cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7333835
title: Supplementary Material for: The Impact of Midodrine on Outcomes in Patients with Intradialytic Hypotension

description: <b><i>Background:</i></b> Intradialytic hypotension (IDH) is a frequent complication of hemodialysis, and is associated with significant morbidity and mortality. Off-label use of the alpha-1 andrenergic receptor agonist midodrine to reduce the frequency and severity of IDH is common. However, limited data exist to support this practice. This study sought to examine real-world efficacy of midodrine with respect to relevant clinical and hemodynamic outcomes. <b><i>Methods:</i></b> Here, we compared a variety of clinical and hemodynamic outcomes among adult patients who were prescribed midodrine (<i>n</i> = 1,046) and matched controls (<i>n</i> = 2,037), all of whom were receiving in-center hemodialysis treatment at dialysis facilities in the United States (July 2015 – September 2016). Mortality, all-cause hospitalization, cardiovascular hospitalization, and hemodynamic outcomes were considered from the month following the initiation of midodrine (or corresponding month for controls) until censoring for discontinuation of dialysis, transplant, loss to follow-up, or study end (September 30, 2016). Rate outcomes were compared using Poisson models and quantitative outcomes using linear mixed models; all models were adjusted for imbalanced patient characteristics. <b><i>Results:</i></b> Compared to non-use, midodrine use was associated with higher rates of death (adjusted incidence rate ratio 1.37, 95% CI 1.15–1.62), all-cause hospitalization (1.31, 1.19–1.43) and cardiovascular hospitalization (1.41, 1.17–1.71). During follow-up, midodrine use tended to be associated with lower pre-dialysis systolic blood pressure (SBP), lower nadir SBP, greater fall in SBP during dialysis, and a greater proportion of treatments affected by IDH. <b><i>Conclusion:</i></b> Although residual confounding may have influenced the results, the associations observed here are not consistent with a potent beneficial effect of midodrine with respect to either clinical or hemodynamic outcomes.
DOI: 10.7284/110317
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1201 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/110327
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1201 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333772
title: Supplementary Material for: An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of <b><i>Akkermansia Muciniphila</i></b>

description: <b><i>Background/Aims:</i></b> The gut microbiota is altered in irritable bowel syndrome (IBS), and microbiota manipulations by diet or antibiotics can reduce its symptoms. As fecal microbiota transfer (FMT) in IBS is still controversial, we investigated the clinical and side effects of FMT in a cohort of IBS patients with recurrent, treatment refractory symptoms, and studied gut microbiota signatures. <b><i>Methods:</i></b> Using an observational, prospective study design, we applied FMTs from one unrelated, healthy donor to 13 IBS patients. Fecal samples of patients and the donor were analyzed by 16S ribosomal RNA amplicon sequencing. <b><i>Results:</i></b> On a symptom level, primarily abdominal pain symptoms were reduced after FMT, and no adverse effects were observed. Studying the microbiome, we found an increase in alpha diversity and changes in the composition of the gut microbiota after FMT. Beta diversity changes after FMT were prominent in a subset of 7 patients with microbiota profiles coming very close to the donor. These patients also showed most pronounced visceral pain reduction. The relative abundance of <i>Akkermansia muciniphila</i> was inversely correlated with pain reduction in our cohort. <b><i>Conclusion:</i></b> Although exploratory in nature and with a pilot character, this study highlights the potential role of microbiota manipulations in IBS and describes a novel association of intestinal <i>Akkermansia</i> and pain modulation.
DOI: 10.6084/m9.figshare.7333796
title: Supplementary Material for: High-Conductance Channel Formation in Yeast Mitochondria is Mediated by F-ATP Synthase e and g Subunits

description: <b><i>Background/Aims:</i></b> The permeability transition pore (PTP) is an unselective, Ca<sup>2+</sup>-dependent high conductance channel of the inner mitochondrial membrane whose molecular identity has long remained a mystery. The most recent hypothesis is that pore formation involves the F-ATP synthase, which consistently generates Ca<sup>2+</sup>-activated channels. Available structures do not display obvious features that can accommodate a channel; thus, how the pore can form and whether its activity can be entirely assigned to F-ATP synthase is the matter of debate. In this study, we investigated the role of F-ATP synthase subunits e, g and b in PTP formation. <b><i>Methods:</i></b> Yeast null mutants for e, g and the first transmembrane (TM) α-helix of subunit b were generated and evaluated for mitochondrial morphology (electron microscopy), membrane potential (Rhodamine123 fluorescence) and respiration (Clark electrode). Homoplasmic C23S mutant of subunit a was generated by <i>in vitro</i> mutagenesis followed by biolistic transformation. F-ATP synthase assembly was evaluated by BN-PAGE analysis. Cu<sup>2+</sup> treatment was used to induce the formation of F-ATP synthase dimers in the absence of e and g subunits. The electrophysiological properties of F-ATP synthase were assessed in planar lipid bilayers. <b><i>Results:</i></b> Null mutants for the subunits e and g display dimer formation upon Cu<sup>2+</sup> treatment and show PTP-dependent mitochondrial Ca<sup>2+</sup> release but not swelling. Cu<sup>2+</sup> treatment causes formation of disulfide bridges between Cys23 of subunits a that stabilize dimers in absence of e and g subunits and favors the open state of wild-type F-ATP synthase channels. Absence of e and g subunits decreases conductance of the F-ATP synthase channel about tenfold. Ablation of the first TM of subunit b, which creates a distinct lateral domain with e and g, further affected channel activity. <b><i>Conclusion:</i></b> F-ATP synthase e, g and b subunits create a domain within the membrane that is critical for the generation of the high-conductance channel, thus is a prime candidate for PTP formation. Subunits e and g are only present in eukaryotes and may have evolved to confer this novel function to F-ATP synthase.
DOI: 10.6084/m9.figshare.7333772.v1
title: Supplementary Material for: An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of <b><i>Akkermansia Muciniphila</i></b>

description: <b><i>Background/Aims:</i></b> The gut microbiota is altered in irritable bowel syndrome (IBS), and microbiota manipulations by diet or antibiotics can reduce its symptoms. As fecal microbiota transfer (FMT) in IBS is still controversial, we investigated the clinical and side effects of FMT in a cohort of IBS patients with recurrent, treatment refractory symptoms, and studied gut microbiota signatures. <b><i>Methods:</i></b> Using an observational, prospective study design, we applied FMTs from one unrelated, healthy donor to 13 IBS patients. Fecal samples of patients and the donor were analyzed by 16S ribosomal RNA amplicon sequencing. <b><i>Results:</i></b> On a symptom level, primarily abdominal pain symptoms were reduced after FMT, and no adverse effects were observed. Studying the microbiome, we found an increase in alpha diversity and changes in the composition of the gut microbiota after FMT. Beta diversity changes after FMT were prominent in a subset of 7 patients with microbiota profiles coming very close to the donor. These patients also showed most pronounced visceral pain reduction. The relative abundance of <i>Akkermansia muciniphila</i> was inversely correlated with pain reduction in our cohort. <b><i>Conclusion:</i></b> Although exploratory in nature and with a pilot character, this study highlights the potential role of microbiota manipulations in IBS and describes a novel association of intestinal <i>Akkermansia</i> and pain modulation.
DOI: 10.6084/m9.figshare.7333796.v1
title: Supplementary Material for: High-Conductance Channel Formation in Yeast Mitochondria is Mediated by F-ATP Synthase e and g Subunits

description: <b><i>Background/Aims:</i></b> The permeability transition pore (PTP) is an unselective, Ca<sup>2+</sup>-dependent high conductance channel of the inner mitochondrial membrane whose molecular identity has long remained a mystery. The most recent hypothesis is that pore formation involves the F-ATP synthase, which consistently generates Ca<sup>2+</sup>-activated channels. Available structures do not display obvious features that can accommodate a channel; thus, how the pore can form and whether its activity can be entirely assigned to F-ATP synthase is the matter of debate. In this study, we investigated the role of F-ATP synthase subunits e, g and b in PTP formation. <b><i>Methods:</i></b> Yeast null mutants for e, g and the first transmembrane (TM) α-helix of subunit b were generated and evaluated for mitochondrial morphology (electron microscopy), membrane potential (Rhodamine123 fluorescence) and respiration (Clark electrode). Homoplasmic C23S mutant of subunit a was generated by <i>in vitro</i> mutagenesis followed by biolistic transformation. F-ATP synthase assembly was evaluated by BN-PAGE analysis. Cu<sup>2+</sup> treatment was used to induce the formation of F-ATP synthase dimers in the absence of e and g subunits. The electrophysiological properties of F-ATP synthase were assessed in planar lipid bilayers. <b><i>Results:</i></b> Null mutants for the subunits e and g display dimer formation upon Cu<sup>2+</sup> treatment and show PTP-dependent mitochondrial Ca<sup>2+</sup> release but not swelling. Cu<sup>2+</sup> treatment causes formation of disulfide bridges between Cys23 of subunits a that stabilize dimers in absence of e and g subunits and favors the open state of wild-type F-ATP synthase channels. Absence of e and g subunits decreases conductance of the F-ATP synthase channel about tenfold. Ablation of the first TM of subunit b, which creates a distinct lateral domain with e and g, further affected channel activity. <b><i>Conclusion:</i></b> F-ATP synthase e, g and b subunits create a domain within the membrane that is critical for the generation of the high-conductance channel, thus is a prime candidate for PTP formation. Subunits e and g are only present in eukaryotes and may have evolved to confer this novel function to F-ATP synthase.
DOI: 10.7284/110557
title: Expendable Probe data collected during research cruise RR1201 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333715
title: Supplementary Material for: Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

description: <b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. <b><i>Methods:</i></b> In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. <b><i>Results:</i></b> A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. <b><i>Conclusion:</i></b> <i>XLOC_046142, XLOC_004398</i> and <i>XLOC_015408</i> may target <i>MAPKAPK2, NR1D2</i> and <i>AKR1C4</i>, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. <i>XLOC_064871</i> and <i>XLOC_011001</i> may play a role in lipid metabolism-related disease via regulating <i>TRIB3</i> and <i>BRCA1</i>. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.
DOI: 10.6084/m9.figshare.7333709
title: Supplementary Material for: Peperomin E Induces Promoter Hypomethylation of Metastatic-Suppressor Genes and Attenuates Metastasis in Poorly Differentiated Gastric Cancer

description: <b><i>Background/Aims:</i></b> Peperomin E (PepE), a natural secolignan isolated from the whole plant of <i>Peperomia dindygulensis</i>, has been reported by ourselves and others to display potent anti-cancer effects in many types cancer cells, especially gastric cancer. However, the effects of PepE on the metastasis of poorly-differentiated gastric cancer cells and the underlying molecular mechanisms have not been well elucidated. <b><i>Methods:</i></b> We evaluated PepE effects on gastric cancer cell invasion and migration <i>in vitro</i> via wound healing and transwell assays and those on growth and metastasis <i>in vivo</i> using an orthotopic xenograft NOD-SCID mouse model. DNA methyltransferase (DNMT) activity was determined using a colorimetric DNMT activity/inhibition assay kit. PepE binding kinetics to DNMTs were determined using the bio-layer interferometry binding assay. Gene and protein levels of DNMTs, AMPKα-Sp1 signaling molecules, and metastatic-suppressor genes in PepE-treated gastric cancer cells were determined using quantitative reverse transcription-PCR arrays and western blotting. The effect of PepE on Sp1 binding to the <i>DNMT</i> promoter was determined by electrophoretic mobility-shift assay. Global DNA methylation levels were determined using liquid chromatography coupled with electrospray ionization tandem mass spectrometry. The methylation status of silenced metastatic-suppressor genes (MSGs) in gastric cancer cells was investigated by methylation-specific PCR. <b><i>Results:</i></b> PepE can dose-dependently suppress invasion and migration of poorly-differentiated gastric cancer cells <i>in vitro</i> and <i>in vivo</i> with low toxicity against normal cells. Mechanistically, PepE not only covalently binds to the catalytic domain of DNMT1 and inhibits its activity (IC<sub>50</sub> value 3.61 μM) but also down-regulates DNMT1, 3a, and 3b mRNA and protein expression in in gastric cancer cells, by disruption of the physical interaction of Sp1 with the <i>DNMT1, 3a</i>, and <i>3b</i> promoter and mediation of the AMPKα-Sp1 signaling pathway. The dual inhibition activity of PepE toward DNMTs renders a relative global DNA hypomethylation, which induces MSG promoter hypomethylation (e.g., E-cadherin and TIMP3) and enhances their expression in gastric cancer cells. <b><i>Conclusion:</i></b> Collectively, our data indicated that PepE may represent a promising therapeutic lead compound for intervention in gastric cancer metastasis and may also exhibit potential as a DNA methylation inhibitor for use in epigenetic cancer therapy.
DOI: 10.7284/110319
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1201 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/110322
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1201 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333616
title: TACAS2019 Artifact Evaluation for paper "J-ReCoVer: Java Reducer Commutativity Verifier"

description: This archive is for the artifact evaluation for the paper "J-ReCoVer: Java Reducer Commutativity Verifier". In this paper, we propose effective heuristics for reducer commutativity analysis and implement them as a tool named J-ReCoVer (Java Reducer Commutativity Verifier). To our knowledge, J-ReCoVer is the first tool specialized in checking reducer commutativity.<br><br>The archive contains the scripts and the benchmarks used to replicate the results showed in the paper, more specifically, to redo the experiments and produce the three result tables and the diagram that we showed in the evaluation chapter of the paper. There are step-by-step instructions included in the README file for how to run the scripts.
DOI: 10.7284/110324
title: Gravimeter data collected during research cruise RR1201 using a Bell BGM-3 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333616.v1
title: TACAS2019 Artifact Evaluation for paper "J-ReCoVer: Java Reducer Commutativity Verifier"

description: This archive is for the artifact evaluation for the paper "J-ReCoVer: Java Reducer Commutativity Verifier". In this paper, we propose effective heuristics for reducer commutativity analysis and implement them as a tool named J-ReCoVer (Java Reducer Commutativity Verifier). To our knowledge, J-ReCoVer is the first tool specialized in checking reducer commutativity.<br><br>The archive contains the scripts and the benchmarks used to replicate the results showed in the paper, more specifically, to redo the experiments and produce the three result tables and the diagram that we showed in the evaluation chapter of the paper. There are step-by-step instructions included in the README file for how to run the scripts.
DOI: 10.6084/m9.figshare.7333610
title: Additional file 5: of Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

description: List of the genes from the conserved syntenic region of npm2 genes. (XLSX 16 kb)
DOI: 10.7284/110321
title: Gyrocompass data collected during research cruise RR1201 using a iXSea Hydrins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333616.v2
title: TACAS2019 Artifact Evaluation for paper "J-ReCoVer: Java Reducer Commutativity Verifier"

description: This archive is for the artifact evaluation for the paper "J-ReCoVer: Java Reducer Commutativity Verifier". In this paper, we propose effective heuristics for reducer commutativity analysis and implement them as a tool named J-ReCoVer (Java Reducer Commutativity Verifier). To our knowledge, J-ReCoVer is the first tool specialized in checking reducer commutativity.<br><br>The archive contains the scripts and the benchmarks used to replicate the results showed in the paper, more specifically, to redo the experiments and produce the three result tables and the diagram that we showed in the evaluation chapter of the paper. There are step-by-step instructions included in the README file for how to run the scripts.
DOI: 10.7284/110323
title: Gyrocompass data collected during research cruise RR1201 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333607
title: Additional file 4: of Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

description: Npm2a and Npm2b protein sequence comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7333607.v1
title: Additional file 4: of Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

description: Npm2a and Npm2b protein sequence comparisons. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7333616.v3
title: TACAS2019 Artifact Evaluation for paper "J-ReCoVer: Java Reducer Commutativity Verifier"

description: This archive is for the artifact evaluation for the paper "J-ReCoVer: Java Reducer Commutativity Verifier". In this paper, we propose effective heuristics for reducer commutativity analysis and implement them as a tool named J-ReCoVer (Java Reducer Commutativity Verifier). To our knowledge, J-ReCoVer is the first tool specialized in checking reducer commutativity.<br><br>The archive contains the scripts and the benchmarks used to replicate the results showed in the paper, more specifically, to redo the experiments and produce the three result tables and the diagram that we showed in the evaluation chapter of the paper. There are step-by-step instructions included in the README file for how to run the scripts.
DOI: 10.7284/110316
title: Meteorological Station data collected during research cruise RR1201 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7333604
title: Additional file 3: of Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

description: qPCR and PCR primers. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7333616.v4
title: TACAS2019 Artifact Evaluation for paper "J-ReCoVer: Java Reducer Commutativity Verifier"

description: This archive is for the artifact evaluation for the paper "J-ReCoVer: Java Reducer Commutativity Verifier". In this paper, we propose effective heuristics for reducer commutativity analysis and implement them as a tool named J-ReCoVer (Java Reducer Commutativity Verifier). To our knowledge, J-ReCoVer is the first tool specialized in checking reducer commutativity.<br><br>The archive contains the scripts and the benchmarks used to replicate the results showed in the paper, more specifically, to redo the experiments and produce the three result tables and the diagram that we showed in the evaluation chapter of the paper. There are step-by-step instructions included in the README file for how to run the scripts.
DOI: 10.6084/m9.figshare.7333604.v1
title: Additional file 3: of Double maternal-effect: duplicated nucleoplasmin 2 genes, npm2a and npm2b, with essential but distinct functions are shared by fish and tetrapods

description: qPCR and PCR primers. (XLSX 9 kb)