cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7813508.v1
title: Supplementary Material for: The Effect of Serum Neutrophil Gelatinase-Associated Lipocalin on the Discontinuation of Continuous Renal Replacement Therapy in Critically Ill Patients with Acute Kidney Injury

description: <b><i>Background:</i></b> To determine the optimal time for discontinuing continuous renal replacement therapy (CRRT) by evaluating serum neutrophil gelatinase-associated lipocalin (NGAL) in critically ill patients with acute kidney injury (AKI). <b><i>Methods:</i></b> A prospective observational study was conducted from September 2015 to March 2018. AKI patients treated with CRRT for at least 24 h were divided into “success” and “failure” groups according to their RRT requirement within 7 days after the initial discontinuation of CRRT. The prefilter and effluent NGAL concentrations were measured to calculate the sieving coefficient (SC) of NGAL in all included subjects from 0 to 72 h. <b><i>Results:</i></b> In total, 110 patients were divided into success (<i>n</i> = 78) and failure groups (<i>n</i> = 32). The mean SC of NGAL during CRRT was less than 0.05. The patients in the failure group were associated with higher mortality compared with patients in the success group (37.5 vs. 12.8%, respectively, <i>p</i> = 0.013). There were significant differences in serum NGAL, creatinine, and urine output at discontinuation. In patients without sepsis (<i>n</i> = 70), serum NGAL and urine output were significant predictors of successful cessation. The area under the receiver operating characteristic to predict the successful discontinuation of CRRT was 0.88 for NGAL and 0.86 for urine output. An NGAL level of 403 ng/mL had the highest sensitivity (81%) and specificity (89%) and a urine output of 695 mL/day had the highest sensitivity (83%) and specificity (88%). However, in septic patients (<i>n</i> = 40), urine output but not serum NGAL (OR 0.999, <i>p</i> = 0.69) was a significant variable (OR 1.002, <i>p</i> = 0.005), with a cutoff of 796 mL/day (sensitivity 83%, specificity 88%). <b><i>Conclusions:</i></b> Serum NGAL was a significant factor for predicting successful CRRT discontinuation in nonseptic AKI patients. However, urine output, rather than serum NGAL, was a significant predictor in septic AKI patients.
DOI: 10.6084/m9.figshare.7813463
title: Supplementary Material for: Characterization of the Blood Microbiota in Korean Females with Rosacea

description: Medicine
DOI: 10.6084/m9.figshare.7813475
title: Raw Database SimFish.xlsx

description: Raw data of SimFish Project. This study was supported by the Biodiversity Foundation of the Spanish Ministry of Agriculture and Fisheries, Food and Environment (Fundación Biodiversidad del Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente) through a research project entitled ‘<i>Herramienta para la gestión pesquera sostenible en distintos escenarios ambientales y climáticos para el área del estrecho de Gibraltar</i>’. Support to activities in the field of terrestrial, marine and coastal biodiversity 2016.
DOI: 10.6084/m9.figshare.7813457
title: Data from: Antioxidant capacity is repeatable across years but does not consistently correlate with a marker of peroxidation in a free-living passerine bird.

description: We investigated the repeatability, within-individual variation and correlation across different conditions of two plasmatic markers of the oxidative balance (reactive oxygen metabolites or ROMs, a marker of lipid and protein peroxidation, and non-enzymatic antioxidant defences measured through the OXY test) in 1108 samples from 635 free-living adult collared flycatchers (Ficedula albicollis). We sought to manipulate energy constraints by increasing wing load in 2012 and 2013 and by providing additional food in 2014. More information can be found in the related research article, published in Journal of Comparative Physiology B (DOI 10.1007/s00360-019-01211-1).<br>
DOI: 10.6084/m9.figshare.7813475.v1
title: Raw Database SimFish.xlsx

description: Raw data of SimFish Project. This study was supported by the Biodiversity Foundation of the Spanish Ministry of Agriculture and Fisheries, Food and Environment (Fundación Biodiversidad del Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente) through a research project entitled ‘<i>Herramienta para la gestión pesquera sostenible en distintos escenarios ambientales y climáticos para el área del estrecho de Gibraltar</i>’. Support to activities in the field of terrestrial, marine and coastal biodiversity 2016.
DOI: 10.6084/m9.figshare.7813445
title: ABC-6 structures (2-16 layers; &lt;= 4 types of cages)

description: 1150 ABC-6 structures generated by the enumeration of their genomic stacking sequences. Only structures constructed by no more than 4 types of cages are kept.
DOI: 10.6084/m9.figshare.7813457.v1
title: Data from: Antioxidant capacity is repeatable across years but does not consistently correlate with a marker of peroxidation in a free-living passerine bird.

description: We investigated the repeatability, within-individual variation and correlation across different conditions of two plasmatic markers of the oxidative balance (reactive oxygen metabolites or ROMs, a marker of lipid and protein peroxidation, and non-enzymatic antioxidant defences measured through the OXY test) in 1108 samples from 635 free-living adult collared flycatchers (Ficedula albicollis). We sought to manipulate energy constraints by increasing wing load in 2012 and 2013 and by providing additional food in 2014. More information can be found in the related research article, published in Journal of Comparative Physiology B (DOI 10.1007/s00360-019-01211-1).<br>
DOI: 10.17045/sthlmuni.7813439
title: Open data and analysis script for 'Attentional bias modification in virtual reality'

description: The zip file contains the data files and R analysis script used in the manuscript titled 'Attentional bias modification in virtual reality - a VR-based dot-probe task with 2D and 3D stimuli'<br>Analysis_script.R is a script file that can be opened by the statistical software R (https://www.r-project.org/) and Rstudio (https://www.rstudio.com/). All analysis steps and codes are found within this file.<br>All files under the Data_files folder are directly called by Analysis_script from R, therefore please ensure that the folder structure and file names remain the same.<br>Folder dot_probe_raw_data_files and its subfolders contain *.xml files with attentional bias (reaction time) data from the participants, generated by the VR program.<br>outcome_measures_and_demographic_data.xlsx contains participant demographic data and questionnaire measures, generated by the iTerapi platform. This data file has been cleaned to remove information irrelevant to the analysis (e.g. number of reminder emails sent etc.).<br>lsas_pre_individual_items.xlsx contains participant responses to individual items of the LSAS-SR questionnaire, generated by the iTerapi platform.<br>
DOI: 10.6084/m9.figshare.7813430
title: Supplementary Material for: Relationship between Adaptive Changing of Lysophosphatidylethanolamine Content in the Bacterial Envelope and Ampicillin Sensitivity of <b><i>Yersinia pseudotuberculosis</i></b>

description: The low permeability of porin channels is the possible reason for Gram-negative bacterial resistance to antibiotics. The adaptive accumulation of lysophosphatidylethanolamine (LPE) in <i>Yersinia pseudotuberculosis</i> induces conformational changes of OmpF porin that may hinder the transport of antibiotics through this channel. The present study was aimed to test whether the changes in LPE content affect the resistance of bacteria to ampicillin. The addition of glucose to the culture medium was shown to simultaneously increase the level of LPE and minimum inhibitory concentration (MIC) for ampicillin of <i>Y. pseudotuberculosis</i> cells 6- and 2-fold, respectively. However, the coadministration of glucose and polyphenol extract from buckwheat husks reduced the content of LPE 2-fold and restored MIC to the control value. Thus, PBEH can be used as antibiotic adjuvant to improve an antibiotic’s ability to cross the outer membrane. The present work demonstrated: (i) the role of adaptive changes in the lipid composition of <i>Y. pseudotuberculosis</i> in<i></i> the development of antibiotic resistance, and (ii) the promising use of PBEH in combination therapy to increase the susceptibility of Gram-negative bacteria to the conventional β-lactam antibiotics, probably attenuating in vivo a previously demonstrated effect of LPE on the conformation and function of the OmpF channel.
DOI: 10.6084/m9.figshare.7813433
title: Supplementary Material for: Isolation and Characterization of Interspersed Repeated Sequences in the Common Lizard, Zootoca vivipara, and Their Conservation in Squamata

description: The common lizard (<i>Zootoca vivipara</i>) displays characteristic cytogenetic, reproductive, molecular, and biogeographic variability. This species comprises oviparous and viviparous populations with disjunct distribution and sex chromosome polymorphisms, from simple ZZ/ZW to complex Z<sub>1</sub>Z<sub>1</sub>Z<sub>2</sub>Z<sub>2</sub>/Z<sub>1</sub>Z<sub>2</sub>W systems with different morphologies of the W chromosome. In this study, we used the primers SINE A and SINE B and a newly designed primer pair to (1) obtain information on the presence and distribution of transposable elements (TEs) in 8 squamate families and (2) assess the chromosomal location of SINE Squam elements in <i>Z. vivipara</i>. PCR amplification with SINE A and SINE B produced single or multiple products in different <i>Z. vivipara</i> populations, subsequently used to design the SINE-Zv primers. Using the newly designed SINE-Zv primers, we identified 2 sequences of about 700 and 300 bp (SINE-Zv 700 and SINE-Zv 300) in all the investigated populations of <i>Z. vivipara</i>. Fluorescence in situ hybridizations showed a preferential localization of SINE-Zv sequences in the peritelomeric regions of almost all chromosomes, with the exception of the W. Both sequences contained a distinct segment of SINE Squam2. SINE-Zv 700 appeared to be restricted to <i>Z</i>. <i>vivipara</i>, while SINE-Zv 300 contained a partial Gypsy sequence that is highly conserved among Squamata and showed high identity values (72-93%) with several transcripts from different species. Using the same primers, we also highlighted the presence of another highly conserved Gypsy-like fragment in snakes which displayed significant similarity with the stomatin-like protein 2 of colubrids. Our results suggest that SINEs and the Gypsy-like elements are widely distributed among squamates and may have played an active role in their genomic evolution and differentiation.
DOI: 10.6084/m9.figshare.7813433.v1
title: Supplementary Material for: Isolation and Characterization of Interspersed Repeated Sequences in the Common Lizard, Zootoca vivipara, and Their Conservation in Squamata

description: The common lizard (<i>Zootoca vivipara</i>) displays characteristic cytogenetic, reproductive, molecular, and biogeographic variability. This species comprises oviparous and viviparous populations with disjunct distribution and sex chromosome polymorphisms, from simple ZZ/ZW to complex Z<sub>1</sub>Z<sub>1</sub>Z<sub>2</sub>Z<sub>2</sub>/Z<sub>1</sub>Z<sub>2</sub>W systems with different morphologies of the W chromosome. In this study, we used the primers SINE A and SINE B and a newly designed primer pair to (1) obtain information on the presence and distribution of transposable elements (TEs) in 8 squamate families and (2) assess the chromosomal location of SINE Squam elements in <i>Z. vivipara</i>. PCR amplification with SINE A and SINE B produced single or multiple products in different <i>Z. vivipara</i> populations, subsequently used to design the SINE-Zv primers. Using the newly designed SINE-Zv primers, we identified 2 sequences of about 700 and 300 bp (SINE-Zv 700 and SINE-Zv 300) in all the investigated populations of <i>Z. vivipara</i>. Fluorescence in situ hybridizations showed a preferential localization of SINE-Zv sequences in the peritelomeric regions of almost all chromosomes, with the exception of the W. Both sequences contained a distinct segment of SINE Squam2. SINE-Zv 700 appeared to be restricted to <i>Z</i>. <i>vivipara</i>, while SINE-Zv 300 contained a partial Gypsy sequence that is highly conserved among Squamata and showed high identity values (72-93%) with several transcripts from different species. Using the same primers, we also highlighted the presence of another highly conserved Gypsy-like fragment in snakes which displayed significant similarity with the stomatin-like protein 2 of colubrids. Our results suggest that SINEs and the Gypsy-like elements are widely distributed among squamates and may have played an active role in their genomic evolution and differentiation.
DOI: 10.6084/m9.figshare.7813427
title: Artifact for TACAS 2019 paper: Minimal-Time Synthesis for Parametric Timed Automata

description: This artifact contains the means to reproduce the experimental results from the<br>paper. In the paper we propose algorithms that synthesize a/all parameter<br>valuation(s) in a PTA, such that the time to reach the target location is<br>minimized. Additionally, we also propose algorithms that synthesize a/all<br>parameter valuation(s) that minimize a specific parameter.<br><br>We consider the following algorithms in our experiments:<br>- Synth: the classical synthesis algorithm (without time minimization)<br>- MTSynth: our minimal-time synthesis algorithm<br>- MPSynth: our minimal-parameter synthesis algorithm (which is used to compute<br> the minimal time)<br>- MTSynth-noRed: Our MTSynth algorithm without using state-space reductions<br>- MTReach: our minimal-time reachability algorithm (that returns at least one<br> parameter valuation that reaches the target location in minimal time)<br>- MPReach: our minimal-parameter reachability algorithm (see MTReach)<br><br>For the experiments, we collected 68 PTA models and properties from the<br>IMITATOR benchmarks library, and ran each experiment (algorithm+model<br>combination).<br><br>The most interesting result is that the minimal-time synthesis version is in<br>general faster in computing results when compared to the classical synthesis<br>algorithm. We can also observe that MTSynth is faster than MPSynth (in MTSynth<br>we use a shortest-path search, and in MPSynth we do not). When comparing<br>reachability with synthesis, we see that the results are fairly similar, with<br>only a few instances in which only reachability is computable in the allowed<br>time.<br><br><br>
DOI: 10.6084/m9.figshare.7813412
title: Supplementary Material for: Overweight and Obesity in the Russian Population: Prevalence in Adults and Association with Socioeconomic Parameters and Cardiovascular Risk Factors

description: <b><i>Objective:</i></b> To evaluate the prevalence and geographic distribution of overweight and obesity in Russian adults aged 25–64 years as well as the association between chronic risk factors and obesity. <b><i>Methods:</i></b> Data were obtained from the survey “Epidemiology of Cardiovascular Diseases and Its Risk Factors in Some Regions of the Russian Federation” (ESSE-RF). This is a large cross-sectional multicenter population-based study that included interviews and medical examination (anthropometry, blood pressure [BP] measurement, and laboratory analysis) applied in 2012–2014. <b><i>Results:</i></b> The sample included 20,190 adults (response rate 79.4%) aged 25–64 years. Approximately one third of participants (30.3%) had obesity and another third (34.3%) were classified as overweight. BMI increased with age in both sexes. The prevalence of obesity between regions ranged from 24.4 to 35.5%. Overweight and obesity levels decreased with higher education (men only). Overall obesity rates were higher in rural than urban populations, but rates of overweight were similar in rural and urban populations. Participants with obesity were more likely to have BP &gt; 160/100 mm Hg (odds ratio &gt; 2.0) and also &gt; 140/90 mm Hg, raised blood glucose, and high triglycerides. <b><i>Conclusion:</i></b> The prevalence of overweight and obesity in Russian adults aged 25–64 years is not evenly distributed geographically, but it is comparable to that of other European countries. Individuals with obesity were also more likely to have indicators of poor cardiovascular and metabolic health.
DOI: 10.6084/m9.figshare.7813427.v1
title: Artifact for TACAS 2019 paper: Minimal-Time Synthesis for Parametric Timed Automata

description: This artifact contains the means to reproduce the experimental results from the<br>paper. In the paper we propose algorithms that synthesize a/all parameter<br>valuation(s) in a PTA, such that the time to reach the target location is<br>minimized. Additionally, we also propose algorithms that synthesize a/all<br>parameter valuation(s) that minimize a specific parameter.<br><br>We consider the following algorithms in our experiments:<br>- Synth: the classical synthesis algorithm (without time minimization)<br>- MTSynth: our minimal-time synthesis algorithm<br>- MPSynth: our minimal-parameter synthesis algorithm (which is used to compute<br> the minimal time)<br>- MTSynth-noRed: Our MTSynth algorithm without using state-space reductions<br>- MTReach: our minimal-time reachability algorithm (that returns at least one<br> parameter valuation that reaches the target location in minimal time)<br>- MPReach: our minimal-parameter reachability algorithm (see MTReach)<br><br>For the experiments, we collected 68 PTA models and properties from the<br>IMITATOR benchmarks library, and ran each experiment (algorithm+model<br>combination).<br><br>The most interesting result is that the minimal-time synthesis version is in<br>general faster in computing results when compared to the classical synthesis<br>algorithm. We can also observe that MTSynth is faster than MPSynth (in MTSynth<br>we use a shortest-path search, and in MPSynth we do not). When comparing<br>reachability with synthesis, we see that the results are fairly similar, with<br>only a few instances in which only reachability is computable in the allowed<br>time.<br><br><br>
DOI: 10.6084/m9.figshare.7813445.v1
title: ABC-6 structures (1150)

description: 1150 ABC-6 structures generated by the enumeration of their genomic stacking sequences. Only structures constructed by no more than 4 types of cages are kept.
DOI: 10.6084/m9.figshare.7813358
title: Supplementary Material for: Effects of L-Menthol and Carbon Dioxide on the Adenoma Detection Rate during Colonoscopy: L-Menthol and Carbon Dioxide on Colonoscopy

description: <b><i>Background and Aims:</i></b> We examined the efficacy of the combined use of L-menthol spraying (L-mentholS) as an antispasmodic agent and carbon dioxide insufflation (CO<sub>2</sub>I) on the adenoma detection rate (ADR) in a prospective, single-center trial with a 2 × 2 factorial design. <b><i>Methods:</i></b> We randomly assigned 611 patients scheduled to undergo colonoscopy to 4 groups: (1) the L-mentholS + CO<sub>2</sub>I (<i>n</i> = 153), (2) L-mentholS + air insufflation (AI; <i>n</i> = 156), (3) CO<sub>2</sub>I (<i>n</i> = 153), and (4) AI (<i>n</i> = 149) groups. We used 20 mL of 0.8%-L-menthol solution for the L-mentholS. The primary outcome was the difference in the ADR, and the secondary outcomes were the differences in colonic peristalsis and abdominal pain. ­<b><i>Results:</i></b> The ADRs were not different among the groups: 1/2/3/4; 39.9%/43.6%/41.2%/51.0%. CO<sub>2</sub>I was associated with a significant decrease in the ADR (OR 0.57; 95% CI 0.35– 0.93) with a multiple logistic regression. The interaction between L-mentholS and CO<sub>2</sub>I was associated with a suppression of the decrease in the ADR. Both L-mentholS and CO<sub>2</sub>I were associated with a significant decrease in abdominal pain, and L-mentholS was associated with a significant improvement of peristalsis. <b><i>Conclusions:</i></b> The fact that CO<sub>2</sub>I was associated with significant decreases in the ADR was a problem. The combined use of L-mentholS and CO<sub>2</sub>I could help to suppress the decrease in the ADR.
DOI: 10.6084/m9.figshare.7813358.v1
title: Supplementary Material for: Effects of L-Menthol and Carbon Dioxide on the Adenoma Detection Rate during Colonoscopy: L-Menthol and Carbon Dioxide on Colonoscopy

description: <b><i>Background and Aims:</i></b> We examined the efficacy of the combined use of L-menthol spraying (L-mentholS) as an antispasmodic agent and carbon dioxide insufflation (CO<sub>2</sub>I) on the adenoma detection rate (ADR) in a prospective, single-center trial with a 2 × 2 factorial design. <b><i>Methods:</i></b> We randomly assigned 611 patients scheduled to undergo colonoscopy to 4 groups: (1) the L-mentholS + CO<sub>2</sub>I (<i>n</i> = 153), (2) L-mentholS + air insufflation (AI; <i>n</i> = 156), (3) CO<sub>2</sub>I (<i>n</i> = 153), and (4) AI (<i>n</i> = 149) groups. We used 20 mL of 0.8%-L-menthol solution for the L-mentholS. The primary outcome was the difference in the ADR, and the secondary outcomes were the differences in colonic peristalsis and abdominal pain. ­<b><i>Results:</i></b> The ADRs were not different among the groups: 1/2/3/4; 39.9%/43.6%/41.2%/51.0%. CO<sub>2</sub>I was associated with a significant decrease in the ADR (OR 0.57; 95% CI 0.35– 0.93) with a multiple logistic regression. The interaction between L-mentholS and CO<sub>2</sub>I was associated with a suppression of the decrease in the ADR. Both L-mentholS and CO<sub>2</sub>I were associated with a significant decrease in abdominal pain, and L-mentholS was associated with a significant improvement of peristalsis. <b><i>Conclusions:</i></b> The fact that CO<sub>2</sub>I was associated with significant decreases in the ADR was a problem. The combined use of L-mentholS and CO<sub>2</sub>I could help to suppress the decrease in the ADR.
DOI: 10.6084/m9.figshare.7813286
title: Additional file 1: of svist4get: a simple visualization tool for genomic tracks from sequencing experiments

description: Svist4get source code and sample data. Python code and samples of yeast data used for generation of figures. (TGZ 5787 kb)
DOI: 10.6084/m9.figshare.7813286.v1
title: Additional file 1: of svist4get: a simple visualization tool for genomic tracks from sequencing experiments

description: Svist4get source code and sample data. Python code and samples of yeast data used for generation of figures. (TGZ 5787 kb)
DOI: 10.6084/m9.figshare.7813253
title: Additional file 8: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: Excel file of DESeq2 results of the mouse RNA dataset comparing normal liver vs liver metastases. (XLSX 4356 kb)
DOI: 10.6084/m9.figshare.7813253.v1
title: Additional file 8: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: Excel file of DESeq2 results of the mouse RNA dataset comparing normal liver vs liver metastases. (XLSX 4356 kb)
DOI: 10.6084/m9.figshare.7813241
title: Additional file 6: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: Excel file with DESeq2 results comparing mammary tumors with liver metastases. (XLSX 28591 kb)
DOI: 10.6084/m9.figshare.7813241.v1
title: Additional file 6: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: Excel file with DESeq2 results comparing mammary tumors with liver metastases. (XLSX 28591 kb)
DOI: 10.6084/m9.figshare.7813214
title: Additional file 1: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: RNA-seq dataset characteristics. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.7813214.v1
title: Additional file 1: of Separation of breast cancer and organ microenvironment transcriptomes in metastases

description: RNA-seq dataset characteristics. (XLSX 38 kb)