cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21368319
title: Supplementary Material for: Plasma Circulating Tumor Necrosis Factor Receptors at Multiple Time Points Can Predict the Outcome of Severe Acute Kidney Injury

description: <b><i>Introduction:</i></b> This prospective cohort study investigated the clinical role of circulating tumor necrosis factor receptor (cTNFR) levels as prognostic biomarkers in severe acute kidney injury (AKI) patients requiring continuous renal replacement therapy (CRRT). <b><i>Methods:</i></b> We enrolled 136 patients from 7 hospitals participating in the VENUS (VolumE maNagement Under body composition monitoring in critically ill patientS on CRRT) trial from July 2017 to October 2019. The levels of cTNFR1 and cTNFR2 were measured using plasma samples collected on days 0 (D0), 2 (D2), and 7 (D7). Patients were divided into high- and low-cTNFR groups based on their receptor concentrations. <b><i>Results:</i></b> D0 concentrations of cTNFR1 and cTNFR2 were positively correlated with one another (<i>R</i><sup>2</sup> = 0.37, <i>p</i> &lt; 0.001). The high-cTNFR1 group displayed a higher in-hospital mortality rate than the low-TNFR1 group (<i>p</i> = 0.002). Moreover, the mortality rate was significantly higher in the high-TNFR1 group than in the low-TNFR1 group after adjusting for age, sex, and acute physiology, and chronic health evaluation II scores (hazard ratio 1.82, 95% confidence interval 1.09–3.03, <i>p</i> = 0.025). D2 and D7 cTNFR1 levels were also associated with in-hospital mortality; contrastingly, cTNFR2 levels were not associated with this outcome. Additionally, patients were divided into three groups according to the change in cTNFR levels from D0 to D2 (ΔcTNFR). Those in the highest ΔcTNFR tertile had a higher mortality rate than the remaining patients (<i>p</i> = 0.033 for ΔcTNFR1; <i>p</i> = 0.025 for ΔcTNFR2). Patients who underwent AKI-to-chronic kidney disease transition had higher concentrations of cTNFR1 (<i>p</i> = 0.014). <b><i>Discussion/Conclusion:</i></b> Plasma cTNFR1 concentrations at CRRT initiation and changes in cTNFR1 and 2 levels immediately following CRRT initiation are significant biomarkers for predicting the outcomes of patients with severe AKI.
DOI: 10.6084/m9.figshare.21908607
title: Supplementary Material for: Impact of Weight Gain on the Subsequent Survival of New Peritoneal Dialysis Patients

description: Introduction: Obesity at the initiation of dialysis was reported to adversely affect the clinical outcome of peritoneal dialysis (PD) patients, and weight gain is common after started on PD. However, there are few studies on the prognostic implications of weight gain after PD. Methods: We reviewed the change in body weight of 954 consecutive patients during the first 2 years of PD in a single Hong Kong center. Their subsequent clinical outcomes, including patient and technique survival rates, hospitalization, and peritonitis rates, were analyzed. Results: The mean age was 60.3 ± 12.2 years; 535 patients (56.1%) were men, and 504 (52.8%) had diabetes. From 1995-1999 to 2015-2019, the percentage of body weight gain during the first 2 years of PD was 1.0 ± 7.9%, 1.6 ± 7.1%, 1.6 ± 7.2%, 3.9 ± 9.5%, to 4.0 ± 10.3% for each 5-year period, respectively (p for linearity &lt;0.0001). The subsequent 5-year patient survival rates were 29.9%, 43.3%, 40.5%, 43.6%, and 43.3% for patients with weight loss &gt;5%, weight loss 2-5%, weight change with 2%, weight gain 2-5%, and weight gain &gt;5% during the first 2 years on PD, respectively (log-rank test, p = 0.035). With multi-variable Cox regression model to adjust for clinical confounders, weight loss &gt;5% during the first 2 years of PD was associated with a worse patient survival rate subsequently (adjusted hazard ratio 4.118, 95% confidence interval 1.040-16.313, p = 0.044), while weight gain was not associated with the subsequent patient survival. Weight change during the first 2 years of PD does not appear to affect subsequent technique survival, hospitalization, decline in residual renal function, or peritonitis rate. Discussion and Conclusions: Weight gain is common during the first two years of PD, but weight gain does not appear to have any significant impact on the subsequent outcome. In contrast, weight loss &gt;5% was significantly associated a worse patient survival subsequently.
DOI: 10.6084/m9.figshare.21929676
title: Supplementary Material for: Evaluation of a web-based intervention for patients with Gestational Trophoblastic Disease: a randomized controlled trial

description: Objective Gestational Trophoblastic Diseases (GTD) comprise a group of rare diseases originating from the trophoblast, affecting women of child-bearing age. Providing optimal information to patients with a rare disease is challenging, because of the small number of patients and limited clinical expertise of many healthcare professionals. Both knowledge and lack of knowledge in patients may influence illness perception. We investigated whether a web-based interactive intervention influences illness perception and knowledge in women with GTD. Design Multicenter randomized control trial. Setting General and academic hospitals in the Netherlands. Population Newly diagnosed GTD patients between 2017-2019. Methods Sixty-nine patients were randomized between direct access or postponed access to an online tool on GTD and received online questionnaires about illness perception, knowledge and anxiety. The main outcome measures were illness perception (primary outcome measure) and knowledge (secondary outcome measure) Results Patients using the online tool were satisfied with the information from the tool (92%). Although they had a higher level of knowledge compared to the control group (p = 0.006), illness perception did not change. Also, no differences in levels of anxiety, depression and distress were observed between the groups. Limitations: Participants had access to other information sources and many searched other websites. It is unknown what kind of websites were visited and when. It is unknown if the increased knowledge levels and low levels of distress will sustain over time as no long term follow-up took place. Healthcare professionals were not interviewed on how they experienced the consultation before and after using the tool by the patients. Conclusions The online tool did not change illness perception, but was shown to be valuable for newly-diagnosed GTD patients to gain knowledge. The improvement in knowledge after digital education, indicates that this tool can be used as an effective method of supporting GTD patients’ informational needs without causing extra distress.
DOI: 10.6084/m9.figshare.22059074
title: Supplementary Material for: Association Between Smoking Cessation and the Risk of Cholangiocarcinoma and Ampulla of Vater Cancer: A Nationwide Cohort Study

description: Introduction: The association between smoking cessation and intrahepatic and extrahepatic cholangiocarcinoma (iCCA and eCCA) risk is unclear. Furthermore, the association in individuals with preexisting risk factors is unknown. We aimed to investigate the association between smoking status (especially smoking cessation) and CCA risk according to individuals’ glycemic status. Methods: In this nationwide cohort study, 9,520,629 adults without cancer who underwent national health screening by the Korean National Health Insurance Service in 2009 were followed up through 2018. The hazard ratios (HRs) and 95% confidence intervals (CIs) for CCA were estimated after adjusting for potential confounders. Results: During the 78.3 person-years of follow-up, 16,236 individuals were newly diagnosed with CCA. Quitters had a significantly lower risk of iCCA and eCCA compared to current smokers in all glycemic status groups (all P&lt;0.01). The HRs (95% CIs) for iCCA in current smokers and quitters were 1.33 (1.24–1.43) vs. 0.98 (0.90–1.06) in individuals with normoglycemia, 1.49 (1.37–1.63) vs. 1.17 (1.06–1.28) in individuals with prediabetes, and 2.15 (1.96–2.37) vs. 1.58 (1.42–1.75) in individuals with diabetes, compared to never-smokers with normoglycemia. Current smokers with diabetes or prediabetes had a synergistically increased risk of iCCA (all P&lt;0.01). However, quitters with diabetes and prediabetes had an iCCA risk comparable to that of never-smokers. Analysis of eCCA yielded similar results. Smoking was not independently associated with the risk of the ampulla of Vater cancer. However, smoking combined with diabetes or prediabetes was associated with an increased risk of the ampulla of Vater cancer (all P&lt;0.05). Discussion/Conclusion: Smoking cessation was associated with a reduced risk of CCA, despite the synergistically increased risk in current smokers with diabetes and prediabetes. Our findings suggest a crucial opportunity to reduce the risk of CCA. More individualized and intensive cancer prevention education is needed against CCA.
DOI: 10.6084/m9.figshare.23041847
title: Hibiscus syriacus cv. Gangneung Draft Genome

description: Draft genome assembly of Hibiscus syriacus var. Gangneung
DOI: 10.6084/m9.figshare.23300687
title: Supplementary Material for: Development and validation of a nomogram for renal survival prediction in patients with autosomal dominant polycystic kidney disease

description: Introduction：Due to the wide variation in the prognosis of autosomal dominant polycystic kidney disease (ADPKD), prediction of risk of renal survival in ADPKD patients is a tough challenge. We aimed to establish a nomogram for the prediction of renal survival in ADPKD patients. Methods: We conducted a retrospective observational cohort study in 263 patients with ADPKD. The patients were randomly assigned to a training set (N= 198) and a validation set (N=65) and demographic and statistical data at baseline were collected. The total kidney volume (TKV) was measured using stereology. A clinical prediction nomogram was developed based on multivariate Cox regression results. The performance and clinical utility of the nomogram were assessed by calibration curves, the concordance index (C-index), and decision curve analysis (DCA). The nomogram was compared with the height-adjusted total kidney volume (htTKV) model by receiver operating characteristic curve analysis, and DCA. Results：The five independent factors used to construct the nomogram for prognosis prediction were age, htTKV, estimated glomerular filtration rate (eGFR), hypertension, and hemoglobin. The calibration curve of predicted probabilities against observed renal survival indicated excellent concordance. The model showed very good discrimination with a C-index of 0.91 (0.83-0.99), and an area under the curve (AUC) of 0.94, which were significantly higher than those of the htTKV model. Similarly, DCA demonstrated that the nomogram had a better net benefit than the htTKV model. Conclusion: The risk prediction nomogram, incorporating easily assessable clinical parameters, was effective for the prediction of renal survival in ADPKD patients. It can be a useful clinical adjunct for clinicians to evaluate the prognosis of ADPKD patients and provide individualized decision-making.
DOI: 10.6084/m9.figshare.24105303
title: Code availability

description: Commands are available.
DOI: 10.6084/m9.figshare.24173733
title: Supplementary Material for: Indocyanine green labeled platelets for survival and recovery studies

description: Introduction: Before being implemented in daily clinical routine, new production strategies for platelet concentrates (PCs) must be validated for their efficacy. Besides in vitro testing, the establishment of new methods requires the labeling of platelets for in vivo studies of platelets’ survival and recovery. Indocyanine green (ICG) is a Food and Drug Administration approved near-infrared fluorescent dye for diagnostic use in vivo, suitable for non-radioactive direct cell labeling of platelets. Methods: Platelets from PCs in storage solutions with different plasma concentrations were labeled with ICG up to concentrations of 200 µM. Whole blood was used as an ex vivo matrix to monitor the labeling stability of ICG-labeled platelets. The impact of labeling processes was assessed by the quantification of CD62P expression and PAC-1 binding as platelet function markers. Platelet aggregation was analyzed by light transmission aggregometry. ICG labeling efficiency and stability of platelets was determined by flow cytometry. Results: Platelets from PCs could be successfully labeled with 10 µM ICG after 1 and 4 days of storage. The best labeling efficiency of 99.8% ± 0.1% (immediately after labeling) and 81% ± 6.2% (after 24 hours incubation with whole blood) was achieved by plasma replacement by 100% platelet additive solution for the labeling process. Since the washing process slightly impaired platelet function, ICG labeling itself did not affect platelets. Immediately after the ICG labeling process plasma was re-added resulting in a recovered platelet function. Conclusion: We developed a Good Manufacturing Practice compatible protocol for ICG fluorescent platelet labeling suitable for survival and recovery studies in vivo as a non-radioactive labeling alternative.
DOI: 10.6084/m9.figshare.24191895
title: Supplementary Material for: Hospital Variation in Mortality and Failure to Rescue after Surgery for High-Risk Neonatal Diagnoses

description: Introduction: A large proportion of postoperative mortality after pediatric surgery occurs among neonates with specific high-risk diagnoses. The extent to which there is hospital-level mortality variation among patients with these diagnoses and whether this variation is associated with differences in failure to rescue (FTR) is unclear. Methods: The Pediatric Health Information System® database (2012–2020) was used to identify patients who underwent surgery for eight high-risk neonatal diagnoses: gastroschisis; volvulus; necrotizing enterocolitis; intestinal atresia; meconium peritonitis; tracheoesophageal fistula; congenital diaphragmatic hernia; perinatal intestinal perforation. Hospitals were stratified into tertiles of reliability adjusted inpatient mortality rates (lower than average mortality— tertile 1 [T1]; higher than average mortality—tertile 3 [T3]). Multivariable hierarchical regression was used to evaluate the association between hospital-level, reliability adjusted mortality and FTR Results: Overall, 20,838 infants were identified across 48 academic, pediatric hospitals. Adjusted hospital mortality rates ranged from 4.0% [95% CI, 0.0–8.2] to 16.3% [12.2–20.4]. Median case volume (range, 80–1238) and number of NICU beds (range, 24–126) were not significantly different across hospital tertiles. Compared to the hospitals with the lowest postoperative mortality (T1), the odds of FTR was significantly higher in hospitals with the highest (T3) postoperative mortality (OR 1.97 [1.50–2.59]). Conclusions: Significant variation in neonatal hospital mortality for high-risk diagnoses does not appear to be explained by hospital structural characteristics. Rather, difference in FTR suggest QI interventions targeting early recognition and management of postoperative complications could improve surgical quality and safety for high-risk neonatal care.
DOI: 10.18112/openneuro.ds004406.v1.0.0
title: RID
DOI: 10.5281/zenodo.4437077
title: Dissociation of task engagement and arousal effects in auditory cortex and midbrain -- dataset.

description: Single neuron data recorded from auditory cortex and midbrain during a tone detection behavior were used to dissociate effects of generalized arousal (as measured by pupil) and specific task engagement on auditory neural coding. These data are provided open-access accompanying the publication: D. Saderi, Z.P. Schwartz, C.R. Heller, J.R. Pennington, S.V. David. (2020) Dissociation of task engagement and arousal effects in auditory cortex and midbrain. <em>bioRxiv</em>. 2020.06.16.155432. Available at: https://doi.org/10.1101/2020.06.16.155432 The authors request that any work using this data cite this publication.
DOI: 10.5281/zenodo.7505421
title: The ER folding sensor UGGT1 acts on TAPBPR-chaperoned peptide-free MHC I

description: Adaptive immune responses are triggered by antigenic peptides presented on major histocompatibility complex class I (MHC I) at the surface of pathogen-infected or cancerous cells. Formation of stable peptide-MHC I complexes is facilitated by tapasin and TAPBPR, two related MHC I-specific chaperones that catalyze selective loading of suitable peptides onto MHC I in a process called peptide editing or proofreading. On their journey to the cell surface, MHC I complexes must pass a quality control step performed by UGGT1, which senses the folding status of the transiting N-linked glycoproteins in the endoplasmic reticulum (ER). UGGT1 reglucosylates non-native glycoproteins and thereby allows them to revisit the ER folding machinery. Here, we describe a reconstituted <em>in-vitro</em> system of purified human proteins that enabled us to delineate the function of TAPBPR during the UGGT1-catalyzed quality control and reglucosylation of MHC I. By combining glycoengineering with liquid chromatography-mass spectrometry, we show that TAPBPR promotes reglucosylation of peptide-free MHC I by UGGT1. Thus, UGGT1 cooperates with TAPBPR in fulfilling a crucial function in the quality control mechanisms of antigen processing and presentation.
DOI: 10.5281/zenodo.8309936
title: Data for figures in "Next-generation ice nucleating particle sampling on aircraft: Characterization of the High-volume flow aERosol particle filter sAmpler (HERA)"

description: Atmospheric ice nucleating particle (INP) concentration data from the free troposphere are sparse, but urgently needed to understand vertical transport processes of INPs and their influence on cloud formation and properties. Here, we introduce the new High-volume flow aERosol particle filter sAmpler (HERA) which was specially developed for installation on research aircraft and subsequent offline INP analysis. HERA is a modular system constisting of a sampling unit and a powerful pump unit and has several features which were integrated specifically for INP sampling. Firstly, the pump unit enables sampling at flow rates exceeding 100 L min<sup>−1</sup>, which is well above typical flow rates of aircraft INP sampling systems described in the literature (~10 L min<sup>−1</sup>). Consequently, required sampling times to capture rare, high-temperature INPs (≥-15 °C) are reduced in comparison to other systems and potential source regions of INPs can be confined more precisely. Secondly, the sampling unit is designed as a seven-way valve, enabling switching between six filter holders and a bypass with one filter being sampled at a time. In contrast to other aircraft INP sampling systems, the valve position is controlled remotely via software so that manual filter changes in-flight are eliminated and the potential for sample contamination is decreased. This design is compatible with a high degree of automation, i.e., triggering filter changes depending on parameters like flight altitude, geographical location, temperature, or time. In addition to the design and principle of operation of HERA, this paper presents laboratory characterization experiments with size-selected test substances, i.e., SNOMAX® and Arizona Test Dust. The particles were sampled on filters with HERA, varying either particle diameter (300 nm to 800 nm) or flow rate (10 L min<sup>−1</sup> to 100 L min<sup>−1</sup>) between experiments. The subsequent offline INP analysis showed good agreement with literature data and comparable sampling efficiencies for all investigated particle sizes and flow rates. Furthermore, the deposition efficiency of atmospheric INPs in HERA was compared to a straightforward filter sampler and good agreement was found. Finally, results from the first campaign of HERA on the High Altitude and LOng range research aircraft (HALO) demonstrate the functionality of the new system in the context of aircraft application. The given csv files contain the data for reproducing the figures in the publication. The data structure of the csv files is explained in the README file.
description: Further information on the dataset is available upon request to grawe@tropos.de. We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), projects 316508271 and 442648163 within PP 1294 (HALO).
DOI: 10.6073/pasta/e0a91c20ee40f73fecc6d9abb2cdc9e6
title: 2018 Priming experiment to investigate dissolved organic matter turnover

description: This dataset is associated with an experiment that was conducted on the University of Florida's campus to evaluate the role of priming in dissolved organic matter turnover. Incubations were established with dissolved organic matter substrates derived from a 13C-labeled algal substrate, mangrove peat derived dissolved organic matter leachate, and a primed condition with both algal and peat substrates. A seawater control was also included. This dataset includes measurements of water chemistry, carbon dioxide, stable isotopes, and gene counts for clusters of orthologous genes (COG). For more information, please refer to Morrison et al., Mangrove peat and algae leachates elicit rapid and contrasting molecular and microbial responses in coastal waters.
DOI: 10.6084/m9.figshare.11961063.v34
title: Dimensions COVID-19 publications, datasets and clinical trials

description: This file contains all relevant publications, datasets and clinical trials from Dimensions that are related to COVID-19. The content has been exported from Dimensions using a query in the openly accessible Dimensions application, which you can access at https://covid-19.dimensions.ai/. Dimensions is updated once every 24 hours, so the latest research can be viewed alongside existing information. With its range of research outputs including datasets and clinical trials, both of which are just as important as journal articles in the face of a potential pandemic, Dimensions is a one-stop shop for all COVID-19 related information. <br>Please share this information with anyone you think would benefit from it. If you have any suggestions as to how we can improve our search terms to maximise the volume of research related to COVID-19, please contact us at support@dimensions.ai.
DOI: 10.6084/m9.figshare.23506005
title: Supplementary Material for: Primary Breast Sarcoma: A Two-Centre Analysis and Review of Literature

description: <b><i>Introduction:</i></b> Primary breast sarcoma is a very rare malignant type of breast tumours with an incidence of 0.1% of all primary breast malignancies. <b><i>Methods:</i></b> We present a retrospective analysis of the case series from two hospitals in the Czech Republic with a review of the diagnostic and treatment approach to primary breast sarcomas with an analysis of published prognostic factors. <b><i>Results:</i></b> Eleven patients were included in the study, 9 women and 2 men. Statistical evaluation revealed that tumour size (<i>p</i> = 0.1964), grade (<i>p</i> = 0.1667), margin distance (<i>p</i> = 0.5403), mitotic activity (<i>p</i> = 0.8577), or age (<i>p</i> = 0.7822) were not prognostic factors in our cohort. <b><i>Conclusion:</i></b> The analysis did not prove any of the factors, such as age, tumour size, grade, or mitotic activity, to be statistically significant prognostic factors. Based on the literature review, the most common published prognostic factors are tumour size, margin status, and grade, but the results are ambiguous.
DOI: 10.6084/m9.figshare.23537901
title: <i>Bifidobacterium longum</i> subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants

description: Supplementary material for '<i>Bifidobacterium longum</i> subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants', a published in <i>International Journal of Systematic and Evolutionary Microbiology</i>
DOI: 10.6084/m9.figshare.24115851
title: Solar-driven waste-to-chemical conversion by wastewater-derived semiconductor biohybrids

description: we propose a strategy that co-utilize pollutants in wastewater to produce semiconductor biohybrids in-situ for scalable solar-to-chemical conversion