cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6561647.v2
title: Measuring autophagosome flux

description: Macroautophagy/autophagy is a proteolytic pathway that is involved in both bulk degradation of cytoplasmic proteins as well as in selective degradation of cytoplasmic organelles. Autophagic flux is often defined as a measure of autophagic degradation activity, and many techniques exist to assess autophagic flux. Although these techniques have generated invaluable information about the autophagic system, the quest continues for developing methods that not only enhance sensitivity and provide a means of quantification, but also accurately reflect the dynamic character of the pathway. Based on the theoretical framework of metabolic control analysis, where the autophagosome flux is the quantitative description of the rate a flow along a pathway, here we treat the autophagy system as a multi-step pathway. We describe a single-cell fluorescence live-cell imaging-based approach that allows the autophagosome flux to be accurately measured. This method characterizes autophagy in terms of its complete autophagosome and autolysosome pool size, the autophagosome flux, J, and the transition time, τ, for autophagosomes and autolysosomes at steady state. This approach provides a sensitive quantitative method to measure autophagosome flux, pool sizes and transition time in cells and tissues of clinical relevance. <b>Abbreviations</b>: ATG5/APG5, autophagy-related 5; GFP, green fluorescent protein; LAMP1, lysosomal-associated membrane protein 1; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; J, flux; MEF, mouse embryonic fibroblast; MTOR, mechanistic target of rapamycin kinase; <i>nA</i>, number of autophagosomes; <i>nAL</i>, number of autolysosomes; <i>nL</i>, number of lysosomes; p-MTOR, phosphorylated mechanistic target of rapamycin kinase; RFP, red fluorescent protein; siRNA, small interfering RNA; τ, transition time; TEM, transmission electron microscopy.
DOI: 10.6084/m9.figshare.6561647.v1
title: Measuring Autophagosome Flux

description: Macroautophagy/autophagy is a proteolytic pathway that is involved in both bulk degradation of cytoplasmic proteins as well as in selective degradation of cytoplasmic organelles. Autophagic flux is often defined as a measure of autophagic degradation activity, and many techniques exist to assess autophagic flux. Although these techniques have generated invaluable information about the autophagic system, the quest continues for developing methods that not only enhance sensitivity and provide a means of quantification, but also accurately reflect the dynamic character of the pathway. Based on the theoretical framework of metabolic control analysis, where the autophagosome flux is the quantitative description of the rate a flow along a pathway, here we treat the autophagy system as a multi-step pathway. We describe a single-cell fluorescence live-cell imaging-based approach that allows the autophagosome flux to be accurately measured. This method characterizes autophagy in terms of its complete autophagosome and autolysosome pool size, the autophagosome flux, J, and the transition time, τ, for autophagosomes and autolysosomes at steady state. This approach provides a sensitive quantitative method to measure autophagosome flux, pool sizes and transition time in cells and tissues of clinical relevance.
DOI: 10.6084/m9.figshare.6561620
title: Wetlands.xlsx

description: Fig.1-Fig.7 data source, How do variations of constructed wetland affect nutrient discharge: resolution from a conceptual model and implications to water quality management.
DOI: 10.6084/m9.figshare.6561620.v1
title: Wetlands.xlsx

description: Fig.1-Fig.7 data source, How do variations of constructed wetland affect nutrient discharge: resolution from a conceptual model and implications to water quality management.
DOI: 10.6084/m9.figshare.6561113
title: Additional file 7: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S3. Results of blastn searches to identify truncated copies of XKol-Tpase genes. Prospective XKol-Tpase CDS used as a query, locus of the CDS, hit locus of the blastn search (e-value &lt;1e-100), and its length (bp) are shown. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.6561113.v1
title: Additional file 7: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S3. Results of blastn searches to identify truncated copies of XKol-Tpase genes. Prospective XKol-Tpase CDS used as a query, locus of the CDS, hit locus of the blastn search (e-value &lt;1e-100), and its length (bp) are shown. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.6561107
title: Additional file 6: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S2. Primer sequences used in PCR to clone XKol-Tpase CDSs from the X. tropicalis Nigerian and Asashima lineages. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.6561107.v1
title: Additional file 6: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S2. Primer sequences used in PCR to clone XKol-Tpase CDSs from the X. tropicalis Nigerian and Asashima lineages. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.6561095
title: Additional file 5: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S1. Name for the Kolobok superfamily transposase query used in the tblastn search. Name for the source transposon in Repbase and protein length are shown. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6561095.v1
title: Additional file 5: of Multiple massive domestication and recent amplification of Kolobok superfamily transposons in the clawed frog Xenopus

description: Table S1. Name for the Kolobok superfamily transposase query used in the tblastn search. Name for the source transposon in Repbase and protein length are shown. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6558971
title: Theoretical ribosomal protein mass fingerprint of Enterobacter cloacae

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Enterobacter cloacae.</i><br><br>
DOI: 10.6084/m9.figshare.6558971.v1
title: Theoretical ribosomal protein mass fingerprint of Enterobacter cloacae

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Enterobacter cloacae.</i><br><br>
DOI: 10.6084/m9.figshare.6558908
title: Theoretical ribosomal protein mass fingerprint of Clostridium perfringens

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Clostridium perfringens.</i><br><br>
DOI: 10.6084/m9.figshare.6558908.v1
title: Theoretical ribosomal protein mass fingerprint of Clostridium perfringens

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Clostridium perfringens.</i><br><br>
DOI: 10.6084/m9.figshare.6558704
title: Theoretical ribosomal protein mass fingerprint of Clostridium botulinum

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Clostridium botulinum</i>.<br><br>
DOI: 10.6084/m9.figshare.6558704.v1
title: Theoretical ribosomal protein mass fingerprint of Clostridium botulinum

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Clostridium botulinum</i>.<br><br>
DOI: 10.6084/m9.figshare.6555761
title: data

description: A repo with all the datasets I've used for my research
DOI: 10.6084/m9.figshare.6555761.v1
title: data

description: A repo with all the datasets I've used for my research
DOI: 10.6084/m9.figshare.6555737
title: HatcheryBacteria_code.txt

description: Mothur script used to analyze bacterial communities on the Lake Sturgeon egg surfaces through their development, and how potential probiotics can direct these egg-associated communities assembly and succession. <br>
DOI: 10.6084/m9.figshare.6555737.v2
title: HatcheryBacteria_code.txt

description: Mothur script used to analyze bacterial communities on the Lake Sturgeon egg surfaces through their development, and how potential probiotics can direct these egg-associated communities assembly and succession. <br>
DOI: 10.6084/m9.figshare.6555203
title: Dataset from Groups and scores: the decline of cooperation

description: All the data collected in the experiment
DOI: 10.6084/m9.figshare.6555203.v1
title: Dataset from Groups and scores: the decline of cooperation

description: All the data collected in the experiment
DOI: 10.6084/m9.figshare.6555200
title: Instructions from Groups and scores: the decline of cooperation

description: Experimental instructions provided to subjects in the lab
DOI: 10.6084/m9.figshare.6555200.v1
title: Instructions from Groups and scores: the decline of cooperation

description: Experimental instructions provided to subjects in the lab
DOI: 10.6084/m9.figshare.6555164
title: Acid suppression in patients treated with endoscopic therapy for the management of gastroesophageal varices: a systematic review and meta-analysis

description: <b>Background and aim</b>: Endoscopic therapy is the cornerstone choice for the management of varices and variceal hemorrhage. The aim of the present systematic review and meta-analysis was to evaluate the efficacy of acid suppression in patients treated with endoscopic therapy for gastroesophageal varices. <b>Methods</b>: All eligible studies were searched via the PubMed, EMBASE, and Cochrane Library databases. Incidence of bleeding, mortality, ulcers, chest pain, and dysphagia after endoscopic therapy and length of stay were analyzed. Subgroup analyses were performed according to the types and major indications of endoscopic treatments. Odds ratios (ORs) with 95% confidence intervals (95%CIs) were calculated. <b>Results</b>: Nine studies with 1470 patients were included. Acid suppression could significantly decrease the incidence of bleeding (OR = 0.39, 95%CI: 0.19–0.81, P = 0.01) and diminish the ulcer size (OR = 0.78, 95%CI: 0.38–1.57, P = 0.48) after endoscopic therapy. The subgroup analyses showed that acid suppression could significantly decrease the incidence of bleeding in patients undergoing prophylactic EVL, rather than in patients undergoing therapeutic EVL. There was no significant difference in the incidence of mortality, ulcers, chest pain, and dysphagia and length of stay between patients treated with and without acid suppression. <b>Conclusion</b>: Acid suppression might be considered in patients undergoing prophylactic EVL for gastroesophageal varices.
DOI: 10.6084/m9.figshare.6555164.v1
title: Acid suppression in patients treated with endoscopic therapy for the management of gastroesophageal varices: a systematic review and meta-analysis

description: <b>Background and aim</b>: Endoscopic therapy is the cornerstone choice for the management of varices and variceal hemorrhage. The aim of the present systematic review and meta-analysis was to evaluate the efficacy of acid suppression in patients treated with endoscopic therapy for gastroesophageal varices. <b>Methods</b>: All eligible studies were searched via the PubMed, EMBASE, and Cochrane Library databases. Incidence of bleeding, mortality, ulcers, chest pain, and dysphagia after endoscopic therapy and length of stay were analyzed. Subgroup analyses were performed according to the types and major indications of endoscopic treatments. Odds ratios (ORs) with 95% confidence intervals (95%CIs) were calculated. <b>Results</b>: Nine studies with 1470 patients were included. Acid suppression could significantly decrease the incidence of bleeding (OR = 0.39, 95%CI: 0.19–0.81, P = 0.01) and diminish the ulcer size (OR = 0.78, 95%CI: 0.38–1.57, P = 0.48) after endoscopic therapy. The subgroup analyses showed that acid suppression could significantly decrease the incidence of bleeding in patients undergoing prophylactic EVL, rather than in patients undergoing therapeutic EVL. There was no significant difference in the incidence of mortality, ulcers, chest pain, and dysphagia and length of stay between patients treated with and without acid suppression. <b>Conclusion</b>: Acid suppression might be considered in patients undergoing prophylactic EVL for gastroesophageal varices.
DOI: 10.6084/m9.figshare.6555071
title: Data and analyses files for "To boldly go where no one has gone before – networks of moons"

description: This fileset provides the basic data and analysis files used for a blogpost on the Genealogical World of Phylogenetic Networks by Guido Grimm and Timothy Holt entitled"To boldy go where no one has gone before – networks of moons"<br><br><br><b>Content<br></b>Figures shown in the blogpost and a 7z-archive (7-zip.org) including<br>— different versions of the basic data matrices including versions with code lines for the performed analysis with PAUP* (in JupiterMatrix99.simple.nex the code lines are explained to facilitate use by newbies)<br>— results of the distance-based and parsimony analyses<br>See Readme.txt for labelling conventions, format, and further information.<br><br><b>!!Important note!!</b> In case you re-use the here provided data, make sure to cite (also) the original publication:<br><br>Holt TR, Brown AJ, Nesvorný D, Horner J, Carter B (2018) Cladistical analysis of the Jovian and Saturnian satellite systems. Astrophysical Journal 859(2): 97, 20 pp<br>Pre-print version at arXiv: 1706.0142<br>
DOI: 10.6084/m9.figshare.6555071.v1
title: Data and analyses files for "To boldly go where no one has gone before – networks of moons"

description: This fileset provides the basic data and analysis files used for a blogpost on the Genealogical World of Phylogenetic Networks by Guido Grimm and Timothy Holt entitled"To boldy go where no one has gone before – networks of moons"<br><br><br><b>Content<br></b>Figures shown in the blogpost and a 7z-archive (7-zip.org) including<br>— different versions of the basic data matrices including versions with code lines for the performed analysis with PAUP* (in JupiterMatrix99.simple.nex the code lines are explained to facilitate use by newbies)<br>— results of the distance-based and parsimony analyses<br>See Readme.txt for labelling conventions, format, and further information.<br><br><b>!!Important note!!</b> In case you re-use the here provided data, make sure to cite (also) the original publication:<br><br>Holt TR, Brown AJ, Nesvorný D, Horner J, Carter B (2018) Cladistical analysis of the Jovian and Saturnian satellite systems. Astrophysical Journal 859(2): 97, 20 pp<br>Pre-print version at arXiv: 1706.0142<br>
DOI: 10.6084/m9.figshare.6554606
title: Energy from Waste (EfW) Ontology - Snapshots & Supplemental Information

description: <i>Energy from Waste</i> (EfW) Ontology - snapshotsScreenshots of first working prototype for corresponding Digital Business Ecosystem
DOI: 10.6084/m9.figshare.6554606.v1
title: Energy from Waste (EfW) Ontology and Digital Business Ecosystem

description: <i>Energy from Waste</i> (EfW) Ontology - snapshotsScreenshots of first working prototype for corresponding Digital Business Ecosystem
DOI: 10.6084/m9.figshare.6554606.v2
title: Energy from Waste (EfW) Ontology and Digital Business Ecosystem

description: <i>Energy from Waste</i> (EfW) Ontology - snapshotsScreenshots of first working prototype for corresponding Digital Business Ecosystem
DOI: 10.6084/m9.figshare.6554606.v3
title: Energy from Waste (EfW) Ontology - Snapshots & Supplemental Information

description: <i>Energy from Waste</i> (EfW) Ontology - snapshotsScreenshots of first working prototype for corresponding Digital Business Ecosystem
DOI: 10.6084/m9.figshare.6554219
title: Additional file 4: of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S3. List of datasets used in this study and their source. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6554219.v1
title: Additional file 4: of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S3. List of datasets used in this study and their source. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6554210
title: Additional file 3:Â of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S2. Human RNAseq, ChIPseq and WGBS allele-specific alignmentÂ results. (TXT 6957 kb)
DOI: 10.6084/m9.figshare.6554210.v1
title: Additional file 3:Â of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S2. Human RNAseq, ChIPseq and WGBS allele-specific alignmentÂ results. (TXT 6957 kb)
DOI: 10.6084/m9.figshare.6554207
title: Additional file 6: of Temporal changes in macrophage phenotype after peripheral nerve injury

description: Table S4a. Gene expression of bone marrow-derived macrophages from 3 mouse strains under 3 in vitro stimulation conditions. Log transformed mRNA transcript count mean +/−standard deviation & Tukey letters from linear mixed effect model with mouse as a random effect and an interaction term of strain*stimulation, followed by Benjamini and Hochberg false discovery rate (FDR) correction. p value for the interaction term is displayed. Table S4b. Gene expression of bone marrow-derived macrophages from 2 mouse strains under 3 in vitro stimulation conditions. Log transformed mRNA transcript count mean +/−standard deviation & Tukey letters from linear mixed effect model with mouse as a random effect and an interaction term of strain*stimulation, followed by Benjamini and Hochberg false discovery rate (FDR) correction. (ZIP 128 kb)
DOI: 10.6084/m9.figshare.6554207.v1
title: Additional file 6: of Temporal changes in macrophage phenotype after peripheral nerve injury

description: Table S4a. Gene expression of bone marrow-derived macrophages from 3 mouse strains under 3 in vitro stimulation conditions. Log transformed mRNA transcript count mean +/−standard deviation & Tukey letters from linear mixed effect model with mouse as a random effect and an interaction term of strain*stimulation, followed by Benjamini and Hochberg false discovery rate (FDR) correction. p value for the interaction term is displayed. Table S4b. Gene expression of bone marrow-derived macrophages from 2 mouse strains under 3 in vitro stimulation conditions. Log transformed mRNA transcript count mean +/−standard deviation & Tukey letters from linear mixed effect model with mouse as a random effect and an interaction term of strain*stimulation, followed by Benjamini and Hochberg false discovery rate (FDR) correction. (ZIP 128 kb)
DOI: 10.6084/m9.figshare.6554195
title: Additional file 2: of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S1. BWA and Bowtie2 allele-specific alignment results. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.6554195.v1
title: Additional file 2: of Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)

description: Table S1. BWA and Bowtie2 allele-specific alignment results. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.6554171
title: Additional file 2: of Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss

description: Table S1. (115 KB)
DOI: 10.6084/m9.figshare.6554171.v1
title: Additional file 2: of Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss

description: Table S1. (115 KB)
DOI: 10.6084/m9.figshare.6554129
title: Additional file 1: of Expression of the glucagon-like peptide-1 receptor and its role in regulating autophagy in endometrial cancer

description: Table S1. Detailed data of participants. Clinicopathological data of 154 patients with endometrial cancer who underwent surgery at the Teikyo University Hospital. These clinical characteristics were obtained by a retrospective review of medical records and the pathological data were obtained by our tissue microarray. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6554129.v1
title: Additional file 1: of Expression of the glucagon-like peptide-1 receptor and its role in regulating autophagy in endometrial cancer

description: Table S1. Detailed data of participants. Clinicopathological data of 154 patients with endometrial cancer who underwent surgery at the Teikyo University Hospital. These clinical characteristics were obtained by a retrospective review of medical records and the pathological data were obtained by our tissue microarray. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6554105
title: Additional file 2: of Mosaicism of the UDP-Galactose transporter SLC35A2 in a female causing a congenital disorder of glycosylation: a case report

description: Figure S2. A, B. A. Length growth over time. B. Weight growth over time. (ZIP 65 kb)
DOI: 10.6084/m9.figshare.6554105.v1
title: Additional file 2: of Mosaicism of the UDP-Galactose transporter SLC35A2 in a female causing a congenital disorder of glycosylation: a case report

description: Figure S2. A, B. A. Length growth over time. B. Weight growth over time. (ZIP 65 kb)
DOI: 10.6084/m9.figshare.6554069
title: Additional file 9: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Temporal versus local genetic differentiation. Temporal genetic change in comparison to local and regional genetic differentiation(F ST and D est ) for each population and sampling time point (historical and present). (XLSX 6 kb)
DOI: 10.6084/m9.figshare.6554069.v1
title: Additional file 9: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Temporal versus local genetic differentiation. Temporal genetic change in comparison to local and regional genetic differentiation(F ST and D est ) for each population and sampling time point (historical and present). (XLSX 6 kb)
DOI: 10.6084/m9.figshare.6554051
title: Additional file 8: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Diversity estimates. Diversity estimates, including heterozygosity (Hexp), allelic richness (Îą), and multi-locus heterozygosity (MLH), for each location and region with standard errors, and inbreeding coefficients F IS with p values for each population. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6554051.v1
title: Additional file 8: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Diversity estimates. Diversity estimates, including heterozygosity (Hexp), allelic richness (Îą), and multi-locus heterozygosity (MLH), for each location and region with standard errors, and inbreeding coefficients F IS with p values for each population. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6554030
title: Additional file 7: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Temporal changes. Estimates of effective population size (Ne), temporal genetic differentiation (F ST and D est ), and p values for temporal changes in diversity measures at each sampling site. (XLSX 6 kb)
DOI: 10.6084/m9.figshare.6554030.v1
title: Additional file 7: of Decadal stability in genetic variation and structure in the intertidal seaweed Fucus serratus (Heterokontophyta: Fucaceae)

description: Temporal changes. Estimates of effective population size (Ne), temporal genetic differentiation (F ST and D est ), and p values for temporal changes in diversity measures at each sampling site. (XLSX 6 kb)