cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1c59zw3v9
title: Adaptations to light contribute to the ecological niches and evolution of the terrestrial avifauna

description: The role of light in structuring the ecological niche remains a frontier
 in understanding how vertebrate communities assemble and respond to global
 change. For birds eyes represent the primary external anatomical structure
 specifically evolved to interpret light, yet eye morphology remains
 understudied compared to movement and dietary traits. Here, I use Stanley
 Ritland’s unpublished measurements of transverse eye diameter from
 preserved specimens to explore the ecological and phylogenetic drivers of
 eye morphology for a third of terrestrial avian diversity (N = 2777
 species). Species with larger eyes specialized in darker understory and
 forested habitats, foraging manoeuvres and prey items requiring
 long-distance optical resolution, and were more likely to occur in
 tropical latitudes. When compared to dietary and movement traits eye size
 was a top predictor for habitat, foraging manoeuvre, diet, and latitude,
 adding 9 – 29% more explanatory power. Eye size was phylogenetically
 conserved (lambda = 0.90), with phylogeny explaining 61% of eye size
 variation. I suggest that light has contributed to the evolution and
 assembly of global vertebrate communities and that eye size provides a
 useful predictor to assess community response to global change.
description: The novel contribution of this dataset is the matrix of eye size
 measurements for 2804 species of terrestrial birds extracted from Stanley
 Ritland's unpublished dissertation (Ritland 1982, University of
 Chicago). SR collected all measurements from specimens of whole eyes
 preserved in formaldehyde and/or alcohol using 0.05 mm Vernier callipers.
 The attached dataset includes the original raw measurements collected by
 SR (per specimen) as well as species-specific averages and residuals
 correcting for body size allometry (using phylogenetic least squares
 regression) for two dimensions of eye size: transverse diameter (TD) and
 axial diameter (AD). The raw data matrix also includes measurements for
 cornea diameter. Please see the associated publication for details on
 species and analysis. The remaining databases are
 composed of subsets from previously published datasets on avian
 ecomorphology, dispersal correlates, and foraging traits (Wilman et al.
 2014, Pigot et al. 2020, Sheard et al. 2020). The classification of
 habitat (forest specialist v. non-forest) is based on Bird Life
 International habitat classifications. Please see the associated
 publication for details. The R scripts allow full
 reconstruction of the analyses described in the associated
 publication. Please see the 'Read Me.doc'
 file for further explanations of all files.
DOI: 10.5061/dryad.mpg4f4qzv
title: Thermal ecology and baseline energetic requirements of a large-bodied ectotherm suggest resilience to climate change

description: Most studies on how rising temperatures will impact terrestrial ectotherms
 have focused on single populations or multiple sympatric species.
 Addressing the thermal and energetic implications of climatic variation on
 multiple allopatric populations of a species will help us better elucidate
 how a species may be impacted by altered climates. We used eight years of
 thermal and behavioral data collected from four populations of Pacific
 rattlesnakes (Crotalus oreganus) living in climatically distinct habitat
 types (inland and coastal) to determine the field-active and lab-preferred
 body temperatures, thermoregulatory metrics, and maintenance energetic
 requirements of snakes from each population. Physical models showed that
 thermal quality was best at coastal sites, but inland snakes
 thermoregulated more accurately despite being in more thermally
 constrained environments. Projected increases of 1 and 2 ºC in ambient
 temperature result in an increase in overall thermal quality at both
 coastal and inland sites. Population differences in modeled standard
 metabolic rate estimates were driven by body size and not field-active
 body temperature, with inland snakes requiring 1.6x more food annually
 than coastal snakes. All snakes thermoregulated with high accuracy,
 suggesting that small increases in ambient temperature are unlikely to
 impact the maintenance energetic requirements of individual snakes and
 that some species of large-bodied reptiles may be robust to modest thermal
 perturbations under conservative climate change predictions.
description: Physical model data and snake field active body temperature data
 were collected via Thermochron iButtons.  Snake preferred body temperature
 data was collection via cloacal thermocouple and data logger. 
 These data are the individual iButton files that have been
 trimmed to exclude temperatures that were collected outside of the
 deployment and field active periods (i.e. when snakes or models were being
 transported to and from study sites) and combined into 3 spreadsheets: 1
 for Physical Model temperatures, 1 for Field Active Snake Body
 Temperatures, and 1 for snake body temperatures from the thermal
 gradient/preferred body temperature trials. There is also an additional
 spreadsheet with snake morphometric data and the additional snake-related
 variables that were included in statistical models.
description: See Thermal_MS_README.txt file.
DOI: 10.5061/dryad.69p8cz920
title: Contributions of wild and provisioned foods to the diets of domestic cats that depredate wild animals

description: Predation of wildlife by domestic cats Felis catus presents a threat to
 biodiversity conservation in some ecological contexts. The proportions of
 wild prey captured and eaten by domestic cats and thus the contributions
 of wild prey to cat diets are hard to quantify. This limits understanding
 of any impacts of cats may have on wild animal populations and confounds
 analyses of the effects of interventions aimed at reducing wildlife
 killing. We used stable isotope analyses to quantify the relative
 contributions of wild and provisioned foods to the diets of domestic cats
 kept as companion animals and which frequently captured wild prey. We
 tested the effects of treatments aimed at reducing killing upon stable
 isotope ratios of cat whiskers and, where treatments had significant
 effects, we estimated variation in the contributions of wild prey to cats’
 diets before and during treatment. We evaluated bells, Birdsbesafe collar
 covers, provision of food in a ‘puzzle feeder’, provision of food in which
 meat was the principal source of protein, object play and a control group.
 As expected, cat diets consisted primarily of provisioned foods, though
 the contribution of wild animals to the diets of these cats, all of which
 regularly caught wild animals, was low (cat food ~96%, wild animals
 ~3–4%). Compared to the pre-treatment period and control group, cats with
 a Birdsbesafe collar cover, exhibited significant reduction in nitrogen
 stable isotope ratios in their whiskers and consumed less wild prey, most
 likely attributable to effective inhibition of hunting, particularly for
 birds. Fitting cats with a Birdsbesafe collar cover, therefore, reduced
 both returns of wild birds and consumption of wild prey. While multiple
 interventions can significantly affect the numbers of wild animals that
 cats capture and return home, the remarkably small dietary contributions
 made by wild animal prey mean dietary change is harder to discern.
 Domestic cats rely almost exclusively on food provided by people even when
 they frequently kill wild animals. This suggests that the hunting behavior
 of domestic cats may be driven by behavioral motivations, or by a need to
 address micronutrient requirements, but is unlikely to alter macronutrient
 intake.
description: Stable isotope analysis of samples from domestic cats and their
 potential food items, comprising wild animals and provisioned pet
 foods.
description: See ReadMe.txt file
DOI: 10.5061/dryad.v41ns1rw4
title: Data from: Concerted morphogenesis of genital ridges and nephric ducts in the mouse captured through whole embryo imaging

description: During development of the mouse urogenital complex, the gonads undergo
 changes in three-dimensional structure, body position, and spatial
 relationship with the mesonephric ducts, kidneys, and adrenals. The
 complexity of genital ridge development obscures potential connections
 between morphogenesis and gonadal sex determination. To characterize the
 morphogenic processes implicated in regulating gonad shape and fate, we
 used whole embryo tissue clearing and light sheet microscopy to assemble a
 time course of gonad development in native form and context. Analysis
 revealed that gonad morphology is determined through anterior-to-posterior
 patterns as well as increased rates of growth, rotation, and separation in
 the central domain that may contribute to regionalization of the gonad. We
 report a close alignment of gonad and mesonephric duct movements and
 delayed duct development in a gonad dysgenesis mutant, which together
 support a mechanical dependency linking gonad and mesonephric duct
 morphogenesis.
description: 3D renderings of whole SF1:eGFP mouse embryos. Samples are
 labelled with antibodies against GFP (green) and PAX8 (red) and cleared
 using iDISCO tissue clearing. Imaris and Imaris viewer software (Bitplane)
 can be used to view .ims files. Further details for
 each sample can be found in the README.txt file.
DOI: 10.5061/dryad.gmsbcc2n6
title: Eco-friendly fluorimetric approaches for the simultaneous estimation of the co-administered ternary mixture: etoposide, moxifloxacin, and nalbuphine

description: Antineoplastic drugs as etoposide (ETO) are widely utilized in leukemia
 cancer. Patient with leukemia cancer has a relative infection with
 pneumonia treated by fluoroquinolones as moxifloxacin HCL (MOX). Because
 opioid analgesic as nalbuphine HCL (NAL) does not have a ceiling dose, it
 is used to manage the distasteful sensory in leukemia cancer. Green
 chemistry advances innovative design to keep a healthy environment.
 Consequently, innovatory green processes for synchronous
 spectrofluorimetric quantification of a ternary mixture of antineoplastic,
 fluoroquinolone, and opioid analgesic drugs. The present study provides
 two eco-friendly synchronous fluorimetric processes (conventional and
 first derivative), conventional for MOX and the first derivative for ETO
 and NAL quantification. Conventional synchronous fluorimetric of MOX was
 monitored at 371 nm, while the first derivative synchronous fluorimetric
 of ETO and NAL was measured at 257 and 273 nm, respectively, in ethanol.
 The synchronous fluorescence was scanned at  λ of 60 nm for both
 processes. Environmentally friendly solvent as ethanol has a major role in
 the sensitivity, reproducibility, and quantitation of innovative
 processes. The outcomes of these designed environmentally friendly
 processes, a linear correlation was described in the ranges of 0.04-0.40,
 0.1-1.0, and 0.5-5.0 g/mL for MOX, ETO, and NAL, respectively.
 Accordingly, several pharmaceutical dosages were achieved within the range
 simply and precisely. Additionally, synchronous assessment of ETO, MOX,
 and NAL in the biological fluid was attained by facile protein
 precipitation technique. These innovatory green processes were evaluated
 as accurate and precise processes regarding ICH roles. Greener innovative
 synchronous fluorimetric processes were corroborated by applying the
 National Environmental Methods Index, Analytical Eco-scale, and Green
 Analytical Procedure Index, which provides a novelty of the current study.
description: Two facile, green, and highly sensitive spectrofluorimetric
 approaches were conducted to simultaneous estimation the antineoplastic drug; etoposide
 (ETO), a fluoroquinolone antibiotic; moxifloxacin HCL (MOX) and opioid
 analgesic; nalbuphine HCL (NAL) in commercial formulations
 and spiked human urine. The first approach relies simply on estimation of
 MOX at 371 nm
 by synchronous fluorimetric technique. The second approach depends on
 applying the first derivative synchronous fluorimetric technique for
 simultaneous estimation of ETO and NAL at 257 and 273 nm,
 respectively. The developed methods are more convenient for routine
 quality control laboratory and therapeutic drug monitoring instead of the
 time-consuming and sophisticated reported techniques.
description: 1- Full validation data of ETO at 257 nm.
 2- Full validation data of MOX at 371 nm.
 3- Full validation data of NAL at 273 nm.
DOI: 10.5061/dryad.2jm63xsp9
title: Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak

description: Leaves interact with a wealth of microorganisms. Among these, fungi are
 highly diverse, and are known to contribute to plant health, leaf
 senescence and early decomposition. However, patterns and drivers of the
 seasonal dynamics of foliar fungal communities are poorly understood. We
 used a multi-factorial experiment to investigate the influence of warming
 and tree genotype on the foliar fungal community on the pedunculate oak
 Quercus robur across one growing season. Fungal species richness
 increased, evenness tended to decrease, and community composition strongly
 shifted during the growing season. Yeasts increased in relative abundance
 as the season progressed, while putative fungal pathogens decreased.
 Warming decreased species richness, reduced evenness and changed community
 composition, especially in the end of the growing season. Warming also
 negatively affected putative fungal pathogens. We only detected a minor
 imprint of tree genotype and warming-by-genotype interactions on species
 richness and community composition. Overall, our findings demonstrate that
 warming plays a larger role than plant genotype in shaping the seasonal
 dynamics of the foliar fungal community on oak. These warming-induced
 shifts in the foliar fungal community may have a pronounced impact on
 plant health, plant-fungal interactions and ecosystem functions.
DOI: 10.5061/dryad.9cnp5hqht
title: On male harm: How it is measured and how it evolves in different environments

description: Males can harm the females they interact with, but populations/species
 vary widely in the occurrence and extent of harm. We consider the merits
 and limitations of two common approaches to investigating male harm and
 apply these to an experimental study of divergence in harm. Different
 physical environments can affect how the sexes interact, causing plastic
 and/or evolved changes in harm. If harmful male phenotypes are less likely
 to evolve in situations where females have more control over sexual
 interactions, populations evolving in environments in which females have
 greater control should have less harmful males. We test this idea using
 experimental populations of Drosophila melanogaster that have evolved in
 either of two environments that vary in the extent to which females can
 avoid males, or in a third environment without mate competition (i.e.,
 enforced monogamy). We demonstrate an evolved reduction in harm in the
 absence of mate competition and also in a mate competition environment in
 which females have greater control. We also show a plastic effect in that
 otherwise harmful males are no longer so when tested in the environment in
 which females have greater control. Our results reveal the different
 perspectives provided by the two methods of studying harm.
description: Data collection protocols are described in detail in the
 accompany manuscript. For the 'experimental_populations' data
 set, rows are replicates from a specific population from the indicated
 larval adaptation set (Adaptation_set) and evolutionary mating treatment
 (Mating_treatment) when tested in a specific assay mating environment
 (Assay_environment) under either low or high exposure to males
 (Male_exposure). For the 'ancestor' data set, rows are
 replicates of the ancestral population tested at the same time as
 experimental populations from one of the laval adaptation sets
 (Adaptation_set) in a specific assay mating environment
 (Assay_environment) and either low or high exposure to males
 (Male_exposure).
DOI: 10.5061/dryad.98sf7m0j3
title: Supporting data: Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

description: The determination of G protein-coupled receptor (GPCR) structures at
 atomic resolution has improved understanding of cellular signaling and
 will accelerate the development of new drug candidates. However,
 experimental structures still remain unavailable for a majority of the
 GPCR family. GPCR structures and their interactions with ligands can also
 be modelled computationally, but such predictions have limited accuracy.
 In this work, we explored if molecular dynamics (MD) simulations could be
 used to refine the accuracy of in silico models of receptor-ligand
 complexes that were submitted to a community-wide assessment of GPCR
 structure prediction (GPCR Dock). Two simulation protocols were used to
 refine 30 models of the D3 dopamine receptor (D3R) in complex with an
 antagonist. Close to 60 µs of simulation time was generated and the
 resulting MD refined models were compared to a D3R crystal structure. In
 the MD simulations, the transmembrane helix region of the models generally
 drifted further away from the crystal structure conformation. However, MD
 refinement was able to improve the accuracy of the ligand binding mode and
 the second extracellular loop region. The best refinement protocol
 improved agreement with the experimentally observed ligand binding mode
 for a majority of the models. Receptor structures with improved virtual
 screening performance, which was assessed by molecular docking of ligands
 and decoys, could also be identified among the MD refined models.
 Application of weak restraints to the transmembrane helixes in the MD
 simulations further improved predictions of the ligand binding mode and
 second extracellular loop. These results provide guidelines for
 application of MD refinement in prediction of GPCR-ligand complexes and
 directions for further method development.
description: Data was obtained by running molecular dynamics simulations on a
 set of models obtained from the GPCR Dock 2010 assessment. Molecular
 dynamics trajectories in the data set has been treated for periodic
 boundary conditions and reduced to approximately 1 frame per 200 ps.
 Solvent has been removed to reduce the size of the files. 
description: Together with the molecular dynamics trajectories and input
 files, analysis results have been uploaded together with example analysis
 scripts. The data has been compressed into tar.gz archives. The archives
 come with README file that describes the contents of the
 archives.
DOI: 10.25349/d99w4t
title: A distributed circuit for associating environmental context to motor choice in retrosplenial cortex

description: During navigation, animals often use recognition of familiar environmental
 contexts to guide motor action selection. The retrosplenial cortex (RSC)
 receives inputs from both visual cortex and subcortical regions required
 for spatial memory, and projects to motor planning regions. However, it is
 not known whether RSC is important for associating familiar environmental
 contexts with specific motor actions. Here, we test this possibility by
 developing a task in which trajectories are chosen based on the context.
 We find that mice exhibit differential pre-decision activity in RSC, and
 that optogenetic suppression of RSC activity impairs task performance.
 Individual RSC neurons encode a range of task variables, often multiplexed
 with distinct temporal profiles. However, the responses are
 spatiotemporally organized, with task variables represented along a
 posterior-to-anterior gradient along RSC during the behavioral
 performance, consistent with histological characterization. These results
 reveal an anatomically-organized retrosplenial cortical circuit for
 associating environmental contexts to appropriate motor outputs.
description: The methods for data collection and processing are described in
 the associated manuscript.
description: The readme.txt file describes variables, units of measurement,
 procedures, and relationships between files.
DOI: 10.7280/d1wq3r
title: Data for: Foundations of a fast, data-driven, machine-learned simulator

description: We introduce Optimal-Transport-based Unfolding and Simulation (OTUS), a
 novel, fast simulator based on unsupervised machine-learning that is
 capable of predicting experimental data from theoretical models.
 Simulations are crucial in science because they map from theoretical
 models to experimental data, allowing scientists to test predictions of
 theoretical models against the reality of experiments.
  Experimental data is often reconstructed from indirect
 measurements causing the aggregate transformation from theoretical models
 to experimental data to be poorly described by analytical methods.
 Scientists instead rely on ad-hoc, numerical simulations at great
 computational cost. Capable of learning directly from data, OTUS trains a
 probabilistic autoencoder to transform directly between theoretical models
 and experimental data. This is achieved by identifying the probabilistic
 autoencoder's latent space with the space of theoretical models,
 causing the decoder network to become a fast, predictive simulator with
 the potential to replace current, computationally costly simulators. Using
 particle physics as an illustrative example, we provide proof-of-principle
 results for Z-boson and top-quark decays, but stress that OTUS can be
 widely applied to other fields.
description: The data is divided into two sets corresponding to the
 experiments in the publication (preprint:
 https://arxiv.org/abs/2101.08944): FinalData_ppzee.hdf5 and
 FinalData_ppttbar.hdf5. The data was generated using
 Madgraph5 v.2.6.3.2 [1], Pythia v.8.240 [2], Delphes v.3.4.1 [3], and ROOT
 v.6.08/00 [4]. Relevant run cards can be found with the code repository
 linked with this dataset. [1] Johan Alwall et al.
 MadGraph 5 : Going Beyond. arxiv:1106.0522. 2011. URL:
 http://arxiv.org/abs/1106.0522. [2] Torbjorn Sjostrand,
 Stephen Mrenna, and Peter Z. Skands. “PYTHIA 6.4 Physics and Manual”. In:
 JHEP 0605 (2006), p. 026. DOI: 10.1088/1126-6708/2006/05/026. arXiv:
 hep-ph/0603175 [hep-ph]. [3] J. de Favereau et al.
 “DELPHES 3, A modular framework for fast simulation of a generic collider
 experiment”. In: JHEP 02 (2014), p. 057. DOI: 10.1007/JHEP02(2014)057.
 arXiv: 1307.6346 [hep-ex]. [4] R. Brun and F.
 Rademakers. “ROOT: An object oriented data analysis framework”. In: Nucl.
 Instrum. Meth. A 389 (1997). Ed. by M. Werlen and D. Perret-Gallix, pp.
 81–86. DOI: 10.1016/S0168-9002(97)00048-X
description: Further detail can be found in attached readme file
 (readme_data.txt), the publication (preprint:
 https://arxiv.org/abs/2101.08944), and the code repository linked with
 this dataset.