cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6176744.v1
title: Infliximab restores colonic barrier to adherent-invasive <i>E. coli</i> in Crohn’s disease via effects on epithelial lipid rafts

description: <b>Objective:</b> Infliximab is important in the therapeutic arsenal of Crohn’s disease (CD). However, its effect on mucosal barrier function is not fully understood. Adherent-invasive <i>Escherichia coli</i> (AIEC) are important in CD pathophysiology, but the transmucosal uptake routes are partly unknown. We investigated effects of infliximab on uptake of colon-specific AIEC HM427 across CD colonic mucosa. <b>Materials and methods:</b> Endoscopic biopsies from non-inflamed colon of seven patients with CD, before and after two infliximab infusions, and eight non-inflammation controls, were mounted in Ussing chambers. Paracellular permeability (<sup>51</sup>Cr-EDTA) and transmucosal passage of GFP-expressing HM427 were studied. Mechanisms of HM427 transepithelial transport were investigated in Caco-2 monolayers treated with TNF, in the presence of infliximab and/or endocytosis inhibitors. <b>Results:</b> Before infliximab treatment, colonic passage of HM427 [CD: 2475 CFU (450–3000); controls 1163(225–1950)] and <sup>51</sup>Cr-EDTA permeability were increased in CD (<i>p</i> <b>Conclusion:</b> Infliximab restored the colonic barrier to AIEC in CD; an effect partially mediated by blocking lipid rafts in epithelial cells. This ability likely contributes to infliximab’s clinical efficacy in colonic CD.
DOI: 10.6084/m9.figshare.6176693
title: Uncropped Western blots

description: Uncropped Western blots of the co-immunoprecipitation experiments.
DOI: 10.6084/m9.figshare.6176693.v1
title: Uncropped Western blots

description: Uncropped Western blots of the co-immunoprecipitation experiments.
DOI: 10.6084/m9.figshare.6176684
title: S2b_Sleuth_analysis_with_TranscriptIDs

description: Sleuth analysis with Trinity transcript IDs.<br>RNA-Seq data available in the NCBI Sequence Read Archive with the bio-project accession number PRJNA407266.
DOI: 10.6084/m9.figshare.6176684.v1
title: S2b_Sleuth_analysis_with_TranscriptIDs

description: Sleuth analysis with Trinity transcript IDs.<br>RNA-Seq data available in the NCBI Sequence Read Archive with the bio-project accession number PRJNA407266.
DOI: 10.17028/rd.lboro.6176582
title: Systems Thinking - A New Direction of Healthcare Incident Investigation

description: 3min 55sec animation on systems thinking in healthcare incident investigation - English and Spanish voice-over
DOI: 10.17028/rd.lboro.6176582.v1
title: Systems Thinking - A New Direction of Healthcare Incident Investigation

description: 3min 55sec animation on systems thinking in healthcare incident investigation - English and Spanish voice-over
DOI: 10.6084/m9.figshare.6176576
title: Results of a randomised trial assessing the effectiveness of different dosages of levofloxacin to cure Helicobacter pylori infection

description: This dataset presents the results of a randomised clinical trial involving 400 participants, which aimed to compare the effectiveness, safety, and compliance of different dosages of levofloxacin used to cure Helicobacter pylori (H. pylori) infection. <br>Patients were assigned to either Group A or Group B, and received esomeprazole, amoxicillin, colloidal bismuth pectin and levofloxacin 500 mg once per day (group A); or levofloxacin 200 mg twice per day (group B) over a 14 day period.<br>The presence of H. pylori was assessed before and after the trial using c-urea breath testing (C-UBT). <br>The dataset is comprised of an Excel spreadsheet with a single tab. Each of the 400 patients is assigned a number, and the dataset includes their baseline C-UBT result, randomised treatment group and follow-up C-UBT; any adverse reactions noted by patients during the trial period; and whether the study was completed per the protocol analysis.
DOI: 10.6084/m9.figshare.6176576.v1
title: Results of a randomised trial assessing the effectiveness of different dosages of levofloxacin to cure Helicobacter pylori infection

description: This dataset presents the results of a randomised clinical trial involving 400 participants, which aimed to compare the effectiveness, safety, and compliance of different dosages of levofloxacin used to cure Helicobacter pylori (H. pylori) infection. <br>Patients were assigned to either Group A or Group B, and received esomeprazole, amoxicillin, colloidal bismuth pectin and levofloxacin 500 mg once per day (group A); or levofloxacin 200 mg twice per day (group B) over a 14 day period.<br>The presence of H. pylori was assessed before and after the trial using c-urea breath testing (C-UBT). <br>The dataset is comprised of an Excel spreadsheet with a single tab. Each of the 400 patients is assigned a number, and the dataset includes their baseline C-UBT result, randomised treatment group and follow-up C-UBT; any adverse reactions noted by patients during the trial period; and whether the study was completed per the protocol analysis.
DOI: 10.6084/m9.figshare.6176567
title: Effects of <i>Daphnia</i> exudates and sodium octyl sulphates on filament morphology and cell wall thickness of <i>Aphanizomenon gracile</i> (Nostocales), <i>Cylindrospermopsis raciborskii</i> (Nostocales) and <i>Planktothrix agardhii</i> (Oscillatoriales)

description: Grazing is recognized as one of the selective factors shaping the morphology and physiology of cyanobacteria. A recent study has shown that the filamentous cyanobacterium <i>Aphanizomenon gracile</i> strain SAG 31.79 thickened in the presence of <i>Daphnia</i> (Cladocera) and its exudates. The aims of our study were: (1) to determine whether this type of response to <i>Daphnia</i> cues is common for other strains of <i>A. gracile</i>, and other species of filamentous cyanobacteria, (2) to test whether the response is due to nutrients recycled by <i>Daphnia</i>, or kairomone induced, and (3) whether it is related to toxin production. Prior to the experiment, cyanobacterial strains were inspected using chromatographic methods for the presence of two toxins, cylindrospermopsin (CYN) and three homologues of microcystin (MC-RR, MC-YR, MC-LR). HPLC analyses showed that all strains were free of cylindrospermopsin, whereas microcystins were detected only in one strain (<i>Planktothrix agardhii</i>). We then tested whether <i>Daphnia</i> exudates can cause thickening of cyanobacterial filaments, which would suggest the morphological changes in cyanobacterial filaments are caused by recycled nutrients. Cyanobacteria were also exposed to sodium octyl sulphate (a commercially available <i>Daphnia</i> kairomone). Transmission electron microscopy (TEM) was used to check whether <i>Daphnia</i> exudates and sodium octyl sulphate trigger thickening of cyanobacterial cell walls, which would be a defence mechanism against grazing. The TEM analysis revealed no significant effect of either <i>Daphnia</i> exudates or kairomone (sodium octyl sulphate) on the cell wall thickness of cyanobacteria. However, our study showed that <i>Daphnia</i> exudates triggered filament thickening in nostocalean cyanobacteria, while filaments of the oscillatorialean strain <i>P. agardhii</i> did not show this response. It was also demonstrated that sodium octyl sulphate alone can also cause filament thickening, which suggests that this might be a specific defence response to the presence of grazers.
DOI: 10.6084/m9.figshare.6176567.v1
title: Effects of <i>Daphnia</i> exudates and sodium octyl sulphates on filament morphology and cell wall thickness of <i>Aphanizomenon gracile</i> (Nostocales), <i>Cylindrospermopsis raciborskii</i> (Nostocales) and <i>Planktothrix agardhii</i> (Oscillatoriales)

description: Grazing is recognized as one of the selective factors shaping the morphology and physiology of cyanobacteria. A recent study has shown that the filamentous cyanobacterium <i>Aphanizomenon gracile</i> strain SAG 31.79 thickened in the presence of <i>Daphnia</i> (Cladocera) and its exudates. The aims of our study were: (1) to determine whether this type of response to <i>Daphnia</i> cues is common for other strains of <i>A. gracile</i>, and other species of filamentous cyanobacteria, (2) to test whether the response is due to nutrients recycled by <i>Daphnia</i>, or kairomone induced, and (3) whether it is related to toxin production. Prior to the experiment, cyanobacterial strains were inspected using chromatographic methods for the presence of two toxins, cylindrospermopsin (CYN) and three homologues of microcystin (MC-RR, MC-YR, MC-LR). HPLC analyses showed that all strains were free of cylindrospermopsin, whereas microcystins were detected only in one strain (<i>Planktothrix agardhii</i>). We then tested whether <i>Daphnia</i> exudates can cause thickening of cyanobacterial filaments, which would suggest the morphological changes in cyanobacterial filaments are caused by recycled nutrients. Cyanobacteria were also exposed to sodium octyl sulphate (a commercially available <i>Daphnia</i> kairomone). Transmission electron microscopy (TEM) was used to check whether <i>Daphnia</i> exudates and sodium octyl sulphate trigger thickening of cyanobacterial cell walls, which would be a defence mechanism against grazing. The TEM analysis revealed no significant effect of either <i>Daphnia</i> exudates or kairomone (sodium octyl sulphate) on the cell wall thickness of cyanobacteria. However, our study showed that <i>Daphnia</i> exudates triggered filament thickening in nostocalean cyanobacteria, while filaments of the oscillatorialean strain <i>P. agardhii</i> did not show this response. It was also demonstrated that sodium octyl sulphate alone can also cause filament thickening, which suggests that this might be a specific defence response to the presence of grazers.
DOI: 10.6084/m9.figshare.6176555
title: Registros de espécies no Parque Ecológico Perequê, Cubatão, São Paulo

description: Registros de ocorrência de espécimes coletadas em expedição de campo dia 16 de abril de 2018 no Parque Ecológico Perequê, Cubatão, São Paulo. Como requisito para cumprimento da disciplina "BIB5759 - O Herbário, suas Coleções e seu Funcionamento", oferecida pelos professores Renato de Mello-Silva, Rafaela C. Forzza e Gregório Ceccantini.
DOI: 10.6084/m9.figshare.6176555.v1
title: Registros de espécies no Parque Ecológico Perequê, Cubatão, São Paulo

description: Registros de ocorrência de espécimes coletadas em expedição de campo dia 16 de abril de 2018 no Parque Ecológico Perequê, Cubatão, São Paulo. Como requisito para cumprimento da disciplina "BIB5759 - O Herbário, suas Coleções e seu Funcionamento", oferecida pelos professores Renato de Mello-Silva, Rafaela C. Forzza e Gregório Ceccantini.
DOI: 10.6084/m9.figshare.6176459
title: DATA_PLOS-ONE

description: - An image raster of Day Land Surface Temperature (LSTDAY) of September 2016;- An image raster of Normalized Difference Vegetation Index (NDVI) of September 2016;- A polygonal shapefile of disease distribution of 'West Nile Disease' in the world in 2016;- A punctual shapefile of outbreaks of 'West Nile Disease' in the world in 2016;- An excel file containing an extract from the 'west nile' outbreaks of 2016 with associated day and night temperature data and vegetation indices, each in a dedicated sheet of the excel file
DOI: 10.6084/m9.figshare.6176459.v1
title: DATA_PLOS-ONE

description: - An image raster of Day Land Surface Temperature (LSTDAY) of September 2016;- An image raster of Normalized Difference Vegetation Index (NDVI) of September 2016;- A polygonal shapefile of disease distribution of 'West Nile Disease' in the world in 2016;- A punctual shapefile of outbreaks of 'West Nile Disease' in the world in 2016;- An excel file containing an extract from the 'west nile' outbreaks of 2016 with associated day and night temperature data and vegetation indices, each in a dedicated sheet of the excel file
DOI: 10.17028/rd.lboro.6176450
title: LEEDR project home energy dataset

description: The LEEDR project (http://leedr-project.co.uk) was funded through the EPSRC (EP/I000267/1) between 2010 to 2014 to understand domestic energy consumption in the context of everyday family life.<br>The project engaged comprehensive, high resolution engineering based empirical monitoring (presented here) with social science and user centered design methods that employed video data, accessible from http://energyanddigitalliving.com.<br>This data set presents the monitoring data from 20 households, maintained by Richard Buswell (r.a.buswell@lboro.ac.uk), Building Energy Research Group (BERG), School of Architecture, Building and Civil Engineering, Loughborough University.<br>Please read the README.TXT file for more information.<br><br>Data was collected using building surveys and home monitoring through proprietary sensors and thorough specially developed devices. It includes:<br>- dimensioned building plans;<br>- images of key appliances;<br>- locations of sensors;<br>- building fabric and incoming energy information; and,<br>- documentation of sensor calibration and data processing procedures.<br><br>The measurements comprise:<br>- window and door opening;<br>- Passive Infra Red based room activity monitoring;<br>- electrical power measurement of incoming supply and appliances;<br>- gas consumption; and,<br>- how water consumption,<br><br>all at a sample at a sample rate of 1 minute, and additionally:<br>- gas consumption; and,<br>- how water consumption,<br>at a sample rate of 1 second.
DOI: 10.6084/m9.figshare.6176399
title: md5HDT.csv

description: mapping all md5 code -&gt; hdt dataset from LODLaundromat.
DOI: 10.6084/m9.figshare.6176399.v1
title: md5HDT.csv

description: mapping all md5 code -&gt; hdt dataset from LODLaundromat.
DOI: 10.6084/m9.figshare.6176303
title: URI_Dataset.tsv

description: mapping all URI -&gt; dataset from LinkLion
DOI: 10.6084/m9.figshare.6176303.v1
title: URI_Dataset.tsv

description: mapping all URI -&gt; dataset from LinkLion
DOI: 10.6084/m9.figshare.6176285
title: Mass balance, velocity and ice thickness data on Nordenskiöldbreen, Svalbard

description: The data is used in the paper "Dynamic response of a high Arctic glacier to melt and runoff variations", published in Geophysical Research Letters. For more details about the data we refer to the manuscript.<br>
DOI: 10.6084/m9.figshare.6176252
title: Supplementary Material for: Pretreatment Neutrophil-Lymphocyte Ratio as a Predictor in Bladder Cancer and Metastatic or Unresectable Urothelial Carcinoma Patients: a Pooled Analysis of Comparative Studies

description: <b><i>Background/Aims:</i></b> Emerging studies have shown that the neutrophil-lymphocyte ratio (NLR) is a potential predictor in various tumors. Our study was conducted to assess the prognostic value of the pretreatment NLR in bladder cancer and metastatic or unresectable urothelial carcinoma (mUC or uUC) patients up to July 2017. The correlation between the pretreatment NLR and pathological characteristics was also evaluated in bladder cancer patients. <b><i>Methods:</i></b> The hazard ratio (HR) and odds ratio (OR) with the 95% confidence interval (CI) were extracted or calculated from the included studies for further pooled analysis. A total of 21 studies were included in a pooled analysis. <b><i>Results:</i></b> The pooled results indicated that a high pretreatment NLR was associated with reduced overall survival (OS) (HR=1.27, 95% CI=1.12-1.43), relapse-free survival (RFS) (HR=1.41, 95% CI=1.23-1.60), progression-free survival (PFS) (HR=1.75, 95% CI=1.36-2.15), disease-specific survival (DSS) and cancer-specific survival (CSS) (HR=1.27, 95% CI=1.19-1.35) in the bladder cancer patients. Additionally, an elevated pretreatment NLR suggested a worse OS rate in the mUC or uUC patients (HR=1.63, 95% CI=1.34-1.91). The pooled ORs and 95% CIs showed that a high pretreatment NLR could be a risk indicator for certain pathological features, such as lymphovascular invasion, a positive margin status and advanced tumor stage. <b><i>Conclusions:</i></b> our results showed that a high pretreatment NLR predicted poor prognosis in bladder cancer, mUC and uUC patients.
DOI: 10.6084/m9.figshare.6176249
title: Supplementary Material for: Inhibition of LncRNA-HRIM Increases Cell Viability by Regulating Autophagy Levels During Hypoxia/Reoxygenation in Myocytes

description: <b><i>Backgrund/Aims:</i></b> Ischemia reperfusion (I/R) promotes the severity of cardiomyocyte injury. Long noncoding RNAs (LncRNAs) are key regulators in cardiovascular diseases. However, the association between LncRNAs and myocardial I/R injury has not been thoroughly characterized to date. We attempted to clarify the potential biological role of a LncRNA (E230034O05Rik), which we named hypoxia/reoxygenation (H/R) injury-related factor in myocytes (HRIM), by investigating the differential expression of LncRNAs between groups of myocytes exposed to either a normal level of oxygen or to H/R. <b><i>Methods:</i></b> Microarray analysis was used to determine analyze the global differential expression of LncRNAs in H9c2 myocytes exposed either to a normal level of oxygen or to H/R. Target LncRNA levels were further verified <i>in vitro</i> and <i>ex vivo</i> by real-time polymerase chain reaction (qPCR). Cell viability was analyzed using the Cell Counting Kit-8 assay. Autophagy levels were confirmed by Western blotting, transmission electron microscopy, and autophagic double-labeled (mRFP-GFP-LC3) adenovirus analyses. <b><i>Results:</i></b> Gene expression profiling revealed that 797 LncRNAs and 1898 mRNAs were differentially expressed in the H/R group compared with the normal oxygen group. Among these LncRNAs and mRNAs, 6 upregulated LncRNAs and 2 downregulated LncRNAs in the H/R group were selected and further validated by qPCR <i>in vitro</i> and <i>ex vivo</i>. Additionally, LncRNA-HRIM was inhibited by specific siRNAs in H9c2 myocytes exposed to H/R. The inhibition of LncRNA-HRIM by siRNA prevented cell death by suppressing excessive autophagic activity in myocytes, This finding suggests a detrimental role of LncRNA-HRIM in the regulation of I/R injury. <b><i>Conclusions:</i></b> <i></i>LncRNAs are involved in H/R injury of H9c2 myocytes. Inhibition of LncRNA-HRIM increased cell viability by reducing autophagy in myocytes during H/R.
DOI: 10.6084/m9.figshare.6176246
title: Supplementary Material for: Urinary and Blood MicroRNA-126 and -770 are Potential Noninvasive Biomarker Candidates for Diabetic Nephropathy: a Meta-Analysis

description: <b><i>Background/Aims:</i></b> Diabetic nephropathy (DN), a major diabetic microvascular complication, has a long and growing list of biomarkers, including microRNA biomarkers, which have not been consistent across preclinical and clinical studies. This meta-analysis aims to identify significant blood- and urine-incident microRNAs as diagnostic/prognostic biomarker candidates for DN. <b><i>Methods:</i></b> PubMed, Web of Science, and Cochrane Library were searched from their earliest records through 12th Dec 2016. Relevant publications for the meta-analysis included (1) human participants; (2) microRNAs in blood and urine; (3) DN studies; and (4) English language. Four reviewers, including two physicians, independently and blindly extracted published data regarding microRNA profiles in blood and/or urine from subjects with diabetic nephropathy. A random-effect model was used to pool the data. Statistical associations between diabetic nephropathy and urinary or blood microRNA expression levels were assessed. <b><i>Results:</i></b> Fourteen out of 327 studies (n=2,747 patients) were selected. Blood or urinary microRNA expression data of diabetic nephropathy were pooled for this analysis. The hsa-miR-126 family was significantly (OR: 0.57; 95% CI: 0.44-0.74; p-value &lt; 0.0001) downregulated in blood from patients with diabetic kidney disease, while its urinary level was upregulated (OR: 2931.12; 95% CI: 9.96-862623.21; p-value = 0.0059). The hsa-miR-770 family microRNA were significantly (OR: 10.24; 95% CI: 2.37-44.25; p-value = 0.0018) upregulated in both blood and urine from patients with diabetic nephropathy. <b><i>Conclusions:</i></b> Our meta-analysis suggests that hsa-miR-126 and hsa-miR-770 family microRNA may have important diagnostic and pathogenetic implications for DN, which warrants further systematic clinical studies.
DOI: 10.6084/m9.figshare.6176210
title: Dataset for: Toxicity and Chemistry of Wastewater from Hydraulic Fracture and Conventional Shale Gas Wells

description: New technology has enabled recovery of inaccessible natural gas shale deposits, however, the human health risks from the migration of brines into drinking water or surface spills are unknown. To provide information that can inform these risks, chemical characterization and in vitro toxicologic testing was conducted using pre- and post-injection waters from conventional and unconventional oil and gas wells. In acute cytotoxicity and wound healing assays, there was dose-dependent toxicity in human and rat cells with growth promotion at low concentrations. Lethality was measured in time studies up to 10 days post-injection. Produced water samples from both well types were equally toxic to human cells and were corrosive at high concentrations. Measurement of protein and gene expression identified metabolic pathways responding to both well types as NQO1 oxidative stress-responsive enzyme and tight junction protein genes. A KCl sample of matched ionic strength showed a different toxicity profile than produced waters, indicating that salts alone were not the cause of toxicity. Organic chemicals and branched alkanes were present in hydraulic fracture wells and mainly branched alkanes were present in conventional wells. One organic substance was still present after 240 days, The known properties of these chemicals include toxicity to multiple human organs, sensitization, irritation, developmental effects and tumor promotion.
DOI: 10.6084/m9.figshare.6176174
title: Supplementary Material for: Serum Obestatin: A Biomarker of Cardiovascular and All-Cause Mortality in Hemodialysis Patients

description: <b><i>Background:</i></b> Recent experimental studies have suggested that obestatin, a proposed anorexigenic gut hormone and a physiological opponent of acyl-ghrelin, has protective cardiovascular effects. We tested the hypothesis that obestatin is independent of inflammatory mediators and/or acyl-ghrelin in predicting outcomes of the maintenance hemodialysis (MHD) population. <b><i>Methods:</i></b> It was a 6-year cohort study on 261 MHD patients. Obestatin, acyl-ghrelin, adipokines (leptin and adiponectin), markers of inflammation and nutrition, prospective all-cause and cardiovascular mortality were studied. <b><i>Results:</i></b> During the follow-up, 160 patients died in total, with 74 deaths due to cardiovascular causes. For each ng/mL increase in baseline obestatin level in fully adjusted models (including malnutrition-inflammation score, Interleukin-6 [IL-6], adipokines and acyl-ghrelin), the hazard for death from all causes was 0.90 (95% CI 0.81–0.99) and for cardiovascular death 0.85 (95% CI 0.73–0.99). However, these associations were more robust in the subgroup of patients aged above 71 years: 0.85 (95% CI 0.73–0.98) for all-cause death and 0.66 (95% CI 0.52–0.85) for cardiovascular death. An interaction between high IL-6 (above median) and low obestatin (below median) levels for increased risk of all-cause mortality (synergy index [SI] 5.14, <i>p</i> = 0.001) and cardiovascular mortality (SI 4.81, <i>p</i> = 0.02) emerged in the development of multivariable adjusted models. Interactions were also observed between obestatin, Tumor necrosis factor-alpha, adipokines and acyl-ghrelin, which were associated with mortality risk. <b><i>Conclusion:</i></b> Serum obestatin behaves as a biomarker for cardiovascular and all-cause mortality in MHD patients. The prognostic ability of obestatin in this regard is independent of inflammation, nutritional status, acyl-ghrelin’s and adipokines’ activity and is modified by age being very prominent in patients older than 71 years.