cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5339986
title: Data "Microbenchmark Selection for Continuous Software Performance Assessment"

description: This is the data used for the paper "Microbenchmark Selection for Continuous Software Performance Assessment". The archive contains all data described in the paper, as well as the R scripts used for analysis.
DOI: 10.6084/m9.figshare.5339986.v1
title: Data "Microbenchmark Selection for Continuous Software Performance Assessment"

description: This is the data used for the paper "Microbenchmark Selection for Continuous Software Performance Assessment". The archive contains all data described in the paper, as well as the R scripts used for analysis.
DOI: 10.6084/m9.figshare.5339980
title: Molecular characterization and phylogenetic analysis of a virulent Marek’s disease virus field strain in broiler chickens in Japan

description: Marek’s disease is a lymphoproliferative disease causing a serious threat in poultry production. Field strains of Marek’s disease virus (MDVs) are continuously re-emerging, causing great economical losses to the poultry industry worldwide in spite of the intensive vaccination and restrictive management policy used. Histopathological and molecular characterizations of MDVs are essential for monitoring the changes of viruses and evaluating the effectiveness of existing vaccines. During 2016, 190 visceral tumour tissues representing 30 vaccinated chicken flocks from the Gifu prefecture, Japan, were analysed. A pathological examination revealed the presence of lymphoproliferative lesions in the visceral organs. Polymerase chain reaction screening of tissue specimens using specific primers for avian leucosis virus, reticuloendotheliosis virus, and MDV was positive only for MDV. The polymerase chain reaction products of meq, pp38, virus-induced IL-8 homology, and glycoprotein MDV genes were sequenced and used for homology, phylogenetic, and similarity level analysis with the published reference of MDVs in the database. The results revealed high similarity between the field isolates, vv and vv+ strains of MDV from the USA and China. Several point mutations in the nucleotide sequence of the field isolates and their deduced amino acid sequences were detected in those genes. The present molecular analyses indicated that nucleotide and amino acid changes could be valuable criteria for differentiation and determination of the pathogenicity and oncogenicity of MDVs according to the Avian Disease and Oncology Laboratory pathotyping in vivo studies. Furthermore, the results suggest that development of a new vaccine must be considered to overcome this devastating avian oncogenic viral disease.
DOI: 10.6084/m9.figshare.5339980.v1
title: Molecular characterization and phylogenetic analysis of a virulent Marek’s disease virus field strain in broiler chickens in Japan

description: Marek’s disease is a lymphoproliferative disease causing a serious threat in poultry production. Field strains of Marek’s disease virus (MDVs) are continuously re-emerging, causing great economical losses to the poultry industry worldwide in spite of the intensive vaccination and restrictive management policy used. Histopathological and molecular characterizations of MDVs are essential for monitoring the changes of viruses and evaluating the effectiveness of existing vaccines. During 2016, 190 visceral tumour tissues representing 30 vaccinated chicken flocks from the Gifu prefecture, Japan, were analysed. A pathological examination revealed the presence of lymphoproliferative lesions in the visceral organs. Polymerase chain reaction screening of tissue specimens using specific primers for avian leucosis virus, reticuloendotheliosis virus, and MDV was positive only for MDV. The polymerase chain reaction products of meq, pp38, virus-induced IL-8 homology, and glycoprotein MDV genes were sequenced and used for homology, phylogenetic, and similarity level analysis with the published reference of MDVs in the database. The results revealed high similarity between the field isolates, vv and vv+ strains of MDV from the USA and China. Several point mutations in the nucleotide sequence of the field isolates and their deduced amino acid sequences were detected in those genes. The present molecular analyses indicated that nucleotide and amino acid changes could be valuable criteria for differentiation and determination of the pathogenicity and oncogenicity of MDVs according to the Avian Disease and Oncology Laboratory pathotyping in vivo studies. Furthermore, the results suggest that development of a new vaccine must be considered to overcome this devastating avian oncogenic viral disease.
DOI: 10.6084/m9.figshare.5339941
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction

description: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction
DOI: 10.6084/m9.figshare.5339941.v1
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction

description: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction
DOI: 10.6084/m9.figshare.5339869
title: pubTEMA.xlsx

description: Dataset para publicação (blind review) na revista TEMA (Trends in Applied and Computational Mathematics)
DOI: 10.6084/m9.figshare.5339941.v3
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction

description: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction
DOI: 10.6084/m9.figshare.5339941.v2
title: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction

description: Adaptive radiotherapy for locally advanced non-small cell lung cancer: dosimetric gain and treatment outcome prediction
DOI: 10.6084/m9.figshare.5339869.v1
title: pubTEMA.xlsx

description: Dataset para publicação (blind review) na revista TEMA (Trends in Applied and Computational Mathematics)
DOI: 10.6084/m9.figshare.5339707
title: Clustergrammer Kinase-Substrate Case Study Data

description: Kinase-substrate network used as a Clustergrammer case study.
DOI: 10.6084/m9.figshare.5339698
title: Clustergrammer Single Cell PBMC CyTOF Case Study Data

description: Single cell PBMC CyTOF data used as a Clustergrammer case study.
DOI: 10.6084/m9.figshare.5339695
title: Proteínas preditas por ESTScan

description: Arquivo contendo as 21.248 preditas por ESTScan para o fungo Phakopsora pachyhizi
DOI: 10.6084/m9.figshare.5339695.v1
title: Proteínas preditas por ESTScan

description: Arquivo contendo as 21.248 preditas por ESTScan para o fungo Phakopsora pachyhizi
DOI: 10.6084/m9.figshare.5339686
title: Dataset CAP

description: <b>Molecular etiological profile of atypical bacterial pathogens, viruses and coinfections among infants and children with community acquired pneumonia admitted to a national hospital in Lima, Peru.<br></b><b>Abstract</b> <b>Objetive: </b>The main objective of this study was to detect the presence of 14 respiratory viruses and atypical bacteria (<i>Mycoplasma pneumoniae, Chlamydia pneumoniae</i>), via Polymerase Chain Reaction in patients under 18 years old hospitalized due to CAP from Lima, Peru. <b>Results:</b> Atypical pathogens were detected in 39.73% (58/146); viral etiologies in 35.62% (52/146) and coinfections in 18.49% (27/146). The most common etiological agent was<i> M. pneumoniae</i> (n=47), followed by <i>C. pneumoniae</i> (n=11). The most frequent respiratory viruses detected were: respiratory syncytial virus A (n= 35), influenza virus C (n= 21) and parainfluenza virus (n= 10). Viral-bacterial and bacterium-bacterium coinfections were found in 27 cases. In our study population, atypical bacteria (39.73%) were detected as frequently as respiratory viruses (35.62%). The presence of <i>M. pneumoniae</i> and <i>C. pneumoniae</i> should not be underestimated as they can be commonly isolated in Peruvian children with CAP.
DOI: 10.6084/m9.figshare.5339689
title: Clustergrammer Lung Cancer PTM Case Study Data

description: Lung cancer post-translational modification data.
DOI: 10.6084/m9.figshare.5339689.v2
title: Clustergrammer Lung Cancer PTM Case Study Data

description: Lung cancer post-translational modification data.
DOI: 10.6084/m9.figshare.5339698.v2
title: Clustergrammer Single Cell PBMC CyTOF Case Study Data

description: Single cell PBMC CyTOF data used as a Clustergrammer case study.
DOI: 10.6084/m9.figshare.5339674
title: High-intensity high-volume swimming induces more robust signaling through PGC-1α and AMPK activation than sprint interval swimming in m. triceps brachii

description: Nine male swimmers enrolled in swimming competitions for at least 8 years (y) and in swimming training for at least 13 y volunteered for the study. Their physical characteristics were as follows: age 23.0 y (range 19-26 y), weight 78.5 kg (range 63-92 kg), height 180 cm (range 174-187 cm), extended upper limb size 187 cm (range 180-197 cm), and a maximal swimming speed of 2.0 m/s (range 1.88-2.10 m/s) (Table 1). Maximal swimming speed was recorded several times before (∼1 wk) the initiation of the study, and an experienced swimming coach, independent of the study, recorded the time required for the 25 m sprint, pushing off from the wall in the swimming pool. All subjects were fully informed of the risks and discomfort associated with the study, and all signed written consent. The study was conducted in accordance with the guidelines contained in the Declaration of Helsinki II and was approved by the local ethics committee of the University of Granada, Spain (protocol: 23/CEIH72015).
DOI: 10.6084/m9.figshare.5339689.v1
title: Clustergrammer Lung Cancer Case Study PTM Data

description: Lung cancer post-translational modification data.
DOI: 10.6084/m9.figshare.5339698.v1
title: Clustergrammer Single Cell PBMC CyTOF Data

description: Single cell PBMC CyTOF data used as a Clustergrammer case study.
DOI: 10.6084/m9.figshare.5339674.v2
title: High-intensity high-volume swimming induces more robust signaling through PGC-1α and AMPK activation than sprint interval swimming in m. triceps brachii

description: Nine male swimmers enrolled in swimming competitions for at least 8 years (y) and in swimming training for at least 13 y volunteered for the study. Their physical characteristics were as follows: age 23.0 y (range 19-26 y), weight 78.5 kg (range 63-92 kg), height 180 cm (range 174-187 cm), extended upper limb size 187 cm (range 180-197 cm), and a maximal swimming speed of 2.0 m/s (range 1.88-2.10 m/s) (Table 1). Maximal swimming speed was recorded several times before (∼1 wk) the initiation of the study, and an experienced swimming coach, independent of the study, recorded the time required for the 25 m sprint, pushing off from the wall in the swimming pool. All subjects were fully informed of the risks and discomfort associated with the study, and all signed written consent. The study was conducted in accordance with the guidelines contained in the Declaration of Helsinki II and was approved by the local ethics committee of the University of Granada, Spain (protocol: 23/CEIH72015).
DOI: 10.6084/m9.figshare.5339647
title: tensile_wet_ambient_100torr.zip

description: Raw data of tensile testing for wet sample, sampled dried at 100 torr (lowest pressure), and two ambient conditions (~40% RH and ~21-22 C) Column format is column #1 : time, #2 : force, #3: unused, #4: cross-head displacement, #5 length as measured from extensometer.First row is usually wrong, file-machine initiating error
DOI: 10.6084/m9.figshare.5339641
title: White_paper_Huan_Lei_DOE_PI.pdf

description: <br>Whitepaper submitted to the 2017 DOE ASCR Applied Math Meeting
DOI: 10.6084/m9.figshare.5339647.v1
title: tensile_wet_ambient_100torr.zip

description: Raw data of tensile testing for wet sample, sampled dried at 100 torr (lowest pressure), and two ambient conditions (~40% RH and ~21-22 C) Column format is column #1 : time, #2 : force, #3: unused, #4: cross-head displacement, #5 length as measured from extensometer.First row is usually wrong, file-machine initiating error
DOI: 10.6084/m9.figshare.5339593
title: ENTLN P2014

description: ENTLN data from old processor
DOI: 10.6084/m9.figshare.5339572
title: ENTLN P2015

description: ENTLN P2015 data for evaluation
DOI: 10.6084/m9.figshare.5339593.v1
title: ENTLN P2014

description: ENTLN data from old processor
DOI: 10.6084/m9.figshare.5339572.v1
title: ENTLN P2015

description: ENTLN P2015 data for evaluation
DOI: 10.6084/m9.figshare.5339641.v3
title: White_paper_Huan_Lei_DOE_PI.pdf

description: <br>Whitepaper submitted to the 2017 DOE ASCR Applied Math Meeting
DOI: 10.6084/m9.figshare.5339641.v2
title: White_paper_Huan_Lei_DOE_PI.pdf

description: <br>Whitepaper submitted to the 2017 DOE ASCR Applied Math Meeting
DOI: 10.6084/m9.figshare.5339497
title: DOE Budget Authority for Energy Research, Development, and Demonstration Database. The Fletcher School, Tufts University; and Department of Politics and International Studies, University of Cambridge, Harvard Kennedy School.

description: U.S. government investments in energy research, development, and demonstration (RD&D) at the Department of Energy (DOE) from 1978
DOI: 10.6084/m9.figshare.5339407
title: Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," published in <i>Ecography</i>: https://onlinelibrary.wiley.com/doi/10.1111/ecog.03641<br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals.<b> </b>We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.
DOI: 10.6084/m9.figshare.5339497.v1
title: DOE Budget Authority for Energy Research, Development, and Demonstration Database 2017

description: U.S. government investments in energy research, development, and demonstration (RD&D) at the Department of Energy (DOE) from 1978
DOI: 10.6084/m9.figshare.5339407.v1
title: A thermal gradient of trait similarity across North America

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," currently in review at <i>Global Ecology and Biogeography</i>. <br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:<b>Aims: </b>Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Individual-level trait data are now available from long-term monitoring networks spanning large geographic extents, enabling trait-based tests of theory at large spatial scales. <b>Location: </b>Continental United States <b>Time period: </b>2015 <b>Taxon: </b>Rodentia <b>Methods: </b>Here we examine variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantify body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. <b>Main conclusions: </b>We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.
DOI: 10.6084/m9.figshare.5339497.v3
title: DOE Budget Authority for Energy Research, Development, and Demonstration Database. The Fletcher School, Tufts University; and Department of Politics and International Studies, University of Cambridge, Harvard Kennedy School.

description: U.S. government investments in energy research, development, and demonstration (RD&D) at the Department of Energy (DOE) from 1978
DOI: 10.6084/m9.figshare.5339497.v2
title: DOE Budget Authority for Energy Research, Development, and Demonstration Database. The Fletcher School, Tufts University; and Department of Politics and International Studies, University of Cambridge, Harvard Kennedy School; June 27, 2017.

description: U.S. government investments in energy research, development, and demonstration (RD&D) at the Department of Energy (DOE) from 1978
DOI: 10.6084/m9.figshare.5336641
title: primary targets bed file of customized short stature panel performed on NimbleDesign

description: primary targets bed file of customized short stature panel performed on NimbleDesign
DOI: 10.6084/m9.figshare.5339407.v2
title: Data from: A thermal gradient of trait similarity across North America

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," currently in review at <i>Global Ecology and Biogeography</i>. <br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:<b>Aims: </b>Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Individual-level trait data are now available from long-term monitoring networks spanning large geographic extents, enabling trait-based tests of theory at large spatial scales. <b>Location: </b>Continental United States <b>Time period: </b>2015 <b>Taxon: </b>Rodentia <b>Methods: </b>Here we examine variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantify body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. <b>Main conclusions: </b>We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.
DOI: 10.6084/m9.figshare.5336638
title: capture targets bed file of customized short stature panel by NimbleDesign

description: capture targets bed file of customized short stature panel by NimbleDesign
DOI: 10.6084/m9.figshare.5336641.v1
title: primary targets bed file of customized short stature panel performed on NimbleDesign

description: primary targets bed file of customized short stature panel performed on NimbleDesign
DOI: 10.6084/m9.figshare.5336557
title: RAST bidirectional best hit output

description: These two files are the output from RAST's bidirectional best hit analysis, using either Halobacteriovorax marinus BE01 or SJ as the reference genome.<br>