cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15022482.v1
title: Data to: The zebrafish multivariate concentric square field (zMCSF): a standardized test for behavioral profiling of zebrafish (Danio rerio)

description: Briefly, videos of the behavioral trials were analyzed with video tracking software (Ethovision XT15, Noldus Information Technology, the Netherlands). Statistical analyses were conducted in R statistical computing software using principal component analyses, (generalized) linear (mixed-effects) models and correlations. Please refer to the articles' methods section for a full description of how the data was collected and processed.<br>For a description of the variables names, please refer to the tab "metadata". The zone names are capitalized and described in the methods section and figure 1 of the article.
DOI: 10.5281/zenodo.6128356
title: A Niclosamide-releasing hot-melt extruded catheter prevents Staphylococcus aureus experimental biomaterial-associated infection

description: Biomaterial-associated infections are a major healthcare challenge as they are responsible for high disease burden in critically ill patients. In this study, we have developed drug-eluting antibacterial catheters to prevent catheter-related infections. Niclosamide (NIC), originally an antiparasitic drug, was incorporated into the polymeric matrix of thermoplastic polyurethane (TPU) via solvent casting, and catheters were fabricated using hot-melt extrusion technology. The mechanical and physicochemical properties of TPU polymers loaded with NIC were studied. NIC was released in a sustained manner from the catheters and exhibited <em>in vitro</em> antibacterial activity against <em>Staphylococcus aureus</em> and <em>Staphylococcus epidermidis</em>. Moreover, the antibacterial efficacy of NIC-loaded catheters was validated in an <em>in vivo</em> biomaterial-associated infection mouse model using a methicillin-susceptible and methicillin-resistant strain of <em>S. aureus. </em>The released NIC from the produced catheters reduced bacterial colonization of the catheter as well as of the surrounding tissue. In summary, the NIC-releasing hot-melt extruded catheters prevented implant colonization and reduced the bacterial colonization of peri-catheter tissue by methicillin sensitive as well as resistant <em>S. aureus</em> in a biomaterial-associated infection mouse model and has good prospects for preclinical development.
DOI: 10.5281/zenodo.6128355
title: A Niclosamide-releasing hot-melt extruded catheter prevents Staphylococcus aureus experimental biomaterial-associated infection

description: Biomaterial-associated infections are a major healthcare challenge as they are responsible for high disease burden in critically ill patients. In this study, we have developed drug-eluting antibacterial catheters to prevent catheter-related infections. Niclosamide (NIC), originally an antiparasitic drug, was incorporated into the polymeric matrix of thermoplastic polyurethane (TPU) via solvent casting, and catheters were fabricated using hot-melt extrusion technology. The mechanical and physicochemical properties of TPU polymers loaded with NIC were studied. NIC was released in a sustained manner from the catheters and exhibited <em>in vitro</em> antibacterial activity against <em>Staphylococcus aureus</em> and <em>Staphylococcus epidermidis</em>. Moreover, the antibacterial efficacy of NIC-loaded catheters was validated in an <em>in vivo</em> biomaterial-associated infection mouse model using a methicillin-susceptible and methicillin-resistant strain of <em>S. aureus. </em>The released NIC from the produced catheters reduced bacterial colonization of the catheter as well as of the surrounding tissue. In summary, the NIC-releasing hot-melt extruded catheters prevented implant colonization and reduced the bacterial colonization of peri-catheter tissue by methicillin sensitive as well as resistant <em>S. aureus</em> in a biomaterial-associated infection mouse model and has good prospects for preclinical development.
DOI: 10.5281/zenodo.6141560
title: Replication package for "Affordable Housing and City Welfare"

description: The package contains all the code necessary to reproduce the figures and tables in Favilukis, Mabille and Van Nieuwerburgh (forthcoming), "Affordable Housing and City Welfare." Review of Economic Studies.
DOI: 10.5281/zenodo.6141896
title: An analytical framework to measure social return of community-supported agriculture

description: Figures of the case studies (original data from CSA websites and staff interviews)
DOI: 10.6084/m9.figshare.19192820.v1
title: Representative chromosomes dataset

description: Representatives chromosomes dataset
DOI: 10.6084/m9.figshare.19192820
title: Representative chromosomes dataset

description: Representatives chromosomes dataset
DOI: 10.6084/m9.figshare.19196579
title: Plastome alignment file of extinsive samples from Poaceae and other monocots

description: Plastome alignment file of extinsive samples from Poaceae and other monocots<br>
DOI: 10.6084/m9.figshare.19196579.v1
title: Plastome alignment file of extinsive samples from Poaceae and other monocots

description: Plastome alignment file of extinsive samples from Poaceae and other monocots<br>
DOI: 10.5281/zenodo.6141936
title: msd-errors - Random walk data

description: The data related to the random walk components of the msd-error work, including truly random and temporarily anti-correlated random walks at a series of system and step size. These have either be analysed numerically or analytically (using kinisi, WLS, or OLS).<br><br>Created using showyourwork from this GitHub repo.<br>
DOI: 10.5281/zenodo.6122610
title: GraphMB datasets

description: Datasets used to test GraphMB. These datasets consist of metagenomic samples sequenced with Oxford Nanopore Technologies (ONT). <em>Strong100</em> is a simulated dataset. <em>Aale</em>, <em>Damh</em>, <em>Mari</em>, <em>Hjor</em>, <em>Hade</em> and <em>Viby</em> are activated sludge datasets from Wastewater treatment plants. <em>Soil</em> is from a soil sample collected for a previous study.
DOI: 10.5281/zenodo.6122609
title: GraphMB datasets

description: Datasets used to test GraphMB. These datasets consist of metagenomic samples sequenced with Oxford Nanopore Technologies (ONT). <em>Strong100</em> is a simulated dataset. <em>Aale</em>, <em>Damh</em>, <em>Mari</em>, <em>Hjor</em>, <em>Hade</em> and <em>Viby</em> are activated sludge datasets from Wastewater treatment plants. <em>Soil</em> is from a soil sample collected for a previous study.
DOI: 10.5517/ccdc.csd.cc26xhm8
title: CCDC 2053180: Experimental Crystal Structure Determination

description: Related Article: Ahmed S. Badr El‐din, Safaa Eldin H. Etaiw, Hassan Marie, Mohamed M. El‐bendary|2021|Appl.Organomet.Chem.|35|e6235|doi:10.1002/aoc.6235
DOI: 10.5517/ccdc.csd.cc26xhn9
title: CCDC 2053181: Experimental Crystal Structure Determination

description: Related Article: Ahmed S. Badr El‐din, Safaa Eldin H. Etaiw, Hassan Marie, Mohamed M. El‐bendary|2021|Appl.Organomet.Chem.|35|e6235|doi:10.1002/aoc.6235
DOI: 10.5517/ccdc.csd.cc2997d8
title: CCDC 2124039: Experimental Crystal Structure Determination

description: Related Article: Himadri Karmakar, Srinivas Anga, Tarun K. Panda, Vadapalli Chandrasekhar|2022|RSC Advances|12|4501|doi:10.1039/D2RA00242F
DOI: 10.5517/ccdc.csd.cc2997f9
title: CCDC 2124040: Experimental Crystal Structure Determination

description: Related Article: Himadri Karmakar, Srinivas Anga, Tarun K. Panda, Vadapalli Chandrasekhar|2022|RSC Advances|12|4501|doi:10.1039/D2RA00242F
DOI: 10.24403/jp.1012985
title: Wirkungen des Betriebssports : ein systematischer Review / Pia Dömling, Robin Heinze & Frank Daumann
DOI: 10.5517/ccdc.csd.cc2997gb
title: CCDC 2124041: Experimental Crystal Structure Determination

description: Related Article: Himadri Karmakar, Srinivas Anga, Tarun K. Panda, Vadapalli Chandrasekhar|2022|RSC Advances|12|4501|doi:10.1039/D2RA00242F
DOI: 10.5517/ccdc.csd.cc2997hc
title: CCDC 2124042: Experimental Crystal Structure Determination

description: Related Article: Himadri Karmakar, Srinivas Anga, Tarun K. Panda, Vadapalli Chandrasekhar|2022|RSC Advances|12|4501|doi:10.1039/D2RA00242F
DOI: 10.5517/ccdc.csd.cc299w9t
title: CCDC 2124656: Experimental Crystal Structure Determination

description: Related Article: Man-Man Xue, Jiarui Chang, Jie Zhang, Xuenian Chen|2022|Dalton Trans.|51|2304|doi:10.1039/D1DT04179G
DOI: 10.5517/ccdc.csd.cc299wbv
title: CCDC 2124657: Experimental Crystal Structure Determination

description: Related Article: Man-Man Xue, Jiarui Chang, Jie Zhang, Xuenian Chen|2022|Dalton Trans.|51|2304|doi:10.1039/D1DT04179G
DOI: 10.24403/jp.1013021
title: Forschungsreport – PAS: Player Agent Study Vol.1 : Spielerberater – eine berufliche Tätigkeit in der Professionalisierung ; eine explorative, empirische Untersuchung zum Berufsfeld des Spielerberaters / Dirk Jungels, Michael Förch & Christian Vogt
DOI: 10.24403/jp.1013026
title: Beeinflusst ein auf Sport, Fitness und eine gesunde Ernährung ausgerichtetes Betriebliches Gesundheitsmanagement die Wahl des zukünftigen Arbeitgebers? / Frank Daumann & Dastin Schulz
DOI: 10.24403/jp.1013032
title: Positive Skaleneffekte in europäischen Fußballligen : eine Analyse auf Basis der UEFA Champions League / Florian Oldenburg-Tietjen, Thomas Hahn, Philipp Reinbacher & Heinz Hönigschmid
DOI: 10.24403/jp.1013034
title: Befristung von Arbeitsverträgen im Spitzenfußball : der Fall „Heinz Müller“ / Hanns-Uwe Richter & Mathias Hick
DOI: 10.24403/jp.1013051
title: Effizienzanalyse professioneller Fußballvereine : eine Untersuchung deutscher Erstligisten der Saisons 2012/13 bis 2014/15 / Marc Schwarzwald & Frank Daumann
DOI: 10.24403/jp.1013057
title: Sport = Arbeit? : neue Rechtsprechung zum Unfallversicherungsschutz im Vereinssport / Jens Blüggel & Rainer Cherkeh
DOI: 10.6084/m9.figshare.19130072
title: Consort Checklist

description: CONSORT Check list
DOI: 10.6084/m9.figshare.19130072.v2
title: Consort Checklist

description: CONSORT Check list
DOI: 10.6084/m9.figshare.19130072.v1
title: Consort Checklist

description: CONSORT Check list
DOI: 10.24403/jp.1013414
title: Eye Tracking als qualitatives Marktforschungsinstrument / Laura Brager
DOI: 10.6084/m9.figshare.19196297
title: Information sheet, consent form, accent form

description: Information sheet is provided to the parents and the study is explained. Children are read and made to understand the procedure. This is followed by obtaining consent from the parents and accent from children
DOI: 10.24403/jp.1013420
title: Eye Tracking in der Sponsoring-Forschung / Carsten Schröer
DOI: 10.24403/jp.1013421
title: Psychologische Prozesse der Werbewirkung im Sportumfeld / Steffen Ronft
DOI: 10.6084/m9.figshare.15090362.v1
title: From crisis to stability and back again: the fragility of environmental governance in the Chilean salmon industry

description: In the last two decades, the 2008 Infectious Salmon Anemia (ISA) virus and the 2016 algal blooms crises have placed the Chilean salmon industry at risk and tested the capacity of its governance mechanisms to solve environmental and economic contradictions and ensure the industry’s continuity and its sustainability. Although in the 2008 crisis the state redefined mechanisms of property, control and access to natural resources to strengthen the resilience of the salmon industry, the lessons learned by the system and the community between one crisis and the next were not enough to avoid a new crisis. Chile’s existing governance mechanisms are reactive and not proactive and, therefore, their capacity to lead the industry towards long-term sustainable practices is flawed.
DOI: 10.6084/m9.figshare.15090362
title: From crisis to stability and back again: the fragility of environmental governance in the Chilean salmon industry

description: In the last two decades, the 2008 Infectious Salmon Anemia (ISA) virus and the 2016 algal blooms crises have placed the Chilean salmon industry at risk and tested the capacity of its governance mechanisms to solve environmental and economic contradictions and ensure the industry’s continuity and its sustainability. Although in the 2008 crisis the state redefined mechanisms of property, control and access to natural resources to strengthen the resilience of the salmon industry, the lessons learned by the system and the community between one crisis and the next were not enough to avoid a new crisis. Chile’s existing governance mechanisms are reactive and not proactive and, therefore, their capacity to lead the industry towards long-term sustainable practices is flawed.
DOI: 10.24403/jp.1013424
title: Die Pressewand : Effektives Werbemittel im Profifußball? / Michael Dinkel & Daniel Schwan
DOI: 10.24403/jp.1013426
title: Wahrnehmung von Sportsponsoring im Web-TV / Laura Brager
DOI: 10.6084/m9.figshare.19196607
title: A scalable hierarchical lasso for gene-environment interactions

description: We describe a regularized regression model for the selection of gene-environment (G × E) interactions. The model focuses on a single environmental exposure and induces a main-effect-before-interaction hierarchical structure. We propose an efficient fitting algorithm and screening rules that can discard large numbers of irrelevant predictors with high accuracy. We present simulation results showing that the model outperforms existing joint selection methods for (G × E) interactions in terms of selection performance, scalability and speed, and provide a real data application. Our implementation is available in the gesso R package.
DOI: 10.6084/m9.figshare.19196607.v1
title: A scalable hierarchical lasso for gene-environment interactions

description: We describe a regularized regression model for the selection of gene-environment (G × E) interactions. The model focuses on a single environmental exposure and induces a main-effect-before-interaction hierarchical structure. We propose an efficient fitting algorithm and screening rules that can discard large numbers of irrelevant predictors with high accuracy. We present simulation results showing that the model outperforms existing joint selection methods for (G × E) interactions in terms of selection performance, scalability and speed, and provide a real data application. Our implementation is available in the gesso R package.
DOI: 10.6084/m9.figshare.14561677
title: Lipotoxicity reduces DDX58/Rig-1 expression and activity leading to impaired autophagy and cell death

description: Nonalcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease globally. NAFLD is a consequence of fat accumulation in the liver leading to lipotoxicity. Increasing evidence has demonstrated the critical role of autophagy in NAFLD. This study uncovers the unexpected role of immune surveillance protein DDX58/Rig-1 (DExD/H box helicase 58) in activating macroautophagy/autophagy and protecting from lipotoxicity associated with NAFLD. Here we show for the first time that DDX58 protein is significantly reduced in nonalcoholic steatohepatitis (NASH) mouse model, an aggressive form of NAFLD characterized by inflammation and fibrosis of the liver. In addition to decreased expression of DDX58, we found that DDX58 activity can be attenuated by treatments with palmitic acid (PA), a saturated fatty acid. To investigate whether PA inhibition of DDX58 is harmful to the cell, we characterized DDX58 function in hepatocytes when exposed to high doses of PA in the presence and/or absence of DDX58. We show that siRNA knockdown of DDX58 promotes apoptosis. Importantly, we show that stable overexpression of DDX58 is protective against toxic levels of PA and stimulates autophagy. This study begins to demonstrate the regulation of the autophagy receptor protein SQSTM1/p62 through DDX58. DDX58 expression directly influences <i>SQSTM1</i> mRNA and protein levels. This work proposes a model in which activating DDX58 increases an autophagic response and this aids in clearing toxic lipid inclusion bodies, which leads to inflammation and apoptosis. Activating a DDX58-induced autophagy response may be a strategy for treating NAFLD. <b>Abbreviations:</b>5ʹpppdsRNA: 5ʹ triphosphate double-stranded RNA; CDAHFD: choline-deficient, L-amino acid defined high-fat diet; CEBPB: CCAAT/enhancer binding protein (C/EBP), beta; CQ: chloroquine; DDX58/retinoic acid inducible gene 1/Rig-1: DExD/H box helicase 58; h: hours; IFIH1/MDA5: interferon induced with helicase C domain 1; IFNB/IFN-β: interferon beta 1, fibroblast; KO: knockout; MAVS: mitochondrial antiviral signaling protein; NAFLD: nonalcoholic fatty liver disease; NASH: nonalcoholic steatohepatitis; NFKB/NF-κB: nuclear factor of kappa light polypeptide gene enhancer in B cells; PA: palmitic acid; poly:IC: polyinosinic:polycytidylic acid; PRR: pattern recognition receptors; PSR: picrosirus red; RAP: rapamycin; RLR: RIG-I-like receptor; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK-binding kinase 1.
DOI: 10.6084/m9.figshare.14371078
title: A NOVEL NOX/PHOX-CD38-NAADP-TFEB AXIS IMPORTANT FOR MACROPHAGE ACTIVATION DURING BACTERIAL PHAGOCYTOSIS

description: Macrophage activation in the presence of bacterial cells and molecules entails complex programs of gene expression. How such triggers elicit specific gene expression programs is incompletely understood. We previously discovered that TFEB (transcription factor EB) is a key contributor to macrophage activation during bacterial phagocytosis. However, the mechanism linking phagocytosis of bacterial cells to TFEB activation and downstream pro-inflammatory cytokine induction remained unknown. We found that macrophages lacking both TFEB and TFE3 (transcription factor E3) were unable to mount a pro-inflammatory phenotype in response to bacterial infection. The NOX/PHOX (NADPH oxidase)-dependent oxidative burst was required for nuclear translocation of TFEB during phagocytosis of Gram-positive or -negative bacteria, and reactive oxygen species (ROS) were sufficient to trigger TFEB activation in a CD38- and NAADP (nicotinic acid adenine dinucleotide phosphate)-dependent manner. Consistent with the Ca<sup>2+</sup>-releasing activity of NAADP, intracellular Ca<sup>2+</sup> chelation and PPP3/calcineurin inhibition prevented TFEB activation by phagocytosis and ROS (reactive oxygen species), impairing the induction of pro-inflammatory cytokines such as IL6 and TNF/TNFα. Therefore, here we describe a previously unknown pathway that links phagocytosis with macrophage pro-inflammatory polarization via TFEB and related transcription factor TFE3. These findings reveal that activation of TFEB and TFE3 is a key regulatory event for the activation of macrophages, and have important implications for infections, inflammation, cancer, obesity, and atherosclerosis.
DOI: 10.6084/m9.figshare.14371078.v1
title: A NOVEL NOX/PHOX-CD38-NAADP-TFEB AXIS IMPORTANT FOR MACROPHAGE ACTIVATION DURING BACTERIAL PHAGOCYTOSIS

description: Macrophage activation in the presence of bacterial cells and molecules entails complex programs of gene expression. How such triggers elicit specific gene expression programs is incompletely understood. We previously discovered that TFEB (transcription factor EB) is a key contributor to macrophage activation during bacterial phagocytosis. However, the mechanism linking phagocytosis of bacterial cells to TFEB activation and downstream pro-inflammatory cytokine induction remained unknown. We found that macrophages lacking both TFEB and TFE3 (transcription factor E3) were unable to mount a pro-inflammatory phenotype in response to bacterial infection. The NOX/PHOX (NADPH oxidase)-dependent oxidative burst was required for nuclear translocation of TFEB during phagocytosis of Gram-positive or -negative bacteria, and reactive oxygen species (ROS) were sufficient to trigger TFEB activation in a CD38- and NAADP (nicotinic acid adenine dinucleotide phosphate)-dependent manner. Consistent with the Ca<sup>2+</sup>-releasing activity of NAADP, intracellular Ca<sup>2+</sup> chelation and PPP3/calcineurin inhibition prevented TFEB activation by phagocytosis and ROS (reactive oxygen species), impairing the induction of pro-inflammatory cytokines such as IL6 and TNF/TNFα. Therefore, here we describe a previously unknown pathway that links phagocytosis with macrophage pro-inflammatory polarization via TFEB and related transcription factor TFE3. These findings reveal that activation of TFEB and TFE3 is a key regulatory event for the activation of macrophages, and have important implications for infections, inflammation, cancer, obesity, and atherosclerosis.
DOI: 10.6084/m9.figshare.14561677.v1
title: Lipotoxicity reduces DDX58/Rig-1 expression and activity leading to impaired autophagy and cell death

description: Nonalcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver disease globally. NAFLD is a consequence of fat accumulation in the liver leading to lipotoxicity. Increasing evidence has demonstrated the critical role of autophagy in NAFLD. This study uncovers the unexpected role of immune surveillance protein DDX58/Rig-1 (DExD/H box helicase 58) in activating macroautophagy/autophagy and protecting from lipotoxicity associated with NAFLD. Here we show for the first time that DDX58 protein is significantly reduced in nonalcoholic steatohepatitis (NASH) mouse model, an aggressive form of NAFLD characterized by inflammation and fibrosis of the liver. In addition to decreased expression of DDX58, we found that DDX58 activity can be attenuated by treatments with palmitic acid (PA), a saturated fatty acid. To investigate whether PA inhibition of DDX58 is harmful to the cell, we characterized DDX58 function in hepatocytes when exposed to high doses of PA in the presence and/or absence of DDX58. We show that siRNA knockdown of DDX58 promotes apoptosis. Importantly, we show that stable overexpression of DDX58 is protective against toxic levels of PA and stimulates autophagy. This study begins to demonstrate the regulation of the autophagy receptor protein SQSTM1/p62 through DDX58. DDX58 expression directly influences <i>SQSTM1</i> mRNA and protein levels. This work proposes a model in which activating DDX58 increases an autophagic response and this aids in clearing toxic lipid inclusion bodies, which leads to inflammation and apoptosis. Activating a DDX58-induced autophagy response may be a strategy for treating NAFLD. <b>Abbreviations:</b>5ʹpppdsRNA: 5ʹ triphosphate double-stranded RNA; CDAHFD: choline-deficient, L-amino acid defined high-fat diet; CEBPB: CCAAT/enhancer binding protein (C/EBP), beta; CQ: chloroquine; DDX58/retinoic acid inducible gene 1/Rig-1: DExD/H box helicase 58; h: hours; IFIH1/MDA5: interferon induced with helicase C domain 1; IFNB/IFN-β: interferon beta 1, fibroblast; KO: knockout; MAVS: mitochondrial antiviral signaling protein; NAFLD: nonalcoholic fatty liver disease; NASH: nonalcoholic steatohepatitis; NFKB/NF-κB: nuclear factor of kappa light polypeptide gene enhancer in B cells; PA: palmitic acid; poly:IC: polyinosinic:polycytidylic acid; PRR: pattern recognition receptors; PSR: picrosirus red; RAP: rapamycin; RLR: RIG-I-like receptor; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK-binding kinase 1.