cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8857763
title: Additional file 2 of Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimerâ s disease

description: Supplemental table. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8857763.v1
title: Additional file 2 of Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimerâ s disease

description: Supplemental table. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8857745
title: Additional file 1: of Tumor regression mediated by oncogene withdrawal or erlotinib stimulates infiltration of inflammatory immune cells in EGFR mutant lung tumors

description: Figure S1. MRI images, histology and representative flow cytometry plots of normal or tumor-bearing lungs before and after erlotinib. (A) Coronal images of CCSPrtTA; TetO-EGFRL858R mouse lungs before (left panel) and after (right panel) treatment with erlotinib. (B) Hematoxylin and eosin (H&E) stain of lungs from control (normal) and tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks. Bar: 50 μm. Absolute number of (C) CD4 and (D) CD8 T cells normalized to weight of lungs of control (normal) and tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks. Representative FACS plot showing percentage of (E) FoxP3+ and FoxP3- CD4+ T cells (F) PD1+ FoxP3+ T cells. (G) Immunofluorescence (IF) stain of lung epithelial cells (green), CD3 T cells (red) and FoxP3 Tregs (Cyan). Nuclei were counterstained with Dapi (blue) (H) Quantification of FoxP3+ CD3 T cells in lung tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks stained by IF. Data are shown as mean ± SD and * is P
DOI: 10.6084/m9.figshare.8857745.v1
title: Additional file 1: of Tumor regression mediated by oncogene withdrawal or erlotinib stimulates infiltration of inflammatory immune cells in EGFR mutant lung tumors

description: Figure S1. MRI images, histology and representative flow cytometry plots of normal or tumor-bearing lungs before and after erlotinib. (A) Coronal images of CCSPrtTA; TetO-EGFRL858R mouse lungs before (left panel) and after (right panel) treatment with erlotinib. (B) Hematoxylin and eosin (H&E) stain of lungs from control (normal) and tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks. Bar: 50 μm. Absolute number of (C) CD4 and (D) CD8 T cells normalized to weight of lungs of control (normal) and tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks. Representative FACS plot showing percentage of (E) FoxP3+ and FoxP3- CD4+ T cells (F) PD1+ FoxP3+ T cells. (G) Immunofluorescence (IF) stain of lung epithelial cells (green), CD3 T cells (red) and FoxP3 Tregs (Cyan). Nuclei were counterstained with Dapi (blue) (H) Quantification of FoxP3+ CD3 T cells in lung tumor bearing CCSP-rtTA; TetO-EGFRL858R mice in the absence (−) and presence (+) of erlotinib for 2 weeks stained by IF. Data are shown as mean ± SD and * is P
DOI: 10.6084/m9.figshare.8857691
title: Additional file 2: of The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback

description: Tables associated with RegulonDB analysis. The tabs of the excel file include M_total, M_TF, M_targets, FF_FB combined, and List of FB loops. (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.8857691.v1
title: Additional file 2: of The engineering principles of combining a transcriptional incoherent feedforward loop with negative feedback

description: Tables associated with RegulonDB analysis. The tabs of the excel file include M_total, M_TF, M_targets, FF_FB combined, and List of FB loops. (XLSX 2199 kb)
DOI: 10.6084/m9.figshare.8857673
title: Additional file 1: of ErbB4 promotes malignant peripheral nerve sheath tumor pathogenesis via Ras-independent mechanisms

description: Figure S1. ErbB4 lysates are sensitive to denaturing detergents. Table S1. Patient demographics for immunostained MPNSTs. Figure S2 Real-time PCR analyses of erbB4 splice variants and mouse MPNST erbB4 expression. Table S2. MPNST locations in P0-GGFÎ˛3;Trp53+/â ;Erbb4flox/flox mice. Figure S3. Validation of Erbb4 ablation and effects on expression of other erbB receptors. Figure S4. Kinase array blots for NRG1Î˛ and unstimulated control and Erbb4-null MPNST cells. Figure S5. Downregulation of WNK1 expression did not affect cell viability. (ZIP 7528 kb)
DOI: 10.6084/m9.figshare.8857673.v1
title: Additional file 1: of ErbB4 promotes malignant peripheral nerve sheath tumor pathogenesis via Ras-independent mechanisms

description: Figure S1. ErbB4 lysates are sensitive to denaturing detergents. Table S1. Patient demographics for immunostained MPNSTs. Figure S2 Real-time PCR analyses of erbB4 splice variants and mouse MPNST erbB4 expression. Table S2. MPNST locations in P0-GGFÎ˛3;Trp53+/â ;Erbb4flox/flox mice. Figure S3. Validation of Erbb4 ablation and effects on expression of other erbB receptors. Figure S4. Kinase array blots for NRG1Î˛ and unstimulated control and Erbb4-null MPNST cells. Figure S5. Downregulation of WNK1 expression did not affect cell viability. (ZIP 7528 kb)
DOI: 10.6084/m9.figshare.8857652
title: Additional file 1: of Prevalence and sociodemographic correlates of common mental disorders among first-year university students in post-apartheid South Africa: implications for a public mental health approach to student wellness

description: Table S1. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for internalising disorder by number of risk factors among first year university students in South Africa (n = 1402). Table S2. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for bipolar disorder by number of risk factors among first year university students in South Africa (n = 1402). Table S3. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for externalising disorder by number of risk factors among first year university students in South Africa (n = 1402). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8857655
title: Additional file 1: of Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014â 2016)

description: Table S1. Sheet 1 â mutations in drug resistance associated genes/loci among MDR M. tuberculosis isolates from Uganda, Somalia and eSwatini that were resistant to any of: Ofloxacin, levofloxacin, moxifloxacin, kanamycin, capreomycin, amikacin; Sheet 2 â primers and sequences used. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8857652.v1
title: Additional file 1: of Prevalence and sociodemographic correlates of common mental disorders among first-year university students in post-apartheid South Africa: implications for a public mental health approach to student wellness

description: Table S1. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for internalising disorder by number of risk factors among first year university students in South Africa (n = 1402). Table S2. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for bipolar disorder by number of risk factors among first year university students in South Africa (n = 1402). Table S3. Prevalence rates and predictors of lifetime, 12-month and 12-month prevalence among lifetime cases for externalising disorder by number of risk factors among first year university students in South Africa (n = 1402). (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8857655.v1
title: Additional file 1: of Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014â 2016)

description: Table S1. Sheet 1 â mutations in drug resistance associated genes/loci among MDR M. tuberculosis isolates from Uganda, Somalia and eSwatini that were resistant to any of: Ofloxacin, levofloxacin, moxifloxacin, kanamycin, capreomycin, amikacin; Sheet 2 â primers and sequences used. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8857637
title: Additional file 9: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The genomic distribution of the uniquely DEGs with over 64 fold change in InVir . (XLS 322 kb)
DOI: 10.6084/m9.figshare.8857634
title: Additional file 8: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Uniquely up- and down-regulated DEGs in high virulent strain InVir at 24 and 120â hai, respectively. (XLS 352 kb)
DOI: 10.6084/m9.figshare.8857628
title: Additional file 7: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The genomic distribution of the overlapping DEGs with over 64 fold change in the two strains. (XLS 205 kb)
DOI: 10.6084/m9.figshare.8857634.v1
title: Additional file 8: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Uniquely up- and down-regulated DEGs in high virulent strain InVir at 24 and 120â hai, respectively. (XLS 352 kb)
DOI: 10.6084/m9.figshare.8857637.v1
title: Additional file 9: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The genomic distribution of the uniquely DEGs with over 64 fold change in InVir . (XLS 322 kb)
DOI: 10.6084/m9.figshare.8857622
title: Additional file 6: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Highly overlapping up- and down-regulated DEGs in both strains. (XLS 306 kb)
DOI: 10.6084/m9.figshare.8857628.v1
title: Additional file 7: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The genomic distribution of the overlapping DEGs with over 64 fold change in the two strains. (XLS 205 kb)
DOI: 10.6084/m9.figshare.8857619
title: Additional file 5: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: All DEGs of the two strains in Planta compared to vegetative growth. (XLSX 944 kb)
DOI: 10.6084/m9.figshare.8857613
title: Additional file 4: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: KEGG analysis of the transcriptome of Foc in vitro samples. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8857622.v1
title: Additional file 6: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Highly overlapping up- and down-regulated DEGs in both strains. (XLS 306 kb)
DOI: 10.6084/m9.figshare.8857610
title: Additional file 3: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The GO annotation of the unigenes of Foc in vitro samples. (EMF 2373 kb)
DOI: 10.6084/m9.figshare.8857613.v1
title: Additional file 4: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: KEGG analysis of the transcriptome of Foc in vitro samples. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.8857619.v1
title: Additional file 5: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: All DEGs of the two strains in Planta compared to vegetative growth. (XLSX 944 kb)
DOI: 10.6084/m9.figshare.8857610.v1
title: Additional file 3: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: The GO annotation of the unigenes of Foc in vitro samples. (EMF 2373 kb)
DOI: 10.6084/m9.figshare.8857589
title: MOESM1 of Characterisation of a niche-specific excretoryâ secretory peroxiredoxin from the parasitic nematode Teladorsagia circumcincta

description: Additional file 1: Table S1. Primers for QPCR and Tci-Prx-1 gene expression construct.
DOI: 10.6084/m9.figshare.8857595
title: Additional file 2: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Transcriptome completeness of transcripts quantified through 290 universal single-copy orthologs using BUSCO. (EMF 79049 kb)
DOI: 10.6084/m9.figshare.8857592
title: Additional file 1: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Statistics of the assembly quality of the transcriptome of Foc in vitro samples. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8857589.v1
title: MOESM1 of Characterisation of a niche-specific excretoryâ secretory peroxiredoxin from the parasitic nematode Teladorsagia circumcincta

description: Additional file 1: Table S1. Primers for QPCR and Tci-Prx-1 gene expression construct.
DOI: 10.6084/m9.figshare.8857595.v1
title: Additional file 2: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Transcriptome completeness of transcripts quantified through 290 universal single-copy orthologs using BUSCO. (EMF 79049 kb)
DOI: 10.6084/m9.figshare.8857583
title: Additional file 11: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Genes of two co-expression modules in InVir. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8857592.v1
title: Additional file 1: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Statistics of the assembly quality of the transcriptome of Foc in vitro samples. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8857577
title: Additional file 10: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: DEGs annotated with transposition function. (XLS 38 kb)
DOI: 10.6084/m9.figshare.8857577.v1
title: Additional file 10: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: DEGs annotated with transposition function. (XLS 38 kb)
DOI: 10.6084/m9.figshare.8857583.v1
title: Additional file 11: of Transcriptome analysis of virulence-differentiated Fusarium oxysporum f. sp. cucumerinum isolates during cucumber colonisation reveals pathogenicity profiles

description: Genes of two co-expression modules in InVir. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.8857490
title: Differential determinants of virulence in two <i>Mycobacterium tuberculosis</i> Colombian clinical isolates of the LAM09 family

description: The heterogeneity of the clinical outcome of <i>Mycobacterium tuberculosis</i> (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.
DOI: 10.6084/m9.figshare.8857490.v1
title: Differential determinants of virulence in two <i>Mycobacterium tuberculosis</i> Colombian clinical isolates of the LAM09 family

description: The heterogeneity of the clinical outcome of <i>Mycobacterium tuberculosis</i> (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.
DOI: 10.6084/m9.figshare.8857490.v3
title: Differential determinants of virulence in two <i>Mycobacterium tuberculosis</i> Colombian clinical isolates of the LAM09 family

description: The heterogeneity of the clinical outcome of <i>Mycobacterium tuberculosis</i> (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.
DOI: 10.6084/m9.figshare.8857490.v2
title: Differential determinants of virulence in two <i>Mycobacterium tuberculosis</i> Colombian clinical isolates of the LAM09 family

description: The heterogeneity of the clinical outcome of <i>Mycobacterium tuberculosis</i> (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.
DOI: 10.6084/m9.figshare.8857436
title: Additional file 6: of Paired-end mappability of transposable elements in the human genome

description: Table S2. Ancient TE families with unusually low mappability and accompanying segmental duplications. This table enumerates a number of ancient TE families which have unusually low mappability scores. Though some of these scores can be accounted for by recent segmental duplications, there still remains a substantial portion of older elements with low mappability scores that could be furthered explored. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.8857430
title: Additional file 5: of Paired-end mappability of transposable elements in the human genome

description: Table S1. TE class and family mappability scores. Percent of elements in each TE class and family with completely unique mappability scores based on Bowtie alignment of 76â bp simulated reads allowing for 3 mismatches. (XLSX 8 kb)