Find research datasets worth reusing

opencc-by-4.0Apr 2023View details →

Data and code: Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome

Data and code to the publication Conrady et al (2023): Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome, PNAS.

opencc-zeroDec 2022View details →

Deep learning unmasks the ECG signature of Brugada Syndrome

One in ten cases of sudden cardiac death strikes without warning as the result of an inherited arrhythmic cardiomyopathy, such as Brugada Syndrome (BrS). Normal physiological variations often obscure visible signs of this and related life-threatening channelopathies in conventional electrocardiograms (ECGs). Sodium channel blockers can reveal previously hidden diagnostic ECG features, however, their use carries the risk of life-threatening proarrhythmic side effects. The absence of a non-invasive test places a grossly underestimated fraction of the population at risk of SCD. Here, we present a machine learning algorithm that extracts, aligns, and classifies ECG waveforms for the presence of BrS. This protocol, which succeeds without the use of a sodium channel blocker (88.4% accuracy, 0.934 AUC in validation), can aid clinicians everywhere to identify the presence of this potentially life-threatening heart disease more easily.

opencc-by-4.0Apr 2023View details →

Datasets: Urbanisation generates multiple trait syndromes for terrestrial animal taxa worldwide

This repository contains the datasets used in the main article: <ul> <li>There is one Excel file per taxonomic group (amphibians, bats, bees, birds, ground beetles, and reptiles).</li> <li>Each file consists of three Excel spreadsheets: "Species" = matrix of species by sites; "Sites" = ID and coordinates of sites + urban and forest land cover variables; "Traits" = matrix of species by traits.</li> <li>Each spreadsheet contains the raw data used for the analyses in the article. For more information on how to handle the data, see the "Method" section.</li> </ul>

opencc-zeroMay 2023View details →

Scores on independence, quality of life, and satisfaction on visual mapping software intervention in children with Down syndrome

Enhancing independence and quality of life are key modifiable outcomes that are short- and long-term goals for children with Down syndrome and for their parents. Here we report the outcome of a 4-week feasibility study in a cohort of 26 children with Down Syndrome, 7–17 years old, who used an assistive technology approach that incorporated smart device software and step-by-step pictures (the MapHabit System). Parents reported improvements in children's activities of daily living, quality of life, and independence. They recommended this technology to other families. This report and its findings underscore the feasibility of using assistive technology in children with Down syndrome within home and family settings. The current findings that assistive technology can be used successfully and effectively in family and home settings set the stage for more informative systematic studies using assistive technology for this population.

opencc-by-4.0Jun 2023View details →

Pharmacokinetic dataset of a randomized controlled trial investigating the efficacy and safety of intravenous imatinib mesylate (Impentri®) in subjects with acute respiratory distress syndrome induced by COVID-19

Abstract Background The coronavirus disease 2019 (COVID-19) pandemic has led to a disruptive increase in the number of intensive care unit (ICU) admissions with acute respiratory distress syndrome (ARDS). ARDS is a severe, life-threatening medical condition characterized by widespread inflammation and vascular leak in the lungs. Although there is no proven therapy to reduce pulmonary vascular leak in ARDS, recent studies demonstrated that the tyrosine kinase inhibitor imatinib reinforces the endothelial barrier and prevents vascular leak in inflammatory conditions, while leaving the immune response intact. Methods This is a randomized, double-blind, parallel-group, placebo-controlled, multicenter clinical trial of intravenous (IV) imatinib mesylate in 90 mechanically ventilated subjects with COVID-19-induced ARDS. Subjects are 18 years or older, admitted to the ICU for mechanical ventilation, meeting the Berlin criteria for moderate-severe ARDS with a positive polymerase chain reaction test for SARS-CoV2. Participants will be randomized in a 1:1 ratio to either imatinib (as mesylate) 200 mg bis in die (b.i.d.) or placebo IV infusion for 7 days, or until ICU discharge or death. The primary study outcome is the change in Extravascular Lung Water Index (EVLWi) between day 1 and day 4. Secondary outcome parameters include changes in oxygenation and ventilation parameters, duration of invasive mechanical ventilation, number of ventilator-free days during the 28-day study period, length of ICU stay, and mortality during 28 days after randomization. Additional secondary parameters include safety, tolerability, and pharmacokinetics. Discussion The current study aims to investigate the efficacy and safety of IV imatinib in mechanically ventilated subjects with COVID-19-related ARDS. We hypothesize that imatinib decreases pulmonary edema, as measured by extravascular lung water using a PiCCO catheter. The reduction in pulmonary edema may reverse hypoxemic respiratory failure and hasten recovery. As pulmonary edema is an important contributor to ARDS, we further hypothesize that imatinib reduces disease severity, reflected by a reduction in 28-day mortality, duration of mechanical ventilation, and ICU length of stay.

opencc-by-4.0Jun 2023View details →

Central obesity, body mass index, metabolic syndrome and mortality in Mediterranean breast cancer patients

Importance:  Obesity and metabolic disorders have been associated with an increased risk of cancer and with  poorer outcomes in many cohorts of breast cancer (BC) patients, with poor evidence from Mediterranean cohorts.  Objective: To investigate the prognostic potential of anthropometric variables, namely body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), as well as Metabolic Syndrome (MetS) and its components, in early BC patients living in a Southern Mediterranean region of Italy. Design: Prospective cohort study enrolling consecutive early BC patients who were treated between January 2009 and December 2013 in Southern Italy. Median follow-up was 11.8 years and ended on June 15th 2022. Physicians who measured the study variables were blinded to patient groupings. Setting: Multicenter study enrolling consecutive, early BC patients referred to specialized cancer centers. Participants: A total of 955 early BC patients consecutively treated at the Istituto Nazionale dei Tumori, “G. Pascale” and at the Policlinico University Hospital “Federico II”, Naples, Italy, were enrolled.  All study subjects provided written informed consent to participate.  Intervention(s) (for clinical trials) and exposure (for observational studies): Anthropometric measurements and indices (BMI, hip circumference and WC) were collected. MetS was defined according to NCEP-ATP III criteria. MetS components were categorized as 0, 1-2 or ≥3.  Main Outcomes  and Measures: Overall survival and BC-specific survival.  Results:  Mean age was 55.3 years (±12.5 years); 61% of patients were post-menopausal. At the end of follow-up, 208 (22%) patients had died, 131 (14%) of whom from BC. Obesity (BMI≥30 kg/m2) was found in 29% of enrolled patients (14% in pre- and 38% in post-menopause); 24% of patients met the criteria for a diagnosis of MetS (7% in pre- and 36% in post-menopause), whereas 1-2 MetS criteria were found in 53% of patients High WC or WHR were associated with a moderately increased risk of all-cause mortality (WC ≥ 88 cm, HR=1.39, 95%CI: 1.00-1.94; WHR > 0.85, HR=1.62, 95%CI: 1.12-2.37). Furthermore, an increased risk of all-cause mortality was observed with the presence of MetS (HR=1.61, 95%CI: 1.12-2.32). An increased BC-specific mortality risk was found in obese patients (BMI≥30 kg/m2, HR=1.72, 95%CI: 1.06-2.78) and in those with WC ≥88 (HR=1.71, 95%CI: 1.12-2.61). High WHR was also associated with increased risk of BC-specific mortality, both when evaluated as a categorical variable (WHR>0.85, HR=1.80, 95%CI: 1.13-2.86) and as a continuous variable (for each 0.1-U increase in WHR, HR=1.33, 95%CI: 1.08-1.63). The presence of MetS was associated with an 81% increased risk of BC-specific mortality (HR=1.81, 95%CI: 1.51-2.85).  These associations varied according to menopausal status. In particular, in pre-menopausal patients higher BMI was associated with an increased risk of both all-cause and BC-specific mortality (HR=1.43 and HR=1.58, respectively). In post-menopausal women an increased risk of all-cause mortality was found only in the presence of ≥3 MetS components (HR=2.77, 95%CI: 1.09-7.06). The associations among anthropometric variables and all-cause and BC-specific mortality also varied according to BC subtype. Triple negative BC was the only disease subtype that wasn’t independently associated with BMI, WC, WHR or MetS or all-cause and BC-specific mortality. Conclusions and Relevance: Central obesity and metabolic disorders result in a highly increased risk of BC death. The magnitude of this effect suggests that obesity may nullify the benefit of effective BC therapies. Active lifestyle interventions to maintain optimal body weight and to prevent MetS should be recommended for several expected beneficial effects, including a potential reduction in BC-specific mortality.

opencc-zeroJul 2023View details →

Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in Drosophila heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit dCHCHD3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with CHCHD3/6 in sensitized fly hearts. Moderate KD of CHCHD3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (E3 ubiquitin ligase), or SPTBN1 (scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially-disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.

opencc-by-4.0Jul 2023View details →

An over-dominant effect associated with an SNP in a TP63 regulatory region is implicated in susceptibility to non-syndromic orofacial clefts.

Background: Non-syndromic orofacial clefts (NSOC) are complex phenotypes, involving multiple low penetrance genetic and environmental factors. Using a candidate gene approach, we aimed to analyze the role of four single nucleotide polymorphisms (SNPs) in the susceptibility to NSOC. Methods: A total of 254 individuals, 120 patients with NSOC, and 134 controls, all of Portuguese origin and non-consanguineous, were recruited. About 92% of patients had cleft lip with or without cleft palate (NSCL/P) and 8% had cleft palate (NSCP).  Four SNPs in the MTHFR, IRF6, PAX7, and TP63 genes were studied, using a real-time approach with TaqMan probes. Statistical analysis was performed with IBM SPSS Statistics and included chi-squared, Cochran test for trend and binomial logistic regression. Bonferroni correction was applied. Statistical significance was set to 0.05. Results: All SNPs were in Hardy-Weinberg equilibrium. A significant statistical association was found for TP63 rs9332461 in an over-dominant model (p = 0.016; OR 1.897 (1.144 - 3.147)). Discussion and conclusion: Few SNPs have been so far identified in TP63 in population association studies. In our sample, a significant association was only highlighted for rs9332461, localized in upstream regulatory region. Mechanisms involved in heterozygous advantage may underlie the association.

opencc-by-4.0Aug 2023View details →

Dataset related to "CFH and CFHR structural variants in atypical Hemolytic Uremic Syndrome: Prevalence, genomic characterization and impact on outcome "

The upload consists of 2 excel files, including genetic and clinical data, and 6 power point files with western blot images. SMRT sequencing data are deposited in the EBI European Nucletide Archive; Accession number: PRJEB44176.

opencc-by-4.0Sep 2023View details →

Data set for early carpal tunnel syndrome diagnostic

This dataset represents the minimum dataset to replicate the results obtained in the article "A coupled electro-mechanical approach for early diagnosis of carpal tunnel syndrome" by Saveliy Peshin, Julia Karakulova, Alex G. Kuchumov. The dataset includes 3D models used in FEM calculations, Python-based code for a motion capture program, MatLab-based code for determining the conductance of a deformed median nerve, and MRI images used to construct 3D geometries. All folders have a README text file that contains a detailed description of usage.

opencc-by-4.0Oct 2023View details →

Hemostasis defects underlying the hemorrhagic syndrome caused by Mammarenaviruses in a cynomolgus macaque model

Abstract: Viral hemorrhagic fevers (HF) are a group of acute febrile diseases with high mortality rates. While hemostatic dysfunction appears to be a major determinant of the severity of the disease, it is still unclear what pathogenic mechanisms lead to it. In clinical studies, arenaviruses such as Lassa, Machupo and Guanarito viruses caused HF that vary in symptoms and biological alterations. In this study we aimed to characterize the hemostatic dysfunction induced by arenaviral HF to determine its implication in the severity of the disease and to elucidate the origin of this syndrome. We found that lethal infection with Machupo, Guanarito and Lassa viruses is associated with cutaneo-mucosal, cerebral, digestive and pulmonary hemorrhages. The affected animals developed a severe alteration of the coagulation system, which was concomitant with acute hepatitis, minor deficit of hepatic factor synthesis, presence of a plasmatic inhibitor of coagulation and dysfunction of the fibrinolytic system. Despite signs of increased vascular permeability, endothelial cell infection was not a determinant factor of the hemorrhagic syndrome. There were also alterations of the primary hemostasis during lethal infection, with moderate to severe thrombocytopenia and platelet dysfunction. Finally, we show that lethal infection is accompanied by a reduced hematopoietic potential of the bone marrow. This study provides an unprecedented characterization of the hemostasis defects induced by several highly pathogenic Arenaviruses. Transcriptomics data presented in Figure 3 and in Supp Figure 2

opencc-by-4.0Sep 2023View details →

A INTERVENTIONAL CROSS SECTIONAL STUDY BETWEEN INTRA VAGINAL PLATELET RICH PLASMA AND ESTROGEN FOR TREATMENT OF GENITO-URINARY SYNDROME IN POST MENOPAUSAL WOMEN.

Genitourinary syndrome of menopause (GSM) is a new term for a condition more renowned as atrophic vaginitis. It is used to describe a variety of menopausal symptoms and signs that are related to the physical changes of the vulva, vagina and lower urinary tract. The etiology of GSM is secondary to decreased levels of endogenous estrogens and represents a common but underreported condition. Currently Intra-Vaginal application of oestrogen has been considered an effective treatment of atrophic vaginitis.Recently, PRP has becoming popular as a non-operative treatment option for GSM symptoms.Our study focuses on the use platelet rich plasma for the treatment of GSM as it has natural mechanisms of cell regeneration and requires less frequent dosing and have better compliance when compared to estrogen creams. Purpose of the study is to compare the effectiveness of intra vaginal estrogen cream with intravaginal PRP in treatment of GSM.

opencc-zeroOct 2023View details →

Data on: Projecting spatiotemporal dynamics of severe fever with thrombocytopenia syndrome in the mainland of China

This dataset is the data used in the paper of Global change biology entitled "Projecting spatiotemporal dynamics of severe fever with thrombocytopenia syndrome in the mainland of China". We use an integrated multi-model, multi-scenario framework to assess the impact of global climate change on SFTS disease in the mainland of China. The SFTS incidence in three time periods (2030-2039, 2050-2059, 2080-2089) is predicted to be increased as compared to the 2010s in the context of various RCPs. The projected spatiotemporal dynamics of SFTS will be heterogeneous across provinces. Notably, we predict possible outbreaks in Xinjiang and Yunnan in the future, where only sporadic cases have been reported previously. These findings highlight the need for population awareness of SFTS in endemic regions, and enhanced monitoring in potential risk areas.

controlledIPD-YESFeb 2026View details →

Exercise Application in the Treatment of Patients With Subacromial Pain Syndrome

ClinicalTrials.gov study NCT02695524. IPD Sharing: YES. Countries: 1. Publications: 15.

restrictedIPD-UNDECIDEDFeb 2026View details →

Acupuncture for Dry Eye Syndrome

ClinicalTrials.gov study NCT00969280. IPD Sharing: Not stated. Countries: 1. Publications: 1.

A 2-Period Crossover Study of BPN14770 in Adults Males With Fragile X Syndrome

ClinicalTrials.gov study NCT03569631. IPD Sharing: NO. Countries: 1. Publications: 2.

controlledIPD-YESFeb 2026View details →

Pandemic Triage Score in Patients With Known or Suspected Severe Acute Respiratory Syndrome (SARS) CoronaVirus (CoV) 2 Infection

ClinicalTrials.gov study NCT04371471. IPD Sharing: YES. Countries: 1. Publications: 7.

Tamibarotene Plus Azacitidine in Participants With Newly Diagnosed RARA-positive Higher-Risk Myelodysplastic Syndrome

ClinicalTrials.gov study NCT04797780. IPD Sharing: NO. Countries: 13. Publications: 2.

Genomic Predictors of Decitabine Response in Patients With Acute Myeloid Leukemia or Myelodysplastic Syndromes

ClinicalTrials.gov study NCT01687400. IPD Sharing: NO. Countries: 1. Publications: 1.

The Effect of Aromatherapy on Neonatal Abstinence Syndrome and Salivary Cortisol Levels

ClinicalTrials.gov study NCT03097484. IPD Sharing: NO. Countries: 1. Publications: 17.