cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12807787.v1
title: BEAST configuration excluding samples from the Czech national museum from Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

description: Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12807784
title: Parameters used for MALT analysis from Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

description: Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12807790.v1
title: BEAST configuration including samples from the Czech national museum from Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

description: Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12807784.v1
title: Parameters used for MALT analysis from Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox

description: Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.12807610
title: CYT UCSC hub hg38

description: Datasets used in the hg38 UCSC session that contains the results from the Nature Genetics article "The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes".
DOI: 10.6084/m9.figshare.12807560
title: Supplementary tables from The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities

description: S1: Full reference metadata for all accessed and analyzed sample data. S2: The top-hits taxonomy for soil-core OTUs from a BLAST search against the NCBI 16S rRNA database and the average abundance of each OTU relative to the total soil-core OTU sequences found among each host.
DOI: 10.6084/m9.figshare.12807560.v1
title: Supplementary tables from The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities

description: S1: Full reference metadata for all accessed and analyzed sample data. S2: The top-hits taxonomy for soil-core OTUs from a BLAST search against the NCBI 16S rRNA database and the average abundance of each OTU relative to the total soil-core OTU sequences found among each host.
DOI: 10.6084/m9.figshare.12807505
title: Supplementary tables from Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities

description: Tables S1-S15
DOI: 10.6084/m9.figshare.12807505.v1
title: Supplementary tables from Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities

description: Tables S1-S15
DOI: 10.6084/m9.figshare.12807209
title: LUCAS_supportDocs.zip

description: Support documents for LUCAS multi-year harmonization workflow. Contents Include:<br>- Mapping CSVs: -- separate file for each year (2006,2009,2012,2015,2018), containing the mapping done between native variable alpha-numerical encoding and the respective label (*year*_lucas_harmo_allVars.csv). -- CSV for mappings column renaming (columnRename.csv) -- CSV for mappings variable recoding (RecodeVars.csv) <br> -- CSV containing a mapping table for manually changed variables (manChangeVars.csv)<br>- Harmonized multi-year legend from native C3 documents (C3_legends_new.csv)<br>- Harmonized updated Record Descriptor (LUCAS_harmo_RD_new.csv)<br>
DOI: 10.6084/m9.figshare.12807209.v1
title: LUCAS_supportDocs.zip

description: Support documents for LUCAS multi-year harmonization workflow. Contents Include:<br>- Mapping CSVs: -- separate file for each year (2006,2009,2012,2015,2018), containing the mapping done between native variable alpha-numerical encoding and the respective label (*year*_lucas_harmo_allVars.csv). -- CSV for mappings column renaming (columnRename.csv) -- CSV for mappings variable recoding (RecodeVars.csv) <br> -- CSV containing a mapping table for manually changed variables (manChangeVars.csv)<br>- Harmonized multi-year legend from native C3 documents (C3_legends_new.csv)<br>- Harmonized updated Record Descriptor (LUCAS_harmo_RD_new.csv)<br>
DOI: 10.6084/m9.figshare.12807068
title: Madingley Outputs: Global rasters

description: global rasters.zip: These are the summarised global (at 1 degree resolution) outputs for the control simulation and the large carnivores removal simulation. Simulations results were produced in the Madingley model.<br><br>
DOI: 10.6084/m9.figshare.12807068.v1
title: Madingley Outputs: Global rasters

description: global rasters.zip: These are the summarised global (at 1 degree resolution) outputs for the control simulation and the large carnivores removal simulation. Simulations results were produced in the Madingley model.<br><br>
DOI: 10.6084/m9.figshare.12807002
title: supplementary material

description: Analysis of mRNA and miRNA sequencing results<br>
DOI: 10.6084/m9.figshare.12806999
title: Multilocus Rickettsia typing and barcoding of BOLD Rickettsia contaminants

description: <i>COI</i> sequences alone provides an impression of the frequency with which<i> Rickettsia </i>associates are found in barcoding studies. However, they have limited value in describing the diversity of the <i>Rickettsia</i> found. To provide further insight into the diversity of <i>Rickettsia </i>using a multilocus approach, we obtained 186 DNA extracts from the archive at the Centre for Biodiversity Genomics (University of Guelph, Canada). We then screened multiple Rickettsia genes via PCR (gltA, 16S, 17KDa) to create strain types. Accession numbers for both Rickettsia and host sequences are provided in this dataset.
DOI: 10.6084/m9.figshare.12806999.v1
title: Multilocus Rickettsia typing and barcoding of BOLD Rickettsia contaminants

description: <i>COI</i> sequences alone provides an impression of the frequency with which<i> Rickettsia </i>associates are found in barcoding studies. However, they have limited value in describing the diversity of the <i>Rickettsia</i> found. To provide further insight into the diversity of <i>Rickettsia </i>using a multilocus approach, we obtained 186 DNA extracts from the archive at the Centre for Biodiversity Genomics (University of Guelph, Canada). We then screened multiple Rickettsia genes via PCR (gltA, 16S, 17KDa) to create strain types. Accession numbers for both Rickettsia and host sequences are provided in this dataset.
DOI: 10.6084/m9.figshare.12807002.v1
title: supplementary material

description: Analysis of mRNA and miRNA sequencing results<br>
DOI: 10.6084/m9.figshare.12806948
title: Risky sexual behaviours among young adults attending Higher Learning Institutions in Mbeya-Tanzania

description: Data was collected from a cross-sectional designed study, conducted from March 2019 to January 2020 in Mbeya region, Tanzania among students attending Higher Learning Institutions (HLIs) in the region registered by the Tanzania Commission for Universities (TCU). Eligible participants included Tanzanian students enrolled in HLIs within Mbeya region in any year of study, aged 18-24 years of age and agreed to provide written informed consent prior to all study-related procedures. Participants were ineligible to take part if they were students attending short-term courses (&lt; 6 months) or elective students. Each HLI in Mbeya region was invited to participate. A complete electronic list of all students registered, aged 18-24 years of age was obtained from the Academic Registrars' offices. Based on the varying number of students from each HLI, and the study desired sample size, probability proportional to size was used to determine the total number of students by gender from each HLI. Students were not selected based on the department or course they are registered for. Each selected student was notified via phone that he/she has been randomly selected to take part in the study and if he/she was willing to take part, he/she was then requested to report to the data collection point within their respective campuses. An individual self-administered questionnaire was used in the study. The questionnaire was administered using a tablet or smart phone through a web-based software (ODK) or hard copy, which ever method the participant preferred. Data was entered in a database, and thereafter cleaned and analysed using statistical software Stata version 14 for Windows. Ethical approval was granted by the Mbeya Medical Research and Ethics Review Committee (MMREC) Reference Number SZEC-2439/R.A/V.1/07, Kilimanjaro Christian Medical College Research Ethics and Review Committee (CRERC) Reference Number 2405, and National Health Research Ethics Committee (NatHREC) Reference Number NIMR/HQ/R.8a/Vol.IX/3092. All eligible participants who agree to participate in this study received study information and were consented prior to any study related activity. Only participant’s study identification number was used in the questionnaire.
DOI: 10.6084/m9.figshare.12806966
title: Supplementary material

description: Analysis of mRNA and miRNA sequencing results<br>
DOI: 10.6084/m9.figshare.12806894
title: Supplementary Material for: The Thioredoxin-Interacting Protein TXNIP Is a Putative Tumour Suppressor in Cutaneous T-Cell Lymphoma

description: <b><i>Background:</i></b> The thioredoxin-interacting protein (TXNIP) is involved in cellular metabolism and cell proliferation, and recently, deficient expression of TXNIP has been associated with progression and poor outcome for cancer patients. <b><i>Objectives:</i></b> To assess TXNIP expression and function in malignant T cells from cutaneous T-cell lymphoma (CTCL). <b><i>Methods:</i></b> CTCL-derived malignant (MyLa2059, PB2B) and non-malignant (MyLa1850) cell lines were analysed by Western blotting and qPCR for TXNIP expression. Subsequently, the malignant CTCL cell lines were treated with GSK126 – an inhibitor of enhancer of zeste homolog 2 (EZH2) methyltransferase activity or assessed by bisulphite sequencing for TXNIP promoter methylation. Methylation was also assessed with the demethylating agent 5-azacytidine (5AZA). Finally, TXNIP was overexpressed in the malignant PB2B cell line via plasmid transduction, and the effect of TXNIP was further analysed by flow cytometry. <b><i>Results:</i></b> We report on low expression of TXNIP protein in all cell lines representing different subtypes and stages of CTCL when compared to non-malignant T cells. Epigenetic silencing and other mechanisms were involved in the repression of TXNIP whereas forced expression of TXNIP strongly inhibited proliferation of malignant T cells. <b><i>Conclusions:</i></b> Epigenetic silencing and other as yet unknown mechanisms repress TXNIP expression in malignant T cells. As forced expression of TXNIP inhibits malignant proliferation, we propose that TXNIP is a putative tumour suppressor in CTCL.
DOI: 10.6084/m9.figshare.12806966.v1
title: Supplementary material

description: Analysis of mRNA and miRNA sequencing results<br>
DOI: 10.6084/m9.figshare.12806870
title: Supplementary Material for: Lipid Droplets Accumulate in the Hypothalamus of Mice and Humans with and without Metabolic Diseases

description: <b><i>Background:</i></b> In peripheral tissues, the lipid droplet (LD) organelle links lipid metabolism, inflammation, and insulin resistance. Little is known about the brain LDs. <b><i>Objectives:</i></b> We hypothesized that hypothalamic LDs would be altered in metabolic diseases. <b><i>Methods:</i></b> We used immunofluorescence labeling of the specific LD protein, PLIN2, as the approach to visualize and quantify LDs. <b><i>Results:</i></b> LDs were abundant in the hypothalamic third ventricle wall layer with similar heterogeneous distributions between control mice and humans. The LD content was enhanced by high-fat diet (HFD) in both wild-type and in low-density lipoprotein receptor deficient (<i>Ldlr</i> –/– HFD) mice. Strikingly, we observed a lower LD amount in type 2 diabetes mellitus (T2DM) patients when compared with non-T2DM patients. <b><i>Conclusions:</i></b> LDs accumulate in the normal hypothalamus, with similar distributions in human and mouse. Moreover, metabolic diseases differently modify LD content in mouse and human. Our results suggest that hypothalamic LD accumulation is an important target to the study of metabolism.
DOI: 10.6084/m9.figshare.12806876
title: CryoEM - Periplasm measurement (ED Fig. 5)

description: Images and data and ImageJ script used for periplasm measurement at the ED Fig. 5
DOI: 10.6084/m9.figshare.12806948.v2
title: Risky sexual behaviours among young adults attending Higher Learning Institutions in Mbeya-Tanzania

description: Data was collected from a cross-sectional designed study, conducted from March 2019 to January 2020 in Mbeya region, Tanzania among students attending Higher Learning Institutions (HLIs) in the region registered by the Tanzania Commission for Universities (TCU). Eligible participants included Tanzanian students enrolled in HLIs within Mbeya region in any year of study, aged 18-24 years of age and agreed to provide written informed consent prior to all study-related procedures. Participants were ineligible to take part if they were students attending short-term courses (&lt; 6 months) or elective students. Each HLI in Mbeya region was invited to participate. A complete electronic list of all students registered, aged 18-24 years of age was obtained from the Academic Registrars' offices. Based on the varying number of students from each HLI, and the study desired sample size, probability proportional to size was used to determine the total number of students by gender from each HLI. Students were not selected based on the department or course they are registered for. Each selected student was notified via phone that he/she has been randomly selected to take part in the study and if he/she was willing to take part, he/she was then requested to report to the data collection point within their respective campuses. An individual self-administered questionnaire was used in the study. The questionnaire was administered using a tablet or smart phone through a web-based software (ODK) or hard copy, which ever method the participant preferred. Data was entered in a database, and thereafter cleaned and analysed using statistical software Stata version 14 for Windows. Ethical approval was granted by the Mbeya Medical Research and Ethics Review Committee (MMREC) Reference Number SZEC-2439/R.A/V.1/07, Kilimanjaro Christian Medical College Research Ethics and Review Committee (CRERC) Reference Number 2405, and National Health Research Ethics Committee (NatHREC) Reference Number NIMR/HQ/R.8a/Vol.IX/3092. All eligible participants who agree to participate in this study received study information and were consented prior to any study related activity. Only participant’s study identification number was used in the questionnaire.
DOI: 10.6084/m9.figshare.12806864
title: Supplementary Material for: Diverse Receptor Tyrosine Kinase Phosphorylation in Urine-Derived Tubular Epithelial Cells from Autosomal Dominant Polycystic Kidney Disease Patients

description: <b><i>Backgrounds:</i></b> The clinical features of autosomal dominant polycystic kidney disease (ADPKD) differ among patients even if they have the same gene mutation in <i>PKD1</i> or <i>PKD2</i>. This suggests that there is diversity in the expression of other modifier genes or in the underlying molecular mechanisms of ADPKD, but these are not well understood. <b><i>Methods:</i></b> We primarily cultured solute carrier family 12 member 3 (SLC12A3)-positive urine-derived distal tubular epithelial cells from 6 ADPKD patients and 4 healthy volunteers and established immortalized cell lines. The diversity in receptor tyrosine kinase (RTK) phosphorylation by phospho-RTK array in immortalized tubular epithelial cells was analyzed. <b><i>Results:</i></b> We noted diversity in the activation of several molecules, including Met, a receptor of hepatocyte growth factor (HGF). Administration of golvatinib, a selective Met inhibitor, or transfection of small interfering RNA for Met suppressed cell proliferation and downstream signaling only in the cell lines in which hyperphosphorylation of Met was observed. In three-dimensional culture of Madin-Darby canine kidney (MDCK) cells as a cyst formation model of ADPKD, HGF activated Met, resulting in an increased total cyst number and total cyst volume. Administration of golvatinib inhibited these phenotypes in MDCK cells. <b><i>Conclusion:</i></b> Analysis of urine-derived tubular epithelial cells demonstrated diverse RTK phosphorylation in ADPKD, and Met phosphorylation was noted in some patients. Considering the difference in the effects of golvatinib on immortalized tubular epithelial cells among patients, this analysis may aid in selecting suitable drugs for individual ADPKD patients.
DOI: 10.6084/m9.figshare.12806876.v1
title: CryoEM - Periplasm measurement (ED Fig. 5)

description: Images and data and ImageJ script used for periplasm measurement at the ED Fig. 5
DOI: 10.6084/m9.figshare.12806864.v1
title: Supplementary Material for: Diverse Receptor Tyrosine Kinase Phosphorylation in Urine-Derived Tubular Epithelial Cells from Autosomal Dominant Polycystic Kidney Disease Patients

description: <b><i>Backgrounds:</i></b> The clinical features of autosomal dominant polycystic kidney disease (ADPKD) differ among patients even if they have the same gene mutation in <i>PKD1</i> or <i>PKD2</i>. This suggests that there is diversity in the expression of other modifier genes or in the underlying molecular mechanisms of ADPKD, but these are not well understood. <b><i>Methods:</i></b> We primarily cultured solute carrier family 12 member 3 (SLC12A3)-positive urine-derived distal tubular epithelial cells from 6 ADPKD patients and 4 healthy volunteers and established immortalized cell lines. The diversity in receptor tyrosine kinase (RTK) phosphorylation by phospho-RTK array in immortalized tubular epithelial cells was analyzed. <b><i>Results:</i></b> We noted diversity in the activation of several molecules, including Met, a receptor of hepatocyte growth factor (HGF). Administration of golvatinib, a selective Met inhibitor, or transfection of small interfering RNA for Met suppressed cell proliferation and downstream signaling only in the cell lines in which hyperphosphorylation of Met was observed. In three-dimensional culture of Madin-Darby canine kidney (MDCK) cells as a cyst formation model of ADPKD, HGF activated Met, resulting in an increased total cyst number and total cyst volume. Administration of golvatinib inhibited these phenotypes in MDCK cells. <b><i>Conclusion:</i></b> Analysis of urine-derived tubular epithelial cells demonstrated diverse RTK phosphorylation in ADPKD, and Met phosphorylation was noted in some patients. Considering the difference in the effects of golvatinib on immortalized tubular epithelial cells among patients, this analysis may aid in selecting suitable drugs for individual ADPKD patients.