cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.79cnp5htr
title: Core outcome set for burn care research: Delphi survey data

description: Background: Collated evidence from systematic reviews supports clinicians
 in identifying optimal treatment for patients. Evidence is created from
 outcomes that, in burn care, include survival, function, cosmesis, pain,
 and psychological well-being. Currently, this is limited because of
 variation in outcomes reported across trials. Improved selection and
 reporting of outcomes in primary research in burn care could improve
 treatment globally by improving data synthesis and the quality of
 evidence. The availability of a Core Outcome Set (COS), a minimum set of
 the most important outcomes to be reported in all trials of a medical
 condition, would resolve this issue. The aim of this study is to develop a
 COS for international burn care research. Methods and findings: Candidate
 outcomes were identified from systematic reviews and stakeholder
 interviews. Through two rounds of a Delphi survey, international
 multi-disciplinary clinicians, researchers, and UK patients and carers
 prioritised the outcomes. Anonymised feedback aimed to achieve consensus.
 Pre-defined criteria for retaining and dropping outcomes were agreed upon.
 A consensus meeting with voting was held to finalise the COS. Examination
 of all data sources identified 1,021 unique outcomes grouped into 88
 candidate outcomes. Stakeholders included 668 health professionals from 77
 countries and 126 UK patients/carers; 25% of clinical participants were
 from low- or low-middle-income countries. After Round 1, one outcome was
 discarded, and 13 new outcomes were added. After Round 2, 69 items were
 discarded, leaving 31 outcomes for the consensus meeting. Discussion and
 voting agreed on seven core outcomes: death, specified complications,
 ability to do daily tasks, time to wound healing, neuropathic pain and
 itch, psychological well-being, and time to return to school/work.
 Conclusions: This is the first COS for international burn care research.
 Implementation is now needed to improve data synthesis, and support
 evidence-based clinical decision-making in global burn care. It is
 recommended that future trials include measures of these seven outcomes.
description: This data was collected through the REDCap datacase after two
 rounds of a Delphi survey to achieve consensus on items to take forward to
 the consensus meeting. This is the raw data and codebook.
description: There should be no missing values and the data is cleaned.
DOI: 10.5061/dryad.jwstqjq85
title: Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Non-Parametric Bootstrap Support

description: Whole genome comparisons based on Average Nucleotide Identities (ANI) and
 the Genome-to-genome distance calculator have risen to prominence in
 rapidly classifying prokaryotic taxa using whole genome sequences. Some
 implementations have even been proposed as a new standard in species
 classification and have become a common technique for papers describing
 newly sequenced genomes. However, attempts to apply whole genome
 divergence data to delineation of higher taxonomic units and to
 phylogenetic inference have had difficulty matching those produced by more
 complex phylogenetic methods. We present a novel method for generating
 statistically supported phylogenies of archaeal and bacterial groups using
 a combined ANI and alignment fraction-based metric. For the test cases to
 which we applied the developed approach we obtained results comparable
 with other methodologies up to at least the family-level.  The
 developed method uses non-parametric bootstrapping to gauge support for
 inferred groups.  This method offers the opportunity to make use
 of whole-genome comparison data, that are already being generated, to
 quickly produce phylogenies including support for inferred groups.
 Additionally, the developed ANI methodology can assist classification of
 higher taxonomic groups. Included herein are supplemental materials, and
 all whole genome datasets used throughout the construction of this work.
description: All genomes (unless noted in table S1) are pulled from NCBI at
 the accession number provided in table S1. All genomes are provided in
 fasta format.
DOI: 10.5061/dryad.9kd51c5gk
title: Data from: Poor endometrial proliferation after clomiphene is associated with altered estrogen action

description: Context: Suboptimal endometrial thickening is associated with
 lower pregnancy rates and occurs in some infertile women treated with
 clomiphene. Objective: To examine cellular and molecular
 differences in the endometrium of women with suboptimal versus optimal
 endometrial thickening following clomiphene.
 Design: Translational prospective cohort study from 2018-2020.
 Setting: University-affiliated clinic. Patients or
 Participants: Reproductive age women with unexplained infertility
 treated with 100mg of clomiphene cycle days 3-7 who developed optimal
 (≥8mm; n=6, controls) or suboptimal (&lt;6mm; n=7, subjects)
 endometrial thickness. Interventions: Pre-ovulatory blood and
 endometrial sampling. Main outcome measures: Endometrial tissue
 architecture, abundance and location of specific proteins, RNA expression,
 ERa binding. Results: The endometrium of suboptimal subjects
 compared to optimal controls was characterized by a reduced volume of
 glandular epithelium (16% vs 24%, P=0.01), decreased immunostaining of
 markers of proliferation (PCNA, ki67) and angiogenesis (PECAM-1),
 increased immunostaining of pan-leukocyte marker CD45 and ERb, but
 decreased ERa immunostaining (all P&lt;0.05). RNASeq identified 398
 differentially expressed genes between groups. Pathway analysis of
 differentially expressed genes indicated reduced proliferation (Z-score=
 -2.2, P&lt;0.01), decreased angiogenesis (Z-score = -2.87,
 P&lt;0.001), increased inflammation (Z-score= +2.2, P&lt;0.01),
 and ERb activation (Z-score= +1.6, P&lt;0.001) in suboptimal subjects.
 ChIP-seq identified 6 genes bound by ERα that were differentially
 expressed between groups (P&lt;0.01), some of which may play a role in
 implantation. Conclusions: Women with suboptimal endometrial thickness
 after clomiphene exhibit aberrant estrogen receptor expression patterns,
 architectural changes and altered gene and protein expression, suggesting
 reduced proliferation and angiogenesis in the setting of increased
 inflammation.
DOI: 10.25349/d9n89m
title: Protecting the global ocean for biodiversity, food and climate

description: The ocean contains unique biodiversity, provides valuable food resources,
 and is a major sink for anthropogenic carbon. Marine protected areas
 (MPAs) are an effective tool for restoring ocean biodiversity and
 ecosystem services but at present only 2.7% of the ocean is
 highly protected. This low level of ocean protection is due largely to
 conflicts with fisheries and other extractive uses. To address this issue,
 here we developed a conservation planning framework to prioritize highly
 protected MPAs in places that would result in multiple benefits today and
 in the future. We find that a substantial increase in ocean protection
 could have triple benefits, by protecting biodiversity, boosting the yield
 of fisheries, and securing marine carbon stocks that are at risk from
 human activities. Our results show that most coastal nations contain
 priority areas that can contribute substantially to achieving these three
 objectives of biodiversity protection, food provision, and carbon storage.
 A globally coordinated effort could be nearly twice as efficient as
 uncoordinated, national-level conservation planning. Our flexible
 prioritization framework could help to inform both national marine spatial
 plans and global targets for marine conservation, food security,
 and climate action.
description: See the methods in the paper and the code in github
DOI: 10.15468/dl.s3hbzp
title: Occurrence Download

description: A dataset containing 32477 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Musa"
 ]
}

 The dataset includes 32477 records from 639 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002778-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dv41ns1xc
title: Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

description: Genomic variation of an invasive species may be affected by complex
 demographic histories and evolutionary changes during invasions. Here, we
 describe the relative influence of bottlenecks, clonality, and population
 expansion in determining genomic variability of the widespread red
 macroalga Agarophyton vermiculophyllum. Its introduction from mainland
 Japan to the estuaries of North America and Europe coincided with shifts
 from predominantly sexual to partially clonal reproduction and rapid
 adaptive evolution. A survey of 62,285 SNPs for 351 individuals from 35
 populations, aligned to 24 chromosome-length scaffolds indicate that
 linkage disequilibrium (LD), observed heterozygosity (Ho), Tajima’s D, and
 nucleotide diversity (Pi) were greater among non-native than native
 populations. Evolutionary simulations indicate LD and Tajima’s D were
 consistent with a severe population bottleneck. Also, the increased rate
 of clonal reproduction in the non-native range could not have produced the
 observed patterns by itself but may have magnified the bottleneck effect
 on LD. A bottleneck or clonality limitedly impact Ho and Pi, rather, the
 increased Ho and Pi in the non-native range is possibly due to elevated
 marker diversity in the genetic source populations. We refined the
 previous invasion source region to a ~50km section of northeastern Honshu
 Island. Outlier detection methods failed to reveal any consistently
 differentiated loci shared among invaded regions, likely because of the
 complex A. vermiculophyllum demographic history. Our results reinforce the
 importance of demographic history, specifically founder effects, in
 driving genomic variation of invasive populations, even when localized
 adaptive evolution and reproductive system shifts are observed.
description: The dataset includes ddRAD-seq data in beagle format produced
 from ANGSD, the assembled <i>Agarophyton vermiculophyllum
 </i>genome, and all scripts used for data analysis and figure
 generation. Download and view README.md for additional dataset
 information.
description: Demultiplexed raw reads are available as an NCBI BioProject
 (PRJNA700770), and the NCBI BioSample accessions are available in the
 BioSampleObjects.txt file included in the dataset.
 The assembled <i>Agarophyton vermiculophyllum </i>genome was
 submitted to NCBI BioSample (SAMN17860744).
DOI: 10.5061/dryad.m0cfxpp31
title: Data from: Organic carbon, grain size, elemental/isotopic composition

description: Salt marshes and seagrass meadows can sequester and store high quantities
 of organic carbon (OC) in their sediments relative to other marine and
 terrestrial habitats. Assessing carbon stocks, carbon sources, and the
 transfer of carbon between habitats within coastal seascapes are each
 integral in identifying the role of blue carbon habitats in coastal carbon
 cycling. Here, we quantified carbon stocks, sources, and exchanges in
 seagrass meadows, salt marshes, and unvegetated sediments in six bays
 along the Pacific coast of California. The salt marshes studied here
 contained approximately twice as much OC as did seagrass meadows, 23.51 ±
 1.77 kg OC m-3 compared to 11.01 ± 1.18 kg OC m-3, respectively. Both
 seagrass and salt marsh sediment carbon stocks were higher than previous
 estimates from this region but lower than global and U.S.-wide averages,
 respectively. Seagrass-derived carbon was deposited annually into adjacent
 marshes during fall seagrass senescence. However, isotope mixing models
 estimate that negligible amounts of this seagrass material were ultimately
 buried in underlying sediment. Rather, the vast majority of OC in sediment
 across sites was likely derived from planktonic/benthic diatoms and C3
 salt marsh plants.
description: See manuscript.
DOI: 10.7280/d11m5q
title: Evaluating Promising Practices in Undergraduate STEM Lecture Courses

description: Observations were collected to examine instructional practices in large
 undergraduate lecture courses at UCI, particularly in STEM (science,
 technology, engineering, and mathematics). The study began in 2012 with
 the intention of documenting the relative presence or absence of practices
 that potentially promote more active and engaged learning (e.g., enhanced
 faculty-student interaction, enhanced peer interaction, greater attention
 to problem-solving strategies, more opportunities for personalized
 learning, opportunities to receive and communicate information across
 diverse channels and modalities, more data-based instruction). 
description: Researchers observed introductory
 STEM courses at UCI to document instructional
 practice. For each observation,
 research assistants videotaped lectures and collected data on
 instructional strategies using a researcher-developed observation protocol
 known as Simple Protocol for Observing Undergraduate Teaching
 (SPROUT). Observations included detailed field notes during the lecture
 that were subsequently transferred to the observation protocol and
 contained both dichotomous indicators and qualitative evidence. Two
 researchers overlapped on 20 percent of the course sessions with
 inter-rater reliability of Cohen's kappa = 0.80. Coding disagreements
 and ambiguities were discussed among the research team as they occurred
 during the data collection process. 
 Student administrative data was collected from the Office of Institutional Research (OIR). In addition to demographic and academic data, OIR provided course enrollments and grades (both in observed courses and in courses that students took in subsequent terms), allowing tracking of student progress toward STEM degrees. Students can enroll in more than one of the observed courses.
description: Papers linked may not use the full dataset.
DOI: 10.5061/dryad.hdr7sqvh7
title: Data from: Flower consumption, ambient temperature and rainfall modulate drinking behavior in a folivorous-frugivorous arboreal mammal

description: In these datasets we provided information on the drinking behavior
 in 14 wild groups of brown howler monkeys (Alouatta guariba
 clamitans) inhabiting small, medium, and large Atlantic Forest fragments
 in southern Brazil. We provided two datasets: (1) full data on the
 drinking behavior of the 14 study groups, and (2) the dataset used to run
 the GLMMs described in the main manuscript. Overall, we found a
 wide variation in the mean rate of drinking among groups (range=0-16
 records/day). Streams (44% of 1,258 records) and treeholes (26%) were the
 major types of water sources, followed by bromeliads in the canopy (16%),
 pools (11%), and rivers (3%). Further details in Chaves et al. (2021).
description: Data on drinking behavior of the fourteen howler groups was
 collected during periods ranging from 12 to 21 months, distributed in five
 year intervals: (i) January to December 1996 (group L5), (ii) June 2002 to
 August 2003 (group M1), (iii) January to December 2005 (groups S7, M2, and
 L4), (iv) June 2011 to June 2014 (groups S1, S2, S3, L1, L2, and L3), and
 (v) June 2018 to July 2019 (S4, S5, and S6). We collected data for all
 groups from dawn to dusk using high-resolution 10 x 42
 binoculars. We monitored the groups on a monthly basis
 during three to eight consecutive days in periods (i), (ii), and (iii),
 during four to five consecutive days on a bimonthly basis in period (iv),
 and during four to nine consecutive days on a monthly basis in period
 (v).
DOI: 10.6084/m9.figshare.28915874
title: NZ Fish Passage Assessment Tool BN model data

description: These data are the results of an expert elicitation process carried out in New Zealand to evaluate the risk to fish passage at different instream structures based on the characteristics of the structure. The data were collected using the four-point elicitation method (best, lower, upper, confidence) and used as the basis of a Bayesian Network model that underpins the New Zealand Fish Passage Assessment Tool. Data are made available for non-commercial uses only.
DOI: 10.6084/m9.figshare.28915874.v1
title: NZ Fish Passage Assessment Tool BN model data

description: These data are the results of an expert elicitation process carried out in New Zealand to evaluate the risk to fish passage at different instream structures based on the characteristics of the structure. The data were collected using the four-point elicitation method (best, lower, upper, confidence) and used as the basis of a Bayesian Network model that underpins the New Zealand Fish Passage Assessment Tool. Data are made available for non-commercial uses only.
DOI: 10.25338/b8wk8f
title: Genetic structure in a cnidarian symbiont is correlated with geographic location, environment, and host species

description: Corals and cnidarians form symbioses with dinoflagellates across a wide
 range of habitats from the tropics to temperate zones. Notably, these
 partnerships create the foundation of coral reef ecosystems and are at
 risk of breaking down due to climate change. This symbiosis couples the
 fitness of the partners, where adaptations in one species can benefit the
 holobiont. However, the scales over which each partner can match their
 current - and future - environment are largely unknown. We investigated
 population genetic patterns of temperate anemones (Anthopleura spp.) and
 their endosymbiont Breviolum ‘muscatinei’, across an extensive geographic
 range to identify the spatial scales over which local adaptation is
 possible. Similar to previously published results, two solitary host
 species exhibited isolation-by-distance across hundreds of kilometers.
 However, symbionts exhibited genetic structure across multiple spatial
 scales, from geographic location to depth in the intertidal zone, and host
 species, suggesting that symbiont populations are more likely than their
 hosts to adaptively mitigate the impact of increasing temperatures.
description: Tentacle samples were collected across the geographic range of
 Anthopleura spp. along the Pacific coast of North America, 16 sites for
 the hosts, 7 sites for the symbionts. Hosts were genotyped using RAD-seq
 and subsequent alignment to the A. sola draft genome. Symbiont populations
 living within tentacles were enriched using FACS, sequenced using RAD-seq,
 and genotyped after alignment to the B. minutum draft genome. We included
 SNPs that were present in at least half of the surveyed populations in at
 least half of the individuals of each population at a coverage of greater
 than 5x. For the symbionts, we excluded SNPs that occurred within 500 bp
 of one another. We also characterized the surrounding
 benthic community around each anemone or aggregation. A matrix of the
 surrounding benthic community is also included, one line per
 individual.
description: Genotype files for both hosts and symbionts were generated using
 plink. ped files contain the genotype information (bed files are binary
 versions), other information regarding locus location on genome assembly
 scaffolds, individual names and geographic groupings are available in
 .map, .famMissing values are present in the genotyping file as
 "0."
DOI: 10.5061/dryad.jsxksn08j
title: Simulation trajectories from ab-initio molecular dynamics of 4x4x4 super cell of Li3OCl with 4 Li concentrations

description: Lithium-rich oxychloride antiperovskites are promising solid electrolytes
 for enabling next-generation batteries. Here, we report a comprehensive
 study varying Li+ concentrations in Li3OCl using ab-initio molecular
 dynamics simulations. The simulations accurately capture the complex
 interactions between Li+ vacancies (V'Li), the dominant mobile
 species in Li3OCl. The V'Li polarize and distort the host
 lattice, inducing additional non-vacancy mediated diffusion mechanisms and
 correlated diffusion events that reduce the activation energy barrier at
 concentrations as low as 1.5% V'Li. Our analyses of discretized
 diffusion events Li in both space and time illustrate the critical
 interplay between correlated dynamics, polarization, and local distortion
 in promoting ionic conductivity in Li3OCl.
description: The simulation trajectories were generated from VASP simulations
 of a Li3OCl 4x4x4 supercell at four Li vacancy concentrations and 5
 temperatures for each concentration (1100 K - 1500K). 
 The XDATCARs from the VASP simulations were unwrapped and the
 trajectories are provided in xyz file format.  The
 entire trajectory is provided, including the equilibration
 steps.
description: Twenty Li3OCl trajectories in the xyz file format (ASCII) can be
 downloaded. These ab-initio molecular dynamics simulations were performed
 on a 4x4x4 supercell of Li3OCl, as descrbied in the manuscript that
 presents this data. The lattice vector was the same for each simulation:
 a=16.08, b=16.08, c=16.08 Angstroms.  The trajectories
 can be visualized with a variety of software packages, including vmd, ase
 gui, ovito, and vesta. The simulations showed the
 effect of increased vacancy concentration on the diffusion mechanism. 
 Four different vacancy concentrations were simulated: out of 192 Li atoms
 1, 2, 3, and 4 vacancies were created by removing Li+.  Five different
 temperatures were simulated at each concentration. The
 tar.gz files are organized based on vacancy concentration and are labled
 1vac, 2vac, 3vac, and 4vac.  Five simualtions at the various temperatures
 are contained in the tar.gz file, organized into subdirectories. Each
 simulation has the same filename - unwrapped.xyz. The entire trajectory
 is provided, including equilibration steps.
DOI: 10.5061/dryad.59zw3r269
title: Data from: Effects of food intake and hydration state on behavioral thermoregulation and locomotor activity in the tropidurid lizard Tropidurus catalanensis

description: Theoretical models predict that lizards adjust their body temperature
 through behavioral thermoregulation as a function of food availability.
 However, behavioral thermoregulation is also governed by interactions
 among physiological and ecological factors other than food availability,
 such as hydration state, and sometimes it can even conflict with the
 locomotor activity of animals. Here, we aimed to investigate the role of
 food intake and hydration state on behavioral thermoregulation and
 voluntary locomotor activity in the lizard Tropidurus catalanensis. We
 hypothesized that food intake can influence behavioral thermoregulation
 via an interaction with hydration state.We also hypothesized that lizards
 should endeavor to spend as little time as possible to reach their
 preferred body temperature to defend other physiological and/or ecological
 functions. We collected lizards in the field and brought them to the
 laboratory to measure the preferred temperature selected in a thermal
 gradient and the total distance traveled by them in fed and unfed
 conditions and with variable hydration state. Our results showed that food
 consumption was the most important predictor of preferred temperature. In
 contrast, either the hydration state alone or its interaction with food
 consumption did not have important effects on the lizards’ thermal
 preference. Also, we found that the total distance traveled by lizards was
 not affected by food intake and was barely affected by the hydration
 state. We provide an experimental approach and a robust analysis of the
 factors that influence behavioral thermoregulation and locomotor activity
 in a tropical lizard.