Find research datasets worth reusing

Epidemiological profile and diabetes control of Type 1 Diabetes Mellitus patients in Karbala Governorate, Iraq

Epidemiological profile and diabetes control of Type 1 Diabetes Mellitus patients in Karbala Governorate, Iraq

Sensor-based telerehabilitation system increases patient adherence after knee surgery

Objectives: Implementing evidence-based recommendations with the option of patient-individualised and situation-specific adaptations in telerehabilitation may increase adherence with improved clinical outcome. Methods: As part of a registry-embedded hybrid design, digital medical device (DMD)-usage in a home-based setting was analysed in a multinational registry. The DMD combines an inertial motion-sensor system with instructions for exercises and functional tests on smartphones. A prospective, single-blinded, patient-controlled, multicentre intervention study (DRKS00023857) compared implementation capacity of the DMD to standard physiotherapy. Usage patterns by health care providers (HCP) were assessed. Results and Conclusion: Registry raw data (10,311 measurements) were analysed from 604 DMD-users, demonstrating clinically expected rehabilitation progression post knee injuries. DMD-users performed tests for range-of-motion, coordination and strength/speed enabling insight to stage-specific rehabilitation (χ2=44.9, p<0.001). Intention-to--treat-analysis revealed DMD-users to have significantly higher adherence to the rehabilitation intervention compared to the matched patient-control-group (86% vs. 74%, p<0.05). DMD-users performed recommended exercises at home with higher intensity (p<0.05). HCP used DMD for clinical decision making. No adverse events related to the DMD were reported. Adherence to standard therapy recommendations can be increased using novel high quality DMD with high potential to improve clinical rehabilitation outcome, enabling evidence-based telerehabilitation.

Identification of glucose-6 phosphate dehydrogenase deficient patients by ATR-FTIR spectroscopy using partial least squares discriminant analysis in aqueous blood samples

Dataset of associated MIR spectra collected in the titled study Baseline: spectrum of air Water: spectrum of deionised water P#_M/F_GD/P/C/T/U_WB/PL/RBC_D/AQ_R: sample spectrum with each section representing the following <ul> <li>P#: patient number 1-30</li> <li>M (male) or F(Female)</li> <li>GD (G6PD deficient), P (Partially G6PD deficient), C & T & ET(Control), U(Unknown) <ul> <li>P10, P28,  P29, & P30 were determined later to be P, C, C, P respectively</li> </ul> </li> <li>WB (whole blood), PL (plasma), RBC (red blood cells)</li> <li>D (dried sample spectrum), AQ (aqueous sample spectrum)</li> </ul>

opencc-zeroDec 2022View details →

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The successful treatment of Enterocytozoon bieneusi Microsporidiosis with nitazoxanide in a patient with B-ALL: A case report

<div> Introduction: Enterocytozoon bieneusi (E. bieneusi) Microsporidia can cause opportunistic infections in immunocompromised patients and is also an emerging disease in these individuals. Its clinical manifestations are chronic diarrhea and severe wasting syndrome, these can be extremely debilitating and carry a significant risk of death for immunocompromised patients. Often, microsporidia cannot be confirmed immediately by routine examination and culture. Effective and available treatment options are limited for infections caused by E. bieneusi in humans. Such cases are very rare in the Chinese Mainland.</div> <div> </div> <div> Case Presentation: A 47-year-old male had recurrent, profuse watery diarrhea and abdominal discomfort for more than 7 months, with a fever for 5 days. Two years earlier, he received treatment with a modified BFM-90 protocol for acute B cell lymphoblastic leukemia and is currently in the final stages of maintenance therapy with oral methotrexate and mercaptopurine. The leukemia was assessed as still in remission two months ago. PET/CT showed massive peritoneal fluid accumulation and a high uptake area in the diffused peritoneum (SUVmax 12.57), suggesting tumor invasion or microbial infections. However, broad-spectrum antibacterial therapies were ineffective. Metagenomic sequencing of plasma and peritoneal fluid showed no suggestion of the existence of a tumor but instead showed a high sequence number of DNA and RNA of the Microsporidia. His albendazole treatment failed and subsequent treatment with nitazoxanide successfully resolved the infection.</div> <div> </div> <div> Conclusion: This case shows that we should consider the possibility of atypical pathogen infection in patients with hematologic malignancy who repeatedly develop unexplained diarrhea with wasting. mNGS can help rule out malignant neoplasms and diagnose infections. Our results suggest that nitazoxanide effectively treats E. bieneusi microsporidia infections. </div>

opencc-by-4.0Jan 2023View details →

Traumatic events, post-traumatic stress disorder, and proxy measures for central sensitization in chronic pain patients of a German university outpatient pain clinic

This dataset was acquired at Hannover Medical School, Hannover, Germany. The study complied with the Declaration of Helsinki, and was approved by the local ethics committee. All subjects gave written informed consent, and consent to use their data anonymously for research purposes. The study was registered at ClinicalTrials.gov (NCT05190367). Between February 2019 and July 2020, 914 patients who visited our outpatient pain department gave written consent to use their routinely collected data anonymously for research purposes. Participants were divided into four groups depending on their trauma severity: (1) no trauma; (2) accidental trauma (e.g. illness, accident, natural disaster); (3) interpersonal trauma (e.g. assault, rape, war); (4) PTSD (diagnosed according to ICD-10). Patients fulfilling two or more categories were assigned to the highest group. Data were collected using the SymptomMapper application [1]. Participants provided information about their traumas, current pain intensity (visual analogue scale, VAS (0-100) [2]), mean and maximal pain in the last 4 weeks (VAS (0-100)), sleep impairment (VAS (0-100)), acceptable pain (VAS (0-100)), pain disability index (PDI [3]), pain area (digital drawings), pain widespreadness (widespread pain index, WPI [4], derived from drawings), stress (patient health questionnaire, German version, PHQ-D [5]), anxiety (PHQ-D), depression (PHQ-D), and somatization symptoms (PHQ-D). This dataset contains the raw data as well as necessary scripts for reproducing the results of this study.   References ########## [1] Neubert TA, Dusch M, Karst M, Beissner F. Designing a Tablet-Based Software App for Mapping Bodily Symptoms: Usability Evaluation and Reproducibility Analysis. JMIR Mhealth Uhealth 2018;6(5):e127. [2] Dworkin RH, Turk DC, Farrar JT et al. Core outcome measures for chronic pain clinical trials: IMMPACT recommendations. Pain 2005;113(1):9-19. [3] Pollard CA. Preliminary Validity Study of the Pain Disability Index. Percept Mot Skills 1984;59(3): 974. [4] Wolfe F, Clauw DJ, Fitzcharles MA et al. The American College of Rheumatology Preliminary Diagnostic Criteria for Fibromyalgia and Measurement of Symptom Severity. Arthritis Care Res 2010;62(5):600-10. [5] Löwe B, Spitzer RL, Zipfel S, Herzog W. Gesundheitsfragebogen für Patienten (PHQ-D). Manual und Testunterlagen (second edition). Pfizer 2002.

opencc-by-4.0Nov 2022View details →

Dataset for comparison of the efficacy of different drug combinations for the treatment of patients with triple negative breast cancer.

Dataset for comparison of the efficacy of different drug combinations for the treatment of patients with triple negative breast cancer.

opencc-by-4.0Jan 2023View details →

Ki-67 and Bcl-2 data by flow cytometry in non-malignant bone marrow aspirates and aspirates from patients with myeloid malignancies.

This Data in Brief article displays a flow cytometric assay that was used for the acquisition and analyses of proliferation and anti-apoptosis in hematopoietic cells. This dataset includes analysis of the Ki-67 positive fraction (Ki-67 proliferation index) and Bcl-2 positive fraction (Bcl-2 anti-apoptotic index) of the different myeloid bone marrow (BM) cell population in non-malignant BM, and the BM disorders myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). The present dataset comprises 1) the percentage of the CD34 positive blast cells, erythroid cells, myeloid cells and monocytic cells, and 2) the determined Ki-67 positive fraction and Bcl-2 positive fraction of these cell populations in tabular form. This allows the comparison and reproduction of the data when these analyses are repeated in a different setting. As gating the Ki-67 positive and Bcl-2 positive cells is a critical step in this assay, different gating approaches were compared to determine the most sensitive and specific approach. BM cells from aspirates of 50 non-malignant, 25 MDS and 50 AML cases were stained with 7 different antibody panels and subjected to flow cytometry for determination of the Ki-67 positive cells and Bcl-2 positive cells of the different myeloid cell populations. The Ki-67 or Bcl-2 positive cells were then divided by the total number of cells of the respective cell population to generate the Ki-67 positive fraction (Ki-67 proliferation index) or the Bcl-2 positive fraction (Bcl-2 anti-apoptotic index). The presented data may facilitate the establishment and standardization of flow cytometric analyses of the Ki-67 proliferation index and Bcl-2 anti-apoptotic index of the different myeloid cell populations in non-malignant BM as well as MDS and AML patients in other laboratories. Directions for proper gating of the Ki-67 positive and Bcl-2 positive fraction are crucial for achieving standardization among different laboratories. In addition, the data and the presented assay allows application of Ki-67 and Bcl-2 in a research and clinical setting and this approach can serve as the basis for optimization of the gating strategy and subsequent investigation of other cell biological processes besides proliferation and anti-apoptosis. These data can also promote future research about the role of these parameters in diagnosis of myeloid malignancies, prognosis of myeloid malignancies and therapeutic resistance against anti-cancer therapies in these malignancies. As specific populations based on cell biological characteristics were identified, these data can be useful for evaluating gating algorithms in flow cytometry in general by confirming the outcome (e.g. MDS or AML diagnosis) with the respective proliferation and anti-apoptotic profile of these malignancies. The Ki-67 proliferation index and Bcl-2 anti-apoptotic index may potentially be used for classification of MDS and AML based on supervised machine learning algorithms, while unsupervised machine learning can be deployed at the level of single cells to potentially distinguish non-malignant from malignant cells to identify minimal residual disease. Therefore, the present dataset may be of interest for internist-hematologists, immunologists with affinity for hemato-oncology, clinical chemists with sub-specialization of hematology and researchers in the field of hemato-oncology.

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Barriers to home exercise for patients with Parkinson's disease – a qualitative study

Objective: This study aimed to explore the barriers to home exercise for patients with Parkinson's disease (PwPDs) and provide guidelines for healthcare providers (HcPs) to build and implement home exercise strategies for PwPDs. Design: A qualitative descriptive method was used. Semi-structured interviews were conducted and thematic analysis was employed. Setting: The study was conducted in the Department of Neurology at a Grade 3 Class A general hospital in China. Participants: A total of 22 participants were interviewed, including 10 PwPDs, seven caregivers, two nurses, one head nurse, and two Parkinson's clinicians. Results: Five themes were identified in this analysis. (1) Psychosomatic stress and low activity; (2) lack of early rehabilitation authorisation; (3) poor "flow" state of home exercise; (4) inaccessibility of continued service; (5) sociocultural impact on family coping. Conclusion: PwPDs, caregivers, and specialised medical staff raised the challenges faced by patients' home exercises from different perspectives. Interventions can improve services and integrate resources through the management of multi-disciplinary, early rehabilitation authorisation, exercise experience, continuous service mode, and family coping strategies under different cultures to gradually adjust the home exercise behaviour of PwPDs.

opencc-zeroJan 2023View details →

opencc-by-4.0Jan 2023View details →

Intra and Inter-Individual Variability in Functional Connectomes of Patients with First Episode of Psychosis

Test-retest functional connectomes for 32 Healthy Controls and 30 First Episode of Psychosis patients. This dataset was originally used in the following article: (Preprint) Tepper, Ángeles and Núñez, Javiera Vásquez and Ramirez-Mahaluf, Juan Pablo and Aguirre, Juan Manuel and Barbagelata, Daniella and Maldonado, Elisa and Dellarossa, Camila Díaz and Nachar, Ruben and Gonzalez-Valderrama, Alfonso and Undurraga, Juan and Goñi, Joaquín and Crossley, Nicolas, Intra and Inter-Individual Variability in Functional Connectomes of Patients with First Episode of Psychosis. Available at SSRN: <a href="https://ssrn.com/abstract=4241607">https://ssrn.com/abstract=4241607</a> or <a href="http://dx.doi.org/10.2139/ssrn.4241607">http://dx.doi.org/10.2139/ssrn.4241607</a> More details and python code used for analyses can be found in this <a href="https://github.com/angietep/Inter-and-Intra-Indiv-Variability">GitHub repository</a>

B-cell receptor data from intratumoural B cells in melanoma patients

This record contains data used in the Crescioli et al. analysis of B-cell response in melanoma, specifically analysis concerning high-throughput BCR repertoire. Files: "Visium_all_Aug22_comboDatBoth.txt": IMGT/HighV-Quest output of the high-throughput intratumoural BCR repertoire from n=5 melanoma tumours. In tab-separated text file format. "HV_EB_COV_MEL_comb_Oct22.RDS": A R data object (readable into R with "readRDS(...)") containing combined data from the melanoma (MEL) data with analogous high-throughput BCR repertoire data from healthy volunteers (HV), Ebola convalescent patients (EB) and hospitalised COVID-19 patients (COV). HV, EB and COV data are taken from <a href="https://dx.doi.org/10.5281/zenodo.5146019">https://dx.doi.org/10.5281/zenodo.5146019</a>. Here the sequences are filtered to contain only unique combinations of isotype and IMGT-numbered V-domain DNA sequence (to remove redundancies due to e.g. capturing BCR transcripts from plasma cells). "BM_Master_Light_Useasreftrue_140325_withPepStats_8.csv". IMGT/HighV-Quest output of the Bone Marrow light chain repertoire data. <a href="https://doi.org/10.3389/fimmu.2016.00388">Published in Townsend et al. Front Immunol 7:388 (2016)</a>. Used here for the comparison of gene conversion frequencies against the melanoma light chain repertoire. "BM_Master_Light_Useasreftrue_140325_withPepStats_8_Vgapped.fasta". The IMGT-gapped V-gene sequence from the Townsend et al. (see above) Bone Marrow light chain repertoire data. This is the raw input to BrepConvert. Provided here for this dataset; same sequences for the melanoma/healthy data are already in the RDS object ("HV_EB_COV_MEL_comb_Oct22.RDS"). "2_IMGT-gapped-nt-sequences_visa.txt", "2_IMGT-gapped-nt-sequences_visb.txt": Raw output of IMGT/HighV-Quest containing IMGT-gapped nucleotide sequences. These files were parsed to extract the IMGT-gapped V-gene sequence for BrepConvert analysis. "BrepConvert.zip": BrepConvert gene conversion analysis results for Healthy and Melanoma repertoires. See code in <a href="https://github.com/josef0731/melanoma-ig">https://github.com/josef0731/melanoma-ig</a> for ways to use these input files for reproducing the analyses.

Raw Data for the article: Brain magnetic resonance imaging radiomics features associated with hepatic encephalopathy in adult cirrhotic patients

Purpose: Hepatic encephalopathy (HE) is a potential complication of cirrhosis. Magnetic resonance imaging (MRI) may demonstrate hyperintense T1 signal in the globi pallidi. The purpose of this study was to evaluate the performance of MRI-based radiomic features for diagnosing and grading chronic HE in adult patients affected by cirrhosis. Methods: Adult patients with and without cirrhosis underwent brain MRI with identical imaging protocol on a 3T scanner. Patients without history of chronic liver disease were the control population. HE grading was based on underlying liver disease, severity of clinical manifestation, and number of encephalopathic episodes. Texture analysis was performed on axial T1-weighted images on bilateral lentiform nuclei at the level of the foramina of Monro. Diagnostic performance of texture analysis for the diagnosis and grading of HE was assessed by calculating the area under the receiver operating characteristics (AUROC) with 95% confidence interval (CI). Results: The final study population consisted of 124 patients, 70 cirrhotic patients, and 54 non-cirrhotic controls. Thirty-eight patients had history of HE with 22 having an HE grade > 1. The radiomic features predicted the presence of HE with an AUROC of 0.82 (95% CI: 0.73, 0.90; P < .0001; 82% sensitivity, 66% specificity). Radiomic features predicted grade 1 HE (AUROC 0.75; 95% CI: 0.61, 0.89; P < .0001; 94% sensitivity, 60% specificity) and grade ≥ 2 HE (AUROC 0.82; 95% CI: 0.71, 0.93; P < .0001, 95% sensitivity, 57% specificity). Conclusion: In cirrhotic patients, MR radiomic is effective in predicting the presence of chronic HE and in grading its severity.

Raw Data for the article: Mortality after transjugular intrahepatic portosystemic shunt in older adult patients with cirrhosis: A validated prediction model

Background and aims: Implantation of a transjugular intrahepatic portosystemic shunt (TIPS) improves survival in patients with cirrhosis with refractory ascites and portal hypertensive bleeding. However, the indication for TIPS in older adult patients (greater than or equal to 70 years) is debated, and a specific prediction model developed in this particular setting is lacking. The aim of this study was to develop and validate a multivariable model for an accurate prediction of mortality in older adults. Approach and results: We prospectively enrolled 411 consecutive patients observed at four referral centers with de novo TIPS implantation for refractory ascites or secondary prophylaxis of variceal bleeding (derivation cohort) and an external cohort of 415 patients with similar indications for TIPS (validation cohort). Older adult patients in the two cohorts were 99 and 76, respectively. A cause-specific Cox competing risks model was used to predict liver-related mortality, with orthotopic liver transplant and death for extrahepatic causes as competing events. Age, alcoholic etiology, creatinine levels, and international normalized ratio in the overall cohort, and creatinine and sodium levels in older adults were independent risk factors for liver-related death by multivariable analysis. Conclusions: After TIPS implantation, mortality is increased by aging, but TIPS placement should not be precluded in patients older than 70 years. In older adults, creatinine and sodium levels are useful predictors for decision making. Further efforts to update the prediction model with larger sample size are warranted.

Raw Data for the article: COVID-19 safety measures at the Radiology Unit of a Transplant Institute: the non-COVID-19 patient's confidence with safety procedures

Purpose: To support the wellbeing of both patients and their families, our aim was to investigate the satisfaction of non-COVID in- and out-patients regarding safety measures implemented at our radiology unit of a transplant institute against COVID infection. Materials and methods: Over a five-month period, adult patients' feedback was obtained by a questionnaire on the fear of contracting COVID-19 during a radiology examination, the perceived delay in treatment, and the following safety measures implemented: modified schedules to limit the number of patients in the waiting area and to maximize social distancing; assistance by staff when visitors were not admitted; cleaning and disinfection of machines; mask wearing and hand hygiene of staff; and staff advice on hand hygiene and infection control precautions. Results: Over a five-month period, our preliminary results (387 patients) showed general patient satisfaction (99.1%) with safety measures applied at our radiology unit. Patients were satisfied with distancing and assistance by staff (100%), cleaning and disinfection (91%), mask wearing and hand hygiene of the staff (97%), and staff advice (94%). There was some criticism of the perceived delay in treatment (7.3%) and in the scheduling of the waiting list (5.4%), with 5.4% fearing contracting the virus. Patients' awareness of safety measures and confidence in the hospital preparedness policy was perceived by all interviewers, and 100% appreciated being questioned. Conclusion: The feedback given by the non-COVID patient helps to measure the quality in health care, to improve the quality service, and to protect and satisfy more vulnerable patients, also during the COVID-19 pandemic.

Adoptive Immune Transfer from Donors Offers Anti-HBV Protection to HBsAb Negative Patients After Allo-HSCT

Original data of the manuscript of "Adoptive Immune Transfer from Donors Offers Anti-HBV Protection to HBsAb Negative Patients After Allo-HSCT " which published in iScience.

Raw Data for the article: How important is the role of iterative liver direct surgery in patients with hepatocellular carcinoma for a transplant center located in an area with a low rate of deceased donation?

Introduction: Hepatocellular carcinoma (HCC) accounts for nearly 90% of primary liver cancers, with estimates of over 1 million people affected by 2025. We aimed to explore the impacting role of an iterative surgical treatment approach in a cohort of HCC patients within the Milan criteria, associated with clinical risk factors for tumor recurrence (RHCC) after liver transplant (LT) and loco-regional therapies (LRT), as well as liver resection (LR) and/or microwave thermal ablation (MWTA). Methods: We retrospectively analyzed our experience performed during an 8-year period between January 2013 and December 2021 in patients treated for HCC, focusing on describing the impact on preoperative end-stage liver disease severity, oncologic staging, tumor characteristics, and surgical treatments. The Cox model was used to evaluate variables that could predict relapse risks. Relapse risk curves were calculated according to the Kaplan-Meier method, and the log-rank test was used to compare them. Results: There were 557 HCC patients treated with a first-line approach of LR and/or LRTs (n = 335) or LT (n = 222). The median age at initial transplantation was 59 versus 68 for those whose first surgical approach was LR and/or LRT. In univariate analysis with the Cox model, nodule size was the single predictor of recurrence of HCC in the posttreatment setting (HR: 1.61, 95% CI: 1.05-2.47, p = 0.030). For the LRT group, we have enlightened the following clinical characteristics as significantly associated with RHCC: hepatitis B virus infection (which has a protective role with HR: 0.34, 95% CI: 0.13-0.94, p = 0.038), number of HCC nodules (HR: 1.54, 95% CI: 1.22-1.94, p < 0.001), size of the largest nodule (HR: 1.06, 95% CI: 1.01-1.12, p = 0.023), serum bilirubin (HR: 1.57, 95% CI: 1.03-2.40, p = 0.038), and international normalized ratio (HR: 16.40, 95% CI: 2.30-118.0, p = 0.006). Among the overall 111 patients with RHCC in the LRT group, 33 were iteratively treated with further curative treatment (12 were treated with LR, two with MWTA, three with a combined LR-MWTA treatment, and 16 underwent LT). Only one of 18 recurrent patients previously treated with LT underwent LR. For these RHCC patients, multivariable analysis showed the protective roles of LT for primary RHCC after IDLS (HR: 0.06, 95% CI: 0.01-0.36, p = 0.002), of the time relapsed between the first and second IDLS treatments (HR: 0.97, 95% CI: 0.94-0.99, p = 0.044), and the impact of previous minimally invasive treatment (HR: 0.28, 95% CI: 0.08-1.00, p = 0.051). Conclusion: The coexistence of RHCC with underlying cirrhosis increases the complexity of assessing the net health benefit of ILDS before LT. Minimally invasive surgical therapies and time to HCC relapse should be considered an outcome in randomized clinical trials because they have a relevant impact on tumor-free survival.

DATASET RELATED TO ARTICLE "MISSENSE MUTATION IN ATXN2 GENE (C.2860C > T) IN AN AMYOTROPHIC LATERAL SCLEROSIS PATIENT WITH AGGRESSIVE DISEASE PHENOTYPE"

NGS_analysis PERFORMED AT fONDAZIONE BESTA AND CARRIED OUT AS PART OF THE STUDY MENTIONED AT TITLE

Transcriptome profiling of human monocytes from accute phase and convalescent patients infected with Plasmodium vivax malaria

RNA sequencing raw data of monocytes obtained from five patients in acute phase of Plasmodium vivax malaria and 45 days after treatment. Individuals from Rondônia (Brazil) were between 18 and 60 years and attended to the exclusion criteria: chronic inflammatory or infectious diseases, pregnancy, and breastfeeding. Diagnostic of malaria by clinical symptoms and thick blood smear was also confirmed by qPCR. According to the recommended protocol of the Brazilian Ministry of Health patients were treated with chloroquine associated to primaquine. Protocols used were approved by the Ethical Committees on Human Experimentation from Instituto Rene ́ Rachou, Fiocruz, and National Ethical Council (CAAE: 59902816.7.0000.5091).            Sequencing was performed in a  NextSeq 500 system using the NextSeq 500/550 High Output Kit v2.5 for 75 cycles (both from Illumina). Before sequencing total mRNA samples were prepared using TruSeq Stranded mRNA Kit (Illumina) according to the manufacturer’s protocol. Files are in FASTQ format, just as they were downloaded from Illumina's cloud environment (BaseSpace) right after sequencing. Files are identified by patient number (1 to 5) and health condition: acute phase of the disease or convalescent (45 days after treatment).

DATASET RELATED TO ARTICLE "Muscle quantitative MRI in adult SMA patients on nusinersen treatment_ a longitudinal study"

Excel file with raw data of muscle fat fraction before and after nusinersen treatment

Investigation of the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients in Jordan

As the world continues to battle the COVID-19 pandemic, Jordan is no exception. In order to improve the accuracy of diagnosis, researchers in Jordan have conducted an investigation into the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients.