cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7064414.v2
title: ATG5 is required for B cell polarization and presentation of particulate antigens

description: The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)<sup>+</sup> and major histocompatibility complex class II (MHC-II)<sup>+</sup> compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [<i>S. cerevisiae</i>]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)–ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. <b>Abbreviations:</b> ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4ʹ,6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1
DOI: 10.6084/m9.figshare.7064414.v1
title: ATG5 is required for B cell polarization and presentation of particulate antigens

description: The involvement of macroautophagy/autophagy proteins in B-cell receptor (BCR) trafficking, although suspected, is not well understood. We show that ATG5 (autophagy related 5) contributes to BCR polarization after stimulation and internalization into LAMP1 (lysosomal-associated membrane protein 1)<sup>+</sup> and major histocompatibility complex class II (MHC-II)<sup>+</sup> compartments. BCR polarization is crucial in the context of immobilized antigen processing. Moreover, antigen presentation to cognate T cells is decreased in the absence of ATG5 when the model antigen OVAL/ovalbumin is provided in an immobilized form in contrast to the normal presentation of soluble OVAL. We further show that ATG5 is required for centrosome polarization and actin nucleation in the immune synapse area. This event is accompanied by an increased interaction between ATG16L1 (autophagy related 16-like 1 [<i>S. cerevisiae</i>]) and the microtubule-organizing center-associated protein PCM1 (pericentriolar material 1). In the human B cell line BJAB, PCM1 is required for BCR polarization after stimulation. We thus propose that the ATG12 (autophagy related 12)–ATG5-ATG16L1 complex under BCR stimulation allows its interaction with PCM1 and consequently facilitates centrosome relocalization to the immune synapse, optimizing the presentation of particulate antigens. <b>Abbreviations:</b> ACTB: actin beta; ACTR2/3: ARP2/3 actin-related protein 2/3; APC: antigen-presenting cells; ATG: autophagy-related; BCR: B cell receptor; BECN1/Beclin 1: beclin 1, autophagy related; CDC42: cell division cycle 42; Cr2: complement receptor 2; CSFE: carboxyfluorescein succinimidyl ester; DAPI: 4ʹ,6-diamidino-2-phenylindole dihydrochloride; EEA1: early endosome antigen 1; ELISA: enzyme-linked immunosorbent assay; FITC: fluorescein isothyocyanate; GC: germinal center; GJA1/CX3: gap junction protein, alpha 1; Ig: immunoglobulin; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; LM: littermate; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK/ERK: mitogen activated protein kinase; MHC-II: major histocompatibility complex class II; MIIC: MHC class II compartment; OVAL: ovalbumin; PBS: phosphate-buffered saline; PCM1: pericentriolar material 1; PtdIns3K: phosphatidylinositol 3-kinase; PTPRC/CD45RB/B220; Protein tyrosine phosphatase, receptor type, C; SYK: spleen tyrosine kinase; TBS: Tris-buffered saline; TCR: T cell receptor; ULK1: unc-51 like kinase 1
DOI: 10.6084/m9.figshare.7064390
title: Data for: Secondhand horror: Effects of direct and indirect predator cues on behavior and reproduction of the bank vole

description: Data sets for Sievert et al. 2019 (Secondhand horror: Effects of direct and indirect predator cues on behavior and reproduction of the bank vole)<br>
DOI: 10.6084/m9.figshare.7064390.v1
title: Sievert et al. 2019 Dataset

description: Data sets for Sievert et al. 2019 (Secondhand horror: Effects of direct and indirect predator cues on behavior and reproduction of the bank vole)<br>
DOI: 10.6084/m9.figshare.7064390.v2
title: Secondhand horror: Effects of direct and indirect predator cues on behavior and reproduction of the bank vole - Dataset

description: Data sets for Sievert et al. 2019 (Secondhand horror: Effects of direct and indirect predator cues on behavior and reproduction of the bank vole)<br>
DOI: 10.6084/m9.figshare.7064261
title: Fitness effects of MA lines at different temperatures

description: Fitness of the derivatives from a mutation accumulation experiment at six temperatures. ID indicates different genotypes; evotemp is the MA temperature; comtemp means the assay temperature and fitness showed the fitness effects of the accumulated mutations. <br>Sheet 1 indicates the fitness of MA lines and Sheet 2 represents all technical replicates.
DOI: 10.6084/m9.figshare.7064261.v1
title: Fitness effects of MA lines at different temperatures

description: Fitness of the derivatives from a mutation accumulation experiment at six temperatures. ID indicates different genotypes; evotemp is the MA temperature; comtemp means the assay temperature and fitness showed the fitness effects of the accumulated mutations. <br>Sheet 1 indicates the fitness of MA lines and Sheet 2 represents all technical replicates.
DOI: 10.6084/m9.figshare.7064255
title: Supplemental Materials for Bhatta et al. 2018_DroughtGWAS

description: Figure S1: Pearson’s correlation of grain yield and yield-related traits of 123 synthetic hexaploid wheat based on adjusted best linear unbiased predictors in 2016 (A) and 2017 (B) growing seasons in Konya, Turkey. Figure S2: Population structure analysis of 123 synthetic hexaploid wheat. Figure S3: Physical distribution of genotyping-by-sequencing derived SNPs within 1 Mb window size on 21 chromosomes of 123 synthetic hexaploid wheat. Figure S4: Manhattan and quantile-quantile plots for 11 traits in 123 synthetic hexaploid wheat germplasm. Table S1: Details of 123 synthetic hexaploid wheat used and subgroups obtained from Bayesian clustering algorithm with population structure matrix (Q) and best linear unbiased predictors (BLUPs) from two-year (2016 and 2017) experiments conducted in Konya, Turkey. Table S2. Crossing scheme of 123 synthetic hexaploid wheat. Table S3. Genotyping-by-Sequencing derived SNP markers of 123 synthetic hexaploid wheats used in this study. Table S4. Combined analysis of variance with means squares and broad sense heritability (<i>H</i><sup>2</sup>) of 123 drought stressed synthetic hexaploid wheats grown in two seasons (2016 and 2017) in Konya, Turkey. Table S5. Details of significant markers associated with 11 traits in 123 synthetic hexaploid wheat grown in two seasons (2016 and 2017) in Konya, Turkey. Table S6. Details of potential candidate gene functions harboring SNPs affecting yield and yield-related traits under drought stress in 123 synthetic hexaploid wheat grown in two seasons (2016 and 2017) in Konya, Turkey.
DOI: 10.6084/m9.figshare.7064255.v1
title: Supplemental Materials for Bhatta et al. 2018_DroughtGWAS

description: Figure S1: Pearson’s correlation of grain yield and yield-related traits of 123 synthetic hexaploid wheat based on adjusted best linear unbiased predictors in 2016 (A) and 2017 (B) growing seasons in Konya, Turkey. Figure S2: Population structure analysis of 123 synthetic hexaploid wheat. Figure S3: Physical distribution of genotyping-by-sequencing derived SNPs within 1 Mb window size on 21 chromosomes of 123 synthetic hexaploid wheat. Figure S4: Manhattan and quantile-quantile plots for 11 traits in 123 synthetic hexaploid wheat germplasm. Table S1: Details of 123 synthetic hexaploid wheat used and subgroups obtained from Bayesian clustering algorithm with population structure matrix (Q) and best linear unbiased predictors (BLUPs) from two-year (2016 and 2017) experiments conducted in Konya, Turkey. Table S2. Crossing scheme of 123 synthetic hexaploid wheat. Table S3. Genotyping-by-Sequencing derived SNP markers of 123 synthetic hexaploid wheats used in this study. Table S4. Combined analysis of variance with means squares and broad sense heritability (<i>H</i><sup>2</sup>) of 123 drought stressed synthetic hexaploid wheats grown in two seasons (2016 and 2017) in Konya, Turkey. Table S5. Details of significant markers associated with 11 traits in 123 synthetic hexaploid wheat grown in two seasons (2016 and 2017) in Konya, Turkey. Table S6. Details of potential candidate gene functions harboring SNPs affecting yield and yield-related traits under drought stress in 123 synthetic hexaploid wheat grown in two seasons (2016 and 2017) in Konya, Turkey.
DOI: 10.6084/m9.figshare.7064240.v1
title: relative abundance

description: Relative abundance
DOI: 10.25919/5f48e66d4a133
title: CSIRO Film Collection: videos 400 - 498 - archival versions

description: CSIRO produced its first film in 1946. It was a two-hour, five-part epic in black and white designed for a specialist audience of Commonwealth scientists meeting in London. It showed them - in the most graphic way possible at the time - the nature and extent of the research facilities of an organisation embarking on the problems of post-war reconstruction. Within a few years, a permanent film unit was established and began to specialise in producing films for the specific audiences on particular areas of research. By the 1960's, it became apparent that many of the films were of interest to a much wider audience. Schools, colleges and universities were beginning to introduce the audio-visual medium to the learning process and CSIRO films were in increasing demand. Makers of television programmes looked to CSIRO films for images of science not yet accessible to the public eye.
DOI: 10.6084/m9.figshare.7063991
title: Additional file 1: of Fasting and time of day independently modulate circadian rhythm relevant gene expression in adipose and skin tissue

description: Table S1. Genes significantly associated with hours of fasting, time of day or seasonality in fat or skin. Table S2. Replicability of literature studies and our study across taxa. Table S3. Replicability of genes associated with hours fasting and time of day. Table S4. Gene ontology enrichment of the hours fasting and solar time in fat and skin using TopGO. Table S5. Gene ontology enrichment of the hours fasting and solar time in fat and skin using ToppFun. Table S6. Ingenuity canonical pathways enrichment of the hours fasting and solar time in fat and skin using Ingenuity software. Table S7. Sensitivity analysis of GO term enrichment using Cut-off P
DOI: 10.6084/m9.figshare.7063991.v1
title: Additional file 1: of Fasting and time of day independently modulate circadian rhythm relevant gene expression in adipose and skin tissue

description: Table S1. Genes significantly associated with hours of fasting, time of day or seasonality in fat or skin. Table S2. Replicability of literature studies and our study across taxa. Table S3. Replicability of genes associated with hours fasting and time of day. Table S4. Gene ontology enrichment of the hours fasting and solar time in fat and skin using TopGO. Table S5. Gene ontology enrichment of the hours fasting and solar time in fat and skin using ToppFun. Table S6. Ingenuity canonical pathways enrichment of the hours fasting and solar time in fat and skin using Ingenuity software. Table S7. Sensitivity analysis of GO term enrichment using Cut-off P
DOI: 10.6084/m9.figshare.7063955
title: Additional file 1: of Lipidomic profiling of extracellular vesicles derived from prostate and prostate cancer cell lines

description: BH Corrected Multiple Comparisons of EV Lipid Species. Lipid species data were analysed using an unpaired t-test, correcting for multiple comparisons using the Benjamini and Hochberg FDR with a q value of 5%. The workbook contains 3 sheets, one for each comparison: RWPE1 v NB26, RWPE1 v PC-3 and NB26 v PC-3. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.7063955.v1
title: Additional file 1: of Lipidomic profiling of extracellular vesicles derived from prostate and prostate cancer cell lines

description: BH Corrected Multiple Comparisons of EV Lipid Species. Lipid species data were analysed using an unpaired t-test, correcting for multiple comparisons using the Benjamini and Hochberg FDR with a q value of 5%. The workbook contains 3 sheets, one for each comparison: RWPE1 v NB26, RWPE1 v PC-3 and NB26 v PC-3. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.7063820
title: Templates for brain bundle recognition

description: This is a copy of templates found in https://figshare.com/articles/Simple_model_bundle_atlas_for_RecoBundles/6483614, but we have uploaded the templates as individual trk files, so that we can download each one separately. Please refer to that repository for references and funding.
DOI: 10.6084/m9.figshare.7063820.v1
title: Templates for brain bundle recognition

description: This is a copy of templates found in https://figshare.com/articles/Simple_model_bundle_atlas_for_RecoBundles/6483614, but we have uploaded the templates as individual trk files, so that we can download each one separately. Please refer to that repository for references and funding.
DOI: 10.6084/m9.figshare.7063823.v1
title: Supplemental materials for Jung et al, 2018

description: Supplemental materials for Jung <i>et al</i>, 2018<br> "Genome-wide screening for enteric colonization factors in carbapenem-resistant ST258 <i>Klebsiella pneumoniae"</i><i><br></i><i>-----------------------</i><i>-----------------------</i><i><br></i><b>Table S1. </b>Essentiality of the MH258 chromosomal genes, determined by EL-ARTIST (19). For the sliding window analysis, 1000 simulations, window size of 10, and <i>p</i>-value of 0.05 were used. 1, non-essential; 2, essential; 3, domain essential. <br><b>Table S2.</b> Mutants with enhanced fitness in gut colonization. Ratios of the read counts to the total read counts are listed for all the mutants that represented more than 2 percent of the total reads (highlighted in yellow) in any of the samples. <br><b>Table S3.</b> Average log2 fold changes in the normalized read counts for all the significant genetic loci in any of the in vivo and in vitro samples. The same color scheme to Fig. 5D was applied. Fold changes for the genes that were not significant in a given sample are not shown; they were treated as unchanged (“0”). <br><b>Table S4.</b> List of primers. <br><b>Text S2.</b> Supplemental methods.
DOI: 10.6084/m9.figshare.7063823.v2
title: Supplemental materials for Jung et al, 2018

description: Supplemental materials for Jung <i>et al</i>, 2019<br> "Genome-wide screening for enteric colonization factors in carbapenem-resistant ST258 <i>Klebsiella pneumoniae"</i><i><br></i><i>-----------------------</i><i>-----------------------</i><i><br></i><b>Table S1.</b> List of MH258 chromosomal essential genes as identified by the EL-ARTIST pipeline (19). For the sliding window analysis, 1000 simulations, window size of 10, and p-value of 0.05 were used. 1, non-essential; 2, essential; 3, domain essential. <br><br><b>Table S2. </b>Mutants with enhanced fitness in gut colonization. Ratios of the read counts to the total read counts are listed for all the mutants that represented more than 2 percent of the total reads (highlighted in yellow) in any of the samples. <br><br><b>Table S3. </b>Average log2 fold changes in the normalized read counts for all the significant genetic loci in any of the in vivo and in vitro samples. The same color scheme to Fig. 5D was applied. Fold changes for the genes that were not significant in a given sample are not shown; they were treated as unchanged (“0”). <br><br><b>Table S4.</b> List of primers. <br><br><b>Text S1.</b> Supplemental Results <br><br><b>Text S2.</b> Supplemental methods. <br><br><b>Figure S11. </b>Genomic comparison of multiple Kp clinical strains. A circos map generated by the Proteome Comparison tool of PATRIC 3.5.27 for Table 1 is shown. <br><br><br>
DOI: 10.6084/m9.figshare.7063808.v1
title: Double-Question Survey Measures for the Analysis of Financial Bubbles and Crashes

description: This paper proposes a new double-question survey whereby an individual is presented with two sets of questions; one on beliefs about current asset values and another on price expectations. A theoretical asset pricing model with heterogeneous agents is advanced and the existence of a negative relationship between price expectations and asset valuations is established, and is then tested using survey results on equity, gold and house prices. Leading indicators of bubbles and crashes are proposed and their potential value is illustrated in the context of a dynamic panel regression of realized house price changes across key Metropolitan Statistical Areas (MSAs) in the US. In an out-of-sample forecasting exercise it is also shown that forecasts of house price changes (pooled across MSAs) that make use of bubble and crash indicators perform significantly better than a benchmark model that only uses lagged and expected house price changes.
DOI: 10.6084/m9.figshare.7063748
title: callable.bed.gz

description: Whitelisted genomic regions
DOI: 10.6084/m9.figshare.7063748.v1
title: callable.bed.gz

description: Whitelisted genomic regions
DOI: 10.6084/m9.figshare.7063637
title: random_mutations.tsv.gz

description: Randomised somatic mutations for 50 donors
DOI: 10.6084/m9.figshare.7063640
title: train_elements.tsv

description: Training genomic elements
DOI: 10.6084/m9.figshare.7063640.v1
title: train_elements.tsv

description: Training genomic elements
DOI: 10.6084/m9.figshare.7063379
title: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health

description: Data from "Gebert et al. Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health" <br>
DOI: 10.6084/m9.figshare.7063379.v1
title: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health

description: Data from "Gebert et al. Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health" <br>
DOI: 10.6084/m9.figshare.7059665
title: GWR air temperature for year 2016

description: Intermediate monthly air temperature product for year 2016 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059659
title: GWR air temperature for year 2013

description: Intermediate monthly air temperature product for year 2013 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059662
title: GWR air temperature for year 2015

description: Intermediate monthly air temperature product for year 2015 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059659.v1
title: GWR air temperature for year 2013

description: Intermediate monthly air temperature product for year 2013 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059653
title: GWR air temperature for year 2012

description: Intermediate monthly air temperature product for year 2012 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059656
title: GWR air temperature for year 2011

description: Intermediate monthly air temperature product for year 2011 calculated using a geographically weighted regression (GWR).
DOI: 10.6084/m9.figshare.7059653.v1
title: GWR air temperature for year 2012

description: Intermediate monthly air temperature product for year 2012 calculated using a geographically weighted regression (GWR).
DOI: 10.15156/bio/sh019304.07fu
title: SH019304.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh019305.07fu
title: SH019305.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.