cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7577639
title: Supplementary Material for: Furosemide Stress Test as a Predicting Biomarker for Delayed Graft Function in Kidney Transplantation

description: <b><i>Background:</i></b> Delayed graft function (DGF) could worsen early and long-term outcomes of kidney transplantation (KT). DGF is caused by several pre-transplantation and perioperative factors in both donors and recipients. At present, there are no biomarkers or tests during the immediate post-KT period that can accurately predict the development of DGF. <b><i>Materials and methods:</i></b> This prospective study was conducted in deceased donor KT (DDKT) at King Chulalongkorn Memorial Hospital, Thailand. All recipients underwent furosemide stress test (FST) by receiving a single dose of intravenous furosemide, 1.5 mg/kg at 3 h after allograft reperfusion. We determined the correlations between DGF (requiring dialysis within the first week after transplantation) and the values of urine volume recorded hourly after FST until 6 h, the parameters of postoperative dynamic tests, including resistive index (RI) of renal arteries and effective renal plasma flow (ERPF), and urine neutrophil gelatinase-associated lipocalin (NGAL). <b><i>Results:</i></b> Of the 59 total DDKT recipients enrolled, 24 developed DGF. The FST is a more accurate biomarker than urine NGAL, RI of renal arteries, and ERPF in the prediction of DGF. The 4-h urine volume less than 350 mL (FST non-responsive) was the best cut-off value in predicting DGF with 87.5% sensitivity, 82.9% specificity, and 82.5% accuracy. Multiple logistic regression analyses showed an odds ratio of 0.993 (0.986–0.999, <i>p</i> = 0.035) for the 4-h urine volume to predict DGF. <b><i>Conclusions:</i></b> The FST is a simple and accurate biomarker for predicting DGF in early post-KT period. Close monitoring and well prepared dialysis are suggested in patients with urine volume &lt; 350 mL after 4 h of FST. The FST non-responsive patients could be the target for further DGF preventive intervention. ClinicalTrials.gov identifier: NCT03071536.
DOI: 10.6084/m9.figshare.7577639.v1
title: Supplementary Material for: Furosemide Stress Test as a Predicting Biomarker for Delayed Graft Function in Kidney Transplantation

description: <b><i>Background:</i></b> Delayed graft function (DGF) could worsen early and long-term outcomes of kidney transplantation (KT). DGF is caused by several pre-transplantation and perioperative factors in both donors and recipients. At present, there are no biomarkers or tests during the immediate post-KT period that can accurately predict the development of DGF. <b><i>Materials and methods:</i></b> This prospective study was conducted in deceased donor KT (DDKT) at King Chulalongkorn Memorial Hospital, Thailand. All recipients underwent furosemide stress test (FST) by receiving a single dose of intravenous furosemide, 1.5 mg/kg at 3 h after allograft reperfusion. We determined the correlations between DGF (requiring dialysis within the first week after transplantation) and the values of urine volume recorded hourly after FST until 6 h, the parameters of postoperative dynamic tests, including resistive index (RI) of renal arteries and effective renal plasma flow (ERPF), and urine neutrophil gelatinase-associated lipocalin (NGAL). <b><i>Results:</i></b> Of the 59 total DDKT recipients enrolled, 24 developed DGF. The FST is a more accurate biomarker than urine NGAL, RI of renal arteries, and ERPF in the prediction of DGF. The 4-h urine volume less than 350 mL (FST non-responsive) was the best cut-off value in predicting DGF with 87.5% sensitivity, 82.9% specificity, and 82.5% accuracy. Multiple logistic regression analyses showed an odds ratio of 0.993 (0.986–0.999, <i>p</i> = 0.035) for the 4-h urine volume to predict DGF. <b><i>Conclusions:</i></b> The FST is a simple and accurate biomarker for predicting DGF in early post-KT period. Close monitoring and well prepared dialysis are suggested in patients with urine volume &lt; 350 mL after 4 h of FST. The FST non-responsive patients could be the target for further DGF preventive intervention. ClinicalTrials.gov identifier: NCT03071536.
DOI: 10.7284/133052
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK190211 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133051
title: Gyrocompass data collected during research cruise FK190211 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7577591
title: Global transcriptomic analysis of a L. monocytogenes agrD mutant

description: Global expression profiles of <i>L. monocytogenes</i> EGDe and an isogenic <i>agrD</i> deletion mutant were analyzed by custom spotted microarrays (Agilent 4x44k arrays, mono-dye setup) covering all genes of the genome.The file set contains a .zip file with raw data including a detailed descriptions of the design of the array and reports on the analysis procedures. The raw data set comprises a second experiment (transcriptomic analysis), which is irrelevant to the comparison of EGDe WT and the <i>agrD</i> mutant. <br>For ease of interpretation and analysis there are further files with raw spot intensities of the relevant samples, a sample key list and a list with background-corrected, normalized log<sub>2</sub>-fold changes in expression in exponential and stationary growth phase for all genes with statistical significance of the change.<br>
DOI: 10.7284/133060
title: Multibeam Echosounder data collected during research cruise FK190211 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7577594
title: Supplementary Material for: External Validation of Different Scoring Systems for Suspected Choledocholithiasis

description: <b><i>Aim of the Study:</i></b> The diagnosis of choledocholithiasis is challenging. Previously published scoring systems designed to calculate the risk of choledocholithiasis were evaluated to appraise the diagnostic performance. <b><i>Patients and Methods</i></b>: Data of patients who were admitted between 2013 and 2015 with the following characteristics were retrieved: bile stone-related symptoms and signs, and indication to laparoscopic cholecystectomy. To validate and appraise the performance of the 6 scoring systems, the acknowledged domains of each metrics were applied to the present cohort. Sensitivity, specificity, positive, negative predictive, Youden index, and receiver operating characteristic curve with the area under the curve (AUC) values of the scores were calculated. <b><i>Results:</i></b> Two-hundred patients were analyzed. The highest sensitivity and specificity were obtained from the Menezes’ (96.6%) and Telem’s (99.3%) metrics respectively. The Telem’s and Menezes’ scores had the best positive (75.0%) and negative (96.4%) predictive values respectively. The best accuracy, as computed by the Youden index and AUC, was found for the Soltan’s scoring system (0.628 and 0.88, respectively). <b><i>Conclusion:</i></b> The available scoring systems are precise only in identifying patients with a negligible risk of common bile duct stone, but overall insufficiently accurate to suggest the routine use in clinical practice.
DOI: 10.6084/m9.figshare.7577588
title: Supplementary Material for: Vancomycin-Associated Acute Kidney Injury in a Large Veteran Population

description: <b><i>Background:</i></b> To determine the association of vancomycin with acute kidney injury (AKI) in relation to its serum concentration value and to examine the risk of AKI in patients treated with vancomycin when compared with a matched cohort of patients receiving non-glycopeptide antibiotics (linezolid/daptomycin). <b><i>Methods:</i></b> From a cohort of &gt; 3 million US veterans with baseline estimated glomerular filtration rate ≥60 mL/min/1.73 m<sup>2</sup>, we identified 33,527 patients who received either intravenous vancomycin (<i>n</i> = 22,057) or non-glycopeptide antibiotics (linezolid/daptomycin, <i>n</i> = 11,470). We examined the association of the serum trough vancomycin level recorded within the first 48 h of administration with subsequent AKI in all patients treated with vancomycin and association of vancomycin vs. non-glycopeptide antibiotics use with the risk of incident AKI. <b><i>Results:</i></b> The overall multivariable adjusted ORs of AKI stages 1, 2, and 3 in patients on vancomycin vs. non-glycopeptides were 1.1 (1.1–1.2), 1.2 (1–1.4), and 1.4 (1.1–1.7), respectively. When examined in strata divided by vancomycin trough level, the odds of AKI were similar or lower in patients receiving vancomycin compared to non-glycopeptide antibiotics as long as serum vancomycin levels were ≤20 mg/L. However, in patients with serum vancomycin levels &gt; 20 mg/L, the ORs of AKI stages 1, 2, and 3 in patients on vancomycin vs. non-glycopeptide antibiotics were 1.5 (1.4–1.7), 1.9 (1.5–2.3), and 2.7 (2–3.5), respectively. <b><i>Conclusions:</i></b> Vancomycin use is associated with a higher risk of AKI when serum levels exceed &gt; 20 mg/L.
DOI: 10.6084/m9.figshare.7577591.v2
title: Global transcriptomic analysis of a L. monocytogenes agrD mutant

description: Global expression profiles of <i>L. monocytogenes</i> EGDe and an isogenic <i>agrD</i> deletion mutant were analyzed by custom spotted microarrays (Agilent 4x44k arrays, mono-dye setup) covering all genes of the genome.The file set contains a .zip file with raw data including a detailed descriptions of the design of the array and reports on the analysis procedures. The raw data set comprises a second experiment (transcriptomic analysis), which is irrelevant to the comparison of EGDe WT and the <i>agrD</i> mutant. <br>For ease of interpretation and analysis there are further files with raw spot intensities of the relevant samples, a sample key list and a list with background-corrected, normalized log<sub>2</sub>-fold changes in expression in exponential and stationary growth phase for all genes with statistical significance of the change.<br>
DOI: 10.6084/m9.figshare.7577588.v1
title: Supplementary Material for: Vancomycin-Associated Acute Kidney Injury in a Large Veteran Population

description: <b><i>Background:</i></b> To determine the association of vancomycin with acute kidney injury (AKI) in relation to its serum concentration value and to examine the risk of AKI in patients treated with vancomycin when compared with a matched cohort of patients receiving non-glycopeptide antibiotics (linezolid/daptomycin). <b><i>Methods:</i></b> From a cohort of &gt; 3 million US veterans with baseline estimated glomerular filtration rate ≥60 mL/min/1.73 m<sup>2</sup>, we identified 33,527 patients who received either intravenous vancomycin (<i>n</i> = 22,057) or non-glycopeptide antibiotics (linezolid/daptomycin, <i>n</i> = 11,470). We examined the association of the serum trough vancomycin level recorded within the first 48 h of administration with subsequent AKI in all patients treated with vancomycin and association of vancomycin vs. non-glycopeptide antibiotics use with the risk of incident AKI. <b><i>Results:</i></b> The overall multivariable adjusted ORs of AKI stages 1, 2, and 3 in patients on vancomycin vs. non-glycopeptides were 1.1 (1.1–1.2), 1.2 (1–1.4), and 1.4 (1.1–1.7), respectively. When examined in strata divided by vancomycin trough level, the odds of AKI were similar or lower in patients receiving vancomycin compared to non-glycopeptide antibiotics as long as serum vancomycin levels were ≤20 mg/L. However, in patients with serum vancomycin levels &gt; 20 mg/L, the ORs of AKI stages 1, 2, and 3 in patients on vancomycin vs. non-glycopeptide antibiotics were 1.5 (1.4–1.7), 1.9 (1.5–2.3), and 2.7 (2–3.5), respectively. <b><i>Conclusions:</i></b> Vancomycin use is associated with a higher risk of AKI when serum levels exceed &gt; 20 mg/L.
DOI: 10.6084/m9.figshare.7577594.v1
title: Supplementary Material for: External Validation of Different Scoring Systems for Suspected Choledocholithiasis

description: <b><i>Aim of the Study:</i></b> The diagnosis of choledocholithiasis is challenging. Previously published scoring systems designed to calculate the risk of choledocholithiasis were evaluated to appraise the diagnostic performance. <b><i>Patients and Methods</i></b>: Data of patients who were admitted between 2013 and 2015 with the following characteristics were retrieved: bile stone-related symptoms and signs, and indication to laparoscopic cholecystectomy. To validate and appraise the performance of the 6 scoring systems, the acknowledged domains of each metrics were applied to the present cohort. Sensitivity, specificity, positive, negative predictive, Youden index, and receiver operating characteristic curve with the area under the curve (AUC) values of the scores were calculated. <b><i>Results:</i></b> Two-hundred patients were analyzed. The highest sensitivity and specificity were obtained from the Menezes’ (96.6%) and Telem’s (99.3%) metrics respectively. The Telem’s and Menezes’ scores had the best positive (75.0%) and negative (96.4%) predictive values respectively. The best accuracy, as computed by the Youden index and AUC, was found for the Soltan’s scoring system (0.628 and 0.88, respectively). <b><i>Conclusion:</i></b> The available scoring systems are precise only in identifying patients with a negligible risk of common bile duct stone, but overall insufficiently accurate to suggest the routine use in clinical practice.
DOI: 10.7284/133061
title: Multibeam Echosounder data collected during research cruise FK190211 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7577561
title: Supplementary Material for: Divergence and Convergence: How Do Income Inequalities in Mortality Change over the Life Course?

description: <b><i>Background:</i></b> Do inequalities in health by income increase or decrease with age? The empirical evidence is not conclusive and competing theories arrive at different conclusions. <b><i>Objective:</i></b> This study examined inequality in mortality by income over the adult life course with longitudinal data on people aged 30–99 between the years 1990 and 2009. Each person was followed for 19 years. <b><i>Methods:</i></b> We used Swedish total population data with 5,011,414 individual observations. We calculated the probability of having died for ages between 31 and 99. This approach to calculating death risk incorporates selective mortality during the follow-up period into the measure. Age and year standardized income positions were calculated for all individuals. Inequality was assessed by comparing the top 10% income group and the bottom 10% income group. Relative inequality was measured by risk ratios (RR) and absolute inequality by percentage point differences. <b><i>Results:</i></b> The results showed that the highest relative income inequality in mortality was at age 56 for men (RR: 4.7) and at age 40 for women (RR: 4.1) with differing patterns across the younger age categories between the sexes. The highest absolute income inequality in mortality was found at age 78 for men (19% difference) and at age 89 for women (14% difference) with similar patterns for both sexes. Both measures of inequality decreased after the peak, with small or no inequalities above age 95. Income inequality in mortality remained in advanced age, with larger absolute inequalities in older ages and larger relative inequalities in younger ages. <b><i>Conclusion:</i></b> The results for absolute and relative measures of inequality differed substantially; this highlights the importance of discussing and making an active choice of inequality measure. To explain and understand the patterns of inequality in mortality over the adult life course, we conclude that the “age-as-leveler” and “cumulative disadvantage” theories are best applied to an absolute measure of inequality.
DOI: 10.6084/m9.figshare.7577591.v1
title: Global transcriptomic analysis of a L. monocytogenes agrD mutant

description: Global expression profiles of <i>L. monocytogenes</i> EGDe and an isogenic <i>agrD</i> deletion mutant were analyzed by custom spotted microarrays (Agilent 4x44k arrays, mono-dye setup) covering all genes of the genome.The file set contains a .zip file with raw data including a detailed descriptions of the design of the array and reports on the analysis procedures. The raw data set comprises a second experiment (transcriptomic analysis), which is irrelevant to the comparison of EGDe WT and the <i>agrD</i> mutant. <br>For ease of interpretation and analysis there are further files with raw spot intensities of the relevant samples, a sample key list and a list with background-corrected, normalized log<sub>2</sub>-fold changes in expression in exponential and stationary growth phase for all genes with statistical significance of the change.<br>
DOI: 10.7284/133062
title: Multibeam Echosounder data collected during research cruise FK190211 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133056
title: Splitbeam Echosounder data collected during research cruise FK190211 using a Kongsberg EK60 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133058
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK190211 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133059
title: TSG (Thermosalinograph) data collected during research cruise FK190211 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133066
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK190315 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133065
title: Expendable Probe data collected during research cruise FK190315 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133067
title: Fluorometer data collected during research cruise FK190315 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133064
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK190315 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25375/uct.7577456
title: Analysis scripts and supplementary files: Rethinking pain threshold as a zone of uncertainty.

description: <b>DESCRIPTION</b><br>This repository contains the analysis scripts and supplementary files for the manuscript <i>Rethinking pain threshold as a zone of uncertainty</i>. The analysis scripts and their outputs are located in pain-threshold.zip. Supplementary files are found in PDF form under the relevant name Suppl-*.pdf. Supplementary figures are found in PDF form under the relevant name SupplFig*.pdf.<br>Please note that participant consent materials did not include consent for public release of data, so data are not made available here. However, we do not wish to restrict access to the data needlessly, so requests for access to the data will be considered on a case-by-case basis and data made available subject to Human Research Ethics Committee approval. Requests can be directed to Tory Madden (torymadden@gmail.com).<br><b>Repository citation</b><br>Kamerman P, Madden V, Catley M, Bellan V, Russek L, Camfferman D, Moseley L. Analysis scripts and supplementary files: Rethinking pain threshold as a zone of uncertainty. Figshare, 2019. DOI: 10.25375/uct.7577456.<br><br>
DOI: 10.25375/uct.7577456.v1
title: Analysis scripts and supplementary files: Rethinking pain threshold as a zone of uncertainty.

description: <b>DESCRIPTION</b><br>This repository contains the analysis scripts and supplementary files for the manuscript <i>Rethinking pain threshold as a zone of uncertainty</i>. The analysis scripts and their outputs are located in pain-threshold.zip. Supplementary files are found in PDF form under the relevant name Suppl-*.pdf. Supplementary figures are found in PDF form under the relevant name SupplFig*.pdf.<br>Please note that participant consent materials did not include consent for public release of data, so data are not made available here. However, we do not wish to restrict access to the data needlessly, so requests for access to the data will be considered on a case-by-case basis and data made available subject to Human Research Ethics Committee approval. Requests can be directed to Tory Madden (torymadden@gmail.com).<br><b>Repository citation</b><br>Kamerman P, Madden V, Catley M, Bellan V, Russek L, Camfferman D, Moseley L. Analysis scripts and supplementary files: Rethinking pain threshold as a zone of uncertainty. Figshare, 2019. DOI: 10.25375/uct.7577456.<br><br>
DOI: 10.7284/133063
title: Gyrocompass data collected during research cruise FK190315 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133570
title: INS (Inertial Navigation System) data collected during research cruise FK190315 using a Applanix POS/MV-320 V5 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133571
title: Meteorological Station data collected during research cruise FK190315 using a Gill MetPak Pro instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133572
title: Meteorological Station data collected during research cruise FK190315 using a Gill MetPak Pro instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133070
title: Multibeam Echosounder data collected during research cruise FK190315 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133071
title: Multibeam Echosounder data collected during research cruise FK190315 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133072
title: Multibeam Echosounder data collected during research cruise FK190315 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133073
title: Multibeam Echosounder data collected during research cruise FK190315 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133568
title: pH data collected during research cruise FK190315 using a SUNBURST SAMI-pH instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/133567
title: Radiometer data collected during research cruise FK190315 using a Eppley RAD instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition