cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1119131
title: Data For: Alisch Et Al Maple Supplementary Materials

description: Archive of experimental data for the manuscript: "MAPLE: a Modular Automated Platform for Large-scale Experiments, a low-cost robot for integrated animal-handling and phenotyping." Data are tracked animal centroids from various arenas, genotypes and experimental groups. Also included are MATLAB scripts for processing this data and producing the plots from the manuscript. A readme file describes the contents of the archive.
DOI: 10.6084/m9.figshare.12588188
title: Supplementary Material for: Prelims

description: Medicine
DOI: 10.6084/m9.figshare.22133492
title: Supplementary Material for: SYSTEMATIC REVIEW AND METANALYSIS OF CLINICAL OUTCOMES AFTER ENUCLEATION OF PANCREATIC METASTASES FROM RENAL CELL CARCINOMA.

description: ABSTRACT. Introduction: A systematic review of the literature was carried out to determine the clinical and oncological outcome of patients who had enucleation of solitary pancreatic metastases from renal cell carcinoma. Methods: Operative mortality, postoperative complications, observed survival and disease free survival were analyzed. The clinical outcomes of patients who had enucleation were compared to those of 857 patients collected from the literature who had standard or atypical pancreatic resection for the same disease using propensity score matching Results: There was no postoperative mortality in the 56 patients who had enucleation of pancreatic metastases from renal cell carcinoma . In 51 patients postoperative complications could be analyzed. Ten patients (10/51=19.6%) had postoperative complications. Three patients (3/51 = 5.9%) had major complications (Clavien-Dindo III or more). Five year observed survival rates and disease free survival for patients with enucleation were 92% and 79% respectively. These results compared favourably with those obtained in patients who had standard resection and other forms of atypical resection (also using propensity score matching). Patients who had partial pancreatic resection (atypical or not) with pancreatic-jejunal anastomosis had increased rates of postoperative complications and local recurrences. Conclusions: Enucleation of pancreatic metastases offers a valid solution in selected patients.
DOI: 10.6084/m9.figshare.22309894
title: Supplementary Material for: The global incidence rate of pemphigus vulgaris: a systematic review and meta-analysis

description: Background: Pemphigus vulgaris is a life-threatening autoimmune bullous disease characterized by flaccid blister formation. As there has been no macroscopic assessment of epidemiological characteristics, its disease burden in the general population remains unknown. Objectives: To assess the global incidence rate of pemphigus vulgaris in the general population. Methods: The search was conducted in databases including Medline, Embase, Web of Science, and The Cochrane Library from inception to May 1st, 2022. We included original studies that either reported incidence of pemphigus vulgaris or provided raw data for calculating. Studies based on a specific population instead of the general population were excluded. Individual studies were summarized using random-effects mode. The pooled incidence rate of pemphigus vulgaris among the general population and subgroups were obtained. Heterogeneity (I2 statistic) was assessed with the χ2 test on Cochrane’s Q statistic. Results: 29 studies were eligible for final analysis and the pooled incidence rate of pemphigus vulgaris was 2.83 per million person-years (95%CI, 2.14-3.61). The incidence rate was similar between men and women and remained stable in the past half-century. Southern Asia showed the highest rate among subcontinents that had more than one study conducted as 4.94 per million person-years (95%CI, 2.55-8.10). Economic levels do not seem to have any bearing on incidence. Conclusions: Despite the substantial heterogeneity among studies, this meta-analysis revealed the worldwide incidence rate of pemphigus vulgaris for the first time and may assist in assessing global disease burden and promoting health policy.
DOI: 10.6084/m9.figshare.23375345
title: Supplementary Material for: Long-Term Prognosis and Related Factors in Patients with Cirrhosis Treated with Balloon-Occluded Retrograde Transvenous Obliteration

description: <b><i>Introduction:</i></b> Balloon-occluded retrograde transvenous obliteration (BRTO) was developed as an effective treatment for gastric varices in patients with cirrhosis. Because liver fibrosis in these patients is assumed to be advanced, their prognosis is expected to be poor. In this study, we investigated the prognosis and characteristics of the patients. <b><i>Methods:</i></b> We enrolled 55 consecutive patients with liver cirrhosis treated with BRTO between 2009 and 2021 at our department. To evaluate factors related to variceal recurrence and long-term prognosis, survival analysis was performed on 45 patients, excluding those who died within 1 month, had an unknown prognosis, or whose treatments were converted to other treatments. <b><i>Results:</i></b> During a mean follow-up period of 2.3 years, esophageal varices recurred in 10 patients and could be treated endoscopically. Non-alcoholic steatohepatitis (NASH) was related to the variceal recurrence (hazard ratio [HR] = 4.27, 95% CI: 1.17–15.5, <i>p</i> = 0.028). The survival rate after the procedure at 1, 3, and 5 years was 94.2%, 74.0%, and 63.5%, respectively, and 10 patients died of hepatocellular carcinoma (<i>n</i> = 6), liver failure (<i>n</i> = 1), sepsis (<i>n</i> = 1), and unknown reasons (<i>n</i> = 2). The estimated glomerular filtration rate (eGFR) level was proved to be a significant poor prognostic factor (HR = 0.96, 95% CI: 0.93–0.99, <i>p</i> = 0.023). The comorbid hypertension (HTN) was the main cause of low eGFR, and HTN was also significantly related to survival (HR = 6.18, 95% CI: 1.57–24.3, <i>p</i> = 0.009). Most of the patients with HTN were treated with calcium channel blocker and/or angiotensin receptor blocker. <b><i>Conclusion:</i></b> The clinical course of patients with cirrhosis treated with BRTO was dependent on the metabolic factors including renal function, comorbid HTN, and NASH.
DOI: 10.6084/m9.figshare.23393267
title: Tidal modulation of Cross-scale Kinetic Energy Fluxes in the Gulf Stream

description: Files to reproduce the figures presented in
DOI: 10.6084/m9.figshare.23799366
title: Supplementary Material for: Validation of E/e’ using the index beat method as an estimate of left atrial pressure in patients with atrial fibrillation

description: Introduction: Echocardiographic assessment of diastolic function during atrial fibrillation (AF) remains challenging due to the irregular cardiac cycle length. We sought to assess whether the index-beat method, the beat following two preceding cardiac cycles of equal duration, could provide a more reliable measurement of E/e′ (mitral E wave/diastolic tissue Doppler velocity) than the conventional averaging of consecutive beats and hence facilitate the non-invasive estimation of elevated left atrial pressure (LAP) in patients with AF. Methods: We prospectively studied 35 patients with persistent AF who had preserved left ventricular ejection fraction and underwent radiofrequency ablation. LAP was measured in conjunction with trans-septal puncture during catheter ablation. Echocardiography was performed 24 h before ablation and E/e′ was determined using the recommended averaging of 10 beats and the index-beat method, with the observers blinded to the clinical details and LAP measurements. Results: Correlation analysis showed a strong positive correlation between two methods in terms of both septal E/e′ (r = 0.841, p &lt; 0.001) and lateral E/e′ (r = 0.930, p &lt; 0.001). Bland-Altman analysis also showed a good agreement between the two measurement methods in terms of E/e′. E/e′ determined using both conventional averaging and the index-beat method was significantly correlated with LAP (p &lt; 0.05). After Fisher Z transformation, we found that the index-beat septal E/e′ had a better correlation with LAP than did the conventional averaging E/e′ (r = 0.736 vs. r = 0.392, Zr = -2.110, p = 0.035). Furthermore, the index-beat method took significantly less time to measure E/e′ (mean 33.6 s; 95% confidence intervals (CI): 32.1s to 36.2s), than did conventional averaging method (mean 96.2 s; 95% CI: 90.2s to 102.3s; p &lt; 0.001). Receiver operating characteristic curve analysis revealed that the optimal cut-off for predicting mean LAP &gt; 12mmHg was 11 (sensitivity 100%; specificity 77.3%) for index-beat septal E/e′ and 16 (sensitivity 61.5%; specificity 95.5%) for index-beat lateral E/e′. Conclusions: Good correlations were found between E/e′ and LAP in patients with AF, particularly with the index-beat method. Moreover, the index-beat method can easily measure E/e′ at an accuracy similar to that for the conventional averaging of consecutive beats, which can therefore be applied to assess the diastolic dysfunction and potentially improve the diagnosis of heart failure in patients with AF.
DOI: 10.6084/m9.figshare.24210435
title: Supplementary Material for: An Intestinal Type Gastric Neuroendocrine Tumor: A Case Report

description: Neuroendocrine tumors (NETs) represent a diverse set of malignancies, originating from the neuroendocrine cells dispersed throughout the body. Their symptoms are associated with the secretion of bioactive peptides by tumor cells. Five-year survival rates depend on the disease stage: 93% for local, 74% for regional, and 19% for metastatic disease. This report describes a case involving a 64-year-old male patient, who was enduring high blood pressure and anemia. His symptomatology included frequent fainting and bloody vomiting without prior bleeding, coupled with persistent abdominal pain and weight loss. A complete blood count revealed microcytic anemia. His condition improved postoperatively after the transfusion of two units of packed red blood cells, normalizing all parameters. Further biochemistry and serology tests did not provide significant insights. However, an upper endoscopy unveiled a deep ulcer below the gastroesophageal junction with ulcer desquamation. A combination of clinical, laboratory, and radiographic data initially indicated a gastric carcinoma of the intestinal type, characterized by extensive extracellular mucin secretion. The surgical intervention led to the extraction of multiple tumors from lymph nodes, culminating in a postoperative diagnosis of a gastrointestinal mesenchymal tumor. NETs predominantly manifest in the gastrointestinal (GI) tract, initiating primarily in the small intestine but can also originate in the stomach, appendix, colon, and other parts of the GI tract. Their development from neuroendocrine cells enables them to produce high concentrations of hormone-like substances such as neuropeptides and amines.
DOI: 10.7488/ds/3427
title: A label-free method to track individuals and lineages of budding cells

description: Single-cell microscopy data and images with manually curated annotations for "A label-free method to track individuals and lineages of budding cells" by Pietsch, Muñoz, Adjavon, Farquhar, Clark and Swain. The data come from fluorescence microscopy experiments where yeast, with fluorescence tags on Sfp1, Nhp6A, or Myo1, were grown in microfluidics devices and subject to changes in nutrients. Cells were segmented and tracked by the BABY algorithm described in the paper. Also included are manually curated image annotations used to train and benchmark both segmentation and tracking performance of the BABY algorithm. Source code for the algorithm is available at https://git.ecdf.ed.ac.uk/swain-lab/baby.
description: All files in this dataset are documented in the attached README.txt file.
DOI: 10.6084/m9.figshare.21982691
title: Supplementary Material for: IL-37 Ameliorates Renal Fibrosis by Restoring CPT1A Mediated Fatty Acid Oxidation in Diabetic Kidney Disease

description: Introduction: Diabetic kidney disease (DKD) is a major source of chronic kidney disease (CKD) and end-stage renal disease (ESRD). The injury of glomerular in DKD is the primary focus, however proximal tubulopathy also is an indispensable factor in the progression of DKD. Interleukin-37 (IL-37), an anti-inflammatory cytokine of IL-1 family member, has been demonstrated to be associated with diabetes and its relative complications in recent years, but the effect of IL-37 on renal fibrosis in DKD is unclear. Methods: We established streptozotocin plus high fat diet (STZ/HFD)-induced DKD mice model with wild type (WT) or IL-37 transgenic (IL-37tg) mice. Masson and HE staining, immunostaining, and Western blot were used to observe renal fibrosis. In addition, RNA-sequencing was applied to explore the potential mechanisms of IL-37. In vitro, treatment of human proximal tubular (HK-2) cells with 30 mmol/L high glucose or 300 ng/ml recombinant IL-37 further elucidated the possible mechanism of IL-37 inhibition of DKD renal fibrosis. Results: In this work, we first verified the decreased expression of IL-37 in kidney of DKD patient and its correlation with clinical features of renal impairment. Moreover, IL-37 expression markedly attenuated proteinuria and renal fibrosis in DKD mice. Using RNA-sequencing, we found and confirmed a novel role of IL-37 in ameliorating fatty-acid oxidation (FAO) reduction of renal tubular epithelial cells both in vivo and in intro. In addition, further mechanistic studies showed that IL-37 alleviated the FAO reduction in HK-2 cells and renal fibrosis in DKD mice through upregulating carnitine palmitoyl-transferase 1A (CPT1A), an important catalyzer for FAO pathway. Conclusion: These data suggest that IL-37 attenuates renal fibrosis via regulating FAO in renal epithelial cells. Upregulation of IL-37 levels might be an effective therapeutic avenue for DKD.
DOI: 10.6084/m9.figshare.22283875
title: Supplementary Material for: Cryotherapy after topical interferon alpha 2b to treat conjunctival primary acquired melanosis

description: When primary acquired melanosis (PAM) with atypia affects the tarsal conjunctiva, a radical surgery can be mutilating, requiring reconstructive surgery of the eyelid. Topical Chemoteraphy associated to local crioteraphy may be an alternative. A 64-year-old Caucasian female presented with diffuse PAM of the right eye involving the inferior tarsal conjunctiva, fornix, and inferotemporal bulbar conjunctiva. Histological study showed a PAM with atypia (C-MIN 5). Given the extent of the lesion and its location, a wide mutilating excision was ruled out. Topical Interferon alpha 2b (IFN-α2b) treatment (1,000,000 IU/mL, 4 times a day) was administered during 10 weeks. However the regression was very slow. Then local cryotherapy was proposed (8s at –80ºC per aplication) to the entire pigmented lesion. This afforded progressive depigmentation, which was complete 2 months later. No recurrence of the lesion has been noted during 3 years of follow-up. The combination of the two procedures reduces IFN-α2b eyedrop administration time, enhancing patient compliance. The combination eradicated the tumour without compromising ocular cosmesis.
DOI: 10.6084/m9.figshare.22567219
title: Supplementary Material for: Optimal Meropenem Dosing Regimens in Patients undergoing Continuous Renal Replacement Therapy: Systematic review and Monte Carlo simulations

description: Introduction The optimal meropenem dosing regimens in critically ill patients receiving continuous renal replacement therapy (CRRT) based on pharmacokinetic and pharmacodynamic concepts are not well established. This study aimed to (1) gather the available published pharmacokinetic studies conducted in septic patients receiving CRRT and (2) to define the optimal meropenem dosing regimens in these populations via Monte Carlo simulations. Methods We used Medical Subject Headings (MeSH) of “meropenem”, “continuous renal replacement therapy” and “pharmacokinetics” or related terms to identify studies for systematic review. A one-compartment pharmacokinetic model was conducted to predict meropenem levels for the initial 48 hours of therapy. The pharmacodynamic (PD) targets were 40% of free drug above a threshold of 1 times the minimum inhibitory concentration (MIC) (40% fT &gt;MIC), 4 times the MIC (40% fT &gt; 4MIC), and an additional target of free drug level above 1 times MIC 100% of the time (fT&gt; MIC). The dose that achieved at least 90% of the probability of target attainment (PTA) was defined as an optimal dose. Results Twenty-one articles were included for our systematic review. The necessary pharmacokinetic parameters such as volume of distribution and CRRT clearance were cited in 90.5 and 71.4% of articles, respectively. None of the published studies reported completed necessary parameters. A regimen of 750 mg q 8 hours was found to be the optimal dose for predilution-CVVH and CVVHD modality using two effluent rates (25 and 35 mL/kg/h) which achieved the PD target of 40% fT &gt; 4MIC. Conclusion None of the published studies showed the necessary pharmacokinetic parameters. Pharmacodynamic target significantly contributed to meropenem dosage regimens in these patients. Differing effluent rates and types of CRRT shared similar dosing regimens. Clinical validation of the recommendation is suggested.
DOI: 10.6084/m9.figshare.24249472
title: Supplementary Material for: Parental experiences of neonatal care – a nationwide study on determinants of excellence

description: INTRODUCTION: Infant- and family-centered developmental care can reduce adverse outcomes in both infants and parents. Parents’ experiences of the care and staff treatment remain to be evaluated. METHODS: Parents of infants admitted to neonatal units in Sweden from July 2020 to May 2022 responded to a questionnaire with standardized questions about in-hospital care. Exposures were hospital, gestational age, length of hospital stay, unit level and bed density. The proportions of parents rating aspects of neonatal care as excellent, defined as five on a Likert scale, and the determinants of excellence were described. The results were benchmarked with ratings in adult somatic care. RESULTS: A total 4,475/13,108 (34%) parents responded. The ratings of excellent care varied by question from 65%-90%. The largest variation in excellence between neonatal units (range 43%–80%) was found for “Participation and Involvement”. The proportion of excellence was significantly lower among parents of extremely preterm infants. Confidence in the staff was lower in parents of extremely preterm than in parents of term infants (56% vs 83%). Longer hospital stay affected the experience of neonatal care adversely, whereas level of care and bed density were overall unrelated to the parental experience. Parents in neonatal care rated the care as excellent to a higher extent than patients cared for in adult medicine. CONCLUSION/DISCUSSION: A majority of parents rated neonatal care in Sweden as excellent. The less frequent ratings of excellence among parents of extremely preterm infants indicate that more could be done to optimize parental involvement and support.
DOI: 10.6084/m9.figshare.24278251
title: Supplementary Material for: Postoperative swallowing function in patients with deep neck infection

description: Introduction: Early detection of dysphagia risk, initiating rehabilitation, and resumption of appropriate diet based on swallowing function is important during deep neck infection control. This study aimed to evaluate the extent of cervical abscess development, particularly in the deep neck space, and its relationship to postoperative swallowing function. Methods: A retrospective chart review was performed for all deep neck infection cases treated between April 2015 and April 2021. Deep neck spaces were divided into categories based on computed tomography (CT) findings. Functional Oral Intake Scale (FOIS) scores of 4 or higher was defined as normal or slight swallowing disorder, and 3 or lower as dysphagia. Results: 17 cases were included in the analysis. Based on FOIS, 14 cases were classified into the dysphagia group at 2 weeks after surgery, 11 cases at 4 weeks, and 8 cases at 8 weeks. There was no significant difference between the location of the abscess and dysphagia at 2 weeks after surgery. Patients with anterior cervical space abscess significantly increased dysphagia 4 weeks (p= 0.018) and 8 weeks (p= 0.036) after surgery. Conclusion: Abscess formation in the anterior cervical space may be associated with prolonged dysphagia after treatment due to inflammation and scarring of the muscles associated with swallowing.
DOI: 10.15784/601695
title: Functional characterization of temperature activated ion channels from Antarctic fishes

description: This dataset is recordings of current, temperature, and voltage for TRPA1b and TRPV1a from Antarctic notothenioids fishes, plus metadata. TRPA1b and TRPV1a were found to be heat activated and multiple modulators of activity were tested. Manuscript is in submission stages and will be posted here when available.
DOI: 10.5281/zenodo.3533431
title: Processed RNA expression count data from Groen et al.: The strength and pattern of natural selection on rice gene expression

description: We assessed transcriptome variation in populations of 216 accessions of rice, <em>Oryza sativa</em>, which represented all major varietal groups including indica and japonica. During the 2016 Philippines dry season the accessions were planted in triplicate (with two accessions planted in triplicate three times as replicated checks) in identical alpha-lattice layouts of 660 plots in two fields: a continuously wet paddy, and a field where plants were exposed to intermittent drought in the vegetative and reproductive stages. We measured transcript levels in leaf blades of 50-day-old plants at 33 days after seedling transplant, and 17 days after withholding water in the dry field, using a liquid automation-based 3’ mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library. Raw sequencing data are available at the SRA in BioProject accession number PRJNA588478. A key to the raw sequencing data in this BioProject can be found in the metadata of the processed RNA expression count data here.