cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14931900.v1
title: Supplementary Material for: Reproducible Naevus Counts Using 3D Total Body Photography and Convolutional Neural Networks

description: <b><i>Background:</i></b> The number of naevi on a person is the strongest risk factor for melanoma; however, naevus counting is highly variable due to lack of consistent methodology and lack of inter-rater agreement. Machine learning has been shown to be a valuable tool for image classification in dermatology. <b><i>Objectives:</i></b> To test whether automated, reproducible naevus counts are possible through the combination of convolutional neural networks (CNN) and three-dimensional (3D) total body imaging. <b><i>Methods:</i></b> Total body images from a study of naevi in the general population were used for the training (82 subjects, 57,742 lesions) and testing (10 subjects; 4,868 lesions) datasets for the development of a CNN. Lesions were labelled as naevi, or not (“non-naevi”), by a senior dermatologist as the gold standard. Performance of the CNN was assessed using sensitivity, specificity, and Cohen’s kappa, and evaluated at the lesion level and person level. <b><i>Results:</i></b> Lesion-level analysis comparing the automated counts to the gold standard showed a sensitivity and specificity of 79% (76–83%) and 91% (90–92%), respectively, for lesions ≥2 mm, and 84% (75–91%) and 91% (88–94%) for lesions ≥5 mm. Cohen’s kappa was 0.56 (0.53–0.59) indicating moderate agreement for naevi ≥2 mm, and substantial agreement (0.72, 0.63–0.80) for naevi ≥5 mm. For the 10 individuals in the test set, person-level agreement was assessed as categories with 70% agreement between the automated and gold standard counts. Agreement was lower in subjects with numerous seborrhoeic keratoses. <b><i>Conclusion:</i></b> Automated naevus counts with reasonable agreement to those of an expert clinician are possible through the combination of 3D total body photography and CNNs. Such an algorithm may provide a faster, reproducible method over the traditional in person total body naevus counts.
DOI: 10.6084/m9.figshare.3119893.v1
title: Hurricane Sandy Anonymised DSO Data
DOI: 10.15468/dl.33qvfb
title: Occurrence Download

description: A dataset containing 6800 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Brachylomia viminalis Fabricius, 1777"
 ]
}

 The dataset includes 6800 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009666-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.19499237.v1
title: patches and local annotations, slide 161, zoom 248x248 um2

description: patches and local annotations: data for slide with ID of the last 3 characters of the file name: local annotations in csv format and a folder with patches at zoom level indicated at the 6th character of the file name
DOI: 10.6084/m9.figshare.22059209.v1
title: Supplementary Material for: Long-term safety, clinical and immunological outcomes in Primary Membranous Nephropathy with Severe Renal Impairment treated with cyclophosphamide and steroid-based regimen

description: Introduction and Aims Therapy of Primary Membranous nephropathy (PMN) with progressive advanced kidney dysfunction is challenging with limited literature and no clear therapeutic strategies. This is due to the scant evidence of effectiveness and uncertainty around the risk-benefit profile of immunosuppression (ImS) when eGFR is less than 30 ml/min. We aimed to determine long term clinical outcomes in patients with PMN and severe renal impairment treated with combined cyclophosphamide and steroids. Methods The study is a single-centre retrospective longitudinal cohort study. All patients (between 2004-2019) with biopsy confirmed PMN who initiated combination therapy with steroids and cyclophosphamide and had an eGFR of ≤30ml/min/1.73m2 at the time of initiation of therapy were included for analysis. Clinical and laboratory parameters including Anti-PLA2R-Ab were monitored as per standard clinical guidance. Primary outcome was achievement of partial remission. Secondary outcomes included immunological remission, need for renal replacement therapy, and adverse effects. Results Eighteen patients with median age of 68 (IQR 58-73) years and 5:1 M:F ratio received the combination therapy when eGFR was ≤30ml/min/1.73m2 (CKD-EPI). At time of immunosuppression, median eGFR and uPCR were 23 (IQR 18-27) ml/min/1.73m2 and 1000 (IQR 838-1285) mg/mmol respectively. Median follow-up was for 67 (IQR 27-80) months. 16 patients (89%) achieved partial Remission and 7 (39%) achieved complete remission. eGFR increased by 7ml/min/1.73m2 (27%) after one year of starting immunosuppression treatment and 12ml/min/1.73m2 at end of follow-up. Two patients (11%) developed end stage renal disease needing renal replacement therapy. 67% achieved both immunological and clinical remission. Two (11%) patients required hospitalization secondary to infections, 4 (22%) patients developed cancer and 4 patients died (22%). Conclusion Combination therapy with cyclophosphamide and steroids is effective in achieving partial remission and improving renal function in PMN with advanced renal dysfunction. Prospective controlled studies are required to provide further evidence and improve outcomes in such patients.
DOI: 10.6084/m9.figshare.26509249.v1
title: Supplementary Material for: Neratinib Alone or in Combination with Immune Checkpoint Inhibitors with or without mTOR Inhibitors in Patients with Fibrolamellar Carcinoma

description: Introduction: Fibrolamellar carcinoma (FLC) displays upregulation of several oncogenes, including HER2, and multiple immune-suppressive mechanisms. We investigated the efficacy and safety of the pan-HER tyrosine kinase inhibitor neratinib as monotherapy (SUMMIT phase 2 basket study) or with immune checkpoint and/or mTOR inhibitors (compassionate-use program) in patients with FLC.
Methods: Patients received neratinib 240 mg/day orally in SUMMIT, or as doublet or triplet combinations with pembrolizumab 2 mg/kg intravenously every 3 weeks, nivolumab 240 mg intravenously every 2 weeks, everolimus 7.5 mg/day orally, or sunitinib 37.5 mg/day orally under compassionate use. The primary endpoint in SUMMIT was objective response rate; safety was a secondary endpoint.
Results: Fifteen patients with FLC received neratinib monotherapy in SUMMIT. The objective response rate was 5% (95% CI 0–21.8) and the disease control rate was 13.3% (95% CI 1.7–40.5). Upon progression, five had added immune checkpoint inhibitors with or without everolimus or sunitinib. Two additional patients received neratinib-based combinations outside of SUMMIT, for a total of 17 neratinib-treated patients. One patient who received neratinib plus pembrolizumab had a confirmed partial response, one treated with neratinib plus everolimus had stable disease lasting 6 months, and one who received neratinib plus pembrolizumab plus sunitinib had stable disease lasting 16 months. Grade 3/4 adverse events with neratinib monotherapy occurred in 10 (66.7%)/2 (13.3%) patients, respectively. Grade 3 adverse events with neratinib-based combinations were hyperglycemia (n = 1; neratinib plus pembrolizumab), hepatic failure, and anaphylaxis (n = 1 each, neratinib plus pembrolizumab plus everolimus). There were no grade 4 adverse events with combination therapy.
Conclusion: In patients with FLC, single-agent neratinib had limited efficacy, but clinical benefit was observed with neratinib in combination with immunotherapy and/or mTOR-targeted agents.
DOI: 10.6084/m9.figshare.26021893.v1
title: Supplementary Material for: Machine-learning-aided decision-making model for the discontinuation of continuous renal replacement therapy

description: ABSTRACT
BACKGROUND. Continuous renal replacement therapy (CRRT) is a primary form of renal support for patients with acute kidney injury in an intensive care unit. Making an accurate decision of discontinuation is crucial for the prognosis of patients. Previous research has mostly focused on the univariate and multivariate analysis of factors in CRRT, without the capacity to capture the complexity of the decision-making process. The present study thus developed a dynamic, interpretable decision model for CRRT discontinuation.
METHODS. The study adopted a cohort of 1234 adult patients admitted to an intensive care unit in the MIMIC-IV database. We used the extreme gradient boosting (XGBoost) machine learning algorithm to construct dynamic discontinuation decision models across four time points. Shapley additive explanation (SHAP) analysis was conducted to show the contribution of an individual feature to the model output.
RESULTS. Of the 1234 included patients with CRRT, 596 (48.3%) successfully discontinued CRRT. The dynamic prediction by the XGBoost model produced an area under the curve of 0.848 and accuracy, sensitivity, and specificity of 0.782, 0.786, and 0.776, respectively. The XGBoost model was thus far superior to other test models. SHAP demonstrated that the features that contributed most to the model results were the sequential organ failure assessment score, serum lactate level, and 24-hour urine output. 
CONCLUSIONS. Dynamic decision models supported by machine learning are capable of dealing with complex factors in CRRT and effectively predicting the outcome of discontinuation. 
KEYWORDS: acute kidney injury, continuous renal replacement therapy, discontinuation, machine learning
DOI: 10.6084/m9.figshare.20938972.v1
title: Data file 5: Genes upregulated upon exposure to ciprofloxacin

description: Genes upregulated upon exposure to 0.5×MIC or 1.0×MIC of ciprofloxacin
DOI: 10.6084/m9.figshare.1197211.v1
title: Dog Canyon Fan Grain-Size and Channel Data

description: This is data collected on Dog Canyon alluvial fan. Details on data collection methods are found in corresponding paper, <em>Generalized sorting patterns on alluvial fans, </em>Geophysical Review Letters, (in review).
DOI: 10.6084/m9.figshare.735899.v1
title: SunPy: Python for Solar Physicists

description: Poster created for SunPy for NAM 2013.
DOI: 10.6084/m9.figshare.12644018.v3
title: Blue Hole Water Column Microbiome: May 2019

description: Illumina MiSeq 500 cycle paired-end 16S rRNA gene amplicon sequence data for eleven water column samples taken from the Amberjack Blue Hole (Gulf of Mexico) in May 2019.
DOI: 10.6084/m9.figshare.16660849.v1
title: Supplemental Data for manuscript currently entitled "Acute and chronic exposure to multiple anthropogenic stressors alters microRNAs, mRNA, and proteins in zebrafish (Danio rerio) liver and muscle "

description: This folder contains all the supplementary data for a thesis chapter and future publication currently entitled "Acute and chronic exposure to multiple anthropogenic stressors alters microRNAs, mRNA, and proteins in zebrafish (Danio rerio) liver and muscle ". The descriptions of the folder contents is found in the word doc or pdf entitled "Supplemental_Data_Legend".
DOI: 10.6084/m9.figshare.8019791.v1
title: 1ss

description: The details about this dataset and how to use them can be found here: https://aksimhal.github.io/astrocytes-synapses-fxs/
DOI: 10.6084/m9.figshare.734277.v14
title: Imperial Workshop on Large Deviations Theory

description: <strong>Workshop on Large Deviations Theory</strong> On Wednesday 10th July 2013, a one day workshop on Large Deviations Theory was held at Imperial College London. It consisted of a series of invited talks by leading researchers and a session of very short talks. The aim was to connect researchers working on different aspects of Large Deviation Theory and those interested in applying these ideas. We covered a wide range of topics, trying to build capacity in this area within the UK. We covered both classical and quantum non-equilibrium systems, and applications both within physics and outside. All material related to this workshop, including some slides from the talks, are in this figshare collection. Funding was provided by the EPSRC NetworkPlus programme on Emergence and Physics far from Equilibrium.
DOI: 10.6084/m9.figshare.2324509.v1
title: Emails to authors and responses (data set 2)

description: Emails to authors and responses from data set 2. Risk of bias assigned in data set 2 based on authors responses.
DOI: 10.6084/m9.figshare.25323421.v3
title: Retinopathy of Prematurity in Neonatal Intensive Care Unit at King Fahd University Hospital, Eastern Province: Prevalence, Risk Factors, and pattern of severity Seven years’ experience.

description: Introduction: Premature newborns are susceptible to retinopathy of prematurity (ROP), a vasoproliferative disease of the developing retinal vessels, which is a major cause of potentially avoidable blindness. Due to geographical variations in newborn care, geographic variations in the epidemiology of ROP have been observed internationally during the last several decades. There was a correlation between the severity of the condition and the number of prenatal, postnatal, and other risk factors. Aim: This study aimed to examine the incidence and risk factors associated with retinopathy of prematurity in preterm infants. Methodology: A retrospective review of preterm newborns evaluated for retinopathy of prematurity between January 2016 and December 2022 was carried out at King Fahd Hospital of the University (KFHU), Khobar, Saudi Arabia. Infants who fulfilled the screening criteria (GA &lt; 34 or Birth Weight (WT) ≤ 1500 g) underwent the screening test, and the International Classification of Retinopathy of Prematurity was used to classify retinopathy of prematurity. Risk factors and demographic information regarding ROP were assessed. Statistical analysis was performed using SPSS (version 20) with a 95% confidence interval (CI). Statistical significance was set at p &lt; 0.05. Results: Among the 200 preterm neonates that were evaluated and admitted to neonatal critical care units, 37% exhibited premature retinopathy, with 46.7% of those cases being in stage 1. The development of ROP was linked to gestational age, length of mechanical ventilation, septicemia, intraventricular hemorrhage, bronchopulmonary dysplasia, respiratory distress syndrome, and septicemia, according to univariate and multivariate logistic regression analyses. Conclusion: The incidence of total retinopathy in premature infants in this population was 37%. Evaluating these risk factors during the screening of high-risk premature infants will help determine the appropriate timing of examinations and treatment.
DOI: 10.6084/m9.figshare.24331537.v1
title: Weibull probability density functions

description: Weibull probability density functionsX columns --&gt; Electric filed in V/umYcolumns--&gt;Probability density{X0;Y0} Virgin material{Xi;Yi} Stretched to the ith level{Xi_j;Yi_j} Stretched for j cycles<br>
DOI: 10.6084/m9.figshare.14931786.v1
title: Supplementary Material for: Post-Progression Survival Influences Overall Survival among Patients with Advanced Non-Small Cell Lung Cancer Undergoing First-Line Pembrolizumab Monotherapy

description: <b><i>Background:</i></b> Among patients with non-small cell lung cancer (NSCLC), the impact of first-line treatment on overall survival (OS) may be influenced by subsequent therapies. Thus, using patient-level data, we assessed the relationships of progression-free survival (PFS) and post-progression survival (PPS) with OS among patients with high-programmed death-ligand 1 (PD-L1) expression undergoing first-line pembrolizumab monotherapy for NSCLC. <b><i>Methods:</i></b> We reviewed data from 133 patients with high PD-L1 expression undergoing first-line pembrolizumab monotherapy for NSCLC at 6 Japanese centers between February 2017 and December 2018. The correlations of PFS and PPS with OS were evaluated at the patient level. <b><i>Results:</i></b> Linear regression analyses and Spearman’s rank correlation coefficient revealed that PPS was strongly correlated with OS (<i>r</i> = 0.76, <i>p</i> &lt; 0.05, <i>R</i><sup>2</sup> = 0.65), while PFS was only moderately correlated with OS (<i>r</i> = 0.71, <i>p</i> &lt; 0.05, and <i>R</i><sup>2</sup> = 0.4). Furthermore, PPS was significantly associated with performance status at the end of pembrolizumab monotherapy, as well as the use of platinum-based combination chemotherapy after pembrolizumab monotherapy (both <i>p</i> &lt; 0.05). <b><i>Conclusions:</i></b> Among patients with high PD-L1 expression undergoing first-line pembrolizumab monotherapy for NSCLC, PPS was more strongly correlated with OS, relative to the relationship between PFS and OS. Therefore, subsequent treatment appears to significantly influence OS in patients with disease progression following first-line pembrolizumab monotherapy.
DOI: 10.6084/m9.figshare.12449645.v1
title: annotation-gtf

description: GENCODE and FANTOM
DOI: 10.6084/m9.figshare.23530926.v1
title: Raw data

description: Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
DOI: 10.6084/m9.figshare.13169348.v1
title: Metadata record for: Lower limb kinematic, kinetic, and EMG data from young healthy humans during walking at controlled speeds

description: This dataset contains key characteristics about the data described in the Data Descriptor Lower limb kinematic, kinetic, and EMG data from young healthy humans during walking at controlled speeds. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.24298600.v1
title: Supplementary Material for: Two cases of exacerbation of asthma during treatment with enfortumab vedotin

description: Enfortumab vedotin is an antibody-drug conjugate against nectin-4 that is recently being used in the management of patients with urothelial carcinoma. The common adverse events include rashes, peripheral neuropathy, and hyperglycemia. Only a few cases of associated respiratory symptoms have been reported. Herein, we describe two patients with advanced urothelial carcinoma who experienced asthma exacerbation after initiating enfortumab vedotin treatment. Both patients improved with inhalation therapy. Since nectin-4 is expressed in the tracheal epithelium, its association with asthma is likely. This study highlights that clinicians should caution patients with a history of asthma against the worsening of respiratory symptoms when enfortumab vedotin is administered.
DOI: 10.6084/m9.figshare.5951566.v1
title: Supplementary Material for: International Consensus Statement on Screening, Diagnosis and Treatment of Substance Use Disorder Patients with Comorbid Attention Deficit/Hyperactivity Disorder

description: Adult attention deficit/hyperactivity disorder (ADHD) often co-occurs with substance use disorders (SUD) and is associated with early onset and more severe development of SUD and with reduced treatment effectiveness. Screening tools allow for a good recognition of possible ADHD in adults with SUD and should be used routinely, followed by an ADHD diagnostic process initiated as soon as possible. Simultaneous and integrated treatment of ADHD and SUD, using a combination of pharmaco- and psychotherapy, is recommended. Long-acting methylphenidate, extended-release amphetamines, and atomoxetine with up-titration to higher dosages may be considered in patients unresponsive to standard doses. This paper includes evidence- and consensus-based recommendations developed to provide guidance in the screening, diagnosis and treatment of patients with ADHD-SUD comorbidity.
DOI: 10.6084/m9.figshare.23849295.v1
title: List of non-English-language journals in ecology and conservation. Version 1.2.

description: This is the list of peer-reviewed journals published in languages other than English in research areas related to ecology and biodiversity conservation.The list was compiled by the translatE project (https://translatesciences.com/) in collaboration with native speakers of 15 languages. Please see the Collaborators sheet for information on those collaborators.If you find any errors, or know any other relevant non-English-language journals, please let us know at: https://translatesciences.com/contact/
DOI: 10.6084/m9.figshare.25524145.v3
title: Dataset for 'Atypical lateralization of visuospatial attention can be associated with better or worse performance on line bisection'

description: Dataset supporting the findings described in the research article titled: 'Atypical lateralization of visuospatial attention can be associated with better or worse performance on line bisection'
DOI: 10.6084/m9.figshare.24198753.v1
title: Supplementary Material for: The cancer cachexia index can be used to prognostically predict patients with gastric cancer undergoing gastrectomy

description: Objective. Cancer cachexia occurs in cancer patients more frequently as the cancer progresses, with a negative impact on treatment outcomes. In this study, we sought to clarify the clinical impact of a cancer cachexia index CXI in patients with gastric cancer (GC) undergoing gastrectomy. Methods. Between January 2013 and December 2018, we reviewed data from 556 patients treated for GC at our hospital. CXI was calculated using skeletal muscle index (SMI), serum albumin, and neutrophil-lymphocyte ratios (NLR). Patients were divided into high (n=414) or low CXI (n=142) groups. We investigated the clinical impact of CXI in patients with GC undergoing gastrectomy. Results. Multivariate analyses of 5-year overall survival (OS) and cancer specific survival (CSS) rates indicated that a low CXI was independently associated with unfavorable outcomes for patients with GC. In multivariate analyses, SMI was independent predictor of OS but not CSS. NLR was not an independent predictor of either OS or CSS. Complication incidences [≥ Clavien Dindo (CD) 3] were non-significantly higher in the low (vs. high) CXI group. Conclusion. CXI was a more valuable prognostic biomarker when compared with SMI or NLR in GC patients undergoing gastrectomy. We suggest that patients with low CXI values should be given more comprehensive treatment, including exercise and nutritional therapy to improve clinical outcomes.