cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14192507
title: A quick and versatile protocol for the 3D visualization of transgene expression across the whole body of larval <i>Drosophila</i>

description: Larval <i>Drosophila</i> are used as a genetically accessible study case in many areas of biological research. Here we report a fast, robust and user-friendly procedure for the whole-body multi-fluorescence imaging of <i>Drosophila</i> larvae; the protocol has been optimized specifically for larvae by systematically tackling the pitfalls associated with clearing this small but cuticularized organism. Tests on various fluorescent proteins reveal that the recently introduced monomeric infrared fluorescent protein (mIFP) is particularly suitable for our approach. This approach comprises an effective, low-cost clearing protocol with minimal handling time and reduced toxicity in the reagents employed. It combines a success rate high enough to allow for small-scale screening approaches and a resolution sufficient for cellular-level analyses with light sheet and confocal microscopy. Given that publications and database documentations typically specify expression patterns of transgenic driver lines only within a given organ system of interest, the present procedure should be versatile enough to extend such documentation systematically to the whole body. As examples, the expression patterns of transgenic driver lines covering the majority of neurons, or subsets of chemosensory, central brain or motor neurons, are documented in the context of whole larval body volumes (using nsyb-Gal4, IR76b-Gal4, APL-Gal4 and mushroom body Kenyon cells, or OK371-Gal4, respectively). Notably, the presented protocol allows for triple-color fluorescence imaging with near-infrared, red and yellow fluorescent proteins.
DOI: 10.6084/m9.figshare.15156818
title: Expression of the <i>foraging</i> gene in adult <i>Drosophila melanogaster</i>

description: The <i>foraging</i> gene in <i>Drosophila melanogaster</i>, which encodes a cGMP-dependent protein kinase, is a highly conserved, complex gene with multiple pleiotropic behavioral and physiological functions in both the larval and adult fly. Adult <i>foraging</i> expression is less well characterized than in the larva. We characterized <i>foraging</i> expression in the brain, gastric system, and reproductive systems using a <i>T2A-Gal4</i> gene-trap allele. In the brain, <i>foraging</i> expression appears to be restricted to multiple sub-types of glia. This glial-specific cellular localization of <i>foraging</i> was supported by single-cell transcriptomic atlases of the adult brain. <i>foraging</i> is extensively expressed in most cell types in the gastric and reproductive systems. We then mapped multiple <i>cis</i>-regulatory elements responsible for parts of the observed expression patterns by a nested cloned promoter-<i>Gal4</i> analysis. The mapped <i>cis</i>-regulatory elements were consistently modular when comparing the larval and adult expression patterns. These new data using the <i>T2A-Gal4</i> gene-trap and cloned <i>foraging</i> promoter fusion <i>GAL4</i>’s are discussed with respect to previous work using an anti-FOR antibody, which we show here to be non-specific. Future studies of <i>foraging</i>’s function will consider roles for glial subtypes and peripheral tissues (gastric and reproductive systems) in <i>foraging</i>’s pleiotropic behavioral and physiological effects.
DOI: 10.6084/m9.figshare.15156818.v1
title: Expression of the <i>foraging</i> gene in adult <i>Drosophila melanogaster</i>

description: The <i>foraging</i> gene in <i>Drosophila melanogaster</i>, which encodes a cGMP-dependent protein kinase, is a highly conserved, complex gene with multiple pleiotropic behavioral and physiological functions in both the larval and adult fly. Adult <i>foraging</i> expression is less well characterized than in the larva. We characterized <i>foraging</i> expression in the brain, gastric system, and reproductive systems using a <i>T2A-Gal4</i> gene-trap allele. In the brain, <i>foraging</i> expression appears to be restricted to multiple sub-types of glia. This glial-specific cellular localization of <i>foraging</i> was supported by single-cell transcriptomic atlases of the adult brain. <i>foraging</i> is extensively expressed in most cell types in the gastric and reproductive systems. We then mapped multiple <i>cis</i>-regulatory elements responsible for parts of the observed expression patterns by a nested cloned promoter-<i>Gal4</i> analysis. The mapped <i>cis</i>-regulatory elements were consistently modular when comparing the larval and adult expression patterns. These new data using the <i>T2A-Gal4</i> gene-trap and cloned <i>foraging</i> promoter fusion <i>GAL4</i>’s are discussed with respect to previous work using an anti-FOR antibody, which we show here to be non-specific. Future studies of <i>foraging</i>’s function will consider roles for glial subtypes and peripheral tissues (gastric and reproductive systems) in <i>foraging</i>’s pleiotropic behavioral and physiological effects.
DOI: 10.6084/m9.figshare.14774426
title: The <i>Drosophila melanogaster foraging</i> gene affects social networks

description: <i>Drosophila melanogaster</i> displays social behaviors including courtship, mating, aggression, and group foraging. Recent studies employed social network analyses (SNAs) to show that <i>D. melanogaster</i> strains differ in their group behavior, suggesting that genes influence social network phenotypes. Aside from genes associated with sensory function, few studies address the genetic underpinnings of these networks. The <i>foraging</i> gene <i>(for)</i> is a well-established example of a pleiotropic gene that regulates multiple behavioral phenotypes and their plasticity. In <i>D. melanogaster,</i> there are two naturally occurring alleles of <i>for</i> called rover and sitter that differ in their larval and adult food-search behavior as well as other behavioral phenotypes. Here, we hypothesize that <i>for</i> affects behavioral elements required to form social networks and the social networks themselves. These effects are evident when we manipulate gene dosage. We found that flies of the rover and sitter strains exhibit differences in duration, frequency, and reciprocity of pairwise interactions, and they form social networks with differences in assortativity and global efficiency. Consistent with other adult phenotypes influenced by <i>for</i>, rover-sitter heterozygotes show intermediate patterns of dominance in many of these characteristics. Multiple generations of backcrossing a rover allele into a sitter strain showed that many but not all of these rover-sitter differences may be attributed to allelic variation at <i>for.</i> Our findings reveal the significant role that <i>for</i> plays in affecting social network properties and their behavioral elements in <i>Drosophila melanogaster</i>.
DOI: 10.6084/m9.figshare.14774426.v1
title: The <i>Drosophila melanogaster foraging</i> gene affects social networks

description: <i>Drosophila melanogaster</i> displays social behaviors including courtship, mating, aggression, and group foraging. Recent studies employed social network analyses (SNAs) to show that <i>D. melanogaster</i> strains differ in their group behavior, suggesting that genes influence social network phenotypes. Aside from genes associated with sensory function, few studies address the genetic underpinnings of these networks. The <i>foraging</i> gene <i>(for)</i> is a well-established example of a pleiotropic gene that regulates multiple behavioral phenotypes and their plasticity. In <i>D. melanogaster,</i> there are two naturally occurring alleles of <i>for</i> called rover and sitter that differ in their larval and adult food-search behavior as well as other behavioral phenotypes. Here, we hypothesize that <i>for</i> affects behavioral elements required to form social networks and the social networks themselves. These effects are evident when we manipulate gene dosage. We found that flies of the rover and sitter strains exhibit differences in duration, frequency, and reciprocity of pairwise interactions, and they form social networks with differences in assortativity and global efficiency. Consistent with other adult phenotypes influenced by <i>for</i>, rover-sitter heterozygotes show intermediate patterns of dominance in many of these characteristics. Multiple generations of backcrossing a rover allele into a sitter strain showed that many but not all of these rover-sitter differences may be attributed to allelic variation at <i>for.</i> Our findings reveal the significant role that <i>for</i> plays in affecting social network properties and their behavioral elements in <i>Drosophila melanogaster</i>.
DOI: 10.6084/m9.figshare.16641799.v2
title: Local ancestry calls for admixed highland mexicana and maize landrace populations in Mexico

description: Publication to cite:Calfee E, Gates D, Lorant A, Perkins MT, Coop G, Ross-Ibarra J (2021). Selective sorting of ancestral introgression in maize and teosinte along an elevational cline. PLOS Genetics. <br>Data here includes posterior probability files of ancestry calls at ~426K ancestry-informative SNPs for individuals from 14 populations of maize and mexicana across Mexico, position information for these SNPs, metadata to identify samples and populations, genomewide ancestry estimates for all samples, input files to ancestry_hmm, and estimated population allele frequencies at these same SNPs. Associated scripts: github.com/ecalfee/hilo. See README file for more information.
DOI: 10.6084/m9.figshare.16641799
title: Local ancestry calls for admixed highland mexicana and maize landrace populations in Mexico

description: Publication to cite:Calfee E, Gates D, Lorant A, Perkins MT, Coop G, Ross-Ibarra J (2021). Selective sorting of ancestral introgression in maize and teosinte along an elevational cline. PLOS Genetics. <br>Data here includes posterior probability files of ancestry calls at ~426K ancestry-informative SNPs for individuals from 14 populations of maize and mexicana across Mexico, position information for these SNPs, metadata to identify samples and populations, genomewide ancestry estimates for all samples, input files to ancestry_hmm, and estimated population allele frequencies at these same SNPs. Associated scripts: github.com/ecalfee/hilo. See README file for more information.
DOI: 10.15151/esrf-es-547535893
title: scanning diffraction on soft matters

description: Xray nano diffraction on the silk and cellulose fibers
DOI: 10.15151/esrf-es-547724236
title: PDF of some oxides

description: PDF of some oxides
DOI: 10.15151/esrf-es-547261238
title: Test scanning diffraction experiments on mouse bone -tendon interface

description: Test scanning diffraction experiments on mouse bone -tendon interface
DOI: 10.6084/m9.figshare.16437026.v2
title: Source Code from Reputation and punishment sustain cooperation in the optional public goods game

description: Python package developed to simulate the discussed models.
DOI: 10.6084/m9.figshare.16437026
title: Source Code from Reputation and punishment sustain cooperation in the optional public goods game

description: Python package developed to simulate the discussed models.
DOI: 10.6084/m9.figshare.16437026.v1
title: Source Code from Reputation and punishment sustain cooperation in the optional public goods game

description: Python package developed to simulate the discussed models.
DOI: 10.5281/zenodo.5518463
title: NicheNet dataset belonging to Saeyslab

description: Dataset belongs to saeyslab (https://github.com/saeyslab/nichenetr/). However, portions of it don't seem to be available to download anymore. Hence this upload.
DOI: 10.5281/zenodo.5518462
title: NicheNet dataset belonging to Saeyslab

description: Dataset belongs to saeyslab (https://github.com/saeyslab/nichenetr/). However, portions of it don't seem to be available to download anymore. Hence this upload.
DOI: 10.5281/zenodo.5517682
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.5281/zenodo.5517681
title: Wikidata Dump

description: RDF dump of wikidata produced with wdumps. <br> View on wdumper <b>entity count</b>: 0, <b>statement count</b>: 0, <b>triple count</b>: 0
DOI: 10.5517/ccdc.csd.cc26w8ft
title: CCDC 2051996: Experimental Crystal Structure Determination

description: Related Article: Udit Kumar, Buthanapalli Ramakrishna, Jisna Varghese, Pitchavel Vidhyapriya, Natarajan Sakthivel, Bala. Manimaran|2021|Inorg.Chem.|60|13284|doi:10.1021/acs.inorgchem.1c01636
DOI: 10.5517/ccdc.csd.cc26w8hw
title: CCDC 2051998: Experimental Crystal Structure Determination

description: Related Article: Udit Kumar, Buthanapalli Ramakrishna, Jisna Varghese, Pitchavel Vidhyapriya, Natarajan Sakthivel, Bala. Manimaran|2021|Inorg.Chem.|60|13284|doi:10.1021/acs.inorgchem.1c01636
DOI: 10.5517/ccdc.csd.cc26w8ds
title: CCDC 2051995: Experimental Crystal Structure Determination

description: Related Article: Udit Kumar, Buthanapalli Ramakrishna, Jisna Varghese, Pitchavel Vidhyapriya, Natarajan Sakthivel, Bala. Manimaran|2021|Inorg.Chem.|60|13284|doi:10.1021/acs.inorgchem.1c01636
DOI: 10.5517/ccdc.csd.cc26w8gv
title: CCDC 2051997: Experimental Crystal Structure Determination

description: Related Article: Udit Kumar, Buthanapalli Ramakrishna, Jisna Varghese, Pitchavel Vidhyapriya, Natarajan Sakthivel, Bala. Manimaran|2021|Inorg.Chem.|60|13284|doi:10.1021/acs.inorgchem.1c01636
DOI: 10.5281/zenodo.5518506
title: Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts

description: Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA All respirometric data that were used for meta-analysis are obtained from the original publications, were converted to SI units, and are available here as a basis for bioenergetic cluster analysis. Inverted regression analysis is illustrated by an example (Figures 1c and d).
description: This work was partially funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 859770, NextGen-O2k project.
description: {"references": ["Gnaiger E (2021) Bioenergetic cluster analysis \u2013 mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA", "Greco M, Villani G, Mazzucchelli F, Bresolin N, Papa S, Attardi G (2003) Marked aging-related decline in efficiency of oxidative phosphorylation in human skin fibroblasts. FASEB J 17:1706-8.", "H\u00fctter E, Renner K, Pfister G, St\u00f6ckl P, Jansen-D\u00fcrr P, Gnaiger E (2004) Senescence-associated changes in respiration and oxidative phosphorylation in primary human fibroblasts. Biochem J 380:919-28.", "Y\u00e9pez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Ko\u0148a\u0159\u00edkov\u00e1 E, Nadel A, Wachutka L, Prokisch H, Gagneur J (2018) OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLOS ONE 13:e0199938. https:// doi.org/10.1371/journal.pone.0199938", "Zdrazilova L, Hanskova H, Gnaiger E (2021) Comparable respiratory activity in attached and suspended fibroblasts. MitoFit Preprints 2021.7. doi:10.26124/mitofit:2021-0007"]}
DOI: 10.5281/zenodo.5517424
title: Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts

description: Gnaiger E (2021) Bioenergetic cluster analysis – mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA All respirometric data that were used for meta-analysis are obtained from the original publications, were converted to SI units, and are available here as a basis for bioenergetic cluster analysis. Inverted regression analysis is illustrated by an example (Figures 1c and d).
description: This work was partially funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No. 859770, NextGen-O2k project.
description: {"references": ["Gnaiger E (2021) Bioenergetic cluster analysis \u2013 mitochondrial respiratory control in human fibroblasts. MitoFit Preprints 2021.8. doi:10.26124/mitofit:2021-0008 - https://www.mitofit.org/index.php/Gnaiger_2021_MitoFit_BCA", "Greco M, Villani G, Mazzucchelli F, Bresolin N, Papa S, Attardi G (2003) Marked aging-related decline in efficiency of oxidative phosphorylation in human skin fibroblasts. FASEB J 17:1706-8.", "H\u00fctter E, Renner K, Pfister G, St\u00f6ckl P, Jansen-D\u00fcrr P, Gnaiger E (2004) Senescence-associated changes in respiration and oxidative phosphorylation in primary human fibroblasts. Biochem J 380:919-28.", "Y\u00e9pez VA, Kremer LS, Iuso A, Gusic M, Kopajtich R, Ko\u0148a\u0159\u00edkov\u00e1 E, Nadel A, Wachutka L, Prokisch H, Gagneur J (2018) OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer. PLOS ONE 13:e0199938. https:// doi.org/10.1371/journal.pone.0199938", "Zdrazilova L, Hanskova H, Gnaiger E (2021) Comparable respiratory activity in attached and suspended fibroblasts. MitoFit Preprints 2021.7. doi:10.26124/mitofit:2021-0007"]}
DOI: 10.18112/openneuro.ds003813.v1.0.0
title: Fitlins - Example
DOI: 10.34740/kaggle/dsv/2635420
title: Dutch News Articles
DOI: 10.6084/m9.figshare.16651852
title: Source Data-GLP-1R and GCGR dual-agonist recovers hepatic fibrosis

description: GLP-1R and GCGR dual-agonist recovers hepatic fibrosis
DOI: 10.6084/m9.figshare.16651852.v1
title: Source Data-GLP-1R and GCGR dual-agonist recovers hepatic fibrosis

description: GLP-1R and GCGR dual-agonist recovers hepatic fibrosis
DOI: 10.6084/m9.figshare.14923527
title: Supplementary Material for: Low corticosterone response to stress in a perimenopausal rat model is associated with the hypoactivation of PaMP region of the PVN and can be corrected by exogenous progesterone supplementation.

description: Medicine
DOI: 10.6084/m9.figshare.16651819
title: Supplementary Material for: Changes in PPAR-γ Expression Are Associated with microRNA Profiles during Fetal Programming due to Maternal Overweight and Obesity

description: <b><i>Background:</i></b> There has been a global increase in the prevalence of obesity in pregnant women in recent years. Animal studies have shown that intrauterine environment associated with maternal obesity leads to epigenetic changes. However, the effects of epigenetic changes occurring before birth in response to maternal conditions have not been clearly characterized in humans. <b><i>Objective:</i></b> The aim of the study was to analyze peroxisome proliferator-activated receptor (PPAR)-γ expression in cell cultures from newborns from mothers with overweight and obesity, in response to in vitro metabolic challenges and their relationship with microRNA profile and cytokine expression. <b><i>Methods/Study design:</i></b> The profile of circulating microRNAs from 72 mother-child pairs (including healthy infants born to normal weight [<i>n</i> = 35], overweight [<i>n</i> = 25], and obese [<i>n</i> = 12] mothers) was determined through real-time PCR, and the PPAR-γ expression in peripheral blood mononuclear cell cultures from offspring was analyzed after in vitro challenges. <b><i>Results:</i></b> miR-146a, miR-155, and miR-378a were upregulated in overweight mothers, while miR-378a was upregulated in obese mothers compared to normal weight mothers. In children from overweight mothers, miR-155 and miR-221 were downregulated and miR-146a was upregulated, while offspring of mothers with obesity showed downregulation of miR-155, miR-221, and miR-1301. These microRNAs have direct or indirect relation with PPAR-γ expression. In vitro exposure to high triglyceride and exposure to miR-378a induced a higher expression of PPAR-γ in cells from offspring of mothers with overweight and obesity. In contrast, cells from offspring of mothers with obesity cultured with high glucose concentrations showed PPAR-γ downregulation. IL-1ß, IL-6, and TNF-α expression in cells of offspring of overweight and obese mothers differed from that of offspring of normal weight mothers. Limitation of our study is the small sample size. <b><i>Conclusion:</i></b> The blood microRNA profile, and in vitro PPAR-γ and inflammatory cytokine expression in cells of newborn infants are associated with maternal obesity indicating that epigenetic marks may be established during intrauterine development. <b><i>Key Message:</i></b> Neonatal microRNA profile is associated with maternal weight. Neonatal microRNA profile is independent of maternal microRNA profile. PPAR-γ expression in newborn cell cultures is affected by maternal weight
DOI: 10.6084/m9.figshare.16651813
title: Supplementary Material for: Perioperative Outcomes of Holmium Laser Enucleation of the Prostate: A Systematic Review

description: <b><i>Introduction:</i></b> The aim of the study was to systematically review the literature and describe perioperative complications of holmium laser enucleation of the prostate (HoLEP), including the Clavien-Dindo classification of surgical complications. <b><i>Methods:</i></b> All English language publications on HoLEP were evaluated. We followed the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analyses) guidelines to evaluate PubMed<sup>®</sup>, Scopus<sup>®</sup>, and Web of Science™ databases from January 1, 1998, to June 1, 2020. <b><i>Results:</i></b> Fifty-seven studies were included, for a total of 10,371 procedures. We distinguished between intra-, peri-, and postoperative complications. Overall, the rate of complications is 0–7%. Intraoperative complications include incomplete morcellation (2.3%), capsular perforation (2.2%), bladder (2.4%), and ureteric orifice (0.4%) injuries. Perioperative complications include postoperative urinary retention (0.2%), hematuria and clot retention (2.6%), and cystoscopy for clot evacuation (0.7%). Postoperative complications include dysuria (7.5%), stress (4.0%), urge (1.8%), transient (7%) and permanent (1.3%) urinary incontinence, urethral stricture (2%) and bladder neck contracture (1%). <b><i>Conclusions:</i></b> HoLEP is a safe procedure, with a satisfactory low complication rate. The most common reported perioperative complications are not severe (Clavien-Dindo classification grades 1–2). Further randomized studies are certainly warranted to fully determine the predictor of surgical complications in order to prevent them and improve this technique.
DOI: 10.26249/fk2/aq02nb/nyeuyh
title: Skalenhandbuch.pdf

description: :unav
DOI: 10.26249/fk2/aq02nb/0gojwn
title: Datensatz.sav

description: :unav
DOI: 10.26249/fk2/aq02nb
title: Replikationsdaten: Erwartungen von Schulleiterinnen und Schulleitern

description: Die durchgeführte Studie stellt eine Replikation der Studie von Schmitz/Voreck (2008) zu den Erwartungen des Schulleiterungspersonals an ihre Lehrkräfte dar. Befragt wurde Schulleitungspersonal an berufsbildenden Schulen in Deutschland zwischen Juli und September 2021. An der Online-Befragung beteiligten sich 170 Personen. Der bereinigte Datensatz umfasst 103 Fälle und ist nicht repräsentativ.
DOI: 10.6084/m9.figshare.16651950
title: supercentenarian-master.zip from Human mortality at extreme age

description: Contains scripts etc. mentioned in SM_reproducibility.pdf
DOI: 10.6084/m9.figshare.16651950.v1
title: supercentenarian-master.zip from Human mortality at extreme age

description: Contains scripts etc. mentioned in SM_reproducibility.pdf