cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13269722.v1
title: Exploring the industrial potential of Lactobacillus delbrueckii subsp. bulgaricus by population genomics and genome-wide association study (GWAS) analysis

description: <i>Lactobacillus</i> <i>delbrueckii</i> subsp. <i>bulgaricus</i> (<i>L. delbrueckii</i> subsp.<i> bulgaricus</i>) is one of the most commonly used starter-cultures for yoghurt production. However, how its genetic background affects the acid production capacity is unclear. This study investigated the industrial potential of <i>L. delbrueckii</i> subsp.<i> bulgaricus</i> by population genomics and genome-wide association study (GWAS) analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced <i>L. delbrueckii</i> subsp.<i> bulgaricus</i> strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation result with sucrose fortified reconstituted skimmed milk revealed significant association between the L-lactate dehydrogenase (<i>lld</i>D; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of <i>L. delbrueckii</i> subsp.<i> bulgaricus </i>by identifying potential targets for further research, development, and utilization of lactic acid bacteria in the dairy industry.
DOI: 10.6084/m9.figshare.13269731
title: Mapping of author institution keywords - discipline

description: mapping of author institution keywords - discipline
DOI: 10.6084/m9.figshare.13269731.v1
title: Mapping of author institution keywords - discipline

description: mapping of author institution keywords - discipline
DOI: 10.5281/zenodo.4283076
title: Meta-Analysis of the transcriptomic profile of human placenta

description: The establishment of a complex multi-scale model of biological tissue is of great significance for the study of related diseases, and the integration of relevant quantitative data is the premise to achieve this goal. Whereas, the systematic collation of data sets related to placental tissue is relatively lacking. In this study, 18 published transcriptomes (a total of 425 samples) datasets of human pregnancy-related tissues (including chorionic villus and decidua, term placenta, endometrium, in vitro cell lines, etc.) from public databases were collected and analyzed. We compared the most widely used dimensionality reduction (DR) methods to generate a 2D-map for visualization of these data. We also compared the effects of different parameter settings and commonly used manifold learning methods on the results. The result indicates that the nonlinear method can better preserve the small differences between different subtypes of placental tissue than the linear method. It led the foundation for the study on accurate computational modeling of placental tissue development in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.
DOI: 10.5281/zenodo.3550751
title: Meta-Analysis of the transcriptomic profile of human placenta

description: The establishment of a complex multi-scale model of biological tissue is of great significance for the study of related diseases, and the integration of relevant quantitative data is the premise to achieve this goal. Whereas, the systematic collation of data sets related to placental tissue is relatively lacking. In this study, 18 published transcriptomes (a total of 425 samples) datasets of human pregnancy-related tissues (including chorionic villus and decidua, term placenta, endometrium, in vitro cell lines, etc.) from public databases were collected and analyzed. We compared the most widely used dimensionality reduction (DR) methods to generate a 2D-map for visualization of these data. We also compared the effects of different parameter settings and commonly used manifold learning methods on the results. The result indicates that the nonlinear method can better preserve the small differences between different subtypes of placental tissue than the linear method. It led the foundation for the study on accurate computational modeling of placental tissue development in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.
DOI: 10.6084/m9.figshare.7392224
title: Stakeholder - Learning Design

description: This dataset 'Stakeholder - Learning Design’ is a component of a Doctor of Philosophy conducted by candidate Alexander Hayes (3919493) titled 'The Socioethical Implications of Body Worn Computers: An Ethnographic Study'. This research was conducted in the Faculty of Engineering and Information Systems, School of Computing and Information Technology (SCIT) at the University of Wollongong with research strength Innovation in Business & Social Research under Principal Supervisor Professor Katina Michael (University of Wollongong) and Associate Supervisor Dr Teemu Leinonen (Aalto University Finland). This thesis explores the socio-ethical implications of body worn computers (BWC) using an ethnographic approach. Furthermore, a subset, body worn cameras (BWCs), combines data with value added constancy through Location Based Services (LBS) over wireless network connections. The aim of this investigation was to engage global leaders from trans-disciplinary stakeholder groups in semi-structured interviews, conversations and events, situating a review of the social impact and ethical implications of BWCs. A critical discourse analysis using a Foucauldian approach reveals power relations, which are then infused through narrative with unique intercultural perspectives, differentiating ‘location’ from ‘place’. The author of this study has subsequently identified through Grounded Theory that BWCs are causal agencies for disconnect from proper culture which can be addressed through the application of Ngikalikarra, a unique framework for empathetic understanding of place and community engagement. The full thesis can be accessed at https://ro.uow.edu.au/theses1/853
DOI: 10.6084/m9.figshare.7392218
title: Stakeholder - Human Computer Interaction

description: This dataset 'Stakeholder - Human Computer Interaction’ is a component of a Doctor of Philosophy conducted by candidate Alexander Hayes (3919493) titled 'The Socioethical Implications of Body Worn Computers: An Ethnographic Study'. This research was conducted in the Faculty of Engineering and Information Systems, School of Computing and Information Technology (SCIT) at the University of Wollongong with research strength Innovation in Business & Social Research under Principal Supervisor Professor Katina Michael (University of Wollongong) and Associate Supervisor Dr Teemu Leinonen (Aalto University Finland). This thesis explores the socio-ethical implications of body worn computers (BWC) using an ethnographic approach. Furthermore, a subset, body worn cameras (BWCs), combines data with value added constancy through Location Based Services (LBS) over wireless network connections. The aim of this investigation was to engage global leaders from trans-disciplinary stakeholder groups in semi-structured interviews, conversations and events, situating a review of the social impact and ethical implications of BWCs. A critical discourse analysis using a Foucauldian approach reveals power relations, which are then infused through narrative with unique intercultural perspectives, differentiating ‘location’ from ‘place’. The author of this study has subsequently identified through Grounded Theory that BWCs are causal agencies for disconnect from proper culture which can be addressed through the application of Ngikalikarra, a unique framework for empathetic understanding of place and community engagement. The full thesis can be accessed at https://ro.uow.edu.au/theses1/853
DOI: 10.6084/m9.figshare.7392218.v1
title: Stakeholder - Human Computer Interaction

description: This dataset 'Stakeholder - Human Computer Interaction’ is a component of a Doctor of Philosophy conducted by candidate Alexander Hayes (3919493) titled 'The Socioethical Implications of Body Worn Computers: An Ethnographic Study'. This research was conducted in the Faculty of Engineering and Information Systems, School of Computing and Information Technology (SCIT) at the University of Wollongong with research strength Innovation in Business & Social Research under Principal Supervisor Professor Katina Michael (University of Wollongong) and Associate Supervisor Dr Teemu Leinonen (Aalto University Finland). This thesis explores the socio-ethical implications of body worn computers (BWC) using an ethnographic approach. Furthermore, a subset, body worn cameras (BWCs), combines data with value added constancy through Location Based Services (LBS) over wireless network connections. The aim of this investigation was to engage global leaders from trans-disciplinary stakeholder groups in semi-structured interviews, conversations and events, situating a review of the social impact and ethical implications of BWCs. A critical discourse analysis using a Foucauldian approach reveals power relations, which are then infused through narrative with unique intercultural perspectives, differentiating ‘location’ from ‘place’. The author of this study has subsequently identified through Grounded Theory that BWCs are causal agencies for disconnect from proper culture which can be addressed through the application of Ngikalikarra, a unique framework for empathetic understanding of place and community engagement. The full thesis can be accessed at https://ro.uow.edu.au/theses1/853
DOI: 10.6084/m9.figshare.13269737
title: Mapping of Subject category (SC) field - ESI discipline category

description: Mapping of Subject category (SC) field - ESI discipline category
DOI: 10.6084/m9.figshare.13269807
title: Additional file 1 of A 300-kb microduplication of 7q36.3 in a patient with triphalangeal thumb-polysyndactyly syndrome combined with congenital heart disease and optic disc coloboma: a case report

description: Additional file 1. Rare protein-changing genetic variants identified in the proband by whole exome sequencing. The table provides information on missense, nonsense, frameshift and splicing genetic variants with gnomAD exome allele frequency &lt; 0.001. The data on the rare variants include genomic coordinates, “rs” ID, homo-/heterozygosity state, allele frequencies based on gnomAD and Kaviar, gene description and tissue specificity including cardiac and muscle specific expression (GTEx), associated clinical conditions, CADD and other predictors of variant functional effect.
DOI: 10.6084/m9.figshare.13269807.v1
title: Additional file 1 of A 300-kb microduplication of 7q36.3 in a patient with triphalangeal thumb-polysyndactyly syndrome combined with congenital heart disease and optic disc coloboma: a case report

description: Additional file 1. Rare protein-changing genetic variants identified in the proband by whole exome sequencing. The table provides information on missense, nonsense, frameshift and splicing genetic variants with gnomAD exome allele frequency &lt; 0.001. The data on the rare variants include genomic coordinates, “rs” ID, homo-/heterozygosity state, allele frequencies based on gnomAD and Kaviar, gene description and tissue specificity including cardiac and muscle specific expression (GTEx), associated clinical conditions, CADD and other predictors of variant functional effect.
DOI: 10.6084/m9.figshare.13269831
title: Additional file 2 of Gut microbiome signature of Viliuisk encephalomyelitis in Yakuts includes an increase in microbes linked to lean body mass and eating behaviour

description: Additional file 2. Microbial taxa differentially abundant between healthy Yakuts and residents of Moscow..
DOI: 10.6084/m9.figshare.13269831.v1
title: Additional file 2 of Gut microbiome signature of Viliuisk encephalomyelitis in Yakuts includes an increase in microbes linked to lean body mass and eating behaviour

description: Additional file 2. Microbial taxa differentially abundant between healthy Yakuts and residents of Moscow..
DOI: 10.6084/m9.figshare.13269866
title: Additional file 1 of Household presentation of influenza and acute respiratory illnesses to a primary care sentinel network: retrospective database studies (2013–2018)

description: Additional file 1.
DOI: 10.6084/m9.figshare.13269873.v1
title: Additional file 2 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 2: Table S1. Data used in the analysis. Contains data sets used in the analyses and URLs to their repositories and additional metadata and quality controls (flow cytometric analyses, Cellranger quality control summaries).
DOI: 10.6084/m9.figshare.13269876
title: Additional file 3 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 3: Table S2. Supporting information related to clustering of cells. Marker genes for clusters in the analysis of B-lymphoid differentiation are listed with statistical analysis of cluster-specificity.
DOI: 10.6084/m9.figshare.13269866.v1
title: Additional file 1 of Household presentation of influenza and acute respiratory illnesses to a primary care sentinel network: retrospective database studies (2013–2018)

description: Additional file 1.
DOI: 10.6084/m9.figshare.13269873
title: Additional file 2 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 2: Table S1. Data used in the analysis. Contains data sets used in the analyses and URLs to their repositories and additional metadata and quality controls (flow cytometric analyses, Cellranger quality control summaries).
DOI: 10.6084/m9.figshare.13269885
title: Additional file 6 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 6: Table S5. Supporting information related to pathway analysis. Genes from ALL vs. pro-B upregulated clusters or up- and downregulated genes in drug vs. ctrl comparisons (related to Figs. 3 and 5) analyzed using Enrichr. Significant terms summarized from GO, MGI Mammalian Phenotype, BioPlanet Reactome and TF perturbations have a combined score &gt; 150. TF motifs from Genome Browser PWMs are listed with nominal p-value &lt;0.05.
DOI: 10.6084/m9.figshare.13269879
title: Additional file 4 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 4: Table S3. Supporting information related to scDD analysis. Cluster membership is indicated for significant genes from leukemic vs. pro-B comparison (against adult and pediatric BM cells), and from drug vs. ctrl (DMSO) cells in the ETS-inhibition experiments carried out in E/R+ REH cells. Includes statistical summaries for cell state comparisons related to Figs. 2 and 5.
DOI: 10.6084/m9.figshare.13269876.v1
title: Additional file 3 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 3: Table S2. Supporting information related to clustering of cells. Marker genes for clusters in the analysis of B-lymphoid differentiation are listed with statistical analysis of cluster-specificity.
DOI: 10.6084/m9.figshare.13269879.v1
title: Additional file 4 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 4: Table S3. Supporting information related to scDD analysis. Cluster membership is indicated for significant genes from leukemic vs. pro-B comparison (against adult and pediatric BM cells), and from drug vs. ctrl (DMSO) cells in the ETS-inhibition experiments carried out in E/R+ REH cells. Includes statistical summaries for cell state comparisons related to Figs. 2 and 5.
DOI: 10.6084/m9.figshare.13269882
title: Additional file 5 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 5: Table S4. Supporting information related to SCENIC analysis. Summary of regulons discovered in healthy BM B-lineage analysis (related to Fig. 2) and the related validation motif analysis results using pro-B ATAC-seq and regulon target gene analysis for PAX5, EBF1 and BCL11A, including respective ChIP-seq peak data used in validation. Summary of regulons discovered upon including ALL cell states and summary of statistical analysis comparing E/R+ to non-E/R ALL based on bulk RNA-seq (related to Fig. 5).
DOI: 10.6084/m9.figshare.13269885.v1
title: Additional file 6 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 6: Table S5. Supporting information related to pathway analysis. Genes from ALL vs. pro-B upregulated clusters or up- and downregulated genes in drug vs. ctrl comparisons (related to Figs. 3 and 5) analyzed using Enrichr. Significant terms summarized from GO, MGI Mammalian Phenotype, BioPlanet Reactome and TF perturbations have a combined score &gt; 150. TF motifs from Genome Browser PWMs are listed with nominal p-value &lt;0.05.
DOI: 10.6084/m9.figshare.13269882.v1
title: Additional file 5 of Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities

description: Additional file 5: Table S4. Supporting information related to SCENIC analysis. Summary of regulons discovered in healthy BM B-lineage analysis (related to Fig. 2) and the related validation motif analysis results using pro-B ATAC-seq and regulon target gene analysis for PAX5, EBF1 and BCL11A, including respective ChIP-seq peak data used in validation. Summary of regulons discovered upon including ALL cell states and summary of statistical analysis comparing E/R+ to non-E/R ALL based on bulk RNA-seq (related to Fig. 5).
DOI: 10.6084/m9.figshare.13269909
title: Additional file 2 of Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

description: Additional file 2: Tables S1- S7. Table S1. Numbers of MiSeq 16 s rRNA amplicon gene sequenced paired reads per sample for Study 1, both pre and post-quality filtering. Table S2. Numbers of MiSeq 16 s rRNA amplicon gene sequenced paired reads per sample for Study 2, both pre- and post-quality filtering. Table S3. Statistical analysis of bacteriome β-diversity of Study 1 and Study 2 Control and FVT groups using Adonis PERMANOVA (Model formula = antibiotic treatment timepoint + Phage/control status). Table S4. Statistically significant differentially abundant taxa between Study 1 FVT and Control Mice. OTUs that differ from CT00 mice are highlighted in blue. Table S5. Statistically significant differentially abundant taxa between Study 2 FVT and Control Mice. OTUs that differ from CT00 mice are highlighted in blue. Table S6. Observed number of contigs/putative viruses in Study 1 and Study 2 mice. Table S7. Summary of Study 1 and Study 2 sample IDs, meta data and corresponding accession numbers.
DOI: 10.6084/m9.figshare.13269909.v1
title: Additional file 2 of Autochthonous faecal viral transfer (FVT) impacts the murine microbiome after antibiotic perturbation

description: Additional file 2: Tables S1- S7. Table S1. Numbers of MiSeq 16 s rRNA amplicon gene sequenced paired reads per sample for Study 1, both pre and post-quality filtering. Table S2. Numbers of MiSeq 16 s rRNA amplicon gene sequenced paired reads per sample for Study 2, both pre- and post-quality filtering. Table S3. Statistical analysis of bacteriome β-diversity of Study 1 and Study 2 Control and FVT groups using Adonis PERMANOVA (Model formula = antibiotic treatment timepoint + Phage/control status). Table S4. Statistically significant differentially abundant taxa between Study 1 FVT and Control Mice. OTUs that differ from CT00 mice are highlighted in blue. Table S5. Statistically significant differentially abundant taxa between Study 2 FVT and Control Mice. OTUs that differ from CT00 mice are highlighted in blue. Table S6. Observed number of contigs/putative viruses in Study 1 and Study 2 mice. Table S7. Summary of Study 1 and Study 2 sample IDs, meta data and corresponding accession numbers.
DOI: 10.6084/m9.figshare.13269779
title: 附件.zip

description: Ca<sup>2+</sup>-regulated Exopolysaccharide Biosynthesis in Probiotic <i>Lactobacillus plantarum</i> K25 as Analyzed by Omics Approach
DOI: 10.6084/m9.figshare.13269779.v1
title: 附件.zip

description: Ca<sup>2+</sup>-regulated Exopolysaccharide Biosynthesis in Probiotic <i>Lactobacillus plantarum</i> K25 as Analyzed by Omics Approach
DOI: 10.21227/mqmt-yq28
title: Coronavirus (COVID-19) Geo-tagged Tweets Dataset

description: This dataset contains IDs and sentiment scores of the geo-tagged tweets related to the COVID-19 pandemic. The tweets are captured by an on-going project deployed at https://live.rlamsal.com.np. The model monitors the real-time Twitter feed for coronavirus-related tweets using 90+ different keywords and hashtags that are commonly used while referencing the pandemic. Complying with Twitter's content redistribution policy, only the tweet IDs are shared. You can re-construct the dataset by hydrating these IDs. The tweet IDs in this dataset belong to the tweets tweeted providing an exact location.The paper associated with this dataset is available here: Design and analysis of a large-scale COVID-19 tweets dataset-------------------------------------Related: Coronavirus (COVID-19) Tweets Sentiment Trend (Global), Coronavirus (COVID-19) Tweets Dataset and Tweets Originating from India During COVID-19 Lockdowns 1, 2, 3, 4-------------------------------------Below is the quick overview of this dataset.— Dataset name: GeoCOV19Tweets Dataset— Number of tweets : 265,976 tweets— Coverage : Global— Language : English (EN)— Dataset usage terms : By using this dataset, you agree to (i) use the content of this dataset and the data generated from the content of this dataset for non-commercial research only, (ii) remain in compliance with Twitter's Developer Policy and (iii) cite the following paper:Lamsal, R. Design and analysis of a large-scale COVID-19 tweets dataset. Applied Intelligence (2020). https://doi.org/10.1007/s10489-020-02029-z— Primary dataset : Coronavirus (COVID-19) Tweets Dataset (COV19Tweets Dataset)— Dataset updates : Everyday— Active keywords and hashtags: keywords.tsvPlease visit this page (primary dataset) for details regarding the collection date and time (and other notes) of each CSV file present in this dataset.