cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25418/crick.28742384.v1
title: Data from a framework analysis of RDM policies to determine openness

description: Data supporting a paper titled "Do data management policies become more open over time?"The data includes three matrices created as part of a framework analysis. The Reasons and Adjectives data show a binary coding of whether a policy contains the term or idea. The Policies matrix contains values from 0 - 4 with 0 representing a very closed policy type and 4 representing a very open policy type. The details of these policies can be found in ...[update when preprint is posted]Associated code can be found at: 10.25418/crick.28788704
DOI: 10.15468/dl.sqyysg
title: Occurrence Download

description: A dataset containing 101470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Amaranthus retroflexus L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 101470 records from 1150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010528-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tq1dk2m
title: Data from: Clinical complications and outcomes of angiographically negative subarachnoid hemorrhage

description: Objective: To define the in-hospital course, complications, short- and
 long-term functional outcomes of patients with angiographically negative
 subarachnoid hemorrhage (anSAH), particularly those with
 aneurysmal-pattern anSAH (aanSAH). Methods: Retrospective cohort study of
 patients with aneurysmal subarachnoid hemorrhage (aSAH), aanSAH and
 perimesencephalic-pattern anSAH (panSAH) treated at a single tertiary
 referral center between January 2006 and April 2018. Ninety-nine patients
 with anSAH (33 aanSAH and 66 panSAH) and 464 patients with aSAH were
 included in this study. Outcomes included symptomatic hydrocephalus
 requiring CSF drainage, need for ventriculoperitoneal shunt (VPS),
 radiographic vasospasm, delayed cerebral ischemia (DCI), radiographic
 infarction, disability level within one year of ictus and at last clinical
 follow-up as defined by modified Rankin Scale (mRS). Results: Patients
 with aanSAH and panSAH had similar rates of DCI and radiologic infarction,
 and patients with aanSAH had significantly lower rates compared to aSAH
 (P≤0.018). Patients with aanSAH were more likely than those with panSAH to
 require temporary CSF diversion and VPS (P≤0.03), with similar rates to
 those seen in aSAH. Only one patient with anSAH died in the hospital.
 Compared to those with aSAH, patients with aanSAH were significantly less
 likely to have a poor functional outcome within one year of ictus (OR
 0.26, 95% CI 0.090 – 0.75) and at last follow-up (HR 0.30, 95% CI 0.19 –
 0.49, P=0.002). Conclusions: DCI is very uncommon in anSAH, but patients
 with aanSAH have a similar need for short- and long-term CSF diversion to
 patients with aSAH. Nevertheless, patients with aanSAH have significantly
 better short- and long-term outcomes.
description: Supplementary
 TablesSupplementary Tables as
 referenced in the manuscript.
DOI: 10.5061/dryad.tf2tr
title: Data from: Modification of Escherichia coli–bacteriophage interactions by surfactants and antibiotics in vitro

description: Although experiments indicate that the abiotic environment plays an
 important role in bacterial interactions with their parasitic viruses
 (bacteriophages or phages), it is not yet clear how exposure to compounds
 present in nature alters the impact of phages on bacterial growth and
 evolution. To address this question, we exposed Escherichia coli K12
 MG1655, in combination with three lytic phages, to various substances that
 natural and clinical microbial populations are likely to encounter: bile
 salts (present in mammalian gastrointestinal tracts), sodium dodecyl
 sulfate (SDS, a common surfactant in cleaning and hygiene products) and
 four antibiotics (present at variable concentrations in natural and
 clinical environments). Our results show that bile salts and SDS can
 reduce the detrimental effect of phages on bacterial growth. In some cases
 these compounds completely mitigated any negative effects of phages on
 bacterial growth and consequently bacteria did not evolve resistance to
 phages in these conditions. The proportional effects of phages were
 unaffected by antibiotics in most combinations, excepting three cases of
 phage-drug synergy. These results suggest that accounting for interactions
 between phages and environmental factors such as surfactants and
 antibiotics will improve understanding of both bacterial growth and
 resistance evolution to phages in vivo and in nature.
description: FEMSME_dataContains datafiles in .csv format for figures and supplementary material in this manuscript. Includes a readme file in .txt format.
DOI: 10.5061/dryad.ts183
title: Data from: Optimal cardiac resynchronization therapy pacing rate in non-ischemic heart failure patients: a randomized crossover pilot trial

description: Background: The optimal pacing rate during cardiac resynchronization
 therapy (CRT) is unknown. Therefore, we investigated the impact of
 changing basal pacing frequencies on autonomic nerve function,
 cardiopulmonary exercise capacity and self-perceived quality of life
 (QoL). Methods: Twelve CRT patients with non-ischemic heart failure (NYHA
 class II–III) were enrolled in a randomized, double-blind, crossover
 trial, in which the basal pacing rate was set at DDD-60 and DDD-80 for 3
 months (DDD-R for 2 patients). At baseline, 3 months and 6 months, we
 assessed sympathetic nerve activity by microneurography (MSNA), peak
 oxygen consumption (pVO2), N-terminal pro-brain natriuretic peptide
 (p-NT-proBNP), echocardiography and QoL. Results: DDD-80 pacing for 3
 months increased the mean heart rate from 77.3 to 86.1 (p = 0.001) and
 reduced sympathetic activity compared to DDD-60 (51±14 bursts/100 cardiac
 cycles vs. 64±14 bursts/100 cardiac cycles, p&lt;0.05). The mean pVO2
 increased non-significantly from 15.6±6 mL/min/kg during DDD-60 to 16.7±6
 mL/min/kg during DDD-80, and p-NT-proBNP remained unchanged. The QoL score
 indicated that DDD-60 was better tolerated. Conclusion: In CRT patients
 with non-ischemic heart failure, 3 months of DDD-80 pacing decreased
 sympathetic outflow (burst incidence only) compared to DDD-60 pacing.
 However, Qol scores were better during the lower pacing rate. Further and
 larger scale investigations are indicated. Trial Registration:
 ClinicalTrials.gov NCT02258061
description: CRT_optimal_DRYADData collected during study period at the different phases (i.e. baseline, 3 months, and 6 months.) Questionnaires are SF-36 and LIfHE, each "@-number" corresponds to standard question. "Ventrikulaer_aktivitet" means ventricular activity.
DOI: 10.5061/dryad.8412
title: Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

description: Measuring the strength of natural selection is tremendously important in
 evolutionary biology, but remains a challenging task. In this work, we
 analyse the characteristics of selection for a morphological change
 (lateral-plate reduction) in the threespine stickleback Gasterosteus
 aculeatus. Adaptation to freshwater, leading to the reduction or loss of
 the bony lateral armor, has indeed occurred in parallel on numerous
 occasions in this species. Completely-plated and low-plated sticklebacks
 were introduced into a pond, and the phenotypic changes were tracked for
 twenty years. Fish from the last generation were genotyped for the
 Ectodysplasin-A (Eda) locus, the major gene involved in armor development.
 We found a strong fitness advantage for the freshwater-type fish (in
 average, 20% for the freshwater morph, and 92% for the freshwater
 genotype). The trend is best explained by assuming that this fitness
 advantage is maximum at the beginning of the invasion and decreases with
 time. Such fitness differences provide a quantifiable example of rapid
 selection-driven phenotypic evolution associated to environmental change
 in a natural population.
description: Genotype at Eda and
 lateral plate phenotypesThe file contains the
 genotypic information used in the manuscript. For each fish are indicated:
 1) the population, 2) the morph according to Bell et al. 2004 definition
 (based on the presence of keel plates), 3) the morph according to
 Zuiganov's definition (based on the number of plates on one side, 4)
 the bilateral number of plates, 5) the genotype at marker Stn382, 6) the
 genotype at marker Stn381. Three populations are indicated, Myrdalsvatn
 and Eikelandsvatn are both parental populations (genotyped in 2008), and
 Nygårdspark is the experimental population. The genotype is not available
 for all fish. Allele code corresponds to rough estimates of fragment sizes
 (more precise information is provided in the
 manuscript)data_dryad.txt
DOI: 10.5061/dryad.2q840
title: Data from: No influence of water limitation on the outcome of competition between diploid and tetraploid Chamerion angustifolium (Onagraceae)

description: 1. Polyploid plants often occupy different geographic ranges than their
 diploid progenitors, but the causes of this segregation are poorly
 understood. Differential competitive abilities of cytotypes across an
 environmental gradient could be responsible for these observed geographic
 range differences. 2. Cytotypes of Chamerion angustifolium (Onagraceae)
 are mostly allopatric, and prior research indicates that tetraploids are
 more physiologically tolerant of water limitation and occupy drier
 habitats than diploids. We hypothesized that tetraploids are stronger
 competitors than diploids in soils where water is limited, which allows
 them to persist in dry habitats while diploids cannot. 3. We grew both
 cytotypes together in competition under water-limited and well-watered
 conditions. We varied both total plant density and the relative frequency
 of cytotypes among pots, which allowed us to separate the effects of
 intra-cytotypic and inter-cytotypic competition. 4. Both diploid and
 tetraploid plants were smaller in the water-limited treatment than in the
 well-watered treatment. Nevertheless, there were no differences in the
 relative strength of intra-cytotypic and inter-cytotypic competition
 experienced by either cytotype across the watering treatments, indicating
 that diploids and tetraploids had equal competitive abilities in both
 treatments. 5. Synthesis. Competition for limiting resources is often
 proposed as a mechanism causing ecological and geographic segregation
 between diploid and polyploid cytotypes. Our results do not support the
 hypothesis that tetraploid Chamerion angustifolium plants are stronger
 competitors than diploids when water is limited. A differential ability to
 compete for water is likely not responsible for the observed ecological
 and geographic segregation between cytotypes in this species. Competition
 may not be a general mechanism that causes segregation between diploid and
 polyploid cytotypes in nature.
description: Competition experiment
 biomass dataThese are the data used
 to analyze the results of the competition experiment. The dataset does not
 include phenology data analyzed in the supplementary materials. This data
 can be accessed by contacting the corresponding author directly (Ken
 Thompson, kthomp1063@gmail.com).2015-02-09-FireweedCompetition_Biomass_Dryad.xlsx
DOI: 10.5061/dryad.6f4qs
title: Data from: Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes

description: Background: Plant survival is a key factor in forest dynamics and survival
 probabilities often vary across life stages. Studies specifically aimed at
 assessing tree survival are unusual and so data initially designed for
 other purposes often need to be used; such data are more likely to contain
 errors than data collected for this specific purpose. Results: We
 investigate the survival rates of ten tree species in a dataset designed
 to monitor growth rates. As some individuals were not included in the
 census at some time points we use capture-mark-recapture methods both to
 allow us to account for missing individuals, and to estimate relocation
 probabilities. Growth rates, size, and light availability were included as
 covariates in the model predicting survival rates. The study demonstrates
 that tree mortality is best described as constant between years and
 size-dependent at early life stages and size independent at later life
 stages for most species of UK hardwood. We have demonstrated that even
 with a twenty-year dataset it is possible to discern variability both
 between individuals and between species. Conclusions: Our work illustrates
 the potential utility of the method applied here for calculating plant
 population dynamics parameters in time replicated datasets with small
 sample sizes and missing individuals without any loss of sample size, and
 including explanatory covariates.
description: Survival of ten tree
 species in the UK - raw dataForest trees monitored
 included 10 species: Acer pseudoplatanus (Sycamore, ACERPS, Nsaplings =
 16, Nadults = 41), Fraxinus excelsior, (European ash, FRAXEX, Nsaplings =
 16, Nadults = 41), Quercus robur (Pedunculate oak, QUERRO, Nsaplings = 5,
 Nadults = 18), Fagus sylvatica, (European beech, FAGUSY, Nsaplings = 5,
 Nadults = 19), Corylus avellana (Common hazel, CORYAV, Nsaplings = 18,
 Nadults = 11), Crataegus monogyna (Common hawthorn, CRATMO, Nsaplings = 8,
 Nadults = 13), Acer campestre (Field maple, ACERCA, Nsaplings = 0, Nadults
 = 13), Betula spp. (Birch, BETUSP, Nsaplings = 0, Nadults = 13), Salix
 spp. (Willow, SALISP, Nsaplings = 4, Nadults = 4), and Sambucus nigra
 (Elder, SAMBINI, Nsaplings = 12, Nadults = 11).Survival raw
 data.xlsx
DOI: 10.5061/dryad.n2s40
title: Data from: Dietary regulation of the gut microbiota engineered by a minimal defined bacterial consortium

description: We have recently reported that Altered Schaedler Flora (ASF) can be used
 to durably engineer the gut microbiota to reduce ammonia production as an
 effective modality to reduce morbidity and mortality in the setting of
 liver injury. Here we investigated the effects of a low protein diet on
 ASF colonization and its ability to engineer the microbiota. Initially,
 ASF inoculation was similar between mice fed a normal protein diet or low
 protein diet, but the outgrowth of gut microbiota differed over the
 ensuing month. Notable was the inability of the dominant Parabacteroides
 ASF taxon to exclude other taxa belonging to the Bacteroidetes phylum in
 the setting of a low protein diet. Instead, a poorly classified yet highly
 represented Bacteroidetes family, S24-7, returned within 4 weeks of
 inoculation in mice fed a low protein diet, demonstrating a reduction in
 ASF resilience in response to dietary stress. Nevertheless, fecal ammonia
 levels remained significantly lower than those observed in mice on the
 same low protein diet that received a transplant of normal feces. No
 deleterious effects were observed in host physiology due to ASF
 inoculation into mice on a low protein diet. In total, these results
 demonstrate that low protein diet can have a pronounced effect on
 engineering the gut microbiota but modulation of ammonia is preserved.
description: Fig 1
 dataFig 5
 data
DOI: 10.5061/dryad.98rf2f1
title: Data from: The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda

description: Understanding the mechanisms that enforce, maintain, or reverse the
 process of speciation is an important challenge in evolutionary biology.
 This study investigates the patterns of divergence and discusses the
 processes that form and maintain divergent lineages of the tsetse fly
 Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites
 spanning known genetic lineages and the four admixture zones between them.
 We apply population genomics, hybrid zone, and approximate Bayesian
 computation to the analysis of three types of genetic markers: 55,267
 double digest restriction-site associated DNA (ddRAD) SNPs to assess
 genome wide admixture, 16 microsatellites to provide continuity with
 published data and accurate biogeographic modeling, and a 491 bp fragment
 of mitochondrial cytochrome oxidase I and II to infer maternal inheritance
 patterns. Admixture zones correspond with regions impacted by the
 reorganization of Uganda’s river networks that occurred during the
 formation of the West African Rift system over the last several hundred
 thousand years. Because tsetse fly population distributions are defined by
 rivers, admixture zones likely represent both old and new regions of
 secondary contact. Our results indicate that older hybrid zones contain
 mostly parental types, while younger zones contain variable hybrid types
 resulting from multiple generations of interbreeding. These findings
 suggest that reproductive barriers are nearly complete in the older
 admixture zones, while nearly absent in the younger admixture zones.
 Findings are consistent with predictions of hybrid zone theory:
 Populations in zones of secondary contact transition rapidly from early to
 late stages of speciation, or collapse all together.
description: Gff-16microsats-251-genepopGff microsatellite data in GenePop format. Data from 251 individuals (that were also included in the ddRAD dataset in the manuscript) from 16 microsatellites loci (A03b, B05, C7b, CAG29, GpCAG133, D05, D101, Gmm8, GpB20b, GpC10, Pgp28, GmL03, GmmA06, GmmH09, GmmL11, GmD15) with varying repeat motifs (of lengths 2, 2, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 2, 2, and 2 bp) and varying repeat lengths (80, 110, 80, 60, 70, 40, 60, 40, 60, 65, 70, 100, 90, 95, 125, and 80).
DOI: 10.5061/dryad.h2162
title: Data from: Genotypic diversity mitigates negative effects of density on plant performance: a field experiment and life-cycle analysis of common evening primrose Oenothera biennis

description: 1.Genotypic diversity in plant populations is known to enhance plant
 performance and ecosystem function. Nonetheless, the effect of genotypic
 diversity has rarely been examined across a population's lifecycle
 despite the expectation that changing conditions, such as population
 density, will alter the benefits of diversity. 2.We simultaneously
 manipulated a component of genotypic diversity (richness, the number of
 genotypes) and density of common evening primrose Oenothera biennis to
 address the consequences for herbivory and lifetime fitness in a two-year
 field experiment that spanned seed germination to life-time fruit
 production. We genotyped &gt;1100 seedlings with microsatellite DNA
 markers to determine realized diversity and density in plots sown with
 O.biennis seeds. Our design achieved quantitative variation in plant
 density and diversity, with one to 44 individuals established in field
 plots and two to eight genotypes per polyculture plot (based on
 microsatellite analysis of reproductive plants). 3.We found a strong
 interaction between seed density and genetic diversity, with germination
 and establishment being 24% higher in genetic polycultures than
 monocultures, but only at low seed density. At high seed density, the
 opposite pattern emerged, with polycultures having 12% fewer individuals
 established than monocultures. Initial effects of emergence on plot
 density persisted through to the fruiting stage. 4.Higher plant densities
 result in increased mortality, decreased probability of reproduction,
 decreased plant height, and lower levels of life-time fruit production per
 plant. Increasing genotypic diversity increased the probability of
 reproduction overall, and showed a significant interaction with plant
 density mitigating the negative effects of high density on individual
 height and lifetime fruit production. 5.Synthesis. Plant density and
 genotypic diversity interacted from the very earliest stages of seed
 germination and establishment of O. biennis. This effect persisted over
 the two-year life-cycle of plants, and genotypic diversity buffered
 against the negative fitness consequences of high plant density. These
 results imply a dynamic interplay between the long-held paradigm of
 density effects in plant ecology and the genetic structure of populations.
description: effects of density and
 diversity on primrose communitiesPlease see the
 associated metadata tab for descriptions of individual columns. These data
 derive from an experimental manipulation of genotypic diversity and
 density in common evening primrose.DENSdata.xlsx
DOI: 10.15468/dl.5dqdnq
title: Occurrence Download

description: A dataset containing 88259 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sphagnum palustre"
 ]
}

 The dataset includes 88259 records from 608 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001090-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p55m7
title: Data from: Functional basis of the sexual dimorphism in the auditory fovea of the duetting bushcricket Ancylecha fenestrata

description: From mammals to insects, acoustic communication is in many species crucial
 for successful reproduction. In the duetting bushcricket Ancylecha
 fenestrata, the mutual acoustic communication between males and females is
 asymmetrical. We investigated how those signalling disparities are
 reflected by sexual dimorphism of their ears. Both sexes have tympanic
 ears in their forelegs, but male ears possess a significantly longer
 crista acustica containing 35% more scolopidia. With more sensory cells to
 cover a similar hearing range, the male hearing organ shows a
 significantly expanded auditory fovea that is tuned to the dominant
 frequency of the female reply to facilitate phonotactic mate finding. This
 sex-specific auditory fovea is demonstrated in the mechanical and neuronal
 responses along the tonotopically organized crista acustica by
 laservibrometric and electrophysiological frequency mapping, respectively.
 Morphometric analysis of the crista acustica revealed an interrupted
 gradient in organ height solely within this auditory fovea region, whereas
 all other anatomical parameters decrease continuously from proximal to
 distal. Combining behavioural, anatomical, biomechanical and
 neurophysiological information, we demonstrate evidence of a pronounced
 auditory fovea as a sex-specific adaptation of an insect hearing organ for
 intraspecific acoustic communication.
description: Scherberich-DataPlease find in the excel file the data for Fig. 1 – 3.