cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5840391
title: Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era

description: <b>Context:</b> Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. <b>Objective:</b> For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. <b>Methods:</b> A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. <b>Results:</b> Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. <b>Conclusions:</b> There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
DOI: 10.6084/m9.figshare.5840391.v2
title: Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era

description: <b>Context:</b> Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. <b>Objective:</b> For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. <b>Methods:</b> A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. <b>Results:</b> Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. <b>Conclusions:</b> There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
DOI: 10.6084/m9.figshare.5840391.v1
title: Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era

description: <b>Context:</b> Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. <b>Objective:</b> For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. <b>Methods:</b> A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. <b>Results:</b> Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. <b>Conclusions:</b> There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
DOI: 10.6084/m9.figshare.5840379
title: Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations

description: <b>Background:</b> Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. <b>Aim:</b> The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. <b>Subjects and methods:</b> Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (<i>n</i> = 4857) were compiled from previous studies. <b>Results:</b> The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. <b>Conclusions:</b> The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.
DOI: 10.6084/m9.figshare.5840379.v1
title: Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations

description: <b>Background:</b> Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. <b>Aim:</b> The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. <b>Subjects and methods:</b> Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (<i>n</i> = 4857) were compiled from previous studies. <b>Results:</b> The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. <b>Conclusions:</b> The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.
DOI: 10.6084/m9.figshare.5840337
title: Additional file 7: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Characterization of HER2E tumors and AR-ness signature. (A) Overview of genes differentially expressed between HER2E and non-HER2E TCGA tumors, accounting for ER expression, PR expression, and PAM50 proliferation score, and omitting genes on chromosome 17. (B) Gene set enrichment results for the C2 gene set collection from MSigDB [22] (KEGG gene sets were removed), for the comparison of HER2E versus non-HER2E TCGA tumors. (C) 45-gene AR-ness signature. (XLSX 6449 kb)
DOI: 10.6084/m9.figshare.5840337.v1
title: Additional file 7: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Characterization of HER2E tumors and AR-ness signature. (A) Overview of genes differentially expressed between HER2E and non-HER2E TCGA tumors, accounting for ER expression, PR expression, and PAM50 proliferation score, and omitting genes on chromosome 17. (B) Gene set enrichment results for the C2 gene set collection from MSigDB [22] (KEGG gene sets were removed), for the comparison of HER2E versus non-HER2E TCGA tumors. (C) 45-gene AR-ness signature. (XLSX 6449 kb)
DOI: 10.6084/m9.figshare.5840322
title: Additional file 6: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Protein-coding genes associated with HER2 amplification. (A) List of 43 protein-coding genes with subtype-independent expression differences between HER2A and non-HER2A breast tumors, after accounting for PAM50 subtype and differences in chromosomal instability, in the TCGA and Metabric cohort. These genes fulfilled the following criteria in at least one cohort: adjusted p value &lt;0.05, and fold change &gt;2 (linear model). (B) List of 14 protein-coding genes with cancer-independent expression differences between HER2A and non-HER2A tumors in a panel of 2838 non-breast TCGA tumors, after accounting for cancer and chromosomal instability. These genes fulfilled the following criteria: adjusted p value &lt;0.001, and fold change &gt;2. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.5840322.v1
title: Additional file 6: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Protein-coding genes associated with HER2 amplification. (A) List of 43 protein-coding genes with subtype-independent expression differences between HER2A and non-HER2A breast tumors, after accounting for PAM50 subtype and differences in chromosomal instability, in the TCGA and Metabric cohort. These genes fulfilled the following criteria in at least one cohort: adjusted p value &lt;0.05, and fold change &gt;2 (linear model). (B) List of 14 protein-coding genes with cancer-independent expression differences between HER2A and non-HER2A tumors in a panel of 2838 non-breast TCGA tumors, after accounting for cancer and chromosomal instability. These genes fulfilled the following criteria: adjusted p value &lt;0.001, and fold change &gt;2. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.5840304
title: Additional file 5: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Mutation and copy number profiles of breast tumors. (A) Mutation profile for 23 genes previously shown to be significantly mutated in breast cancer [13] in 679 TCGA breast tumors with exome-seq data. (B) Mutation profile for 21 genes (FOXA1 and MLL3 are not available) in 1039 Metabric tumors with targeted sequence data. (C) Copy number profile for 28 genes previously shown to have subtype-specific copy number alterations [13], in 864 TCGA breast tumors. (D) Copy number profile for 28 genes in 1107 Metabric tumors. PAM50 subtype and HER2A status are provided. (XLSX 417 kb)
DOI: 10.6084/m9.figshare.5840304.v1
title: Additional file 5: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Mutation and copy number profiles of breast tumors. (A) Mutation profile for 23 genes previously shown to be significantly mutated in breast cancer [13] in 679 TCGA breast tumors with exome-seq data. (B) Mutation profile for 21 genes (FOXA1 and MLL3 are not available) in 1039 Metabric tumors with targeted sequence data. (C) Copy number profile for 28 genes previously shown to have subtype-specific copy number alterations [13], in 864 TCGA breast tumors. (D) Copy number profile for 28 genes in 1107 Metabric tumors. PAM50 subtype and HER2A status are provided. (XLSX 417 kb)
DOI: 10.6084/m9.figshare.5840298
title: Additional file 1: of Integrin-uPAR signaling leads to FRA-1 phosphorylation and enhanced breast cancer invasion

description: Oligonucleotides utilized in this manuscript. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.5840298.v1
title: Additional file 1: of Integrin-uPAR signaling leads to FRA-1 phosphorylation and enhanced breast cancer invasion

description: Oligonucleotides utilized in this manuscript. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.5840271
title: Additional file 2: Table S2. of Current epidemiological evidence for predisposition to high or low intensity human helminth infection: a systematic review

description: Summary of statistical results for all included papers. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5840271.v1
title: Additional file 2: Table S2. of Current epidemiological evidence for predisposition to high or low intensity human helminth infection: a systematic review

description: Summary of statistical results for all included papers. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.5840259
title: Additional file 1: Table S1. of Increase of MZB1 in B cells in systemic lupus erythematosus: proteomic analysis of biopsied lymph nodes

description: Proteomic information of 465 proteins detected by LC-MS. (XLSX 127 kb)
DOI: 10.6084/m9.figshare.5840259.v1
title: Additional file 1: Table S1. of Increase of MZB1 in B cells in systemic lupus erythematosus: proteomic analysis of biopsied lymph nodes

description: Proteomic information of 465 proteins detected by LC-MS. (XLSX 127 kb)
DOI: 10.6084/m9.figshare.5840250
title: Additional file 1: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Flow chart summarizing sample size and available data for the TCGA, Metabric and USO1062 cohort; Clinical metadata, subtype information, HER2A status, AR-ness score, HER2 copy number, and expression levels of ERBB2, ER, PR and AR for the tumors in these three cohorts. (XLSX 669 kb)
DOI: 10.6084/m9.figshare.5840250.v1
title: Additional file 1: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: Flow chart summarizing sample size and available data for the TCGA, Metabric and USO1062 cohort; Clinical metadata, subtype information, HER2A status, AR-ness score, HER2 copy number, and expression levels of ERBB2, ER, PR and AR for the tumors in these three cohorts. (XLSX 669 kb)
DOI: 10.6084/m9.figshare.5840247
title: Additional file 1 of Teaching and learning mathematics through error analysis

description: Additional file 1: Error analysis data.
DOI: 10.6084/m9.figshare.5840247.v2
title: Additional file 1 of Teaching and learning mathematics through error analysis

description: Additional file 1: Error analysis data.
DOI: 10.6084/m9.figshare.5840247.v1
title: MOESM1 of Teaching and learning mathematics through error analysis

description: Additional file 1: Error analysis data.
DOI: 10.6084/m9.figshare.12894959
title: Hunting_GS.xlsx

description: Data on hunting in Gran Sabana
DOI: 10.6084/m9.figshare.12894959.v1
title: Hunting_GS.xlsx

description: Data on hunting in Gran Sabana
DOI: 10.6084/m9.figshare.5840187
title: Additional file 10: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: HER2 co-amplification events: 14 regions with 931 genes are significantly co-amplified with HER2 in TCGA and Metabric combined cohorts (Fisherâ s exact FDR p value &lt;0.05). Percentage of amplification in the HER2A vs. non-HER2A tumors, Fisherâ s exact FDR p value, and gene annotation are shown. Genes in the core or broad HER2 amplicon are listed, and known cancer genes as reported previously [44, 45] are highlighted. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.5840187.v1
title: Additional file 10: of HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

description: HER2 co-amplification events: 14 regions with 931 genes are significantly co-amplified with HER2 in TCGA and Metabric combined cohorts (Fisherâ s exact FDR p value &lt;0.05). Percentage of amplification in the HER2A vs. non-HER2A tumors, Fisherâ s exact FDR p value, and gene annotation are shown. Genes in the core or broad HER2 amplicon are listed, and known cancer genes as reported previously [44, 45] are highlighted. (XLSX 104 kb)
DOI: 10.6084/m9.figshare.5840181
title: Additional file 6: Table S6. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Detailed statistical analysis results. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.5840181.v1
title: Additional file 6: Table S6. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Detailed statistical analysis results. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.5840160
title: Additional file 5: Table S5. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on pirimiphos-methyl sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5840160.v1
title: Additional file 5: Table S5. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on pirimiphos-methyl sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5840157
title: Additional file 3: of Built environmental characteristics and diabetes: a systematic review and meta-analysis

description: Sensitivity analyses (ZIP 120 kb)
DOI: 10.6084/m9.figshare.5840157.v1
title: Additional file 3: of Built environmental characteristics and diabetes: a systematic review and meta-analysis

description: Sensitivity analyses (ZIP 120 kb)
DOI: 10.6084/m9.figshare.5840142
title: Additional file 4: Table S4. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on bendiocarb sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.5840142.v1
title: Additional file 4: Table S4. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on bendiocarb sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.5840115
title: Additional file 3: Table S3. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on deltamethrin sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.5840115.v1
title: Additional file 3: Table S3. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis and wild Anopheles gambiae (s.l.) after WHO standard cone bioassay tests on deltamethrin sprayed surfaces by country, mosquito source and surface type, 2010â 2015. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.5840109
title: Additional file 2: of Laquinimod attenuates inflammation by modulating macrophage functions in traumatic brain injury mouse model

description: Gene dataâ TBI and laquinimod. Sheet 1: nCounter CodeSet Design. Sheet 2: MG468 Isoform Coverage. Sheet 3: MG468 Annotated genes. Sheet 4: Normalized data. Sheet 5: List of all detected genes. (XLSX 953Â kb)
DOI: 10.6084/m9.figshare.5840109.v1
title: Additional file 2: of Laquinimod attenuates inflammation by modulating macrophage functions in traumatic brain injury mouse model

description: Gene dataâ TBI and laquinimod. Sheet 1: nCounter CodeSet Design. Sheet 2: MG468 Isoform Coverage. Sheet 3: MG468 Annotated genes. Sheet 4: Normalized data. Sheet 5: List of all detected genes. (XLSX 953Â kb)
DOI: 10.6084/m9.figshare.5840100
title: Additional file 2: Table S2. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis after WHO standard cone bioassay tests on alpha-cypermethrin sprayed surfaces by country and surface type, 2008â 2012. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.5840100.v1
title: Additional file 2: Table S2. of Multi-country assessment of residual bio-efficacy of insecticides used for indoor residual spraying in malaria control on different surface types: results from program monitoring in 17 PMI/USAID-supported IRS countries

description: Summary of monthly number exposed and percent mortality of insectary reared susceptible colony of Anopheles gambiae and Anopheles arabiensis after WHO standard cone bioassay tests on alpha-cypermethrin sprayed surfaces by country and surface type, 2008â 2012. (XLSX 48 kb)