cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g2t66
title: Data from: Population characteristics, mechanisms of primary care and premature mortality in England: a cross-sectional study

description: Objectives. Health systems with strong primary care tend to have better
 population outcomes, but in many countries demand for care is growing. We
 sought to identify mechanisms of primary care that influence premature
 mortality. Design. We developed a conceptual model of the mechanisms by
 which primary care influences premature mortality, and undertook a
 cross-sectional study in which population and primary care variables
 reflecting the model were used to explain variations in mortality under
 aged 75 years. The premature standardised mortality ratios (SMRs) for each
 practice, available from the Department of Health, had been calculated
 from numbers of deaths in the five years 2006-10. A regression model was
 undertaken with explanatory variables for the year 2009/10, and repeated
 to check stability using data for 2008/09 and 2010/11. Setting: All
 general practices in England were eligible for inclusion, and of the total
 of 8290, complete data were available for 7858. Results. Population
 variables, particularly deprivation, were the most powerful predictors of
 premature mortality, but the mechanisms of primary care depicted in our
 model also affected mortality. The number of GPs/1000 population and
 detection of hypertension were negatively associated with mortality. In
 less deprived practices, continuity of care was also negatively associated
 with mortality. Conclusions. Greater supply of primary care is associated
 with lower premature mortality even in a health system that has strong
 primary care (England). Health systems need to sustain the capacity of
 primary care to deliver effective care, and should assist primary care
 providers in identifying and meeting the needs of socio-economically
 deprived groups.
description: mechanisms of general
 practice 2016An excel file containing
 the variables used in the study
DOI: 10.5061/dryad.1tk3d
title: Data from: Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard, Carlia amax

description: High-throughput sequencing approaches offer opportunities to better
 understand the evolutionary processes driving diversification,
 particularly in nonmodel organisms. In particular, the 100–1000's of
 loci that can now be sequenced are providing unprecedented power in
 population, speciation and phylogenetic studies. Here, we apply an exon
 capture approach to generate &gt;99% complete sequence and SNP data
 across &gt;2000 loci from a tropical skink, Carlia amax, and exploit
 these data to identify divergent lineages and infer their relationships
 and demographic histories. This is especially relevant to low-dispersal
 tropical taxa that often have cryptic diversity and spatially dynamic
 histories. For C. amax, clustering of nuclear SNPs and coalescent-based
 species delimitation analyses identify four divergent lineages, one fewer
 than predicted based on geographically coherent mtDNA clades (&gt;9.4%
 sequence divergence). Three of these lineages are widespread and
 parapatric on the mainland, whereas the most divergent is restricted to
 islands off the northeast Northern Territory. Tests for population
 expansion reject an equilibrium isolation-by-distance model for two of the
 three widespread lineages and infer refugial expansion sources in the
 relatively mesic northeast Top End and northwest Kimberley. The latter is
 already recognized as a hotspot of endemism, but our results also suggest
 that a stronger focus on the northeast Top End, and adjacent islands is
 warranted. More generally, our results show how genome-reduction methods
 such as exon capture can yield insights into the pattern and dynamics of
 biodiversity across complex landscapes with as yet poorly understood
 biogeographic history and how exon data can link between population and
 phylogenetic questions.
description: Datasets used in this
 studyThis is a compressed zip
 file of all the datasets used in this study grouped by
 analysis.Dryad
 Repository.zip
DOI: 10.15468/dl.vw52k7
title: Occurrence Download

description: A dataset containing 3158148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Africa",
 "Country is South Africa",
 "DatasetKey is iNaturalist Research-grade Observations",
 "Year 2010-2026"
 ]
}

 The dataset includes 3158148 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001409-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s8r4n
title: Data from: Root-lesion nematodes suppress cabbage aphid population development by reducing aphid daily reproduction

description: Empirical studies have shown that belowground feeding herbivores can
 affect the performance of aboveground herbivores in different ways. Often
 the critical life-history parameters underlying the observed performance
 effects remain unexplored. In order to better understand the cause for the
 observed effects on aboveground herbivores, these ecological mechanisms
 must be better understood. In this study we combined empirical experiments
 with a modelling approach to analyse the effect of two root feeding
 endoparasitic nematodes with different feeding strategies on the
 population growth of the aboveground feeding specialist aphid Brevicoryne
 brassicae on Brassica nigra. The aim was to test whether emerging
 differences in life history characteristics (days until reproduction,
 daily reproduction) would be sufficient to explain observed differences in
 aphid population development on plants with and without two species of
 nematodes. Aphid numbers were lower on plants with Pratylenchus penetrans
 in comparison to aphid numbers on plants with Meloidogyne spp. A dedicated
 experiment showed that aphid daily reproduction was lower on plants with
 P. penetrans (3.08 offspring per female per day) in comparison to both
 uninfested plants and plants with Meloidogyne spp. (3.50 offspring per
 female per day). The species-specific reduction of aphid reproduction
 appeared independent of changes in amino acids, soluble sugars or the
 glucosinolate sinigrin in the phloem. An individual-based model revealed
 that relatively small differences in reproduction rate per female were
 sufficient to yield a similar difference in aphid populations as was found
 in the empirical experiments.
description: Brassica_nigra_with_nematodes_and_aphidsThis file contains data from a greenhouse experiment with nematodes and aphids in a full factorial design on the plant Brassica nigra. There is data on plant quality (glucosinolates, sugars, amino acids), numbers of herbivores (nematodes, aphids) and results from a simulation model.Master_data_Bnigra.xlsx
DOI: 10.25446/oxford.26937448
title: PandemicPACT Dataset & Data Dictionary Files

description: Comprehensive PandemicPACT Dataset, Data Dictionary, and Documentation Guide
DOI: 10.25446/oxford.26937448.v1
title: PandemicPACT Dataset & Data Dictionary Files

description: Comprehensive PandemicPACT Dataset, Data Dictionary, and Documentation Guide
DOI: 10.5061/dryad.6hb49
title: Data from: IgM-enriched immunoglobulin attenuates systemic endotoxin activity in early severe sepsis: a before-after cohort study

description: Introduction: Sepsis remains associated with a high mortality rate.
 Endotoxin has been shown to influence viscoelastic coagulation parameters,
 thus suggesting a link between endotoxin levels and the altered
 coagulation phenotype in septic patients. This study evaluated the effects
 of systemic polyspecific IgM-enriched immunoglobulin (IgM-IVIg)
 (Pentaglobin® [Biotest, Dreieich, Germany]) on endotoxin activity (EA),
 inflammatory markers, viscoelastic and conventional coagulation
 parameters. Methods: Patients with severe sepsis were identified by daily
 screening in a tertiary, academic, surgical ICU. After the inclusion of 15
 patients, the application of IgM-IVIg (5 mg/kg/d over three days) was
 integrated into the unit’s standard operation procedure (SOP) to treat
 patients with severe sepsis, thereby generating “control” and “IgM-IVIg”
 groups. EA assays, thrombelastometry (ROTEM®) and impedance aggregometry
 (Multiplate®) were performed on whole blood. Furthermore, routine
 laboratory parameters were determined according to unit’s standards.
 Results: Data from 26 patients were included. On day 1, EA was
 significantly decreased in the IgM-IVIg group following 6 and 12 hours of
 treatment (0.51 ±0.06 vs. 0.26 ±0.07, p&lt;0.05 and 0.51 ±0.06 vs.
 0.25 ±0.04, p&lt;0.05) and differed significantly compared with the
 control group following 6 hours of treatment (0.26 ±0.07 vs. 0.43 ±0.07,
 p&lt;0.05). The platelet count was significantly higher in the
 IgM-IVIg group following four days of IgM-IVIg treatment (200/nl ±43 vs.
 87/nl ±20, p&lt;0.05). The fibrinogen concentration was significantly
 lower in the control group on day 2 (311 mg/dl ±37 vs. 475 mg/dl ±47 (p =
 0.015)) and day 4 (307 mg/dl ±35 vs. 420 mg/dl ±16 (p = 0.017)). No
 differences in thrombelastometric or aggregometric measurements, or
 inflammatory markers (interleukin-6 (IL-6), leukocyte, lipopolysaccharide
 binding protein (LBP)) were observed. Conclusion: Treatment with
 IgM-enriched immunoglobulin attenuates the EA levels in patients with
 severe sepsis and might have an effect on septic thrombocytopenia and
 fibrinogen depletion. Viscoelastic, aggregometric or inflammatory
 parameters were not influenced. Trial Registration: clinicaltrials.gov
 NCT02444871
description: Raw data with
 demographics, laboratory and point of care parametersRawdata
 IgMIVIg.csvDT1d1-1_aptem_130104142730000Original ROTEM DataDT1d1-1_extem_130104142635000Original ROTEM DataDT1d1-1_heptem_130104142820000Original ROTEM DataDT1d1-2_aptem_130104202109000Original ROTEM DataDT1d1-2_extem_130104202027000Original ROTEM DataDT1d1-2_extem_130104202027000Original ROTEM DataDT1d1-2_heptem_130104202155000Original ROTEM DataDT1d2-1_aptem_130105084339000Original ROTEM DataDT1d2-1_extem_130105084248000Original ROTEM DataDT1d2-1_heptem_130105084418000Original ROTEM DataOriginal ROTEM DataZip file of all original ROTEM dataOriginal Multiplate DataZip file of original Multiple data
DOI: 10.5061/dryad.f5f1t
title: Data from: A new Upper Cretaceous titanosaur nesting site from La Rioja (NW Argentina), with implications for titanosaur nesting strategies

description: Cretaceous titanosaur nesting sites are currently known only from Europe,
 Asia and South America. In the latter, only the Auca Mahuevo and Sanagasta
 nesting sites have been confidently assigned to this clade of sauropod
 dinosaurs. Here we report the discovery of the first eggs and egg clutches
 found at Tama, a new Upper Cretaceous fossiliferous locality in the Los
 Llanos Formation, Sierra de Los Llanos (La Rioja, NW Argentina). At least
 five egg clutches, several partially preserved, isolated eggs and many
 eggshell fragments were discovered in a single outcrop of a sandstone
 horizon which represents a cumulative palaeosol profile. Although the
 mechanical and digital preparation of eggs did not reveal any embryonic
 remains in ovo, the morphology of the eggs and eggshells closely matches
 that of titanosaur eggs and eggshells found worldwide. The morphology and
 spatial grouping of the titanosaur eggs from Tama, along with geological
 observations support a burrow-nesting strategy for these dinosaurs.
 Although the Sanagasta and Tama eggs were found in the same
 stratigraphical unit and share several morphological characters, they
 clearly differ in shell thickness and egg size. This, coupled with the
 interpretation of different sedimentary contexts for these nesting sites,
 strongly suggests that at least two different titanosaur species nested in
 La Rioja during the Late Cretaceous, using different nesting strategies.
 The occurrence of this new titanosaur nesting site in a semiarid
 palaeoenvironment represents an interesting case study for the
 reproductive biology of the titanosaur dinosaurs, particularly their
 labile nesting behaviour.
description: CT scan renderings of
 the jacket #2 of CRILAR-Pv 530/1The video shows a 3D
 reconstruction of the 5 eggs present in the jacket #2 of CRILAR-Pv 530/1.
 In addition, it is shown in detail an external and internal view of e1.
 Inside it, the slices show several cracks that are normal to the bedding
 plane and describe a slightly concentric pattern.Hechenleitner_et_al_2016_VS1.mp4
DOI: 10.5061/dryad.g7805
title: Data from: Genetic specificity of a plant-insect food web: implications for linking genetic variation to network complexity

description: Theory predicts that intraspecific genetic variation can increase the
 complexity of an ecological network. To date, however, we are lacking
 empirical knowledge of the extent to which genetic variation determines
 the assembly of ecological networks, as well as how the gain or loss of
 genetic variation will affect network structure. To address this knowledge
 gap, we used a common garden experiment to quantify the extent to which
 heritable trait variation in a host plant determines the assembly of its
 associated insect food web (network of trophic interactions). We then used
 a resampling procedure to simulate the additive effects of genetic
 variation on overall food-web complexity. We found that trait variation
 among host-plant genotypes was associated with resistance to insect
 herbivores, which indirectly affected interactions between herbivores and
 their insect parasitoids. Direct and indirect genetic effects resulted in
 distinct compositions of trophic interactions associated with each
 host-plant genotype. Moreover, our simulations suggest that food-web
 complexity would increase by 20% over the range of genetic variation in
 the experimental population of host plants. Taken together, our results
 indicate that intraspecific genetic variation can play a key role in
 structuring ecological networks, which may in turn affect network
 persistence.
description: Interaction network,
 gall size, and plant traitstree_level_interaxn_all_plants_traits_size.csvFood-web complexity simulation datafood web complexity simulation 50 reps of 200 sims 4 reps.csvMonoculture simulation 4 repsfood web complexity simulation 1000 monosims 4 reps.csvMonoculture simulation 3 repsfood web complexity simulation 1000 monosims 3 reps.csvMonoculture simulation 2 repsfood web complexity simulation 1000 monosims 2 reps.csvMonoculture simulation 1 repfood web complexity simulation 1000 monosims 1 reps.csv
DOI: 10.6084/m9.figshare.31157479
title: msdata

description: Data Description and Naming ConventionThe raw GC-MS data files are categorized into three batches corresponding to distinct clinical centers, identified by unique file prefixes: supsh1 (Center 1), sh2 (Center 2), and sz (Center 3).Sample groups are distinguished by their suffix structure:<br>Hemodialysis Patients (Paired): Identified by a timepoint suffix. Files ending in .1 represent pre-dialysis samples (e.g., supsh1.1.1, sz1.1), while files ending in .2 represent post-dialysis samples (e.g., supsh1.1.2, sz1.2).Healthy Controls: Identified by the absence of a timepoint suffix (e.g., supsh1.1, sz1).A total of approximately 20 paired patient samples and 10-12 healthy controls were collected from each center.
DOI: 10.6084/m9.figshare.31157479.v1
title: msdata

description: Data Description and Naming ConventionThe raw GC-MS data files are categorized into three batches corresponding to distinct clinical centers, identified by unique file prefixes: supsh1 (Center 1), sh2 (Center 2), and sz (Center 3).Sample groups are distinguished by their suffix structure:<br>Hemodialysis Patients (Paired): Identified by a timepoint suffix. Files ending in .1 represent pre-dialysis samples (e.g., supsh1.1.1, sz1.1), while files ending in .2 represent post-dialysis samples (e.g., supsh1.1.2, sz1.2).Healthy Controls: Identified by the absence of a timepoint suffix (e.g., supsh1.1, sz1).A total of approximately 20 paired patient samples and 10-12 healthy controls were collected from each center.
DOI: 10.5061/dryad.f3d4f
title: Data from: Not going with the flow: a comprehensive time-calibrated phylogeny of dragonflies (Anisoptera: Odonata: Insecta) provides evidence for the role of lentic habitats on diversification

description: Ecological diversification of aquatic insects has long been suspected to
 have been driven by differences in freshwater habitats, which can be
 classified into flowing (lotic) waters and standing (lentic) waters. The
 contrasting characteristics of lotic and lentic freshwater systems imply
 different ecological constraints on their inhabitants. The ephemeral and
 discontinuous character of most lentic water bodies may encourage
 dispersal by lentic species in turn reducing geographical isolation among
 populations. Hence, speciation probability would be lower in lentic
 species. Here, we assess the impact of habitat use on diversification
 patterns in dragonflies (Anisoptera: Odonata). Based on the eight nuclear
 and mitochondrial genes, we inferred species diversification with a
 model-based evolutionary framework, to account for rate variation through
 time and among lineages and to estimate the impact of larval habitat on
 the potentially nonrandom diversification among anisopteran groups.
 Ancestral state reconstruction revealed lotic fresh water systems as their
 original primary habitat, while lentic waters have been colonized
 independently in Aeshnidae, Corduliidae and Libellulidae. Furthermore, our
 results indicate a positive correlation of speciation and lentic habitat
 colonization by dragonflies: speciation rates increased in lentic
 Aeshnidae and Libellulidae, whereas they remain mostly uniform among lotic
 groups. This contradicts the hypothesis of inherently lower speciation in
 lentic groups and suggests species with larger ranges are more likely to
 diversify, perhaps due to higher probability of larger areas being
 dissected by geographical barriers. Furthermore, larger range sizes may
 comprise more habitat types, which could also promote speciation by
 providing additional niches, allowing the coexistence of emerging species.
description: MEC_Letsch_etal_2016MEC_Letsch.zip
DOI: 10.15468/dl.qreb9j
title: Occurrence Download

description: A dataset containing 388941 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Coordinated Waterbird Counts"
 ]
}

 The dataset includes 388941 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001429-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2gf23
title: Data from: Comparison of social structures within cities of very different sizes

description: People make a city, making each city as unique as the combination of its
 inhabitants. However, some cities are similar and some cities are
 inimitable. We examine the social structure of 10 different cities using
 Twitter data. Each city is decomposed to its communities. We show that in
 many cases one city can be thought of as an amalgamation of communities
 from another city. For example, we find the social network of Manchester
 is very similar to the social network of a virtual city of the same size,
 where the virtual city is composed of communities from the Bristol
 network. However, we cannot create Bristol from Manchester since Bristol
 contains communities with a social structure that are not present in
 Manchester. Some cities, such as Leeds, are outliers. That is, Leeds
 contains a particularly wide range of communities, meaning we cannot build
 a similar city from communities outside of Leeds. Comparing communities
 from different cities, and building virtual cities that are comparable to
 real cities, is a novel approach to understand social networks. This has
 implications when using social media to inform or advise residents of a
 city.
description: Social networks for 10
 citiesThe giant component for
 Tweets during October 1st 2014 through to October 28th 2014, separated by
 city. The first column relates to the city (1:Edinburgh; 2:Glasgow;
 3:Cardiff; 4:Bristol; 5:Nottingham; 6: Birmingham; 7:Sheffield; 8:Leeds;
 9:Manchester; 10:London), and the other two columns indicate an edge
 between the two listed nodes.10cityGCs.txt
DOI: 10.5061/dryad.bg41s
title: Data from: Genome-wide patterns of regulatory divergence revealed by introgression lines

description: Understanding the genetic basis for changes in transcriptional regulation
 is an important aspect of understanding phenotypic evolution. Using
 interspecific introgression lines, we infer the mechanisms of divergence
 in genome-wide patterns of gene expression between the nightshades Solanum
 pennellii and S. lycopersicum (domesticated tomato). We find that cis- and
 trans-regulatory changes have had qualitatively similar contributions to
 divergence in this clade, unlike results from other systems. Additionally,
 expression data from four tissues (shoot apex, ripe fruit, pollen, and
 seed) suggest that introgressed regions in these hybrid lines tend to be
 down-regulated, while background (non-introgressed) genes tend to be
 up-regulated. Finally, we find no evidence for an association between the
 magnitude of differential expression in NILs and previously determined
 sterility phenotypes. Our results contradict previous predictions of the
 predominant role of cis- over trans-regulatory divergence between species,
 and do not support a major role for gross genome-wide misregulation in
 reproductive isolation between these species.
description: R source, markdown and
 helper fileThe zip file contains
 all the source code used in our study (Guerrero_etal_source.R), as well as
 the R markdown file (Guerrero_etal_SuppInfo.Rmd) used to produce the
 Supporting Information (the .pdf output is also included). Two more files
 necessary for running the scripts (isNIL_bool_*) are included. These have
 the information on the state of each gene in the S. lycopersicum genome
 with respect to the introgressed regions in each introgression line. An
 allele can be introgressed (coded "true") or background (coded
 "false")Guerrero_etal_scripts.zipAnther (pollen) gene expression dataGene expression in pollen (microarray data) for 4 S. lycopersicum x S. pennellii introgression lines, and for S. lycopersicum. Protocols described in the GEO entry.Carpel (seed) gene expression dataGene expression in seed (from microarrays) for 3 S. lycopersicum x S. pennellii introgression lines, and for S. lycopersicum. Protocols described in the GEO entry.Gene expression in vegetative tissueProcessed data generated from RNA-Seq data from apices of 74 S. lycopersicum x S. pennellii introgression lines, and the two parents, from Chitwood et al. (2013; The Plant Cell, 25). Please see Readme.txt for further details on how to obtain the raw data.Leaf_sun_expression.txt