cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w6m905qn8
title: Coexistence of predators in time: effects of season and prey availability on species activity within a Mediterranean carnivore guild

description: 1. The degree of coexistence among predators can determine the structure
 of ecological communities. Niche partitioning is a common strategy applied
 by species to enhance their coexistence. Diet, habitat or time use can be
 responsible for segregation among carnivore species, the latter factor
 being the least studied in Mediterranean ecosystems. Terrestrial
 medium-sized carnivores (i.e. mesocarnivores) carry out important
 functions in ecosystems and identifying their interactions is essential
 for their conservation. 2. In this study, we explore the activity of a
 terrestrial mesocarnivore guild in order to determine seasonal differences
 on daily activity patterns of competitors and prey. We also investigate
 how the abundance of a common mesocarnivore prey in the region, small
 mammals, influences the activity of predators. 3. During a year, camera
 trap devices (n=18) were installed in Montseny Natural Park (Catalan
 Pre-Coastal Range, Nort-East Iberian Peninsula), a region that hosts five
 mesocarnivore species. Camera trapping detections were used to estimate
 their daily activity patterns and corresponding overlaps. We also surveyed
 small mammal plots (n=5) in order to calculate prey abundance and test its
 effect on the relative activity of each carnivore species. 4. Despite all
 target mesocarnivores are mainly nocturnal, the activity overlap among
 them varies according to species particularities and season. Red fox
 (Vulpes vulpes) appears as a generalist species in terms of time use,
 whereas stone marten (Martes foina) and genet (Genetta genetta) show the
 most similar activity patterns and both of them seem to be positively
 influenced by small mammal abundance. Overall, the diversity found in the
 way mesocarnivore species use time could facilitate their coexistence. 5.
 Despite activity pattern similarities among carnivore species should not
 be directly translated to negative interactions, they can have a strong
 influence in habitat and resource-limited ecosystems. Therefore, activity
 overlaps should be taken into account when discussing wildlife management
 actions.
description: <strong>Table 1</strong>. It includes camera trap
 data, showing each mesocarnivore and small mammal contact indicating site,
 season, date and time of the corresponding picture.
 <strong>Table 2.</strong> It includes the Relative
 Activity Indices (RAI) of each species per site and season (RAI is
 expressed as the number of contacts per 100 sampling days).
 <strong>Table 3</strong>. It includes the number of
 small mammal individuals of each species captured in the five small mammal
 plots.
DOI: 10.5061/dryad.rbnzs7h95
title: Using a new video rating tool to crowd-source analysis of behavioural reaction to stimuli

description: Quantifying the intensity of animals’ reaction to stimuli is notoriously
 difficult as classic unidimensional measures of responses such as latency
 or duration of looking, can fail to capture the overall strength of
 behavioural responses. More holistic rating can be useful but have the
 inherent risks of subjective bias and lack of repeatability. Here, we
 explored whether crowdsourcing could be used to efficiently and reliably
 overcome these potential flaws. A total of 396 participants watched online
 videos of dogs reacting to auditory stimuli and provided 23,248 ratings of
 the strength of the dogs’ responses from zero (default) to 100 using an
 online survey form. We found that raters achieved very high inter-rater
 reliability across multiple datasets (although their responses were
 affected by their sex and attitude towards animals) and that as few as 10
 raters could be used to achieve a reliable result. A linear mixed model
 applied to PCA factors of behaviours discovered that the dogs’ facial
 expressions and head orientation influenced strength of behaviour ratings
 the most. Further linear mixed models showed that that strength of
 behaviour ratings were moderately correlated to the duration of dogs’
 reactions but not to dogs’ reaction latency (from the stimulus onset).
 This suggests that observers’ ratings captured consistent dimensions of
 animals’ responses that are not fully represented by more classic
 unidimensional metrics. Finally, we report that overall participants
 strongly enjoyed the experience. Thus, we suggest that using crowdsourcing
 can offer a useful, repeatable tool to assess behavioural intensity in
 experimental or observational studies where unidimensional coding may miss
 nuance, or where coding multiple dimensions may be too time-consuming.
description: File names represent the dogs’ names, breeds, and trial. All
 stimuli sounds were replaced by a pop.  See
 "Data_from_‘Using_a_new_video_rating_tool_to_crowd-source_analysis_of_behavioural_reaction_to_stimuli’_README.rtf" for more information.
DOI: 10.5061/dryad.qrfj6q5d2
title: Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks

description: We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp.
 from the Famennian (Late Devonian) of the Maïder region in Morocco. This
 chondrichthyan is exceptionally well preserved and displays not only
 mineralized soft tissues but also undeformed cartilages of the head,
 gills, and shoulder girdle. A reconstruction of the head using 3D-prints
 revealed a previously unknown kind of jaw articulation. Here, we make the
 original cropped image stack and PLY-files of the single cartilaginous
 elements accessible. Additionally, a nexus-file with the character matrix
 used for the cladogram shown in the article is included.
description: Most of this text is copied from the article: The holotype of
 Ferromirum oukherbouchi n.gen. et sp. was scanned using an industrial
 computed tomography scanner (Nikon XT H 225 ST) at the University of
 Zurich, Switzerland. Data acquisition and image reconstruction parameters
 are: 224 kV, 474µA; filter: 4 mm of copper; isotropic voxel dimensions of
 0.091 mm; 16-bit TIFF images were acquired; XX 8-bit TIFF images were used
 for reconstruction. Images were analysed and 3D models reconstructed using
 Mimics v.17 (http://www.biomedical.materialise.com/mimics; Materialise,
 Leuven, Belgium). The 3D-object was edited (smoothing, colours and
 lightning) in MeshLab v. 2016 (http://www.meshlab.net; 41) and blender
 v2.79b (https://www.blender.org; Amsterdam, Netherlands). PLY-files of the
 main cartilages were produced using Mimics v.17.
DOI: 10.5061/dryad.q573n5tgr
title: Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

description: Simultaneous molecular dating of population and species divergences
 is essential in many biological investigations,
 including phylogeography, phylodynamics, and species delimitation studies.
 In these investigations, multiple sequence alignments consist of
 both intra- and inter-species samples (mixed samples). As a
 result, the phylogenetic trees contain inter-species, inter-population,
 and within-population divergences. Bayesian relaxed clock methods are
 often employed in these analyses, but they assume the same tree prior for
 both inter- and intra-species branching processes and require
 specification of a clock model for branch rates (independent vs.
 autocorrelated rates models). We evaluated the impact of a single tree
 prior onBayesian divergence time estimates by
 analyzing computer-simulated datasets. We also examined
 the effectof the assumption of independence of evolutionary rate
 variation among branches when the branch rates are autocorrelated.
 Bayesian approach with coalescent tree priors generally
 produced excellent molecular dates and highest posterior
 densities with high coverage probabilities. We also evaluated the
 performance of a non-Bayesian method, RelTime, which does not require the
 specification of a tree prior or a clock model. RelTime's performance
 was similar to that of the Bayesian approach, suggesting that it is also
 suitable to analyze datasets containing both populations and species
 variation when its computational-efficiency is needed.
description: These are simulated data and settings used to perform divergence
 time estimation in BEAST and RelTime.  
 The dataset consists of xml files used to perform BEAST2 (and
 StarBEAST2) analyses. For RelTime analyses, the file
 "reltime_ml_nucleotide.mao" was used as the configuration file
 to run RelTime in megacc (with the same alignments and tree topologies
 contained in the xml files).
DOI: 10.34740/kaggle/dsv/14644435
title: 🇰🇷 🇰🇵 Reddit r/Korea Subreddit Dataset 2026
DOI: 10.5061/dryad.6djh9w0zs
title: RNAseq raw counts FLCN positive vs. FLCN negative renal proximal tubular epithelial cells (RPTEC)

description: Germline inactivating mutations in Folliculin (FLCN) cause Birt–Hogg–Dubé
 (BHD) syndrome, a rare autosomal dominant disorder predisposing to kidney
 tumors. FLCN is a conserved, essential gene linked to diverse cellular
 processes but the mechanisms by which FLCN prevents kidney cancer remain
 unknown. Here we show that deleting FLCN activates TFE3, upregulating its
 downstream E-box genes in human renal tubular epithelial cells
 (RPTEC/TERT1), including RRAGD and GPNMB, without modifying mTORC1
 activity. Surprisingly, deletion of FLCN or its binding partners
 FNIP1/FNIP2 also induces interferon response genes, but independently of
 interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to
 chromatin and slows cellular proliferation. Our integrated analysis
 identifies STAT1/2 signaling as a novel target of FLCN in renal cells and
 BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed
 hyper-proliferation and may influence the immune response. These findings
 shed light on unique roles of FLCN in human renal tumorigenesis and
 pinpoint candidate prognostic biomarkers.
description: See material & methods section RNA extraction, sequencing
 & qRT-PCR of DOI: 10.7554/eLife.61630  RNA was
 extracted from dry cell pellet (~1.5E6 cells) according to the High Pure
 RNA Isolation Kit (Roche, Penzberg, Germany) manual. For Illumina-based
 sequencing samples were prepped using TruSeq Stranded mRNA Library
 Preparation Kit according to TruSeq Stranded mRNA Sample Preparation
 Guide. Sequencing was performed on an Illumina HiSeq 4000 (Illumina, San
 Diego, California, USA) using run mode SR50. Reads were trimmed using
 sickle-1.33 (Joshi & Fass, 2011) and aligned to hg19 using
 hisat2-2.0.4 (Kim, Langmead, & Salzberg, 2015). The alignments
 were assigned to genes and exons using feature count-1.5.0-p3 (Liao,
 Smyth, & Shi, 2014) using the gene annotation provided by the
 iGenomes resource (Illumina, 2020).
description: See material & methods section differential expression
 analysis of RNAseq data of DOI: 10.7554/eLife.61630<br> <br>
 We used the R package edgeR (Robinson, McCarthy, & Smyth, 2010) to
 compare RNA sequencing profiles between FLCNPOS and FLCNNEG replicates, as
 well as between TP53POS and TP53NEG. This involved reading in the
 gene-level counts, computing library size normalizing factors using the
 trimmed-mean of M-values (TMM) method and then fitting a model to estimate
 the group effect. Obtained p-values were corrected for multiple testing
 using the Benjamini-Hochberg false discovery rate (FDR) step-up procedure
 (Benjamini & Hochberg, 1995).
DOI: 10.5061/dryad.qfttdz0fb
title: Adaptive associations among life history, reproductive traits, environment, and origin in the Wisconsin angiosperm flora

description: PREMISE OF THE STUDY: We tested 25 classic and novel hypotheses
 regarding trait-origin, trait-trait, and trait-environment relationships
 to account for flora-wide variation in life history, habit, and especially
 reproductive traits using a plastid DNA phylogeny of most native (96.6%,
 or 1494/1547 species) and introduced (87.5%, or 690/789 species)
 angiosperms in Wisconsin, USA. METHODS: We assembled data on life
 history, habit, flowering, dispersal, mating system, and occurrence across
 open/closed/mixed habitats across species in the state phylogeny. We used
 phylogenetically structured analyses to assess the strength and
 statistical significance of associations predicted by our models. KEY
 RESULTS: Introduced species are more likely to be annual herbs,
 occupy open habitats, have large, visually conspicuous hermaphroditic
 flowers, and bear passively dispersed seeds.  Among
 native species, hermaphroditism is associated with larger, more
 conspicuous flowers; monoecy, with small inconspicuous flowers and passive
 seed dispersal; and dioecy, with small inconspicuous flowers and fleshy
 fruits. Larger flowers with more conspicuous colors are more common in
 open habitats, and in understory species flowering under open (spring)
 canopies; fleshy fruits are more common in closed habitats. Wind
 pollination may help favor dioecy in open habitats.
 CONCLUSIONS: These findings support predictions regarding how
 breeding systems depend on flower size, flower color, and fruit type, and
 how those traits depend on habitat. This study is the first to combine
 flora-wide phylogenies with complete trait databases and phylo­genetically
 structured analyses to provide powerful tests of evolutionary hypotheses
 about reproductive traits and their variation with geographic source, each
 other, and environmental conditions.
description: The dataset was collected from the literature and from herbarium
 specimens.
description: See attached README for additional information.
DOI: 10.5061/dryad.7sqv9s4qw
title: Root associated fungi in Arctic Glacier Forlands raw sequences

description: Climate change causes Arctic glaciers to retreat faster, exposing new
 areas for colonization. Several pioneer plants likely to colonize recent
 deglaciated, nutrient-poor areas depend on fungal partners for successful
 establishment. Little is known about general patterns or characteristics
 of facilitating fungal pioneers and how they vary with regional climate in
 the Arctic. The High Arctic Archipelago Svalbard represents an excellent
 study system to address these questions, as glaciers cover ∼60% of the
 land surface and recent estimations suggest at least 7% reduction of
 glacier area since 1960s. Roots of two ectomycorrhizal
 (ECM) plants (Salix polaris and Bistorta vivipara ) were sampled in eight
 glacier forelands. Associated ECM fungi were assessed using DNA
 metabarcoding. About 25% of the diversity was unknown at family level,
 indicating presence of undescribed species. Seven genera dominated based
 on richness and abundance, but their relative importance varied with local
 factors. The genus Geopora showed surprisingly high richness and
 abundance, particularly in dry, nutrient-poor forelands. Such forelands
 will diminish along with increasing temperature and precipitation, and
 faster succession. Our results support a taxonomical shift in pioneer ECM
 diversity with climate change, and we are likely to lose unknown fungal
 diversity, without knowing their identity or ecological importance.
description: DNA was extracted from the entire plant root system using a
 modified CTAB extraction protocol , and further purified using the
 E.Z.N.A. Soil DNA kit (Omega Bio-tek, USA) following the
 manufacturer's protocol. A negative control was used during
 extraction procedure and included in PCR and sequencing. We amplified the
 internal transcribed space 2 (ITS2) region of the nuclear ribosomal rDNA
 using primers fITS7a and ITS4. PCR procedures, library preparation and
 Multiplex Identification DNA-tags. Paired-end sequencing (2 × 300) was
 performed on an Illumina MiSeq sequencer
DOI: 10.5061/dryad.tmpg4f4wk
title: Association between Procalcitonin Levels and Duration of Mechanical Ventilation in COVID-19 Patients

description: Background Patients diagnosed with COVID-19 frequently require mechanical
 ventilation. Knowledge of laboratory tests associated with the prolonged
 need for mechanical ventilation may guide resource allocation. We
 hypothesized that an elevated plasma procalcitonin level (&gt;0.1
 ng/ml) would be associated with the duration of invasive mechanical
 ventilation. Methods Patients diagnosed with COVID-19, who were admitted
 to any of our health system’s hospitals between March 9th-April 20th, 2020
 and required invasive mechanical ventilation, were eligible for this
 observational cohort study. Demographics, comorbidities, components of the
 Sequential Organ Failure Assessment score, and procalcitonin levels on
 admission were obtained from the electronic health record. The primary
 outcome was the duration of mechanical ventilation; secondary outcomes
 included 28-day mortality and time to intubation. Outcomes were assessed
 within the first 28 days of admission. Baseline demographics and
 comorbidities were summarized by descriptive statistics. Univariate
 comparisons were made using Pearson’s chi-square test for binary outcomes
 and Mann-Whitney U test for continuous outcomes. A multiple linear
 regression was fitted to assess the association between procalcitonin
 levels and the duration of mechanical ventilation.  Results
 Patients with an initial procalcitonin level &gt;0.1 ng/ml required a
 significantly longer duration of mechanical ventilation than patients with
 a level of ≤0.1 ng/ml (p=0.021) in the univariate analysis. There was no
 significant difference in 28-day mortality or time to intubation between
 the two groups. After adjusted analysis using multivariable linear
 regression, the duration of mechanical ventilation was, on average, 5.6
 (p=0.016) days longer in patients with an initial procalcitonin level
 &gt;0.1 ng/ml. Conclusion In this cohort of 93 mechanically ventilated
 COVID-19 patients, we found an association between an initial plasma
 procalcitonin level &gt;0.1 ng/ml and the duration of mechanical
 ventilation. These findings may help to identify patients at risk for
 prolonged mechanical ventilation upon admission.
description: To further protect patients' identities, we provide only
 categorical variable information for body mass index (BMI) and age in this
 data set.
DOI: 10.5061/dryad.xsj3tx9cr
title: The promise and the perils of resurveying to understand global change impacts

description: Historical datasets can be useful tools to aid in understanding the
 impacts of global change on natural ecosystems. Resampling of historically
 sampled sites (“snapshot resampling”) has often been used to detect
 long-term shifts in ecological populations and communities, because it
 allows researchers to avoid long-term monitoring costs and investigate a
 large number of potential trends. But recent simulation-based research has
 called the reliability of resampling into question, and its utility has
 not been comprehensively evaluated. Here we combine long-term empirical
 datasets with novel community-level simulations to explore the accuracy of
 snapshot resampling of both population- and community-level metrics under
 a variety of conditions. We show that snapshot resampling often yields
 spurious conclusions, but the accuracy of results increases when
 inter-annual variability in the response variable is low or the magnitude
 of change through time is high. Snapshot resampling also generally
 performs better for community-level metrics (e.g. species richness) as
 opposed to population-level metrics pertaining to a single species (e.g.
 abundance). Finally, we evaluated strategies to improve the accuracy of
 snapshot resampling, including sampling multiple years at the end of the
 study, but these produced mixed results. Ultimately, we found that
 snapshot resampling should be used with caution, but under certain
 circumstances, can be a useful for understanding long-term global change
 impacts.
DOI: 10.5061/dryad.zkh189380
title: Data from: Heat tolerance in ectotherms scales predictably with body size

description: This study analyses how heat stress varies with body size in ectothermic
 organisms. The analytical approach is based on thermal death time (TDT)
 curves, which take into consideration both the intensity and the duration
 of a thermal stress, and result in a linear relationship between
 temperature and the logarithm of time. We analyzed two separate
 heat tolerance datasets measured in mollusk, arthropod, fish, amphibian
 and reptile species, covering nearly 9 orders of magnitude in size.
 Datasets ware intrinsically different but ultimately convey the same type
 of information on thermal tolerance. The first dataset comprised
 individual measurements of heat stress (i.e., data points expressed in
 temperature and time coordinates) whereas the second dataset described the
 intercept and slope of TDT curves. In both cases, smaller organisms
 exhibited a higher tolerance to an acute heat stress than larger ones, but
 their tolerance declined faster in time.We then combined the results from
 our scaling analyses with geographic information to quantify
 thermal safety margins standardized by mass and time. 
description: All the data employed in this study was compiled from the literature. Dataset 1 includes estimates of critical thermal limits, complemented with information on the duration of each assay obtainedfrom the original sources (<i>n</i>= 328 measurements), whereas Dataset 2 describes slopes and intercepts of individual TDT curves in a different and more restricted sample (<i>n</i>= 62 curves). We combined these datasets with information on the collection sites and wet body mass. Collection sites were then employed to retrieve maximum mean monthly air and sea surface temperatures for terrestrial and marine organisms, respectively. The detailed sources are provided in the attached Readme.txt and in the original paper.     
description: See attached Readme.txt for additional information.
DOI: 10.25349/d9ns4w
title: Tsimane physiological dysregulation data

description: Humans have the longest post-reproductive lifespans and lowest rates of
 actuarial aging among primates. Understanding the links between slow
 actuarial aging and physiological change is critical for improving the
 human “healthspan”. Physiological dysregulation may be a key feature of
 aging in industrialized populations with high burdens of chronic “diseases
 of civilization”, but little is known about age trajectories of
 physiological condition in subsistence populations with limited access to
 public health infrastructure. To better characterize human physiological
 dysregulation, we examined age trajectories of 40 biomarkers spanning the
 immune (n=13 biomarkers), cardiometabolic (n=14), musculoskeletal (n=6),
 and other (n=7) systems among Tsimane forager-horticulturalists of the
 Bolivian Amazon using mixed cross-sectional and longitudinal data
 (n=22,115 observations). We characterized age-related changes using a
 multi-system statistical index of physiological dysregulation (Mahalanobis
 distance; Dm) that increases with age in both humans and other primates.
 Although individual biomarkers showed varied age-profiles, we found a
 robust increase in age-related dysregulation for Tsimane (β=0.17-0.18)
 that was marginally faster than that reported for an industrialized
 Western sample (β=0.14-0.16), but slower than that of other non-human
 primates. We found minimal sex differences in the pace or average level of
 dysregulation for Tsimane. Our findings highlight some conserved patterns
 of physiological dysregulation in humans, consistent with the notion that
 somatic aging exhibits species-typical patterns, despite cross-cultural
 variation in environmental exposures, lifestyles and mortality.
description: Data collection methods are detailed in the associated paper. The
 data here are pre-processed analysis data that can be used to reproduce
 the main analyses of the paper.
description: For details, see the metadata file
 "Metadata_for_Dm_dat.docx".