cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7861280.v1
title: Additional file 4: of MGSEA – a multivariate Gene set enrichment analysis

description: Table S1. Number of significantly enriched gene sets using top 100 genes from each feature score. The table shows the number of significantly enriched gene sets by querying top 100 genes from each feature score. A gene set is significantly enriched if the p-value of the Fisher’s exact test &lt;0.05. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7861286.v1
title: Additional file 5: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S2. Parameters settings for analysis presented in this study. The table shows the parameters used for MGSEA and REVIGO in the analysis. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.7861256
title: Additional file 20: of MGSEA â a multivariate Gene set enrichment analysis

description: Supplementary File S1. The R source codes of the MGSEA program, a toy example dataset, and a brief explanation for running the program. (ZIP 1832 kb)
DOI: 10.6084/m9.figshare.7861244
title: Additional file 19: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S15. Number of significant gene set overlap between TCGA GBM and REMBRANDT data and their combinatorial patterns. The table shows the number and combinatorial pattern of significantly enriched gene set overlap between TCGA GBM and REMBRANDT data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861256.v1
title: Additional file 20: of MGSEA â a multivariate Gene set enrichment analysis

description: Supplementary File S1. The R source codes of the MGSEA program, a toy example dataset, and a brief explanation for running the program. (ZIP 1832 kb)
DOI: 10.6084/m9.figshare.7861235
title: Additional file 18: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S14. Identities of significant gene set overlap between TCGA GBM and REMBRANDT data. The table shows the list of significantly enriched gene set overlap between TCGA GBM and REMBRANDT data. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7861235.v1
title: Additional file 18: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S14. Identities of significant gene set overlap between TCGA GBM and REMBRANDT data. The table shows the list of significantly enriched gene set overlap between TCGA GBM and REMBRANDT data. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7861244.v1
title: Additional file 19: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S15. Number of significant gene set overlap between TCGA GBM and REMBRANDT data and their combinatorial patterns. The table shows the number and combinatorial pattern of significantly enriched gene set overlap between TCGA GBM and REMBRANDT data. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861217
title: Additional file 16: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S12. Dominant and redundant features of enrichment in 381 functional classes of REMBRANDT data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for REMBRANDT data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7861226
title: Additional file 17: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S13. Dominant and redundant features of enrichment in 161 reduced functional classes of REMBRANDT data. The table shows the reduced list of significantly enriched gene sets and their combinatorial relations for REMBRANDT data. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7861226.v1
title: Additional file 17: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S13. Dominant and redundant features of enrichment in 161 reduced functional classes of REMBRANDT data. The table shows the reduced list of significantly enriched gene sets and their combinatorial relations for REMBRANDT data. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7861211
title: Additional file 15: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S11. Number of significant gene set overlap between TCGA breast cancer and METABRIC data and their combinatorial patterns. The table shows the number and combinatorial pattern of significantly enriched gene set overlap between TCGA breast cancer and METABRIC data. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7861217.v1
title: Additional file 16: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S12. Dominant and redundant features of enrichment in 381 functional classes of REMBRANDT data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for REMBRANDT data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7861205
title: Additional file 14: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S10. Identities of significant gene set overlap between TCGA breast cancer and METABRIC data. The table shows the full list of significantly enriched gene set overlap between TCGA breast cancer and METABRIC data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7861193
title: Additional file 12: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S8. Dominant and redundant features of enrichment in 278 functional classes of METABRIC data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for METABRIC data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7861196
title: Additional file 13: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S9. Dominant and redundant features of enrichment in 143 reduced functional classes of METABRIC data. The table shows the reduced list of significantly enriched gene sets and their combinatorial relations for METABRIC data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7861199
title: Additional file 1: of Clinical impact of a cytological screening system using cyclin D1 immunostaining and genomic analysis for the diagnosis of thyroid nodules

description: Table S1. First round PCR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861205.v1
title: Additional file 14: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S10. Identities of significant gene set overlap between TCGA breast cancer and METABRIC data. The table shows the full list of significantly enriched gene set overlap between TCGA breast cancer and METABRIC data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7861211.v1
title: Additional file 15: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S11. Number of significant gene set overlap between TCGA breast cancer and METABRIC data and their combinatorial patterns. The table shows the number and combinatorial pattern of significantly enriched gene set overlap between TCGA breast cancer and METABRIC data. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7861190
title: Additional file 11: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S7. Subtype-specific CNV and their values in TCGA and external dataset. The table show the previously reported subtype-specific CNV and their values (mean and standard deviation) for (A) breast cancer and (B) GBM TCGA and external dataset. The values were CDFs (ranged from 0 to 1) for TCGA data, log2 of estimated copy numbers (centered at 0) for METABRIC, and estimated copy numbers (centered at 2) for REMBRANDT, respectively. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861193.v1
title: Additional file 12: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S8. Dominant and redundant features of enrichment in 278 functional classes of METABRIC data. The table shows the full list of significantly enriched gene sets and their combinatorial relations for METABRIC data. The reduced functional category for each gene set is also reported. An NA entry denotes that the gene set and its reduced functional category are identical. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7861196.v1
title: Additional file 13: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S9. Dominant and redundant features of enrichment in 143 reduced functional classes of METABRIC data. The table shows the reduced list of significantly enriched gene sets and their combinatorial relations for METABRIC data. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7861199.v1
title: Additional file 1: of Clinical impact of a cytological screening system using cyclin D1 immunostaining and genomic analysis for the diagnosis of thyroid nodules

description: Table S1. First round PCR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861181
title: Additional file 2: of Assessment of the use and need for an integrated molecular surveillance of tuberculosis: an online survey in Germany

description: Qualitative answers to the survey between different groups of PHOs. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7861190.v1
title: Additional file 11: of MGSEA â a multivariate Gene set enrichment analysis

description: Table S7. Subtype-specific CNV and their values in TCGA and external dataset. The table show the previously reported subtype-specific CNV and their values (mean and standard deviation) for (A) breast cancer and (B) GBM TCGA and external dataset. The values were CDFs (ranged from 0 to 1) for TCGA data, log2 of estimated copy numbers (centered at 0) for METABRIC, and estimated copy numbers (centered at 2) for REMBRANDT, respectively. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7861181.v1
title: Additional file 2: of Assessment of the use and need for an integrated molecular surveillance of tuberculosis: an online survey in Germany

description: Qualitative answers to the survey between different groups of PHOs. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7861118
title: Additional file 2: of GMASS: a novel measure for genome assembly structural similarity

description: Table S1. Statistics of a reference assembly and 11 descendant assemblies, as well as CSBs constructed between them. AS denotes the scaffolds contained each assembly, and SF represents the CSBs constructed between each assembly and the reference assembly. Table S2. Statistics of analyzed assemblies and reference sequences. In the case of the GAGE dataset, the statistics of the reference sequences were calculated using the human chromosome 14 (HG38/GRCh38 assembly) downloaded from the UCSC genome browser [30]. In the case of the Assemblathon 1 dataset, the teams’ names constructed each assembly are written in parentheses, and the statistics of reference are the averages of statistics of two haplotypes used in the study. Table S3. Li(A1, A2), Ci(A1, A2) and Si scores of assembly pairs obtained from the GAGE dataset in different resolutions. In the “Combination” column, the name of an assembly used as reference appears first. Table S4. Statistics of each assembly and CSBs of assembly pairs obtained from the GAGE dataset. AS denotes the scaffolds in each assembly, and SF represents the CSBs constructed between each assembly pair. In combination column, front assembly is used as reference assembly and rear assembly is used as target assembly. Table S5. Li(A1, A2), Ci(A1, A2) and Si scores of assembly pairs obtained from the Assemblathon 1 dataset in different resolutions. In the “Combination” column, the name of an assembly used as reference appears first. Table S6. Statistics of each assembly and CSBs of assembly pairs obtained from the Assemblathon1 dataset. AS denotes the scaffolds in each assembly, and SF represents the CSBs constructed between each assembly pair. In combination column, front assembly is used as reference assembly and rear assembly is used as target assembly. Used assemblers are omitted. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.7861118.v1
title: Additional file 2: of GMASS: a novel measure for genome assembly structural similarity

description: Table S1. Statistics of a reference assembly and 11 descendant assemblies, as well as CSBs constructed between them. AS denotes the scaffolds contained each assembly, and SF represents the CSBs constructed between each assembly and the reference assembly. Table S2. Statistics of analyzed assemblies and reference sequences. In the case of the GAGE dataset, the statistics of the reference sequences were calculated using the human chromosome 14 (HG38/GRCh38 assembly) downloaded from the UCSC genome browser [30]. In the case of the Assemblathon 1 dataset, the teams’ names constructed each assembly are written in parentheses, and the statistics of reference are the averages of statistics of two haplotypes used in the study. Table S3. Li(A1, A2), Ci(A1, A2) and Si scores of assembly pairs obtained from the GAGE dataset in different resolutions. In the “Combination” column, the name of an assembly used as reference appears first. Table S4. Statistics of each assembly and CSBs of assembly pairs obtained from the GAGE dataset. AS denotes the scaffolds in each assembly, and SF represents the CSBs constructed between each assembly pair. In combination column, front assembly is used as reference assembly and rear assembly is used as target assembly. Table S5. Li(A1, A2), Ci(A1, A2) and Si scores of assembly pairs obtained from the Assemblathon 1 dataset in different resolutions. In the “Combination” column, the name of an assembly used as reference appears first. Table S6. Statistics of each assembly and CSBs of assembly pairs obtained from the Assemblathon1 dataset. AS denotes the scaffolds in each assembly, and SF represents the CSBs constructed between each assembly pair. In combination column, front assembly is used as reference assembly and rear assembly is used as target assembly. Used assemblers are omitted. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.7861019
title: Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of <i>Bacillus licheniformis</i> using RNA-Seq

description: RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of <i>B. licheniformis</i> isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.
DOI: 10.6084/m9.figshare.7861019.v1
title: Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of <i>Bacillus licheniformis</i> using RNA-Seq

description: RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of <i>B. licheniformis</i> isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.
DOI: 10.6084/m9.figshare.7860956
title: Antarctic_Shipwrecks.csv

description: The dataset represents a complete collection of know shipwrecks, lost vessels and/or debilitating incidents located in the Antarctic region (between -60 and -80 latitude) between the years 1578 to 2016. The dataset maintains information on the vessel name, year of incident, location of incident, coordinates, country of registration, purpose of expedition, and, when available, the cause of the incident. A large portion of this dataset was originally collected and organized by The Australian Antarctic Data Centre (AADC) and was modified by the author in March, 2019. The main purpose of this dataset is to provide new insight, or at least new tools for viewing the history of Antarctic exploration through the lens of shipwreck data. <br>
DOI: 10.6084/m9.figshare.7860989.v1
title: Suppl Table 1.docx

description: Supplemental Table 1 of paper titled "Attenuated Dentin Matrix Protein 1 Enhance Fibroblast Growth Factor 23 in Carvaria in Primary Hyperparathyroidism Model"<br>
DOI: 10.6084/m9.figshare.7860836
title: Testing Statebuilding’s ‘Missing Link’: Effects of Government Communications in Colombia

description: Research from developed countries indicates that improving how government communicates with the public can increase trust in government and satisfaction with public services. In countries affected by violent conflict, communication has even been described as the ‘missing link’ necessary to rebuild a positive relationship between citizen and state. Does this approach work? This paper presents a field experiment implemented in partnership with a Colombian government agency, to test two communication interventions in statebuilding areas. The results suggest limits to these programmes. One treatment – provision of information on service delivery via text messages – led to a reduction in satisfaction with services. For the second treatment – an invitation for citizens to vote on service provision priorities – we can detect no effect. We find evidence that people’s prior beliefs are strong drivers of these results: both treatments had negative effects among people with low political interest and knowledge, suggesting that informational interventions may backfire among precisely the sub-populations that statebuilders seek to engage. Instead of improving perceptions of service delivery, they may have raised expectations among this otherwise apathetic population.
DOI: 10.6084/m9.figshare.7860941
title: Fluorescence microscopy of piezo1 in droplet hydrogel bilayers

description: Mechanosensitive ion channels are membrane gated pores which are activated by mechanical stimuli. The focus of this study is on Piezo1, a newly discovered, large, mammalian, mechanosensitive ion channel, which has been linked to diseases such as dehydrated hereditary stomatocytosis (<i>Xerocytosis</i>) and lymphatic dysplasia. Here we utilize an established <i>in-vitro</i> artificial bilayer system to interrogate single Piezo1 channel activity. The droplet-hydrogel bilayer (DHB) system uniquely allows the simultaneous recording of electrical activity and fluorescence imaging of labelled protein. We successfully reconstituted fluorescently labelled Piezo1 ion channels in DHBs and verified activity using electrophysiology in the same system. We demonstrate successful insertion and activation of hPiezo1-GFP in bilayers of varying composition. Furthermore, we compare the Piezo1 bilayer reconstitution with measurements of insertion and activation of KcsA channels to reproduce the channel conductances reported in the literature. Together, our results showcase the use of DHBs for future experiments allowing simultaneous measurements of ion channel gating while visualising the channel proteins using fluorescence.
DOI: 10.6084/m9.figshare.7860836.v2
title: Testing Statebuilding’s ‘Missing Link’: Effects of Government Communications in Colombia

description: Research from developed countries indicates that improving how government communicates with the public can increase trust in government and satisfaction with public services. In countries affected by violent conflict, communication has even been described as the ‘missing link’ necessary to rebuild a positive relationship between citizen and state. Does this approach work? This paper presents a field experiment implemented in partnership with a Colombian government agency, to test two communication interventions in statebuilding areas. The results suggest limits to these programmes. One treatment – provision of information on service delivery via text messages – led to a reduction in satisfaction with services. For the second treatment – an invitation for citizens to vote on service provision priorities – we can detect no effect. We find evidence that people’s prior beliefs are strong drivers of these results: both treatments had negative effects among people with low political interest and knowledge, suggesting that informational interventions may backfire among precisely the sub-populations that statebuilders seek to engage. Instead of improving perceptions of service delivery, they may have raised expectations among this otherwise apathetic population.
DOI: 10.6084/m9.figshare.7860941.v1
title: Fluorescence microscopy of piezo1 in droplet hydrogel bilayers

description: Mechanosensitive ion channels are membrane gated pores which are activated by mechanical stimuli. The focus of this study is on Piezo1, a newly discovered, large, mammalian, mechanosensitive ion channel, which has been linked to diseases such as dehydrated hereditary stomatocytosis (<i>Xerocytosis</i>) and lymphatic dysplasia. Here we utilize an established <i>in-vitro</i> artificial bilayer system to interrogate single Piezo1 channel activity. The droplet-hydrogel bilayer (DHB) system uniquely allows the simultaneous recording of electrical activity and fluorescence imaging of labelled protein. We successfully reconstituted fluorescently labelled Piezo1 ion channels in DHBs and verified activity using electrophysiology in the same system. We demonstrate successful insertion and activation of hPiezo1-GFP in bilayers of varying composition. Furthermore, we compare the Piezo1 bilayer reconstitution with measurements of insertion and activation of KcsA channels to reproduce the channel conductances reported in the literature. Together, our results showcase the use of DHBs for future experiments allowing simultaneous measurements of ion channel gating while visualising the channel proteins using fluorescence.
DOI: 10.6084/m9.figshare.7860164
title: macosko_dropseq_control.h5ad

description: Negative control data for Drop-seq
DOI: 10.6084/m9.figshare.7860095
title: klein_indrops_control_GSM1599501.h5ad

description: InDrops negative control data
DOI: 10.6084/m9.figshare.7860164.v1
title: macosko_dropseq_control.h5ad

description: Negative control data for Drop-seq
DOI: 10.6084/m9.figshare.7860086
title: zheng_gemcode_control.h5ad

description: GemCode negative control data
DOI: 10.6084/m9.figshare.7860092
title: svensson_chromium_control.h5ad

description: Chromium negative control data
DOI: 10.6084/m9.figshare.7860095.v1
title: klein_indrops_control_GSM1599501.h5ad

description: InDrops negative control data
DOI: 10.6084/m9.figshare.7860080
title: 190319Test

description: 190319Test
DOI: 10.6084/m9.figshare.7860086.v1
title: zheng_gemcode_control.h5ad

description: GemCode negative control data
DOI: 10.6084/m9.figshare.7860080.v1
title: 190319Test

description: 190319Test
DOI: 10.6084/m9.figshare.7860071
title: Example damage function.xlsx

description: This is an example of implementation of the damage function proposed by Estrada F, Tol RSJ and Botzen WJW in EXTENDING INTEGRATED ASSESSMENT MODELS' DAMAGE FUNCTIONS TO INCLUDE ADAPTATION AND DYNAMIC SENSITIVITY.