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126,115 results for “Patients”
Surface electromyography data set of knee osteoarthritis patients undergoing hydrotherapy and physiotherapy rehabilitation routines
<p>Osteoarthritis is one of the most prevalent degenerative diseases in the elderly that affects the structural and functional integrity of the musculoskeletal system. Currently, hydrotherapy is taking relevance for osteoarthritis treatment due to its possible efficacy on pain relief and functionality. This therapy can be evaluated by means of an electromyographic analysis. The objective is to show a database of lower limbs muscles electrical activity in charge of postural stability, comparing the difference between hydrotherapy and conventional therapy through surface electromyography. A signal acquisition methodology was developed measuring electromyographic activity of the Tibialis Anterior, Soleus, Vastus Medialis, Biceps Femoris, Medial Gastrocnemius and Lateral Gastrocnemius muscles, before and after applying a specific exercise routine for knee osteoarthritis. This routine consisted of 12 therapy sessions spread over 4 weeks and could be done in water and on land. </p> <p>The data is organized according to the attendance of 28 patients to the therapy sessions. There are two records per person, before and after each hydrotherapy or physiotherapy session, obtaining a total of 1344 records at the end of the 12 sessions, and 56 data for each session. However, a total of 864 complete records were obtained for both therapies, withdrawing those who missed any of the sessions. There is a personal information database in .CSV format and electromyographic records with a .MAT extension.</p>
Patient Representatives' Perspective on Informed Consent: Nominal Group Data
<p>For Task 1.6 of the i-CONSENT project, a one day workshop was organised with nine attendees from eight European patient groups. During the workshop, Nominal Group Technique (NGT) was used to explore issues that were considered pertinent within each of the four themes (comprehension, patient expectations, gender and assent), and to reach a consensus in terms of their significance. During this exercise, the workshop facilitator presented a short introduction to the theme, before each participant was given sticky notes and instructed to write down as many individual issues as possible using a separate sticky note for each idea. There was no limit to the number of ideas the participants could generate. This stage was conducted in silence and repeated for each of the four themes. The attached documents include the list of all the ideas collected on sticky notes notes during this stage and the ranking of the items done by the participants.</p>
Significance of the relationship between BIRC5 and the expression of other genes in AML patients
<p>BIRC5 expression levels were examined in relationship to the expression of other genes in the MILE dataset.</p>
SASC: A Simple Approach to Synthetic Cohorts. Applying COVID-19 clinical data to generate longitudinal observational patient cohorts and comparison with alternative synthetic cohort approaches as well as real patient data
<p>Subset from COVID-19 Dataset from https://zenodo.org/record/3766350#.YVcfyTFBxgA. Used as reference for a publication dealing with synthetic patient cohort generation.</p>
Modelling Cyclic Stretch of Patient-Derived Alveolar Epithelial Cells from Organoids using a New Alveoli-on-Chip Platform
<p><span>The data originates from lung tumor samples obtained at the University Hospital Bern. Patient-derived alveolar epithelial type 2 cells (AEC2) were isolated and cultured into organoids. Grown organoids where dissociated and seeded onto a novel alveoli-on-chip system submerged in medium. After 24 h of either no mechanical stimulus (control) or cyclic breathing stretch (stretch), RNA was isolated and sequenced. The RNA-seq data underwent quality control, alignment to the reference genome, read counting, DGE and GSEA. All analyses were run in R version 4.2.1.</span></p>
The impact of cefuroxime prophylaxis on human intestinal microbiota in surgical oncological patients - Dataset (FASTQ FILES)
<p>Dataset containing FASTQ files of the sequenced samples, generated by the Illumina MiSeq platform. </p> <p><span>This data is freely available under a CC-BY license; if you use it in your work, please cite our paper, "The impact of cefuroxime prophylaxis on human intestinal microbiota in surgical oncological patients" (DOI 10.3389/frmbi.2022.1092771).</span></p>
Patient-Centric Reddit Cancer Dataset
<p>The Patient-Centric Reddit Cancer Dataset (PCRCD) consists of all posts from r/Cancer during the period 01/01/2014 and 04/30/2020. A total of 23,028 unique posts were extracted. These posts were labelled according to three patient demographic traits: patient versus caregiver, sex and age. Each post was independently labelled by three annotators. PCRCD can help with the understanding of the challenges and concerns being reported by the patients and caregivers dealing with cancer. It also exemplifies the potential and limitations associated with the translation of raw posts from online health forums into a common resource for researchers.</p>
Raman spectra of urine from patients with diabetes mellitus and other pathologies
<p>This dataset contains raw (<strong>unprocessed Raman spectra</strong>) of urine from de-identified human patients. Analysis of this dataset is included in our journal article, "<em><strong>Analysis of urine Raman spectra differences from patients with diabetes mellitus and other pathologies</strong></em>." The dataset includes urine Raman spectra from (1) healthy volunteers, (2) patients with chronic kidney disease and diabetes mellitus, (3) patients with chronic kidney disease and without diabetes mellitus, (4) patients with biopsy-confirmed diabetic nephropathy, (5) patients with biopsy-confirmed immune-mediated nephropathy, (5) patients with biopsy-confirmed membranous nephropathy, (6) patients with biopsy-confirmed renal neoplasm, (7) patients with other glomerular pathologies, and (8) Surine (urinalysis control).</p> <p>Raman spectra were obtained with the following parameters:</p> <ul> <li>Raman spectrometer: Agiltron PeakSeeker PRO-785</li> <li>Mode: Bulk liquid scanning</li> <li>Wavelength: 785 nm</li> <li>Wavenumber range: 200-2000 cm-1</li> <li>Laser power: 30 mW</li> <li>Spectral resolution: 8 cm-1</li> <li>Laser spot size: 0.2 mm</li> <li>Excitation time: 30 s</li> </ul> <p>Raman spectral data and de-identified metadata are present in tab-separated value (tsv) files. Each urine sample is bar-code identified and linked to a disease state (or control) in the metadata tsv file. Ten (10) independent Raman scan replicates exist for each urine sample and are identified by bar-code in the spectral data tsv file. The study IRB approval and a sample blank patient consent form are also included here.</p>
SUDMEX_CONN: The Mexican dataset of cocaine use disorder patients.
<p>The SUDMEX_CONN is a Mexican open dataset of CUD patients and matched healthy controls that includes demographic, cognitive, clinical and magnetic resonance imaging (MRI) data.</p> <p>The study was done at the National Institute of Psychiatry in Mexico City</p> <p>The MRI sequences are available at https://openneuro.org/datasets/ds003346/versions/1.1.1</p> <p>If you require more information about data or scales, please contact us. </p> <p><em>LANIREM (</em><em>National MRI Laboratory)</em><em>, Institute of Neurobiology, </em></p> <p><em>Universidad Nacional Autónoma de México (UNAM), </em><em>Querétaro, México.</em></p> <p><strong>Diego Angeles Valdez, M. Sc. </strong></p> <ul> <li>diego.ang.val@gmail.com</li> <li>diego.ang.val@inb.unam.mx</li> </ul> <p><br> <strong>Eduardo A. Garza-Villarreal, M.D., Ph.D.</strong></p> <ul> <li>egarza@gmail.com</li> <li>egarza@comunidad.unam.mx</li> </ul> <p> </p> <p><strong>Updates</strong></p> <p>October 11-12, 2022</p> <p>The MINI PLUS was coded to reflect all the possible answers we had for questions about substance use as columns. For example, if the patient said to use more than 1 hallucinogen, we would mark the first one in Mini.L1.d1, then d2 is the second hallucinogen, then d3 is the third one.</p> <p>We updated the databases of the variables Addiction Severity Index (ASI), Barratt's Impulsivity Scale version 11 (BIS-11). and Clinical Global Impressions (CGI) Scale.</p> <p> </p> <pre> </pre>
Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
<p>Spatial transcriptomic data (counts.csv) derived using the Nanostring GeoMx digital spatial profiler platform to analyse matched colonic primary and liver metastases from 4 patients with metastatic colorectal cancer. 48 AOIs of cancer transcriptome atlas data. Normalised using Q3 normalisation. In addition, normalised data (Counts - ncounter.csv) from ncounter bulk experiment comparing matched colonic primary and liver metastases</p>
Underestimation of Body Size in Patients with Obesity
<p>The database includes real and estimated measures (in centimeters) of shoulders, waist, and hips widths and circumferences of 22 female inpatients with obesity and 21 healthy-weight women. The database includes also their age and years of education, and a measure of estimation accuracy (Delta), that is the difference between the real and estimated size of each body part.</p>
dataset relate to article "Quality of life assessment in adult spinal muscular atrophy patients treated with nusinersen"
<p>Excel file with raw data of the INQoL scale scores for each domain, for each patient, before and after nusinersen treatment</p>
dATASET RELATED TO ARTICLE "Complement Activation Profile in Myasthenia Gravis Patients: Perspectives for Tailoring Anti-Complement Therapy"
<p><strong>raw data derived by quantification of complement components and activation products in plasma samples of myasthenia gravis (MG) patients positive for anti-achr and anti-musk autoantibodies and healthy controls, using multiplex immunoassays and elisa</strong></p>
dataset related to article: "PMCA-Based Detection of Prions in the Olfactory Mucosa of Patients With Sporadic Creutzfeldt-Jakob Disease"
<ol> <li>ESTIMATING PRION CONCENTRATION IN THE OM OF SCJD MM1, MV2 AND VV2 PATIENTS BY MEANS OF QUANTITATIVE PMCA (QPMCA)</li> <li>EVALUATION OF THE BIOCHEMICAL PROPERTIES OF PMCA GENERATED PRODUCTS</li> <li>PMCA ANALYSIS OF SCJD BRAIN HOMOGENATES</li> <li>PMCA ANALYSIS OF SCJD OLFACTORY MUCOSA</li> <li>RT-QuIC ANALYSIS OF OM AND BH OF SCJD PATIENTS AND CONTROLS</li> <li>WESTERN BLOT ANALYSIS OF BRAIN HOMOGENATES</li> <li>STATISTICAL ANALYSIS</li> </ol>
The effect of Vitamin D levels on the course of COVID-19 in hospitalized patients – a 1-year prospective cohort study
<p>Background: The aim of the current study was to assess the patients with COVID-19 and the impact of vitamin D supplementation on the course of COVID-19.<br> Methods: This prospective cohort study included patients hospitalized due to COVID-19 between December 2020 and December 2021. Patients' demographic, clinical, and laboratory parameters were analysed. <br> Results: 301 participants were enrolled in the study. 46 (15,3%) had moderate, and 162 (53,8%) had severe COVID-19. 14 (4,7%) patients died, and 30 (10,0%) were admitted to the ICU due to disease worsening. The majority needed oxygen therapy (n=224; 74,4%). Average vitamin 25(OH)D3 levels were below optimal at the admittance, and vitamin D deficiency was detected in 205 individuals. More male patients were suffering from vitamin D deficiency. Patients with the more severe disease showed lower levels of vitamin 25(OH)D3 in their blood. The most severe group of patients had more symptoms that lasted significantly longer with progressing disease severity. This group of patients also suffered from more deaths, ICU admissions, and treatments with dexamethasone, remdesivir, and oxygen.<br> Conclusion: Patients with the severe course of COVID-19 were shown to have increased inflammatory parameters, increased mortality, and higher incidence of vitamin D deficiency. The results suggest that the vitamin D deficiency might represent a significant risk factor for a severe course of COVID-19.</p> <p> </p>
Patient-specific induced pluripotent stem cell properties implicate Ca2+-homeostasis in clinical arrhythmia associated with combined heterozygous RYR2 and SCN10A variants
<p class="MsoNormal"><span>We illustrate the use of induced pluripotent stem cells (iPSCs) as platforms for investigating cardiomyocyte phenotypes in a human family pedigree exemplified by novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants occurring alone and in combination. The proband, a four-month-old boy, presented with </span><span>polymorphic</span><span> ventricular tachycardia (</span><span>P</span><span>VT). Genetic tests revealed double novel heterozygous RYR2-A1855D and SCN10A-Q1362H variants inherited from his father (F) and mother (M) respectively. His father showed ventricular premature beats (VPB); his mother was asymptomatic. Molecular biological characterisations demonstrated greater <em>TNNT2</em> mRNA expression in the iPSCs-induced cardiomyocytes (iPS-CMs) than in the iPSCs</span><span>.</span><span> </span><span>c</span><span>TNTs became progressively organised, but cytoplasmic RYR2 and SCN10A aggregations occurred in the iPS-CMs. Proband-specific iPS-CMs showed decreased <em>RYR2</em> and <em>SCN10A</em> mRNA expression. The RYR2-A1855D variant resulted in premature spontaneous sarcoplasmic reticular (SR) Ca<sup>2+</sup> transients (PCTs), Ca<sup>2+</sup> oscillations (COs), and increased action potential durations (APDs). SCN10A-Q1362H did not confer any specific phenotype. However, the </span><span>combined </span><span>heterozygous RYR2-A1855D and SCN10A-Q1362H variants in the proband iPS-CMs resulted in accentuated Ca<sup>2+</sup> homeostasis disorders, AP prolongation and susceptibility to early afterdepolarisations (EADs) at high stimulus frequencies. These findings attribute the clinical phenotype in the proband to effects of the heterozygous <em>RYR2</em> variant exacerbated by heterozygous <em>SCN10A</em> modification. </span></p>
Raw Counts: A protocol for low-input RNA-sequencing of patients with febrile neutropenia captures relevant immunological information
<p>Raw counts for scientific article: </p> <p><em>"A protocol for low-input RNA-sequencing of patients with febrile neutropenia captures relevant immunological information"</em></p> <p>Victoria Probst*<sup>1</sup>, Lotte Møller Smedegaard*<sup>2</sup>, Arman Simonyan<sup>1</sup>, Yuliu Guo<sup>1</sup>, Olga Østrup<sup>1</sup>, Kia Hee Schultz Dungu<sup>2</sup><sub>, </sub>Nadja Hawwa Vissing<sup>2</sup><sub>, </sub>Ulrikka Nygaard<sup>2</sup><sub> </sub>and<sub> </sub>Frederik Otzen Bagger<sup>1</sup></p> <p><sup>*Shared first authorship</sup></p> <p>Data description: </p> <p>The raw counts are from 88 samples of 22 patients with leukaemia and suspected infection sequenced by a low-input protocol (Takara SMART-seq HT) (96% succeeded) and 15 of these were also processed by the standard protocol (Truseq).</p> <p> </p> <p><sup>CLI.CSV: Raw counts of control samples processed using a low input RNA sequencing protocol. 15 samples processed by the low-input protocol. </sup></p> <p><sup>CRNA.CSV: Raw counts of control samples processed using a standard RNA sequencing protocol. 15 samples processed by the standard protocol. </sup></p> <p><sup>FEB.CSV: Raw gene counts from patients. 88 samples processed by the low input protocol. 4 samples failed sequencing.</sup></p> <p> </p> <p> </p> <p> </p>
Polygenic risk scores validated in patient-derived cells stratify for mitochondrial subtypes of Parkinson's disease
<p><strong>Background</strong> Parkinson’s disease (PD) is the fastest growing neurodegenerative disorder, with affected individuals expected to double during the next 20 years. This raises the urgent need to better understand the genetic architecture and downstream cellular alterations underlying PD pathogenesis, in order to identify more focused therapeutic targets. While only ∼10% of PD cases can be clearly attributed to monogenic causes, there is mounting evidence that additional genetic factors could play a role in idiopathic PD (iPD). In particular, common variants with low to moderate effect size in multiple genes regulating key neuroprotective activities may act as risk factors for PD. In light of the well-established involvement of mitochondrial dysfunction in PD, we hypothesized that a fraction of iPD cases may harbour a pathogenic combination of common variants in nuclear-encoded mitochondrial genes, ultimately resulting in neurodegeneration.</p> <p><strong>Methods</strong> to capture this mitochondria-related “missing heritability”, we leveraged on existing data from previous genome-wide association studies (GWAS) – i.e., the large PD GWAS from Nalls and colleagues. We then used computational approaches based on mitochondria-specific polygenic risk scores (mitoPRSs) for imputing the genotype data obtained from different iPD case-control datasets worldwide, including the Luxembourg Parkinson’s Study (412 iPD patients and 576 healthy controls) and the COURAGE-PD cohorts (7270 iPD cases and 6819 healthy controls).</p> <p><strong>Results</strong> applying this approach to gene sets controlling mitochondrial pathways potentially relevant for neurodegeneration in PD, we demonstrated that common variants in genes regulating <em>Oxidative Phosphorylation (OXPHOS</em>-PRS<em>)</em> were significantly associated with a higher PD risk both in the Luxembourg Parkinson’s Study (odds ratio, OR=1.31[1.14-1.50], <em>p</em>=5.4e-04) and in COURAGE-PD (OR=1.23[1.18-1.27], <em>p</em>=1.5e-29). Functional analyses in primary skin fibroblasts and in the corresponding induced pluripotent stem cells-derived neuronal progenitor cells from Luxembourg Parkinson’s Study iPD patients stratified according to the <em>OXPHOS</em>-PRS, revealed significant differences in mitochondrial respiration between high and low risk groups (<em>p</em> < 0.05). Finally, we also demonstrated that iPD patients with high <em>OXPHOS</em>-PRS have a significantly earlier age at disease onset compared to low-risk patients.</p> <p><strong>Conclusions</strong> our findings suggest that OXPHOS-PRS may represent a promising strategy to stratify iPD patients into pathogenic subgroups – in which the underlying neurodegeneration is due to a genetically defined mitochondrial burden – potentially eligible for future, more tailored mitochondrially targeted treatments.</p>
Processed data and scripts supporting the manuscript "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma"
<p>This submission contains the compiled count table, processed R objects and various scripts and output files accompanying our manuscript "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma" (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-38886-8)</p>
Processed Vectra images for primary central nervous system lymphoma (PCNSL) patients
<ul> <li>FFPE materials</li> </ul> <p>Formalin-fixed paraffin-embedded (FFPE) tumor samples and clinical data were obtained from PCNSL patients enrolled in the HOVON105/ALLG NHL 24 intergroup, multicenter, open-label, randomized phase 3 study (NTR2437 and ACTRN12610000908033) through the HOVON Pathology Facility and Biobank. </p> <ul> <li>Muiltiplex imaging</li> </ul> <p>Multiplex immunofluorescence was performed on 4-µm-thick formalin-fixed, paraffin-embedded whole tissue sections using the Opal 7-color fluorescence immunohistochemistry (IHC) kit (Akoya biosciences, USA), as previously described. In brief, slides were deparaffinized and rehydrated, followed by a blocking step for endogenous peroxidase using 0.3% H<sub>2</sub>O<sub>2</sub>/methanol and fixation with 10% neutral buffered formalin (Leica Biosystems, Germany). Slides were washed in Milli-Q water and 0.05% Tween20 in 1x Tris-Buffered Saline (TBS-T). Antigen retrieval was done by placing the slides in 0.05% ProClin300/Tris–EDTA buffer pH 9.0 in a microwave at 100% power until boiling, followed by 15 min at 30% power. Slides were cooled in Milli-Q water, washed in 1x TBS-T and blocked with Antibody Diluent (Agilent, USA). The slides were then incubated with primary antibody diluted in Normal Antibody Diluent, followed by incubation with the broad spectrum HRP from the SuperPicture Polymer Detection Kit (Life Technologies, USA). Next, the slides were incubated with Opal TSA fluorochromes diluted in an amplification buffer (Akoya biosciences, USA). The primary and secondary antibody complex was stripped by microwave treatment with 0.05% ProClin300/Tris–EDTA buffer at pH 9.0. Finally, DAPI working solution (Akoya biosciences, USA) was applied and the slides were mounted with Prolong Diamond Anti-fade mounting medium (#P36965; Life Technologies).</p> <ul> <li>Image processing</li> </ul> <p>Stained slides were scanned using the Vectra Polaris Automated Quantitative Pathology Imaging System (Akoya biosciences, USA). From each slide, representative tumor regions and regions at the junction of tumor and surrounding cerebral tissue were selected and multispectral imaging (MSI) images were acquired at 40x resolution. After image capture, the images were spectrally unmixed and analyzed, using supervised machine learning algorithms within Inform 4.2.2. (Akoya biosciences). Cells were assigned into ten different phenotype categories: “PAX5+PD-L1-”, “PAX5+PD-L1+”, “CD163+PD-L1-”, “CD163+PD-L1+”, “CD3+CD8-PD-1-”, “CD3+CD8+PD-1-”, “CD3+CD8-PD-1+”, “CD3+CD8+PD-1+”, “other PD-L1+” or “other”, based on the size of the cells and positivity of markers in the panel. </p> <p> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.