Find research datasets worth reusing

opencc-by-4.0May 2020View details →

Data package from "Regional Mapping and Spatial Distribution Analysis of Canopy Palms in an Amazon Forest Using Deep Learning and VHR Images"

This data package contains the very high resolution maps of canopy palms from the paper "Regional Mapping and Spatial Distribution Analysis of Canopy Palms in an Amazon Forest Using Deep Learning and VHR Images". These maps have been produced with two GeoEye-1 very high resolution images (0.5 m) and a Deep Learning method for image segmentation called U-net, methods and data are fully described in the article. The total size of the decompressed archive is 2.56 Go and is distributed in two shapefiles, one for each GeoEye-1 image. When using this dataset, please cite the original article https://doi.org/10.3390/rs12142225

opencc-by-4.0Jun 2020View details →

Supplemental data S1 to accompany Marin et al 2020 "Connectomics analysis reveals first, second, and third order thermosensory and hygrosensory neurons in the adult Drosophila brain"

Neuronal skeletons and meshes. Related to STAR Methods. marin2020-skeletons contains files describing the morphology of each neuron in this study (in FAFB14 space, .swc format). glomeruli_meshes contains the glomerular meshes (in FAFB14 space, .stl format). neuropil_meshes contains the glomerular meshes (in FAFB14 space, .stl format).

opencc-zeroMay 2020View details →

Data from: Molecular evolutionary analysis of nematode Zona Pellucida (ZP) modules reveals disulfide-bond reshuffling and standalone ZP-C domains

Zona pellucida (ZP) modules mediate extracellular protein-protein interactions and contribute to important biological processes including syngamy and cellular morphogenesis. While some biomedically-relevant ZP modules are well-studied, little is known about the protein family's broad-scale diversity and evolution. The increasing availability of sequenced genomes from "non-model" systems provides a valuable opportunity to address this issue, and to use comparative approaches to gain new insights into ZP module biology. Here, through phylogenetic and structural exploration of ZP module diversity across the nematode phylum, I report evidence that speaks to two important aspects of ZP module biology. First, I show that ZP-C domains—which in some modules act as regulators of ZP-N domain-mediated polymerization activity, and which have never before been found in isolation—can indeed be found as standalone domains. These standalone ZP-C domain proteins originated in independent (paralogous) lineages prior to the diversification of extant nematodes, after which they evolved under strong stabilizing selection, suggesting the presence of ZP-N domain-independent functionality. Second, I provide a much-needed phylogenetic perspective on disulfide bond variability, uncovering evidence for both convergent evolution and disulfide-bond reshuffling. This result has implications for our evolutionary understanding and classification of ZP module structural diversity and highlights the usefulness of phylogenetics and diverse sampling for protein structural biology. All told, these findings set the stage for broad-scale (cross-phyla) evolutionary analysis of ZP modules and position Caenorhabditis elegans and other nematodes as important experimental systems for exploring the evolution of ZP modules and their constituent domains.

opencc-by-4.0May 2020View details →

Accompanied data files used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis"

lists of source file used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis" by Jing Yang, Amanda McGovern, Paul Martin, Kate Duffus, Xiangyu Ge, Peyman Zarrineh, Andrew P Morris, Antony Adamson, Peter Fraser, Magnus Rattray & Stephen Eyre. The paper has been accepted by Nature Communications.

opencc-by-nc-4.0Apr 2020View details →

Image analysis data for the study of the reactivity of the phases in Nd-Fe-B magnets etched with HCl-saturated Cyphos IL 101

Scanning electronic microscopy (SEM), Energy dispersive X-rays Spectroscopy (EDS) and image analysis have been used as techniques to analyse the results of etching experiments carried on NdFeB permanent magnets by using the ionic liquid Cyphos IL 101 saturated with HCl. Image analysis is for the first time reported in the literature as a technique for corrosion studies. Operational conditions of the analysis equipment were the following: -  The samples were analyzed via electron microscopy and image analysis. Scanning electron microscope (SEM) pictures and energy dispersed spectra (EDS) were collected with a JEOL JSM 5800 microscope, operating at 20 kV. The polished samples were made conductive by spraying a carbon layer on them using a Balzer SCD 050 sputter coater. - The EDS analysis were collected as average on 5 points per each SEM picture - A commercial software, ImageJ®, was used for the image analysis. Two data were analysed: the Feret diameter, dF, and the percentage of etched area, %area. The SEM images were converted to 8-bit grayscale, from 0 to 255 number of grey ranges. Simple linear scaling was applied

opencc-by-4.0Jun 2020View details →

Insights into the operation of the solid Earth system from analysis of compiled geochemical data (Video)

This is the first session video recording of the Goldschmidt 2020 Virtual Workshop: Earth Science meets Data Science - Services & Systems, Policies & Procedures, Tools & Techniques for Geochemistry. Moderated by Kerstin Lehnert (Columbia University)

openother-openJul 2020View details →

ekoraytascilar/naturecommunicationscovid: Data and analysis code to accompany "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"

This release contains raw datasets and analysis code for the research paper titled "Patients with immune-mediated inflammatory diseases receiving cytokine inhibitors have low prevalence of SARS-CoV-2 seroconversion"

opencc-by-4.0Jul 2020View details →

Data & Open Science analysis of citizen science projects related with pollution

These two spreadsheets contain the analysis done from a Data & Open Science perspective of citizen science projects related with pollution

opencc-zeroFeb 2020View details →

Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination

Wolbachia are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced Wolbachia strains in the A, B, C, D, E and F supergroups. Phylogenomic analysis with these core genes indicate that all 33 Wolbachia strains maintain the supergroup relationship classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (9 events), but also between A and E supergroups (5 events). Maintenance of such transfers suggests possible roles in Wolbachia infection related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in Wolbachia.

opencc-zeroJul 2020View details →

Data from: A meta-analysis of factors influencing the strength of mate choice copying in animals

Davies et al., (2020) All data and R code Mate-choice copying is a form of social learning in which an individual's choice of mate is influenced by the apparent choices of other individuals of the same sex, and has been observed in more than 20 species across a broad taxonomic range. Though fitness benefits of copying have proven difficult to measure, theory suggests that copying should not be beneficial for all species or contexts. However, the factors influencing the evolution and expression of copying have proven difficult to resolve. We systematically searched the literature for studies of mate-choice copying in non-human animals, and then performed a phylogenetically-controlled meta-analysis to explore which factors influence the expression of copying across species. Across 58 published studies in 23 species, we find strong evidence that animals copy the mate choice of others. The strength of copying was significantly influenced by taxonomic group, however sample size limitations mean it is difficult to draw firm conclusions regarding copying in mammals and arthropods. The strength of copying was also influenced by experimental design: copying was stronger when choosers were tested before and after witnessing a conspecific's mate choice, compared to when choosers with social information were compared to choosers without. Importantly, we did not detect any difference in the strength of copying between males and females, or in relation to the rate of multiple mating. Our search also highlights that more empirical work is needed to investigate copying in a broader range of species, especially those with differing mating systems and levels of reproductive investment.

opencc-zeroMay 2020View details →

Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry

The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus Deuveia is the sister group of other epicopeiid genera. Epicopeia and Nossa are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that the last common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution.

opencc-zeroJul 2020View details →

Data from: Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages

Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 different sites around Bielefeld in Germany revealed little in the way of population structure over a geographic scale of several kilometers. However, on a more local scale we found evidence for elevated relatedness as well as inbreeding. We also observed a significant negative association between the genetic diversity of fruit and the age of the trees under which they were sampled. Taken together, our results suggest that as genets mature, they compete and potentially create conditions under which further spores struggle to become established. By implication, even though this species is widely picked, propagules remain common enough to create strong competition when new habitats become available.

opencc-zeroJun 2020View details →

Data from: Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020

Background: Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. Methods: We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29-May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. Results: 491 of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% CI 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% CI 2.73-3.69] to 1.77 [95% CI 1.49-2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CI 0.84-0.94]) by national lockdown measure. Conclusions: Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

opencc-zeroMay 2020View details →

Data from: City sicker? a meta-analysis of wildlife health and urbanization

Urban development can alter resource availability, land use, and community composition, in turn influencing wildlife health. Generalizable relationships between wildlife health and urbanization have yet to be quantified, and could vary across health metrics and animal taxonomy. We present a phylogenetic meta-analysis of 516 records spanning 81 wildlife species from 106 studies comparing the toxicant loads, parasitism, body condition, or stress of urban and non-urban wildlife populations in 30 countries. We find a significantly negative relationship between urbanization and wildlife health, driven by higher toxicant loads and greater parasitism by parasites transmitted through close contact. Invertebrates and amphibians were particularly affected, with higher toxicant loads and physiological stress in urban populations as compared to their non-urban counterparts. We also found strong geographic and taxonomic bias in research effort, highlighting future research needs. Our results suggest urban wildlife experience several health risks with potential threats to conservation.

Data from: Evaluation of a pharmacist-led actionable audit and feedback intervention for improving medication safety in primary care: an interrupted time series analysis

Background. We evaluated the impact of a pharmacist-led Safety Medication dASHboard (SMASH) intervention on medication safety in primary care. Methods and findings. SMASH comprised: (1) training of clinical pharmacists to deliver the intervention; (2) a web-based dashboard providing actionable, patient-level feedback; and (3) pharmacists reviewing individual at-risk patients, and initiating remedial actions or advising general practitioners on doing so. It was implemented in forty-three general practices covering a population of 235,595 people in Salford (Greater Manchester), UK. All practices started receiving the intervention between 18 April 2016 and 26 September 2017. We used an interrupted time series analysis of rates of potentially hazardous prescribing and inadequate blood-test monitoring, comparing observed rates post-intervention to extrapolations from a 24-month pre-intervention trend. The number of people registered to participating practices and having one or more risk factors for being exposed to hazardous prescribing or inadequate blood-test monitoring at the start of the intervention was 47,413 (males: 23,073 [48.7%]; mean age: 60 [standard deviation: 21]). At baseline, 95% of practices had rates of potentially hazardous prescribing (composite of 10 indicators) between 0.88% and 6.19%. The prevalence of potentially hazardous prescribing reduced by 27.9% (95% confidence interval [CI], 20.3% to 36.8%) at 24 weeks and by 40.7% (95% CI, 29.1% to 54.2%) at twelve months after introduction of SMASH. The rate of inadequate blood-test monitoring (composite of 2 indicators) reduced by 22.0% (95% CI, 0.2% to 50.7%) at 24 weeks and by 23.5% (95% CI, -4.5% to 61.6%) at 12 months. After 12 months, 95% of practices had rates of potentially hazardous prescribing between 0.74% and 3.02%. We did not randomise practices but enrolled them in a naturalistic fashion. All our measurements were based on routinely kept electronic health records. Conclusions. The SMASH intervention was associated with reduced rates of potentially hazardous prescribing and inadequate blood-test monitoring in general practices. This reduction was sustained over 12 months after start of the intervention for prescribing but not for monitoring of medication. There was a marked reduction in the variation in rates of high-risk prescribing between practices.

opencc-by-4.0Aug 2020View details →

CO2 Reduction Tafel Dataset for Bayesian Data Analysis

This dataset contains 344 different digitized and tagged Tafel slope datasets from the CO2 reduction literature. We re-analyze this data with a Bayesian data analysis procedure that estimates a Tafel slope and yields distributional uncertainty information about its value. We are releasing this dataset along with our study to facilitate re-analyzing and refitting our data using different models and approaches.

Data from: Trophic plasticity in a common reef-building coral: Insights from δ13C analysis of essential amino acids

1. Reef-building corals are mixotrophic organisms that can obtain nutrition from endosymbiotic microalgae (autotrophy) and particle capture (heterotrophy). Heterotrophic nutrition is highly beneficial to many corals, particularly in times of stress. Yet the extent to which different coral species rely on heterotrophic nutrition remains largely unknown because it is challenging to quantify. 2. We developed a quantitative approach to investigate coral nutrition using carbon isotope (δ13C) analysis of six essential amino acids (AAESS) in a common Indo-Pacific coral (Pocillopora meandrina) from the fore reef habitat of Palmyra Atoll. We sampled particulate organic matter (POM) and zooplankton as the dominant heterotrophic food sources in addition to the coral host and endosymbionts. We also measured bulk tissue carbon (δ13C) and nitrogen (δ15N) isotope values of each sample type. 3. Patterns among δ13C values of individual AAESS provided complete separation between the autotrophic (endosymbionts) and heterotrophic nutritional sources. In contrast, bulk tissue δ13C and δ15N values were highly variable across the putative food sources and among the coral and endosymbiont fractions, preventing accurate estimates of coral nutrition on Palmyra. 4. We used linear discriminant analysis to quantify differences among patterns of AAESS δ13C values, or 'fingerprints', of the food resources available to corals. This allowed for the development of a quantitative continuum of coral nutrition that can identify the relative contribution of autotrophic and heterotopic nutrition to individual colonies. Our approach revealed exceptional variation in conspecific colonies at scales of meters to kilometers. On average, 41% of AAESS in P. meandrina on Palmyra are acquired via heterotrophy but some colonies appear capable of obtaining the majority of AAESS from one source or the other. 5. The use of AAESS δ13C fingerprinting analysis offers a significant improvement on the current methods for quantitatively assessing coral trophic ecology. We anticipate that this approach will facilitate studies of coral nutrition in the field, which are essential for comparing coral trophic ecology across taxa and multiple spatial scales. Such information will be critical for understanding the role of heterotrophic nutrition in coral resistance and/or resilience to ongoing environmental change.

Data from: Detecting and quantifying social transmission using network-based diffusion analysis

1. Although social learning capabilities are taxonomically widespread, demonstrating that freely interacting animals (whether wild or captive) rely on social learning has proved remarkably challenging. 2. Network-based diffusion analysis (NBDA) offers a means for detecting social learning using observational data on freely interacting groups. Its core assumption is that if a target behaviour is socially transmitted, then its spread should follow the connections in a social network that reflects social learning opportunities. 3. Here, we provide a comprehensive guide for using NBDA. We first introduce its underlying mathematical framework and present the types of questions that NBDA can address. We then guide researchers through the process of: selecting an appropriate social network for their research question; determining which NBDA variant should be used; and incorporating other variables that may impact asocial and social learning. Finally, we discuss how to interpret an NBDA model's output and provide practical recommendations for model selection. 4. Throughout, we highlight extensions to the basic NBDA framework, including incorporation of dynamic networks to capture changes in social relationships during a diffusion and using a multi-network NBDA to estimate information flow across multiple types of social relationship. 5. Alongside this information, we provide worked examples and tutorials demonstrating how to perform analyses using the newly developed NBDA package written in the R programming language.

Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function

Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3.

Data for Analysis of Keystone Predation - trait based or driven by extrinsic processes?

Keystone predation can be a determinant of community structure, including species diversity, but factors underlying "keystoneness" have been minimally explored. Using the system in which the original keystone, the sea star Pisaster ochraceus, was discovered, we focused on two potential (but overlapping) determinants of keystoneness: intrinsic traits or state variables of the species (e.g., size, density), and extrinsic environmental parameters (e.g., prey productivity) that may provide conditions favorable for keystone predator evolution. Using a comparative-experimental approach, with repeated field experiments at multiple sites across a variable coastal environment, we tested predation rates, or how quickly predators consumed prey, and predation effects, or community response to predator presence or absence. We tested five hypotheses: (H1) predation rates and effects will vary in space but not time; (H2) per population predation rates will vary primarily with individual traits and population variables; (HJHH3) per capita predation rates will vary only with individual traits; (H4) predation effects will vary with traits, variables, and external drivers; and (H5) as predicted by the keystone predation hypothesis, diversity will vary unimodally with predation pressure. As hypothesized, predation rates differed among sites but not over time (H1), and in caging exclusion experiments, predation effect varied with both intrinsic and extrinsic factors (H4). Unexpectedly, predation rates varied with both intrinsic and extrinsic (H2, per population), or only with extrinsic (H3, per capita) factors. Further, in large-plot exclusion experiments, predation effect was most closely associated with individual traits (contra H4). Finally, taxon diversity varied unimodally with proxies of predation pressure (sessile prey abundance) and was sensitive to extrinsic factors (mussel growth, temperature, and upwelling) (H5). Hence, keystoneness depended on predator individual traits, predator population variables, and environmental parameters. However, temporal differences in caging experiments suggested that environmental characteristics underlying prey dynamics may be preeminent. Compared to prior experiments, predation was weaker with low prey input compared to periods with high prey input. Collectively, our results suggest that keystone predator evolution depends on the coalescence of species-specific characteristics, and environmental parameters favoring high prey productivity. Our approach may be a model for future studies exploring the generality of keystoneness.