cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70rxwdbz8
title: Shaped by the sun: the effect of exposure to sunlight on the evolution of spider bodies

description: Body temperature strongly influences fitness. Some sun-exposed ectotherms
 thermoregulate by adjusting body posture according to the sun's
 position. To evaluate the impact of body shape, size and posture on body
 temperature, we first built a model combining traditional heat transfer
 models with models of thermoregulatory postures in spiders. The model
 indicates that both body size and shape determine thermoregulation
 efficiency by affecting heat gain via solar irradiance. These estimates
 corroborate previous empirical studies on spider thermoregulation. We then
 coupled meteorological data to our heat transfer model. The model predicts
 that body elongation in large orb-web spiders decreases the risk of high
 body temperatures. Lastly, we measured the elongation of orb-web spiders
 across 1,024 species and found that sun-exposed species evolved more
 elongate bodies than sun-protected species. Overall, our results suggest
 that thermoregulation influenced the evolution of body shapes of orb-web
 spiders.
description: We estimated body elongation and area of spiders by measuring
 dorsal images extracted from taxonomical articles on Neotropical species.
 These images were processed using ImageJ software (v. 1.8.0). We drew over
 the abdomen with the polygon feature and recorded two outputs: total area
 and roundness [38]. Roundness may vary between 0 and 1, with the latter
 being a perfectly round shape (equal minor and major axes; Supplementary
 Material eq. 6). We classified spider genera as either
 sun-exposed or sun-protected primarily based on the scientific
 literature. We classified diurnal spiders that sit on the web hub during
 the day as sun-exposed and nocturnal and diurnal spiders that hide from
 the sun (by shelter construction or waiting on vegetation) as
 sun-protected. We built a heat transfer model to
 estimate the equilibrium temperature of animals of varying elongations
 (roundness), volumes, and angles of exposure to sunlight. We coupled
 classical models on heat exchange of ectotherms with a model on
 thermoregulatory postures of orb-web spiders plus a body elongation
 parameter. Further, we estimated the number of days per
 year sun-exposed orb-web spiders would reach ≥35°C and ≥40°C. We applied
 the heat transfer model to 10 years of meteorological data (2011-2020)
 collected hourly (wind speed, solar radiation and air temperature) in
 automatic stations (-34° to 0° Lat. and -36° to -73° Long.).
description: Code and analyses were run in R. Package 'brms' needs
 to be installed to open statistical models. Open RDS files using the
 readRDS function. Data are stored in model_name$data.
DOI: 10.5061/dryad.dz08kprz9
title: Bat phylogenetic responses to regenerating Amazonian forests

description: 1. Throughout the tropics, regenerating secondary forests occupy vast
 areas previously cleared for agriculture and cattle ranching. However,
 despite the importance of regenerating forests in mitigating the pervasive
 negative consequences of forest loss and fragmentation on
 forest-associated biodiversity, longitudinal studies on species’
 phylogenetic responses to matrix regeneration are rare. 2. We surveyed
 bats in continuous primary forest, primary forest fragments and in the
 regenerating secondary forest matrix of a whole-ecosystem Amazonian
 fragmentation experiment, ~15 and ~30 years after forest clearance, to
 investigate how changes in matrix quality through forest recovery affect
 phylogenetic α- and β-diversity. 3. We found that temporal changes in
 phylogenetic α-richness were more marked in the secondary forest matrix
 than in forest fragments and continuous forest, evidencing a significant
 increase in total evolutionary history over time. However, when the
 effects of species richness were accounted for, the phylogenetic structure
 of each assemblage was reduced close to zero, evincing a random pattern of
 lineages in all habitat types. Temporal differences in phylogenetic
 β-diversity were driven mainly by βreplacement in secondary forest and
 continuous forest ~30 years after forest clearance. Both habitats also
 clustered together in terms of βrichness, indicating similar levels of
 evolutionary heritage. Consequently, regenerating secondary forest showed
 a reduction in the extinction probability of lineages over time. 4.
 Synthesis and applications. Approximately 30 years of secondary forest
 regeneration were sufficient for phylogenetic richness to recover to
 levels similar to those observed in continuous forest. Promoting forest
 succession on degraded land through a combination of natural and active
 restoration, while ensuring the long-term protection of secondary forests
 regardless of their age is of key importance for conserving tropical bat
 diversity and their associated ecosystem services. Such restoration
 measures would stimulate the recolonization of fragments and matrix
 habitats by evolutionarily distinct bat species, safeguarding
 phylogenetically diverse assemblages and ecological functions. Our study
 suggests that forest restoration in tropical degraded areas should be
 encouraged and secondary forests be protected by law, especially in
 countryside ecosystems with high primary forest cover, and in the
 surroundings of protected areas.
DOI: 10.5061/dryad.6djh9w123
title: Current and future plant invasions in protected areas: Does clonality matter?

description: Aim: Protected areas (PAs) play an important role in biodiversity
 conservation, but remain increasingly threatened by invasive alien plant
 species (IAPS) in conjunction with global climate change. The latter is
 modifying the distribution of the former, and the magnitude and direction
 of distributional changes are predicted to vary depending on species
 dispersal mode. Here we address the question of whether clonality is
 expected to affect the future invasion pattern in PAs. Location:
 World-wide. Time period: 1950–2100. Major taxa studied: 36 invasive alien
 plant species Methods: We used ensembles of three species distribution
 models (GLM, GAM and Maxent) based on &gt; 70,000 occurrence records
 to project the distribution of 36 of the world’s most invasive clonal and
 non-clonal plants in &gt; 20,000 PAs. Projections were based on three
 greenhouse gas concentration scenarios (low, medium and high) for 2080.
 Results: Climate change showed little impact on the global invasion
 pattern in PAs and clonality showed little effect when all biomes were
 processed in concert. However, we discerned that the future invasion risk
 of clonal IAPS markedly increased in biomes located at high elevation and
 high latitude compared to non-clonal IAPS, while the risk decreased in
 lower-elevation tropical and subtropical biomes where asexual reproduction
 may be a less successful trait. We also showed that invasion hotspots
 overlapped with biodiversity hotspots and two realms (i.e., Nearctic and
 Palearctic), which calls for bridging the gap between invasion and
 conservation sciences and for more concerted management strategies. Main
 conclusions: We suggest that effective management of IAPS in PAs should
 consider in which biomes PAs are located as well as the reproductive
 traits of IAPS that are present or may become so.
DOI: 10.5061/dryad.cjsxksn6g
title: Data for: Perceived risk structures the space use of competing carnivores

description: Competition structures ecological communities. In carnivorans, competitive
 interactions are disproportionately costly to subordinate carnivores who
 must account for risk of interspecific killing when foraging. Accordingly,
 missed opportunity costs for meso-carnivores imposed by risk can benefit
 the smallest-bodied competitors. However, the extent to which the risk
 perpetuates into spatial partitioning in hierarchically structured
 communities remains unknown. To determine how risk-avoidance behaviors
 shape the space-use of carnivore communities, we studied a simple
 community of carnivores in northern Patagonia, Argentina: pumas (Puma
 concolor; an apex carnivore), culpeo foxes (Lycalopex culpaeus; a
 meso-carnivore), and chilla foxes (Lycalopex griseus; a small carnivore).
 We used multi-species occupancy models to quantify the space use within
 the carnivore community and giving-up densities to understand the
 behaviors that structure space use. Notably, we applied an analytical
 framework that tests whether actual or perceived risk of predation most
 strongly influences the space use of subordinate carnivores while
 accounting for their foraging and vigilance behaviors. We found that there
 was a dominance hierarchy from the apex carnivore through the
 meso-carnivore to the subordinate small carnivore, which was reflected in
 space. Although both meso- and small carnivores exhibited similar predator
 avoidance behavioral responses to apex carnivores, the habitat
 associations of apex carnivores only altered meso-carnivore space use. The
 biases in risk management we observed for meso-carnivores likely
 translates into stable co-existence of this community of competing
 carnivores. We believe our analytical framework can be extended to other
 communities to quantify the spatial-behavioral tradeoffs of risk.
description: This data was collected in the field using camera traps and a
 pseudo-experimental giving-up density experiment. See our publication
 "Perceived risk structures the space use of competing
 carnivores" for details.
DOI: 10.5061/dryad.qnk98sfhk
title: Semantic competency as a marker of clinical reasoning performance

description: Purpose: This study sought to explore the relationship between semantic
 competence (or dyscompetence) displayed during think alouds performed by
 resident and attending physicians and clinical reasoning performance.
 Methods: Internal medicine resident physicians and practicing internists
 participated in “think-alouds” performed after watching videos of typical
 presentations of common diseases in internal medicine. The
 think-alouds were evaluated for the presence of semantic competence and
 dyscompetence and these results were correlated with clinical reasoning
 performance.  Results: We found that the length of think-aloud
 was negatively correlated with clinical reasoning
 performance. Beyond this finding, however, we did not find any
 other significant correlations between semantic competence or
 dyscompetence and clinical reasoning performance. Conclusion: While this
 study did not produce the previously hypothesized findings of correlation
 between semantic competence and clinical reasoning performance, we discuss
 the possible implications and areas of future study regarding the
 relationship between semantic competency and clinical reasoning
 performance.
description: Data was collected by review of transcripts from think-alouds
 performed by participants in the study. Data was coded by a group of
 authors using the coding rules included in the paper, with results
 included on the spreadsheet.
DOI: 10.5061/dryad.4f4qrfjd0
title: Data from: A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes

description: Background: The large inter-individual variability in immune-cell
 cell composition and function determines immune responses in general and
 susceptibility to immune-mediated diseases in particular. While much has
 been learned about the genetic variants relevant for type 1 diabetes
 (T1D), the pathophysiological mechanisms through which these variations
 exert their effects remain unknown. Methods: Blood samples were
 collected from 243 patients with T1D of Dutch descent. We applied genetic
 association analysis on &gt; 200 immune cell traits and &gt;100
 cytokine production profiles in response to stimuli measured to identify
 genetic determinants of immune function, and compared the results obtained
 in T1D to healthy controls. Results: Genetic variants that
 determine susceptibility to T1D significantly affect T cell composition.
 Specifically, the CCR5+ regulatory T cells associate with T1D through the
 CCR region, suggesting a shared genetic regulation. Genome-wide
 quantitative trait loci (QTL) mapping analysis of immune traits revealed
 15 genetic loci that influence immune responses in T1D, including 12 that
 have never been reported in healthy population studies, implying a
 disease-specific genetic regulation. Conclusion: This study
 provides new insights into the genetic factors that affect immunological
 responses in T1D.
description: The QTL dataset was generated by mapping immune phenotypes (cell
 proportion and cytokine production in response to stimulation) to either
 heathy donors (500FG) or Type 1 diabetes patients (300DM).
description: All donor information was Anonymized.
DOI: 10.5061/dryad.stqjq2c46
title: Cold-water species deepen to escape warm water temperatures

description: Aim. Whether marine species can respond to ocean warming by changing their
 depth remains controversial. While some evidence suggests that species can
 deepen to cope with warming climates, other studies found ecologically
 constrained depth distributions. Our study focuses on generalizing species
 depth response to warming, and elucidating whether some species display
 larger depth change than others. This may help in understanding the future
 distribution of marine species and communities. Location. The
 Mediterranean Sea Time period. 1985-2017 Major taxa studied. Fish,
 malacostracans, and cephalopods Methods. We compiled species depth records
 from bottom-trawl surveys encompassing 236 marine species across the steep
 climatic gradient of the Mediterranean Sea. This data, represents the
 largest assessment, to date, of the potential of species to modify their
 depth distribution in response to spatially-varying climate. Using
 environmental variables (e.g. sea surface temperature, bottom temperature,
 and salinity) we elucidate species depth change across different climatic
 gradients. We then test whether species traits (e.g. thermal preference,
 depth affinity, and taxonomic relation) explain the variation in
 depth-response. Results. We revealed a significant deepening of minimum
 depths (shallow depth limits) with increasing sea temperatures across the
 Mediterranean Sea. Moreover, we show that this deepening is uneven among
 species, as cold-water species, and eurytherms, deepen more than
 warm-water species, and stenotherms. In addition, deep-water species
 deepen more than shallow-water species. We also find surprising changes
 towards shallower maximal depths (deep depth limits) with warming, but
 this pattern was not entirely supported by our sensitivity analyses. Main
 conclusions. These large changes across the Mediterranean Sea imply that
 progressively warmer oceans will compress the vertical distribution of
 marine organisms. However, as different species will respond
 differentially, the future vertical distribution of marine communities
 will change in complex ways.
description: We extracted data on the depth range of Mediterranean marine
 species from published literature based on bottom trawl surveys across
 multiple depths. We used the search terms “depth” and “Mediterranean” and
 “trawl*” on the ‘Web of Science’ database in September 2020, resulting in
 437 publications. These publications were screened for papers containing
 data on the depth ranges (minimum and maximum) of surveyed
 species.
DOI: 10.5061/dryad.wpzgmsbnp
title: Disentangling the effects of male age and mating history: contrasting effects of mating history on pre-copulatory mating behaviour and paternity success

description: Many studies ask whether older males are better at acquiring mates. Even
 so, how age affects reproductive success is still poorly understood
 because male age and mating history are confounded in most studies: older
 males usually have more mating experience. To what extent does mating
 history rather than age explain variation in male mating success? And how
 do mating history and male age determine paternity when there is also
 post-copulatory sexual selection? Here we experimentally manipulated the
 mating history of old and young males in the eastern mosquitofish
 (Gambusia holbrooki). We then recorded male mating behaviour and share of
 paternity (1259 offspring from 232 potential sires) when they competed for
 mates and fertilizations. Old males, and males with no mating experience,
 spent significantly more time approaching females, and attempting to mate,
 than did young males and those with greater mating experience. Male age
 and mating history interacted to affect paternity: old males benefited
 from having previous mating experience, but young males did not. Our
 results highlight that the age-related changes in male reproductive traits
 and in paternity that have been described in many taxa, may be partly
 attributable to male mating history and not simply to age itself.
DOI: 10.5061/dryad.fj6q573vz
title: Nitrogen addition, rather than altered precipitation, stimulates nitrous oxide emissions in an alpine steppe

description: Anthropogenic-driven global change, including changes in atmospheric
 nitrogen (N) deposition and precipitation patterns, is dramatically
 altering N cycling in soil. How long-term N deposition, precipitation
 changes, and their interaction influence nitrous oxide (N2O) emissions
 remains unknown, especially in the alpine steppes of the Qinghai-Tibetan
 Plateau (QTP). To fill this knowledge gap, a platform of N addition (10 g
 m−2 yr−1) and altered precipitation (± 50% precipitation) experiments was
 established in an alpine steppe of the QTP in 2013. Long-term N addition
 significantly increased N2O emissions. However, neither long-term
 alterations in precipitation nor the co-occurrence of N addition and
 altered precipitation significantly affected N2O emissions. These
 unexpected findings indicate that N2O emissions are particularly
 susceptible to N deposition in the alpine steppes. Our results further
 indicated that both biotic and abiotic properties had significant effects
 on N2O emissions. N2O emissions occurred mainly due to nitrification,
 which was dominated by ammonia-oxidizing bacteria, rather than
 ammonia-oxidizing archaea. Furthermore, the alterations in belowground
 biomass and soil temperature induced by N addition modulated N2O
 emissions. Overall, this study provides pivotal insights to aid the
 prediction of future responses of N2O emissions to long-term N deposition
 and precipitation changes in alpine ecosystems. The underlying microbial
 pathway and key predictors of N2O emissions identified in this study may
 also be used for future global-scale model studies.
description: The experiments consisted of six different treatments (NP:
 ambient nitrogen with ambient precipitation; NP−: ambient nitrogen with
 50% reduced precipitation; NP+: ambient nitrogen with 50% increased
 precipitation; N+P: nitrogen addition with ambient precipitation; N+P−:
 nitrogen addition with 50% reduced precipitation; N+P+: nitrogen addition
 with 50% increased precipitation). We monitored the
 N<sub>2</sub>O flux during the 2020 growing season (May to
 October) based on in-situ experiments. To identify the key abiotic and
 biotic factors regulating N<sub>2</sub>O emissions, we
 measured N<sub>2</sub>O flux on six consecutive days in
 mid-August (during peak plant growth). Soils were also collected to
 measure abiotic parameters and functional microbes, including nitrifiers
 (ammonia-oxidizing bacteria: AOB; ammonia-oxidizing archaea: AOA) and
 denitrifiers (<i>nirS</i>-, <i>nirK</i>-, and
 <i>nosZ</i> gene-containing microorganisms).
DOI: 10.5061/dryad.t4b8gtj33
title: Raw microscopy data from: Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers

description: Protein folding homeostasis in the endoplasmic reticulum (ER) is regulated
 by a signaling network, termed the unfolded protein response (UPR).
 Inositol-requiring enzyme 1 (IRE1) is an ER membrane-resident kinase/RNase
 that mediates signal transmission in the most evolutionarily conserved
 branch of the UPR. Dimerization and/or higher-order oligomerization of
 IRE1 are thought to be important for its activation mechanism, yet the
 actual oligomeric states of inactive, active, and attenuated mammalian
 IRE1 complexes remained unknown. We developed an automated two-color
 single-molecule tracking approach to dissect the oligomerization of tagged
 endogenous human IRE1 in live cells. In contrast to previous models, our
 data indicate that IRE1 exists as a constitutive homodimer at baseline and
 assembles into small oligomers upon ER stress. We demonstrate that the
 formation of inactive dimers and stress-dependent oligomers is fully
 governed by IRE1’s lumenal domain. Phosphorylation of IRE1’s kinase domain
 occurs more slowly than oligomerization and is retained after oligomers
 disassemble back into dimers. Our findings suggest that assembly of IRE1
 dimers into larger oligomers specifically enables trans-
 autophosphorylation, which in turn drives IRE1’s RNase activity.
  
description: Please see the attached Readme file, as well as the detailed
 README.md file distributed with the associated analysis code
 repository.
DOI: 10.5061/dryad.b5mkkwhdw
title: Impact of the malaria comprehensive case management programme in Odisha, India

description: Background The Comprehensive Case Management Project (CCMP), was a
 collaborative implementation research initiative to strengthen malaria
 early detection and complete treatment in Odisha State, India. Methods A
 two-arm quasi-experimental design was deployed across four districts in
 Odisha, representing a range of malaria endemicity: Bolangir (low
 transmission), Dhenkanal (moderate transmission), Angul (high
 transmission), and Kandhamal (hyper transmission). In each district, a
 control block received routine malaria control measures, whereas a CCMP
 block received a range of interventions to intensify surveillance,
 diagnosis, and case management. Impact was evaluated by
 difference-in-difference (DID) analysis and interrupted time-series (ITS)
 analysis of monthly blood examination rate (MBER) and monthly parasite
 index (MPI) over three phases: phase 1 pre-CCMP (2009–2012) phase 2 CCMP
 intervention (2013–2015), and phase 3 post-CCMP (2016–2017). Results
 During CCMP implementation, adjusting for control blocks, DID and ITS
 analysis indicated a 25% increase in MBER and a 96% increase in MPI,
 followed by a –47% decline in MPI post-CCMP, though MBER was maintained.
 Level changes in MPI between phases 1 and 2 were most marked in Dhenkanal
 and Angul with increases of 976% and 287%, respectively, but declines in
 Bolangir (−57%) and Kandhamal (−22%). Between phase 2 and phase 3, despite
 the MBER remaining relatively constant, substantial decreases in MPI were
 observed in Dhenkanal (−78%), and Angul (−59%), with a more modest decline
 in Bolangir (−13%), and an increase in Kandhamal (14%). Conclusions
 Overall, CCMP improved malaria early detection and treatment through the
 enhancement of the existing network of malaria services which positively
 impacted case incidence in three districts. In Kandhamal, an area of hyper
 transmission, the impact was not evident. However, in Dhenkanal and Angul,
 areas of moderate-to-high transmission, CCMP interventions precipitated a
 dramatic increase in case detection and a subsequent decline in malaria
 incidence, particularly in previously difficult-to-reach communities.