cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.prr4xgxhf
title: Data from: Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets

description: There are considerable phylogenetic incongruencies between morphological
 and phylogenomic data for the deep evolution of animals. This has
 contributed to a heated debate over the earliest-branching lineage of the
 animal kingdom: The sister to all other Metazoa (SOM). Here we use
 published phylogenomic datasets (∼45,000-400,000 characters in size with
 ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the
 impact of incorporating morphological datasets (∼15-275 characters). We
 additionally use small exemplar datasets to quantify how increased taxon
 sampling can help stabilize phylogenetic inferences. We apply a plethora
 of common methods, i.e. likelihood models and their "equivalent"
 under parsimony: character weighting schemes. Our results are at odds with
 the typical view of phylogenomics, i.e., that genomic-scale datasets will
 swamp out inferences from morphological data. Instead, weighting
 morphological data 2-10× in both likelihood and parsimony can in some
 cases "flip" which phylum is inferred to be the SOM. This
 typically results in the molecular hypothesis of Ctenophora as the SOM
 flipping to Porifera (or occasionally Placozoa). However, greater taxon
 sampling improves phylogenetic stability, with some of the larger
 molecular datasets (&gt;200,000 characters and up to ∼100 taxa)
 showing node stability even with ≧100× up-weighting of morphological data.
 Accordingly, our analyses have three strong messages. A) The assumption
 that genomic data will automatically "swamp out" morphological
 data is not always true for the SOM question. Morphological data have a
 strong influence in our analyses of combined datasets, even when
 outnumbered thousands of times by morphological data. Morphology therefore
 should not be counted out a priori. B.) We here quantify for the first
 time how the stability of the SOM node improves for several genomic
 datasets when the taxon sampling is increased. C.) The patterns of
 "flipping points" (i.e., the weighting of morphological data it
 takes to change the inferred SOM) carry information about the phylogenetic
 stability of matrices. The weighting space is an innovative way to assess
 comparability of datasets that should be developed into a new sensitivity
 analysis tool.
description: See ReadMe files in Supplemental Files 1 and 2.
DOI: 10.5061/dryad.44j0zpc9h
title: Low first-year apparent survival of passerines in abandoned fields in northwestern Russia

description: First-year survival probability of migratory passerines during the period
 between fledging and first reproduction is a highly variable parameter
 having a major effect on population dynamics. We used a long-term
 mark–recapture dataset (2002–2018) to examine first-year survival of three
 passerine species breeding in abandoned agricultural fields of
 northwestern Russia: the Booted Warbler Iduna caligata, the Whinchat
 Saxicola rubetra and the Western Yellow Wagtail Motacilla flava. We banded
 3457 nestlings including 1363 Booted Warblers, 1699 Whinchats and 395
 Yellow Wagtails and resighted 12 Booted Warblers, 29 Whinchats and 13
 Yellow Wagtails in the year after fledging. We evaluated first-year
 apparent survival rates using Cormack-Jolly-Seber models in MARK within
 the multispecies approach. We tested effect of fledge date on the
 first-year apparent survival. In all focal species first-year apparent
 survival rates were extremely low and reached the lower limits known for
 migratory passerines. We found no differences in first-year survival rates
 among the three species: estimated average first-year apparent survival
 rate of all species was 0.05±0.01. The fledge date had a considerable
 impact on first-year survival rate: later fledge dates negatively affected
 first-year survival. We suggest that first-year apparent survival rates in
 our study were low due to low natal philopatry and high mortality in the
 postfledging period. Low apparent first-year survival may be a specific
 feature of open-nesting birds breeding in abandoned fields that are
 low-quality habitats because of high predation pressure.
DOI: 10.15468/dl.ten3hp
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus dakini",
 "Year 1900-2026"
 ]
}

 The dataset includes 7 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002176-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.73n5tb2tb
title: Notochord vacuoles absorb compressive bone growth during zebrafish spine formation

description: The vertebral column or spine assembles around the notochord rod which
 contains a core made of large vacuolated cells. Each vacuolated cell
 possesses a single ﬂuid-ﬁlled vacuole, and loss or fragmentation of these
 vacuoles in zebrafish leads to spine kinking. Here, we identified a
 mutation in the kinase gene dstyk that causes fragmentation of notochord
 vacuoles and a severe congenital scoliosis-like phenotype in zebrafish.
 Live imaging revealed that Dstyk regulates fusion of membranes with the
 vacuole. We find that localized disruption of notochord vacuoles causes
 vertebral malformation and curving of the spine axis at those sites.
 Accordingly, in dstyk mutants the spine curves increasingly over time as
 vertebral bone formation compresses the notochord asymmetrically, causing
 vertebral malformations and kinking of the axis. Together, our data show
 that notochord vacuoles function as a hydrostatic scaffold that guides
 symmetrical growth of vertebrae and spine formation.
description: This dataset includes all raw imaging data for all figures and
 supplementary figures. All whole mount images and
 confocal files have not been processed.     Also
 included is the raw micro-ct data for figure 2E and 2F and the cropped
 lightsheet movies. Lightsheet files were cropped to only include the slice
 of interest.  All data collected for quantifications is
 located in the excel file in the figure 1 folder.   
  
description: Each tab in the excel file refers the the raw data from the
 cooresponding figure.
DOI: 10.25349/d9sp43
title: Land use change in California, 2001-2100

description: The SLEUTH urbanization and land use change model was used to produce
 century-long forecasts of California’s land uses to the year 2100. We
 describe how data were assembled and conflated for the model, how the
 model was applied to the very large and high resolution dataset, and how
 calibration of the model was performed using a genetic algorithm. The
 calibration results showed that the model accuracy was high, and suitable
 for simulations, which used Monte Carlo methods to capture both future
 land uses and their modeling uncertainty. The simulations showed the
 amount and location of anticipated futures changes in land use, dominated
 by changes to urban and a few other pairs of land use transitions. The
 proportion of urban land was 6.7% in 2001, 8.8% in 2011, and is forecast
 to reach 14.5% in 2050 and 17.6% in 2100, converting some 4,456,160
 hectares of land. Farmland lost 224,135 Ha. between 2001 and 2011, but is
 projected to lose another 1,346,912 Ha by 2100, a decline over the century
 from 10.05% to 6.76% of the total land area. Of the 15 top land
 transitions by land area, accounting for 88% of the expected change by
 area from 2001-2100, only 6 of them are expected to be transitions to
 urban, the remainder are combinations of changes among shrublands,
 grassland and forest that will also have major consequences for
 California’s future. The authors hope that the projections of land use
 change will be of use to other scientists, land managers and policy
 makers.
description: The data set consists of the full set of inputs for the SLEUTH
 land use change model for California for the period 2001-2100. The primary
 data source is the 2001 and 2011 land use data from the National Land
 Cover Database. The model was calibrated using methods described in the
 paper, and forecasts of future land use produced for each decade from 2020
 to 2100. Also included are the SLEUTH calibration results and individual
 forecasts by data tile, along with uncertainty estimates for the model
 forecasts. Forecast data sets are in GeoTIFF format, recificed to the
 Albers Conformal Conic projection and NAD83.
description: Three folders are archived.  CA_Zones_GeoTIFF
 contains the forecast and data images, with WRL files as
 metadata. SLEUTHGAInput contains the raw GIF format
 input files for SLEUTH modeling, structured by zone and subtile, with the
 calibration results. SLEUTHOutput contains the same
 structure, but includes the SLEUTH output tiles before their assembly in
 GeoTIFF format.
DOI: 10.25338/b8j61w
title: The non-traditional Coriolis terms and tropical convective clouds

description: The full, three-dimensional Coriolis force includes the familiar
 sine-of-latitude terms as well as frequently dropped cosine-of-latitude
 terms (Nontraditional Coriolis Terms [NCT]).  The latter are
 often ignored because they couple the zonal and vertical momentum
 equations which in the large-scale limit of weak vertical velocity is
 considered insignificant almost everywhere.  Here, we ask whether
 equatorial mesoscale clouds which fall outside the large-scale limit are
 affected by the NCT.  A simple scaling indicates that a
 Lagrangian parcel convecting at 10m/s through the depth of the
 troposphere should be deflected over 2km to the west.  To
 understand the real impact of NCT, we develop a mathematical framework
 which describes an azimuthally symmetric convective circulation with an
 analytical expression for an incompressible poloidal flow.
  Because the model incorporates the full 3-dimensional flow
 associated with convection, it uniquely predicts not only the westward
 tilt of clouds but also a  meridional diffluence of western cloud
 outflow.  To test these predictions, we perform a set of
 cloud-resolving simulations whose results show preferential lifting of
 surface parcels with positive zonal momentum and zonal asymmetry in
 convective strength.  RCE simulations show changes to the
 organization of coherent precipitation regions and a decrease in mean
 convective intensity of approximately 2m/s above the freezing
 level.  An additional pair of dry cloud-resolving simulations
 designed to mimic the steady state flow of the model show maximum
 perturbations to the upper level zonal flow of 8m/s.  Together,
 the numerical and analytic results suggest the NCT consequentially alter
 equatorial mesoscale convective circulations and should be considered in
 conceptual models.
description: These simulations are described fully in Igel and Biello
 (2020).
description: These are standard, full RAMS output files stored in HDF5
 format.
DOI: 10.5061/dryad.t4b8gthz3
title: The vulnerability of shellfish aquaculture to climate change and ocean acidification– a global assessment

description: Human-induced climate change and ocean acidification (CC-OA) is changing
 the physical and biological processes occurring within the marine
 environment, with poorly understood implications for marine life. Within
 the aquaculture sector, molluscan culture is a relatively benign method of
 producing a high-quality, healthy and sustainable protein source for the
 expanding human population.  We modelled the Vulnerability of
 global bivalve mariculture to impacts of CC-OA over the period 2020 to
 2100, under RCP8.5.  Vulnerability, assessed at the national
 level, was dependent on CC-OA-related Exposure, taxon-specific Sensitivity
 and Adaptive capacity in the sector.  Exposure risk increased
 over time from 2020 to 2100, with ten nations predicted to experience
 Very-high Exposure to CC-OA in at least one decade during the period 2020
 - 2100. Predicted high Sensitivity in developing countries resulted,
 primarily, from the cultivation of species that have a narrow habitat
 tolerance, whilst in some European nations (France, Ireland, Italy,
 Portugal and Spain) high Sensitivity was attributable to the relatively
 high economic value of the shellfish production sector. 
 Predicted Adaptive capacity was low in developing countries primarily due
 to governance issues, while in some developed countries (Denmark, Germany,
 Iceland, Netherlands, Sweden, and the United Kingdom) it was linked to
 limited species diversity in the sector.  Developing and least
 developed nations (n = 15) were predicted to have the highest overall
 Vulnerability.  Across all nations, 2060 was identified as a
 tipping point where predicted CC-OA will be associated with the greatest
 challenge to shellfish production.  However, rapid declines in
 mollusc production are predicted to occur in the next decade for some
 nations, notably North Korea.  Shellfish culture offers human
 society a low-impact source of sustainable protein.  This
 research highlights, on a global scale, the likely extent and nature of
 the CC-OA related threat to shellfish culture and this sector enabling
 early-stage adaption and mitigation.
description: The source of these data are described in the
 'Data_availability' document, while processing details are
 contained within the 'README' and 'R_Script'
 files.
description: Please note the "README",
 "Data_availability", and "R_Script" files.
DOI: 10.15468/dl.vvfck8
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-80.36371 -2.60881,-77.14477 -2.60881,-77.14477 0.89963,-80.36371 0.89963,-80.36371 -2.60881))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Azolla filiculoides"
 ]
}

 The dataset includes 30 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002177-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k3j9kd543
title: Direct oral anticoagulants in atrial fibrillation patients with concomitant hyperthyroidism

description: Objective Patients with hyperthyroidism were excluded from randomized
 clinical trials of direct oral anticoagulants(DOACs) for stroke prevention
 in patients with non-valvular atrial fibrillation (NVAF). Methods We
 performed a nationwide retrospective cohort study using data from the
 Taiwan National Health Insurance Research Database. We enrolled 3,213 and
 1,181 NVAF patients with hyperthyroidism taking DOACs and warfarin,
 respectively, from June 1, 2012 to December 31, 2017. We also enrolled
 53,591 and 16,564 NVAF patients without hyperthyroidism taking DOACs and
 warfarin, respectively. We used propensity score-based stabilized weights
 (PSSWs) to balance covariates across the study groups. We also used 1:4
 matching on both taking DOACs, with (n=3,213) and without hyperthyroidism
 (n=12,852); and both taking warfarin, with (n=1,181) and without
 hyperthyroidism (n=4,724). Results After PSSW, DOAC had a comparable risk
 of ischemic stroke/systemic embolism (IS/SE) and a lower risk of major
 bleeding (hazard ratio (HR):0.65; [95% confidential interval
 (CI):0.44-0.96]; P=0.0295) than warfarin among patients with
 hyperthyroidism.  There were comparable risks of IS/SE and major
 bleeding between those patients with and without hyperthyroidism. However,
 patients taking warfarin with hyperthyroidism had a lower risk of IS/SE
 than those without hyperthyroidism (HR:0.61; [95%CI:0.43-0.86]; P=0.0050).
 Conclusion Among NVAF Asian patients with concomitant hyperthyroidism,
 DOACs may be an effective and safer alternative to warfarin.
 Thromboprophylaxis with DOACs may be considered for such patients, and it
 is important to validate this finding in further prospective study.
description: We performed a nationwide retrospective cohort study using data
 from the Taiwan National Health Insurance Research Database. We enrolled
 3,213 and 1,181 NVAF patients with hyperthyroidism taking DOACs and
 warfarin, respectively, from June 1, 2012 to December 31, 2017.
description: Supplemental materials (figures and tables) for the article of
 "Direct Oral Anticoagulants in Atrial Fibrillation Patients with
 Concomitant Hyperthyroidism"
DOI: 10.7910/dvn/nmgzet
title: Chemotherapy-induced nausea and vomiting and patient characteristics in older adult cancer patients

description: These data were collected as part of a larger longitudinal study aiming to examine treatment effects of moderately- or highly-emetogenic chemotherapies among cancer patients at 24 hours and 5 days post-infusion. This anonymized dataset includes sociodemographic and clinical characteristics and both patient- and clinician-reported outcome measures of nausea and vomiting among 803 cancer patients.
DOI: 10.6086/d18q2j
title: Role of endogenous and exogenous attention in task-relevant visual perceptual learning

description: The present study examined the role of exogenous and endogenous attention
 in task relevant visual perceptual learning (TR-VPL). VPL performance was
 assessed by examining the learning to a trained stimulus feature and
 transfer of learning to an untrained stimulus feature. To assess the
 differential role of attention in VPL, two types of attentional cues were
 manipulated; exogenous and endogenous. In order to assess the
 effectiveness of the attentional cue, the two types of attentional cues
 were further divided into three cue-validity conditions. Participants were
 trained, on a novel task, to detect the presence of a complex gabor patch
 embedded in fixed Gaussian contrast noise while contrast thresholds were
 varied. The results showed initial differences were found prior to
 training, and so the magnitude of learning was assessed. Exogenous and
 endogenous attention were both found to facilitate learning and feature
 transfer when investigating pre-test and post-test thresholds. However,
 examination of training data indicate attentional differences; with
 endogenous attention showing consistently lower contrast thresholds as
 compared to exogenous attention suggesting greater impact of training with
 endogenous attention. We conclude that several factors, including the use
 of stimuli that resulted in rapid learning, may have contributed to the
 generalization of learning found in the present study.
DOI: 10.15139/s3/ed2jke
title: Data Management and Sharing Plan for: Creating a novel place-based measure to explain racial disparities in naloxone access to reduce opioid overdose deaths

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.25349/d9p014
title: Engineering crack tortuosity in polymer-polymer composites through ordered pores

description: Multimaterial additive manufacturing (or 3D printing) is an enabling tool
 for exploring structure-property relationships. In this work, a recently
 developed multimaterial printing approach, solution mask liquid
 lithography (SMaLL), is used to produce polymer-polymer composites
 inspired by tough, hierarchical structures found in nature. Triphasic
 composites comprised of a hard exterior “cuticle”, a soft interior “core,”
 and controlled pore size/structure are printed in a single step and their
 mechanical properties evaluated. The results of these tests demonstrate
 that varying the size and packing of pores in the core structure leads to
 significant enhancement in crack deflection. Finite element analysis
 reveals that this enhancement is linked to geometry-dependent stress
 distribution in each material. These results provide design cues for
 increasing resilience in multimaterial polymer-polymer composites.
DOI: 10.5061/dryad.9w0vt4bbd
title: Non-linear variation in clinging performance with surface roughness in geckos

description: Understanding the challenges faced by organisms moving within their
 environment is essential to comprehending the evolution of locomotor
 morphology and habitat use. Geckos have developed adhesive toe pads that
 enable exploitation of a wide range of microhabitats. These toe pads, and
 their adhesive mechanisms, have typically been studied using a range of
 artificial substrates, usually significantly smoother than those available
 in nature. Although these studies have been fundamental in understanding
 the mechanisms of attachment in geckos, it is unclear whether gecko
 attachment simply gradually declines with increased roughness as some
 researchers have suggested, or whether the interaction between the
 gekkotan adhesive system and surface roughness produces non-linear
 relationships. To understand ecological challenges faced in their natural
 habitats, it is essential to use test surfaces that are more like surfaces
 used by geckos in nature. We tested gecko shear force (i.e., frictional
 force) generation as a measure of clinging performance on three artificial
 substrates. We selected substrates that exhibit microtopographies with
 peak-to-valley heights similar to those of substrates used in nature, to
 investigate performance on a range of surfaces smooth (glass), and
 fine-grained (fine sandpaper) to rough (coarse sandpaper). We found that
 shear force did not decline monotonically with roughness, but varied
 non-linearly among substrates. Clinging performance was greater on glass
 and coarse sandpaper than on fine sandpaper, and clinging performance was
 not significantly different between glass and coarse sandpaper. Our
 results demonstrate that performance on different substrates varies,
 probably depending on the underlying mechanisms of the adhesive apparatus
 in geckos.
DOI: 10.15468/dl.fk8s97
title: Occurrence Download

description: A dataset containing 129 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sprattus antipodum",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 129 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002178-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.