cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p148m
title: Data from: Environmental and genetic determinants of transcriptional plasticity in Chinook salmon

description: Variation in gene transcription is widely believed to be the mechanistic
 basis of phenotypically plastic traits; however, comparatively little is
 known about the inheritance patterns of transcriptional variation that
 would allow us to predict its response to selection. In addition,
 acclimation to different environmental conditions influences acute
 transcriptional responses to stress and it is unclear if these effects are
 heritable. To address these gaps in knowledge, we assayed levels of
 messenger RNA for 14 candidate genes at rest and in response to a 24-hour
 confinement stress for 72 half-sib families of Chinook salmon reared in
 two different environments (hatchery and semi-natural stream channel). We
 observed extensive plasticity for mRNA levels of metabolic and stress
 response genes and demonstrated that mRNA-level plasticity due to rearing
 environment affects mRNA-level plasticity in response to stress. These
 effects have important implications for natural populations experiencing
 multiple stressors. We identified genotype-by-environment interactions for
 mRNA levels that were dominated by maternal-effects; however, mRNA level
 response to challenge also exhibited a non-additive genetic basis. Our
 results indicate that while plasticity for mRNA-levels can evolve,
 predicting the outcome of selection will be difficult. The inconsistency
 in genetic architecture among treatment groups suggests there is
 considerable cryptic genetic variation for gene expression.
description: raw_dataRaw qPCR data for all analyzed genes (Detectors) for all individuals (Samples). Values are cycle relative threshold (Cq) output by QuantStudio 12K Flex instrument including technical replicates for each gene.Kyle_Methyl6x6_Chinook_OA_20161027_143113_good_genes_tech_reps.txtsample_annotationData file containing family, rearing environment, stress treatment and tank associations for each individual.pcr_efficienciesPCR efficiencies calculated for each gene using LinRegPCREfficiency.txtR_codeR code to perform analyses described in the paper.Wellband_Heredity_Sept2017.R
DOI: 10.17632/34dmwxdsrk.1
title: Long-Term Efficacy, Predictors of Response, and Safety of Abrocitinib in Atopic Dermatitis: A Prospective Real-World Study

description: In this dataset, we have provided supplementary information for the study titled "Long-Term Efficacy, Predictors of Response, and Safety of Abrocitinib in Atopic Dermatitis: A Prospective Real-World Study." The supplementary materials include supplementary document, figures and tables. A detailed description is provided below:
Supplementary Methods: Provides additional methodological details on the Treatment, Outcome measure, and Serum biomarker profiles upon abrocitinib treatment.
Supplementary Figure Legend S1-5.
Supplementary Figure 1. Dynamic changes of multiple outcome measures during abrocitinib treatment. 
Supplementary Figure 2. Dynamic changes in EASI scores of different body sites during abrocitinib treatment.
Supplementary Figure 3. Changes in blood eosinophil counts during abrocitinib treatment.
Supplementary Figure 4. Association between early treatment response and long-term efficacy of abrocitinib.
Supplementary Figure 5. Cumulative incidence of abrocitinib discontinuation stratified by reason for treatment discontinuation.
Supplementary Table S1-11:
Table S1. Baseline demographic and clinical characteristics of AD patients;
Table S2. Rate of changes in EASI scores stratified by different body sites;
Table S3. Clinical factors stratified by patient-reported reflare episodes;
Table S4. Clinical factors stratified by clinician-assessed reflare episodes;
Table S5. Clinical factors stratified by successful versus unsuccessful dose reduction;
Table S6. Overall and subgroup drug survival rates of abrocitinib;
Table S7. Baseline predictors of treatment discontinuation;
Table S8. Reasons for treatment discontinuation;
Table S9. Adverse events during abrocitinib treatment;
Table S10. Adverse events with abrocitinib after week 12, stratified by age group (&lt;60 vs ≥60 years);
Table S11. Baseline cytokine and chemokine levels in early responders and delayed responders.
DOI: 10.7284/100751
title: Meteorological Station data collected during research cruise NH0919 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.1sg4j
title: Data from: Species traits as drivers of food web structure

description: The use of functional traits to describe community structure is a
 promising approach to reveal generalities across organisms and ecosystems.
 Plant ecologists have demonstrated the importance of traits in explaining
 community structure, competitive interactions as well as ecosystem
 functioning. The application of trait-based methods to more complex
 communities such as food webs is however more challenging owing to the
 diversity of animal characteristics and of interactions. The objective of
 this study was to determine how functional structure is related to food
 web structure. We consider that food web structure is the result of 1) the
 match between consumer and resource traits, which determine the occurence
 of a trophic interaction between them, and 2) the distribution of
 functional traits in the community. We implemented a statistical approach
 to assess whether or not 35 466 pairwise interactions between soil
 organisms are constrained by trait-matching and then used a Procrustes
 analysis to investigate correlations between functional indices and
 network properties across 48 sites. We found that the occurrence of
 trophic interactions is well predicted by matching the traits of the
 resource with those of the consumer. Taxonomy and body mass of both
 species were the most important traits for the determination of an
 interaction. As a consequence, functional evenness and the variance of
 certain traits in the community were correlated to trophic complementarity
 between species, while trait identity, more than diversity, was related to
 network topology. The analysis was however limited by trait data
 availability, and a coarse resolution of certain taxonomic groups in our
 dataset. These limitations explain the importance of taxonomy, as well as
 the complexity of the statistical model needed. Our results outline the
 important implications of trait composition on ecological networks,
 opening promising avenues of research into the relationship between
 functional diversity and ecosystem functioning in multi-trophic systems.
description: traits and interactions
 datasetConsumer and resource
 traits and taxonomy with their respective interactions.Dataset.xls
DOI: 10.7284/107721
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise NH1211 using a Hawaii UHDAS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.9bs8n
title: Data from: Patterns of local community composition are linked to large-scale diversification and dispersal of clades

description: At any location, a group of organisms may be represented by several
 clades. What determines which clades will dominate local communities in
 terms of their species richness? Here, this relatively neglected question
 is addressed by analyzing 166 local assemblages of snakes distributed
 globally. For most regions, local assemblages are dominated by clades with
 higher global-scale diversification rates and more frequent dispersal into
 each region, and not by clades that have been present in that region
 longer. This result contrasts with many other studies of local richness
 (in other organisms), which show strong impacts of regional colonization
 time on overall local species richness of clades. Furthermore, even though
 local assemblages are assembled independently on different continents,
 most regions have converged on similar patterns of proportional richness.
 Specifically, a few rapidly diversifying clades dominate most communities
 around the world. The high diversification rates of these clades are then
 linked to their high dispersal rates. Similar patterns may occur in many
 groups, such as plants, frogs, salamanders, birds, and mammals.
description: Online Appendix
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 COnline Appendix
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 EOnline Appendix
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 IOnline Appendix
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 KOnline Appendix
 LOnline Appendix
 MOnline Appendix
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DOI: 10.7284/107724
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1211 using a Furuno GP-150 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/cwtk32p8rm.1
title: Physical Parameters of Iron Meteoroids

description: This dataset provides posterior distribution of the physical characteristics of 15 iron-rich meteoroids inferred via dynamic nested sampling from meteor observations. All the simulations runs are organized in 3 different folders based on the three luminous-efficiency (Tau) assumptions used (3%, 0.3%, 0.08%). For events with CAMO narrow-field tracking, wake plots (observed vs. best-guess lag/deceleration) and available spectra are included. Preferred solutions are in the Results folder and they satisfy both an observational fit criterion and a melting-temperature admissibility test (two events likely require an intermediate luminous efficiency).
DOI: 10.7284/107726
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1211 using a Garmin GPS-17HVS instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.5061/dryad.sk0q2
title: Data from: Robust clustering of languages across Wikipedia growth

description: Wikipedia is the largest existing knowledge repository that is growing on
 a genuine crowdsourcing support. While the English Wikipedia is the most
 extensive and the most researched one with over 5 million articles,
 comparatively little is known about the behaviour and growth of the
 remaining 283 smaller Wikipedias, the smallest of which, Afar, has only
 one article. Here, we use a subset of these data, consisting of 14 962
 different articles, each of which exists in 26 different languages, from
 Arabic to Ukrainian. We study the growth of Wikipedias in these languages
 over a time span of 15 years. We show that, while an average article
 follows a random path from one language to another, there exist six
 well-defined clusters of Wikipedias that share common growth patterns. The
 make-up of these clusters is remarkably robust against the method used for
 their determination, as we verify via four different clustering methods.
 Interestingly, the identified Wikipedia clusters have little correlation
 with language families and groups. Rather, the growth of Wikipedia across
 different languages is governed by different factors, ranging from
 similarities in culture to information literacy.
description: Wikipedia
 dataTime stamps of 14962
 Wikipedia articles across 26 different languages over a span of 15
 years.data.txt
DOI: 10.7284/107727
title: GNSS (Global Navigation Satellite System) data collected during research cruise NH1211 using a Ashtech ADU2 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/k3bdvmh7wz
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.5061/dryad.dg072
title: Data from: American black bears perceive the risks of crossing roads

description: Roadways may negatively impact wildlife species through vehicular-related
 mortality and spatial displacement or obstruction. Here we investigated
 physiological responses, which provide insights into the animal’s
 perception of its environment. We deployed GPS-collars in combination with
 cardiac biologgers on American black bears (Ursus americanus; 18
 bear-years) in areas with differing road densities across Minnesota, USA.
 We tested whether bears exhibited acute stress responses, as defined by
 significant increases in heart rate (HR), associated with road crossings.
 Maximum HR between successive telemetry locations were, on average, 13 bpm
 higher when bears were known to cross a road. They crossed a road, on
 average, once per day. Different demographic groups (males, females with
 and without cubs) responded similarly. We found stronger HR responses when
 crossing high-traffic roads relative to low-traffic in half of the
 bear-year combinations we sampled. Bears crossed high-traffic roads mainly
 at night, but low traffic roads during daylight. Bear HRs first became
 elevated when 73−183 meters away from roadways. Our findings suggest that
 roadways act as an acute stressor, but the magnitude of the stress
 response appears to be mild. Elevated HRs may reflect an increased
 vigilance and recognition of threat when preparing to cross a road. Bears’
 recognition and alertness to human-related threats is adaptive for living
 in human-altered landscapes.
description: Variables in model
 examining effect of road crossing on bear max. heart
 rateThis csv file contains
 all of the processed values of variables included in the first model
 (generalized additive model) examining the influence of road crossings on
 bears' maximum heart rate (MAXHRstep), including other considered
 covariates.RoadX_MaxHRstep_091217_v2.csvVariables in model examining effect of distance to roadway on bear max. heart rateThis csv file contains all of the processed values of variables included in the second model (generalized additive model) examining the influence distance to roadways on bears' maximum heart rate (MAXHRstep), including other considered covariates.DistToRoad_MaxHRpt_091517.csv
DOI: 10.17632/k3bdvmh7wz.1
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.7284/107725
title: Gyrocompass data collected during research cruise NH1211 using a Sperry MK-37 instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/b4pyjc8ybt
title: Experimental data analysis
DOI: 10.5061/dryad.2p6b5
title: Data from: Trunk dental tissue evolved independently from underlying dermal bony plates but is associated to surface bones in living odontode-bearing catfish

description: Although oral dental tissue is a vertebrate attribute, trunk dental tissue
 evolved in several extinct vertebrate lineages but is rare among living
 species. The question of which processes trigger dental-tissue formation
 in the trunk remains open, and would shed light on odontogenesis
 evolution. Extra-oral dental structures (odontodes) in the trunk are
 associated with underlying dermal bony plates, leading us to ask whether
 the formation of trunk bony plates is necessary for trunk odontodes to
 emerge. To address this question, we focus on Loricarioidei: an extant,
 highly diverse group of catfish whose species all have odontodes. We
 examined the location and cover of odontodes and trunk dermal bony plates
 for all six loricarioid families and 17 non-loricarioid catfish families
 for comparison. We inferred the phylogeny of Loricarioidei using a new
 10-gene dataset, eight time-calibration points, and noise-reduction
 techniques. Based on this phylogeny, we reconstructed the ancestral states
 of odontode and bony plate cover, and find that trunk odontodes emerged
 before dermal bony plates in Loricarioidei. Yet we discovered that when
 bony plates are absent, other surface bones are always associated with
 odontodes, suggesting a link between osteogenic and odontogenic
 developmental pathways, and indicating a remarkable trunk odontogenic
 potential in Loricarioidei.
description: Raw
 sequencesAll the markers which
 were newly sequenced for this study.Raw_sequences.tarGene_AlignmentsThe sequence data used in our analyses, already aligned with areas of ambiguous alignment removed, and separated by gene.DS1-DS4_alignmentsConcatenated alignment of our data, from DS1 to DS4. DS1 is all the concatenated data in nucleotides, in DS2, all the coding genes have been translated to amino acids, in DS3, the nucleotide sites in the non-coding genes belonging to the fastest gamma rate category have been removed, and in DS4 the nucleotide sites in the non-coding genes belonging to the *two* fastest gamma rate categories have been removed.TreesAll the trees obtained in this study, with the sequence data that can be found in this submission: A Maximum-Likelihood tree with 1000 bootstraps for each of the four datasets (DS1-DS4), and a Bayesian Inference consensus tree after 20M generations, also for each of the four datasets. Finally, we also include the final time tree obtained with the DS4 dataset, with the time calibration points mentioned in the publications, and after 30M generations, using BEAST v1.8.4. This last file has all the parameter information in the nodes, and has to be visualized with a program like figtree.Sequence ID tableThis table was also included as Supplementary Data in the publication, and shows the GenBank accession numbers for all of the sequences used in this study which came from that service.Sequences_table.xlsx
DOI: 10.7284/107722
title: Meteorological Station data collected during research cruise NH1211 using a SIO MET-System instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/b4pyjc8ybt.1
title: Experimental data analysis
DOI: 10.5061/dryad.gq93s
title: Data from: Historical biogeography of endemic seed plant genera in the Caribbean: did GAARlandia play a role?

description: The Caribbean archipelago is a region with an extremely complex geological
 history and an outstanding plant diversity with high levels of endemism.
 The aim of this study is to better understand the historical assembly and
 evolution of endemic seed plant genera in the Caribbean, by first
 determining divergence times of endemic genera to test whether the
 hypothesized Greater Antilles and Aves Ridge (GAARlandia) land bridge
 played a role in the archipelago colonization, and second by testing South
 America as the main colonization source as expected by the position of
 landmasses and recent evidence of an asymmetrical biotic interchange. We
 reconstructed a dated molecular phylogenetic tree for 625 seed plants
 including 32 Caribbean endemic genera using Bayesian inference and ten
 calibrations. To estimate the geographic range of the ancestors of endemic
 genera we performed a model selection between a null and 2 complex
 biogeographical models that included timeframes based on geological
 information, dispersal probabilities and directionality among regions.
 Crown ages for endemic genera ranged from Early Eocene (53.1 Ma) to Late
 Pliocene (3.4 Ma). Confidence intervals for divergence times (crown and/or
 stem ages) of 22 endemic genera occurred within the GAARlandia time frame.
 Contrary to expectations, the Antilles appears as the main ancestral area
 for endemic seed plant genera and only five genera had a South American
 origin. In contrast with patterns shown for vertebrates and other
 organisms and based on our sampling we conclude that GAARlandia did not
 act as a colonization route for plants between South America and the
 Antilles. Further studies on Caribbean plant dispersal at the species and
 population levels will be required to reveal finer-scale biogeographic
 patterns and mechanisms.
description: concatenated DNA
 matrixDNA matrix used for
 BEAST analysis4reg_concatenated.nexMCC_17.7.2Maximum Clade Credibility obtained in BEAST
DOI: 10.7284/107720
title: Singlebeam Echosounder data collected during research cruise NH1211 using a Knudsen 320B/R instrument system onboard the platform RV New Horizon

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/2j27m2b7td
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.7284/159551
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR2303 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17632/2j27m2b7td.2
title: Teaching First-Grade Students Addition Using Web-Based Interactive Digital Simulations

description: The dataset used in this study consists of quantitative and qualitative data collected during the implementation of web-based interactive digital simulations for teaching addition to first-grade students. The quantitative data include students’ pre-test and post-test scores, which were used to measure learning outcomes before and after the instructional intervention. The qualitative data comprise teachers’ and students’ responses collected through questionnaires administered after the use of the web-based interactive digital simulations. All data were collected for research purposes and anonymized to protect participants’ identities.
DOI: 10.7284/166978
title: Multibeam Echosounder data collected during research cruise SKQ202519S using a Kongsberg EM710 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition