cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25338/b8gg8p
title: Data and code for simulation study and case study in "A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity"

description: This dataset contains the R and JAGS code underlying the simulation study,
 as well as the data and code underlying the case study on bird occurrence
 in Murchison Falls National Park, presented in the paper "A Bayesian
 Dirichlet process community occupancy model to estimate community
 structure and species similarity".
description: The zip file "Code and Data.zip" contains data, R and
 JAGS code to run the simulation study and the analysis of the point count
 dataset on Ugandan birds described in “A Bayesian Dirichlet process community
 occupancy model to estimate community structure and species
 similarity”. Please refer to main text for model details. The
 zip file contains the following files: (1)
 simulation_script_DPoccupancy.R: R script to simulate community occupancy
 data and analyze it with a Dirichlet Process (DP) community occupancy
 model (COM), under 15 scenarios determined by (1) the degree of
 distinctiveness among clusters (omega) and the number of parameters used
 in the probit-linear predictor of occupancy probability (m).
 (2) simulation_script_Normal.R: R script to analyze community
 occupancy data generated with (1) using a COM with a Normal random species
 level effect, under the same 15 scenarios as described under (1)
 (3) Simulation summary script DPoccupancy.R: R script to
 summarize simulation results generated with (1) (4)
 Simulation summary script Normal occupancy.R: R script to summarize
 simulation results generated with (2) (5)
 env_dat4V.R: simulated environmental predictor variables used in the
 simulation study; needs to be in the working directory to execute (1) and
 (2) (6) DPSim2mv.txt: JAGS
 code for the DP COM for a multivariate DP (i.e., including at least the
 intercept + one predictor variable)
 (7) DPSim2uv.txt: JAGS code for the DP COM for a
 univariate DP (i.e., including only the intercept)
 (8) NormalSim2mv.txt: JAGS code for the Normal COM
 for a multivariate Normal species random effect (i.e., including at least
 the intercept + one predictor variable)
 (9) NormalSim2uv.txt: JAGS code for the Normal COM
 for a univariate Normal species random effect (i.e., including only the
 intercept) (10)
 RunCommunityOccupancyModels.R: R script to analyze point count data for
 Ugandan birds in JAGS with DP COM and Normal COM
 (11) UgandaBirdData.R: Formatted bird point count
 data, needs to be in the working directory to execute
 (10) (12)
 JAGS.occu.DP2.Multivar.txt: JAGS code for DP COM for Ugandan bird
 data (13)
 CommOccNormal.Multivar.txt: JAGS code for Normal COM for Ugandan bird
 data
DOI: 10.5061/dryad.jdfn2z38j
title: Tobacco smoke exposure exacerbated crystalline silica-induced lung toxicity in rats

description: Smoking may modify the lung response to silica exposure including cancer
 and silicosis. Nevertheless, the precise role of exposure to tobacco smoke
 (TS) on the lung response to crystalline silica (CS) exposure and the
 underlying mechanisms need further clarification. The objectives of the
 present study were to determine the role of TS on lung response to CS
 exposure and the underlying mechanism(s). Male Fischer 344 rats were
 exposed by inhalation to air, CS (15 mg/m3, 6 hrs/day, 5 days), TS (80
 mg/m3, 3 hrs/day, twice weekly, 6 months), or CS (15 mg/m3, 6 hrs/day, 5
 days) followed by TS (80 mg/m3, 3 hrs/day, twice weekly, 6 months). The
 rats were euthanized 6 months and 3 weeks following initiation of the
 first exposure and the lung response was assessed. Silica exposure
 resulted in significant lung toxicity as evidenced by lung histological
 changes, enhanced neutrophil infiltration, increased LDH levels, enhanced
 oxidant production, and increased cytokine levels.  The TS
 exposure alone had only a minimal effect on these toxicity parameters.
 However, the combined exposure to TS and CS exacerbated the lung response,
 compared to TS or CS exposure alone. Global gene expression changes in the
 lungs correlated with the lung toxicity severity. Bioinformatic analysis
 of the gene expression data demonstrated significant enrichment in
 functions, pathways, and networks relevant to the response to silica
 exposure which correlated with the lung toxicity detected. Collectively
 our data demonstrated an exacerbation of CS-induced lung toxicity by TS
 exposure and the molecular mechanisms underlying the exacerbated toxicity.
DOI: 10.5061/dryad.3bk3j9kh1
title: Supplemental Material for "Biomechanical analyses of Cambrian euarthropod limbs reveal their effectiveness in mastication and durophagy"

description: Durophagy arose in the Cambrian and greatly influenced the diversification
 of biomineralised defensive structures throughout the Phanerozoic. Spinose
 gnathobases on protopodites of Cambrian euarthropod limbs are considered
 key innovations for shell-crushing, yet few studies have demonstrated
 their effectiveness with biomechanical models. Here we present finite
 element analysis models of two Cambrian trilobites with prominent
 gnathobases—Redlichia rex and Olenoides serratus—and compare these to the
 protopodites of the Cambrian euarthropod Sidneyia inexpectans and the
 modern American horseshoe crab, Limulus polyphemus. Results show that L.
 polyphemus, S. inexpectans and R. rex have broadly similar microstrain
 patterns, reflecting effective durophagous abilities. Conversely, low
 microstrain values across the O. serratus protopodite suggest that the
 elongate gnathobasic spines transferred minimal strain, implying that this
 species was less well-adapted to masticate hard prey. These results
 confirm that Cambrian euarthropods with transversely elongate protopodites
 bearing short, robust gnathobasic spines were likely durophages.
 Comparatively, taxa with shorter protopodites armed with long spines, such
 as O. serratus, were more likely restricted to a soft food diet. The
 prevalence of Cambrian gnathobase-bearing euarthropods and their various
 feeding specialisations may have accelerated the development of complex
 trophic relationships within early animal ecosystems, especially the ‘arms
 race’ between predators and biomineralised prey.
description: The .st7 files can be opened using Strand7, the biomechanical
 software used to conduct the finite element analyses considered in
 this research project.
DOI: 10.5061/dryad.573n5tb5d
title: Predicting incremental and future visual change in neovascular age-related macular degeneration using deep learning

description: Purpose To evaluate the predictive utility of quantitative imaging
 biomarkers, acquired automatically from optical coherence tomography (OCT)
 scans, of cross-sectional and future visual outcomes of patients with
 neovascular age-related macular degeneration (AMD) starting anti-vascular
 endothelial growth factor (VEGF) therapy. Design Retrospective cohort
 study. Methods Automatic segmentation was carried out by applying
 a deep learning segmentation algorithm to 137,379 OCT scans from 6467 eyes
 of 3261 patients with neovascular AMD between 2007 and 2017 at Moorfields
 Eye Hospital (a large, UK single-centre). Treatment-naïve, first-treated
 eyes were taken forward for analysis - 926 eyes of 926 patients. Main
 outcome measures were correlation coefficients (R2) and mean absolute
 error (MAE) between quantitative OCT (qOCT) parameters and cross-sectional
 visual-function; VA at distant timepoints (up to 12 months post-baseline);
 the incremental VA-change from an individual injection.
 Results VA at distant timepoints could be predicted: R2 0.79 (MAE
 5.0 ETDRS letters) and R2 0.63 (MAE 7.2) post-injection 3 and at 12 months
 post-baseline (both p &lt; 0.001), respectively. Best performing
 models included both baseline qOCT parameters and treatment-response.
 Furthermore, we present proof-of-principle evidence that the incremental
 change in VA from an injection can be predicted: R2 0.13 (MAE 5.6) for
 injection 2 and R2 0.07 (MAE 5.0) for injection 3 (both p &lt; 0.01).
 Conclusions Automatic segmentation enables rapid acquisition of
 quantitative and reproducible OCT biomarkers with potential to inform
 treatment decisions in the care of neovascular AMD. This furthers
 development of point-of-care decision-aid systems for personalized
 medicine.
DOI: 10.5061/dryad.8cz8w9gn7
title: Target-capture phylogenomics provide insights on gene and species tree discordances in Old World Treefrogs (Anura: Rhacophoridae)

description: Genome-scale data have greatly facilitated the resolution of recalcitrant
 nodes that Sanger-based datasets have been unable to resolve. However,
 phylogenomic studies continue to utilize traditional methods such as
 bootstrapping to estimate branch support; and high bootstrap values are
 still interpreted as providing strong support for the correct topology.
 Furthermore, relatively little attention is given to assessing
 discordances between gene and species trees, and the underlying processes
 that produce phylogenetic conflict. We generated novel genomic datasets to
 characterize and determine the causes of discordance in Old World
 Treefrogs (Family: Rhacophoridae)—a group that is fraught with conflicting
 and poorly supported topologies among major clades. We showed that
 incomplete lineage sorting was present at all nodes that exhibited high
 levels of discordance, which was caused by extremely short internal
 branches. We also clearly demonstrate that bootstrap values do not reflect
 uncertainty or confidence for the correct topology, and hence, should not
 be used as a measure of branch support in phylogenomic datasets. Overall,
 we showed that species tree inference can be improved using a
 total-evidence and multi-faceted approach that utilizes the most amount of
 data and considers results from different analytical methods and datasets.
description: This repository includes all relevant files required for
 reproducibility of the study: 1) Alignments (phylip
 format) 2) Partition files (for partitioned analysis of
 concatenated data) 3) IQ-TREE consensus trees
 4) ASTRAL-III species trees 5) SVDQuartets
 species trees 6) Individual gene trees (estimated using
 IQ-TREE).
DOI: 10.5061/dryad.73n5tb2v5
title: Data from: Testing multiple drivers of the temperature-size rule with nonlinear temperature increase

description: The temperature-size rule (TSR) describes the inverse relationship between
 organism size and environmental temperature in uni- and multicellular
 species. Despite the TSR being widespread, the mechanisms for shrinking
 body size with warming remain elusive. Here, we experimentally test three
 hypotheses (differential development and growth [DDG], maintain aerobic
 scope and regulate oxygen supply [MASROS] and the supply-demand hypothesis
 [SD]) potentially  explaining the TSR using the aquatic protist
 Colpidium striatum in three gradually changing and one constant
 temperature environment crossed with three different nutrient levels. We
 find that the constant and slowly warming environments show similar
 responses in terms of population dynamics, whereas populations with linear
 and fast warming quickly decline and  show a stronger
 temperature-size response. Our analyses suggest that acclimation may have
 played a role in observing these differences among treatments. The SD
 hypothesis is most parsimonious with the data, however, neither the DDG
 nor the MASROS hypothesis can be firmly dismissed. We conclude that the
 TSR is driven by multiple ecological and acclimatory responses, hence
 multicausal.
description: Data were collected from an aquatic microcosm experiment. The
 experiment has a full-factorial design of four levels of temperature
 treatment (constant 15°C, three rising temperature between 15-30°C and
 three levels of nutrient concentration (low = 0.28, medium = 0.56, and
 high = 1.12 g Protist Pellet medium per liter). We chose constant 15°C as
 the reference temperature as this is representative for the temperature
 <em>Colpidium striatum</em> experiences in natural freshwater
 environments. All three rising temperature treatments start at 15°C and
 end at 30°C. The linear speed is +1°C per day, while the fast nonlinear
 rising temperature increases at the beginning of the experiment (growth
 phase) faster then it slows down and the slow nonlinear rising temperature
 treatment goes in reversed fashion. During the
 experiment, 5 mL of medium (of a total of 100 mL medium) was taken every
 day and replaced with 5 mL of sterile medium. 1 mL of the sample was
 transferred to a counting chamber and filmed under a stereo microscope
 with a 25× magnification mounted digital CMOS camera (Hamamatsu Orca
 C11440; Hamamatsu Photonics, Japan) to take a 5s video (25 frames per
 second). The following properties were measured with the R package BEMOVI:
 individual morphology (cell size and shape), and population size
 (individuals per mL). Furthermore, samples were processed to measure
 bacterial abundance using flow cytometry with an Accuri C6 flow cytometer
 and dissolved oxygen (DO) concentration with oxygen sensors (from PreSens
 - Precision Sensing GmbH); for details refer to Pennekamp et al
 2015.
description: Missing data is coded as NA.
DOI: 10.5061/dryad.3j9kd51g2
title: Data offspring performance following two-donor crosses at different floral stages and with different competitor types in greenhouse studies of Collinsia heterophylla

description: Data on two offspring performance traits (seeds per capsule and flower
 number) in greenhouse studies of Collinsia heterophylla to investigate
 indirect benefits of mate choice. We performed two-donor pollinations
 during successive floral stages and with different competitor types
 (outcross and self) to assess how stigma receptivity and two pollen traits
 known to affect siring success influence offspring performance. We also
 investigated the link between seed production in mothers and offspring as
 an indication of heritability of this trait, and differential resource
 allocation by studying the influence of sibling performance in the same
 capsule.
DOI: 10.82294/dvnkofc45
title: Entrevistas semiestructuradas. Territorio: Norte de Santander. Sector: Cultura. Año: 2032

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2023, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Norte de Santander
DOI: 10.5061/dryad.wdbrv15m7
title: Chimpanzees use least-cost routes to out-of-sight goals

description: While the ability of naturally ranging animals to recall the location of
 food resources and use straight-line routes between them has been
 demonstrated in several studies [1, 2], it is not known whether animals
 can use knowledge of their landscape to walk least-cost routes [3]. This
 ability is likely to be particularly important for animals living in
 highly variable energy landscapes, where movement costs are exacerbated
 [4, 5].  Here, we used least-cost modelling, which determines the
 most efficient route assuming full knowledge of the environment, to
 investigate whether chimpanzees (Pan troglodytes) living in a rugged,
 montane environment walk least-cost routes to out of sight goals. We
 compared the ‘costs’ and geometry of observed movements with predicted
 least-cost routes and local knowledge (agent-based) and straight-line null
 models.  The least-cost model performed better than the local
 knowledge and straight-line models across all parameters, and linear mixed
 modelling showed a strong relationship between the cost of observed
 chimpanzee travel and least-cost routes.  Our study provides the
 first example of the ability to take least-cost routes to out of sight
 goals by chimpanzees and suggests they have spatial memory of their home
 range landscape. This ability may be a key trait that has enabled
 chimpanzees to maintain their energy balance in a low-resource
 environment.  Our findings provide a further example of how the
 advanced cognitive complexity of hominins may have facilitated their
 adaptation to a variety of environmental conditions and lead us to
 hypothesise that landscape complexity may play a role in shaping
 cognition.
DOI: 10.6078/d16d9p
title: Supplementary Materials - Adaptive Tree Proposals for Bayesian Phylogenetic Inference

description: Bayesian inference of phylogeny with MCMC plays a key role in the study of
 evolution. Yet, this method still suffers from a practical challenge
 identified more than two decades ago: designing tree topology proposals
 that efficiently sample tree spaces. In this study, I introduce the
 concept of adaptive tree proposals for unrooted topologies, that is tree
 proposals adapting to the posterior distribution as it is estimated. I use
 this concept to elaborate two adaptive variants of existing proposals and
 an adaptive proposal based on a novel design philosophy in which the
 structure of the proposal is informed by the posterior distribution of
 trees. This dataset contains a document (PDF) detailing the key concepts
 presented in this study: How to approximate the posterior distribution of
 trees How to build "ergodic" adaptive tree proposals An example
 of how to build path-based adaptive tree proposals Additionally, this
 document contains extended results (with absolute value), and an
 additional result showing the relation between the amount phylogenetic
 information contained in an alignment and the behavior of adaptive tree
 proposals.
description: The file 'SupMatAdaptiveTreeProposals.pdf' contains the supplemental methods, figures and tables referenced in the main text. The data and software used for this study can be found at the following URL: https://bitbucket.org/XavMeyer/coevrj/src/master/. The README.md file in this GIT repository provides you all the information required to replicate the simulation conducted in this study.
DOI: 10.15468/dl.qncafh
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Guyana",
 "MediaType is Image",
 "TaxonKey is Vanilla"
 ]
}

 The dataset includes 64 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002519-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.612jm641r
title: A multidimensional approach to the expression of phenotypic plasticity

description: Phenotypic plasticity is increasingly recognized as a key element of
 eco-evolutionary dynamics, but it remains challenging to assess because of
 its multidimensional nature. Indeed, organisms live in complex
 environments where numerous factors can impact the phenotypic expression
 of traits (inter-environment axis), possess multiple traits that can
 influence each other’s expression (inter-trait axis), and differ in their
 genetic background (inter-genotype axis), which can not only impact the
 traits’ values but also their plasticity. We addressed six questions
 related to phenotypic plasticity: (1) do different environmental gradients
 show similar effects on a given trait? (2) Are the effects of two
 environmental gradients on a trait additive? (3) Do different traits show
 similar plastic response to a given environmental gradient? (4) Do the
 (co)variances between traits vary across environmental gradients? (5) Do
 genotypes differ in their plastic response to a given environmental
 gradient? (6) Are some genotypes more plastic than others across all
 traits? We designed a microcosm experiment using the protist Tetrahymena
 thermophila aimed at encompassing all these aspects of phenotypic
 plasticity. We exposed 15 distinct genotypes to 25 combinations of
 temperature and nutrient availability and assessed the plasticity of five
 phenotypic traits. Our results show strong differences in the plastic
 response depending on the environmental gradient, not only regarding the
 shape of the reaction norm of the different traits tested, but also in the
 overall plasticity of the organisms. We did not find any covariance
 between traits that was consistent across all environments. Overall, our
 results suggest independent impacts of the environmental dimension
 considered on the observed plastic response. These results underline
 potential difficulties in generalising findings about plasticity to all
 environments and all traits.
description: This dataset was collected throughout the experiment presented in
 the article : <em>A multidimensional approach to the expression of
 phenotypic plasticity</em> (see Methods section)
DOI: 10.26255/heal.9e48b606
title: test-metadata
DOI: 10.5061/dryad.73n5tb2v6
title: Soil dissolved organic carbon in terrestrial ecosystems: global budget, spatial distribution and controls

description: Aims: Soil dissolved organic carbon (DOC) is a primary form of labile
 carbon in terrestrial ecosystems and therefore plays a vital role in soil
 carbon cycling. This study aims to quantify the budgets of soil DOC at
 biome- and global levels and to examine the variations in soil DOC and
 their environmental controls. Location: Global Time period: 1981 - 2019
 Method: We compiled a global dataset and analyzed the concentration and
 distribution of DOC across 10 biomes. Results: Large variations in DOC are
 found among biomes across space and the soil DOC concentration declines
 exponentially along soil depths. Tundra has the highest soil DOC
 concentration in 0 - 30 cm soils (453.75 (95% confidence interval: 324.95
 – 633.5) mg·kg-1); whereas tropical and temperate forests have relatively
 lower DOC concentrations, ranging from 30.20 (24.78 - 36.80) mg·kg-1 to
 54.54 (49.77 – 59.77) mg·kg-1. DOC generally accounts for &lt; 1% of
 total organic carbon in soils, and DOC in 0 - 30 cm contributes more than
 half of total DOC in 0 - 100 cm soil profile. Furthermore, variations in
 DOC are primarily controlled by soil texture, moisture, and total organic
 carbon. Main conclusion: A global synthesis is combined with an empirical
 model to extrapolate the DOC concentration along soil profiles across the
 globe, and global budgets of DOC are estimated as 7.20 Pg C in top 0 - 30
 cm and 12.97 Pg C in 0 - 100 cm, respectively, with a considerable
 variation among biomes. The strong soil texture control but weak TOC
 control on DOC variations suggest that the investigation of physical
 protection of soil organic carbon might need to expand to consider the
 labile C in soils. The global maps of DOC concentration serve as a
 benchmark for validating land surface models in estimating carbon storage
 in soils.
description: The data for DOC concentrations were collected from the
 publications by searching “soil DOC” in Google Scholar and the Web of
 Science. The data points were derived from tables containing soil DOC or
 extracted by the Engauge Digitizer software (Version 4.1) from figures in
 collected publications. The data points with reported soil DOC
 concentrations greater than total organic C (TOC) concentration were
 excluded from the database. In total, 3869 data points were retrieved from
 107 papers published during 1981 - 2019.
description: The database represents 171 sites from 33 countries, of which
 34.1% in Europe, 34.6% in Asia, 27.2% in America and &lt; 4% in other
 continents. These data points represent soil samples from various depths
 of 0-100 cm. Available auxiliary information of the sampling sites was
 also retrieved, including the latitude and longitude, mean annual air
 temperature (MAT), mean annual precipitation (MAP), soil pH, TOC, total
 nitrogen concentration (TN), vegetation type, soil texture type, and
 sampling date. The database used in this study was organized in April 2019
 and was updated and finalized on November 20<sup>th</sup>,
 2019.