cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9204584.v1
title: ESCRT-mediated phagophore sealing during mitophagy

description: Inactivation of the endosomal sorting complex required for transport (ESCRT) machinery has been reported to cause autophagic defects, but the exact functions of ESCRT proteins in macroautophagy/autophagy remain incompletely understood. Using live-cell fluorescence microscopy we found that the filament-forming ESCRT-III subunit CHMP4B was recruited transiently to nascent autophagosomes during starvation-induced autophagy and mitophagy, with residence times of about 1 and 2 min, respectively. Correlative light microscopy and electron tomography revealed CHMP4B recruitment at a late step in mitophagosome formation. The autophagosomal dwell time of CHMP4B was strongly increased by depletion of the regulatory ESCRT-III subunit CHMP2A. Using a novel optogenetic closure assay we observed that depletion of CHMP2A inhibited phagophore sealing during mitophagy. Consistent with this, depletion of CHMP2A and other ESCRT-III subunits inhibited both PRKN/PARKIN-dependent and -independent mitophagy. We conclude that the ESCRT machinery mediates phagophore closure, and that this is essential for mitophagic flux. <b>Abbreviations:</b> BSA: bovine serum albumin; CHMP: chromatin-modifying protein; CLEM: correlative light and electron microscopy; EGFP: enhanced green fluorescent protein; ESCRT: endosomal sorting complex required for transport; HEPES: 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid; HRP: horseradish peroxidase; ILV: intralumenal vesicle; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; LOV2: light oxygen voltage 2; MLS: mitochondrial localization sequence; MT-CO2: mitochondrially encoded cytochrome c oxidase II; O+A: oligomycin and antimycin A; PBS: phosphate-buffered saline; PIPES: piperazine-N,N-bis(2-ethanesulfonic acid); PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; RAB: RAS-related in brain; SD: standard deviation; SEM: standard error of the mean; TOMM20: TOMM20: translocase of outer mitochondrial membrane 20; VCL: vinculin; VPS4: vacuolar protein sorting protein 4; Zdk1: Zdark 1; TUBG: Tubulin gamma chain
DOI: 10.15131/shef.data.9204509
title: International survey of research data management in libraries

description: Anonymised results of an international survey of Research Data Services provided by academic libraries.<br>The survey was distributed Feb-April 2018 in the following countries: Australia, Canada, Germany, Ireland, Netherlands, New Zealand, UK, USA - primarily by direct invitation to a library director.<br>A similar survey was distributed in 2014.<br>Supports the following articles:-Cox, A., Kennan, M., Lyon, L., Pinfield, S. and Sbaffi, L. (2019), "Maturing research data services and the transformation of academic libraries", Journal of Documentation, Vol. 75 No. 6, pp. 1432-1462. https://doi.org/10.1108/JD-12-2018-0211Cox, A., Kennan, M., Lyon, L., Pinfield, S. and Sbaffi, L. "Progress in Research Data Services: An international survey of university libraries (2019), VOL 14 NO 1 (2019) http://www.ijdc.net/article/view/595<br>
DOI: 10.6084/m9.figshare.9204485
title: Distinct pattern of peripheral lymphocyte subsets in Graves’ disease with persistency of anti-TSHR autoantibodies

description: <b>Background:</b> Graves’ disease (GD) is characterized by the production of autoantibodies against the TSHR (TRAbs). With long-term treatment, serum concentrations of TRAbs decline but in some patients, despite being clinically stable, TRAbs persist for many years. <b>Objective:</b> To investigate whether GD patients with persistence of TRAbs constitute a subset of patients that could be identified by phenotypic analysis of circulating lymphocytes, suggesting disease heterogeneity. <b>Materials and methods:</b> Peripheral blood lymphocytes (including naïve, memory and effector T and B cells, Th17, regulatory T cells (Treg), recent thymic emigrants (RTEs) and double positive CD4<sup>+</sup>CD8<sup>+</sup> (DP) cells) were analysed by flow cytometry in a cross-sectional study in 25 clinically stable GD patients, five patients at onset of GD disease and 40 healthy donors (HDs). <b>Results:</b> GD patients with persistence of TRAbs showed a lower percentage of Treg and lower absolute numbers of central and effector memory CD8<sup>+</sup> T cells than HD. No differences in RTEs were found in peripheral blood from GD patients compared to HD. Stable GD patients had higher percentage of DP cells of effector phenotype than HD. <b>Conclusions:</b> Using extensive phenotypic analysis of lymphocyte subpopulations, it is possible to detect changes that help to identify patients with persistent TSHR antibodies and may contribute to understand why the autoimmune response is maintained.
DOI: 10.15131/shef.data.9204509.v1
title: International survey of research data management in libraries

description: Anonymised results of an international survey of Research Data Services provided by academic libraries.<br>The survey was distributed Feb-April 2018 in the following countries: Australia, Canada, Germany, Ireland, Netherlands, New Zealand, UK, USA - primarily by direct invitation to a library director.<br>A similar survey was distributed in 2014.<br>Supports the following articles:-Cox, A., Kennan, M., Lyon, L., Pinfield, S. and Sbaffi, L. (2019), "Maturing research data services and the transformation of academic libraries", Journal of Documentation, Vol. 75 No. 6, pp. 1432-1462. https://doi.org/10.1108/JD-12-2018-0211Cox, A., Kennan, M., Lyon, L., Pinfield, S. and Sbaffi, L. "Progress in Research Data Services: An international survey of university libraries (2019), VOL 14 NO 1 (2019) http://www.ijdc.net/article/view/595<br>
DOI: 10.6084/m9.figshare.9204485.v1
title: Distinct pattern of peripheral lymphocyte subsets in Graves’ disease with persistency of anti-TSHR autoantibodies

description: <b>Background:</b> Graves’ disease (GD) is characterized by the production of autoantibodies against the TSHR (TRAbs). With long-term treatment, serum concentrations of TRAbs decline but in some patients, despite being clinically stable, TRAbs persist for many years. <b>Objective:</b> To investigate whether GD patients with persistence of TRAbs constitute a subset of patients that could be identified by phenotypic analysis of circulating lymphocytes, suggesting disease heterogeneity. <b>Materials and methods:</b> Peripheral blood lymphocytes (including naïve, memory and effector T and B cells, Th17, regulatory T cells (Treg), recent thymic emigrants (RTEs) and double positive CD4<sup>+</sup>CD8<sup>+</sup> (DP) cells) were analysed by flow cytometry in a cross-sectional study in 25 clinically stable GD patients, five patients at onset of GD disease and 40 healthy donors (HDs). <b>Results:</b> GD patients with persistence of TRAbs showed a lower percentage of Treg and lower absolute numbers of central and effector memory CD8<sup>+</sup> T cells than HD. No differences in RTEs were found in peripheral blood from GD patients compared to HD. Stable GD patients had higher percentage of DP cells of effector phenotype than HD. <b>Conclusions:</b> Using extensive phenotypic analysis of lymphocyte subpopulations, it is possible to detect changes that help to identify patients with persistent TSHR antibodies and may contribute to understand why the autoimmune response is maintained.
DOI: 10.6084/m9.figshare.9203450
title: Structure and diversity of the <i>Araucaria</i> forest in southern Brazil: biotic homogenisation hinders the recognition of floristic assemblages related to altitude

description: Forest structure and species abundance may respond to environmental features triggered by geomorphology, altitude gradients and human impacts. In this study we investigated if data from a large-area inventory would support the segregation of floristic assemblages related to altitude-oriented forest physiognomies established for the Brazilian <i>Araucaria</i> forest, even after decades of intense logging and degradation by canopy opening, burning and cattle grazing/trampling inside forests. We applied cluster analysis and non-metric multidimensional scaling (NMDS) to group 143 systematically distributed 0.4 ha plots, located in the southern Brazilian <i>Araucaria</i> forest, according to their species abundance. Subsequently, forest structure attributes, species richness and diversity were assessed. We found 368 species and an average of ∼34 species per sample plot. Our estimations yielded a mean basal area per sample plot of 24.4 ± 2.1 m<sup>²</sup> ha<sup>−1</sup>, and a mean aboveground biomass of 86.9 ± 7.3 Mg ha<sup>−1</sup> (± 95% confidence interval). Besides a subtle differentiation of the sample plots’ species abundance along the altitudinal gradient (514–1 560 m above sea level) revealed by the NMDS, we did not find ecologically meaningful floristic assemblages related to altitude. Possibly, this result is a consequence of floristic and stand structure homogenisation caused by intensive historical (and ongoing) logging, cattle grazing inside stands and general land-use changes. In turn, forest structure attributes, such as total tree height, tree density and basal area, were more evidently related to the altitude gradient, most likely due to lower temperatures, stronger winds, greater cloud cover and frost frequency occurring at high-altitude sites.
DOI: 10.6084/m9.figshare.9203450.v2
title: Structure and diversity of the <i>Araucaria</i> forest in southern Brazil: biotic homogenisation hinders the recognition of floristic assemblages related to altitude

description: Forest structure and species abundance may respond to environmental features triggered by geomorphology, altitude gradients and human impacts. In this study we investigated if data from a large-area inventory would support the segregation of floristic assemblages related to altitude-oriented forest physiognomies established for the Brazilian <i>Araucaria</i> forest, even after decades of intense logging and degradation by canopy opening, burning and cattle grazing/trampling inside forests. We applied cluster analysis and non-metric multidimensional scaling (NMDS) to group 143 systematically distributed 0.4 ha plots, located in the southern Brazilian <i>Araucaria</i> forest, according to their species abundance. Subsequently, forest structure attributes, species richness and diversity were assessed. We found 368 species and an average of ∼34 species per sample plot. Our estimations yielded a mean basal area per sample plot of 24.4 ± 2.1 m<sup>²</sup> ha<sup>−1</sup>, and a mean aboveground biomass of 86.9 ± 7.3 Mg ha<sup>−1</sup> (± 95% confidence interval). Besides a subtle differentiation of the sample plots’ species abundance along the altitudinal gradient (514–1 560 m above sea level) revealed by the NMDS, we did not find ecologically meaningful floristic assemblages related to altitude. Possibly, this result is a consequence of floristic and stand structure homogenisation caused by intensive historical (and ongoing) logging, cattle grazing inside stands and general land-use changes. In turn, forest structure attributes, such as total tree height, tree density and basal area, were more evidently related to the altitude gradient, most likely due to lower temperatures, stronger winds, greater cloud cover and frost frequency occurring at high-altitude sites.
DOI: 10.6084/m9.figshare.9203450.v1
title: Structure and diversity of the <i>Araucaria</i> forest in southern Brazil: biotic homogenisation hinders the recognition of floristic assemblages related to altitude

description: Forest structure and species abundance may respond to environmental features triggered by geomorphology, altitude gradients and human impacts. In this study we investigated if data from a large-area inventory would support the segregation of floristic assemblages related to altitude-oriented forest physiognomies established for the Brazilian <i>Araucaria</i> forest, even after decades of intense logging and degradation by canopy opening, burning and cattle grazing/trampling inside forests. We applied cluster analysis and non-metric multidimensional scaling (NMDS) to group 143 systematically distributed 0.4 ha plots, located in the southern Brazilian <i>Araucaria</i> forest, according to their species abundance. Subsequently, forest structure attributes, species richness and diversity were assessed. We found 368 species and an average of ∼34 species per sample plot. Our estimations yielded a mean basal area per sample plot of 24.4 ± 2.1 m<sup>²</sup> ha<sup>−1</sup>, and a mean aboveground biomass of 86.9 ± 7.3 Mg ha<sup>−1</sup> (± 95% confidence interval). Besides a subtle differentiation of the sample plots’ species abundance along the altitudinal gradient (514–1 560 m above sea level) revealed by the NMDS, we did not find ecologically meaningful floristic assemblages related to altitude. Possibly, this result is a consequence of floristic and stand structure homogenisation caused by intensive historical (and ongoing) logging, cattle grazing inside stands and general land-use changes. In turn, forest structure attributes, such as total tree height, tree density and basal area, were more evidently related to the altitude gradient, most likely due to lower temperatures, stronger winds, greater cloud cover and frost frequency occurring at high-altitude sites.
DOI: 10.6084/m9.figshare.9202991
title: MOESM1 of Beyond sequencing: re-visiting annotations for PJL as a test case

description: Additional file 1. Overview of the status of sequenced PJL samples, This file contains information regarding the sequencing, family data (trio statuses) and analysis of PJL samples.
DOI: 10.6084/m9.figshare.9202991.v1
title: MOESM1 of Beyond sequencing: re-visiting annotations for PJL as a test case

description: Additional file 1. Overview of the status of sequenced PJL samples, This file contains information regarding the sequencing, family data (trio statuses) and analysis of PJL samples.
DOI: 10.6084/m9.figshare.9202982
title: Additional file 1: of Iranian neonatal diabetes mellitus due to mutation in PDX1 gene: a case report

description: Figures S1 and S2: Molecular genetic laboratory reports. (ZIP 2090 kb)
DOI: 10.6084/m9.figshare.9202982.v1
title: Additional file 1: of Iranian neonatal diabetes mellitus due to mutation in PDX1 gene: a case report

description: Figures S1 and S2: Molecular genetic laboratory reports. (ZIP 2090 kb)
DOI: 10.6084/m9.figshare.9202955
title: Additional file 8: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mutational signatures for all MPA/DMBA-induced tumors. (ZIP 142 kb)
DOI: 10.6084/m9.figshare.9202955.v1
title: Additional file 8: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mutational signatures for all MPA/DMBA-induced tumors. (ZIP 142 kb)
DOI: 10.6084/m9.figshare.9202943
title: Additional file 6: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Comparative mutation rates in MPA/DMBA-induced tumors and human breast tumors in the TCGA cohort. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.9202934
title: Additional file 5: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Driver gene mutations in MPA/DMBA-induced tumors observed in the COSMIC database. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.9202943.v1
title: Additional file 6: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Comparative mutation rates in MPA/DMBA-induced tumors and human breast tumors in the TCGA cohort. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.9202934.v1
title: Additional file 5: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Driver gene mutations in MPA/DMBA-induced tumors observed in the COSMIC database. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.9202928
title: Additional file 4: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mutations observed in MPA/DMBA-induced tumors. (XLSX 405 kb)
DOI: 10.6084/m9.figshare.9202928.v1
title: Additional file 4: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mutations observed in MPA/DMBA-induced tumors. (XLSX 405 kb)
DOI: 10.6084/m9.figshare.9202913
title: Additional file 5: of Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing

description: Table S1. Results of DMCs from ACPA Positive vs. Negative comparison after blood composition adjustment. (XLSX 408T1 kb)
DOI: 10.6084/m9.figshare.9202916
title: Additional file 2: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Gene lists used for gene expression scores. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9202919
title: Additional file 3: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Subtype correlations for MPA/DMBA-induced tumors. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9202910
title: Additional file 1: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mouse characteristics and histopathological data. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9202913.v1
title: Additional file 5: of Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing

description: Table S1. Results of DMCs from ACPA Positive vs. Negative comparison after blood composition adjustment. (XLSX 408T1 kb)
DOI: 10.6084/m9.figshare.9202919.v1
title: Additional file 3: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Subtype correlations for MPA/DMBA-induced tumors. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.9202910.v1
title: Additional file 1: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Mouse characteristics and histopathological data. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9202916.v1
title: Additional file 2: of Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

description: Gene lists used for gene expression scores. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9202823
title: MOESM4 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 4. Statistics of volumes of whole grains and internal compartments.
DOI: 10.6084/m9.figshare.9202820
title: MOESM3 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 3. File contains statistical result of grain dimensions.
DOI: 10.6084/m9.figshare.9202817
title: MOESM2 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 2. Image processing and analysis workflow. This file contains all image processing and analysis source code and adetailed instruction explaining input and output of our method.
DOI: 10.6084/m9.figshare.9202823.v1
title: MOESM4 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 4. Statistics of volumes of whole grains and internal compartments.
DOI: 10.6084/m9.figshare.9202817.v1
title: MOESM2 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 2. Image processing and analysis workflow. This file contains all image processing and analysis source code and adetailed instruction explaining input and output of our method.
DOI: 10.6084/m9.figshare.9202820.v1
title: MOESM3 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 3. File contains statistical result of grain dimensions.
DOI: 10.6084/m9.figshare.9202811
title: MOESM1 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 1. Overview of dataset used.
DOI: 10.6084/m9.figshare.9202811.v1
title: MOESM1 of Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development

description: Additional file 1. Overview of dataset used.
DOI: 10.6084/m9.figshare.9202742
title: Additional file 9: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S8. Differentially expressed genes related to osmoprotectans in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202739
title: Additional file 8: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S7. Differentially expressed genes related to fatty acid in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202733
title: Additional file 7: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S6. Differentially expressed genes related to free radical scavengers and flavonoid in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202742.v1
title: Additional file 9: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S8. Differentially expressed genes related to osmoprotectans in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202733.v1
title: Additional file 7: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S6. Differentially expressed genes related to free radical scavengers and flavonoid in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202739.v1
title: Additional file 8: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S7. Differentially expressed genes related to fatty acid in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202721
title: Additional file 5: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S4. Differentially expressed transcription factors (TFs) in response to cold treatment of SCZ and YH 9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202727
title: Additional file 6: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S5. Differentially expressed cold response genes in response to cold treatment of SCZ and YH9 leaves. Significant (Pâ
DOI: 10.6084/m9.figshare.9202721.v1
title: Additional file 5: of Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

description: Table S4. Differentially expressed transcription factors (TFs) in response to cold treatment of SCZ and YH 9 leaves. Significant (Pâ