cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.19603
title: Data from: Consumer-resource interactions and the evolution of migration

description: Theoretical studies have demonstrated that selection will favor increased
 migration when fitnesses vary both temporally and spatially, but it is far
 from clear how pervasive those theoretical conditions are in nature. While
 consumer-resource interactions are omnipresent in nature and can generate
 spatial and temporal variation, it is unknown even in theory whether these
 dynamics favor the evolution of migration. We develop a mathematical model
 to address whether and how migration evolves when variability in fitness
 is determined at least in part by consumer-resource coevolutionary
 interactions. Our analyses show that such interactions can drive the
 evolution of migration in the resource, consumer, or both species and thus
 supplies a general explanation for the pervasiveness of migration. Over
 short time scales, we show the direction of change in migration rate is
 determined primarily by the state of local adaptation of the species
 involved: rates increase when a species is locally maladapted and decrease
 when locally adapted. Our results reveal that long-term evolutionary
 trends in migration rates can differ dramatically depending on the
 strength or weakness of interspecific interactions and suggest an
 explanation for the evolutionary divergence of migration rates among
 interacting species.
description: Coevolution and
 Migration code and dataMATLAB code used to
 numerically iterate the full recursions in the main paper. Raw data for
 each of the five figures in the main paper. Each figure has its own
 file.Drown_etal_Coevolution_Migration_Code_and_Data.zip
DOI: 10.5061/dryad.k5sj288
title: Data from: Spatial distribution, movements, and geographic range of Steller sea lions (Eumetopias jubatus) in Alaska

description: The two stocks of Steller sea lions (Eumetopias jubatus) in Alaska include
 an endangered western stock, recently recovering in parts of its range
 following decades of decline, and an eastern stock which was removed from
 the U.S. Endangered Species List in 2013 following increasing numbers
 since the 1970s. Information on overlapping distributions of eastern and
 western sea lions is needed for management considerations. We analyzed
 &gt;30,000 sightings collected from 2000-2014 of 2,385 sea lions that
 were branded as pups at 10 Alaskan rookeries to examine mesoscale (mostly
 &lt;500km) spatial distribution, geographic range, and geographic
 population structure based on natal rookery, sex, and age during breeding
 and non-breeding seasons. Analyses of summary movement measures (e.g.,
 natal rookery, sex, and age-class differences in spatial distribution and
 geographic range) indicate wide variation in rookery-specific movement
 patterns. Correlations between movement measures and population dynamics
 suggested movement patterns could be a function of density dependence.
 Animals from larger rookeries, and rookeries with slower population growth
 and lower survival, had wider dispersion than animals from smaller
 rookeries, or rookeries with high growth and survival. Sea lions from the
 largest rookery, Forrester Island, where survival and population trends
 are lowest, were the most widely distributed. Analysis of geographic
 population structure indicated that animals born in the eastern Aleutian
 Islands had the most distinct movements and had little overlap with other
 western sea lions. Northern Southeast Alaska, within the eastern stock, is
 the area of greatest overlap between stocks, and is important to western
 animals, especially those born in Prince William Sound. Detailed knowledge
 of distribution and movements of western sea lions is useful for defining
 recovery and population trend analysis regions that better reflect
 dispersion and population structure and provides valuable information to
 managers as critical habitat is re-evaluated and the location of the stock
 boundary reconsidered.
description: SSL
 dist_mvmt_range
DOI: 10.5061/dryad.p0t0b
title: Data from: Cytonuclear discordance among the Southeast Asian Black rats (Rattus rattus complex)

description: Black rats are major invasive vertebrate pests with severe ecological,
 economic and health impacts. Remarkably, their evolutionary history has
 received little attention, and there is no firm agreement on how many
 species should be recognized within the black rat complex. This species
 complex is native to India and Southeast Asia. According to current
 taxonomic classification, there are three taxa living in sympatry in
 several parts of Thailand, Cambodia and Lao People's Democratic
 Republic, where this study was conducted: two accepted species (Rattus
 tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of
 unclear taxonomic status referred to here as ‘Rattus R3’. We used
 extensive sampling, morphological data and diverse genetic markers
 differing in rates of evolution and parental inheritance (two
 mitochondrial DNA genes, one nuclear gene and eight microsatellite loci)
 to assess the reproductive isolation of these three taxa. Two close Asian
 relatives, Rattus argentiventer and Rattus exulans, were also included in
 the genetic analyses. Genetic analyses revealed discordance between the
 mitochondrial and nuclear data. Mitochondrial phylogeny studies identified
 three reciprocally monophyletic clades in the black rat complex. However,
 studies of the phylogeny of the nuclear exon interphotoreceptor
 retinoid-binding protein gene and clustering and assignation analyses with
 eight microsatellites failed to separate R. tanezumi and R3. Morphometric
 analyses were consistent with nuclear data. The incongruence between
 mitochondrial and nuclear (and morphological) data rendered R. tanezumi/R3
 paraphyletic for mitochondrial lineages with respect to R. sakeratensis.
 Various evolutionary processes, such as shared ancestral polymorphism and
 incomplete lineage sorting or hybridization with massive mitochondrial
 introgression between species, may account for this unusual genetic
 pattern in mammals.
description: IRBP-Pages-2012Fasta alignment of IRBP sequences used in Pages et al., 2012Mito-Pages-2012Fasta alignment of mitochondrial data used in Pages et al., 2012Microsat-Pages-2012Microsatellite data used in Pages et al., 2012Morphological dataWe assessed the morphological differences between 328 adult specimens from the R3 and R. tanezumi mt lineages. Five linear measurements were considered: head + body length, tail length, hind-foot length, ear length and head length. All measurements were made with a ruler (precision 1 mm), with the exception of head length, which was measured with a caliper (precision 0.1 mm). Specimens were sexed and classified as adults on the basis of both complete development of the mandibular row of teeth and sexual maturity (full development of seminal vesicles and vulva opening, for males (M) and females (F), respectively)Morphological-Data.xls
DOI: 10.5281/zenodo.18353473
title: Rapid Personalized Computational Modeling of the Wrist - Data

description: Project Description

This work was performed at Mayo Clinic in Rochester, MN, USA.

It is part of a bigger project to use four-dimensional computed tomography data to develop and calibrate computational models of the human hand and wrist for recreating joint dynamics, with the ultimate goal being to improve the diagnosis and treatment of soft-tissue injuries of the hand and wrist. The work is funded by several NIH grants, as well as internal funding from Mayo Clinic. The project includes a data collected from a previous study on in vivo healthy controls collected with previous IRB approval (NCT03193996) using a combination of static computed tomography (3DCT) and dynamic computed tomography (4DCT = 3DCT + time). In this case, a subset of three asymptomatic individuals from that dataset were used. A novel computational workflow was used that combined non-linear morphing algorithms based on generalized regression neural networks (GRNNs) with algorithmic techniques to automatically create computational finite element models of each individuals native geometries. This workflow was applied to the three asymptomatic participants to develop models with personalized wrist bone geometries and material properties. Each model was then used with an optimization routine as well as a Monte Carlo (MC) analysis to demonstrate the utility of these models towards developing Digital Twins and for in silico clinical trials.

In total the work has provided the raw geometries and kinematics for the three participants, the calibrated computational model for Participant 2, and the working MATLAB code to develop new personalized models from the original bony geometries. This work is shared with IRB approval (25-012254).

This repository contains all of the raw data including the geometries and the kinematics for the three participants. The full set of deliverables are including in the following links:

Data: https://doi.org/10.5281/zenodo.18166548

Model: https://doi.org/10.5281/zenodo.18166610

Software/Code: https://doi.org/10.5281/zenodo.18166628

Licensing

This work is provided under a Creative Commons Attribution 4.0 International. You are free to use the work for your own purposes; however, we ask that you cite the work that made it possible:

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Development of Efficient Participant-Specific Computational Models of the Wrist", arXiv, 25 May 2025, DOI: 10.48550/arXiv.2505.19282

and

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Personalized Computational Modeling of the Wrist - Data", Zenodo, 14 January 2026, DOI: 10.5281/zenodo.18166548

File Structure

All files are organized within folders and name accordingly. For descriptions of the files and folder, please download the README.txt file to see the details.
DOI: 10.5281/zenodo.18166548
title: Rapid Personalized Computational Modeling of the Wrist - Data

description: Project Description

This work was performed at Mayo Clinic in Rochester, MN, USA.

It is part of a bigger project to use four-dimensional computed tomography data to develop and calibrate computational models of the human hand and wrist for recreating joint dynamics, with the ultimate goal being to improve the diagnosis and treatment of soft-tissue injuries of the hand and wrist. The work is funded by several NIH grants, as well as internal funding from Mayo Clinic. The project includes a data collected from a previous study on in vivo healthy controls collected with previous IRB approval (NCT03193996) using a combination of static computed tomography (3DCT) and dynamic computed tomography (4DCT = 3DCT + time). In this case, a subset of three asymptomatic individuals from that dataset were used. A novel computational workflow was used that combined non-linear morphing algorithms based on generalized regression neural networks (GRNNs) with algorithmic techniques to automatically create computational finite element models of each individuals native geometries. This workflow was applied to the three asymptomatic participants to develop models with personalized wrist bone geometries and material properties. Each model was then used with an optimization routine as well as a Monte Carlo (MC) analysis to demonstrate the utility of these models towards developing Digital Twins and for in silico clinical trials.

In total the work has provided the raw geometries and kinematics for the three participants, the calibrated computational model for Participant 2, and the working MATLAB code to develop new personalized models from the original bony geometries. This work is shared with IRB approval (25-012254).

This repository contains all of the raw data including the geometries and the kinematics for the three participants. The full set of deliverables are including in the following links:

Data: https://doi.org/10.5281/zenodo.18166548

Model: https://doi.org/10.5281/zenodo.18166610

Software/Code: https://doi.org/10.5281/zenodo.18166628

Licensing

This work is provided under a Creative Commons Attribution 4.0 International. You are free to use the work for your own purposes; however, we ask that you cite the work that made it possible:

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Development of Efficient Participant-Specific Computational Models of the Wrist", arXiv, 25 May 2025, DOI: 10.48550/arXiv.2505.19282

and

Thor E. Andreassen, Taylor P. Trentadue, Andrew R. Thoreson, Kai-Nan An, Sanjeev Kakar, Kristin D. Zhao, "Rapid Personalized Computational Modeling of the Wrist - Data", Zenodo, 14 January 2026, DOI: 10.5281/zenodo.18166548

File Structure

All files are organized within folders and name accordingly. For descriptions of the files and folder, please download the README.txt file to see the details.
DOI: 10.5061/dryad.m010p
title: Data from: Simple versus complex models of trait evolution and stasis as a response to environmental change

description: Previous analyses of evolutionary patterns, or modes, in fossil lineages
 have focused overwhelmingly on three simple models: stasis, random walks,
 and directional evolution. Here we use likelihood methods to fit an
 expanded set of evolutionary models to a large compilation of
 ancestor–descendant series of populations from the fossil record. In
 addition to the standard three models, we assess more complex models with
 punctuations and shifts from one evolutionary mode to another. As in
 previous studies, we find that stasis is common in the fossil record, as
 is a strict version of stasis that entails no real evolutionary changes.
 Incidence of directional evolution is relatively low (13%), but higher
 than in previous studies because our analytical approach can more
 sensitively detect noisy trends. Complex evolutionary models are often
 favored, overwhelmingly so for sequences comprising many samples. This
 finding is consistent with evolutionary dynamics that are, in reality,
 more complex than any of the models we consider. Furthermore, the timing
 of shifts in evolutionary dynamics varies among traits measured from the
 same series. Finally, we use our empirical collection of evolutionary
 sequences and a long and highly resolved proxy for global climate to
 inform simulations in which traits adaptively track temperature changes
 over time. When realistically calibrated, we find that this simple model
 can reproduce important aspects of our paleontological results. We
 conclude that observed paleontological patterns, including the prevalence
 of stasis, need not be inconsistent with adaptive evolution, even in the
 face of unstable physical environments.
description: paleoTS files - zip
 archiveThis zip archive holds
 771 plain text files in paleoTS format. Each stores the raw data for a
 trait time-series, with columns for trait sample sizes, trait means, trait
 variances, and sample ages.paleoTS
 files.zippaleoTS data - RData
 formatSame data as
 'paleoTS files.zip', but all combined into a single file
 readable by R. Double-clinking this file will open R and make available in
 the R Workspace an object called 'tsList' which is a list of the
 771 time-series (paleoTS) objects.paleoTS
 files.RDatapaleoTS summary - XLSX
 formatExcel spreadsheet with
 auxiliary data for these files, including the number of samples,
 environmental context, and taxonomic group of the fossils. Includes also
 reference information for the published papers from which these data were
 drawn.paleoTS
 summary.xlsxpaleoTS summary - CSV
 formatSame as paleoTS
 'summary.xlsx' but in Comma-separated-value
 format.paleoTS
 summary.csvpaleoTS
 referencesSame as information in
 second worksheet of "paleoTS summary.xlsx", here separated out
 as CSV format.
DOI: 10.5061/dryad.9bg43
title: Data from: Women’s preference for masculine traits is disrupted by images of male-on-female aggression

description: Women’s preferences for men’s masculinized faces and voices were assessed
 after women (n = 331) were primed with images of male-on-male aggression,
 male-on-female aggression, pathogens, and neutral scenes. Male-on-male
 aggression and pathogen primes were associated with increased preference
 for masculine traits, but the same effect emerged in the neutral
 condition. We show the increased preference for masculine traits was due
 to repeated exposure to these traits, not the priming images themselves.
 Images of male-on-female aggression were an exception; these elicited
 feelings of disgust and anger appeared to disrupt the preference for
 masculinized traits. The results suggest women process men’s facial and
 vocal traits as signals of aggressive potential and lose any preference
 for these traits with cues indicating men might direct this aggression
 toward them.  
description: Li et al. PLoS ONE Raw
 DataRaw data for two main
 studies, and supplementary masculinity discrimination and working memory
 studies
DOI: 10.5061/dryad.1m004jc
title: Data from: Risk factors for respiratory illness in a community of wild chimpanzees (Pan troglodytes schweinfurthii)

description: Respiratory disease has caused significant mortality in African great ape
 populations. While much effort has been given to identifying the
 responsible pathogens, little is known about the factors that influence
 disease transmission or individual susceptibility. In the Kanyawara
 community of wild chimpanzees, respiratory illness has been the leading
 cause of mortality over 30 years, contributing to 27% of deaths. Deaths
 were common in all age groups except juveniles. Over 22 years of health
 observations, respiratory signs were rare among infants and most common
 among older adults of both sexes. Signs were also common among males
 during the transition to adulthood (ages 10-20 years), particularly among
 those of low rank. Respiratory signs peaked conspicuously in March, a
 pattern that we could not explain after modeling climatic factors, group
 sizes, diet, or exposure to humans. Furthermore, rates of respiratory
 illness in the chimpanzees did not track seasonal rates of disease in the
 nearby village. Our data indicate that the epidemiology of chimpanzee
 respiratory illness warrants more investigation but clearly differs in
 important ways between humans and chimpanzees. Findings on individual
 susceptibility patterns suggest that respiratory signs are a robust
 indicator for investigating immunocompetence in wild chimpanzees.
description: Kanyawara Respiratory
 Data PublicDatasheet with monthly
 risk factors for respiratory signs in wild chimpanzees.
DOI: 10.7910/dvn/ff66rn
title: Distorted Political Behavior under Sectarian Party Systems: Misaligned Dissent, Participation, and Silence in Post-conflict Iraq

description: Distorted Political Behavior under Sectarian Party Systems: Misaligned Dissent, Participation, and Silence in Post-conflict Ira
DOI: 10.5061/dryad.ns8v4
title: Data from: Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants

description: Ecologists increasingly rely on molecular delimitation methods (MMs) to
 identify species boundaries, thereby potentially increasing the number of
 putative species because of the presence of morphologically cryptic
 species. It has been argued that cryptic species could challenge our
 understanding of what determine large-scale biodiversity patterns which
 have traditionally been documented from morphology alone. Here, we used
 morphology and three MMs to derive four different sets of putative species
 among the European groundwater crustaceans. Then, we used regression
 models to compare the relative importance of spatial heterogeneity,
 productivity and historical climates, in shaping species richness and
 range size patterns across sets of putative species. We tested three
 predictions. First, MMs would yield many more putative species than
 morphology because groundwater is a constraining environment allowing
 little morphological changes. Second, for species richness, MMs would
 increase the importance of spatial heterogeneity because cryptic species
 are more likely along physical barriers separating ecologically similar
 regions than along resource gradients promoting ecologically-based
 divergent selection. Third, for range size, MMs would increase the
 importance of historical climates because of reduced and asymmetrical
 fragmentation of large morphological species ranges at northern latitudes.
 MMs yielded twice more putative species than morphology and decreased by
 10-fold the average species range size. Yet, MMs strengthened the
 mid-latitude ridge of high species richness and the Rapoport effect of
 increasing range size at higher latitudes. Species richness predictors did
 not vary between morphology and MMs but the latter increased the
 proportion of variance in range size explained by historical climates.
 These findings demonstrate that our knowledge of groundwater biodiversity
 determinants is robust to overlooked cryptic species because the latter
 are homogeneously distributed along environmental gradients. Yet, our
 findings call for incorporating multiple species delimitation methods into
 the analysis of large-scale biodiversity patterns across a range of taxa
 and ecosystems.
description: Appendix1COI data set.DataAlignments and COI phylogenetic trees for the Niphargidae and Aselloidea.
DOI: 10.5281/zenodo.18381313
title: Pneumonia and antibiotic use in a northern Pakistani village

description: Data describing the use of antibiotics to treat cases of pneumonia in children in Oshikhandass, a village in northern Pakistan
DOI: 10.5061/dryad.d1f0d
title: Data from: A global perspective on the trophic geography of sharks

description: Sharks are a diverse group of mobile predators that forage across varied
 spatial scales and have the potential to influence food web dynamics. The
 ecological consequences of recent declines in shark biomass may extend
 across broader geographic ranges if shark taxa display common behavioural
 traits. By tracking the original site of photosynthetic fixation of carbon
 atoms that were ultimately assimilated into muscle tissues of 5,394 sharks
 from 114 species, we identify globally consistent biogeographic traits in
 trophic interactions between sharks found in different habitats. We show
 that populations of shelf-dwelling sharks derive a substantial proportion
 of their carbon from regional pelagic sources, but contain individuals
 that forage within additional isotopically diverse local food webs, such
 as those supported by terrestrial plant sources, benthic production and
 macrophytes. In contrast, oceanic sharks seem to use carbon derived from
 between 30° and 50° of latitude. Global-scale compilations of stable
 isotope data combined with biogeochemical modelling generate hypotheses
 regarding animal behaviours that can be tested with other methodological
 approaches.
description: Bird_etal_shark_trophic_geographyCarbon isotope data compiled from muscle tissues of 5394 sharks from 114 species. Data provided include d13C values, latitude of capture, designation as shelf, slope or oceanic shark, length, depth of capture (where available), C/N ratios of muscle, and lipid extraction method if used. Also included are phytoplankton d13C data modelled from Magozzi et al 2016 (Ecosphere 8(5):e01763. 10.1002/ecs2.1763). Model data expressed as the median and standard deviation d13C value for the Longhurst Biogeographic province corresponding to the location of shark capture