cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18402806
title: Synch2-Cal: Dataset

description: A dataset of synthetic data for evaluating marker-based multi-view calibration.

 

Github:  https://github.com/andriani-st/Synch2-Cal

Synch2-Cal Parts links:

    Part A: https://zenodo.org/records/17598149

    Part B: https://zenodo.org/records/17609423

    Part C: https://zenodo.org/records/17623803
DOI: 10.5061/dryad.nvx0k6dzb
title: Behavioural thermoregulation and food availability drives fine-scale seasonal habitat partitioning in limpets

description: Small-scale spatial variation in temperature plays a key role in limiting
 the distribution of organisms in thermally heterogeneous environments. In
 the rocky intertidal zone, intra-day temperature variation at small scales
 (cm-m) can easily exceed 30°C. To experimentally test the impact of this
 small-scale temperature heterogeneity on the distribution of an
 ecologically important limpet species (Cellana denticulata), boulders on
 an intertidal rocky reef in New Zealand were rotated, and small-scale
 temperature variability and food availability were measured throughout one
 year. Small-scale variability in thermal tolerance, heart rate, and heat
 shock protein expression was also measured to relate in situ limpet
 distributions with environmental conditions. Temperature variability was
 measured using limpet bio-mimics and HOBO pendant temperature loggers,
 while food availability (chlorophyll a concentration) was measured on in
 situ concrete fiberboard tiles. To measure limpet distributions, every
 tagged limpet on each of 18 boulders was followed from June 2021–2022.
 During each sampling, the location of each limpet, compass direction, and
 slope of the surface that each limpet inhabited were measured. To test for
 physiological differences among limpets from each microhabitat, thermal
 tolerance, and heat shock protein expression were measured in collected
 limpets; in situ heart rates and body temperatures were also measured
 sporadically on hot days. Maximum predicted body temperatures (36–39°C),
 heart rates, and actual body temperatures were greatest on equatorial
 surfaces (i.e., surfaces facing the equator) whereas food availability was
 greatest on poleward-facing surfaces. During summer, limpets moved towards
 surfaces that minimised their body temperatures and maximised food
 availability, namely vertical and poleward facing surfaces and undersides
 of boulders. Thermal tolerance, measured using Arrhenius breakpoint
 temperatures (mean ± SE: 34.7–35.8 ± 0.4–0.7°C) and flat line temperatures
 (36.2–37.4 ± 0.3–0.4°C), were similar among limpets facing different
 directions. Surprisingly, heat shock protein expression was relatively
 consistent throughout the year and among directions. Overall, limpet
 populations are resilient to thermal stress because they effectively use
 behavioural thermoregulation to exploit cooler microhabitats that also
 have greater food availability during summer.
DOI: 10.5061/dryad.nzs7h44x5
title: Signal detection theory applied to giant pandas: Do pandas go out of their way to make sure their scent marks are found?

description: Inter-animal communication allows signals released by an animal to be
 perceived by others. Scent-marking is the primary mode of such
 communication in giant pandas (Ailuropoda melanoleuca). Signal detection
 theory propounds that animals choose the substrate and location of their
 scent marks so that the signals released are transmitted more widely and
 last longer. We believe that pandas trade off scent-marking because they
 are an energetically marginal species and it is costly to generate and
 mark chemical signals. Existing studies only indicate where pandas mark
 more frequently, but their selection preferences remain unknown. This
 study investigates whether the marking behavior of pandas is consistent
 with signal detection theory. Feces count, reflecting habitat use
 intensity, was combined with mark count to determine the selection
 preference for marking. The results showed that pandas preferred to mark
 ridges with animal trails and that most marked tree species were locally
 dominant. In addition, marked plots and species were selected for lower
 energy consumption and a higher chance of being detected. Over 90% of the
 marks used were the longest-surviving anogenital gland secretion marks,
 and over 80% of the marks were oriented toward animal trails. Our research
 demonstrates that pandas go out of their way to make sure their marks are
 found. This study not only sheds light on the mechanisms of scent-marking
 by pandas but also guides us toward more precise conservation of the panda
 habitat.
DOI: 10.13140/rg.2.2.23229.12005
title: Certificate of Participation Celebration of the International Friendship Organization (I.F.O.) Kingdom of Sweden
DOI: 10.15468/dl.nbymd6
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-86.55537 -22.52836,-56.44463 -22.52836,-56.44463 -10.47164,-86.55537 -10.47164,-86.55537 -22.52836))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lupinus munzianus"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003616-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k98sf7mcv
title: Data from: Climate micro-mobilities as adaptation practice in the Pacific: the case of Samoa

description: These data are part of a data portal that accompanies the special issue
 'Climate change adaptation needs a science of culture,'
 published in Philosophical Transactions of the Royal Society B in 2023. To
 access the data portal, please visit 10.5061/dryad.bnzs7h4h4. This data
 set provides the summary of translated interviews with 20 participants
 from the two research sites in the small Pacific island state of Samoa.
 The field data was collected between June and August 2021.
description: Talanoa Methodology: This study employs a comparative qualitative
 case study approach using talanoa style conversational interviews. Talanoa
 literally means ‘talk freely’ and is a term used across the Pacific
 Islands. It has been developed into a research methodology suitable to
 conduct interviews in Pacific Island communities as it replicates a space
 of everyday life on islands in which people share stories and experiences
 (Vaioleti, 2006; Suaali’i-Sauni, 2012). This method helps remove
 psychological distance and reduces the power differential
 between interviewer and interviewee and allowed the participants to share
 their stories in a relaxed atmosphere.
DOI: 10.15468/dl.my8r33
title: Occurrence Download

description: A dataset containing 11122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lacerta agilis",
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 2005-2020"
 ]
}

 The dataset includes 11122 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003614-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p5hqbzkvb
title: Data from: The macroevolutionary singularity of snakes

description: Snakes and lizards (Squamata) represent a third of terrestrial vertebrates
 and exhibit spectacular innovations in locomotion, feeding, and sensory
 processing. However, the evolutionary drivers of this dramatic radiation
 remain poorly known. We infer potential causes and ultimate consequences
 of squamate macroevolution by combining individual-based natural history
 observations (&gt;60,000 animals) with a comprehensive time-calibrated
 phylogeny that we anchored with genomic data (5,400 loci) from 1,018
 species. Through concerted changes in the dynamics of phenotypic evolution
 and speciation, snakes have transformed the macroecological landscape
 through their impact on the trophic architecture of animal communities.
 Squamate biodiversity reflects a legacy of singular events that occurred
 during the early history of snakes and reveals the profound impact of
 historical contingency on vertebrate biodiversity.
description: # The macroevolutionary singularity of snakes This repository contains all
 data and code used to infer the squamate phylogeny, prepare trait and
 other datasets, run comparative analyses, and generate all main and
 supplemental figures. README files with additional information are
 provided within repository subfolders. ## Description of the data and file
 structure Data files are provided via Data Dryad and R/Python scripts are
 provided in the associated Zenodo repository, but the data folder and
 scripts folder are intended to be placed in a common directory so that
 file paths in the scripts can point to the appropriate data files. Data
 are organized into several subfolders that are aligned with the different
 stages of analysis. Scripts generally mirror this structure. Code for
 comparative analyses and main or supplemental figures should be runnable
 by the user. Code for other stages of analysis are shared for the sake of
 transparency, but are not runnable as provided. Phylogenies can be found
 in the data repository, in 1.tree_inference &gt; mainTrees Diversification
 and trait data can be found in alldat.csv (see associated readme).
DOI: 10.5281/zenodo.18403826
title: Methotrexate-Induced Liver Injury Is Associated with Oxidative Stress, Impaired Mitochondrial Respiration, and Endoplasmic Reticulum Stress In Vitro

description: Low-dose methotrexate (MTX) is a standard therapy for rheumatoid arthritis due to its low cost and efficacy. Despite these benefits, MTX has been reported to cause chronic drug-induced liver injury, namely liver fibrosis. The hallmark of liver fibrosis is excessive scarring of liver tissue, triggered by hepatocellular injury and subsequent activation of hepatic stellate cells (HSCs). However, little is known about the precise mechanisms through which MTX causes hepatocellular damage and activates HSCs. Here, we investigated the mechanisms leading to hepatocyte injury in HepaRG and used immortalized stellate cells (hTERT-HSC) to elucidate the mechanisms leading to HSC activation by exposing mono- and co-cultures of HepaRG and hTERT-HSC to MTX. The results showed that at least two mechanisms are involved in MTX-induced toxicity in HepaRG: (i) oxidative stress through depletion of glutathione (GSH) and (ii) impairment of cellular respiration in a GSH-independent manner. Furthermore, we measured increased levels of endoplasmic reticulum (ER) stress in activated HSC following MTX treatment. In conclusion, we established a human-relevant in vitro model to gain mechanistical insights into MTX-induced hepatotoxicity, linked oxidative stress in HepaRG to a GSH-dependent and -independent pathway, and hypothesize that not only oxidative stress in hepatocytes but also ER stress in HSCs contribute to MTX-induced activation of HSCs.
DOI: 10.5281/zenodo.18403827
title: Methotrexate-Induced Liver Injury Is Associated with Oxidative Stress, Impaired Mitochondrial Respiration, and Endoplasmic Reticulum Stress In Vitro

description: Low-dose methotrexate (MTX) is a standard therapy for rheumatoid arthritis due to its low cost and efficacy. Despite these benefits, MTX has been reported to cause chronic drug-induced liver injury, namely liver fibrosis. The hallmark of liver fibrosis is excessive scarring of liver tissue, triggered by hepatocellular injury and subsequent activation of hepatic stellate cells (HSCs). However, little is known about the precise mechanisms through which MTX causes hepatocellular damage and activates HSCs. Here, we investigated the mechanisms leading to hepatocyte injury in HepaRG and used immortalized stellate cells (hTERT-HSC) to elucidate the mechanisms leading to HSC activation by exposing mono- and co-cultures of HepaRG and hTERT-HSC to MTX. The results showed that at least two mechanisms are involved in MTX-induced toxicity in HepaRG: (i) oxidative stress through depletion of glutathione (GSH) and (ii) impairment of cellular respiration in a GSH-independent manner. Furthermore, we measured increased levels of endoplasmic reticulum (ER) stress in activated HSC following MTX treatment. In conclusion, we established a human-relevant in vitro model to gain mechanistical insights into MTX-induced hepatotoxicity, linked oxidative stress in HepaRG to a GSH-dependent and -independent pathway, and hypothesize that not only oxidative stress in hepatocytes but also ER stress in HSCs contribute to MTX-induced activation of HSCs.
DOI: 10.5061/dryad.h44j0zprr
title: Collections of small urban parks consistently support higher species richness but not higher phylogenetic or functional diversity

description: When prioritizing regions for conservation protection, decisions are often
 based on the principle that a single large (SL) reserve should support
 more species than several small (SS) reserves of the same total area
 (SLOSS). This principle remains a central paradigm in conservation
 planning despite conflicting empirical evidence and methodological
 concerns. In urban areas where small parks tend to dominate and policies
 to promote biodiversity are becoming increasingly popular, determining the
 most appropriate prioritization method is critical. Here, we document the
 role of SLOSS in defining the seasonal diversity of birds in 475 parks in
 21 US cities. Collections of small parks were consistently associated with
 higher species richness, spatial turnover, and rarity. Collections of both
 small and large parks were associated with higher phylogenetic and
 functional diversity whose patterns varied across seasons and cities.
 Thus, collections of small parks are a reliable source of species richness
 driven by higher spatial turnover and rarity, whereas collections of both
 small and large parks contain the potential to support higher phylogenetic
 and functional diversity. The presence of strong intra-annual and
 geographic variation emphasizes the need for regional prioritization
 strategies where multiple diversity metrics are examined across parks and
 seasons.
description: # Collections of small urban parks consistently support higher species
 richness but not higher phylogenetic or functional diversity
 Three CSV files containing
 city and urban park information, bird occurrence data, and five avian
 diversity metrics. ## Description of the data and file structure
 **urban-park-id-area.csv** The names of the 21 cities and 475 urban parks
 and each park's identification number (POLYFID) and surface area in
 square meters. **species-composition.csv** Species composition of bird
 assemblages in 475 urban parks (POLYFID) during four seasons: (1)
 nonbreeding, (2) spring migration, (3) breeding, and (4) autumn migration.
 **diversity-metrics.csv** Five diversity metrics calculated for bird
 assemblages in 475 urban parks (POLYFID) during four seasons: (1)
 nonbreeding, (2) spring migration, (3) breeding, and (4) autumn migration.
 The diversity metrics include: species richness (S), phylogenetic
 diversity (PD), mean pairwise distance (MPD), mean nearest taxon distance
 (MNTD), and functional diversity (FD). ## Sharing/Access information The
 park data is publicly available here
 The bird occurrence data
 is publicly available here
DOI: 10.15468/dl.ftt36g
title: Occurrence Download

description: A dataset containing 1723 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Plantae [GBIF Backbone Taxonomy])",
 "GadmGid is one of (COL.2.34_2)"
 ]
 }
 ]
}

 The dataset includes 1723 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003617-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kwh70rz9t
title: River drainage reorganization and reticulate evolution in the Two-Lined Salamander (Eurycea bislineata) species complex

description: The origin and eventual loss of biogeographic barriers can create
 alternating periods of allopatry and secondary contact, facilitating gene
 flow among distinct metapopulations and generating reticulate evolutionary
 histories that are not adequately described by a bifurcating evolutionary
 tree. One such example may exist in the two-lined salamander (Eurycea
 bislineata) species complex, where discordance among morphological and
 molecular datasets has created a “vexing taxonomic challenge”. Previous
 phylogeographic analyses of mitochondrial DNA (mtDNA) suggested that the
 reorganization of Miocene paleodrainages drove vicariance and dispersal,
 but the inherent limitations of a single-locus dataset precluded the
 evaluation of subsequent gene flow. Here, we generate triple-enzyme
 restriction site-associated DNA sequencing (3RAD) data for &gt;100
 individuals representing all major mtDNA lineages and use a suite of
 complementary methods to demonstrate that discordance among earlier
 datasets is best explained by a reticulate evolutionary history influenced
 by river drainage reorganization. Systematics of such groups should
 acknowledge these complex histories and relationships that are not
 strictly hierarchical.
DOI: 10.5061/dryad.tht76hf4v
title: Yeast species and abundances in beetle adult, larva, and environmental samples

description: Yeast species and abundances in beetle adult, larva, and environmental
 samples. Values are given in CFUs (colony forming units) per organ for the
 midgut, hindgut, mycangium, and ovaries; or CFU per gram for the larval
 tunnel, cocoon wall, and new wood flakes. - = absence of yeast.
DOI: 10.15468/dl.tq7zvn
title: Occurrence Download

description: A dataset containing 2865 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kallima inachus"
 ]
}

 The dataset includes 2865 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003618-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21223/p3/f8igi9
title: Dataset for: Participatory Varietal Selection of 20 late blight resistant clones (B3C2) in the locality of Chaquicocha in La Libertad, Peru

description: The Mother and Baby (M&B) trial methodology was adapted by CIP for Participatory Variety Selection (PVS) through decentralized evaluation networks and multi-year evaluations in potato growing areas in the Andean region. The M&B trial design encourages active participation of farmers through the application of treatments through systematic evaluations and selections of treatments in their own plots called "Baby trials" (i.e. farmer managed trials) and in fields with an experimental design called "Mother trials" (i.e. researcher managed trials). Objective: Analyze characteristics, attributes and preferences that men and women have when selecting a new potato variety at the phase of flowering and harvesting. A M&B trial was performed to evaluate 20 clones of the population B3C2 with late blight resistance at the locality of Chaquicocha, Pataz province in La Libertad department, Peru. The trial design was a Randomized Complete Block Design (RCBD) with 3 replicates during 2009-2010. In this experiment, characteristics of plant (size, type of foliage) and resistance to diseases during flowering and harvesting were evaluated.
DOI: 10.5061/dryad.1rn8pk10p
title: Puke or poop? Comparison of regurgitate and faecal samples to infer alpine grasshopper (Paprides nitidus Hutton) diet in experimental plant communities

description: Characterising plant-herbivore interactions is important to understanding
 the processes that influence community structure and ecosystem
 functioning. Traditional methods used to identify plant-herbivore
 interactions are being superseded by non-destructive molecular approaches
 that can infer interactions with greater resolution and accuracy from
 environmental DNA (e.g., faeces and regurgitate). However, few studies
 have compared the use of different types of samples and whether they
 provide similar or contrasting information about species’ diet. Here we
 compared the success of DNA amplification and host plant species
 identification using restriction fragment length polymorphism (RFLP) of
 faecal and regurgitate samples collected from alpine grasshoppers Paprides
 nitidus Hutton during a grassland community mesocosm experiment. We found
 that DNA amplification success was 23% and 86% higher for faecal than
 regurgitate samples from female and male grasshoppers, respectively,
 whereas successful host plant identification using RFLP was 9% higher for
 regurgitate than faecal samples. The mean number of host plant species
 identified per sample (1.40) did not differ between sample types or
 grasshopper sexes. Of the 136 paired faecal-regurgitate samples, just 41%
 and 74% produced exactly or partially matching host plant identifications,
 respectively, indicating that different sample types provided
 complementary information about herbivore diet. Some plant species were
 more likely to be identified from faecal samples than expected by chance,
 and this identification bias skewed towards greater representation in
 faecal samples for plant species with higher investment in leaf tissue. We
 conclude that multiple sample types may be required to fully characterise
 an invertebrate herbivore species’ diet.
DOI: 10.57745/neas5i
title: eco2adapt_Soil MicroResp_T0_Finland.tab

description: :unav
DOI: 10.57745/vldorw
title: eco2adapt_Soil MicroResp_T0_Finland

description: This dataset presents the results of soil CLPP (Community-Level Physiological Profile) analyses performed using the MicroResp™ technique for Finish LL (North Karelia) (Time zero - June 2023)
DOI: 10.5061/dryad.8pk0p2ntm
title: Systematic review of post-fire forest recovery at high latitudes

description: Through this systematic review, we sought to determine the general
 relationship between post-fire tree regeneration densities and latitude in
 forests above 40º N/S. We expected regeneration densities post-fire would
 decrease with increasing latitude, and that forest regeneration would be
 negatively impacted by high burn severities, forest management, harsh site
 conditions, and unprotected microsites. We also anticipated that
 light-demanding species with adaptations to fire would replace
 shade-tolerant species that lack such adaptations post-fire. To achieve
 our objective and test our hypotheses, we analyzed 93 articles that
 directly measured post-fire regeneration at or above 40º N/S.