Caledonian crow astonished the world when she 'spontaneously' bent straight pieces of garden wire into hooked foraging tools. Recent field experiments have revealed that tool bending is part of the species' natural behavioural repertoire, providing important context for interpreting Betty's iconic wire-bending feat. More generally, this discovery provides a compelling illustration of how natural history observations can inform laboratory-based research into the cognitive capacities of non-human animals.},
}

@article {pmid27639565,
year = {2016},
author = {van Horik, JO and Emery, NJ},
title = {Transfer of physical understanding in a non-tool-using parrot.},
journal = {Animal cognition},
volume = {19},
number = {6},
pages = {1195-1203},
pmid = {27639565},
issn = {1435-9456},
mesh = {Animals ; Cognition ; *Comprehension ; Cues ; *Parrots ; Passeriformes ; },
abstract = {Physical cognition has generally been assessed in tool-using species that possess a relatively large brain size, such as corvids and apes. Parrots, like corvids and apes, also have large relative brain sizes, yet although parrots rarely use tools in the wild, growing evidence suggests comparable performances on physical cognition tasks. It is, however, unclear whether success on such tasks is facilitated by previous experience and training procedures. We therefore investigated physical comprehension of object relationships in two non-tool-using species of captive neotropical parrots on a new means-end paradigm, the Trap-Gaps task, using unfamiliar materials and modified training procedures that precluded procedural cues. Red-shouldered macaws (Diopsittaca nobilis) and black-headed caiques (Pionites melanocephala) were presented with an initial task that required them to discriminate between pulling food trays through gaps while attending to the respective width of the gaps and size of the trays. Subjects were then presented with a novel, but functionally equivalent, transfer task. Six of eight birds solved the initial task through trial-and-error learning. Four of these six birds solved the transfer task, with one caique demonstrating spontaneous comprehension. These findings suggest that non-tool-using parrots may possess capacities for sophisticated physical cognition by generalising previously learned rules across novel problems.},
}

Animals
Cognition
*Comprehension
Cues
*Parrots
Passeriformes

@article {pmid27629645,
year = {2016},
author = {Rutz, C and Klump, BC and Komarczyk, L and Leighton, R and Kramer, J and Wischnewski, S and Sugasawa, S and Morrissey, MB and James, R and St Clair, JJ and Switzer, RA and Masuda, BM},
title = {Discovery of species-wide tool use in the Hawaiian crow.},
journal = {Nature},
volume = {537},
number = {7620},
pages = {403-407},
pmid = {27629645},
issn = {1476-4687},
mesh = {Aging ; Animals ; Animals, Zoo/physiology ; Biological Evolution ; Cognition ; Crows/classification/*physiology ; Female ; Hawaii ; Male ; Phylogeny ; Species Specificity ; *Tool Use Behavior ; },
abstract = {Only a handful of bird species are known to use foraging tools in the wild. Amongst them, the New Caledonian crow (Corvus moneduloides) stands out with its sophisticated tool-making skills. Despite considerable speculation, the evolutionary origins of this species' remarkable tool behaviour remain largely unknown, not least because no naturally tool-using congeners have yet been identified that would enable informative comparisons. Here we show that another tropical corvid, the 'Alalā (C. hawaiiensis; Hawaiian crow), is a highly dexterous tool user. Although the 'Alalā became extinct in the wild in the early 2000s, and currently survives only in captivity, at least two lines of evidence suggest that tool use is part of the species' natural behavioural repertoire: juveniles develop functional tool use without training, or social input from adults; and proficient tool use is a species-wide capacity. 'Alalā and New Caledonian crows evolved in similar environments on remote tropical islands, yet are only distantly related, suggesting that their technical abilities arose convergently. This supports the idea that avian foraging tool use is facilitated by ecological conditions typical of islands, such as reduced competition for embedded prey and low predation risk. Our discovery creates exciting opportunities for comparative research on multiple tool-using and non-tool-using corvid species. Such work will in turn pave the way for replicated cross-taxonomic comparisons with the primate lineage, enabling valuable insights into the evolutionary origins of tool-using behaviour.},
}

Aging
Animals
Animals, Zoo/physiology
Biological Evolution
Cognition
Crows/classification/*physiology
Female
Hawaii
Male
Phylogeny
Species Specificity
*Tool Use Behavior

@article {pmid27437926,
year = {2016},
author = {Jacobs, IF and von Bayern, A and Osvath, M},
title = {A novel tool-use mode in animals: New Caledonian crows insert tools to transport objects.},
journal = {Animal cognition},
volume = {19},
number = {6},
pages = {1249-1252},
pmid = {27437926},
issn = {1435-9456},
mesh = {Animals ; *Crows ; *Tool Use Behavior ; },
abstract = {New Caledonian crows (Corvus moneduloides) rely heavily on a range of tools to extract prey. They manufacture novel tools, save tools for later use, and have morphological features that facilitate tool use. We report six observations, in two individuals, of a novel tool-use mode not previously reported in non-human animals. Insert-and-transport tool use involves inserting a stick into an object and then moving away, thereby transporting both object and tool. All transported objects were non-food objects. One subject used a stick to transport an object that was too large to be handled by beak, which suggests the tool facilitated object control. The function in the other cases is unclear but seems to be an expression of play or exploration. Further studies should investigate whether it is adaptive in the wild and to what extent crows can flexibly apply the behaviour in experimental settings when purposive transportation of objects is advantageous.},
}

Animals
*Crows
*Tool Use Behavior

@article {pmid26955788,
year = {2016},
author = {Matsui, H and Hunt, GR and Oberhofer, K and Ogihara, N and McGowan, KJ and Mithraratne, K and Yamasaki, T and Gray, RD and Izawa, E},
title = {Adaptive bill morphology for enhanced tool manipulation in New Caledonian crows.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {22776},
pmid = {26955788},
issn = {2045-2322},
mesh = {Animals ; Beak/*anatomy & histology ; *Behavior, Animal ; Biological Evolution ; Crows/*anatomy & histology/*physiology ; Principal Component Analysis ; Tomography, X-Ray Computed ; *Tool Use Behavior ; },
abstract = {Early increased sophistication of human tools is thought to be underpinned by adaptive morphology for efficient tool manipulation. Such adaptive specialisation is unknown in nonhuman primates but may have evolved in the New Caledonian crow, which has sophisticated tool manufacture. The straightness of its bill, for example, may be adaptive for enhanced visually-directed use of tools. Here, we examine in detail the shape and internal structure of the New Caledonian crow's bill using Principal Components Analysis and Computed Tomography within a comparative framework. We found that the bill has a combination of interrelated shape and structural features unique within Corvus, and possibly birds generally. The upper mandible is relatively deep and short with a straight cutting edge, and the lower mandible is strengthened and upturned. These novel combined attributes would be functional for (i) counteracting the unique loading patterns acting on the bill when manipulating tools, (ii) a strong precision grip to hold tools securely, and (iii) enhanced visually-guided tool use. Our findings indicate that the New Caledonian crow's innovative bill has been adapted for tool manipulation to at least some degree. Early increased sophistication of tools may require the co-evolution of morphology that provides improved manipulatory skills.},
}

Animals
Beak/*anatomy & histology
*Behavior, Animal
Biological Evolution
Crows/*anatomy & histology/*physiology
Principal Component Analysis
Tomography, X-Ray Computed
*Tool Use Behavior

@article {pmid26793670,
year = {2015},
author = {Habibzadeh, A and Pourabdol, S and Saravani, S},
title = {The effect of emotion regulation training in decreasing emotion failures and self-injurious behaviors among students suffering from specific learning disorder (SLD).},
journal = {Medical journal of the Islamic Republic of Iran},
volume = {29},
number = {},
pages = {279},
pmid = {26793670},
issn = {1016-1430},
abstract = {BACKGROUND: A great deal of attention has been given to the study of learning disorders. Hence, the aim of this research was to study the effect of emotion regulation training in decreasing emotion failures and self-injurious behaviors among students suffering from specific learning disorder.

METHODS: This was an experimental study with the pre-test, post-test and a control group. Research population included all 5th grade male students suffering from specific learning disorder (case study: 5th grade students in Ardabil in 2015). Research sample included 40 male students suffering from specific learning disorder (SLD) who were selected through multi-step cluster sampling and classified into two groups: Experimental group (n= 20) and control group (n= 20). The following tools were used for data collection: Kay Math mathematic Test, Raven Intelligence Test, Reading Test of Shafiei et al, Falahchay Writing Expression, Emotion Failures Scale, Self-Injurious Behavior Questionnaire and Diagnostic Interview based on DSM-5. Data were analyzed by multivariate of variance analysis (MANOVA) model in the SPSS software version 22.

RESULTS: The results of MANOVA revealed that emotion regulation training was effective in decreasing emotion failures in all parameters (difficulty in describing feelings, difficulty in identifying feelings, and externally oriented thinking style) and self-injurious behaviors in students suffering from specific learning disorder (p< 0.001).

CONCLUSION: In this study, it was found that since emotion regulation training can have a remarkable effect on reducing negative emotions and increasing the positive ones; this treatment can play an eminent role in decreasing emotion failures and self-injurious behaviors in such students.},
}

@article {pmid26701755,
year = {2015},
author = {Troscianko, J and Rutz, C},
title = {Activity profiles and hook-tool use of New Caledonian crows recorded by bird-borne video cameras.},
journal = {Biology letters},
volume = {11},
number = {12},
pages = {20150777},
pmid = {26701755},
issn = {1744-957X},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G023913/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Acacia ; Animals ; *Appetitive Behavior ; Crows/*physiology ; Feeding Behavior ; Melaleuca ; New Caledonia ; *Tool Use Behavior ; Video Recording ; },
abstract = {New Caledonian crows are renowned for their unusually sophisticated tool behaviour. Despite decades of fieldwork, however, very little is known about how they make and use their foraging tools in the wild, which is largely owing to the difficulties in observing these shy forest birds. To obtain first estimates of activity budgets, as well as close-up observations of tool-assisted foraging, we equipped 19 wild crows with self-developed miniature video cameras, yielding more than 10 h of analysable video footage for 10 subjects. While only four crows used tools during recording sessions, they did so extensively: across all 10 birds, we conservatively estimate that tool-related behaviour occurred in 3% of total observation time, and accounted for 19% of all foraging behaviour. Our video-loggers provided first footage of crows manufacturing, and using, one of their most complex tool types--hooked stick tools--under completely natural foraging conditions. We recorded manufacture from live branches of paperbark (Melaleuca sp.) and another tree species (thought to be Acacia spirorbis), and deployment of tools in a range of contexts, including on the forest floor. Taken together, our video recordings reveal an 'expanded' foraging niche for hooked stick tools, and highlight more generally how crows routinely switch between tool- and bill-assisted foraging.},
}

Acacia
Animals
*Appetitive Behavior
Crows/*physiology
Feeding Behavior
Melaleuca
New Caledonia
*Tool Use Behavior
Video Recording

@article {pmid26683184,
year = {2015},
author = {Malik, A and Mallajosyula, VV and Mishra, NN and Varadarajan, R and Gupta, SK},
title = {Generation and Characterization of Monoclonal Antibodies Specific to Avian Influenza H5N1 Hemagglutinin Protein.},
journal = {Monoclonal antibodies in immunodiagnosis and immunotherapy},
volume = {34},
number = {6},
pages = {436-441},
doi = {10.1089/mab.2015.0047},
pmid = {26683184},
issn = {2167-9436},
mesh = {Animals ; Antibodies, Monoclonal/*biosynthesis ; Antibodies, Viral/*biosynthesis ; Antibody Specificity ; Ascites/immunology ; Cross Reactions ; Female ; Hemagglutination Inhibition Tests ; Hemagglutinin Glycoproteins, Influenza Virus/administration & dosage/*analysis/genetics/immunology ; Humans ; Influenza A Virus, H1N1 Subtype/chemistry/immunology ; Influenza A Virus, H3N2 Subtype/chemistry/immunology ; Influenza A Virus, H5N1 Subtype/chemistry/*immunology ; Influenza A Virus, H7N9 Subtype/chemistry/immunology ; Kinetics ; Mice ; Mice, Inbred BALB C ; Protein Binding ; Recombinant Proteins/administration & dosage/analysis/genetics/immunology ; },
abstract = {Highly pathogenic avian influenza (HPAI) H5N1 virus has in the past breached the species barrier from infected domestic poultry to humans in close contact. Although human-to-human transmission has previously not been reported, HPAI H5N1 virus has pandemic potential owing to gain of function mutation(s) and/or genetic reassortment with human influenza A viruses. Monoclonal antibodies (MAbs) have been used for diagnosis as well as specific therapeutic candidates in several disease conditions including viral infections in humans. In this study, we describe the preliminary characterization of four murine MAbs developed against recombinant hemagglutinin (rHA) protein of avian H5N1 A/turkey/Turkey/1/2005 virus that are either highly specific or broadly reactive against HA from other H5N1 subtype viruses, such as A/Hong Kong/213/03, A/Common magpie/Hong Kong/2256/2006, and A/Barheaded goose/Quinghai/14/2008. The antibody binding is specific to H5N1 HAs, as none of the antibodies bound H1N1, H2N2, H3N2, or B/Brisbane/60/2008 HAs. Out of the four MAbs, one of them (MA-7) also reacted weakly with the rHA protein of H7N9 A/Anhui/1/2013. All four MAbs bound H5 HA (A/turkey/Turkey/1/2005) with high affinity with an equilibrium dissociation constant (KD) ranging between 0.05 and 10.30 nM. One of the MAbs (MA-1) also showed hemagglutination inhibition activity (HI titer; 31.25 μg/mL) against the homologous A/turkey/Turkey/1/2005 H5N1 virus. These antibodies may be useful in developing diagnostic tools for detection of influenza H5N1 virus infection.},
}

Animals
Antibodies, Monoclonal/*biosynthesis
Antibodies, Viral/*biosynthesis
Antibody Specificity
Ascites/immunology
Cross Reactions
Female
Hemagglutination Inhibition Tests
Hemagglutinin Glycoproteins, Influenza Virus/administration & dosage/*analysis/genetics/immunology
Humans
Influenza A Virus, H1N1 Subtype/chemistry/immunology
Influenza A Virus, H3N2 Subtype/chemistry/immunology
Influenza A Virus, H5N1 Subtype/chemistry/*immunology
Influenza A Virus, H7N9 Subtype/chemistry/immunology
Kinetics
Mice
Mice, Inbred BALB C
Protein Binding
Recombinant Proteins/administration & dosage/analysis/genetics/immunology

@article {pmid26582537,
year = {2015},
author = {Klump, BC and Sugasawa, S and St Clair, JJ and Rutz, C},
title = {Hook tool manufacture in New Caledonian crows: behavioural variation and the influence of raw materials.},
journal = {BMC biology},
volume = {13},
number = {},
pages = {97},
pmid = {26582537},
issn = {1741-7007},
support = {BB/G023913/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biological Evolution ; Crows/*physiology ; New Caledonia ; *Tool Use Behavior ; },
abstract = {BACKGROUND: New Caledonian crows use a range of foraging tools, and are the only non-human species known to craft hooks. Based on a small number of observations, their manufacture of hooked stick tools has previously been described as a complex, multi-stage process. Tool behaviour is shaped by genetic predispositions, individual and social learning, and/or ecological influences, but disentangling the relative contributions of these factors remains a major research challenge. The properties of raw materials are an obvious, but largely overlooked, source of variation in tool-manufacture behaviour. We conducted experiments with wild-caught New Caledonian crows, to assess variation in their hooked stick tool making, and to investigate how raw-material properties affect the manufacture process.

RESULTS: In Experiment 1, we showed that New Caledonian crows' manufacture of hooked stick tools can be much more variable than previously thought (85 tools by 18 subjects), and can involve two newly-discovered behaviours: 'pulling' for detaching stems and bending of the tool shaft. Crows' tool manufactures varied significantly: in the number of different action types employed; in the time spent processing the hook and bending the tool shaft; and in the structure of processing sequences. In Experiment 2, we examined the interaction of crows with raw materials of different properties, using a novel paradigm that enabled us to determine subjects' rank-ordered preferences (42 tools by 7 subjects). Plant properties influenced: the order in which crows selected stems; whether a hooked tool was manufactured; the time required to release a basic tool; and, possibly, the release technique, the number of behavioural actions, and aspects of processing behaviour. Results from Experiment 2 suggested that at least part of the natural behavioural variation observed in Experiment 1 is due to the effect of raw-material properties.

CONCLUSIONS: Our discovery of novel manufacture behaviours indicates a plausible scenario for the evolutionary origins, and gradual refinement, of New Caledonian crows' hooked stick tool making. Furthermore, our experimental demonstration of a link between raw-material properties and aspects of tool manufacture provides an alternative hypothesis for explaining regional differences in tool behaviours observed in New Caledonian crows, and some primate species.},
}

Animals
Biological Evolution
Crows/*physiology
New Caledonia
*Tool Use Behavior

@article {pmid26529116,
year = {2015},
author = {St Clair, JJH and Burns, ZT and Bettaney, EM and Morrissey, MB and Otis, B and Ryder, TB and Fleischer, RC and James, R and Rutz, C},
title = {Experimental resource pulses influence social-network dynamics and the potential for information flow in tool-using crows.},
journal = {Nature communications},
volume = {6},
number = {},
pages = {7197},
pmid = {26529116},
issn = {2041-1723},
support = {BB/G023913/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G023913/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Computer Simulation ; *Crows ; Environment ; *Information Dissemination ; *Social Behavior ; *Social Learning ; *Tool Use Behavior ; },
abstract = {Social-network dynamics have profound consequences for biological processes such as information flow, but are notoriously difficult to measure in the wild. We used novel transceiver technology to chart association patterns across 19 days in a wild population of the New Caledonian crow--a tool-using species that may socially learn, and culturally accumulate, tool-related information. To examine the causes and consequences of changing network topology, we manipulated the environmental availability of the crows' preferred tool-extracted prey, and simulated, in silico, the diffusion of information across field-recorded time-ordered networks. Here we show that network structure responds quickly to environmental change and that novel information can potentially spread rapidly within multi-family communities, especially when tool-use opportunities are plentiful. At the same time, we report surprisingly limited social contact between neighbouring crow communities. Such scale dependence in information-flow dynamics is likely to influence the evolution and maintenance of material cultures.},
}

Animals
Computer Simulation
*Crows
Environment
*Information Dissemination
*Social Behavior
*Social Learning
*Tool Use Behavior

@article {pmid26342705,
year = {2016},
author = {Saakian, DB and Hu, CK},
title = {Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics.},
journal = {Current topics in microbiology and immunology},
volume = {392},
number = {},
pages = {121-139},
doi = {10.1007/82_2015_471},
pmid = {26342705},
issn = {0070-217X},
mesh = {*Evolution, Molecular ; Models, Genetic ; *Models, Theoretical ; Mutation ; },
abstract = {We formulate the Crow-Kimura, discrete-time Eigen model, and continuous-time Eigen model. These models are interrelated and we established an exact mapping between them. We consider the evolutionary dynamics for the single-peak fitness and symmetric smooth fitness. We applied the quantum mechanical methods to find the exact dynamics of the evolution model with a single-peak fitness. For the smooth symmetric fitness landscape, we map exactly the evolution equations into Hamilton-Jacobi equation (HJE). We apply the method to the Crow-Kimura (parallel) and Eigen models. We get simple formulas to calculate the dynamics of the maximum of distribution and the variance. We review the existing mathematical tools of quasi-species theory.},
}

*Evolution, Molecular
Models, Genetic
*Models, Theoretical
Mutation

@article {pmid26308874,
year = {2014},
author = {Taylor, AH and Gray, RD},
title = {Is there a link between the crafting of tools and the evolution of cognition?.},
journal = {Wiley interdisciplinary reviews. Cognitive science},
volume = {5},
number = {6},
pages = {693-703},
doi = {10.1002/wcs.1322},
pmid = {26308874},
issn = {1939-5086},
abstract = {UNLABELLED: The ability to craft tools is one of the defining features of our species. The technical intelligence hypothesis predicts that tool-making species should have enhanced physical cognition. Here we review how the physical problem-solving performance of tool-making apes and corvids compares to closely related species. We conclude that, while some performance differences have been found, overall the evidence is at best equivocal. We argue that increased sample sizes, novel experimental designs, and a signature-testing approach are required to determine the effect tool crafting has on the evolution of intelligence. WIREs Cogn Sci 2014, 5:693-703. doi: 10.1002/wcs.1322 For further resources related to this article, please visit the WIREs website.

CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article.},
}

@article {pmid26301340,
year = {2015},
author = {Schmelz, M and Krüger, O and Call, J and Krause, ET},
title = {A comparison of spontaneous problem-solving abilities in three estrildid finch (Taeniopygia guttata, Lonchura striata var. domestica, Stagonopleura guttata) species.},
journal = {Journal of comparative psychology (Washington, D.C. : 1983)},
volume = {129},
number = {4},
pages = {356-365},
doi = {10.1037/a0039646},
pmid = {26301340},
issn = {1939-2087},
mesh = {Animals ; Behavior, Animal/*physiology ; Female ; Finches/*physiology ; Male ; Problem Solving/*physiology ; },
abstract = {Cognition has been extensively studied in primates while other, more distantly related taxa have been neglected for a long time. More recently, there has been an increased interest in avian cognition, with the focus mostly on big-brained species like parrots and corvids. However, the majority of bird species has never systematically been studied in diverse cognitive tasks other than memory and learning tasks, so not much can yet be concluded about the relevant factors for the evolution of cognition. Here we examined 3 species of the estrildid finch family in problem-solving tasks. These granivorous, non-tool-using birds are distributed across 3 continents and are not known for high levels of innovation or spontaneous problem solving in the wild. In this study, our aim was to find such abilities in these species, assess what role domestication might play with a comparison of 4 genetically separated zebra finch strains, and to look for between-species differences between zebra finches, Bengalese finches, and diamond firetails. Furthermore, we established a 3-step spontaneous problem-solving procedure with increasing levels of complexity. Results showed that some estrildid finches were generally capable of spontaneously solving problems of variable complexity to obtain food. We found striking differences in these abilities between species, but not between strains within species, and offer a discussion of potential reasons. Our established methodology can now be applied to a larger number of bird species for phylogenetic comparisons on the behavioral level to get a deeper understanding of the evolution of cognitive abilities.},
}

Animals
Behavior, Animal/*physiology
Female
Finches/*physiology
Male
Problem Solving/*physiology

@article {pmid26276368,
year = {2016},
author = {Logan, CJ and Breen, AJ and Taylor, AH and Gray, RD and Hoppitt, WJ},
title = {How New Caledonian crows solve novel foraging problems and what it means for cumulative culture.},
journal = {Learning & behavior},
volume = {44},
number = {1},
pages = {18-28},
pmid = {26276368},
issn = {1543-4508},
support = {BB/I007997/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Communication ; *Crows ; *Learning ; *Social Behavior ; Tool Use Behavior ; },
abstract = {New Caledonian crows make and use tools, and tool types vary over geographic landscapes. Social learning may explain the variation in tool design, but it is unknown to what degree social learning accounts for the maintenance of these designs. Indeed, little is known about the mechanisms these crows use to obtain information from others, despite the question's importance in understanding whether tool behavior is transmitted via social, genetic, or environmental means. For social transmission to account for tool-type variation, copying must utilize a mechanism that is action specific (e.g., pushing left vs. right) as well as context specific (e.g., pushing a particular object vs. any object). To determine whether crows can copy a demonstrator's actions as well as the contexts in which they occur, we conducted a diffusion experiment using a novel foraging task. We used a nontool task to eliminate any confounds introduced by individual differences in their prior tool experience. Two groups had demonstrators (trained in isolation on different options of a four-option task, including a two-action option) and one group did not. We found that crows socially learn about context: After observers see a demonstrator interact with the task, they are more likely to interact with the same parts of the task. In contrast, observers did not copy the demonstrator's specific actions. Our results suggest it is unlikely that observing tool-making behavior transmits tool types. We suggest it is possible that tool types are transmitted when crows copy the physical form of the tools they encounter.},
}

Animals
*Communication
*Crows
*Learning
*Social Behavior
Tool Use Behavior

@article {pmid26266937,
year = {2015},
author = {Jelbert, SA and Singh, PJ and Gray, RD and Taylor, AH},
title = {New Caledonian crows rapidly solve a collaborative problem without cooperative cognition.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0133253},
pmid = {26266937},
issn = {1932-6203},
mesh = {Animals ; Biological Evolution ; Cognition/physiology ; *Cooperative Behavior ; Crows/*physiology ; Problem Solving/*physiology ; Tool Use Behavior/*physiology ; },
abstract = {There is growing comparative evidence that the cognitive bases of cooperation are not unique to humans. However, the selective pressures that lead to the evolution of these mechanisms remain unclear. Here we show that while tool-making New Caledonian crows can produce collaborative behavior, they do not understand the causality of cooperation nor show sensitivity to inequity. Instead, the collaborative behavior produced appears to have been underpinned by the transfer of prior experience. These results suggest that a number of possible selective pressures, including tool manufacture and mobbing behaviours, have not led to the evolution of cooperative cognition in this species. They show that causal cognition can evolve in a domain specific manner-understanding the properties and flexible uses of physical tools does not necessarily enable animals to grasp that a conspecific can be used as a social tool.},
}

Animals
Biological Evolution
Cognition/physiology
*Cooperative Behavior
Crows/*physiology
Problem Solving/*physiology
Tool Use Behavior/*physiology

@article {pmid26246543,
year = {2015},
author = {Taylor, AH and Cheke, LG and Waismeyer, A and Meltzoff, A and Miller, R and Gopnik, A and Clayton, NS and Gray, RD},
title = {No conclusive evidence that corvids can create novel causal interventions.},
journal = {Proceedings. Biological sciences},
volume = {282},
number = {1813},
pages = {20150796},
pmid = {26246543},
issn = {1471-2954},
mesh = {Animals ; *Biological Evolution ; *Cognition ; Crows/*physiology ; Female ; Humans ; *Learning ; Male ; *Tool Use Behavior ; },
}

Animals
*Biological Evolution
*Cognition
Crows/*physiology
Female
Humans
*Learning
Male
*Tool Use Behavior

@article {pmid25994674,
year = {2015},
author = {Klump, BC and van der Wal, JE and St Clair, JJ and Rutz, C},
title = {Context-dependent 'safekeeping' of foraging tools in New Caledonian crows.},
journal = {Proceedings. Biological sciences},
volume = {282},
number = {1808},
pages = {20150278},
pmid = {25994674},
issn = {1471-2954},
support = {BB/G023913/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Biological Evolution ; Crows/*physiology ; *Feeding Behavior ; Female ; Male ; *Tool Use Behavior ; },
abstract = {Several animal species use tools for foraging, such as sticks to extract embedded arthropods and honey, or stones to crack open nuts and eggs. While providing access to nutritious foods, these behaviours may incur significant costs, such as the time and energy spent searching for, manufacturing and transporting tools. These costs can be reduced by re-using tools, keeping them safe when not needed. We experimentally investigated what New Caledonian crows do with their tools between successive prey extractions, and whether they express tool 'safekeeping' behaviours more often when the costs (foraging at height), or likelihood (handling of demanding prey), of tool loss are high. Birds generally took care of their tools (84% of 176 prey extractions, nine subjects), either trapping them underfoot (74%) or storing them in holes (26%)--behaviours we also observed in the wild (19 cases, four subjects). Moreover, tool-handling behaviour was context-dependent, with subjects: keeping their tools safe significantly more often when foraging at height; and storing tools significantly more often in holes when extracting more demanding prey (under these conditions, foot-trapping proved challenging). In arboreal environments, safekeeping can prevent costly tool losses, removing a potentially important constraint on the evolution of habitual and complex tool behaviour.},
}

Animals
Biological Evolution
Crows/*physiology
*Feeding Behavior
Female
Male
*Tool Use Behavior

@article {pmid25984564,
year = {2014},
author = {Auersperg, AM and Oswald, N and Domanegg, M and Gajdon, GK and Bugnyar, T},
title = {Unrewarded Object Combinations in Captive Parrots.},
journal = {Animal behavior and cognition},
volume = {1},
number = {4},
pages = {470-488},
pmid = {25984564},
issn = {2372-5052},
support = {J 3404/FWF_/Austrian Science Fund FWF/Austria ; Y 366/FWF_/Austrian Science Fund FWF/Austria ; },
abstract = {In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea.},
}

@article {pmid25982732,
year = {2015},
author = {Zhu, Y and Sun, L and Garbarino, A and Schmidt, C and Fang, J and Chen, J},
title = {PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways.},
journal = {BMC bioinformatics},
volume = {16},
number = {1},
pages = {165},
pmid = {25982732},
issn = {1471-2105},
mesh = {Computer Graphics ; Computer Simulation ; *Gene Expression ; Genomics/*methods ; Humans ; *Internet ; *Metabolic Networks and Pathways ; Proteins/metabolism ; Proteomics/*methods ; Signal Transduction ; *Software ; Species Specificity ; },
abstract = {BACKGROUND: High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses. Since humans can interpret visual information rapidly, a means for interactive visual exploration that lets biologists interpret such data in a comprehensive and exploratory manner would be invaluable. However, humans have limited memory capacity. Current visualization tools have limited viewing and manipulation capabilities to address complex data analysis problems, and visual exploratory tools are needed to reduce the high mental workload imposed on biologists.

RESULTS: We present PathRings, a new interactive web-based, scalable biological pathway visualization tool for biologists to explore and interpret biological pathways. PathRings integrates metabolic and signaling pathways from Reactome in a single compound graph visualization, and uses color to highlight genes and pathways affected by input data. Pathways are available for multiple species and analysis of user-defined species or input is also possible. PathRings permits an overview of the impact of gene expression data on all pathways to facilitate visual pattern finding. Detailed pathways information can be opened in new visualizations while maintaining the overview, that form a visual exploration provenance. A dynamic multi-view bubbles interface is designed to support biologists' analytical tasks by letting users construct incremental views that further reflect biologists' analytical process. This approach decomposes complex tasks into simpler ones and automates multi-view management.

CONCLUSIONS: PathRings has been designed to accommodate interactive visual analysis of experimental data in the context of pathways defined by Reactome. Our new approach to interface design can effectively support comparative tasks over substantially larger collection than existing tools. The dynamic interaction among multi-view dataset visualization improves the data exploration. PathRings is available free at http://raven.anr.udel.edu/~sunliang/PathRings and the source code is hosted on Github: https://github.com/ivcl/PathRings .},
}

Computer Graphics
Computer Simulation
*Gene Expression
Genomics/*methods
Humans
*Internet
*Metabolic Networks and Pathways
Proteins/metabolism
Proteomics/*methods
Signal Transduction
*Software
Species Specificity