cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.02v6wwq4p
title: Niche differentiation within a cryptic pathogen complex: climatic drivers and hyperparasitism at multiple spatial scales

description: Pathogens are embedded in multi-trophic food webs, which often include
 co-occurring cryptic species within the same pathogen complex.
 Nonetheless, we still lack an understanding of what dimensions of the
 ecological niche might allow these cryptic species to coexist. We explored
 the role of climate, host characteristics (tree autumn phenology) and
 attack by the fungal hyperparasite Ampelomyces (a group of fungi attacking
 plant pathogens) in defining the niches of three powdery mildew species
 (Erysiphe alphitoides, E. hypophylla and E. quercicola) within a cryptic
 pathogen complex on the pedunculate oak Quercus robur at the continental
 (Europe), national (Sweden and France) and landscape scales (a 5 km2
 island in southwestern Finland). Previous studies have shown that climate
 separated the niches of three powdery mildew species (E. alphitoides, E.
 hypophylla and E. quercicola) in Europe and two species (E.
 alphitoides and E. quercicola) in France. In our study, we did
 not detect a significant relationship between temperature or precipitation
 and the distribution of E. alphitoides and E. hypophylla present in
 Sweden, while at the landscape scale, temperature, but not relative
 humidity, negatively affected disease incidence of E. alphitoides in an
 exceptionally warm year. Tree variation in autumn phenology did not
 influence disease incidence of powdery mildew species, and hyperparasite
 presence did not differ among powdery mildew species at the continental,
 national and landscape scale. Climate did not affect the distribution of
 the hyperparasite at the continental scale and at the national scale in
 Sweden. However, climate affected the hyperparasite distribution in
 France, with a negative relationship between non-growing season
 temperature and presence of the hyperparasite. Overall, our findings, in
 combination with earlier evidence, suggest that climatic factors are more
 important than species interactions in defining the niches of cryptic
 species within a pathogen complex on oak.
DOI: 10.5061/dryad.kkwh70s62
title: Temporomandibular joints disorders TMDs prevalence and its relation to anxiety in dental students

description: Introduction: Temporomandibular disorders TMDs are very common disorders
 affecting the population and causing pain. Researches have reported a high
 prevalence of TMDs among university students due to increased distress.
 Aim: To determine the frequency of TMDs in Umm al-Qura University UQU
 dental students using Diagnostic Criteria for Temporomandibular Disorders
 (DC/TMD). Also, to examine the relationship between anxiety, bruxism, and
 TMDs among those students. Methods: RDC / TMD pain screener questionnaire
 was completed by dental students. Students who reported TMD pain or had at
 least one positive TMD symptom were invited to the dental clinic for a
 full TMJ evaluation. History of bruxism was documented and an ultra-brief
 tool for detecting anxiety and depression (Patient Health Questionnaire-4
 PHQ) was completed by all students. Results: A total of 240 students
 responded to the TMJ pain screener in which 119 reported at least one TMJ
 symptom. Only 93 dental students presented to clinical examination in
 which 64.5% (n=60) of them had temporomandibular joint disorders. Disc
 displacement with reduction and local myalgia (38.7 % & 32.25%
 respectively) were the most frequent diagnosis. A total of 29%(n=27) of
 students had more than one diagnosis. Forty-one participants (44.09 %)
 reported a positive response to the anxiety scale and (n=38) 40% of
 participants reported parafunctional habit. Both the history of bruxism
 and anxiety were significantly related to TMDs (P=0.0002) and also
 significantly higher in females of higher academic years(P ≤0.01).
 Conclusion: High prevalence of TMDs among UQU dental students. Disc
 displacement with reduction was the most prevalent disorder. Bruxism and
 anxiety were associated with painful TMDs
description: Data were collected through paper quetionnair and through
 interview and clinical exam of the participants. all collcted data were
 entered in an Excel sheet.The data analysis was performed
 using Statistical Package for the Social Sciences (SPSS, Version 22, and
 SPSS Inc., Chicago, IL, USA), student T-test and chi-square analysis were
 used to relate the existence of TMD problem to age, gender, academic year,
 history of bruxism and anxiety level. Also, to compare the anxiety scores
 among male and female groups. Statistical significance was set
 at <em>P </em>≤
 0.05.
DOI: 10.5061/dryad.c866t1g88
title: Data from: Creation of photocyclic vertebrate rhodopsin by single amino acid substitution

description: Opsins are universal photoreceptive proteins in animals and can be
 classified into three types based on their photoreaction properties. Upon
 light irradiation, vertebrate rhodopsin forms a metastable active state,
 which cannot revert back to the original dark state via either
 photoreaction or thermal reaction. By contrast, after photoreception, most
 opsins form a stable active state which can photo-convert back to the dark
 state. Moreover, we recently found a novel type of opsins whose activity
 is regulated by photocycling. However, the molecular mechanism underlying
 this diversification of opsins remains unknown. In this study, we showed
 that vertebrate rhodopsin acquired the photocyclic and photoreversible
 properties upon introduction of a single mutation at position 188. This
 revealed that the residue at position 188 contributes to the
 diversification of photoreaction properties of opsins by its regulation of
 the recovery from the active state to the original dark state.
DOI: 10.5061/dryad.fxpnvx0t9
title: Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks

description: In the past two decades genomic data have been widely used to detect
 historical gene flow between species in a variety of plants and animals.
 The Tamias quadrivittatus group of North America chipmunks, which
 originated through a series of rapid speciation events, are known to
 undergo massive amounts of mitochondrial introgression. Yet in a recent
 analysis of targeted nuclear loci from the group, no evidence for
 cross-species introgression was detected, indicating widespread
 cytonuclear discordance. The study used the heuristic method HyDe to
 detect gene flow, which may suffer from low power. Here we use the
 Bayesian method implemented in the program bpp to reanalyze these data. We
 develop a Bayesian test of introgression, calculating the Bayes factor via
 the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC)
 sample under the model of introgression. We take a stepwise approach to
 constructing an introgression model by adding introgression events onto a
 well-supported binary species tree. The analysis detected robust evidence
 for multiple ancient introgression events affecting the nuclear genome,
 with introgression probabilities reaching 63%. We estimate population
 parameters and highlight the fact that species divergence times may be
 seriously underestimated if ancient cross-species gene flow is ignored in
 the analysis. We examine the assumptions and performance of HyDe, and
 demonstrate that it lacks power if gene flow occurs between sister
 lineages or if the mode of gene flow does not match the assumed hybrid
 speciation model with symmetrical population sizes. Our analyses highlight
 the power of likelihood-based inference of cross-species gene flow using
 genomic sequence data.
description: Please see the accompanying published article: 
 Ji J, Jackson DJ, Leache AD, Yang Z. (2023) Power of Bayesian and
 heuristic tests to detect cross-species introgression with reference to
 gene flow in the Tamias quadrivittatus group of North American chipmunks.
 Systematic Biology 72:446-465.
  https://doi.org/10.1093/sysbio/syac077
description: The files are plain text files.  They are used to run the BPP
 program, which is available at  https://github.com/bpp/
DOI: 10.5061/dryad.j0zpc86g3
title: Longitudinal trends of EHR concepts in pediatric patients

description: The longitudinal nature of the data motivated temporal trend
 identification in the pediatric EHR datatypes. Over the past
 three decades (1980-2018), we identified and quantified the temporal trend
 of 16,460 EHR concepts across measurement, visit, diagnosis,
 drug, and procedure datatypes. 
description: See the Methods of the associated JAMIA Open
 manuscript.  We defined trends for clinical concepts
 per EHR datatype per year across participants. We first calculated a
 standardized z-score (x-mu)/sd, where x was the percent of a concept or
 the number of participants with a recorded concept within a year and for a
 datatype out of the total number of concepts for that datatype, mu was the
 average percent across concepts for a year, and sd was the sample standard
 deviation of the percent across concepts. We then calculated a linear
 model to estimate the association of concept z-scores across time. We
 quantified the slope and R squared coefficient between the z-score and a
 year, across all years where EHR data was provided. This generated a beta
 coefficient for each year representing a trend in clinical concepts,
 relative to other EHR concepts, recorded in participant’s EHRs.
 Significant trends were defined as the linear model beta coefficient
 greater than 0, beta coefficient confidence interval not containing the
 null association, and R squared coefficient between the date and z scores
 greater than 0.8. We performed summarization, visualization, and
 statistical analyses using R packages
 including tidyverse and data.table and Python3 libraries Numpy,
 Matplotlib, Pandas, Sklearn, and Seaborn.
description: Field : Description datatype : The
 OMOP-defined EHR domain. concept_id : The OMOP-defined
 concept identifier.  concept_name : The OMOP-defined
 concept name. lwr: The 95% lower bound of the odds
 ratio quantified by the linear model. odds: The odds
 ratio of the EHR concept z-score across three decades (year units)
 quantified by the linear model. upr: The 95% upper
 bound of the odds ratio quantified by the linear model.
DOI: 10.5061/dryad.x0k6djhm1
title: Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences

description: The data presented here are those used in the paper : CAYUELA H., JACOB
 S., SCHTICKZELLE N., VERDONCK R., PHILIPPE H., LAPORTE M., HUET M.,
 BERNATCHEZ L., LEGRAND D. Transgenerational plasticity of
 dispersal-related traits in a ciliate: genotype-dependency and fitness
 consequences. Oikos. DOI: 10.1111/oik.08846 Phenotypic plasticity, the
 ability of one genotype to produce different phenotypes in different
 environments, plays a central role in species’ response to environmental
 changes. Transgenerational plasticity (TGP) allows the transmission of
 this environmentally-induced phenotypic variation across generations, and
 can influence adaptation. To date, the genetic control of TGP, its
 long-term stability, and its potential costs remain largely unknown,
 mostly because empirical demonstrations of TGP across many generations in
 several genetic backgrounds are scarce. In the paper of Cayuela et al., we
 examined how genotype determines the TGP of phenotypic traits related to
 dispersal, a fundamental process in ecology and evolution. We used an
 experimental approach in Tetrahymena thermophila, a ciliate model-species,
 to determine if and how phenotypic changes expressed following a dispersal
 treatment are inherited over multiple generations. The data include
 morphological and movement traits, dispersal rates, and cell growth data
 measured before and after dispersal trials. We considered different
 genotypes and different populations within each genotype.
description: The txt files are attached. The files "IGP" are those
 used in the analyses on intra-generational plasticity of fitness and
 phenotypic traits before ("pre-trial") and after
 ("post-trial") the dispersal. The files
 "Reversibility" correspond to reversibility analyses (fitness
 and phenotypic traits) for cells with dispersing and non-dispersing
 ancestors. The files "TGP" are those used for
 transgenerational plasticity analyses (fitness and phenotypic
 traits).
DOI: 10.5061/dryad.9kd51c5jj
title: Cold winters have morph-specific effects on natal dispersal distance in a wild raptor

description: Dispersal is a key process with crucial implications in spatial
 distribution, density and genetic structure of species’ populations.
 Dispersal strategies can vary according to both individual and
 environmental features, but putative phenotype-by-environment interactions
 have rarely been accounted for. Melanin-based color polymorphism is a
 phenotypic trait associated with specific behavioral and physiological
 profiles and is therefore a good candidate trait to study dispersal
 tactics in different environments. Here, using a 40 years dataset of a
 population of color polymorphic tawny owls (Strix aluco), we investigated
 natal dispersal distance of recruiting gray and pheomelanic reddish-brown
 (hereafter brown) color morphs in relation to post-fledging winter
 temperature and individual characteristics. Since morphs are differently
 sensitive to cold winters, we predicted that morphs’ natal dispersal
 distances vary according to winter conditions. Winter temperature did not
 affect the proportion of brown (or gray) among recruits. We found that
 dispersal distances correlate with winter temperature in an opposite
 manner in the two morphs. While the gray morph undertakes larger movements
 in harsher conditions, likely because it copes better with winter
 severity, the brown morph disperses shorter distances when winters are
 harsher. We discuss this morph-specific natal dispersal pattern in a
 context of competition for territories between morphs and in terms of
 costs and benefits of these alternative strategies. Our results stress the
 importance of considering the interaction between phenotype and
 environment to fully disentangle dispersal movement patterns and provide
 further evidence that climate affects behavior and local distribution of
 this species.
DOI: 10.5061/dryad.bzkh189b6
title: Data from: Psychedelic mushrooms in the USA: knowledge, patterns of use, and association with health outcomes

description: This was a cross-sectional nationwide survey of adults in the US in 2021.
 The survey targeted a representative sample of US adults. The rate of
 psychedelic us, comorbid conditions, mental and physical health, and
 factors predictive of psychedlic use were assessed.
description: Data was collected through an on-line cross-sectional survey of
 adults (18 years or older) in the US. The survey was conducted in
 accordance with Acumen Health Research Institute's (AHRI) established
 SOPs. A random stratified sampling framework ensured a community-based
 sample with a demographic composition representative of the US adult
 population by region, gender, age, and race, according to the US Census
 (US Census American Community Survey 5-year estimate, 2011-2015). To
 participate in the study, respondents were required to be 18 years old or
 older, reside in the United States, and confirm their voluntarily
 agreement to participate (participants were informed they could leave the
 survey at any time). The survey was open to the general population.
 Participants were recruited through AHRI’s online research panels.
 Analysis was carried out with SPSS v27.0.1.0.
description: See ReadMe file (code book).
DOI: 10.5061/dryad.c2fqz619g
title: The dynamics of social cohesion in response to simulated intergroup conflict in banded mongooses

description: Intergroup conflict is widespread in nature and is proposed to have strong
 impacts on the evolution of social behaviour. The conflict-cohesion
 hypothesis predicts that exposure to intergroup conflict should lead to
 increased social cohesion to improve group success or resilience in future
 conflicts. There is evidence to support this prediction from studies of
 affiliative responses to outgroup threats in some animal societies.
 However, most of these studies have focused on behavioural changes over
 short time periods (minutes and hours after exposure to an outgroup), and
 hence very little is known about the dynamics and durability of responses
 to intergroup conflict over the longer term. We investigated this question
 by simulating intergroup encounters in wild banded mongooses (Mungos
 mungo) and measuring social behaviour before, during, and after these
 encounters over a five day period. We also ran control trials with
 non-threatening stimuli. Banded mongooses reacted immediately to intrusion
 stimuli by vocalising, grouping together and advancing on the stimulus. In
 the first five minutes after simulated intrusions, we saw an elevation in
 grooming levels, but in the hour after exposure grooming rates declined
 sharply, contrary to our expectation. In the two subsequent days grooming
 rates remained at this depressed rate. In control trials, the initial
 increase in grooming was not seen, but grooming declined compared in the
 longer term time periods. Grooming changed across time, but not in the
 same pattern as during intrusions, suggesting that intrusions had an
 impact above and beyond that of the experimental set-up. The dynamics of
 grooming responses were short-lived and more complex than we initially
 expected. We suggest this unexpected result may be linked to the frequency
 of aggressive intergroup encounters in this system. Our results indicate
 short-lived impacts of outgroup threat on measures of social cohesion in
 this species, but cannot confirm longer term changes.
description: See methods section of the associated paper for details of the
 experimental methods, and data processing for analysis.
DOI: 10.5061/dryad.j0zpc86g4
title: Engagement with indigenous people preserves local knowledge and biodiversity alike

description: Recent events have brought increasing attention to social inequities in
 the sciences, including those stemming from the legacy of colonialism. In
 biological classification, Western scientists have long benefitted from
 traditional indigenous knowledge but have usually not engaged with it on
 equal footing, often providing a biased assessment of biodiversity. We
 illustrate how adopting a collaborative approach results in a better, more
 complete understanding of biodiversity that promotes conservation of both
 the environment and indigenous knowledge. This study concerns the Bornean
 fruit tree species, Artocarpus odoratissimus, which has remained a single
 species in Western diagnosis but corresponds to two species in the
 traditional taxonomy of the Iban people. Molecular data from newly
 collected and historical specimens unequivocally support the Iban
 two-species framework. We advocate a more expansive approach to
 standardized scientific taxonomy that welcomes indigenous peoples as equal
 partners and that integrates diverse forms of taxonomic knowledge,
 ultimately resulting in improved understanding of evolutionary history and
 more effective conservation and management of biodiversity.
description: Illumina sequencing or target genes SSR
 fragment-length analysis
DOI: 10.5061/dryad.cz8w9gj4t
title: Insect herbivory for Catula gettyi, a late Cretaceous laurel from Utah, USA

description: The Upper Cretaceous (Campanian Stage) Kaiparowits Formation of southern
 Utah, USA, preserves abundant plant, invertebrate, and vertebrate fossil
 taxa. Taken together, these fossils indicate that the ecosystems preserved
 in the Kaiparowits Formation were characterized by high biodiversity.
 Hundreds of vertebrate and invertebrate species and over 80 plant
 morphotypes are recognized from the formation, but insects and their
 associations with plants are largely undocumented. Here, we describe a new
 fossil leaf taxon, Catula gettyi gen et. sp. nov. in the family Lauraceae
 from the Kaiparowits Formation. Catula gettyi occurs at numerous
 localities in this deposit that represent ponded and distal floodplain
 environments. The type locality for C. gettyi has yielded 1,564 fossil
 leaf specimens of this species, which provides the opportunity to
 circumscribe this new plant species. By erecting this new genus and
 species, we are able to describe ecological associations on C. gettyi and
 place these interactions within a taxonomic context. We describe an
 extensive archive of feeding damage on C. gettyi caused by herbivorous
 insects, including more than 800 occurrences of insect damage belonging to
 five functional feeding groups indicating that insect-mediated damage on
 this taxon is both rich and abundant. Catula gettyi is one of the
 best-sampled host plant taxa from the Mesozoic Era, a poorly sampled time
 interval, and its insect damage is comparable to other Lauraceae taxa from
 the younger Late Cretaceous Hell Creek Flora of North Dakota, USA.
description: Collection made with standard paleobotanical bench quarry
 techniques. Only specimens of <em>Catula gettyi </em>and Hell
 Creek laurels were included in these datasets.
DOI: 10.5061/dryad.g1jwstqs9
title: Data from: Intrapopulation differences in polar bear movement and step selection patterns

description: Background: The spatial ecology of individuals often varies within a
 population or species. Identifying how individuals in different classes
 interact with their environment can lead to a better understanding of
 population responses to human activities and environmental change and
 improve population estimates. Most inferences about polar bear (Ursus
 maritimus) spatial ecology are based on data from adult females due to
 morphological constraints on applying satellite radio collars to other
 classes of bears. Recent studies, however, have provided limited movement
 data for adult males and sub-adults of both sexes using ear-mounted and
 glue-on tags. We evaluated class-specific movements and step selection
 patterns for polar bears in the Chukchi Sea subpopulation during spring.
 Methods: We developed hierarchical Bayesian models to evaluate polar bear
 movement (i.e., step length and directional persistence) and step
 selection at the scale of 4-day step lengths. We assessed differences in
 movement and step selection parameters among the three classes of polar
 bears (i.e., adult males, sub-adults, and adult females without
 cubs-of-the-year). Results: Adult males had larger step lengths and less
 directed movements than adult females. Sub-adult movement parameters did
 not differ from the other classes but point estimates were most similar to
 adult females. We did not detect differences among polar bear classes in
 step selection parameters and parameter estimates were consistent with
 previous studies. Conclusions: Our findings support the use of estimated
 step selection patterns from adult females as a proxy for other classes of
 polar bears during spring. Conversely, movement analyses indicated that
 using data from adult females as a proxy for the movements of adult males
 is likely inappropriate. We recommend that researchers consider whether it
 is valid to extend inference derived from adult female movements to other
 classes, based on the questions being asked and the spatial and temporal
 scope of the data. Because our data were specific to spring, these
 findings highlight the need to evaluate differences in movement and step
 selection during other periods of the year, for which data from
 ear-mounted and glue-on tags are currently lacking.