cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11405589
title: MOESM1 of Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings

description: Additional file 1 The frequency distribution of DDIs observed in training and test sets for each fold in 10-fold disjoint cross-validation and Chi-square test results for each fold, the file is in XLSX format.
DOI: 10.6084/m9.figshare.11405589.v1
title: MOESM1 of Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings

description: Additional file 1 The frequency distribution of DDIs observed in training and test sets for each fold in 10-fold disjoint cross-validation and Chi-square test results for each fold, the file is in XLSX format.
DOI: 10.6084/m9.figshare.11405580
title: MOESM1 of Relationship between ethanol consumption and TBL2 rs17145738 on LDL-C concentration in Japanese adults: a four season 3-day weighed diet record study

description: Additional file 1. Genome-wide association studies for LDL cholesterol concentration among East Asians (Japanese, Chinese, Korean). Abbreviations: SNPs, single nucleotide polymorphisms; CHR, chromosome; MAF, minor allele frequency. aAlleles were presented as major/minor or reference/alternative. bEffect sizes are shown as β ± standard error (SE) or β [95% confidence interval (CI)].
DOI: 10.6084/m9.figshare.11405580.v1
title: MOESM1 of Relationship between ethanol consumption and TBL2 rs17145738 on LDL-C concentration in Japanese adults: a four season 3-day weighed diet record study

description: Additional file 1. Genome-wide association studies for LDL cholesterol concentration among East Asians (Japanese, Chinese, Korean). Abbreviations: SNPs, single nucleotide polymorphisms; CHR, chromosome; MAF, minor allele frequency. aAlleles were presented as major/minor or reference/alternative. bEffect sizes are shown as β ± standard error (SE) or β [95% confidence interval (CI)].
DOI: 10.6084/m9.figshare.11405556
title: Soil microbial respiration and carbon use efficiency data

description: Microbial respiration and carbon use efficiency data for 285 cropland soils, data used in ArticalCompensatory thermal adaptation of soil microbial respiration rates in global croplandshttps://doi.org/10.1029/2019GB006507<br>
DOI: 10.6084/m9.figshare.11405523
title: data

description: A sample dataset and relative software that support the findings of the present study are available. Exploring the impact factors and their interactions of dockless bike sharing usage: A case study in Shenzhen, China
DOI: 10.6084/m9.figshare.11405556.v1
title: Soil microbial respiration and carbon use efficiency data

description: Microbial respiration and carbon use efficiency data for 285 cropland soils, data used in ArticalCompensatory thermal adaptation of soil microbial respiration rates in global croplandshttps://doi.org/10.1029/2019GB006507<br>
DOI: 10.6084/m9.figshare.11402691
title: Dataset for paper titled "Surface Heat Flux Induced by Mesoscale Eddies Cools the Kuroshio-Oyashio Extension Region" by Shan et al.

description: This repository contains data, analysis codes, and model configuration files used for the paper titled "Surface Heat Flux Induced by Mesoscale Eddies Cools the Kuroshio-Oyashio Extension Region" by Shan et al.
DOI: 10.6084/m9.figshare.11402166
title: Proteome database of Proteus vulgaris ATCC 49132

description: Known for its swarming motility, <i>Proteus vulgaris</i> is a Gram-negative, rod-shaped bacterium that inhabits a variety of environments ranging from the human gastrointestinal tract to soil and water. Ability to thrive in a variety of environmental and nutritional environments may partially explain why <i>P. vulgaris </i>is also an opportunistic human pathogen causing, for example, wound infections. But, the defining feature of this bacterium remains its coordinate movement across surfaces known as swarming motility, which endows it with model organism status in this field of research. This work sought to provide some fundamental information of <i>P. vulgaris</i> ATCC 49132 through parsing the organism’s UniProt proteome file through an in-house MATLAB software. Altogether, a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence was constructed that, in addition to providing key features of each protein in <i>P. vulgaris </i>ATCC 49132, also informs researchers of the metabolic and signalling pathways present in the species. Such information should find use in a variety of basic microbiological investigations seeking to decipher the question: why and how <i>P. vulgaris</i> moves on surfaces in coordinated fashion? <br><br>
DOI: 10.6084/m9.figshare.11402247.v1
title: A Matrix–free Likelihood Method for Exploratory Factor Analysis of High-dimensional Gaussian Data

description: This paper proposes a novel profile likelihood method for estimating the covariance parameters in exploratory factor analysis of high-dimensional Gaussian datasets with fewer observations than number of variables. An implicitly restarted Lanczos algorithm and a limited-memory quasi-Newton method are implemented to develop a matrix-free framework for likelihood maximization. Simulation results show that our method is substantially faster than the expectation-maximization solution without sacrificing accuracy. Our method is applied to fit factor models on data from suicide attempters, suicide ideators and a control group.
DOI: 10.6084/m9.figshare.11402115
title: Validation of the Lymphoedema Quality of Life Questionnaire (LYMQOL) in Swedish cancer patients

description: <b>Background:</b> The aim of this study was to validate a translated Swedish version of the lymphoedema-specific quality of life questionnaire (LYMQOL) in a cohort of Swedish cancer patients with secondary lymphoedema of the limbs after cancer treatment. <b>Material and methods:</b> We recruited 102 patients with lymphoedema of the arms or legs after cancer treatment who were visiting lymphoedema therapists at the departments of oncology at the university hospitals in Linköping and Umeå. The LYMQOL questionnaires were translated forward and backward from English to Swedish. Content and face validity were evaluated. The construct validity was assessed by comparing the LYMQOL with the Short Form Health Survey (SF-36) and the perceived degree of lymphoedema of the limbs, respectively. Reliability was determined through test-retest. The internal consistency was assessed by determining Cronbach’s alpha and by factor analysis. <b>Results:</b> The content and face validity assessments showed that LYMQOL was an easy, clear and not too long questionnaire to use for patients with lymphoedema. Construct validity was high in both versions when compared with the SF-36. The association between the degrees of perceived lymphoedema and the LYMQOL was only significant in the domains Function and Body Image in the arm version, whereas all domains in the leg version were significant. The reliability was good for the arm version (intra-class-correlation coefficients 0.53–0.87) and very good for the leg version (intra-class-correlation coefficients 0.78–0.90). The internal consistency was acceptable to excellent, with Cronbach’s alpha values between 0.79–0.93 (arm-version) and 0.87–0.94 (leg-version). The factor analysis confirmed the usefulness of the four domains in the LYMQOL versions. <b>Conclusions:</b> This study confirmed the validity of the Swedish version of LYMQOL and demonstrated that LYMQOL may be a simple and useful tool for use in clinical practice and scientific contexts for evaluating QoL in patients with lymphoedema of the limbs.
DOI: 10.6084/m9.figshare.11402115.v1
title: Validation of the Lymphoedema Quality of Life Questionnaire (LYMQOL) in Swedish cancer patients

description: <b>Background:</b> The aim of this study was to validate a translated Swedish version of the lymphoedema-specific quality of life questionnaire (LYMQOL) in a cohort of Swedish cancer patients with secondary lymphoedema of the limbs after cancer treatment. <b>Material and methods:</b> We recruited 102 patients with lymphoedema of the arms or legs after cancer treatment who were visiting lymphoedema therapists at the departments of oncology at the university hospitals in Linköping and Umeå. The LYMQOL questionnaires were translated forward and backward from English to Swedish. Content and face validity were evaluated. The construct validity was assessed by comparing the LYMQOL with the Short Form Health Survey (SF-36) and the perceived degree of lymphoedema of the limbs, respectively. Reliability was determined through test-retest. The internal consistency was assessed by determining Cronbach’s alpha and by factor analysis. <b>Results:</b> The content and face validity assessments showed that LYMQOL was an easy, clear and not too long questionnaire to use for patients with lymphoedema. Construct validity was high in both versions when compared with the SF-36. The association between the degrees of perceived lymphoedema and the LYMQOL was only significant in the domains Function and Body Image in the arm version, whereas all domains in the leg version were significant. The reliability was good for the arm version (intra-class-correlation coefficients 0.53–0.87) and very good for the leg version (intra-class-correlation coefficients 0.78–0.90). The internal consistency was acceptable to excellent, with Cronbach’s alpha values between 0.79–0.93 (arm-version) and 0.87–0.94 (leg-version). The factor analysis confirmed the usefulness of the four domains in the LYMQOL versions. <b>Conclusions:</b> This study confirmed the validity of the Swedish version of LYMQOL and demonstrated that LYMQOL may be a simple and useful tool for use in clinical practice and scientific contexts for evaluating QoL in patients with lymphoedema of the limbs.
DOI: 10.6084/m9.figshare.11402091
title: Impact of the non-native locariid fish <i>Pterygoplichthys pardalis</i> in native fish community on a seasonal tropical floodplain in Mexico

description: The present study reports the seasonal dynamics of the fish community structure in the presence of a non-native fish (<i>Pterygoplichthys pardalis</i>) in tropical waterbodies of southern Mexico. The studied floodplain existed in both connected pools and disconnected pools “to the Palizada river”. Local fish fauna showed consistent assemblages across seasons, but among the 17 local fish species recorded, the non-native species <i>P</i>. <i>pardalis</i> showed the highest percentage of contribution to the fish community (ca. 20%). Conversely, the frequency of occurrence and density of the non-native species showed variation in relation to the type of waterbody and seasonality; its density was approximately four times higher in disconnected pools than in connected pools in the rainy season and its predominant size class in both pool types was 21-30 cm in standard length. Interestingly, the diversity of the native species was negatively related to the density of the non-native species, indicating that the presence of <i>P. pardalis</i> can be a factor involved in the decline of native fish diversity in these local communities. Currently, the possible impacts of the presence of <i>P. pardalis</i> on local fish diversity at the regional scale are unknown, but our results suggest that hydrological dynamics regulate the establishment of the non-native species in this region. However, future studies are needed to provide insights into the actual scenario of <i>P</i>. <i>pardalis</i> distribution in Yucatan Peninsula and the possible impacts on the native fish fauna in southern Mexico.
DOI: 10.6084/m9.figshare.11402061
title: Geometric morphometric analysis of Ichneumonidae (Hymenoptera: Apocrita) with two new Mesozoic taxa from Myanmar and China

description: A new genus and species of Labenopimplinae (Ichneumonidae), <i>Heteropimpla megista</i> Li, Shih, Kopylov & Ren gen. et sp. nov., is erected based on a specimen in mid-Cretaceous Myanmar (Burmese) amber. A key to genera of Labenopimplinae is provided. In addition, a new species, <i>Amplicella abbreviata</i> Li, Shih, Kopylov & Ren (Tanychorinae) from the Lower Cretaceous Yixian Formation is described. Geometric morphometric analysis (GMA) was applied to study forewing venation of 24 Cretaceous species of Ichneumonidae and the results are presented for the first time. The GMA results not only confirm the taxonomic position of new taxa and relationships among these genera consistent with subfamily classifications, but also clarify the methodological differences between classical taxonomy and the GMA. http://zoobank.org/urn:lsid:zoobank.org:pub:DC98459D-45C1-4B78-B59E-F32787B787F1
DOI: 10.6084/m9.figshare.11402061.v1
title: Geometric morphometric analysis of Ichneumonidae (Hymenoptera: Apocrita) with two new Mesozoic taxa from Myanmar and China

description: A new genus and species of Labenopimplinae (Ichneumonidae), <i>Heteropimpla megista</i> Li, Shih, Kopylov & Ren gen. et sp. nov., is erected based on a specimen in mid-Cretaceous Myanmar (Burmese) amber. A key to genera of Labenopimplinae is provided. In addition, a new species, <i>Amplicella abbreviata</i> Li, Shih, Kopylov & Ren (Tanychorinae) from the Lower Cretaceous Yixian Formation is described. Geometric morphometric analysis (GMA) was applied to study forewing venation of 24 Cretaceous species of Ichneumonidae and the results are presented for the first time. The GMA results not only confirm the taxonomic position of new taxa and relationships among these genera consistent with subfamily classifications, but also clarify the methodological differences between classical taxonomy and the GMA. http://zoobank.org/urn:lsid:zoobank.org:pub:DC98459D-45C1-4B78-B59E-F32787B787F1
DOI: 10.6084/m9.figshare.11401677
title: Proteome database of Saccharomyces cerevisiae ATCC 204508

description: Used in brewing beer and making bread, <i>Saccharomyces cerevisiae</i> is not alien to people’s daily life. But, a wealth of mysteries remains to be discovered concerning the fundamental physiology and gene regulation mechanisms in this model eukaryotic organism. Specifically, relatively little is known about why a genetic complement of 6008 genes would endow <i>S. cerevisiae</i> an eukaryotic lifestyle, while other microorganisms with larger genetic repertoire adopt a prokaryotic lifestyle. This work sought to provide fundamental information of the proteome of <i>S. cerevisiae </i>ATCC 204508. A compendium of protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence, this resource was obtained by processing the UniProt proteome of <i>S. cerevisiae</i> ATCC 204508 through an in-house MATLAB software. In terms of utility, this proteome database should complement many aspects of fundamental and applied biology research seeking to answer a variety of questions concerning protein and pathway function in this single-cell minimal eukaryotic species. <br><br>
DOI: 10.6084/m9.figshare.11401677.v1
title: Proteome database of Saccharomyces cerevisiae ATCC 204508

description: Used in brewing beer and making bread, <i>Saccharomyces cerevisiae</i> is not alien to people’s daily life. But, a wealth of mysteries remains to be discovered concerning the fundamental physiology and gene regulation mechanisms in this model eukaryotic organism. Specifically, relatively little is known about why a genetic complement of 6008 genes would endow <i>S. cerevisiae</i> an eukaryotic lifestyle, while other microorganisms with larger genetic repertoire adopt a prokaryotic lifestyle. This work sought to provide fundamental information of the proteome of <i>S. cerevisiae </i>ATCC 204508. A compendium of protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence, this resource was obtained by processing the UniProt proteome of <i>S. cerevisiae</i> ATCC 204508 through an in-house MATLAB software. In terms of utility, this proteome database should complement many aspects of fundamental and applied biology research seeking to answer a variety of questions concerning protein and pathway function in this single-cell minimal eukaryotic species. <br><br>
DOI: 10.6084/m9.figshare.11401158
title: Longitudinal gene expression dataset [The immuno-pathogenesis of progressive scarring trachoma: results of a four-year longitudinal study in Tanzanian children]

description: Longitudinal data is provided for the following article "The immuno-pathogenesis of progressive scarring trachoma: results of a four-year longitudinal study in Tanzanian children".<br>id = participant ID number visit = time-point (from 1 to 17) tsprog_1_ = Trachomatous scarring progression over 4-year study period (1=scarring progression, 0=no progression)sex (1 = male, 2=female)age = in years at start of studyinf_ = C. trachomatis detection <br>The following variables are delta CT values for gene expression of 45 genes (gene names provided), tested in ocular swab samples at each timepoint.
DOI: 10.6084/m9.figshare.11401137
title: The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (<i>Oryzias latipes</i>)

description: Primordial germ cells (PGCs) are precursors of eggs and sperm. How the PGCs epigenetically reprogram during early embryonic development in fish is currently unknown. Here we generated a series of PGC methylomes using whole genome bisulfite sequencing across key stages from 8 days post fertilization (dpf) to 25 dpf coinciding with germ cell sex determination and gonadal sex differentiation in medaka (<i>Oryzias latipes</i>) to elucidate the dynamics of DNA methylation during epigenetic reprogramming in germ cells. Our high-resolution DNA methylome maps show a global demethylation taking place in medaka PGCs in a two-step strategy. The first step occurs between the blastula and 8-dpf stages, and the second step occurs between the 10-dpf and 12-dpf stages. Both demethylation processes are global, except for CGI promoters which remain hypomethylated throughout the stage of PGC specification. <i>De novo</i> methylation proceeded at 25-dpf stage with the process in male germ cells superseding female germ cells. Gene expression analysis showed that <i>tet2</i> maintains high levels of expression during the demethylation stage, while <i>dnmt3ba</i> expression increases during the <i>de novo</i> methylation stage during sexual fate determination in germ cells. The present results suggest that medaka PGCs undergo a bi-phasic epigenetic reprogramming process. Global erasure of DNA methylation marks peaks at 15-dpf and <i>de novo</i> methylation in male germ cells takes precedence over female germ cells at 25 dpf. Results also provide important insights into the developmental window of susceptibility to environmental stressors for multi- and trans-generational health outcomes in fish.
DOI: 10.6084/m9.figshare.11401158.v1
title: Longitudinal gene expression dataset [The immuno-pathogenesis of progressive scarring trachoma: results of a four-year longitudinal study in Tanzanian children]

description: Longitudinal data is provided for the following article "The immuno-pathogenesis of progressive scarring trachoma: results of a four-year longitudinal study in Tanzanian children".<br>id = participant ID number visit = time-point (from 1 to 17) tsprog_1_ = Trachomatous scarring progression over 4-year study period (1=scarring progression, 0=no progression)sex (1 = male, 2=female)age = in years at start of studyinf_ = C. trachomatis detection <br>The following variables are delta CT values for gene expression of 45 genes (gene names provided), tested in ocular swab samples at each timepoint.
DOI: 10.6084/m9.figshare.11401137.v1
title: The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (<i>Oryzias latipes</i>)

description: Primordial germ cells (PGCs) are precursors of eggs and sperm. How the PGCs epigenetically reprogram during early embryonic development in fish is currently unknown. Here we generated a series of PGC methylomes using whole genome bisulfite sequencing across key stages from 8 days post fertilization (dpf) to 25 dpf coinciding with germ cell sex determination and gonadal sex differentiation in medaka (<i>Oryzias latipes</i>) to elucidate the dynamics of DNA methylation during epigenetic reprogramming in germ cells. Our high-resolution DNA methylome maps show a global demethylation taking place in medaka PGCs in a two-step strategy. The first step occurs between the blastula and 8-dpf stages, and the second step occurs between the 10-dpf and 12-dpf stages. Both demethylation processes are global, except for CGI promoters which remain hypomethylated throughout the stage of PGC specification. <i>De novo</i> methylation proceeded at 25-dpf stage with the process in male germ cells superseding female germ cells. Gene expression analysis showed that <i>tet2</i> maintains high levels of expression during the demethylation stage, while <i>dnmt3ba</i> expression increases during the <i>de novo</i> methylation stage during sexual fate determination in germ cells. The present results suggest that medaka PGCs undergo a bi-phasic epigenetic reprogramming process. Global erasure of DNA methylation marks peaks at 15-dpf and <i>de novo</i> methylation in male germ cells takes precedence over female germ cells at 25 dpf. Results also provide important insights into the developmental window of susceptibility to environmental stressors for multi- and trans-generational health outcomes in fish.
DOI: 10.6084/m9.figshare.11400924
title: Sequence Files

description: Because of the sequence analyses were done at three different time points, the samples are labeled (1), (2) and (3) in two group K562 and IR (K562-IR). For four Bcr-Abl kinase domain overlapping fragments, the samples are labeled P1, P2, P3, P4 with R (reverse) and F (forward) primer abbreviations.<br>
DOI: 10.6084/m9.figshare.11400924.v2
title: Sequence Files

description: Because of the sequence analyses were done at three different time points, the samples are labeled (1), (2) and (3) in two group K562 and IR (K562-IR). For four Bcr-Abl kinase domain overlapping fragments, the samples are labeled P1, P2, P3, P4 with R (reverse) and F (forward) primer abbreviations.<br>
DOI: 10.6084/m9.figshare.11400924.v1
title: Sequence Files

description: Because of the sequence analyses were done at three different time points, the samples are labeled (1), (2) and (3) in two group K562 and IR (K562-IR). For four Bcr-Abl kinase domain overlapping fragments, the samples are labeled P1, P2, P3, P4 with R (reverse) and F (forward) primer abbreviations.<br>
DOI: 10.6084/m9.figshare.11400840
title: Land cover classification of Galapagos agroecosystems and their surrounding protected areas (2018)

description: This is the first high-resolution land cover classification map of the agricultural zone of the Galapagos Islands and the surrounding protected humid highlands. The classification scheme includes categories that are relevant for both agricultural and conservation sectors. The dataset is provided in Shapefile and GeoJSON formats. An additional metadata file is included as well. For information on methods, please refer to: <br><br>Laso, F. J., Benitez, F. L., Rivas-torres, G., Sampedro, C., & Arce-Nazario, J. (2019). Land cover classification of complex agroecosystems in the non-protected highlands of the Galapagos Islands. <i>Remote Sensing</i>, 1–40.<br>
DOI: 10.6084/m9.figshare.11400561
title: Dependencies between drivers of compound floods in observations and models

description: This datasets contains estimates of depedency between storm surge height (with and without wave component) and precipitation amount or river discharge, daily resolution over Europe, based on observations and a set models containing climate reanalysis and hindcast, and climate model-driven hydrodynamic models.