cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6158117
title: Additional file 6: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S6. Data for time to influenza peak. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6158117.v1
title: Additional file 6: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S6. Data for time to influenza peak. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6158105
title: Additional file 5: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S5. Data for percentage reduction in peak influenza attack rate in the general population. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6158105.v1
title: Additional file 5: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S5. Data for percentage reduction in peak influenza attack rate in the general population. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6158099
title: Additional file 4: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S6. Detailed information for DE genes displaying significant homology to genes described in viruses, yeasts and fungi: mean normalized counts per experimental set-up, model effects (host plant, moth species, interaction) and functional annotations. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6158099.v1
title: Additional file 4: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S6. Detailed information for DE genes displaying significant homology to genes described in viruses, yeasts and fungi: mean normalized counts per experimental set-up, model effects (host plant, moth species, interaction) and functional annotations. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6158081
title: Additional file 3: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S4. Detailed information for all DE genes: mean normalized counts per experimental set-up, significant effects in the GLM model (host plant, moth species, interaction) and functional annotations. (XLSX 1085Â kb)
DOI: 10.6084/m9.figshare.6158081.v1
title: Additional file 3: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S4. Detailed information for all DE genes: mean normalized counts per experimental set-up, significant effects in the GLM model (host plant, moth species, interaction) and functional annotations. (XLSX 1085Â kb)
DOI: 10.6084/m9.figshare.6158078
title: Additional file 4: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S4. Data for percentage reduction in cumulative influenza attack rate in the general population, by compliance with intervention. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6158078.v1
title: Additional file 4: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S4. Data for percentage reduction in cumulative influenza attack rate in the general population, by compliance with intervention. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.6158072
title: Additional file 1: of A Recurrent Silent Mutation Implicates fecA in Ethanol Tolerance by Escherichia coli

description: Table S1. List of observed nucleotide changes in FBR5 and the twenty mutant strains derived from FBR5. Escherichia coli K-12 MG1655 (GenBank: U00096.2) was used as the reference genome. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6158072.v1
title: Additional file 1: of A Recurrent Silent Mutation Implicates fecA in Ethanol Tolerance by Escherichia coli

description: Table S1. List of observed nucleotide changes in FBR5 and the twenty mutant strains derived from FBR5. Escherichia coli K-12 MG1655 (GenBank: U00096.2) was used as the reference genome. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.6158069
title: Additional file 3: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S3. Data for percentage reduction in cumulative influenza attack rate in the general population, by threshold for triggering intervention. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6158069.v1
title: Additional file 3: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S3. Data for percentage reduction in cumulative influenza attack rate in the general population, by threshold for triggering intervention. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.6158057
title: Additional file 2: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S3. Common and private DE genes in analyses with and without the inclusion of the one outlier sample (ECB_Mug2). (XLSX 403Â kb)
DOI: 10.6084/m9.figshare.6158057.v1
title: Additional file 2: of Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

description: Table S3. Common and private DE genes in analyses with and without the inclusion of the one outlier sample (ECB_Mug2). (XLSX 403Â kb)
DOI: 10.6084/m9.figshare.6158054
title: Additional file 2: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S2. Data for percentage reduction in cumulative influenza attack rate. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6158054.v1
title: Additional file 2: of Effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review

description: Table S2. Data for percentage reduction in cumulative influenza attack rate. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.6157772
title: Electronic Supplementary Material 3.zip

description: This folder contains the data and R code used for the titular manuscript. <br><br>There is an RStudio Project file ('pretreatment study.Rproj') which will allow for easy navigation of all the data within the two scripts ('pretreatment study master script.R' and 'Figures master script.R').<br><br>The 'final figures' folder is empty for sake of file size, but the figures (used in the manuscript) can be generated with the associated code.<br><br>If one should spot any errors, want more clarification, or have any question, please feel free to contact me (Zach; zpsimpso@gmail.com).
DOI: 10.6084/m9.figshare.6157691
title: Simulation dataset

description: Dataset used to evaluate sample size to estimate genomic kinship.
DOI: 10.6084/m9.figshare.6157691.v1
title: Simulation dataset

description: Dataset used to evaluate sample size to estimate genomic kinship.
DOI: 10.6084/m9.figshare.6157679
title: Neighbourhood Adjusted Wallace Coefficient: supporting data

description: Supporting information for the manuscript entitled <b><i>"Rapid Identification of Stable Clusters in Bacterial Populations Using the Adjusted Wallace Coefficient"</i></b> <b>doi:</b> https://doi.org/10.1101/299347<br>Files included in the zip archive:<br><b>README.txt:</b> Description of the various files in the archive<b>campylobacter_accessions.txt:</b> List of C jejuni genome accessions<b>salmonella_accessions.txt:</b> List of S enterica genome accessions<b>campylobacter (folder):</b><br><b>campylobacter_calls.csv:</b> allele call results<b>campylobacter_clusters.txt:</b> goeBURST cgmlst profile clusters<b>campylobacter_donor_recipient.txt:</b> donor-recipient merger table<b>campylobacter_stats_table.txt:</b> partitions statistics over goeburst thresholds<b>campylobacter_st_definitions.tsv:</b> Sequence Type definitions<b>campylobacter_strain_st.tsv:</b> Strain vs. Sequence Type lookups<b>Alleles (folder):</b> contains 697 multifasta files with allelic data for loci in C jejuni cgMLST scheme<br><b>salmonella (folder):</b><br><b>salmonella_calls.csv:</b> allele call results<b>salmonella_clusters.txt:</b> goeBURST cgmlst profile clusters<b>salmonella_donor_recipient.txt:</b> donor-recipient merger table<b>salmonella_stats_table.txt:</b> partitions statistics over goeburst thresholds<b>salmonella_st_definitions.tsv:</b> Sequence Type definitionssalmonella_strain_st.tsv: Strain vs. Sequence Type lookups
DOI: 10.6084/m9.figshare.6157679.v1
title: Neighbourhood Adjusted Wallace Coefficient: supporting data

description: Supporting information for the manuscript entitled <b><i>"Rapid Identification of Stable Clusters in Bacterial Populations Using the Adjusted Wallace Coefficient"</i></b> <b>doi:</b> https://doi.org/10.1101/299347<br>Files included in the zip archive:<br><b>README.txt:</b> Description of the various files in the archive<b>campylobacter_accessions.txt:</b> List of C jejuni genome accessions<b>salmonella_accessions.txt:</b> List of S enterica genome accessions<b>campylobacter (folder):</b><br><b>campylobacter_calls.csv:</b> allele call results<b>campylobacter_clusters.txt:</b> goeBURST cgmlst profile clusters<b>campylobacter_donor_recipient.txt:</b> donor-recipient merger table<b>campylobacter_stats_table.txt:</b> partitions statistics over goeburst thresholds<b>campylobacter_st_definitions.tsv:</b> Sequence Type definitions<b>campylobacter_strain_st.tsv:</b> Strain vs. Sequence Type lookups<b>Alleles (folder):</b> contains 697 multifasta files with allelic data for loci in C jejuni cgMLST scheme<br><b>salmonella (folder):</b><br><b>salmonella_calls.csv:</b> allele call results<b>salmonella_clusters.txt:</b> goeBURST cgmlst profile clusters<b>salmonella_donor_recipient.txt:</b> donor-recipient merger table<b>salmonella_stats_table.txt:</b> partitions statistics over goeburst thresholds<b>salmonella_st_definitions.tsv:</b> Sequence Type definitionssalmonella_strain_st.tsv: Strain vs. Sequence Type lookups
DOI: 10.6084/m9.figshare.6157631
title: Complete data set for 2018 CellReports Zhang Succinate Ischemia Paper

description: Complete data set for each of the Figures in Zhang et al. paper in Press in Cell Reports<br>
DOI: 10.6084/m9.figshare.6157604
title: Residential inter-zonal ventilation rates for exposure modeling

description: Residential inter-zonal (e.g., between rooms) ventilation is comprised of fresh air infiltration in and exfiltration out of the whole house plus the “fresh” air that is entering (and exiting) the room of interest from other rooms or areas within the house. Clearly, the inter-zone ventilation rate in any room of interest will be greater than the infiltration/exfiltration ventilation rate of outdoor air for the whole house. The purpose of this study is to determine how much greater the inter-zonal ventilation rate is in typical U.S. residences compared to the whole house ventilation rate from outdoor air. The data for this statistical analysis came from HouseDB, a 1995 EPA database of residential ventilation rates. Analytical results indicate that a lognormal distribution provides the best fit to the data. Lognormal probability distribution functions (PDFs) are provided for various inter-zonal ventilation rates for comparison to the PDF for the whole house ventilation rates. All ventilation rates are expressed as air change rates per hour (ACH). These PDFs can be used as inputs to exposure models. This analysis suggests that if one were performing a deterministic analysis for unknown housing stocks in the U.S., a default mean and median ACH values of 0.4/hr and 0.3/hr, respectively, for whole house ventilation would be appropriate; and 0.7/hr and 0.6/hr, respectively, for inter-zonal ventilation.
DOI: 10.6084/m9.figshare.6157604.v1
title: Residential inter-zonal ventilation rates for exposure modeling

description: Residential inter-zonal (e.g., between rooms) ventilation is comprised of fresh air infiltration in and exfiltration out of the whole house plus the “fresh” air that is entering (and exiting) the room of interest from other rooms or areas within the house. Clearly, the inter-zone ventilation rate in any room of interest will be greater than the infiltration/exfiltration ventilation rate of outdoor air for the whole house. The purpose of this study is to determine how much greater the inter-zonal ventilation rate is in typical U.S. residences compared to the whole house ventilation rate from outdoor air. The data for this statistical analysis came from HouseDB, a 1995 EPA database of residential ventilation rates. Analytical results indicate that a lognormal distribution provides the best fit to the data. Lognormal probability distribution functions (PDFs) are provided for various inter-zonal ventilation rates for comparison to the PDF for the whole house ventilation rates. All ventilation rates are expressed as air change rates per hour (ACH). These PDFs can be used as inputs to exposure models. This analysis suggests that if one were performing a deterministic analysis for unknown housing stocks in the U.S., a default mean and median ACH values of 0.4/hr and 0.3/hr, respectively, for whole house ventilation would be appropriate; and 0.7/hr and 0.6/hr, respectively, for inter-zonal ventilation.
DOI: 10.6084/m9.figshare.6157601
title: Microbial hazards during harvesting and processing at an outdoor United States cannabis farm

description: Cannabis cultivation is an emerging industry within the United States. Organic dust derived in part from naturally occurring microorganisms is known to cause byssinosis in the hemp industry. In this pilot study, bacteria and fungi encountered by workers at an outdoor cannabis farm that utilized organic practices were elucidated by 16 S ribosomal RNA (rRNA) and Internal Transcribed Spacer (ITS) region sequencing, respectively. Area (n = 14) and personal air samples (n = 12) were collected during harvesting and processing activities. 16 S rRNA and ITS regions of extracted bacterial and fungal genomic DNA were amplified and sequenced using Sanger sequencing. Bacterial sequencing resolved 1,077 sequences that were clustered into 639 operational taxonomic units (OTUs) and predominantly placed in the phylum, Actinobacteria (46%). Personal air samples revealed higher bacterial and Actinobacteria diversity compared to outdoor area samples collected within the facility (<i>p</i> &lt; 0.05). A high degree of dissimilarity between bacteria was identified within and between samples. Fungal sequences (n = 985) were identified and predominantly clustered in the phylum Ascomycota (53%). Of the 216 fungal OTUs elucidated, the cannabis plant pathogenic species, <i>Botrytis cinerea</i>, was the most prevalent and accounted for 34% of all fungal sequences. The relative abundance of <i>B. cinerea</i> was highest in personal air samples (59%) compared to area samples collected in the drying room (19%), greenhouse (18%), and outdoor environment (6%). There was 49% sample similarity between fungi identified within personal air samples, but higher dissimilarity coefficients were observed within and between greenhouse, drying room, and outdoor area air samples. The results of this pilot study suggest that the cannabis farm workers are potentially exposed to Actinobacteria as well as the cannabis plant pathogen, <i>B. cinerea</i> during harvesting, bud-stripping, and hand-trimming processes.
DOI: 10.6084/m9.figshare.6157601.v1
title: Microbial hazards during harvesting and processing at an outdoor United States cannabis farm

description: Cannabis cultivation is an emerging industry within the United States. Organic dust derived in part from naturally occurring microorganisms is known to cause byssinosis in the hemp industry. In this pilot study, bacteria and fungi encountered by workers at an outdoor cannabis farm that utilized organic practices were elucidated by 16 S ribosomal RNA (rRNA) and Internal Transcribed Spacer (ITS) region sequencing, respectively. Area (n = 14) and personal air samples (n = 12) were collected during harvesting and processing activities. 16 S rRNA and ITS regions of extracted bacterial and fungal genomic DNA were amplified and sequenced using Sanger sequencing. Bacterial sequencing resolved 1,077 sequences that were clustered into 639 operational taxonomic units (OTUs) and predominantly placed in the phylum, Actinobacteria (46%). Personal air samples revealed higher bacterial and Actinobacteria diversity compared to outdoor area samples collected within the facility (<i>p</i> &lt; 0.05). A high degree of dissimilarity between bacteria was identified within and between samples. Fungal sequences (n = 985) were identified and predominantly clustered in the phylum Ascomycota (53%). Of the 216 fungal OTUs elucidated, the cannabis plant pathogenic species, <i>Botrytis cinerea</i>, was the most prevalent and accounted for 34% of all fungal sequences. The relative abundance of <i>B. cinerea</i> was highest in personal air samples (59%) compared to area samples collected in the drying room (19%), greenhouse (18%), and outdoor environment (6%). There was 49% sample similarity between fungi identified within personal air samples, but higher dissimilarity coefficients were observed within and between greenhouse, drying room, and outdoor area air samples. The results of this pilot study suggest that the cannabis farm workers are potentially exposed to Actinobacteria as well as the cannabis plant pathogen, <i>B. cinerea</i> during harvesting, bud-stripping, and hand-trimming processes.
DOI: 10.6084/m9.figshare.6157583
title: Structuring Wikipedia Articles with Section Recommendations

description: Output generated by the method described in: https://arxiv.org/abs/1804.05995<br><br>Category based recommendation using category–section counts (4.1)
DOI: 10.6084/m9.figshare.6157445
title: WCNPruning input set

description: Wikipedia Category network Sept 17. <br>Input files for: https://github.com/epfl-dlab/WCNPruning<br>Input files:<i>article_types_dbpedia.tsv.gz<br></i><i>category_graph_sept17.tsv.gz<br></i><i>article_categories_sept17.tsv.gz</i><br><br>Output file:articles_scores_gini_coefficient0.966.json.gz<br>
DOI: 10.6084/m9.figshare.6155189
title: 15GRNT25560038 Ligand-Specific Gene Regulation by Liver X Receptors.

description: AHA data set
DOI: 10.6084/m9.figshare.6155189.v1
title: 15GRNT25560038 Ligand-Specific Gene Regulation by Liver X Receptors.

description: AHA data set
DOI: 10.6084/m9.figshare.6155009
title: Supplementary Material for: The Role of Proteasome Inhibitor MG132 in 2,4-Dinitrofluorobenzene-Induced Atopic Dermatitis in NC/Nga Mice

description: <b><i>Background:</i></b> Although immunosuppressants for therapy of atopic dermatitis (AD) are still being sought, proteasome inhibitors are also potential candidates for the treatment of AD. Proteasome inhibitors exert various effects by blocking proteasomal degradation and help regulate processes such as apoptosis induction via caspase-9, cell cycle progression via cyclins, NF-κB inactivation via IκB, and downregulation of antigen cross-presentation. The cells targeted by proteasome inhibitors are therefore activated cells undergoing proliferation or differentiation, and antigen-presenting cells carrying out protein degradation. <b><i>Objectives:</i></b> This study investigated the therapeutic effects and side effects of a proteasome inhibitor, MG132, on the treatment of AD. <b><i>Methods:</i></b> AD-like disease in NC/Nga mice housed under specific pathogen-free conditions was induced by repeated application of 2,4-dinitrofluorobenzene (DNFB). Disease progression was evaluated by inflammation score, histopathology, and serum IgE level, and the effects of systemic MG132 administration were investigated. The percentages and absolute numbers for each population of Th1, Th2, and Th17 cells in the axillary lymph nodes were analyzed by flow cytometry. <b><i>Results:</i></b> DNFB application increased the expression of a unique major histocompatibility complex class I mutant molecule D/L<sup>dm7</sup> in dendritic cells (DCs), and increased Th1 and Th17 cells in NC/Nga mice. In vivo MG132 administration to NC/Nga mice with DNFB-induced dermatitis reduced Th17 cells but maintained the level of Th1 cells, resulting in the alleviation of dermatitis lesions by decreasing both serum IgE hyperproduction and mast cell migration. To understand the mechanisms maintaining Th1 cell levels following in vivo MG132-administration, we focused on the role of proteasomes regulating D/L<sup>dm7</sup> expression. Interestingly, 20S proteasome activity was higher in NC/Nga DCs than in BALB/c DCs. In vitro MG132 administration partially increased D/L<sup>dm7</sup> expression in a dose-dependent manner during DC maturation, and induced IFN-γ production from autoreactive CD8+ T cells but not from CD4+ T cells following coculturing with D/L<sup>dm7</sup>-upregulated DCs. <b><i>Conclusion:</i></b> Although MG132 administration temporarily alleviated AD pathogenesis in NC/Nga mice, prolonged MG132 treatment may result in immunopathogenesis leading to chronic AD due to its side effect of maintaining Th1 levels via autoreactive CD8+ T cells.
DOI: 10.6084/m9.figshare.6154928
title: galleria.csv

description: Raw data for survival analysis on galleria
DOI: 10.6084/m9.figshare.6154928.v1
title: galleria.csv

description: Raw data for survival analysis on galleria
DOI: 10.6084/m9.figshare.6154925
title: sgRNA libraries for representative model microbes

description: Using the developed software package, we designed sgRNA libraries for six model bacteria (protein- and ncRNA-coding genes). Totally 12 libraries.
DOI: 10.6084/m9.figshare.6154925.v1
title: sgRNA libraries for representative model microbes

description: Using the developed software package, we designed sgRNA libraries for six model bacteria (protein- and ncRNA-coding genes). Totally 12 libraries.
DOI: 10.6084/m9.figshare.6154877
title: MouseHeadFixRestraintSytem

description: Dimensions of head holder, arms, and restraint frames for headfix behavioral experiments with mice.<br>Files with .vsdx extension are for the MS Visio software.
DOI: 10.6084/m9.figshare.6154877.v1
title: MouseHeadFixRestraintSytem

description: Dimensions of head holder, arms, and restraint frames for headfix behavioral experiments with mice.<br>Files with .vsdx extension are for the MS Visio software.
DOI: 10.6084/m9.figshare.6154841
title: statistic

description: statistic
DOI: 10.6084/m9.figshare.6154841.v1
title: statistic

description: statistic
DOI: 10.17637/rh.6154811
title: Segmented Image Data for Fontainebleau and Berea Sandstones

description: This data contain 3D segmented images of two different sandstones. Three different data sets are contained and are outlined as follows, dry Fontainebleau sandstone, dry Berea sandstone, and saturated Berea sandstone. The 2D images for each data set were segmented using PerGeos (fromThermo Fisher). .am files were generated in PerGeos. .raw files can be opened using multiple applications.<br><br>Also, see the associated archive of pore-network modeling results from these samples at<br>Thomson, Paul-Ross, Aituar-Zhakupova, Aizhan, & Hier-Majumder, Saswata. (2018). Pore network modeling data for Fontainebleau and Berea Sandstones [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1184144<br><br><b>Dry_Fontainebleau.zip<br></b>connected pore space only<b><br></b>Pore-space3.connected-Pore-Space.am<br>Pore-space3.connected-Pore-Space.raw<br><br><b>Dry_Berea.zip<br></b>connected pore space<br>Pore.Connected-Pore-Space.am<br>Pore.Connected-Pore-Space.raw<br>all segmented phases<br>all-phases.labels.am<br>all-phases.labels.raw<br><br><b>Saturated_Berea</b><br>connected pore space<br>Water-phase.Connected-Pore-Space.am<br>Water-phase.Connected-Pore-Space.raw<br>all segmented phases<br>A-filtered.labels.am<br>A-filtered.labels.raw<br><br><br><br><br><b><br><br></b><br><br>