cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.km038
title: Data from: History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data

description: Two major ecological transitions marked the history of the Black Sea after
 the last Ice Age. The first was the postglacial transition from a
 brackish-water to a marine ecosystem dominated by porpoises and dolphins,
 once this basin was reconnected back to the Mediterranean Sea (ca. 8,000
 years B.P.). The second occurred during the last decades, when overfishing
 and hunting activities brought these predators close to extinction, deeply
 impacting the structure and dynamics of the ecosystem. Estimating the
 extent of this decimation is essential for characterizing this
 ecosystem's dynamics and for formulating restoration plans. However
 this extent is poorly documented in historical records. We addressed this
 issue for one of the main Black Sea predators, the harbor porpoise, using
 a population genetics approach. Analyzing its genetic diversity using an
 Approximate Bayesian Computation approach, we show that only a demographic
 expansion (at most 5,000 years ago) followed by a contemporaneous
 population collapse can explain the observed genetic data. We demonstrated
 that both the postglacial settlement of harbor porpoises in the Black Sea
 and the recent anthropogenic activities have left a clear footprint on
 their genetic diversity. Specifically, we inferred a strong population
 reduction (~90%) that occurred within the last five decades, which can
 therefore clearly be related to the recent massive killing of small
 cetaceans and to the continuing incidental catches in commercial
 fisheries. Our study thus provides a first quantitative assessment of
 these demographically catastrophic events, while also showing that two
 separate historical events can be inferred from contemporary genetic data.
description: DataDRYAD_Fontaine_etalPNAS_PlusGenotype data for 10 autosomal microsatellite loci are provided as well as sequences for the mtDNA DLOOP-Control region from the 89 harbor porpoises from the Black Sea and Aegean Sea. Data are formatted following the modified version of the genepop format (Rousset 2008, Mol Ecol Res 8: 103) described in Diy-ABC 1.X (Cornuet et al. BMC Bioinformatics 2010, 11:401)
DOI: 10.5061/dryad.d9q57
title: Data from: Grazing intensity affects insect diversity via sward structure and heterogeneity in a long-term experiment

description: In the past, insect diversity in grasslands showed a severe decline due to
 management intensification or abandonment. In this study, we investigate
 the long-term influence of grazing and the potential for spatial patterns
 created by different grazing intensities to enhance insect diversity. In a
 long-term experiment (2002–2011), three grazing intensities were applied
 to 1-ha paddocks in a triplicate block design: moderate grazing (MC),
 lenient grazing (LC) and very lenient grazing (VLC, since 2005). The
 experiment was conducted in a moderately species-rich grassland at the
 edge of the Solling Uplands in Lower Saxony, Germany. Orthoptera
 (grasshoppers) and Lepidoptera (butterflies) on three 50-m transects per
 paddock were counted in 2002–2004 and again in 2010 and 2011. Statistics
 were performed using linear mixed modelling. Grasshopper diversity
 measures (species richness and abundance) were significantly affected by
 grazing intensity; abundance increased from 2002 to 2011 more strongly in
 the LC than in the MC treatment. Butterfly species richness response to
 grazing intensity varied among years. Data from 2010 and 2011 did not
 reveal any advantage of the lowest grazing intensity (VLC) compared to the
 intermediate grazing intensity treatment (LC) in either insect group.
 Multiple regressions were used to investigate diversity patterns. Along
 with compressed sward height, spatial patchiness was important for
 grasshopper species richness and abundance as well as for butterfly
 species numbers. Butterfly abundance was mainly influenced by vertical
 sward height heterogeneity in addition to the significant effects of
 thistle abundance and number of nectar plant species. Synthesis and
 applications. Cattle grazing intensity affects the proportions and spatial
 heterogeneity of short and tall sward patches on pastures. The less mobile
 grasshoppers particularly benefitted from the structural modifications
 created by cattle at lenient grazing levels (stocking rate 1.14 SLU ha-1,
 SLU: standard livestock unit = 500 kg). In the final study years, areas
 with intermediate grazing intensity revealed high diversity indices and
 the most distinct patchiness, therefore a further reduction of grazing
 intensity is not recommended. This indicates that commercial livestock
 production may be compatible with conservation targets.
description: grasshopperssee ReadMebutterfliessee ReadMeEnvVariablessee ReadMe
DOI: 10.5061/dryad.gt5m884
title: Data from: An investigation of sepsis surveillance and emergency treatment on patient mortality outcomes: an observational cohort study

description: Objective. To determine the prevalence of initiating the sepsis 3-hour
 bundle of care and estimate effects of bundle completion on risk-adjusted
 mortality among ED patients screened-in by electronic surveillance.
 Materials and Methods. This was a multiple center observational cohort
 study conducted in 2016. The study population was comprised of patients
 screened-in by St. John Sepsis Surveillance Agent within four hours of ED
 arrival, had a sepsis bundle initiated, and admitted to hospital. We built
 multivariable logistic regression models to estimate impact of a 3-hour
 bundle completed within three hours of arrival on mortality outcomes.
 Results. Approximately 3% ED patients were screened-in by electronic
 surveillance within four hours of arrival and admitted to hospital. Nearly
 7 in 10 (69%) patients had a bundle initiated, with most bundles completed
 within three hours of arrival. The fully-adjusted risk model achieved good
 discrimination on mortality outcomes (AUROC = .82, 95% CI = .79 to .85)
 and estimated 34% reduced mortality risk among patients with a bundle
 completed within three hours of arrival compared to non-completers.
 Discussion. The sepsis bundle is an effective intervention for many
 vulnerable patients, and likely to be completed within three hours after
 arrival when electronic surveillance with reliable alert notifications are
 integrated into clinical workflow. Beginning at triage, the platform and
 sepsis program enables identification and management of patients with
 greater precision, and increases the odds of good outcomes. Conclusion.
 Sepsis surveillance and clinical decision support accelerate accurate
 recognition and stratification of patients, and facilitate timely delivery
 of healthcare.
description: Dryad_data_1508Use Data for "sepsis surveillance and emergency treatment"
DOI: 10.5061/dryad.5f95s
title: Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite

description: Theory indicates that spatial scale and habitat configuration are
 fundamental for coevolutionary dynamics and how diversity is maintained in
 host–pathogen interactions. Yet, we lack empirical data to translate the
 theory to natural host–parasite systems. In this study, we conduct a
 multiscale cross-inoculation study using the specialist wild plant
 pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We
 apply the same sampling scheme to a region with highly fragmented (Åland)
 and continuous (Saaremaa) host populations. Although theory predicts
 higher parasite virulence in continuous regions, we did not detect
 differences in traits conferring virulence among the regions. Patterns of
 adaptation were highly scale dependent. We detected parasite maladaptation
 among regions, and among populations separated by intermediate distances
 (6.0–40.0 km) within the fragmented region. In contrast, parasite
 performance did not vary significantly according to host origin in the
 continuous landscape. For both regions, differentiation among populations
 was much larger for genetic variation than for phenotypic variation,
 indicating balancing selection maintaining phenotypic variation within
 populations. Our findings illustrate the critical role of spatial scale
 and habitat configuration in driving host–parasite coevolution. The
 absence of more aggressive strains in the continuous landscape, in
 contrast to theoretical predictions, has major implications for long-term
 decision making in conservation, agriculture, and public health.
description: Inoculation
 matrixInoculation_matrix.txtGenetic dataGenetic_data.txt
DOI: 10.5061/dryad.kp497
title: Data from: Nest fidelity is driven by multi-scale information in a long-lived seabird

description: Although the reproductive success of most organisms depends on factors
 acting at several spatial scales, little is known about how organisms are
 able to synthesize multi-scale information to optimize reproduction. Using
 longitudinal data from a long-lived seabird, Monteiro's storm-petrel,
 we show that average breeding success is strongly related to oceanic
 conditions at the population level, and we postulate that (i) individuals
 use proximal information (their own reproduction outcome in year t) to
 assess the qualities of their mate and nest and to decide to retain them
 or not in year t + 1; (ii) the intensity of these responses depends on the
 quality of the oceanic environment in year t, which affects the
 predictability of reproduction outcome in year t + 1. Our results confirm
 that mate and nest fidelities are higher following successful reproduction
 and that the relationship between the success of a given pair and
 subsequent nest fidelity is stronger in years with unfavourable oceanic
 conditions, suggesting that individuals rely on distant information to
 modulate their use of proximal information and adjust their breeding
 strategy.
description: demographic and
 environemental data for the Monteiro’s Storm-petrel population monitored
 on Praia Islet (2000–2012)dataForDryad.xls
DOI: 10.5061/dryad.8374
title: Data from: A study of canalization and developmental stability in the sternopleural bristle system of Drosophila melanogaster

description: Among the explanations for minimizing the effects of extraneous variation
 has been canalization and developmental stability. However, there is
 little agreement as to whether these two processes reflect a common set of
 mechanisms. This confusion is inflated due to the lack of consensus as to
 a precise definition of canalization. In this study, canalization in the
 sternopleural bristle system is used to investigate the relationships
 between measures of canalization and developmental stability by comparing
 how a panel of naturally derived lines responds to both genetic and
 environmental perturbations. No evidence for a common mechanism between
 the different measures of canalization was observed. Furthermore, a
 hypothesis regarding a common mechanism for environmental and genetic
 canalization was tested, and no evidence was found to support it. However,
 there is evidence for a relationship between at least one form of
 canalization and developmental stability.
description: sp
DOI: 10.5061/dryad.77pq8
title: Data from: Effects of hypoxia and ocean acidification on the upper thermal niche boundaries of coral reef fishes

description: Rising ocean temperatures are predicted to cause a poleward shift in the
 distribution of marine fishes occupying the extent of latitudes tolerable
 within their thermal range boundaries. A prevailing theory suggests that
 the upper thermal limits of fishes are constrained by hypoxia and ocean
 acidification. However, some eurythermal fish species do not conform to
 this theory, and maintain their upper thermal limits in hypoxia. Here we
 determine if the same is true for stenothermal species. In three coral
 reef fish species we tested the effect of hypoxia on upper thermal limits,
 measured as critical thermal maximum (CTmax). In one of these species we
 also quantified the effect of hypoxia on oxygen supply capacity, measured
 as aerobic scope (AS). In this species we also tested the effect of
 elevated CO2 (simulated ocean acidification) on the hypoxia sensitivity of
 CTmax. We found that CTmax was unaffected by progressive hypoxia down to
 approximately 35 mmHg, despite a substantial hypoxia-induced reduction in
 AS. Below approximately 35 mmHg, CTmax declined sharply with water oxygen
 tension (PwO2). Furthermore, the hypoxia sensitivity of CTmax was
 unaffected by elevated CO2. Our findings show that moderate hypoxia and
 ocean acidification do not constrain the upper thermal limits of these
 tropical, stenothermal fishes.
description: Data for individual
 animalsCritical thermal maximum
 (CTmax), maximum metabolic rate (MMR), standard metabolic rate (SMR),
 aerobic scope (AS), critical oxygen tension (Pcrit), body mass (BM) and
 experimental conditions for individual animals.Raw data for SMR and
 PcritIndividual MO2 points as
 a function of time for estimates of SMR Individual MO2 points as a
 function of water oxygen tension for estimates of Pcrit
DOI: 10.5061/dryad.77r3p
title: Data from: Environmental conditions affect spatial genetic structures and dispersal patterns in a solitary rodent

description: The study of the spatial distribution of relatives in a population under
 contrasted environmental conditions provides critical insights into the
 flexibility of dispersal behaviour and the role of environmental
 conditions in shaping population relatedness and social structure. Yet few
 studies have evaluated the effects of fluctuating environmental conditions
 on relatedness structure of solitary species in the wild. The aim of this
 study was to determine the impact of interannual variations in
 environmental conditions on the spatial distribution of relatives [spatial
 genetic structure (SGS)] and dispersal patterns of a wild population of
 eastern chipmunks (Tamias striatus), a solitary rodent of North America.
 Eastern chipmunks depend on the seed of masting trees for reproduction and
 survival. Here, we combined the analysis of the SGS of adults with direct
 estimates of juvenile dispersal distance during six contrasted years with
 different dispersal seasons, population sizes and seed production. We
 found that environmental conditions influences the dispersal distances of
 juveniles and that male juveniles dispersed farther than females. The
 extent of the SGS of adult females varied between years and matched the
 variation in environmental conditions. In contrast, the SGS of males did
 not vary between years. We also found a difference in SGS between males
 and females that was consistent with male-biased dispersal. This study
 suggests that both the dispersal behaviour and the relatedness structure
 in a population of a solitary species can be relatively labile and change
 according to environmental conditions.
description: data and
 matricesdryad-data.zip
DOI: 10.5061/dryad.5m0m5
title: Data from: Components of phylogenetic signal in antagonistic and mutualistic networks

description: Recent studies have shown a phylogenetic signal in the structure of
 ecological networks, making the point that evolutionary history is
 important in explaining network architecture. However, this previous work
 has focused on either antagonistic (i.e., predator-prey) or mutualistic
 networks and has used different methodologies. Thus, a comparative
 assessment of both the frequency and the strength of phylogenetic signal
 across network types and components of network structure has been
 precluded. Here, we address this issue using a data set comprising 60
 antagonistic and mutualistic networks. By quantifying simultaneously the
 matching and centrality components of network architecture—capturing the
 modular and nested structure, respectively—we test the presence and
 quantify the strength of phylogenetic signal across network types, species
 sets, and components of network structure. We find contrasting differences
 across such groups. First, phylogenetic signal is stronger in antagonistic
 webs than in mutualistic webs. Second, resources are more strongly
 constrained than consumers in food webs, while animals show more
 constraints than plants in mutualistic networks. Third, phylogenetic
 constraints are stronger for the matching component than for the
 centrality component of network structure. These results can shed light on
 the contrasting evolutionary constraints shaping network structure across
 interaction types and species sets.
description: Network
 datadata.zip
DOI: 10.5061/dryad.6r19m91
title: Data from: Immune checkpoint inhibitor–related myositis and myocarditis in patients with cancer

description: Objective: To report the clinicopathological features and outcome of
 myositis in patients treated with immune checkpoint inhibitors
 (irMyositis). Methods: We retrospectively analyzed patients diagnosed with
 irMyositis in tertiary centers in Paris, France, and Berlin, Germany, from
 January 2015, to July 2017. Main outcomes were clinical manifestations and
 muscle histology, which included MHC-I, C5b-9, CD3, CD4, CD8, CD20, CD68,
 PD-1, PD-L1 and PD-L2 immunohistochemical stains. Results: Ten patients
 with metastatic cancer were included; median age was 73 years (range,
 56-87). Median follow-up duration was 48 weeks (range 16-88). Six patients
 developed myositis during nivolumab therapy, one during pembrolizumab, one
 during durvalumab, and two during combined nivolumab and ipilimumab.
 Median delay between immune checkpoint inhibitor (ICI) initiation and
 myositis onset was 25 days (range, 5-87). Clinical manifestations were
 dominated by acute or subacute myalgia (8 patients), limb-girdle (7),
 axial (7) and oculomotor (7) weakness. Four patients had evidence of
 myocarditis. In all patients, CK levels were elevated (median 2668 U/L,
 range 1059-16620), while anti-acetylcholine receptor and
 myositis-associated antibodies were negative. Electrodiagnostic studies
 showed myopathic process without decrement in all patients. Muscle biopsy
 constantly showed multifocal necrotic myofibers, sarcolemmal MHC-I and
 endomysial inflammation, mainly consisting of CD68+ cells expressing PD-L1
 and CD8+ cells expressing PD-1. ICI treatment was withdrawn in all
 patients; nine patients received immunosuppressive therapy, which
 consistently led to marked clinical improvement. Conclusions: irMyositis
 presents with remarkably homogeneous and unique clinicopathological
 features, expanding the nosological spectrum of inflammatory myopathies in
 patients with cancer. ICI withdrawal and treatment with corticosteroids
 improve outcome.
description: Supplementary Table 1.
 Detailed auto-antibodies work-up in patients with
 irMyositis.Touat et al_irMyositis_R1_Suppl
 Table 1.pdf
DOI: 10.5061/dryad.4fq5vr6
title: Data from: Rainfall pulse response of carbon fluxes in a temperate grass ecosystem in the semiarid Loess Plateau

description: Rainfall pulses can significantly influence carbon cycling in water
 limited ecosystems. The magnitude of carbon flux component responses to
 precipitation may vary depending on precipitation amount and antecedent
 soil moisture, associated with nonlinear responses of plants and soil
 microbes. The present study was carried out in a temperate grass ecosystem
 during 2013–2015 in the semiarid Loess Plateau of China, to examine the
 response of carbon fluxes to precipitation using the “threshold-delay”
 model. The unique contribution of environmental variables, such as
 precipitation amount and antecedent soil moisture before rainfall
 (SWC_antecedent) to carbon fluxes in response to rainfall were also
 investigated. The lower threshold of effective rainfall was 6.6 mm for
 gross ecosystem production (GEP), 8.5 mm for net ecosystem production
 (NEP) and 4.5 mm for ecosystem respiration (RE); and the upper threshold
 of effective rainfall was 21.4 mm for GEP and NEP, and 16.8 mm for RE.
 Rainfall amount was positively affected the relative rainfall responses of
 GEP, NEP and RE. However, SWC_antecedent at 20 cm soil depth offset the
 response of GEP to rainfall pulses, and SWC_antecedent at 5 cm depth
 offset the response of NEP and RE to rainfall pulses, with corresponding
 partial slopes of linear regressions of −0.50, −0.40 and −0.52. These
 results indicated that NEP was more sensitive to rainfall pulses and RE
 was more sensitive to SWC_antecedent. These results demonstrate the
 importance of rainfall events of &lt; 10 mm, and that the negative
 effect of SWC_antecedent should also be considered when estimating
 ecosystem carbon fluxes in this semiarid region.
description: Carbon flux
 dataCarbon flux data. All
 the abbreviation and the unit can be observed in the
 manuscript.Rainfall and soil water
 content dataRainfall and soil water
 content data. All the abbreviation and the unit can be observed in the
 manuscript.Root surface area of A.
 scoparia and G. uralensisRoot surface area of A.
 scoparia and G. uralensis. All the abbreviation and the unit can be
 observed in the manuscript.
DOI: 10.5061/dryad.8v234
title: Data from: Bacterial competition and quorum-sensing signalling shapes the eco-evolutionary outcomes of model in vitro phage therapy

description: The rapid rise of antibiotic resistance has renewed interest in phage
 therapy – the use of bacteria-specific viruses (phages) to treat bacterial
 infections. Even though phages are often pathogen-specific, little is
 known about the efficiency and eco-evolutionary outcomes of phage therapy
 in polymicrobial infections. We studied this experimentally by exposing
 both quorum sensing (QS) signalling PAO1 and QS-deficient lasR Pseudomonas
 aeruginosa genotypes (differing in their ability to signal
 intra-specifically) to lytic PT7 phage in the presence and absence of two
 bacterial competitors: Staphylococcus aureus and Stenotrophomonas
 maltophilia – two bacteria commonly associated with P. aeruginosa in
 polymicrobial cystic fibrosis lung infections. Both the P. aeruginosa
 genotype and the presence of competitors had profound effects on bacteria
 and phage densities and bacterial resistance evolution. In general,
 competition reduced the P. aeruginosa frequencies leading to a lower rate
 of resistance evolution. This effect was clearer with QS-signalling PAO1
 strain due to lower bacteria and phage densities and relatively larger
 pleiotropic growth cost imposed by both phage and competitors.
 Unexpectedly, phage selection decreased the total bacterial densities in
 the QS-deficient lasR pathogen communities, while an increase was observed
 in the QS-signalling PAO1 pathogen communities. Together these results
 suggest that bacterial competition can shape the eco-evolutionary outcomes
 of phage therapy.
description: PseudomonasdensitydataTotalbacterialdensitydataPhagedensitydataFitnessdata