Find research datasets worth reusing

opencc-by-4.0May 2024View details →

Database on chemotherapy-induced cognitive impairment and its long-term development in patients with breast cancer - results from the observational CICARO Study

Raw data and edited data on the observational CICARO-study on chemotherapy-induced cognitive impairment and its long-term development in patients with breast cancer

opencc-by-4.0Sep 2024View details →

A 4,302-patient cohort study of association of rare genetic alterations with endocrine disorders

Endocrine pathologies including disorders such as diabetes and dysfunctions of endocrine glands, are frequently associated with genetic predisposition. This study investigated the association of endocrine diseases with genetic variants, copy number variations (CNVs), and mutational load of molecular pathways in 4302 patients with 409 ICD-10 diagnoses who underwent DNA testing using next-generation sequencing at the National Medical Research Center for Endocrinology (Moscow) from November 2017 till January 2024. We analyzed rare protein-altering genetic variants using three control cohorts (gnomAD3, RUSeq healthy, experimental).  We identified 143 associated variants for diabetes mellitus and 188 genetic variants across other 18 different ICD-10 groups of diagnoses, including 25% and 30% of previously undescribed variants, respectively. In addition, we investigated the aggregation of genetic variants across individual genes and their functional ensembles (molecular pathways) and identified 105 and 101 associations with ICD-10 diagnoses, respectively. In addition, we identified 35 pathogenic and 91 likely pathogenic CNVs in 925 patients with whole exome sequencing profiles. Among them, 9 and 44 CNVs, respectively, were not previously described. Totally, we found statistically significant associations between CNVs and endocrine pathologies for 168 genes. These results expand our understanding of endocrine disease mechanisms and may indicate new potential therapeutic targets.

Simulated Object-Centric Event Logs (OCEL 2.0) for Order-to-Cash, Procure-to-Pay, Hiring, and Hospital Patient Lifecycle Processes

This dataset contains simulated object-centric event logs for four distinct business processes: Order-to-Cash (O2C), Procure-to-Pay (P2P), Hiring, and Hospital Patient Lifecycle. Each process is designed to reflect realistic workflows, encompassing multiple object types and capturing key activities, decision points, and process dynamics. The dataset is aimed at providing a rich source of data for process mining, analysis, and modeling activities. 1. Order-to-Cash (O2C):    The O2C process simulates an end-to-end business flow starting from customer order placement to payment receipt. It includes diverse activities such as order approval, fulfillment, invoice generation, and payment processing, involving object types like Customers, Orders, Products, and Invoices. The dataset captures variability through random decisions, synchronization between departments, and workarounds in credit checks and inventory adjustments. Attributes such as customer tiers, order values, and shipment statuses add further depth, allowing for detailed analysis of this complex process. 2. Procure-to-Pay (P2P):    The P2P process simulates the procurement lifecycle, from requisition creation to payment of suppliers. Key activities include purchase order creation, three-way matching, goods receipt, and payment processing. The event log records object types such as Purchase Requisitions, Purchase Orders, Suppliers, and Invoices. Variability is introduced through approval decisions, batching, and potential mismatches in the matching process. The dataset represents the inherent complexities of real-world procurement operations, including batching and synchronization issues between different process stages. 3. Hiring Process:    The hiring process log tracks the recruitment lifecycle, from job requisition creation to onboarding. It includes object types like Candidates, Job Requisitions, Recruiters, and Interviewers. The process covers activities such as resume screening, interviews, assessments, and offer management. Variability in the hiring process is introduced through random delays, candidate decisions, and background check durations. Batching occurs in stages like resume screening and onboarding, while synchronization challenges arise during interview scheduling. 4. Hospital Patient Lifecycle:    This log represents the lifecycle of patients within a hospital, capturing interactions with multiple resources such as physicians, beds, and medical equipment. The process begins with pre-admission activities, followed by diagnosis, treatment, and discharge. The dataset includes object types like Patients, Physicians, and Medical Equipment, with attributes related to patient demographics and event severity. The process reflects the dynamic nature of hospital operations, including synchronization of resources and the occurrence of workarounds in case of delays or resource unavailability. Each process simulation captures high variability, synchronization issues, and batching, making this dataset suitable for analyzing real-world operational challenges. The logs provide a comprehensive view of complex workflows, supporting advanced analysis, including object-centric process mining. This description will provide the necessary details about the dataset, highlighting its structure, purpose, and potential uses for researchers and process analysts. Object-centric event logs conceived and simulated by the o1-preview-2024-09-12 LRM, using the https://github.com/fit-alessandro-berti/llm-ocel-simulator project.

opencc-by-4.0Jan 2024View details →

Reduced mortality in patients over 65 years old that undergo surgery for degenerative spine disease

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Assessment of the expression level of selected genes and protein phosphorylation of the PI3K/Akt signaling pathway in patients with colorectal cancer

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High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations

This repository contains: all code, phenomic data, extracted features, calculated stats, normalised z-scores and timerseries data for all of the disease mutant phenologs and data in our paper: High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations.

Impact of CYP3A5 Genotypes on Tacrolimus Pharmacokinetics in Colombian Liver Transplant Patients

Impact of CYP3A5 Genotypes on Tacrolimus Pharmacokinetics in Colombian Liver Transplant Patients

opencc-by-4.0Nov 2024View details →

Data and Code from: Dysregulation of zebrin-II cell subtypes is a shared feature across polyglutamine ataxia mouse models and human patients

<div> <div> <div> Abstract Spinocerebellar ataxia type 7 (SCA7) is a genetic neurodegenerative disorder caused by a CAG- polyglutamine repeat expansion. Purkinje cells (PCs) are central to the pathology of ataxias, but their low abundance in the cerebellum underrepresents their transcriptomes in sequencing assays. To address this issue, we developed a PC enrichment protocol and sequenced individual nuclei from mice and patients with SCA7. Single-nucleus RNA sequencing in SCA7-266Q mice revealed dysregulation of cell identity genes affecting glia and PCs. Specifically, genes marking zebrin-II PC subtypes accounted for the highest proportion of DEGs in symptomatic SCA7-266Q mice. These transcriptomic changes in SCA7-266Q mice were associated with increased numbers of inhibitory synapses as quantified by immunohistochemistry and reduced spiking of PCs in acute brain slices. Dysregulation of zebrin-II cell subtypes was the predominant signal in PCs of SCA7-266Q mice and was associated with the loss of zebrin-II striping in the cerebellum at motor symptom onset. We furthermore demonstrated zebrin-II stripe degradation in additional mouse models of polyglutamine ataxia and observed decreased zebrin-II expression in cerebellum of patients with SCA7. Our results suggest that a breakdown of zebrin subtype regulation is a shared pathological feature of polyglutamine ataxias. Data and Code Availability Here you will find data and code associated with our manuscript "Dysregulation of zebrin-II cell subtypes is a shared feature across polyglutamine ataxia mouse models and human patients", Bartelt et al., Sci. Trans. Med. 16, eadn5449 (2024). The data file labeled "HuCb_filtered.rds" is a processed and annotated single-nucleus RNA-seq Seurat object, containing the gene-level count data for the multiplexed snRNA-seq experiment performed on post-mortem human cerebellar tissues from patients with SCA7 and unaffected controls. Data obtained from WT and SCA7-266Q mice as described in our paper can be accessed in the NIH Gene Expression Omnibus under accession number GSE269430. There are three code files numbered 00 through 02 which contain analysis code for snRNA-seq data applied to both the mouse and human datasets. These files are sequential and will take the user from CellRanger output, to filtered and annotated Seurat objects, and include details for subclustering analysis as well as our pseudobulk DEseq2 differential expression approach. There are places where the user may need to modify the code based on their computer system, version of R or Seurat, and whether they are processing the 5 week, 8 week, or human data sets; these locations in the code are marked with comments. <ul> <li>The first file, 00_Preprocessing_MULTIseq, begins with CellRanger filtered_feature_barcode_matrix output, extracts cell barcodes, utilizes the MULTIseq deMULTIplex software to match cell barcodes to oligo barcodes from MULTIseq fastq files, and annotates the Seurat file with metadata. Cell type identification and annotation also takes place in this file. Note: the deMULTIplex step will likely need to be run on a high performance compute cluster.</li> <li>The second file, 01_Seurat_Analysis, uses the filtered and annotated Seurat file to calculate useful QC metrics, investigate disease signals, and perform cell type subclustering analyses.</li> <li>The third file, 02_Pseudobulk_DEseq2, contains custom analysis code to extract raw counts for each cell type and each animal from the Seurat file, and uses the DEseq2 package to calculate DEGs, taking into account biological replicates, and raw read count differences between control and SCA7 animals.</li> </ul> </div> </div> </div>

opencc-zeroMar 2020View details →

Data from: Discharge communication for chronic disease patients in three hospitals in India

OBJECTIVES Poor discharge communication is associated with negative health outcomes in high-income countries. However, quality of discharge communication has received little attention in India and many other low and middle-income countries. Primary Objective To investigate verbal and documented discharge communication for chronic non-communicable disease (NCD) patients. Secondary objective To explore the relationship between quality of discharge communication and health outcomes. METHODS: Design Prospective study. Setting: Three public hospitals in Himachal Pradesh and Kerala states, India. Participants: 546 chronic NCD (chronic respiratory disease, cardiovascular disease or diabetes) patients. Piloted questionnaires were completed at admission, discharge and Five and eighteen-week follow-up covering health status, health-seeking behaviour and healthcare information exchange practices. Logistic regression was used to explore the relationship between quality of discharge communication and health outcomes. Outcome Measures: Primary: Patient recall and experiences of verbal and documented discharge communication. Secondary: Death, hospital readmission and self-reported deterioration of NCD/s. RESULTS All patients received discharge notes, which were predominantly on minimally structured sheets of paper (71%); 31% of notes contained all of the following information required for facilitating continuity of care: diagnosis, medication information, lifestyle advice, and follow-up instructions. Patient reports indicated notable variations in verbal information provided during discharge consultations; 50% received ongoing treatment/management information and 23% received lifestyle advice. Within 18 weeks of follow-up, 25 (5%) patients had died, 69 (13%) had been readmitted and 62 (11%) reported that their chronic NCD/s had deteriorated. Significant associations were found between low-quality documented discharge communication and death (AOR=3.00; 95% CI 1.27,7.06) and low-quality verbal discharge communication and self-reported deterioration of chronic NCD/s (AOR=0.46; 95% CI 0.25,0.83) within 18-weeks of follow-up. CONCLUSIONS Sub-optimal discharge practices may be compromising the continuity and safety of chronic NCD patient care. Structured protocols, documents and training are required to improve discharge communication, healthcare integration and overall NCD management.

opencc-by-4.0Jun 2021View details →

Analysis of DNA methylation profile of Korean chronic lymphocytic leukaemia (CLL) patients with MeDIP-Seq

In this study, we performed genome-wide methylation profiling of eight CLL patients and five control subjects, in an Asian cohort. Methyl-CpG-binding domain sequencing (MBD-Seq) was used as the profiling method. Differential methylation analysis identified a number of differentially methylated regions (DMRs) and genes (DMGs). More regions were hypomethylated than were hypermethylated. Promoters contained the highest proportion of DMRs, while distal intergenic and intron regions contained the largest number of DMRs. Gene Ontology, pathway analysis, and network-based prioritization of DMGs were also performed.

opencc-zeroDec 2020View details →

Concentration of selected proteins in plasma of patient with soft tissue infections or sepsis

The dataset includes two tabular sets of concentration measurements of selected proteins in plasma samples from patients with soft tissue infections or sepsis. Patients with soft tissue infections are classified into three groups: Patients with necrotizing soft tissue infections (NSTI), suspected NSTI cases but where no necrotic tissue was found during surgical exploration (Non-NSTI) and cellulitis. The sepsis patient cohort has heterogeneous etiologies and location of infection. Additionally, we included a group of patients that had surgery related to non-infectious conditions as a healthy cohort of patients (Surgical control). The measurements were performed by Luminex® multiplex immunoassay or ELISA. Each of the two sets were obtained from independent rounds of measurements and differ in the panel of analytes measured and samples included. The first set of measurements (Set01) covers 39 analytes measured in two sets of customized multiplex plates (32-plex and 5-plex), and two in independent ELISA assays. These analytes were measured in 251 NSTI samples, 20 Non-NSTI, 19 cellulitis and 20 surgical controls. The second set of measurements (Set02) consist of a subset of 10 analytes included in the first set and were measured in two multiplex plates (4-plex and 6-plex). The second round of measurements were carried out in 60 additional NSTI patients and 24 sepsis patients. Lastly, imputation of censored data was carried out only in the first set of measurements and the resulting data is also available in the current data set (Set01_imputed).

opencc-by-4.0Jul 2021View details →

MRI versus CT in the detection of brain lesions in patients with infective endocarditis before/after cardiac surgery

Imaging of brain involvement in infective endocarditis can drive the clinical management of this serious condition. MRI is very sensitive, but CT is more readily available. In this retrospective study, we compared the detection rate of CT and MRI. After Ethics Committee approval, we retrospectively reviewed a series of 20 patients (13 males, median age 64 years) who underwent both CT and MRI before or after cardiac surgery for definite infective endocarditis. Unenhanced CT and MRI were evaluated for acute ischemic lesions, both punctuate and large, intraparenchymal hemorrhages, cerebral microbleeds, subarachnoid hemorrhages, abscesses, microabscesses and meningitis. Qualitative and Cohen κ analysis were performed. The value of contrast-enhanced scans (MRI, n = 14; CT, n = 9) and cognitive status were also assessed. While CT rapidly excludes large hemorrhages before cardiac surgery for infective endocarditis, MRI accurately distinguishes the whole spectrum of brain lesions.

opencc-by-4.0Dec 2020View details →

Dataset on preferences of patients with diabetes towards EQ-5D-5L health states in Spain

The dataset includes data of patients with diabetes preferences toward EQ-5D-5L health states.

opencc-zeroJul 2021View details →

HINC dataset from: Homeopathic treatment as an add-on therapy may improve quality of life and prolong survival in patients with non-small cell lung cancer: A prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter study

Background: Patients with advanced non-small cell lung cancer (NSCLC) have limited treatment options. Alongside conventional anticancer treatment, additive homeopathy might help to alleviate side effects of conventional therapy. The aim of the present study was to investigate whether additive homeopathy might influence quality of life (QoL) and survival in NSCLC patients. Methods: In this prospective, randomized, placebo-controlled, double-blind, three-arm, multicenter, phase III study, we evaluated the possible effects of additive homeopathic treatment compared with placebo in NSCLC stage IV patients with respect to QoL in the two randomized groups and survival time in all three groups. Treated patients visited the outpatients' centers every 9 weeks. 150 Patients with stage IV NSCLC were included in the study. 98 received either individualized homeopathic remedies (n=51) or placebo (n=47) in a double-blinded fashion. 52 control patients without any homeopathic treatment were observed for survival only. The constituents of the different homeopathic remedies were mainly of plant, mineral or animal origin. The remedies were manufactured by stepwise dilution and succussion, thereby preparing stable Good Manufacturing Practice grade formulations. Results: QoL as well as functional and symptom scales showed significant improvement in the homeopathy group when compared with placebo after 9 and 18 weeks of homeopathic treatment (p<0.001). Median survival time was significantly longer in the homeopathy group (435 days) vs placebo (257 days; p=0.010) as well as vs control (228 days; p<0.001). Survival rate in the homeopathy group differed significantly from placebo (p=0.020) and from control (p<0.001). Conclusion: QoL improved significantly in the homeopathy group compared with placebo. In addition, survival was significantly longer in the homeopathy group versus placebo and control. A higher QoL might have contributed to the prolonged survival. The study suggests that homeopathy positively influences not only QoL but also survival. Further studies including other tumor entities are warranted.

opencc-by-4.0Jul 2021View details →

Accuracy of ultrasonography and magnetic resonance imaging for preoperative staging of cervical cancer – analysis of patients from the prospective study on total mesometrial resection.

This is supplementary material to the manuscript published in the Diagnostics (MDPI) journal.  Diagnostics 2021, 11, 1749 https://doi.org/10.3390/diagnostics11101749 Videos present examples of ultrasound examinations of patients with cervical cancer.

opencc-by-4.0Aug 2021View details →

Clinical outcome prediction in COVID-19 patients by lymphocyte subsets analysis and monocytes' iTNF-α expression

Raw Box & Whiskers plot related to a manuscript submitted to "Biology" journal - MDPI - https://www.mdpi.com/journal/biology - https://doi.org/10.3390/biology10080735 Manuscript Title: Clinical outcome prediction in COVID-19 patients by lymphocyte subsets analysis and monocytes’ iTNF-α expression Authors: Gabriele Madonna 1&dagger;, Silvia Sale 2&dagger;, Mariaelena Capone 1, Chiara De Falco 2, Valentina Santocchio 2, Tiziana Di Matola 2, Giuseppe Fiorentino 3, Caterina Pirozzi 2, Anna D’Antonio 2, Rocco Sabatino 2, Lidia Atripaldi4, Umberto Atripaldi 4, Marcello Raffone 5, Marcello Curvietto 1, Antonio Maria Grimaldi 1, Vito Vanella 1, Lucia Festino 1, Luigi Scarpato 1, Marco Palla 1, Michela Spatarella 6, Francesco Perna 7, Pellegrino Cerino 8, Gerardo Botti 9, Roberto Parrella 10, Vincenzo Montesarchio 11, Paolo Antonio Ascierto 1&dagger;&dagger;* and Luigi Atripaldi 2&dagger;&dagger; Affiliations: 1 Melanoma, Cancer Immunotherapy and Development Therapeutics Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 2 UOC Biochimica Clinica, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 3 UOC Fisiopatologia e Riabilitazione respiratoria, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 4 University of Campania "Luigi Vanvitelli", Naples, Italy 5 UOC Microbiologia e Virologia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 6 UOSD di Farmacia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy 7 Università degli Studi di Napoli "Federico II", Naples, Italy. 8 Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici (Na), Italy. 9 Scientific Direction, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 10 UOC Malattie Infettive ad Indirizzo Respiratorio, AORN Ospedali dei Colli - Monaldi – Cotugno -CTO, Napoli, Italy 11 UOC Oncologia, AORN Ospedali dei Colli - Monaldi – Cotugno - CTO, Napoli, Italy &dagger;These authors have contributed equally to this work and share first authorship &dagger;&dagger;These authors have contributed equally to this work and share senior authorship *Correspondence: Abstract of submitted Manuscript: T In December 2019 a novel coronavirus, “SARS-CoV-2”, was recognized as the cause of Coronavirus disease-2019 (COVID-19-disease). Several studies have explored the changes and the role of inflammatory cells and cytokines in the immunopathogenesis of disease, but until today the results have been controversial. Based on these premises, we carried out a retrospective assessment of monocytes’ intracellular TNF-α expression (iTNF-α) and on frequencies of lymphocyte sub-populations in twenty-five patients with moderate/severe COVID-19-disease. We found lymphopenia in all COVID-19 infected subjects compared with healthy subjects. On initial observation, in patients with favorable outcome we detected high absolute eosinophils count and high CD4+/CD8+ T lymphocytes ratio, while in the exitus group we observed high neutrophils and CD8+ T lymphocytes counts. During infection, in patients with favorable outcome we observed a rise in lymphocyte count, in monocytes and in Treg lymphocytes counts, in CD4+ and in CD8+ T lymphocytes count but a reduction in CD4+/CD8+ T lymphocytes ratio. Instead, in the exitus group we observed a reduction in Treg lymphocytes counts and a decrease in iTNF-α expression. Our preliminary findings point to a modulation of the different cellular mediators of immune system, which probably have a key role in the outcome of the COVID-19-disease. Funding: This work was supported by Grants from “Regione Campania” through “POR FESR CAMPANIA 2014-2020”, CUP H64I20000300002. Cite: Madonna, G.; Sale, S.; Capone, M.; De Falco, C.; Santocchio, V.; Di Matola, T.; Fiorentino, G.; Pirozzi, C.; D’Antonio, A.; Sabatino, R.; Atripaldi, L.; Atripaldi, U.; Raffone, M.; Curvietto, M.; Grimaldi, A.M.; Vanella, V.; Festino, L.; Scarpato, L.; Palla, M.; Spatarella, M.; Perna, F.; Cerino, P.; Botti, G.; Parrella, R.; Montesarchio, V.; Ascierto, P.A.; Atripaldi, L. Clinical Outcome Prediction in COVID-19 Patients by Lymphocyte Subsets Analysis and Monocytes’ iTNF-α Expression. Biology 2021, 10, 735. doi: <a href="https://doi.org/10.3390/biology10080735">10.3390/biology10080735</a>

opencc-zeroAug 2021View details →

Phase-contrast MRI data of 18 Chiari-I malformation patients and 21 controls

We collected phase-contrast MRI data (5-mm midline sagittal section, rostro-caudal direction) and obtained average velocity in certain Regions-0f-Interest (ROIs). The measured ROIs are cerebellar tonsil, ventral spinal subarachnoid space, dorsal spinal subarachnoid space, upper portion of syrinxes, upper cervical cord, and medulla. Data obtained from 18 Chiari-I patients (preoperative and postoperative) and 21 controls are included. Because the preoperative MRI data was missing in one patient, the preoperative studies included 17 MRI sessions. The unit of the data is cm/sec. The data are synchronized with pre-processing so that the rise of the caudal CSF movement be placed at the center of the cardiac cycle.

opencc-by-4.0Aug 2021View details →

Raw data fort the article: FLUOROSCOPY-GUIDED BILIARY PROCEDURES IN A PREGNANT, LIVER TRANSPLANT PATIENT: FETUS RADIATION PROTECTION

We report three cases of clinically necessary, fluoroscopy-guided, percutaneous biliary procedures performed safely in a pregnant, liver transplant recipient using three different angiography suites. The uterine cumulative equivalent dose was 0.25 mSv, a value obtained by adding the doses of the three procedures described above, and which is relatively low when compared with the naturally occurring background radiation exposure for a 9-month pregnancy (~0.5-1 mSv). Our experience shows that staff knowledge, awareness and liaison promote the application of all dose reduction strategies possible while still achieving the clinical aim despite using different angiographic equipment.

opencc-zeroAug 2021View details →

Innate immune activation by checkpoint inhibition in patient-derived lung cancer tissues

Although Pembrolizumab-based immunotherapy has significantly improved lung cancer patient survival, many patients show variable efficacy and resistance development. A better understanding of the drug's action is needed to improve patient outcomes. Functional heterogeneity of the tumor microenvironment (TME) is crucial to modulating drug resistance; understanding of individual patients' TME that impacts drug response is hampered by lack of appropriate models. Lung organotypic tissue slice cultures (OTC) with patients' native TME procured from primary and brain-metastasized (BM) non-small cell lung cancer (NSCLC) patients were treated with Pembrolizumab and/or beta-glucan (WGP, an innate immune activator). Metabolic tracing with 13C6-Glc/13C5,15N2-Gln, multiplex immunofluorescence (mIF), and digital spatial profiling (DSP) were employed to interrogate metabolic and functional responses to Pembrolizumab and/or WGP. Primary and BM PD-1+ lung cancer OTC responded to Pembrolizumab and Pembrolizumab + WGP treatments, respectively. Pembrolizumab activated innate immune metabolism and functions in primary OTC, which were accompanied by tissue damage. DSP analysis indicated an overall decrease in immunosuppressive macrophages and T cells but revealed microheterogeneity in immune responses and tissue damage. Two TMEs with altered cancer cell properties showed resistance. Pembrolizumab or WGP alone had negligible effects on BM-lung cancer OTC but Pembrolizumab + WGP blocked central metabolism with increased pro-inflammatory effector release and tissue damage. In depth metabolic analysis and multiplex TME imaging of lung cancer OTC demonstrated overall innate immune activation by Pembrolizumab but heterogeneous responses in the native TME of a patient with primary NSCLC. Metabolic and functional analysis also revealed synergistic action of Pembrolizumab and WGP in OTC of metastatic NSCLC.