cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8318738
title: Additional file 5: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S4. Co-localization of CNVRs and cis-eQTLs in the gluteus medius muscle (eQTL and gene positions are expressed in Mb). Table S5. Co-localization of CNVRs and cis-eQTLs in liver tissue (eQTL and gene positions are expressed in Mb). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8318747.v1
title: Additional file 6: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S6. Sequences of the primers used to validate CNVRs by qPCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8318738.v1
title: Additional file 5: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S4. Co-localization of CNVRs and cis-eQTLs in the gluteus medius muscle (eQTL and gene positions are expressed in Mb). Table S5. Co-localization of CNVRs and cis-eQTLs in liver tissue (eQTL and gene positions are expressed in Mb). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8318729
title: Additional file 4. of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S3. Positional coincidence of the copy number variant regions (CNVR) detected in the current work with CNVRs reported in other pig populations. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8318723
title: Additional file 3: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S2. Locations, absolute frequencies, lengths and status of CNVRs detected in 350 Duroc pigs with the PennCNV and GADA softwares. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8318729.v1
title: Additional file 4. of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S3. Positional coincidence of the copy number variant regions (CNVR) detected in the current work with CNVRs reported in other pig populations. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8318723.v1
title: Additional file 3: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S2. Locations, absolute frequencies, lengths and status of CNVRs detected in 350 Duroc pigs with the PennCNV and GADA softwares. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8318705
title: Additional file 1: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S1. List of genes that are differentially expressed (DE) in the gluteus medius muscle and the liver (q-value &lt; 0.05). (XLSX 353 kb)
DOI: 10.6084/m9.figshare.8318705.v1
title: Additional file 1: of About the existence of common determinants of gene expression in the porcine liver and skeletal muscle

description: Table S1. List of genes that are differentially expressed (DE) in the gluteus medius muscle and the liver (q-value &lt; 0.05). (XLSX 353 kb)
DOI: 10.6084/m9.figshare.8318657
title: Additional file 1: of Ethiodized poppyseed oil versus ioversol for image quality and adverse events in hysterosalpingography: a prospective cohort study

description: RAW DATA. (XLS 157 kb)
DOI: 10.6084/m9.figshare.8318657.v1
title: Additional file 1: of Ethiodized poppyseed oil versus ioversol for image quality and adverse events in hysterosalpingography: a prospective cohort study

description: RAW DATA. (XLS 157 kb)
DOI: 10.6084/m9.figshare.8318642
title: Additional file 1: of Comparison of vaginal hysterectomy and laparoscopic hysterectomy: a systematic review and meta-analysis

description: The raw data of the enrolled studies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8318642.v1
title: Additional file 1: of Comparison of vaginal hysterectomy and laparoscopic hysterectomy: a systematic review and meta-analysis

description: The raw data of the enrolled studies. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8318519
title: MOESM3 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

description: Additional file 3. Processed document IDs during the TIPS competition.
DOI: 10.6084/m9.figshare.8318519.v1
title: MOESM3 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

description: Additional file 3. Processed document IDs during the TIPS competition.
DOI: 10.6084/m9.figshare.8318507
title: MOESM1 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

description: Additional file 1. Description of the structure and the restrictions of the supported formats.
DOI: 10.6084/m9.figshare.8318507.v1
title: MOESM1 of Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

description: Additional file 1. Description of the structure and the restrictions of the supported formats.
DOI: 10.6084/m9.figshare.8317142
title: Factors influencing farmers’ decision to participate in Bilateral Agricultural Projects in Africa: Case study of smallholder farmers in Ghana

description: This data was gotten for a study using questionnaires to interview farmers in Ghana on their challenges,priorities, and willingness to particpate in donro funded agricultural projects. <br>
DOI: 10.6084/m9.figshare.8317142.v1
title: Factors influencing farmers’ decision to participate in Bilateral Agricultural Projects in Africa: Case study of smallholder farmers in Ghana

description: This data was gotten for a study using questionnaires to interview farmers in Ghana on their challenges,priorities, and willingness to particpate in donro funded agricultural projects. <br>
DOI: 10.6084/m9.figshare.8317124
title: Consecutive Experimental Determination of Stress-Dependent Fluid Flow Properties of Berea Sandstone and Implications for Two-phase Flow Modelling

description: Stress-Dependent Fluid Flow Properties<br>
DOI: 10.6084/m9.figshare.8317109
title: Annotation of Amphibalanus amphitrite

description: Annotation of Amphibalanus amphitrite containing gff, ffn, faa and annotation file
DOI: 10.6084/m9.figshare.8317106
title: Assembly of Amphibalanus amphitrite

description: Assembly of Amphibalanus amphitrite
DOI: 10.6084/m9.figshare.8317124.v1
title: Stress-Dependent Fluid Flow Properties

description: Consecutive Experimental Determination of Stress-dependent Static and Dynamic Properties of Berea Sandstone and Implications for Two-phase Flow Modelling
DOI: 10.6084/m9.figshare.8317079
title: Global Atmospheric Rivers (Historic and Future)

description: This data set include netcdf (.nc) and matlab (.mat) files of the CMIP5 and ERA-Interim data used to calculate this study. The data are global AR frequency and intensity (IVT) maps, for the historic records as well as the future simulations (RCP45 and RCP85).<br>Atmospheric rivers (ARs) are narrow jets of integrated water vapor transport that are important for the global water cycle, and also have large impacts on local weather and regional hydrology. Uniformly-weighted multi-model averages have been used to describe how ARs will change in the future, but this type of estimate does not consider skill or independence of the climate models of interest. Here, we utilize information from various model averaging approaches to evaluate 21 global climate models from the Coupled Model Intercomparison Project Phase 5 (CMIP5). Model ensemble weighting strategies based on atmospheric river model independence and performance skill relative to reanalysis data (ERA-Interim) result in lower uncertainties in the future estimates compared to the equal weighting strategy. These weighted models show that the frequency of ARs is expected to increase by the end of the century, with high certainty, by ~50% on average globally.<br><br><br>
DOI: 10.6084/m9.figshare.8317124.v2
title: Stress-Dependent Fluid Flow Properties

description: Consecutive Experimental Determination of Stress-dependent Static and Dynamic Properties of Berea Sandstone and Implications for Two-phase Flow Modelling
DOI: 10.6084/m9.figshare.8317124.v3
title: Stress-Dependent Fluid Flow Properties

description: Stress-Dependent Fluid Flow Properties<br>
DOI: 10.6084/m9.figshare.8317079.v1
title: Global Atmospheric Rivers (Historic and Future)

description: Atmospheric rivers (ARs) are narrow jets of integrated water vapor transport that are important for the global water cycle, and also have large impacts on local weather and regional hydrology. Uniformly-weighted multi-model averages have been used to describe how ARs will change in the future, but this type of estimate does not consider skill or independence of the climate models of interest. Here, we utilize information from various model averaging approaches to evaluate 21 global climate models from the Coupled Model Intercomparison Project Phase 5 (CMIP5). Model ensemble weighting strategies based on atmospheric river model independence and performance skill relative to reanalysis data (ERA-Interim) result in lower uncertainties in the future estimates compared to the equal weighting strategy. These weighted models show that the frequency of ARs is expected to increase by the end of the century, with high certainty, by ~50% on average globally.<br><br>This data set include netcdf (.nc) and matlab (.mat) files of the CMIP5 and ERA-Interim data used to calculate this study. The data are global AR frequency maps, for the historic records as well as the future simulations (RCP45 and RCP85).
DOI: 10.6084/m9.figshare.8317124.v5
title: Consecutive Experimental Determination of Stress-Dependent Fluid Flow Properties of Berea Sandstone and Implications for Two-phase Flow Modelling

description: Stress-Dependent Fluid Flow Properties<br>
DOI: 10.6084/m9.figshare.8317085.v2
title: AIBECS-OCIM0.1

description: This file contains the circulation output and grid information from the Ocean Circulation Inverse Model (OCIM) version 0.1 [DeVries and Primeau, 2011; Primeau et al., 2013].<br>The data was converted for use by the Algebraic Implicit Biogeochemical Element Cycling System (AIBECS).<br>References: <br>- Primeau, F. W., Holzer, M., and DeVries, T. ( 2013), Southern Ocean nutrient trapping and the efficiency of the biological pump, <i>J. Geophys. Res. Oceans</i>, 118, 2547– 2564, doi:10.1002/jgrc.20181. - DeVries, T. and F. Primeau, 2011: Dynamically and Observationally Constrained Estimates of Water-Mass Distributions and Ages in the Global Ocean. <i>J. Phys. Oceanogr.,</i> <b>41</b>, 2381–2401, https://doi.org/10.1175/JPO-D-10-05011.1<br>- Benoit Pasquier. (2019, May 23). AIBECS.jl: The ideal tool for exploring global marine biogeochemical cycles (v0.2.0). Zenodo. http://doi.org/10.5281/zenodo.3192180
DOI: 10.6084/m9.figshare.8317124.v4
title: Consecutive Experimental Determination of Stress-Dependent Fluid Flow Properties of Berea Sandstone and Implications for Two-phase Flow Modelling

description: Stress-Dependent Fluid Flow Properties<br>
DOI: 10.6084/m9.figshare.8317046
title: Dataset for: On the analysis of two-phase designs in cluster--correlated settings

description: In public health research information that is readily available may be insufficient to address the primary question(s) of interest. One cost-efficient way forward, especially in resource-limited settings, is to conduct a two-phase study in which the population is initially stratified, at phase I, by the outcome and/or some categorical risk factor(s). At phase II detailed covariate data is ascertained on a sub-sample within each phase I strata. While analysis methods for two-phase designs are well established, they have focused exclusively on settings in which participants are assumed to be independent. As such, when participants are naturally clustered (e.g. patients within clinics) these methods may yield invalid inference. To address this we develop a novel analysis approach based on inverse-probability weighting (IPW) that permits researchers to specify some working covariance structure, appropriately accounts for the sampling design and ensures valid inference via a robust sandwich estimator. In addition, to enhance statistical efficiency, we propose a calibrated IPW estimator that makes use of information available at phase I but not used in the design. A comprehensive simulation study is conducted to evaluate small-sample operating characteristics, including the impact of using na\"{i}ve methods that ignore correlation due to clustering, as well as to investigate design considerations. Finally, the methods are illustrated using data from a one-time survey of the national anti-retroviral treatment program in Malawi.
DOI: 10.6084/m9.figshare.8316956
title: Mode-1 M2 internal tides in the North Atlantic Ocean

description: Mode-1 M2 internal tides in the North Atlantic Ocean, constructed using about 20 years of altimeter data made by multiple satellite missions. The mapping technique is described in Zhao et al. (2016) (doi: 10.1175/JPO-D-15-0105.1). Three waves are fitted at each grid point. For each wave, parameters here include propagation direction (dir), and depth-integrated energy flux (Flux). The horizontal grid is at 0.1 lon by 0.1 lat.
DOI: 10.6084/m9.figshare.8317046.v1
title: Dataset for: On the analysis of two-phase designs in cluster--correlated settings

description: In public health research information that is readily available may be insufficient to address the primary question(s) of interest. One cost-efficient way forward, especially in resource-limited settings, is to conduct a two-phase study in which the population is initially stratified, at phase I, by the outcome and/or some categorical risk factor(s). At phase II detailed covariate data is ascertained on a sub-sample within each phase I strata. While analysis methods for two-phase designs are well established, they have focused exclusively on settings in which participants are assumed to be independent. As such, when participants are naturally clustered (e.g. patients within clinics) these methods may yield invalid inference. To address this we develop a novel analysis approach based on inverse-probability weighting (IPW) that permits researchers to specify some working covariance structure, appropriately accounts for the sampling design and ensures valid inference via a robust sandwich estimator. In addition, to enhance statistical efficiency, we propose a calibrated IPW estimator that makes use of information available at phase I but not used in the design. A comprehensive simulation study is conducted to evaluate small-sample operating characteristics, including the impact of using na\"{i}ve methods that ignore correlation due to clustering, as well as to investigate design considerations. Finally, the methods are illustrated using data from a one-time survey of the national anti-retroviral treatment program in Malawi.
DOI: 10.6084/m9.figshare.8316929
title: Dataset for: Bayesian time-varying quantile regression to extremes

description: Maximum analysis consists of modeling the maximums of a data set by considering a specific distribution. Extreme value theory (EVT) shows that for a sufficiently large block size, the maxima distribution is approximated by the generalized extreme value (GEV) distribution. Under EVT, it is important to observe the high quantiles of the distribution. %, which shows the probability of a risk event occurring in every $t$ period. In this sense, quantile regression techniques fit the data analysis of maxima by using the GEV distribution. In this context, this work presents the quantile regression extension for the GEV distribution. In addition, a time-varying quantile regression model is presented and the important properties of this approach are displayed. The parameter estimation of these new models is carried out under the Bayesian paradigm. The results of the temperature data and river quota application show the advantage of using this model, which allows us to estimate directly the quantiles as a function of the covariates. This shows which of them influences the occurrence of extreme temperature and the magnitude of this influence.
DOI: 10.6084/m9.figshare.8316929.v1
title: Dataset for: Bayesian time-varying quantile regression to extremes

description: Maximum analysis consists of modeling the maximums of a data set by considering a specific distribution. Extreme value theory (EVT) shows that for a sufficiently large block size, the maxima distribution is approximated by the generalized extreme value (GEV) distribution. Under EVT, it is important to observe the high quantiles of the distribution. %, which shows the probability of a risk event occurring in every $t$ period. In this sense, quantile regression techniques fit the data analysis of maxima by using the GEV distribution. In this context, this work presents the quantile regression extension for the GEV distribution. In addition, a time-varying quantile regression model is presented and the important properties of this approach are displayed. The parameter estimation of these new models is carried out under the Bayesian paradigm. The results of the temperature data and river quota application show the advantage of using this model, which allows us to estimate directly the quantiles as a function of the covariates. This shows which of them influences the occurrence of extreme temperature and the magnitude of this influence.
DOI: 10.6084/m9.figshare.8316863
title: Monitoring data of restoration areas in the Brazilian Atlantic Forest

description: Monitoring data collected in 550 areas undergoing restoration in the Brazilian Atlantic Forest.
DOI: 10.6084/m9.figshare.8316827
title: Species trees of 571 Rhizobiaceae genomes, with a focus on 41 Pseudorhizobium and Neorhizobium, based on core genome gene concatenates

description: Genomic dataset and gene family classificationWe assembled a complete bacterial genome dataset covering all known representative of the subgroup in the alphaproteobacterial families Rhizobiaceae and (sister group) Aurantimonadaceae. This dataset comprises all 564 genomes available from the NCBI RefSeq Assembly database on the 23 Apr 2018, filtering anomalous genomes and those with a contig N50 &lt; 98kb using query: ‘(txid82115[Organism:exp] OR txid255475[Organism:exp]) AND ("latest refseq"[filter] NOT anomalous[filter]) AND ("98000"[ContigN50] : "20000000"[ContigN50])’. From this dataset we removed assembly GCF_002000045.1 (R. flavum YW14) for which we had a newer, higher quality assembly. To these we added the new genome sequences from the eight strains mentioned above, for a total of 571 genomes (dataset ‘571Rhizob’).<br>Reference species treesFrom the 571Rhizob genome dataset, we define the pseudo-core genome as genes occurring only in a single copy and present in at least 561 out of the 571 genomes (98%). The resulting pseudo-core genome gene set (thereafter referred as pCG<sub>571</sub>) includes 155 loci, which protein alignments were concatenated. This concatenated protein alignment was used to compute a reference species tree (S<sub>ML571</sub>) with RAxML (Stamatakis 2014) under the model PROTCATLGX; branch supports were estimated by generating 200 rapid bootstraps under the same parameters. From the S<sub>ML571</sub> tree, we identified the well-supported clade grouping 41 genomes including all representative of Neorhizobium spp. and Pseudorhizobium spp. and our new isolates (dataset ‘41NeoPseudo’). To gain further phylogenetic resolution in this clade of interest, we restricted the pCG<sub>571</sub> concatenated alignment to the 41 genomes of this smaller genomic dataset, which we used as input to the Phylobayes program for a more accurate (but computationally more expensive) Bayesian phylogenetic inference under the CAT-GTR+G4 model (Lartillot et al. 2007). This provided us with a robust non-ultrametric tree for the 41 genomes (S<sub>BA41</sub>). We finally used this S<sub>BA41</sub> tree as a fixed input topology for Phylobayes to infer an ultrametric tree (unitless ‘time’ tree) under the CIR clock model (Lepage et al. 2007), further referred to as T<sub>BA41</sub>.
DOI: 10.6084/m9.figshare.8316863.v1
title: Monitoring data of restoration areas in the Brazilian Atlantic Forest

description: Monitoring data collected in 550 areas undergoing restoration in the Brazilian Atlantic Forest.
DOI: 10.6084/m9.figshare.8316803
title: NaCl Plate phenotype Pseudorhizobium strains

description: Growth of strains was assayed at 28°C in liquid R2A medium (DSMZ medium 830) supplemented with increasing concentrations of NaCl (0–9% range was tested) to determine their minimum inhibitory NaCl concentration (MIC<sub>NaCl</sub>).
DOI: 10.6084/m9.figshare.8316818
title: Genome-wide association testing of Biolog GenIII phenotypes vs. accessory genome presence/absence

description: The association of accessory gene occurrence with phenotypic profiles obtained with the Biolog GenIII (continuous values) was tested using the phylogenetic framework implemented in the ‘treeWAS’ R package (Collins & Didelot 2018). The test was performed on 9,621 non-trivial OG presence/absence profiles using the ML method for ancestral state reconstruction. Significance was assessed by comparing test scores to those obtained by simulating random genotype profiles along the 10-taxon species tree for 100 times more loci than the tested dataset (ca. 105 simulations) and scaling the p-values using FDR correction. Phenotypes with significant hits were then tested again with more stringent parameters, using 1,000 times more loci than the tested dataset and Bonferroni p-value correction.
DOI: 10.6084/m9.figshare.8316803.v1
title: NaCl Plate phenotype Pseudorhizobium strains

description: Growth of strains was assayed at 28°C in liquid R2A medium (DSMZ medium 830) supplemented with increasing concentrations of NaCl (0–9% range was tested) to determine their minimum inhibitory NaCl concentration (MIC<sub>NaCl</sub>).
DOI: 10.6084/m9.figshare.8316770
title: API 20 NE biochemical profiling of Pseudorhizobium strains

description: The commercial biochemical identification system for Gram-negative bacteria ‘Api 20 NE’ (BioMérieux) was used for an initial analysis of the biochemical capacities.