cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.525988k
title: Data from: Acute ischemic stroke thrombi have an outer shell that impairs fibrinolysis

description: Objectives. Thrombi responsible for large vessel occlusion (LVO) in the
 setting of acute ischemic stroke (AIS) are characterized by a low
 recanalization rate after intravenous thrombolysis. To test whether AIS
 thrombi have inherent common features that limit their susceptibility to
 thrombolysis, we analyzed the composition and ultrastructural organization
 of AIS thrombi causing LVO. Methods. A total of 199 endovascular
 thrombectomy-retrieved thrombi were analyzed by immunohistology, scanning
 electron microscopy (SEM), and subjected to ex vivo thrombolysis assay.
 The relationship between thrombus organization and thrombolysis resistance
 was further investigated in vitro using thrombus produced by
 recalcification of citrated whole blood. Results. SEM and immunohistology
 analyses revealed that, although AIS thrombus composition and organization
 was highly heterogeneous. AIS thrombi shared a common remarkable
 structural feature in the form of an outer shell made of densely compacted
 thrombus components including fibrin, von Willebrand factor, and
 aggregated platelets. In vitro thrombosis experiments using human blood
 indicated that platelets were essential to the formation of the thrombus
 outer shell. Finally, in both AIS and in vitro thrombi, the thrombus outer
 shell showed a decreased susceptibility to t-PA-mediated thrombolysis as
 compared to the thrombus inner core. Interpretation. Irrespective of their
 etiology and despite their heterogeneity, intracranial thrombi causing LVO
 have a core-shell structure that influences their susceptibility to
 thrombolysis.
description: Supplemental Data
 FinalSupplemental Figures
 e1-4 and Table e1Revised Supplemental
 Data2.pdf
DOI: 10.5061/dryad.mv32031
title: Data from: Species-specific effects of passive warming in an Antarctic moss system

description: Polar systems are experiencing rapid climate change and the high
 sensitivity of these Arctic and Antarctic ecosystems make them especially
 vulnerable to accelerated ecological transformation. In Antarctica,
 warming regions result in a mosaic of ice-free terrestrial habitats
 dominated by a diverse assemblage of cryptogamic plants (i.e. mosses and
 lichens). Although these plants provide key habitat for a wide array of
 microorganisms and invertebrates, we have little understanding of the
 interaction between trophic levels in this terrestrial ecosystem, and
 whether there are functional effects of plant species on higher trophic
 levels that may alter with warming. Here, we used Open Top Chambers (OTCs)
 on Fildes Peninsula, King George Island, Antarctica, to examine the
 effects of passive warming and moss species on the abiotic environment and
 ultimately on higher trophic levels. For the dominate mosses,
 Polytrichastrum alpinum and Sanionia georgicouncinata, we found
 species-specific effects on the abiotic environment, including moss canopy
 temperature and soil moisture. Additionally, we found distinct
 reproductive shifts in P. alpinum plants under warming compared to mosses
 without warming, and invertebrate communities in this moss species were
 strongly correlated with plant reproduction. Mosses under warming had
 substantially larger total invertebrate communities, and some invertebrate
 taxa were influenced differentially by moss species. However, warmed moss
 plants showed lower fungal biomass than control moss plants, and fungal
 biomass differed between moss species. Our results indicate that continued
 warming will differentially impact the reproductive output of Antarctic
 moss species, potentially altering terrestrial ecosystems dynamics from
 the bottom up. Understanding these effects requires clarifying the
 foundational, mechanistic role that individual plant species play in
 mediating complex interactions in Antarctica’s terrestrial food-webs.
description: King George Island
 Antarctica, Bryophyte Community Dataset These data were
 collected on a bryophyte (moss) community under 8 years of experimental
 passive warming on King George Island, South Shetland Islands, Antarctica.
 These data quantify changes in moss canopy characteristics, moss
 invertebrate communities and moss fungal biomass under passive
 warming.
DOI: 10.5061/dryad.r2nd550
title: Data from: High-speed motility originates from cooperatively pushing and pulling flagella bundles in bilophotrichous bacteria

description: Bacteria propel and change direction by rotating long, helical filaments,
 called flagella. The number of flagella, their arrangement on the cell
 body and their sense of rotation hypothetically determine the locomotion
 characteristics of a species. The movement of the most rapid
 microorganisms has in particular remained unexplored because of additional
 experimental limitations. We show that magnetotactic cocci with two
 flagella bundles on one pole swim faster than 500 μm·s-1 along a double
 helical path, making them one of the fastest natural microswimmers. We
 additionally reveal that the cells reorient in less than 5 ms, an order of
 magnitude faster than reported so far for any other bacteria. Using
 hydrodynamic modeling, we demonstrate that a mode where a pushing and a
 pulling bundle cooperate is the only possibility to enable both helical
 tracks and fast reorientations. The advantage of sheathed flagella bundles
 is the high rigidity, making high swimming speeds possible.
description: MC1_3DtracksExperimental data from the lab; created with MatLab, saved as .mat files. The .mat files include structs. Most important is the Bugs cell that includes 5 columns, first column is the line number, second to fourth is x,y,z coordinates and fifth is the correlation value as a representation of the certainty of the finding. Created with an adapted version from the Nature Communication article by Taute et al. from 2015. Comes with 2 example reading and analysing scripts for MatLab.
DOI: 10.5061/dryad.48p658n
title: Data from: A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius

description: Hybridization and convergent evolution are phenomena of broad interest in
 evolutionary biology, but their occurrence poses challenges for
 reconstructing evolutionary affinities among affected taxa. Sticklebacks
 in the genus Pungitius are a case in point: evolutionary relationships and
 taxonomic validity of different species and populations in this
 circumpolarly distributed species complex remain contentious due to
 convergent evolution of traits regarded as diagnostic in their taxonomy,
 and possibly also due to frequent hybridization among taxa. To clarify the
 evolutionary relationships among different Pungitius species and
 populations globally, as well as to study prevalence and extent of
 introgression among recognized species, genomic datasets of both reference
 genome-anchored SNPs and de novo assembled RAD-tag loci were constructed
 with RAD-seq data. Both datasets yielded topologically identical and
 well-supported species trees. Incongruence between nuclear and
 mitochondrial DNA-based trees was found and suggested frequent
 hybridization and mitogenome capture during the evolution of Pungitius
 sticklebacks. Further analyses revealed evidence for frequent nuclear
 genetic introgression among Pungitius species, although the estimated
 proportions of autosomal introgression were low. Apart from providing
 evidence for frequent hybridization, the results challenge earlier
 mitochondrial and morphology-based hypotheses about the number of species
 and their affinities in this genus: at least seven extant species can be
 recognized on the basis of genetic data. The results also shed new light
 on the biogeographic history of the Pungitius-complex, including
 suggestion of several trans-Arctic invasions of Europe from the Northern
 Pacific. The well-resolved phylogeny should facilitate the utility of this
 genus as a model system for future comparative evolutionary studies.
description: The
 maximum-clade-credibility summary treesThe
 maximum-clade-credibility summary trees of SNAPP
 phylogenies.Maximum likelihood-based
 phylogenyMaximum likelihood-based
 phylogeny constructed using RAxML.ML_tree_individual-level(RAxML).treeXML files and PHYLIP fileAll the XML files and a PHYLIP format SNP-matrix used in the SNAPP analyses.XML_and_PHYLIP_files.zipPerl script.A custom Perl script used for transforming heterozygous sites to standard ambiguity codes.consensus.plThe concatenated alignment of five mitochondrial regionsThe concatenated alignment of five mitochondrial regions, and their positions.Pungitius_MT_sequences_Figure3.zip
DOI: 10.5061/dryad.7r5t6p5
title: Data from: Age and growth of stocked juvenile Shoal Bass in a tailwater: environmental variation and accuracy of daily age estimates

description: Otolith microanalysis is often used to assess population age structure and
 growth of fishes during their early stages. Shoal Bass Micropterus
 cataractae is a recently described species of conservation concern and
 little is known regarding factors affecting their recruitment. In 2004,
 Georgia Department of Natural Resources (GADNR) and the US National Park
 Service (NPS) stocked Shoal Bass marked with oxytetracycline (OTC) in the
 Chattahoochee River near Atlanta, Georgia in an effort to restore this
 population, creating known-age fish to examine the effect of environment
 on daily age accuracy. We obtained samples of stocked juvenile
 (&lt;150 mm) Shoal Bass from standard monitoring that occurred
 approximately 30-60 days after stocking in the Chattahoochee River to 1)
 validate daily rings for estimating age, hatch dates, and growth rates for
 stocked age-0 Shoal Bass, and 2) evaluate the effect of habitat (location)
 on age bias. Shoal Bass otoliths were examined for OTC marks and daily
 rings were counted in reference to OTC marks to assess age estimation
 accuracy. Age estimation accuracy ranged from -2 to -25 days and was
 influenced by the environment where Shoal Bass were captured, with greater
 inaccuracy in colder water temperatures. Fish collected from locations
 with colder temperatures displayed closer spacing of daily rings,
 potentially leading to greater underestimation of age. Growth rates of
 stocked Shoal Bass, corrected for age estimation error, ranged from 0.5
 mm/day to 0.8 mm/day. This study demonstrates the effect of environmental
 variability on age inaccuracy and subsequent interpretation of results.
 Incorporating methods to assess age estimation accuracy is needed to
 understand interspecific differences in recruitment among black bass
 species in the variety of natural and human-modified environments they
 inhabit.
description: juvenile bass age and
 growth_for Dryad measures of age for
 shoal bass (Micropterus cataractae) collected from the Chattahoochee
 River, Atlanta, Georiga, USA
DOI: 10.5061/dryad.6fv8fb4
title: Data from: Comparing methods for SNP calling from Genotyping-By-Sequencing (GBS) data for a large-genome conifer without a published genome sequence

description: Reduced-representation restriction-enzyme-based sequencing methods have
 been demonstrated to be robust and cost-effective genotyping methods to
 identify Single Nucleotide Polymorphisms (SNPs). While alignment of the
 short-read fragments to a genome sequence of the same species results in
 better SNP calling than de novo approaches, only a few tree species - and
 few conifers in particular - have an annotated sequence. Many conifer
 genomes are huge (&gt;19 GB) and include a large proportion of repeat
 sequences, making assembly difficult. While the sequence of a related
 species could be used, choosing the proper pipeline for SNP calling is
 still challenging. Here we compare the performance of four bioinformatics
 pipelines, two of which require a reference genome (TASSEL-GBS V2 and
 Stacks), two of which are de novo pipelines (UNEAK and Stacks). We used
 Illumina GBS data from 94 ponderosa pines. Using loblolly pine genome as
 the reference greatly increased the number of SNPs called (62 -196
 thousand vs. 2.1 - 2.7 million SNPs). UNEAK was fastest and identified
 more SNPs than Stacks de novo. Reference-based Stacks produced the highest
 number of SNPs with lowest proportion of paralogs, TASSEL-GBS V2 exhibited
 the highest proportion of paralogs. The Stacks reference-based approach
 produced the best results overall, while UNEAK is the better de novo
 method. However, all four pipelines had distinct benefits and limitations.
 Differences in observed and expected heterozygosity between the SNP sets
 generated by the pipelines could lead to different conclusions when they
 are used for population genetics analyses.  
description: <strong>GBS_96</strong><br> VCF file produced
 by TASSEL-GBS V2 pipeline for 94 ponderosa pine using loblolly pine as the
 reference genome
 <strong>Stacks_denovo_96.snps</strong><br> VCF
 file produced by Stacks de novo pipeline for 94 ponderosa pine
 <strong>Stacks_ref_96.snps</strong><br> VCF
 file produced by Stacks reference based pipeline for 94 ponderosa pine
 using loblolly pine as the reference genome
 <strong>UNEAK_denovo_96</strong><br> VCF file
 produced by UNEAK pipeline for 94 ponderosa pine
DOI: 10.5061/dryad.j7h6f69
title: Data from: One-shot learning and behavioral eligibility traces in sequential decision making

description: In many daily tasks we make multiple decisions before reaching a goal. In
 order to learn such sequences of decisions, a mechanism to link earlier
 actions to later reward is necessary. Reinforcement learning theory
 suggests two classes of algorithms solving this credit assignment problem:
 In classic temporal-difference learning, earlier actions receive reward
 information only after multiple repetitions of the task, whereas models
 with eligibility traces reinforce entire sequences of actions from a
 single experience (one-shot). Here we show one-shot learning of sequences.
 We developed a novel paradigm to directly observe which actions and states
 along a multi-step sequence are reinforced after a single reward. By
 focusing our analysis on those states for which RL with and without
 eligibility trace make qualitatively distinct predictions, we find direct
 behavioral (choice probability) and physiological (pupil dilation)
 signatures of reinforcement learning with eligibility trace across
 multiple sensory modalities.
description: Behaviour and Pupil
 Dilation during Human learningPupil dilations and
 behavioral data recorded during a sequential decision making task. Matlab
 (mat) and Text (csv) files.DataDryadUpload.zip
DOI: 10.5061/dryad.34b1466
title: Data from: Loser-effect duration evolves independently of fighting ability

description: Winning or losing contests can impact subsequent competitive behaviour and
 the duration of these effects can be prolonged. While it is clear effects
 depend on social and developmental environments, the extent to which they
 are heritable, and hence evolvable, is less clear and remains untested.
 Furthermore, theory predicts that winner and loser effects should evolve
 independently of actual fighting ability, but again tests of this
 prediction are limited. Here we used artificial selection on replicated
 beetle populations to show that the duration of loser effects can evolve,
 with a realized heritability of about 17%. We also find that naïve
 fighting ability does not co-evolve with reductions in the duration of the
 loser effect. We discuss the implications of these findings and how they
 corroborate theoretical predictions.
description: Raw data for
 Loser-effect duration evolves independently of fighting
 ability
DOI: 10.5061/dryad.41gm638
title: Data from: Outcomes of stroke patients treated with thrombolysis according to prestroke Rankin Scale scores

description: Background: It is common practice to withhold intravenous thrombolysis
 (IVT) for acute ischemic stroke in patients with preexisting disabilities.
 To test the hypothesis of an association of IVT and good clinical outcome
 also in patients with preexisting disabilities without an increase in
 mortality we analyzed data of 52,741 patients (15,317 treated with IVT)
 depending on prestroke Rankin Scale (pRS) score. Methods: We performed an
 observational study based on a consecutive stroke registry covering 10.8
 million inhabitants. The outcome at discharge of stroke patients admitted
 in the time window of potential eligibility for IVT (&lt;4.5h after
 stroke onset) was compared between patients treated and not treated with
 thrombolysis, stratified by pRS. Logistic regression analysis was used to
 estimate adjusted odds ratios (OR) along with 95% confidence intervals
 (CI) for favorable clinical outcome, defined as returning to the baseline
 pRS score or a score of 0 or 1 and mortality. Sensitivity analyses for
 subgroups of mildly and severely affected stroke patients were performed
 and influence of treatment duration was assessed. Results: Among included
 patients IVT rates were 32% for patients with pRS 0-1 and 20% for patients
 with pRS 2-5. IVT in patients with pRS of 0-4 was associated with a higher
 chance of returning to the baseline pRS (or a modified RS of 0/1), with
 ORs ranging between 1.42 (pRS 2; CI 1.16-1.73) and 1.73 (pRS 0; CI
 1.61-1). The OR observed in patients with a pRS of 5 was 0.65 (CI
 0.25-1.70). Observed associations remained consistent in sensitivity
 analyses. Subgroup analyses revealed no evidence of bias due to potential
 floor and ceiling effects. No evidence of elevated in-hospital mortality
 of patients treated with thrombolysis was observed. Conclusions: Our study
 suggests that IVT can be effective even in patients with severe
 preexisting disabilities, provided that they were not bedridden before
 stroke onset. Withholding IVT on the sole ground of prestroke disabilities
 may not be justified.
description: IVT prestroke rankin
 table 3-5Table 3. Detailed
 characteristics of the study population according to mRS and IVT. Table 4.
 Outcomes measured by score on modified Rankin scale (mRS) without
 adjustment for LOS for favorable outcome and mortality of patients treated
 and not treated with tissue plasminogen activator. Table 5. Subgroup
 analyses - outcomes measured by score on modified Rankin scale (mRS) of
 patients treated and not treated with tissue plasminogen
 activator
DOI: 10.5061/dryad.nh1s3k3
title: Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities

description: 1. Anthropogenic environmental changes are known to affect the Earth’s
 ecosystems. However, how these changes influence assembly trajectories of
 the impacted communities remains a largely open question. 2. In this
 study, we investigated the effect of elevated nitrogen (N) deposition and
 increased precipitation on plant taxonomic and phylogenetic β-diversity in
 a 9-year field experiment in the temperate semi-arid steppe of Inner
 Mongolia, China. 3. We found that both N and water addition significantly
 increased taxonomic β-diversity, whereas N, not water, addition
 significantly increased phylogenetic β-diversity. After the differences in
 local species diversity were controlled using null models, the standard
 effect size of taxonomic β-diversity still increased with both N and water
 addition, while water, not N, addition, significantly reduced the standard
 effect size of phylogenetic β-diversity. The increased phylogenetic
 convergence observed in the water addition treatment was associated with
 the colonization of different, but phylogenetically closely related,
 species into different replicate plots of the treatment. Species
 colonization in this treatment was found to be trait-based, with leaf
 nitrogen concentration being the key functional trait. 4. Synthesis. Our
 analyses demonstrate that anthropogenic environmental changes may affect
 the assembly trajectories of plant communities at both taxonomic and
 phylogenetic scales. Our results also suggest that while stochastic
 processes may cause communities to diverge in species composition,
 deterministic process could still drive communities to converge in
 phylogenetic community structure.
description: β-diversityTaxonomic β-diversity, phylogenetic β-diversity, and their respective standardized effect sizes among replicate plots within each treatment.beta_diversity.csvPhylogenetic treePhylogenetic tree for the species that were observed in the experimental area.phylogeny.treDissimilarity between new colonists/extinct species and final species compositionThe taxonomic (β-deviation) and phylogenetic dissimilarity (SES.Dpw) between new colonists and extinct species of each plot and final species composition in the other three replicate plots within the same treatment.ses_beta_colonization_extinction.csv
DOI: 10.5061/dryad.760jg17
title: Data from: Soil CO2 and O2 concentrations illuminate the relative importance of weathering and respiration to seasonal soil gas fluctuations

description: [No abstract entered]
description: Shale Hills and Garner
 Run 2015 - 2017 Soil CO2 and O2Hand-collected soil CO2
 and O2 from soil gas wells at the Susquehanna Shale Hills CZO. These data
 were collected from the Shale Hills (SPVF, SPMS, SPRT, NPMS sites) and the
 Garner Run (LRVF, LRMS, LRRT, TMMS sites) watersheds. Data were collected
 from the valley floors (SPVF, LRVF), south midslopes (SPMS, LRMS), north
 midslopes (NPMS, TMMS), and ridgetops (SPRT, LRRT) and analyzed using
 methods detailed in Hodges et al., 2019.shalehills_garnerrun_handsamples_alldata_fordryad.xlsx
DOI: 10.15468/dl.5gwyfu
title: Occurrence Download

description: A dataset containing 38484427 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 38484427 records from 4633 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001831-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s36zyh
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Arctictis binturong (Raffles, 1821))",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 101 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016067-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.