cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57770/82shwr
title: Mitocytosis, a migrasome-mediated mitochondrial quality-control process.

description: Damaged mitochondria need to be cleared to maintain the quality of the mitochondrial pool. Here, we report mitocytosis, a migrasome-mediated mitochondrial quality-control process. We found that, upon exposure to mild mitochondrial stresses, damaged mitochondria are transported into migrasomes and subsequently disposed of from migrating cells. Mechanistically, mitocytosis requires positioning of damaged mitochondria at the cell periphery, which occurs because damaged mitochondria avoid binding to inward motor proteins. Functionally, mitocytosis plays an important role in maintaining mitochondrial quality. Enhanced mitocytosis protects cells from mitochondrial stressor-induced loss of mitochondrial membrane potential (MMP) and mitochondrial respiration; conversely, blocking mitocytosis causes loss of MMP and mitochondrial respiration under normal conditions. Physiologically, we demonstrate that mitocytosis is required for maintaining MMP and viability in neutrophils in vivo. We propose that mitocytosis is an important mitochondrial quality-control process in migrating cells, which couples mitochondrial homeostasis with cell migration.
DOI: 10.57770/fqgyxm
title: Therapeutic perspectives of thermogenic adipocytes in obesity and related complications.

description: There is a rapidly increasing prevalence of obesity and related metabolic disorders such as type 2 diabetes worldwide. White adipose tissue (WAT) stores excess energy, whereas brown and beige adipose tissues consume energy to generate heat in the process of thermogenesis. Adaptive thermogenesis occurs in response to environmental cues as a means of generating heat by dissipating stored chemical energy. Due to its cumulative nature, very small differences in energy expenditure from adaptive thermogenesis can have a significant impact on systemic metabolism over time. Targeting brown adipose tissue (BAT) activation and converting WAT to beige fat as a method to increase energy expenditure is one of the promising strategies to combat obesity. In this review, we discuss the activation of the thermogenic process in response to physiological conditions. We highlight recent advances in harnessing the therapeutic potential of thermogenic adipocytes by genetic, pharmacological and cell-based approaches in the treatment of obesity and metabolic disorders in mice and the human.
DOI: 10.6084/m9.figshare.21803445
title: Processed CCLE CNA 21Q3 data

description: Processed CCLE CNA 21Q3 data
DOI: 10.6084/m9.figshare.21801097
title: Processed CCLE mutation 21Q3 data

description: Processed CCLE mutation 21Q3 data
DOI: 10.6084/m9.figshare.21801094
title: Processed CCLE mutation 19Q3 data

description: Processed CCLE mutation 19Q3 data
DOI: 10.5281/zenodo.7499290
title: Impact of Passive Voice in Requirements Engineering

description: This repository contains instrumentation material and results for the experiment described in the paper "On The Impact of Passive Voice Requirements on Domain Modelling" by Henning Femmer, Jan Kucera, and Antonio Vetrò from Technische Universität München.
description: This repository was disclosed with the explicit permission of the first author of the work, Henning Femmer. It is a data recovery since the original hosting (https://www.in.tum.de/i04/~femmer/data/passives_experiment.zip) has become unavailable.
description: {"references": ["Femmer, H., Ku\u010dera, J., & Vetr\u00f2, A. (2014, September). On the impact of passive voice requirements on domain modelling. In Proceedings of the 8th ACM/IEEE International Symposium on Empirical Software Engineering and Measurement (pp. 1-4)."]}
DOI: 10.6084/m9.figshare.21801091
title: Processed CCLE gene expression 21Q3 data

description: Processed CCLE gene expression 21Q3 data
DOI: 10.6084/m9.figshare.21801079
title: Processed CCLE gene expression 19Q3 data

description: Processed CCLE gene expression 19Q3 data
DOI: 10.6084/m9.figshare.21801079.v1
title: Processed CCLE gene expression 19Q3 data

description: Processed CCLE gene expression 19Q3 data
DOI: 10.6084/m9.figshare.21801073.v1
title: Processed CCLE CNA 19Q3 data

description: Processed CCLE CNA 19Q3 dataset
DOI: 10.6084/m9.figshare.21801073
title: Processed CCLE CNA 19Q3 data

description: Processed CCLE CNA 19Q3 dataset
DOI: 10.6084/m9.figshare.21801070
title: Processed PPI data

description: Protein-protein interaction network filtered by expression data.
DOI: 10.6084/m9.figshare.21801070.v1
title: Processed PPI data

description: Protein-protein interaction network filtered by expression data.
DOI: 10.6084/m9.figshare.21801061
title: Processed DepMap RNAi screen 19Q3 data

description: RNAi screen data generated based on DepMap 19Q3 expression data.
DOI: 10.6084/m9.figshare.21801061.v1
title: Processed DepMap RNAi screen 19Q3 data

description: RNAi screen data generated based on DepMap 19Q3 expression data.
DOI: 10.5281/zenodo.7418228
title: Flora of Cerrado Pé-de-Gigante: a protected area from Vassununga State Park, Santa Rita do Passa Quatro, São Paulo State, Brazil

description: <strong>This dataset is part of the manuscript: "<em>Systematic review of the Cerrado Pé-de-Gigante flora, one of the largest protected Cerrado fragments in São Paulo state, Brazil</em>".</strong><br> <br> The Cerrado Pé-de-Gigante is located in the State of São Paulo, southeastern Brazil, and it comprises a part of the Vassununga State Park, a integral protection conservation unit. This study presents an updated list of the flora of Cerrado Pé-de-Gigante which was developed through a systematic search in the literature, consultations to virtual herbaria, and field validation. In the state of São Paulo, the original vegetation of the remaining Cerrado is mostly in small fragments and in areas not properly protected. In this regard, we emphasize the relevance in the context of conservation of biodiversity as a whole of Cerrado Pé-de-Gigante, since our results pointed to the record of 681 plant species for this area of just over 1200 ha. The final list includes angiosperms, ferns and bryophytes and their respective conservation status, habit and herbarium deposit vouchers. <pre> </pre>
DOI: 10.6084/m9.figshare.21801058
title: Processed DepMap CRISPR screen 21Q3 data

description: DepMap CRISPR screen data generated based on 21Q3 expression data.
DOI: 10.7303/syn50558757.1
title: Cohort Canine Melanoma - whole slide images
DOI: 10.7303/syn34393627.1
title: Cohort 0 - whole slide images
DOI: 10.6084/m9.figshare.21744605.v1
title: Table 1. Distribution of the decreased-susceptibility-to-DDAC phenotype in the study panel (n=168) according to the year of strain isolation (A), animal species (B), and sample type (C).

description: P-values of Fisher's test of independence comparing the category against the rest of the population (B) and (C). <em>DDAC: didecyldimethylammonium chloride; DS: decreased susceptibility</em>
DOI: 10.7303/syn33514579.1
title: Cohort 0 - single-cell annotations
DOI: 10.5281/zenodo.7499294
title: Dataset related to article "Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules"

description: This record contains raw data related to article “Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules" The humoral arm of innate immunity includes diverse molecules with antibody-like functions, some of which serve as disease severity biomarkers in coronavirus disease 2019 (COVID-19). The present study was designed to conduct a systematic investigation of the interaction of human humoral fluid-phase pattern recognition molecules (PRMs) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of 12 PRMs tested, the long pentraxin 3 (PTX3) and mannose-binding lectin (MBL) bound the viral nucleocapsid and spike proteins, respectively. MBL bound trimeric spike protein, including that of variants of concern (VoC), in a glycan-dependent manner and inhibited SARS-CoV-2 in three in vitro models. Moreover, after binding to spike protein, MBL activated the lectin pathway of complement activation. Based on retention of glycosylation sites and modeling, MBL was predicted to recognize the Omicron VoC. Genetic polymorphisms at the MBL2 locus were associated with disease severity. These results suggest that selected humoral fluid-phase PRMs can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.
DOI: 10.5281/zenodo.7499293
title: Dataset related to article "Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules"

description: This record contains raw data related to article “Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules" The humoral arm of innate immunity includes diverse molecules with antibody-like functions, some of which serve as disease severity biomarkers in coronavirus disease 2019 (COVID-19). The present study was designed to conduct a systematic investigation of the interaction of human humoral fluid-phase pattern recognition molecules (PRMs) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of 12 PRMs tested, the long pentraxin 3 (PTX3) and mannose-binding lectin (MBL) bound the viral nucleocapsid and spike proteins, respectively. MBL bound trimeric spike protein, including that of variants of concern (VoC), in a glycan-dependent manner and inhibited SARS-CoV-2 in three in vitro models. Moreover, after binding to spike protein, MBL activated the lectin pathway of complement activation. Based on retention of glycosylation sites and modeling, MBL was predicted to recognize the Omicron VoC. Genetic polymorphisms at the MBL2 locus were associated with disease severity. These results suggest that selected humoral fluid-phase PRMs can play an important role in resistance to, and pathogenesis of, COVID-19, a finding with translational implications.
DOI: 10.6084/m9.figshare.21744611
title: Appendix A. Table A1. Distribution of the decreased susceptibility-to-DDAC phenotype in the panel for genomic characterization (n = 41), according to the year of strain isolation, animal species and sampling.

description: DDAC: didecyldimethylammonium chloride; DS: decreased susceptibility.
DOI: 10.6084/m9.figshare.21744611.v2
title: Appendix A. Table A1. Distribution of the decreased susceptibility-to-DDAC phenotype in the panel for genomic characterization (n = 41), according to the year of strain isolation, animal species and sampling.

description: DDAC: didecyldimethylammonium chloride; DS: decreased susceptibility.
DOI: 10.6084/m9.figshare.21744611.v1
title: Appendix B. Distribution of the decreased susceptibility-to-DDAC phenotype in the panel for genomic characterization (n=41) according to year of strain isolation (A), animal species (B) and sample type (C).

description: <em>DDAC: didecyldimethylammonium chloride; DS: decreased susceptibility</em>
DOI: 10.6084/m9.figshare.21728319
title: Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

description: Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images. <b>Abbreviations:</b> 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
DOI: 10.6084/m9.figshare.21728319.v1
title: Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

description: Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images. <b>Abbreviations:</b> 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.
DOI: 10.6084/m9.figshare.19182029
title: Uip4p modulates nuclear pore complex function in <i>Saccharomyces cerevisiae</i>

description: A double membrane bilayer perforated by nuclear pore complexes (NPCs) governs the shape of the nucleus, the prominent distinguishing organelle of a eukaryotic cell. Despite the absence of lamins in yeasts, the nuclear morphology is stably maintained and shape changes occur in a regulated fashion. In a quest to identify factors that contribute to regulation of nuclear shape and function in <i>Saccharomyces cerevisiae</i>, we used a fluorescence imaging based approach. Here we report the identification of a novel protein, Uip4p, that is required for regulation of nuclear morphology. Loss of Uip4 compromises NPC function and loss of nuclear envelope (NE) integrity. Our localization studies show that Uip4 localizes to the NE and endoplasmic reticulum (ER) network. Furthermore, we demonstrate that the localization and expression of Uip4 is regulated during growth, which is crucial for NPC distribution.
DOI: 10.6084/m9.figshare.19182029.v1
title: Uip4p modulates nuclear pore complex function in <i>Saccharomyces cerevisiae</i>

description: A double membrane bilayer perforated by nuclear pore complexes (NPCs) governs the shape of the nucleus, the prominent distinguishing organelle of a eukaryotic cell. Despite the absence of lamins in yeasts, the nuclear morphology is stably maintained and shape changes occur in a regulated fashion. In a quest to identify factors that contribute to regulation of nuclear shape and function in <i>Saccharomyces cerevisiae</i>, we used a fluorescence imaging based approach. Here we report the identification of a novel protein, Uip4p, that is required for regulation of nuclear morphology. Loss of Uip4 compromises NPC function and loss of nuclear envelope (NE) integrity. Our localization studies show that Uip4 localizes to the NE and endoplasmic reticulum (ER) network. Furthermore, we demonstrate that the localization and expression of Uip4 is regulated during growth, which is crucial for NPC distribution.
DOI: 10.6084/m9.figshare.19245913.v1
title: Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study

description: Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes. <b>Abbreviations:</b> NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.
DOI: 10.6084/m9.figshare.19376651.v2
title: <i>Dictyostelium</i> spastin is involved in nuclear envelope dynamics during semi-closed mitosis

description: Dictyostelium amoebae perform a semi-closed mitosis, in which the nuclear envelope is fenestrated at the insertion sites of the mitotic centrosomes and around the central spindle during karyokinesis. During late telophase the centrosome relocates to the cytoplasmic side of the nucleus, the central spindle disassembles and the nuclear fenestrae become closed. Our data indicate that Dictyostelium spastin (DdSpastin) is a microtubule-binding and severing type I membrane protein that plays a role in this process. Its mitotic localization is in agreement with a requirement for the removal of microtubules that would hinder closure of the fenestrae. Furthermore, DdSpastin interacts with the HeH/ LEM-family protein Src1 in BioID analyses as well as the inner nuclear membrane protein Sun1, and shows subcellular co-localizations with Src1, Sun1, the ESCRT component CHMP7 and the IST1-like protein filactin, suggesting that the principal pathway of mitotic nuclear envelope remodeling is conserved between animals and Dictyostelium amoebae.
DOI: 10.6084/m9.figshare.19245913
title: Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study

description: Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study, we tested whether NS exhibit any stable association with chromatin and show that limited DNAse-1 nicking of chromatin leads to the collapse of NS into isotropic distribution or aggregates of constituent proteins without affecting other nuclear structures. Further biochemical probing revealed that NS proteins were tightly associated with chromatin, extractable only by high-salt treatment just like histone proteins. NS were also co-released with solubilised mono-dinucleosomal chromatin fraction following the MNase digestion of chromatin. We propose a model that NS-chromatin constitutes a “putative stable association” whose coupling might be subject to the combined regulation from both chromatin and NS changes. <b>Abbreviations:</b> NS: Nuclear speckles; DSB: double strand breaks; PTM: posttranslational modifications; DDR: DNA damage repair; RBP-RNA binding proteins; TAD: topologically associated domains; LCR: low complexity regions; IDR: intrinsically disordered regions.
DOI: 10.6084/m9.figshare.19376651
title: <i>Dictyostelium</i> spastin is involved in nuclear envelope dynamics during semi-closed mitosis

description: Dictyostelium amoebae perform a semi-closed mitosis, in which the nuclear envelope is fenestrated at the insertion sites of the mitotic centrosomes and around the central spindle during karyokinesis. During late telophase the centrosome relocates to the cytoplasmic side of the nucleus, the central spindle disassembles and the nuclear fenestrae become closed. Our data indicate that Dictyostelium spastin (DdSpastin) is a microtubule-binding and severing type I membrane protein that plays a role in this process. Its mitotic localization is in agreement with a requirement for the removal of microtubules that would hinder closure of the fenestrae. Furthermore, DdSpastin interacts with the HeH/ LEM-family protein Src1 in BioID analyses as well as the inner nuclear membrane protein Sun1, and shows subcellular co-localizations with Src1, Sun1, the ESCRT component CHMP7 and the IST1-like protein filactin, suggesting that the principal pathway of mitotic nuclear envelope remodeling is conserved between animals and Dictyostelium amoebae.