cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8275463.v1
title: Supplementary Material for: Microbleeds after Carotid Artery Stenting: Small Embolism May Induce Cerebral Microbleeds

description: <b><i>Background:</i></b> Since the advent of magnetic resonance imaging technology, cerebral microbleeds can be diagnosed in vivo. However, the underlying mechanism of cerebral microbleed formation is not fully understood. <b><i>Objectives:</i></b> This study aimed to identify the factors associated with cerebral microbleeds after carotid artery stenting (CAS). <b><i>Method:</i></b> We retrospectively examined 125 patients who underwent CAS for carotid stenosis. Cerebral microbleeds were investigated using T2*-weighted gradient-echo (GRE) imaging before and after CAS. We analyzed the possible association of new microbleeds with the following risk factors: the number of baseline microbleeds and ischemic cerebral lesions, the occurrence of cerebral hyperperfusion syndrome, and new ischemic cerebral lesions after CAS. <b><i>Results:</i></b> Baseline cerebral microbleeds were detected in 53 patients (42.4%). New cerebral microbleeds after CAS were observed in 13 of 125 patients (10.4%) and were exclusively associated with new ischemic lesions but not with other risk factors. No patient showed a merged image of a new cerebral microbleed on GRE imaging or a new ischemic lesion on diffusion-weighted imaging. Lobar and deep microbleeds were noted in 12/13 (92.3%) and 1 patient (7.7%), respectively. Of 12 patients with new microbleeds, 10 (76.9%) and 2 (15.4%) had a new microbleed in the ipsilateral and contralateral hemispheres, respectively. <b><i>Conclusions:</i></b> We found that new cerebral microbleeds developed after CAS and that these might be associated with new ischemic lesions, mostly in the territory of the treated carotid artery. We speculate that these microbleeds result from the deoxygenation of hemoglobin in the embolus or, alternatively, small hemorrhagic transformation of ischemic lesions.
DOI: 10.6084/m9.figshare.8275499.v1
title: Three new serine-protease autotransporters of <i>Enterobacteriaceae</i> (SPATEs) from extra-intestinal pathogenic <i>Escherichia coli</i> and combined role of SPATEs for cytotoxicity and colonization of the mouse kidney

description: Serine protease autotransporters of <i>Enterobacteriaceae</i> (SPATEs) are secreted proteins that contribute to virulence and function as proteases, toxins, adhesins, and/or immunomodulators. An extra-intestinal pathogenic <i>E. coli</i> (ExPEC) O1:K1 strain, QT598, isolated from a turkey, was shown to contain <i>vat, tsh</i>, and three uncharacterized SPATE-encoding genes. Uncharacterized SPATEs: Sha (<i>S</i>erine-protease <i>h</i>emagglutinin <i>a</i>utotransporter), TagB and TagC (<i>t</i>andem <i>a</i>utotransporter <i>g</i>enes <i>B</i> and <i>C</i>) were tested for activities including hemagglutination, autoaggregation, and cytotoxicity when expressed in <i>E. coli</i> K-12. Sha and TagB conferred autoaggregation and hemagglutination activities. TagB, TagC, and Sha all exhibited cytopathic effects on a bladder epithelial cell line. In QT598, <i>tagB</i> and <i>tagC</i> are tandemly encoded on a genomic island, and were present in 10% of UTI isolates and 4.7% of avian <i>E. coli</i>. Sha is encoded on a virulence plasmid and was present in 1% of UTI isolates and 20% of avian <i>E. coli</i>. To specifically examine the role of SPATEs for infection, the 5 SPATE genes were deleted from strain QT598 and tested for cytotoxicity. Loss of all five SPATEs abrogated the cytopathic effect on bladder epithelial cells, although derivatives producing any of the 5 SPATEs retained cytopathic activity. In mouse infections, <i>sha</i> gene-expression was up-regulated a mean of sixfold in the bladder compared to growth <i>in vitro</i>. Loss of either <i>tagBC</i> or <i>sha</i> did not reduce urinary tract colonization. Deletion of all 5 SPATEs, however, significantly reduced competitive colonization of the kidney supporting a cumulative role of SPATEs for QT598 in the mouse UTI model.
DOI: 10.6084/m9.figshare.8275433
title: Supplementary Material for: Formulation and Artificial Sebum Effects on the Percutaneous Absorption of Zinc Pyrithione through Excised Human Skin

description: <b><i>Background:</i></b> Zinc pyrithione (ZnPT) is deposited on the skin as a fine particulate and must reach microorganisms localized in the stratum corneum and hair follicles in molecular form to exert its broad-spectrum antimicrobial/antifungal activity. Dissolution of ZnPT particles followed by molecular speciation results in the organic portion, i.e. pyrithione, being more susceptible to skin penetration than the inorganic component, i.e. zinc, or the chelate itself, i.e. ZnPT. <b><i>Objectives:</i></b> To further test the hypothesis that ZnPT skin penetration is rate-limited by dissolution and molecular speciation, the effect of different formulations and artificial sebum on the in vitro percutaneous absorption of radiolabel associated with Zn[<sup>14</sup>C]PT was investigated. <b><i>Method:</i></b> In vitro penetration of [<sup>14</sup>C]PT into and through excised human skin was measured following application of Zn[<sup>14</sup>C]PT prepared as suspensions in distinct vehicles including water-based carboxymethylcellulose (CMC), diluted body wash comprised of surfactants, and castor oil, in the presence and absence of artificial sebum. <b><i>Results:</i></b> The steady-state flux and cumulative absorption of Zn[<sup>14</sup>C]PT increased 4- to 5-fold when deposited from a body wash or castor oil compared to a water-based CMC suspension. Tritiated water flux measured before and after treatment showed that neither the surfactant vehicle nor castor oil significantly altered barrier function versus water alone. An artificial sebum layer on the skin potentiated Zn[<sup>14</sup>C]PT and <sup>3</sup>H<sub>2</sub>O absorption when dosed from both aqueous formulations, but not from castor oil. <b><i>Conclusion:</i></b> These data are consistent with the hypothesis that ZnPT percutaneous absorption, as measured by [<sup>14</sup>C]PT kinetics, is controlled by particle dissolution and molecular speciation.
DOI: 10.6084/m9.figshare.8275445
title: Epidemiological investigation of non-fermentative bacterial infection in cirrhotic patients

description: <b>Background</b>: This study aimed to describe the clinical characteristics of NFGNB in patients with cirrhosis as well as the risk factors for short-term mortality. <b>Methods</b>: A retrospective analysis was performed in patients with cirrhosis and NFGNB infections from 2011 to 2016 . <b>Results</b>: 144 episodes in 134 patients with liver cirrhosis and NFGNB infections were found in total. Of these, 81.2% were hospital-acquired or healthcare- associated infections, while only 18.8% of NFGNB infections originated from the community. <i>A. baumannii</i> were the most frequently isolated bacteria (39 episodes), followed by <i>S. maltophilia (38 episodes)</i> and <i>P. aeruginosa</i> (31 episodes). MDR- and non-MDR-NFGNB comprised 62.5% and 37.5% of infections respectively. The Kaplan-Meier survival curve showed no significant difference between MDR and non-MDR NFGNB patients (74.1% vs 75.5%, P = 0.811). Neither MDR or the subgroup of common NFGNB (<i>P. aeruginosa, A. baumannii, S. maltophilia</i>) was associated with the 28-day mortality (all P &gt;0.05). Low albumin levels and high Tbil levels were both independent risk factors for 28-day mortality (HR = 0.930, 95%CI (0.869, 0.995), P = 0.035; HR = 1.003, 95%CI (1.002, 1.005), P <b>Conclusions</b>: Diabetes increased 28-day mortality significantly, however, MDR status, site of infection and bacteria type did not.
DOI: 10.6084/m9.figshare.8275496.v1
title: WIsamples.correct.Final.map.recode.vcf

description: 180K SoyaSNP array genotype data for construction of genetic maps in WH, HI, WI, and II populations
DOI: 10.6084/m9.figshare.8275445.v1
title: Epidemiological investigation of non-fermentative bacterial infection in cirrhotic patients

description: <b>Background</b>: This study aimed to describe the clinical characteristics of NFGNB in patients with cirrhosis as well as the risk factors for short-term mortality. <b>Methods</b>: A retrospective analysis was performed in patients with cirrhosis and NFGNB infections from 2011 to 2016 . <b>Results</b>: 144 episodes in 134 patients with liver cirrhosis and NFGNB infections were found in total. Of these, 81.2% were hospital-acquired or healthcare- associated infections, while only 18.8% of NFGNB infections originated from the community. <i>A. baumannii</i> were the most frequently isolated bacteria (39 episodes), followed by <i>S. maltophilia (38 episodes)</i> and <i>P. aeruginosa</i> (31 episodes). MDR- and non-MDR-NFGNB comprised 62.5% and 37.5% of infections respectively. The Kaplan-Meier survival curve showed no significant difference between MDR and non-MDR NFGNB patients (74.1% vs 75.5%, P = 0.811). Neither MDR or the subgroup of common NFGNB (<i>P. aeruginosa, A. baumannii, S. maltophilia</i>) was associated with the 28-day mortality (all P &gt;0.05). Low albumin levels and high Tbil levels were both independent risk factors for 28-day mortality (HR = 0.930, 95%CI (0.869, 0.995), P = 0.035; HR = 1.003, 95%CI (1.002, 1.005), P <b>Conclusions</b>: Diabetes increased 28-day mortality significantly, however, MDR status, site of infection and bacteria type did not.
DOI: 10.6084/m9.figshare.8275406
title: Data associated with analysis of beta myosin sequence changes associated with body mass

description: The files available here are associated with a research project that investigated sequence changes in beta myosin that are associated with reduced heart rate as mammal body mass increases.<br>myh7.fasta contains the multiple sequence alignment of the beta myosin sequences.<br>myh7_plot_H_3.csv is a comma separated file that contains the body masses of the species and the alignment in a a CSV format.<br>Source file for Nat Comms - this file contains the raw experimental data for the project.
DOI: 10.6084/m9.figshare.8275397
title: Supplementary Material for: A Body Mass Index-Based Cross-Classification Approach for the Assessment of Prognostic Factors in Chronic Kidney Disease Progression

description: <b><i>Background/Aims:</i></b> Cross-classification analyses are rarely reported. We investigated the prognostic factors for chronic kidney disease (CKD) progression using a body mass index (BMI)-based cross-classification approach. <b><i>Methods:</i></b> Patients’ renal outcome (≥50% decline in the estimated glomerular filtration rate or end-stage renal disease) in each subcohort was examined. <b><i>Results:</i></b> The number of prognostic factors identified in the multivariate Cox analysis was smaller in the “BMI ≥25, female” and CKD stage 3 subcohorts than in other subcohorts. Prognostic factors identified in the “BMI ≥25, CKD stage 3” subcohort only comprised albuminuria and male sex, and those in the “BMI ≥25, female” subcohort only comprised albuminuria, hyperphosphatemia, and anemia. Albuminuria, kidney impairment, male sex, hyperphosphatemia, anemia, and increased pulse pressure × heart rate product (PP × HR; pulsatile stress) were stable renal prognostic factors in almost all subcohorts. On the other hand, the prognostic value of increased BMI, younger age, hypoalbuminemia, increased intact parathyroid hormone, and decreased estimated 24-h urinary potassium excretion (e24hUK) differed according to subcohort. BMI was positively associated with CKD progression in the “BMI ≥25, age ≥65 years” and “BMI ≥25, CKD stages 4–5” subcohorts, whereas it was negatively associated with CKD progression in the “BMI &lt;25, diabetes mellitus” subcohort. PP × HR was independently associated with CKD progression in the “BMI &lt;25, CKD stage 3” subcohort, which had relatively few identified renal prognostic factors. Decreased e24hUK was a renal prognostic factor for CKD progression in the “BMI &lt;25, CKD stages 4–5” subcohort, while no significant factors were observed in the “BMI ≥25, CKD stages 4–5” subcohort. <b><i>Conclusion:</i></b> A BMI-based cross-classification approach, which provides more comprehensive findings than that in previous approaches, is expected to be an effective method for evaluating renal prognostic factors in patients with CKD who are affected by multiple risk factors.
DOI: 10.6084/m9.figshare.8275406.v2
title: Data associated with analysis of beta myosin sequence changes associated with body mass

description: The files available here are associated with a research project that investigated sequence changes in beta myosin that are associated with reduced heart rate as mammal body mass increases.<br>myh7.fasta contains the multiple sequence alignment of the beta myosin sequences.<br>myh7_plot_H_3.csv is a comma separated file that contains the body masses of the species and the alignment in a a CSV format.<br>Source file for Nat Comms - this file contains the raw experimental data for the project.
DOI: 10.6084/m9.figshare.8275388
title: Reviewing the discoverability and accessibility to data and information products linked to Essential Climate Variables

description: Essential Climate Variables (ECVs) are geophysical records generated from systematic Earth Observations associated with climate variations, changes, and impacts. ECVs products support the data and information needs of international frameworks and policies such as the work of the United Nations Framework Convention on Climate Change (UNFCCC) and the Intergovernmental Panel on Climate Change (IPCC). We map the main networks and initiatives publishing ECVs, by presenting an overview of existing satellite-based ECVs, their general data creation characteristics, discoverability and accessibility methods from an end-user perspective. We investigate key initiatives providing or coordinating access to ECV data records, such as the Global Climate Observing System (GCOS), the Committee on Earth Observation Satellites (CEOS), the Coordination Group for Meteorological Satellites (CGMS), Joint Working Group on Climate (WGClimate), the Remote Sensing Systems (REMSS), and the European Space Agency Climate Change Initiative (ESA CCI). We find that ECV data discovery and access is difficult and time consuming due to the lack of common data and metadata catalogues. In addition, the selection of fit-for-purpose data records by end-users requires the implementation of interoperable standards and scalable data infrastructures to allow the generation of tailored applications and data-driven information products in support of decision-making processes.
DOI: 10.6084/m9.figshare.8275406.v1
title: Data associated with analysis of beta myosin sequence changes associated with body mass

description: The files available here are associated with a research project that investigated sequence changes in beta myosin that are associated with reduced heart rate as mammal body mass increases.<br>myh7.fasta contains the multiple sequence alignment of the beta myosin sequences.<br>myh7_plot_H_3.csv is a comma separated file that contains the body masses of the species and the alignment in a a CSV format.
DOI: 10.6084/m9.figshare.8275385
title: HIsamples.correct.Final.map.recode.vcf

description: 180K SoyaSNP array genotype data for construction of genetic maps in WH, HI, WI, and II populations
DOI: 10.6084/m9.figshare.8275388.v1
title: Reviewing the discoverability and accessibility to data and information products linked to Essential Climate Variables

description: Essential Climate Variables (ECVs) are geophysical records generated from systematic Earth Observations associated with climate variations, changes, and impacts. ECVs products support the data and information needs of international frameworks and policies such as the work of the United Nations Framework Convention on Climate Change (UNFCCC) and the Intergovernmental Panel on Climate Change (IPCC). We map the main networks and initiatives publishing ECVs, by presenting an overview of existing satellite-based ECVs, their general data creation characteristics, discoverability and accessibility methods from an end-user perspective. We investigate key initiatives providing or coordinating access to ECV data records, such as the Global Climate Observing System (GCOS), the Committee on Earth Observation Satellites (CEOS), the Coordination Group for Meteorological Satellites (CGMS), Joint Working Group on Climate (WGClimate), the Remote Sensing Systems (REMSS), and the European Space Agency Climate Change Initiative (ESA CCI). We find that ECV data discovery and access is difficult and time consuming due to the lack of common data and metadata catalogues. In addition, the selection of fit-for-purpose data records by end-users requires the implementation of interoperable standards and scalable data infrastructures to allow the generation of tailored applications and data-driven information products in support of decision-making processes.
DOI: 10.6084/m9.figshare.8275397.v1
title: Supplementary Material for: A Body Mass Index-Based Cross-Classification Approach for the Assessment of Prognostic Factors in Chronic Kidney Disease Progression

description: <b><i>Background/Aims:</i></b> Cross-classification analyses are rarely reported. We investigated the prognostic factors for chronic kidney disease (CKD) progression using a body mass index (BMI)-based cross-classification approach. <b><i>Methods:</i></b> Patients’ renal outcome (≥50% decline in the estimated glomerular filtration rate or end-stage renal disease) in each subcohort was examined. <b><i>Results:</i></b> The number of prognostic factors identified in the multivariate Cox analysis was smaller in the “BMI ≥25, female” and CKD stage 3 subcohorts than in other subcohorts. Prognostic factors identified in the “BMI ≥25, CKD stage 3” subcohort only comprised albuminuria and male sex, and those in the “BMI ≥25, female” subcohort only comprised albuminuria, hyperphosphatemia, and anemia. Albuminuria, kidney impairment, male sex, hyperphosphatemia, anemia, and increased pulse pressure × heart rate product (PP × HR; pulsatile stress) were stable renal prognostic factors in almost all subcohorts. On the other hand, the prognostic value of increased BMI, younger age, hypoalbuminemia, increased intact parathyroid hormone, and decreased estimated 24-h urinary potassium excretion (e24hUK) differed according to subcohort. BMI was positively associated with CKD progression in the “BMI ≥25, age ≥65 years” and “BMI ≥25, CKD stages 4–5” subcohorts, whereas it was negatively associated with CKD progression in the “BMI &lt;25, diabetes mellitus” subcohort. PP × HR was independently associated with CKD progression in the “BMI &lt;25, CKD stage 3” subcohort, which had relatively few identified renal prognostic factors. Decreased e24hUK was a renal prognostic factor for CKD progression in the “BMI &lt;25, CKD stages 4–5” subcohort, while no significant factors were observed in the “BMI ≥25, CKD stages 4–5” subcohort. <b><i>Conclusion:</i></b> A BMI-based cross-classification approach, which provides more comprehensive findings than that in previous approaches, is expected to be an effective method for evaluating renal prognostic factors in patients with CKD who are affected by multiple risk factors.
DOI: 10.6084/m9.figshare.8275355
title: Supplementary Material for: Free 25-Vitamin D Is Correlated with Cardiovascular Events in Prevalent Hemodialysis Patients but Not with Markers of Renal Mineral Bone Disease

description: Free vitamin D is the biologically active form of vitamin D. Vitamin D deficiency is associated with cardiovascular disease, the most common cause of mortality in hemodialysis patients. The goal of our current study was to investigate the relation between blood concentrations of free 25-hydroxyvitamin D with cardiovascular events in end-stage chronic kidney disease patients on hemodialysis, because this is unknown so far. We measured free vitamin D levels in 117 stable consecutive prevalent patients in September as a surrogate of vitamin D exposure during the past 6 months, and recorded the number of cardiovascular events during the previous 6 months defined as hospitalization due to heart failure, episodes of acute coronary syndrome, and stroke. Fourteen events occurred during the observation period. In patients without any cardiovascular events the free vitamin D levels were significantly higher as compared to those with cardiovascular events (patients without events: 5.68 [4.37–9.27] pg/mL; patients with events: 4.74 [3.46–5.37] pg/mL, <i>p</i> = 0.015). This finding remained stable after multiple regression analysis considering confounding factors such as age, time on dialysis, preexisting diabetes, hypertension, and coronary heart disease. In conclusion, our study shows that free vitamin D serum concentrations are independently associated with major cardiovascular events in chronic kidney disease patients on dialysis.
DOI: 10.6084/m9.figshare.8275385.v1
title: HIsamples.correct.Final.map.recode.vcf

description: 180K SoyaSNP array genotype data for construction of genetic maps in WH, HI, WI, and II populations
DOI: 10.6084/m9.figshare.8275340
title: Supplementary Material for: Biomarker Predictors of Adverse Acute Kidney Injury Outcomes in Critically Ill Patients: The Dublin Acute Biomarker Group Evaluation Study

description: <b><i>Background:</i></b> The Dublin Acute Biomarker Group Evaluation (DAMAGE) Study is a prospective 2-center observational study investigating the utility of urinary biomarker combinations for the diagnostic and prognostic assessment of acute kidney injury (AKI) in a heterogeneous adult intensive care unit (ICU) population. The objective of this study is to evaluate whether serial urinary biomarker measurements, in combination with a simple clinical model, could improve biomarker performance in the diagnostic prediction of severe AKI and clinical outcomes such as death and need for renal replacement therapy (RRT). <b><i>Methods:</i></b> Urine was collected daily from patients admitted to the ICU, for a total of 7 post-admission days. Urine biomarker concentrations (neutrophil gelatinase-associated lipocalin [NGAL], α-glutathione S-transferase [GST], π-GST, kidney injury molecule-1 [KIM-1], liver-type fatty acid-binding protein [L-FABP], Cystatin C, creatinine, and albumin) were measured. Urine biomarkers were combined with a clinical prediction of AKI model, to determine ability to predict AKI (any stage, within 2 days or 7 days of ICU admission), or a ­30-day composite clinical outcome (RRT – or death). <b><i>Results:</i></b> A total of 257 (38%) patients developed AKI within 7 days of ICU admission. Of those who developed AKI, 106 (41%) patients met stage 3 AKI within 7 days of ICU admission and 208 patients of the entire study cohort (31%) met the composite clinical endpoint of in-hospital mortality or RRT within 30 days of ICU admission. The addition of urinary NGAL/albumin to the clinical model modestly improved the prediction of AKI, in particular severe stage 3 AKI (area under the curve [AUC] of 0.9 from 0.87, <i>p</i> = 0.369) and the prediction of 30-day RRT or death (AUC 0.83 from 0.79, <i>p</i> = 0.139). <b><i>Conclusion:</i></b> A clinical model incorporating severity of illness, patient demographics, and chronic illness with currently available clinical biomarkers of renal function was strongly predictive of development of AKI and associated clinical outcomes in a heterogeneous adult ICU population. The addition of urinary NGAL/albumin to this simple clinical model improved the prediction of severe AKI, need for RRT and death, but not at a statistically or clinically significant level, when compared to the clinical model alone.