cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ngf1vhhr2
title: Data from: Examining differences in phylogenetic composition enhances understanding of the phylogenetic structure of the shrub community in the northeastern Qinghai-Tibetan Plateau

description: Abstract: Periodic climatic oscillations and species dispersal during the
 post-glacial period are two important causes of plant assemblage and
 distribution on the Qinghai-Tibet Plateau (QTP). To improve our
 understanding of the bio-geological histories of shrub communities on the
 QTP, we tested two hypotheses. First, the intensity of climatic
 oscillations played a filtering role during community structuring. Second,
 species dispersal during the post-glacial period contributed to the
 recovery of species and phylogenetic diversity and the emergence of
 phylogenetic overdispersion. To test these hypotheses, we investigated and
 compared the shrub communities in the alpine and desert habitats of the
 northeastern QTP. Notably, we observed higher levels of species and
 phylogenetic diversity in the alpine habitat than in the desert habitat,
 leading to phylogenetic overdispersion in the alpine shrub communities
 versus phylogenetic clustering in the desert shrub communities. This
 phylogenetic overdispersion increased with greater climate anomalies.
 These results suggest that 1) although climate anomalies strongly affect
 shrub communities, these phenomena do not act as a filter for shrub
 community structuring, and 2) species dispersal increases phylogenetic
 diversity and overdispersion in a community. Moreover, our investigation
 of the phylogenetic community composition revealed a larger number of
 plant clades in the alpine shrub communities than in the desert shrub
 communities, which provided insights into plant clade-level differences in
 the phylogenetic structures of alpine and desert shrub communities in the
 northeastern QTP.
description: We surveyed 20 sampling sites from the desert habitat and 41 from
 the alpine habitat with little or no disturbance (total = 61; Figure 1).
 Three 10-m × 10-m subplots were established at each sampling site to
 investigate the species composition of the community, identify species and
 collect plant specimens. Eventually, a combination of the species found in
 the three subplots was used to represent the species composition of the
 community at each site.
description: We constructed a phylogenetic tree to present the evolutionary
 relationships between the 285 species found at our sampling sites. As in
 many previous studies, we used the megatree containing 32,223 plant
 species published by Zanne et al. (2014) as a backbone, and used the
 Phylomatic platform to prune this megatree to include only the species
 found at our sampling sites. To identify differences in
 phylogenetic diversity, we used the PD index. We assessed differences in
 the phylogenetic community structures of shrub communities between the two
 habitats using the net relatedness index (NRI) and nearest taxon index
 (NTI) based on this dataset. Specific method seen in picante
 package.
DOI: 10.5061/dryad.sxksn030q
title: Data from: Deconstructing species richness–environment relationships in Neotropical lianas

description: Abstract Aim: Studying species richness patterns by considering all
 species as equivalent units may prevent a deeper understanding of the
 origin and maintenance of biodiversity. Here, we deconstructed the species
 richness of Neotropical lianas by specific attributes of species to study
 richness–environment relationships. Location: Neotropics Taxon: Tribe
 Bignonieae (Bignoniaceae), the largest clade of Neotropical lianas
 Methods: We used five morphological, one geographical and two evolutionary
 attributes of species, each with 2–7 attribute states. We compared the
 environmental response of species richness of each attribute state to the
 response of overall Bignonieae species richness. For those groups of
 species that differed in their environmental response to three-dimensional
 habitat structure, climate, and soil we assessed: (i) the magnitude and
 direction of the environmental response; and (ii) the variation in species
 richness explained by environmental variables and spatial filters using
 variation partitioning analysis. Results: We identified eight attribute
 states whose richness–environment relationship differed from the overall
 richness pattern: three morphological (species with shrubby habit, lacking
 tendrils, and with seeds bearing ellipsoid wings), three geographical
 (species with small, small to medium, and medium to large range sizes),
 and two evolutionary (species of the genera Amphilophium and Cuspidaria)
 attribute states. Areas with high species richness of these eight
 attribute states did not overlap with the centers of Neotropical diversity
 in the tribe Bignonieae. A high fraction of the variation in species
 richness of these eight attribute states was accounted for by spatial
 filters or remained unexplained. Main conclusions: The
 richness-deconstruction approach revealed that richness–environment
 relationships of species with specific attribute states differ from the
 overall species richness pattern. These morphological, geographical and
 evolutionary attribute states are mostly related to the survival and
 persistence in savanna habitats, and show that ecological strategies and
 evolutionary histories need to be taken into account to fully understand
 richness–environment relationships.
description: For more details see "Database_README.txt".
description: For more details see "Database_README.txt".
DOI: 10.5061/dryad.8931zcrmr
title: Data from: Rapid within- and transgenerational changes in thermal tolerance and fitness in variable thermal landscapes

description: Phenotypic plasticity may increase performance and fitness and allow
 organisms to cope with variable environmental conditions. We studied
 within-generation plasticity and transgenerational effects of thermal
 conditions on temperature tolerance and demographic parameters in
 Drosophila melanogaster. We employed a fully factorial design, in which
 both parental (P) and offspring generations (F1) were reared in a constant
 or a variable thermal environment. Thermal variability during ontogeny
 increased heat tolerance in P, but with demographic cost as this treatment
 resulted in substantially lower survival, fecundity and net reproductive
 rate. The adverse effects of thermal variability (V) on demographic
 parameters were less drastic in flies from the F1, which exhibited higher
 net reproductive rates than their parents. These compensatory responses
 could not totally overcome the challenges of the thermally variable
 regime, contrasting with the offspring of flies raised in a constant
 temperature (C) that showed no reduction in fitness with thermal
 variation. Thus, the parental thermal environment had effects on thermal
 tolerance and demographic parameters in fruit-fly. These results
 demonstrate how transgenerational effects of environmental conditions on
 heat tolerance, as well as their potential costs on other fitness
 components, can have a major impact on populations’ resilience to warming
 temperatures and more frequent thermal extremes.
DOI: 10.5061/dryad.msbcc2fvk
title: Data from: Insights on the concept of indicator populations derived from parentage-based tagging in a large-scale coho salmon application in British Columbia, Canada

description: For Pacific salmon, the key fisheries management goal in British Columbia
 (BC) is to maintain and restore healthy and diverse Pacific salmon
 populations, making conservation of salmon biodiversity the highest
 priority for resource management decision-making. Salmon status
 assessments are often conducted on coded-wire tagged subsets of indicator
 populations based on assumptions of little differentiation within or among
 proximal populations. In the current study of southern BC coho salmon
 (Oncorhynchus kisutch) populations, parentage-based tagging (PBT) analysis
 provided novel information on migration and life history patterns to test
 the assumptions of biological homogeneity over limited (generally &lt;
 100km) geographic distances and, potentially, to inform management of
 fisheries and hatchery broodstocks. Heterogeneity for location and timing
 of fishery captures, family productivity, and exploitation rate was
 observed over small geographic scales, within regions that are, or might
 be expected to be, within the area encompassed by a single tagged
 indicator population. These results provide little support for the
 suggestion that information gained from tagged indicator populations is
 representative of marine distribution, productivity, and exploitation
 patterns of proximal populations.
description: 2018_Coho_brood_rubias This is multi-locus
 genotype data for the coho brood collected in 2018. These were sampled
 when they returned to the Hatchery. These are in Rubias format.
 2018_Coho_fishery_rubias This is multi-locus
 genotype data for the coho collected in 2018. These were samples taken in
 fisheries. These are in Rubias format.
 2018_Coho_escapement_rubias This is
 multi-locus genotype data for the coho escapements collected in 2018.
 These were sampled when they returned. These are in Rubias
 format.
DOI: 10.5061/dryad.37pvmcvgn
title: Direct oral anticoagulants in treatment of cerebral venous thrombosis: systematic review

description: Objectives Current guidelines do not recommend direct oral anticoagulants
 (DOAC) to treat cerebral venous thrombosis (CVT) despite their benefits
 over standard therapy. We performed a systematic review to summarize the
 published experience of DOAC therapy in CVT. Data sources MEDLINE, EMBASE,
 and COCHRANE databases up to November 18, 2020. Eligibility criteria All
 published articles of patients with CVT treated with DOAC were included.
 Studies without follow-up information were excluded. Data extraction and
 synthesis Two independent reviewers screened articles and extracted data.
 A risk of bias analysis was performed. Primary and secondary outcome
 measures Safety data included mortality, intracranial hemorrhage (ICH), or
 other adverse events. Efficacy data included recurrent CVT, recanalization
 rates, and disability by modified Rankin Scales (mRS). Results 33 studies
 met inclusion criteria. One randomized controlled trial, 5 observational
 cohorts, and 27 case series or studies reported 279 patients treated with
 DOAC for CVT: 41% dabigatran, 47% rivaroxaban, 10% apixaban, and 2%
 edoxaban, in addition to 315 patients treated with standard therapy. The
 observational cohorts showed a similar risk of death in DOAC and standard
 therapy arms (RR 2.12, 95%CI 0.29-15.59). New ICH was reported in 2 (0.7%)
 DOAC-treated patients and recurrent CVT occurred in 4 (1.5%). A favourable
 mRS between 0 and 2 was reported in 94% of DOAC-treated patients, more
 likely than standard therapy in observational cohorts (RR 1.13, 95% CI:
 1.02-1.25). Conclusion The evidence for DOAC use in CVT is limited
 although suggests sufficient safety and efficacy despite variability in
 timing and dose of treatment. This systematic review highlights that
 further rigorous trials are needed to validate these findings and to
 determine optimal treatment regimens. PROSPERO ID: CRD42017078398
description: The search strategy was iteratively developed with assistance of
 a research librarian (RS). We searched Ovid MEDLINE, Epub Ahead of Print,
 In-Process & Other Non-Indexed Citations, Ovid MEDLINE(R) Daily
 and Ovid MEDLINE(R), EMBASE, Web of Science, and the Cochrane Central
 Register of Controlled Trials for original reports of patients with a
 diagnosis of CVT treated with a DOAC up to November 18, 2020. We included
 all available peer-reviewed studies including RCTs, prospective or
 retrospective observational cohorts, case series and case studies. Studies
 without follow-up data were excluded. Two authors (GB, JG) independently
 reviewed titles and abstracts for inclusion.  Authors were contacted for
 additional information if necessary.
description: Please see the attached ReadMe file for information on use of
 this dataset.
DOI: 10.7280/d1hx1n
title: Transforming knowledge, transforming libraries research project dataset

description: In Spring 2017, the University of California Irvine (UCI) Libraries were
 awarded a 3-year Instituteof Museum and Library Services (IMLS) grant in
 the community anchors category for “Transforming Knowledge/Transforming
 Libraries” (TKTL). Our research team (Audra EagleYun, Jimmy Zavala,
 Krystal Tribbett, and Thuy Vo Dang) sought to explore how libraries can
 fill the gap between calls to diversify the historical record and actually
 diversifying the profession through student-led action research. The
 project design for TKTL is rooted in the social justice imperatives and
 theoretical frameworks of community-based archives and ethnic studies,
 arguing that together these frameworks can transform the historical record
 and how we learn about our history. Working with people who identify with
 members of marginalized communities was central to our approach to the
 TKTL research project. The themes that emerged from our research provide
 key insights into the outcomes of student engagement with library,
 archives, and community building, as well as affective responses
 to the experience of students seeing (or not seeing) themselves
 in the archives. We discovered patterns and divergences in the personal,
 social, and cultural observations of community archives work by all
 involved in community-centered work. The data analysis, along with the
 novel approach of community-centered archives partnerships, articulates
 how participatory, student-centered approaches in building
 community-centered archives can transform engagement between ethnic
 studies, community-based archives, and libraries.
description: For this grant we partnered with the UCI
 departments of African American Studies, Chicano/Latino Studies, and Asian
 American Studies. Overall, the research team collaborated with 12
 different faculty members from the ethnic studies departments at UC Irvine
 for the project and hosted a total of 18 workshops. In some cases, the
 research team collaborated more than once with a faculty member for the
 same course. Over 700 students participated in the project, including 718
 students completing an entrance survey; 686 participating in an in-class
 workshop; 418 completing an exit survey; and 30 students participating in
 an intensive summer cohort experiential learning opportunity.
DOI: 10.5061/dryad.0cfxpnvzh
title: Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data

description: The growing availability of genetic datasets, in combination with machine
 learning frameworks, offer great potential to answer long-standing
 questions in ecology and evolution. One such question has intrigued
 population geneticists, biogeographers, and conservation biologists: What
 factors determine intraspecific genetic diversity? This question
 is challenging to answer because many factors may influence genetic
 variation, including life history traits, historical influences, and
 geography, and the relative importance of these factors varies across
 taxonomic and geographic scales. Furthermore, interpreting the influence
 of numerous, potentially correlated variables is difficult with
 traditional statistical approaches. To address these challenges, we
 analyzed repurposed data using machine learning and investigated
 predictors of genetic diversity, focusing on Nearctic amphibians as a case
 study. We aggregated species traits, range characteristics, and
 &gt;42,000 genetic sequences for 299 species using open-access scripts
 and various databases. After identifying important predictors of
 nucleotide diversity with random forest regression, we conducted follow-up
 analyses to examine the roles of phylogenetic history, geography, and
 demographic processes on intraspecific diversity. Although life history
 traits were not important predictors for this dataset, we found
 significant phylogenetic signal in genetic diversity within amphibians. We
 also found that salamander species at northern latitudes contain lower
 genetic diversity. Data repurposing and machine learning provide valuable
 tools for detecting patterns with relevance for conservation, but
 concerted efforts are needed to compile meaningful datasets with greater
 utility for understanding global biodiversity.
description: Data were compiled from open-access databases and were processed
 using a series of python and R scripts (included with the Dryad
 package).
description: A README file is provided to orient users to the files included.
 The final datasets analyzed are provided in a single directory with
 commented R scripts which can be opened and run in RStudio.
DOI: 10.5061/dryad.3r2280gd2
title: Simulated ONT libraries for genome assembly experimental design

description: Background: High quality reference genome sequences are the core of modern
 genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA
 sequences in excess of 100,000 nucleotides but high error rates make
 sequence assembly and analysis a non-trivial problem as genome size and
 complexity increases. Robust experimental design is necessary for ONT
 genome sequencing and assembly but few studies have attempted to address
 eukaryotic organisms. Here, we present novel results using a combination
 of simulated and empirical ONT and DNA libraries and identify best
 practices for ONT sequencing and assembly. We simulate ONT and Illumina
 DNA sequence reads for Escherichia coli, Caenorhabditis elegans,
 Arabidopsis thaliana, and Drosophila melanogaster and assemble with Canu,
 Flye, and MaSuRCA software to quantify the influence of sequencing
 coverage and assembly approach. We show broad applicability of our methods
 using real ONT data generated for four strains of the nematode
 Caenorhabditis remanei and C. latens. Results: ONT libraries have a unique
 error structure and high sequence depth is necessary to assemble
 contiguous genome sequences.  As sequence depth increases errors
 accumulate and assembly statistics plateau. High-quality assembled
 sequences require high molecular weight DNA extractions that increase
 sequence read length and computational protocols that reduce error through
 pre-assembly correction, read selection and post-assembly ‘polishing.’ Our
 robust experimental design results in highly contiguous and accurate
 genome assemblies for the four strains of C. remanei and C. latens.
 Conclusions: ONT sequencing is inexpensive and accessible but the
 technology’s error structure requires informed experimental design. Our
 quantitative results will be helpful for a broad array of researchers
 seeking guidance for de novo assembly projects.
description: Data were simulated from reference genomes and ONT flowcell data
 with the NanoSim program; assembled with either Canu or Masurca.
DOI: 10.5061/dryad.w6m905qmk
title: Data from: Demography, life history trade-offs, and the gastrointestinal virome of wild chimpanzees

description: In humans, senescence increases susceptibility to viral infection.
 However, comparative data on viral infection in free-living non-human
 primates—even in our closest living relatives, chimpanzees and bonobos
 (Pan troglodytes and P. paniscus)—are relatively scarce, thereby
 constraining an evolutionary understanding of age-related patterns of
 viral infection. We investigated a population of wild eastern chimpanzees
 (P. t. schweinfurthii), using metagenomics to characterize viromes (full
 viral communities) in the feces of 42 sexually mature chimpanzees (22
 males, 20 females) from the Kanyawara and Ngogo communities in Kibale
 National Park, Uganda. We identified 12 viruses from at least four
 families with genomes of both single-stranded RNA and single-stranded DNA.
 Although fecal viromes of both sexes varied with chimpanzee age, viral
 richness increased with age in males but not in females. This effect was
 largely due to three viruses, salivirus, porprismacovirus, and chimpanzee
 stool-associated RNA virus (chisavirus), which occurred more frequently in
 samples from older males. This finding is consistent with the hypothesis
 that selection on males for early-life reproduction compromises investment
 in somatic maintenance, which has delayed consequences for health later in
 life, in this case reflected in viral infection and/or shedding. Fecal
 viromes may be useful for studying processes related to the divergent
 reproductive strategies of males and females, aging, and sex differences
 in longevity.
description: The following data sheets contain data on viral presence and load
 generated from metagenomic analyses of fecal samples from 42 wild
 chimpanzees. Fecal samples were collected from the Kanyawara and Ngogo
 chimpanzee communities in 2016. Pooled reads were sequenced on an Illumina
 MiSeq.
description: Viral loads were calculated as the proportion of reads mapping to
 a given virus out of the total number of trimmed reads per sample. This
 value was then normalized to one million reads and to the length of the
 target sequence (i.e., viral contig length). This final value is the
 number of viral reads per million per kilobase of target
 (vRPM/kb). For more information on the generation and
 analysis of these data, please consult the following:
 http://dx.doi.org/10.1098/rstb.2019.0613
DOI: 10.15468/dl.vdx696
title: Occurrence Download

description: A dataset containing 17721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Hymenoptera Collection - Instituto Nacional de Pesquisas da Amazônia (INPA)",
 "TaxonKey is Apidae"
 ]
}

 The dataset includes 17721 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001565-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00010188.0
title: Available datapackage for study 'A Phase 3b/4 Randomized Double Blind Study Of 5 Mg Of Tofacitinib With And Without Methotrexate In Comparison To Adalimumab With Methotrexate In Subjects With Moderately To Severely Active Rheumatoid Arthritis'

description: To assess the efficacy of tofacitinib monotherapy or tofacitinib with methotrexate as compared to adalimumab with methotrexate. To compare the efficacy of tofacitinib monotherapy compared to tofacitinib combined with methotrexate. To compare effects on all health outcomes measures in the study. To evaluate the safety and tolerability of tofacitinib and adalimumab. To evaluate the safety of the zoster vaccine given prior to the initiation of tofacitinb or adalimumab.
DOI: 10.15468/dl.vqx7ha
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alepidea natalensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 111 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007520-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcxyzs
title: Occurrence Download

description: A dataset containing 1853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Populus simonii",
 "Year 1970-1999"
 ]
}

 The dataset includes 1853 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007521-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.