Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Experimental data for "A Novel Clinical-Driven Design for Robotic Hand Rehabilitation: Combining Sensory Training, Effortless Setup and Large Range of Motion in a Palmar Device"

Experimental data for the interaction force benchmark test of the PRIDE haptic hand rehabilitation device.

opencc-zeroJan 2023View details →

Data from: Decreased cerebrospinal fluid orexin levels not associated with clinical sleep disturbance in Parkinson's disease: A retrospective study

Patients with Parkinson's disease (PD) often suffer from sleep disturbances, including excessive daytime sleepiness (EDS) and rapid eye movement sleep behavior disorder (RBD). These symptoms are also experienced by patients with narcolepsy, which is characterized by orexin neuronal loss. In PD, a decrease in orexin neurons is observed pathologically, but the association between sleep disturbance in PD and cerebrospinal fluid (CSF) orexin levels is still unclear. This study aimed to clarify the role of orexin as a biomarker in patients with PD. CSF samples were obtained from a previous cohort study conducted between 2015 and 2020. We cross-sectionally and longitudinally examined the association between CSF orexin levels, sleep, and clinical characteristics. We analyzed 78 CSF samples from 58 patients with PD and 21 samples from controls. CSF orexin levels in patients with PD (median = 272.0 [interquartile range = 221.7–334.5] pg/mL) were lower than those in controls (352.2 [296.2–399.5] pg/mL, p = 0.007). There were no significant differences in CSF orexin levels according to EDS, RBD, or the use of dopamine agonists. Moreover, no significant correlation was observed between CSF orexin levels and clinical characteristics by multiple linear regression analysis. Furthermore, the longitudinal changes in orexin levels were also not correlated with clinical characteristics. This study showed decreased CSF orexin levels in patients with PD, but these levels did not show any correlation with any clinical characteristics. Our results suggest the limited efficacy of CSF orexin levels as a biomarker for PD, and that sleep disturbances may also be affected by dysfunction of the nervous system other than orexin, or by dopaminergic treatments in PD. Understanding the reciprocal role of orexin among other neurotransmitters may provide a better treatment strategy for sleep disturbance in patients with PD.

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Right vs left portal branch puncture in TIPS creation with controlled expansion covered stent: comparison of hemodynamic and clinical outcomes

Purpose: To retrospectively compare outcomes of TIPS performed by puncturing left portal vein (LPV) vs right portal vein (RPV) to access the portal system. Materials and methods: One hundred ninety-three consecutive patients underwent TIPS with controlled expansion covered stent by using the LPV (37 patients) or the RPV (156 patients). Patients were followed until the last clinical evaluation, liver transplantation, or death. Results: Demographics and clinical characteristics of the two groups were comparable. The median follow-up was 9.6 months (range 0.1-50.6). Portosystemic pressure gradient (PSG) before TIPS 15.7 mmHg ± 4.7 in RPV group (RPVG) vs 15.4 mmHg ± 4.5 in LPV group (LPVG) (p = 0.725). After TIPS, PSG 6.3 mmHg ± 2.8 in RPVG vs 6.2 mmHg ± 2.2 (p = 0.839). In LPVG, the stent was dilated to 8-mm in 95% of patients vs 77% of RPVG (p = 0.015). Two (5.4%) and 22 (14%) patients underwent TIPS revision in LPVG and RPVG (p = 0.15). The incidence of overt HE was 13% in LPVG and 24% in RPVG (p = 0.177). Rebleeding occurred in 3 of 49 patients (6%) with variceal bleeding as an indication: 2/41 patients (4.9%) in RPVG vs 1/8 patients (12.5%) in LPVG (p = 0.417). Among 126 patients with refractory ascites 20 patients (15.9%) needed paracentesis 3 months after the procedure: 18/101 patients (17.8%) in RPVG vs 2/25 patients (8%) in LPVG (p = 0.231). Thirty-seven patients (19%) died: 32 (21%) in RPVG and 5 (14%) in LPVG (p = 0.337). Conclusion: Compared with RPV puncture, in TIPS created through the LPV, the targeted PSG was reached with a smaller stent diameter. However, no significant difference in clinical outcomes was observed.

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Clinical outcomes of transjugular intrahepatic portosystemic shunt with PTFE-covered stents after liver transplantation and technical results in split and whole liver graft recipients

Objectives: To assess the outcomes of transjugular intrahepatic portosystemic shunt (TIPS) creation using PTFE-covered stents in liver transplant (LT) recipients and to analyze the technical result of TIPS creation in split grafts (SG) compared with whole liver grafts (WG). Methods and materials: Single-center, retrospective study, analyzing LT patients who underwent TIPS using PTFE-covered stents. Clinical and technical variables were analyzed. Results: Between 2005 and 2021, TIPS was created using PTFE-covered stents in 48 LT patients at a median of 43 months (range, 0.5-192) after LT. TIPS indications were refractory ascites (RA) in 33 patients (69%), variceal bleeding (VB) in 9 patients (19%), others in 6 (12%). Ten patients (21%) received a SG. Technical success rate was 100% in both groups: in two WG recipients, (5%) a second attempt was required. An unconventional approach (combined transhepatic or transplenic access) was needed in 2 WG (5%) and 2 SG recipients (20%). Two procedure-related death occurred in the WG group. After a median follow-up of 22 months (range, 0,1-144), 16 patients (48%) in the RA group did not require post-TIPS paracentesis, in the VB group rebleeding occurred in 3 patients (33%). Fifteen patients (31%) underwent TIPS revision. Overt hepatic encephalopathy occurred in 14 patients (29%). Patient survival at 6 months, 1 year, and 3 years was 77%, 66%, and 43%, respectively. Conclusions: The feasibility and safety of TIPS creation in SG are comparable to that of WG. TIPS creation using PTFE-covered stents represents a viable option to treat portal hypertensive complications in LT recipients.

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Clinical Insights to Complete and Incomplete Surgical Revascularization in Atrial Fibrillation and Multivessel Coronary Disease

Objectives: Although endorsed by international guidelines, complete revascularization (CR) with Coronary Artery Bypass Grafting (CABG) remains underused. In higher-risk patients such as those with pre-operative atrial fibrillation (AF), the effects of CR are not well studied. Methods: We analyzed patients' data from the HEIST (HEart surgery In AF and Supraventricular Tachycardia) registry. Between 2012 and 2020 we identified 4770 patients with pre-operative AF and multivessel coronary artery disease who underwent isolated CABG. We divided the cohort according to the completeness of the revascularization and used propensity score matching (PSM) to minimize differences between baseline characteristics. The primary endpoint was all-cause mortality. Results: Median follow-up was 4.7 years [interquartile range (IQR) 2.3-6.9]. PSM resulted in 1,009 pairs of complete and incomplete revascularization. Number of distal anastomoses varied, accounting for 3.0 + -0.6 vs. 1.7 + -0.6, respectively. Although early (< 24 h) and 30-day post-operative mortalities were not statistically different between non-CR and CR patients [Odds Ratio (OR) and 95% Confidence Intervals (CIs): 1.34 (0.46-3.86); P = 0.593, Hazard Ratio (HR) and 95% CIs: 0.88 (0.59-1.32); P = 0.542, respectively] the long term mortality was nearly 20% lower in the CR cohort [HR (95% CIs) 0.83 (0.71-0.96); P = 0.011]. This benefit was sustained throughout subgroup analyses, yet most accentuated in low-risk patients (younger i.e., < 70 year old, with a EuroSCORE II < 2%, non-diabetic) and when off-pump CABG was performed. Conclusion: Complete revascularization in patients with pre-operative AF is safe and associated with improved survival. Particular survival benefit with CR was observed in low-risk patients undergoing off-pump CABG.

opencc-zeroApr 2023View details →

Data for: Defining the relationship between phylogeny, clinical manifestation and phenotype for Trichophyton mentagrophytes/interdigitale complex; a literature review and taxonomic recommendations

This study looked for correlations between molecular identification, clinical manifestation and morphology for Trichophyton interdigitale and T. mentagrophytes. For this purpose, a total of 110 isolates were obtained from Czech patients with various clinical manifestations of dermatophytosis. Micro- and macromorphology and physiology were analysed, and the strains were characterized using multilocus sequence typing. Among the 12 measured/scored phenotypic features, statistically significant differences between species were found only in growth rates at 37°C and in the production of spiral hyphae but none of these features was diagnostic. Correlations were found between T. interdigitale and higher age of patients and between clinical manifestations such as tinea pedis or onychomychosis. The MLST approach showed that ITS genotyping of T. mentagrophytes isolates has limited practical benefits because of extensive gene flow between sublineages. Based on our results and previous studies, there are few taxonomic arguments for preserving both species' names. The species show a lack of monophyly and unique morphology. On the other hand, some genotypes are associated with predominant clinical manifestations and sources of infections, which keep those names alive. This practice is questionable because the use of both names confuses identification, leading to difficulty in comparing epidemiological studies. The current identification method using ITS genotyping is ambiguous for some isolates and is not user-friendly. Additionally, identification tools such as MALDI-TOF MS fail to distinguish these species. To avoid further confusion and simplify identification in practice, we recommend using the name T. mentagrophytes for the entire complex. When clear differentiation of populations corresponding to T. interdigitale and T. indotineae is possible based on molecular data, we recommend optionally using a variety rank: T. mentagrophytes var. interdigitale and T. mentagrophytes var. indotineae.

opencc-by-4.0May 2023View details →

TCGA RNA-Seq normalized rsem data, TCGA clinical data and mutational signature profiles

Normalized rsem RNA-Seq data for each of the 33 TCGA tumor types named as "tumortypernaSeq.tar", a file containing TCGA clinical data ("cliDat_tcga_18.tar") and a text file with single base substitution mutational signatures for each sample from COSMIC (https://cancer.sanger.ac.uk/cosmic, “signatureProfileSample.txt.zip”).

opencc-by-4.0Jul 2023View details →

TCGA Kidney Renal Clear Cell Carcinoma (KIRC) Clinical Data

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset includes curated survival data from the Pan-cancer Atlas paper titled <a href="http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0">"An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics"</a>. The paper highlights four types of carefully curated survival endpoints, and <a href="http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl3&pii=S0092867418302290">recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type</a>. The dataset also includes phenotypic information about KIRC. The Sample IDs are unique identifiers, which can be paired with the gene expression dataset.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The survival and phenotype data were merged into one file. Empty columns were removed. Columns with the same value for every sample were also removed.  Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 Liu, Jianfang, Caesar-Johnson, Samantha J. et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, Volume 173, Issue 2, 400 - 416.e11. <a href="https://doi.org/10.1016/j.cell.2018.02.052">https://doi.org/10.1016/j.cell.2018.02.052</a> The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

opencc-by-4.0Jul 2023View details →

TCGA Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Clinical Data

Abstract: The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. This dataset includes curated survival data from the Pan-cancer Atlas paper titled <a href="http://www.cell.com/cell/fulltext/S0092-8674(18)30229-0">"An Integrated TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR) to drive high quality survival outcome analytics"</a>. The paper highlights four types of carefully curated survival endpoints, and <a href="http://www.cell.com/action/showFullTableImage?isHtml=true&tableId=tbl3&pii=S0092867418302290">recommends the use of the endpoints of OS, PFI, DFI, and DSS for each TCGA cancer type</a>. The dataset also includes phenotypic information about CESC. The Sample IDs are unique identifiers, which can be paired with the gene expression dataset.  Inspiration: This dataset was uploaded to UBRITE for GTKB project.  Instruction: The survival and phenotype data were merged into one file.  Acknowledgments: Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8 Liu, Jianfang, Caesar-Johnson, Samantha J. et al. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, Volume 173, Issue 2, 400 - 416.e11. <a href="https://doi.org/10.1016/j.cell.2018.02.052">https://doi.org/10.1016/j.cell.2018.02.052</a> The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764 U-BRITE last update: 07/13/2023

opencc-zeroOct 2023View details →

Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro

<div> <div> <div> Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics. </div> </div> </div>

closedIPD-NOFeb 2026View details →

Assessing the Performance of Artificial Intelligence (AI)-Augmented Electronic Health Record (EHR) Data Abstraction for Clinical Trial Patient Screening

ClinicalTrials.gov study NCT06561217. IPD Sharing: NO. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

A Non-interventional, International, Multicentre Clinical Research Study to Build the Largest Collection of Multimodal Data (Including Clinical Data, Imaging Data and Omics Data) in Oncology

ClinicalTrials.gov study NCT06625203. IPD Sharing: YES. Countries: 4. Publications: 7.

controlledIPD-YESFeb 2026View details →

Recommendations of Enhanced Recovery Interventions for Patient's Clinical Team and Collection of Associated Data

ClinicalTrials.gov study NCT04606264. IPD Sharing: YES. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Acupuncture for ADHD: Acupoint Data Mining, Clinical Effectiveness, and Interviews to Explore Treatment Outcomes.

ClinicalTrials.gov study NCT06860763. IPD Sharing: NO. Countries: 1. Publications: 19.

restrictedIPD-UNDECIDEDFeb 2026View details →

Post-Market Clinical Follow Up Study to Collect Additional Data and Imaging

ClinicalTrials.gov study NCT04880070. IPD Sharing: Not stated. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

Digital Data Linkage and Scheduling to Track Pregnancy With or Without Community Data Use to Increase Antenatal Clinic Uptake in Western Kenya.

ClinicalTrials.gov study NCT05929586. IPD Sharing: YES. Countries: 1. Publications: 0.

closedIPD-NOFeb 2026View details →

Post Market Clinical Follow Up Study to Collect Additional Data and Imaging

ClinicalTrials.gov study NCT04881058. IPD Sharing: NO. Countries: 1. Publications: 1.

publicJul 2022View details →

Single-cell expression and TCR data from CD19-specific CAR T cells in a phase I/II clinical trial

Open the record for dataset details and reuse information.

publicOct 2023View details →

Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro

Open the record for dataset details and reuse information.