cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p14g62b3
title: Pd Surveillance DNA Extraction by Sample Type Experiment Data Release

description: These data were collected as part of a research project to compare commonly used DNA extraction methods for subsequent detection of Pseudogymnoascus destructans (Pd), the causative fungus of white-nose syndrome in bats, from bat guano samples, skin swabs, and environmental/sediment swabs. Swab samples were used to evalute DNA extraction protocols based on either a MagMAX™ Total Nucleic Acid Isolation Kit or PrepMan™ Ultra Sample Reagent. Guano samples additionally included the use of a DNeasy PowerLyzer PowerSoil Kit-based DNA extraction protocol. Data_Average_Standard_Curve_v2.csv includes qPCR results (Cq values) from standard curves included on 274 reaction plates. Standards were created from 1:10 dilution series containing 85.296 to 8,529,575 copies of Pd gBlock (i.e., synthetic, double-stranded DNA that contains a near-identical sequence to the intergenic spacer region of the type strain for Pd). A new dilution series was created from a stock aliquot of Pd gBlock at least for each date, but reaction plates processed on the same date may have used the same dilution series. The qPCR methodology for each plate followed that described by Verant et al. (2016). These data were used to create an averaged standard curve, which was used to convert Cq values to copy numbers of target DNA for the remaining datasets in this research project, in which the same qPCR methodology was used. Data_Inoculated_Samples_v2.csv contains qPCR results from a laboratory experiment where guano samples and sediment-coated swabs were inoculated with between 10 and 100,000 Pd conidia and extracted with either a PrepMan, MagMAX, or PowerLyzer-based DNA extraction method. Data_Field-collected_Env_Swabs_v2.csv contains qPCR results from environmental substrate swabs that were collected as part of national Pd surveillance efforts from underground and above-ground bat roosts that were naturally infected with Pd. These environmental swabs were extracted with a PrepMan-based method and qPCR was conducted on both undiluted and a ten-fold dilution of extract from each swab. Data_Bat_Skin_Swabs_v2.csv contains qPCR results from skin swabs collected from bat carcasses that had previously been submitted for diagnostic evaluation of white-nose syndrome infection and were re-sampled for this research project. These skin swabs were extracted with either a PrepMan or MagMAX-based method.
DOI: 10.15468/dl.zkyyze
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Abelmoschus esculentus"
 ]
}

 The dataset includes 61 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003404-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtj53g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((98.03 2.720176, 97.959659 2.714607, 97.891051 2.698038, 97.825868 2.670877, 97.765716 2.633793, 97.71207699999999 2.5877, 97.66627200000001 2.533735, 97.629428 2.473227, 97.602451 2.407666, 97.586005 2.338667, 97.580493 2.26793, 97.58604800000001 2.197196, 97.60253299999999 2.128207, 97.629541 2.062661, 97.666405 2.002172, 97.712217 1.948228, 97.765849 1.902157, 97.825981 1.865092, 97.891133 1.837946, 97.95970199999999 1.821387, 98.03 1.815821, 98.100298 1.821387, 98.16886700000001 1.837946, 98.234019 1.865092, 98.294151 1.902157, 98.34778300000001 1.948228, 98.393595 2.002172, 98.430459 2.062661, 98.45746699999999 2.128207, 98.473952 2.197196, 98.479507 2.26793, 98.473995 2.338667, 98.457549 2.407666, 98.430572 2.473227, 98.393728 2.533735, 98.34792299999999 2.5877, 98.294284 2.633793, 98.234132 2.670877, 98.168949 2.698038, 98.100341 2.714607, 98.03 2.720176))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003405-260120142942310/datasets/export for details.
DOI: 10.6084/m9.figshare.27316262
title: Predictive role of Oxford Classification for prognosis in children with IgA nephropathy: a systematic review and meta-analysis

description: The Oxford Classification was proposed as an independent prognostic indicator in IgA nephropathy (IgAN). However, most studies on the subject focus on adults instead of children. Using a meta-analysis to appraise the predictive roles of the Oxford classification for the prognosis of pediatric patients with IgAN. All cohort studies regarding the analysis of the association between poor kidney-related prognosis (GFR categories G2-G5) according to the Kidney Disease Improving Global Outcomes (KDIGO) Guideline in pediatric patients with IgAN and five pathologic lesions in the Oxford Classification were included. Hazard ratios (HRs) regarding the association between the Oxford classification and prognosis of pediatric patients with IgAN were synthesized using random effect models. The risk of bias in studies was assessed based on the Newcastle-Ottawa scale. Fourteen articles were included with 5679 IgAN patients and 710 endpoint outcome events occurred. M1 was associated with a higher risk of poor kidney-related prognosis compared with M0, pooled HR (1.79; 95%CI, 1.46–2.19; <i>p</i> &lt; 0.001, random effect model). S1 and T1 or T2 increased the risk of poor kidney-related prognosis (pooled HR, 2.13; 95%CI, 1.68–2.70; <i>p</i> &lt; 0.001; pooled HR, 2.64; 95%CI, 1.81–3.86; <i>p</i> &lt; 0.001, respectively, estimated by random effect model). Compared with C0, C1, or C2 was also associated with an increased risk of poor kidney-related prognosis in the subgroup analysis of Asian and other populations. Evidence to indicate that E1 increased the risk of poor kidney-related prognosis was marginal.
DOI: 10.6084/m9.figshare.27316262.v1
title: Predictive role of Oxford Classification for prognosis in children with IgA nephropathy: a systematic review and meta-analysis

description: The Oxford Classification was proposed as an independent prognostic indicator in IgA nephropathy (IgAN). However, most studies on the subject focus on adults instead of children. Using a meta-analysis to appraise the predictive roles of the Oxford classification for the prognosis of pediatric patients with IgAN. All cohort studies regarding the analysis of the association between poor kidney-related prognosis (GFR categories G2-G5) according to the Kidney Disease Improving Global Outcomes (KDIGO) Guideline in pediatric patients with IgAN and five pathologic lesions in the Oxford Classification were included. Hazard ratios (HRs) regarding the association between the Oxford classification and prognosis of pediatric patients with IgAN were synthesized using random effect models. The risk of bias in studies was assessed based on the Newcastle-Ottawa scale. Fourteen articles were included with 5679 IgAN patients and 710 endpoint outcome events occurred. M1 was associated with a higher risk of poor kidney-related prognosis compared with M0, pooled HR (1.79; 95%CI, 1.46–2.19; <i>p</i> &lt; 0.001, random effect model). S1 and T1 or T2 increased the risk of poor kidney-related prognosis (pooled HR, 2.13; 95%CI, 1.68–2.70; <i>p</i> &lt; 0.001; pooled HR, 2.64; 95%CI, 1.81–3.86; <i>p</i> &lt; 0.001, respectively, estimated by random effect model). Compared with C0, C1, or C2 was also associated with an increased risk of poor kidney-related prognosis in the subgroup analysis of Asian and other populations. Evidence to indicate that E1 increased the risk of poor kidney-related prognosis was marginal.
DOI: 10.6084/m9.figshare.27367492
title: Development and validation of an early acute kidney injury risk prediction model for patients with sepsis in emergency departments

description: In this study, we aimed to develop and validate a nomogram to predicting the risk of sepsis-associated acute kidney injury (SA-AKI) in patients admitted to emergency departments (EDs). We randomly divided a retrospective dataset of 391 patients with sepsis into a 294-person training cohort and a 97-person validation cohort, and developed three predictive models using multivariate logistic regression analysis and clinical insight. No difference was observed between the three models using the DeLong test and Model 3 was selected as the risk prediction model based on the principle of least inclusion indicators. The use of vasopressor drugs, patient age, platelet count, procalcitonin, and D-dimer levels were included. The training and validation cohorts had a consistency index of 0.832 and 0.866, respectively, indicating high accuracy and stability in predicting SA-AKI risk. The area under the receiver operating characteristic curve was 0.832, showing excellent discrimination. The calibration curves for the training and validation cohorts showed excellent calibration. The decision curve and clinical impact curve analyses showed that the net clinical benefit of using the nomogram was greatest over a probability threshold of 0.05–0.90. In addition, the model showed moderate validity in predicting the 30-day survival and the incidence of major adverse renal events within 30 days. The nomogram developed for SA-AKI risk assessment in patients in EDs showed good discriminability and clinical utility. It can provide a theoretical basis for emergency physicians to prevent SA-AKI.
DOI: 10.6084/m9.figshare.27367492.v1
title: Development and validation of an early acute kidney injury risk prediction model for patients with sepsis in emergency departments

description: In this study, we aimed to develop and validate a nomogram to predicting the risk of sepsis-associated acute kidney injury (SA-AKI) in patients admitted to emergency departments (EDs). We randomly divided a retrospective dataset of 391 patients with sepsis into a 294-person training cohort and a 97-person validation cohort, and developed three predictive models using multivariate logistic regression analysis and clinical insight. No difference was observed between the three models using the DeLong test and Model 3 was selected as the risk prediction model based on the principle of least inclusion indicators. The use of vasopressor drugs, patient age, platelet count, procalcitonin, and D-dimer levels were included. The training and validation cohorts had a consistency index of 0.832 and 0.866, respectively, indicating high accuracy and stability in predicting SA-AKI risk. The area under the receiver operating characteristic curve was 0.832, showing excellent discrimination. The calibration curves for the training and validation cohorts showed excellent calibration. The decision curve and clinical impact curve analyses showed that the net clinical benefit of using the nomogram was greatest over a probability threshold of 0.05–0.90. In addition, the model showed moderate validity in predicting the 30-day survival and the incidence of major adverse renal events within 30 days. The nomogram developed for SA-AKI risk assessment in patients in EDs showed good discriminability and clinical utility. It can provide a theoretical basis for emergency physicians to prevent SA-AKI.
DOI: 10.6084/m9.figshare.27957529
title: Exploring the causal effect of complement and IgA nephropathy—a Mendelian randomization study

description: IgA nephropathy, one of the most common primary glomerulonephritis worldwide, is still under investigation for its precise etiology. The widely accepted theory is the ‘four-hit model’ and subsequent complement and inflammatory responses. Recent studies have reported correlations between specific complement components and IgA nephropathy. However, the causal effects of genetically predicted complement components on IgA nephropathy require further elucidation. Our study aimed to determine the causal relationship between genetic predictors of complement and IgA nephropathy using the Mendelian randomization method. The primary analysis was initially conducted, examining heterogeneity and horizontal pleiotropy tests in each subgroup. Complement components with positive results were further analyzed using the MR-PRESSO test and co-localization analysis. Subsequently, the positive results were further analyzed using the cML-MA method to validate the previous studies. Finally, a Bi‑directional analysis was performed, providing a brief evaluation of the causal effect of IgA nephropathy on complement components. We found a causal effect between C1QBP, C3b, C3d, C2, and C7 and IgA nephropathy, but did not identify any reverse causality. Results from co-localization analysis suggest intricate pathway interactions between the complement system and IgA nephropathy. Our findings provide possible directions for subsequent complement research, which will contribute to further exploration of the etiology of IgA nephropathy.
DOI: 10.6084/m9.figshare.27957529.v1
title: Exploring the causal effect of complement and IgA nephropathy—a Mendelian randomization study

description: IgA nephropathy, one of the most common primary glomerulonephritis worldwide, is still under investigation for its precise etiology. The widely accepted theory is the ‘four-hit model’ and subsequent complement and inflammatory responses. Recent studies have reported correlations between specific complement components and IgA nephropathy. However, the causal effects of genetically predicted complement components on IgA nephropathy require further elucidation. Our study aimed to determine the causal relationship between genetic predictors of complement and IgA nephropathy using the Mendelian randomization method. The primary analysis was initially conducted, examining heterogeneity and horizontal pleiotropy tests in each subgroup. Complement components with positive results were further analyzed using the MR-PRESSO test and co-localization analysis. Subsequently, the positive results were further analyzed using the cML-MA method to validate the previous studies. Finally, a Bi‑directional analysis was performed, providing a brief evaluation of the causal effect of IgA nephropathy on complement components. We found a causal effect between C1QBP, C3b, C3d, C2, and C7 and IgA nephropathy, but did not identify any reverse causality. Results from co-localization analysis suggest intricate pathway interactions between the complement system and IgA nephropathy. Our findings provide possible directions for subsequent complement research, which will contribute to further exploration of the etiology of IgA nephropathy.
DOI: 10.5281/zenodo.18331411
title: Hydrographic conditions and fluorescence peaks of dissolved organic matter along a transect at the Brazil–Malvinas Confluence

description: This dataset comprises hydrographic conditions and fluorescence peak–resolved dissolved organic matter (DOM) properties measured along an oceanographic transect at the Brazil–Malvinas Confluence (Southwestern Atlantic Ocean) during a low-productivity period. The dataset includes geographic coordinates (longitude and latitude in decimal degrees), depth, seawater density, temperature, salinity, dissolved oxygen, bulk fluorescence, and optical indices of DOM (BIX, FI and HIX). In addition, fluorescence intensities of DOM peaks A, B, C, M and T (sensu Coble et al., 1996) are provided, reported in Raman-normalized units.

These data allow the characterization of the hydrographic setting and the sources, composition and transformation state of dissolved organic matter under low-productivity conditions in a key oceanographic region influenced by the interaction between subtropical and subantarctic water masses. The dataset is suitable for studies addressing DOM optical properties, water mass structure, biogeochemical gradients and physical–biological coupling at the Brazil–Malvinas Confluence.
DOI: 10.5281/zenodo.18331410
title: Hydrographic conditions and fluorescence peaks of dissolved organic matter along a transect at the Brazil–Malvinas Confluence

description: This dataset comprises hydrographic conditions and fluorescence peak–resolved dissolved organic matter (DOM) properties measured along an oceanographic transect at the Brazil–Malvinas Confluence (Southwestern Atlantic Ocean) during a low-productivity period. The dataset includes geographic coordinates (longitude and latitude in decimal degrees), depth, seawater density, temperature, salinity, dissolved oxygen, bulk fluorescence, and optical indices of DOM (BIX, FI and HIX). In addition, fluorescence intensities of DOM peaks A, B, C, M and T (sensu Coble et al., 1996) are provided, reported in Raman-normalized units.

These data allow the characterization of the hydrographic setting and the sources, composition and transformation state of dissolved organic matter under low-productivity conditions in a key oceanographic region influenced by the interaction between subtropical and subantarctic water masses. The dataset is suitable for studies addressing DOM optical properties, water mass structure, biogeochemical gradients and physical–biological coupling at the Brazil–Malvinas Confluence.
DOI: 10.6084/m9.figshare.27928809
title: The impact of angiotensin-receptor neprilysin inhibitors on cardiovascular events and solute transport function in peritoneal dialysis patients: a multicenter retrospective controlled study

description: Whether angiotensin receptor-neprilysin inhibitor (ARNI) can reduce the incidence of cardiovascular events and improve peritoneal function in peritoneal dialysis (PD) patients remains unclear. Thus, this study aims to clarify the role of ARNI in PD patients. This was a multicenter retrospective study. A total of 102 patients were enrolled for analysis. Patients who continuously used ARNI for 12 months were assigned to the ARNI group (<i>n</i> = 55), while those who never used ARNI to the control group (<i>n</i> = 47). Clinical indicators and cardiovascular risk factors were analyzed, along with <i>in vitro</i> experiments on neoangiogenesis to investigate the underlying molecular mechanisms of peritoneal protection by ARNI. Systolic blood pressure (<i>p</i> = 0.001), diastolic blood pressure (<i>p</i> = 0.001), and left ventricular ejection fraction (<i>p</i> = 0.008) were statistically improved after 12 months of ARNI therapy, whereas these metrics did not change in control patients. The risk factors for the occurrence of cardiac events in PD patients included the use of ARNI [hazard ratio (HR) 0.053; 95% confidence interval (CI), 0.006–0.492] and NT-proBNP level (HR 2.317; 95% CI, 1.179–4.554). Additionally, there was a decrease in 4-hour ratio of creatinine concentration in dialysate to plasma (4h Scr D/P) in the ARNI group (<i>p</i> = 0.020). The <i>in vitro</i> experiments showed that LCZ696, a combination of sacubitril and valsartan, inhibited neoangiogenesis <i>via</i> the VEGFR2/ERK1/2 and Notch1 pathways. ARNI may play a protective role in reducing the incidence of cardiovascular events and decreasing solute transport in PD patients.
DOI: 10.6084/m9.figshare.27928809.v1
title: The impact of angiotensin-receptor neprilysin inhibitors on cardiovascular events and solute transport function in peritoneal dialysis patients: a multicenter retrospective controlled study

description: Whether angiotensin receptor-neprilysin inhibitor (ARNI) can reduce the incidence of cardiovascular events and improve peritoneal function in peritoneal dialysis (PD) patients remains unclear. Thus, this study aims to clarify the role of ARNI in PD patients. This was a multicenter retrospective study. A total of 102 patients were enrolled for analysis. Patients who continuously used ARNI for 12 months were assigned to the ARNI group (<i>n</i> = 55), while those who never used ARNI to the control group (<i>n</i> = 47). Clinical indicators and cardiovascular risk factors were analyzed, along with <i>in vitro</i> experiments on neoangiogenesis to investigate the underlying molecular mechanisms of peritoneal protection by ARNI. Systolic blood pressure (<i>p</i> = 0.001), diastolic blood pressure (<i>p</i> = 0.001), and left ventricular ejection fraction (<i>p</i> = 0.008) were statistically improved after 12 months of ARNI therapy, whereas these metrics did not change in control patients. The risk factors for the occurrence of cardiac events in PD patients included the use of ARNI [hazard ratio (HR) 0.053; 95% confidence interval (CI), 0.006–0.492] and NT-proBNP level (HR 2.317; 95% CI, 1.179–4.554). Additionally, there was a decrease in 4-hour ratio of creatinine concentration in dialysate to plasma (4h Scr D/P) in the ARNI group (<i>p</i> = 0.020). The <i>in vitro</i> experiments showed that LCZ696, a combination of sacubitril and valsartan, inhibited neoangiogenesis <i>via</i> the VEGFR2/ERK1/2 and Notch1 pathways. ARNI may play a protective role in reducing the incidence of cardiovascular events and decreasing solute transport in PD patients.
DOI: 10.6084/m9.figshare.26975159
title: Association between serum calcium level and the risk of acute kidney injury in patients with acute myocardial infarction: evidences from the MIMIC-IV database

description: This cohort study was to assess the association between serum calcium levels and the risk of acute kidney injury (AKI) in acute myocardial infarction (AMI) patients. This study was analyzed using data of 1286 AMI patients aged ≥18 years who stayed in ICU more than 24 h in Medical Information Mart for Intensive Care IV (MIMIC-IV) database. Univariable logistic regression model was established to identify potential covariates. Univariate and multivariable logistic regression models were used to analyze the association between serum calcium and the risk of AKI in patients with AMI. The association between serum calcium and the risk of AKI in patients with AMI was also shown by restricted cubic spline (RCS) plot. Odds ratio (OR) and 95% confidence interval (CI) were calculated. The median follow-up time was 1.61 (1.23, 2.30) days, and 436 (33.90%) participants had AKI at the end of follow-up. After adjusting for covariates, elevated level of serum calcium level was related to reduced risk of AKI in AMI patients (OR = 0.88, 95%CI: 0.80–0.98). Decreased risk of AKI was found in AMI patients with serum calcium level of 8.40–8.90 mg/dL (OR = 0.54, 95%CI: 0.34–0.86) or ≥8.90 mg/dL (OR = 0.60, 95%CI: 0.37–0.99). The RCS plot depicted that serum calcium level was negatively correlated with the risk of AKI in patients with AMI. AMI patients with AKI had lower serum calcium levels compared with those without AKI. Increased serum calcium level was associated with decreased risk of AKI in patients with AMI.