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126,115 results for “Patients”
Digitized patient level time to event data of overall survival
<p>This dataset contains digitized patient level time to event data for overall survival of patients with locally advanced and metastatic (stage IIIB/IV) Non-small cell lung cancer (NSCLC). The data can be used to recreate the original Kaplan-Meier survival curves that were published in randomized controlled trials, in order to perform secondary analysis on the survival data. In order to recreate a survival curve, you need two csv.files per trial arm that are in this <br> database: (1) starting with 'surv_', containing the individual patient level time to event data, and (2) starting with 'natrisk_', containing the corresponding numbers at risk table. For the methodology and r-code that can be used for this purpose we refer to article that is linked to this dataset. </p>
Identification of co-infections in a cohort of patients diagnosed with Lyme Disease
<p>Serlogy test data used in the study: Identification of co-infections in a cohort of patients diagnosed with Lyme Disease</p>
Synthetic Patient Appointment Dataset
<p>A synthetic dataset of patient appointments, referrals, and journeys to a fictional service in the North East of England. The code can be adjusted to incorporate any area on mainland Great Britain. NI or the islands can be integrated too, however the structure of postcode, GP and OSA public data is different, and data input handlers will need to be adjusted.</p> <p>The behaviour of the patients (visiting their nearby GP followed by attending a</p> <p>specialist clinic), appointments (clinic appointments within 7day-6weeks of the referral (gp appointment)), and facilities (one major facility taking the load, along with minor facilities) is meant to mirror the real data used under Pilot 2 of the Track & Know Project.</p> <p>Real postcodes, from Royal Mail, are used to generate the appointment population, real facilities are used based on the British Lung Foundations study of Obstructive Sleep Apnoea, and real GP's are used based on public data from the NHS.</p>
Experiment data in support of "Segmentation analysis and the recovery of queuing parameters via the Wasserstein distance: a study of administrative data for patients with chronic obstructive pulmonary disease"
<p>This archive contains a ZIP archive, `data.zip`, that itself contains the data used in the final sections of the paper. The remainder of the paper's supporting files are available at <a href="https://github.com/daffidwilde/copd-paper/">github.com/daffidwilde/copd-paper/</a></p> <p>The ZIP archive is structured as follows:</p> <ul> <li>There is a directory, `wasserstein`, for the parameter sweep described in the model construction section of the paper. Its contents are: (i) a file, `main.csv`, describing each parameter and their maximal Wasserstein distance to the observed data, and (ii) three directories, `best`, `median` and `worst`, each containing the simulated queuing results (in `main.csv`) from that sweep with the best, median and worst found parameter sets, respectively (in `params.txt`).</li> <li>The remaining three directories correspond to the experiments conducted in the final section of the paper. Each directory contains two files: (i) `system_times.csv` which holds trial parameters and system time records for every patient to pass through the model in that experiment, and (ii) `utilisations.csv` which holds trial parameters and utilisations for each server in the model for that experiment.</li> </ul>
Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study
<p>This is the dataset of the study called "Epidemiology, risk factors and clinical course of SARS-CoV-2 infected patients in a Swiss university hospital: an observational retrospective study". <br> <br> <strong>Abstract: </strong></p> <p>Background<br> Coronavirus disease 2019 (COVID-19) is now a global pandemic with Europe and the USA at its epicenter. Little is known about risk factors for progression to severe disease in Europe. This study aims to describe the epidemiology of COVID-19 patients in a Swiss university hospital.</p> <p>Methods<br> This retrospective observational study included all adult patients hospitalized with a laboratory confirmed SARS-CoV-2 infection from March 1 to March 25, 2020. We extracted data from electronic health records. The primary outcome was the need to mechanical ventilation at day 14. We used multivariate logistic regression to identify risk factors for mechanical ventilation. Follow-up was of at least 14 days. <br> <br> Results<br> 200 patients were included, of whom 37 (18·5%) needed mechanical ventilation at 14 days. The median time from symptoms onset to mechanical ventilation was 9·5 days (IQR 7.00, 12.75). Multivariable regression showed increased odds of mechanical ventilation in males (3.26, 1.21-9.8; p=0.025), in patients who presented with a qSOFA score ≥2 (6.02, 2.09-18.82; p=0.001), with bilateral infiltrate (5.75, 1.91-21.06; p=0.004) or with a CRP of 40 mg/l or greater (4.73, 1.51-18.58; p=0.013). <br> <br> Conclusions<br> This study gives some insight in the epidemiology and clinical course of patients admitted in a European tertiary hospital with SARS-CoV-2 infection. Male sex, high qSOFA score, CRP of 40 mg/l or greater and a bilateral radiological infiltrate could help clinicians identify patients at high risk for mechanical ventilation.</p>
A Chinese female Morvan patient with LGI1 and CASPR2 antibodies: a case report
<p>Figure 1-2 of the case and the original photos under fluorescence microscope. Fig. 1 Cranial MRI of our patient. Fig. 2 The immunoreactivity of patient’s serum to CASPR2 and LGI1 proteins.</p>
MicroRNA Panel Predicts Lung Adenocarcinoma in Patients Presenting with Ground-Glass Nodules
<p>MicroRNA (miRNA) expression is correlated with tumor histology, differentiation, invasiveness and treatment outcome. We aimed to identify miRNAs whose differential expression might enable early diagnosis of lung adenocarcinoma in patients presenting with ground-glass nodules (GGNs). To identify potential miRNAs of interest, we analyzed the miRNA expression profile of tumor and adjacent non para-tumor tissue in 3 participants by next-generation sequencing (NGS). We then assessed the expression levels of the miRNAs of interest in 73 lung adenocarcinoma presenting with GGNs with matched adjacent non-tumor tissue by quantitative real-time polymerase chain reaction (qRT-PCR). Target genes of our selected miRNA panel were predicted using Miranda with default parameters. Twenty-three miRNAs showed differential expression between tumor and adjacent non-tumor tissue by NGS. Five miRNAs exhibited higher expression in tumor tissue compared to adjacent non-tumor tissue (P＜0.05), eighteen miRNAs demonstrated lower expression in tumor tissue versus adjacent non-tumor tissue (P＜0.05). When qRT-PCR was performed for the 23 miRNAs identified by NGS in the pilot stage, seven were found to have statistically significant expression in tumor versus adjacent non-tumor tissue (P＜0.05). The predicted targets of our miRNAs of interest are frequently associated with cancer signaling pathways. We developed a miRNA panel that could potential predict the presence of lung adenocarcinoma in patients presenting with GGNs. </p>
Raw BRCA1/2 variants in breast cancer patients and healthy relatives produced with GATK.
<p>Aligned sequencing data is available in the NCBI Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) under accession SRP095082. Variants were called using GATK HaplotypeCaller (version 3.6). After joint performing joint genotyping multi-sample vcf file was generated. Next, SNPs and indels were extracted into two different vcf files and specific set of filters were applied for each case.</p> <p> </p> <p><strong>File descriptions</strong></p> <p><strong><em>Datasets</em></strong></p> <p><strong>BRCA_SNVs.vcf</strong> - this file contains SNPs called with GATK and hard filters applied. Following filtering options were applied: "QD < 2.0", "FS > 60.0", "MQ < 40.0", "MQRankSum < -12.5", "ReadPosRankSum < -8.0", "SB < -0.10" , "DP < 10" , "GQ < 30" , and "SOR > 3.0"</p> <p><strong>BRCA_indels.vcf</strong> - This file contains indels called with GATK and hard filters applied. Following filtering options were applied: "QD < 2.0", "FS > 200.0", "ReadPosRankSum < -20.0", "InbreedingCoeff < -0.8", "SOR > 10.0".</p> <p> </p> <p><strong><em>Scripts package (scritps.zip)</em></strong></p> <p>Scripts.zip file contains scripts and supporting files for genotype calling and filtering. </p> <p><strong>raw.variant.caling.sh </strong>– bam files preprocessing, alignment refining and raw genotype calling with HaplotypeCaller.</p> <p><strong>genotyping_and_filtering.sh </strong>– joint genotyping, variant hard filtering and callset refinement.</p> <p><strong>LIST.txt</strong> – supporting file that contains bam filenames containing aligned reads.</p> <p><strong>sample_order.txt</strong> – supporting file for sample renaming.</p> <p> </p> <p><strong><em>Reference files (hg19) used in variant calling scripts</em></strong></p> <p>Reference files can be downloaded from GATK bundle web-site at https://software.broadinstitute.org/gatk/download/bundle. </p> <p><strong>ucsc.hg19.fasta</strong> - human genome assembly;</p> <p><strong>Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment;</p> <p><strong>1000G_phase1.indels.hg19.sites.vcf.gz</strong> – set of known indels to be used for local realignment;</p> <p><strong>dbsnp_138.hg19.vcf.gz</strong> – a recent dbSNP release (build 138); </p> <p><strong>1000G_phase3_v4_20130502.hg19.lifted.sites.vcf</strong> – the latest set from 1000G phase 3 (v4) for genotype refinement.</p> <p> </p>
Dataset of the scientific paper "A Comparative Analysis of 2D and 3D Tasks for Virtual Reality Therapies Based on Robotic-Assisted Neurorehabilitation for Post-stroke Patients" (Front. Aging Neurosci.)
<p> There are three files with the following information:<br> - data_2d.bin, binary file with information of the different parameters of the nine subjects during 2d tasks<br> - data_3d.bin, binary file with information of the different parameters of the nine subjects during 3d tasks<br> - survey.bin, binary file with the score of the System Usability Scale (SUS) survey of each subject</p>
Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)
<p>Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.</p> <p> </p> <p>This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.</p> <p> </p> <p><strong>Baylor Scott and White (BSW) cohort</strong>: <strong>10x.visium.tar.gz</strong>, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. </p> <p>Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. </p> <p> </p> <p>For <strong>Georgia validation cohort</strong>, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file <strong>georgia.validation.visium.tar.gz</strong>. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.</p> <p> </p> <p>As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. <strong>GSM_giotto_processed.tar.gz</strong> refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.</p>
A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling
<p>Collection of auxiliary data to reproduce the results from "<strong>A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling</strong>". Source code is available at: https://github.com/saezlab/reheat2_pub<br><br>We provide processed data to facilitate access to the results, for the original count data, please see the associated manuscript for references to the original datasets. </p> <p> </p> <p> </p>
Twenty four hour continuous tympanic temperature recordings in healthy volunteers and patients presented with Undifferentiated fever
<p>Twenty-four-hour continuous tympanic temperature recordings were obtained using high-accuracy tympanic probes placed at the auditory canal. Measurements were recorded at one-minute intervals over a 24-hour period, yielding 1,440 data points per subject and enabling high-resolution temporal profiling of body temperature.</p> <p>In Phase I, a total of 100 healthy adult volunteers were recruited to establish baseline circadian thermoregulatory patterns. These recordings were stratified by gender to examine physiological variability among individuals without fever.</p> <p>In Phase II, 184 adult patients presenting with undifferentiated fever of seven or more days’ duration were enrolled. Based on clinical examination and laboratory confirmation, the temperature profiles were analysed across a range of conditions, including tuberculosis, non-tubercular bacterial infections, dengue fever, malaria, leptospirosis, pyogenic sepsis, thyroiditis, malignancies, and non-infectious inflammatory diseases. This dual-phase dataset facilitated a comparative analysis between normative and pathological thermoregulatory patterns, supporting the development of classification models for diagnostic differentiation.</p>
Antimicrobial Stewardship & Patient Safety Improvements: Introducing the NIVAS Line Flushing Guidance
<p>Recent published literature highlights that as much as 35% [1] of medication may remain in the infusion line as residual volume. The line is not commonly flushed outside of paediatric and oncology settings and therefore the total prescribed dose is not administered to patients, and this residual medication is discarded, raising the issue of underdosing. [2]</p><p> </p><p>At Salisbury NHS Foundation Trust, the Medical Device Management Services team is actively working towards improving patient safety and recovery through antimicrobial stewardship and compliance with new NIVAS guidelines [3]. We were keen to understand the implications of current intravenous administration practice at our Trust. We were particularly interested in assessing the prevalence and extent to which patients are underdosed, and the cost implications of discarded medication.</p>
Single-cell mouse and PC9 data for "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability"
<p>This repository includes the processed data (including copy number profiles and related analysis) for the E/EP mouse tumors and for the PC9 resistance cell lines for all the analyses of the manuscript "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability".</p><p>The code for the related analyses is available in GitHub at https://github.com/zaccaria-lab/TP53loss_WGD</p>
A statistical shape model of craniosynostosis patients and 100 model instances of each pathology
<p>This dataset is part of the publication "A statistical shape model for radiation-free assessment and classification of craniosynostosis" (M. Schaufelberger et al.). It includes several 3D head models constructed of surface scans of craniosynostosis patients: The full shape model, a texture model, and submodels of four classes: sagittal suture fusion (scaphocephaly), metopic suture fusion (trigonocephaly), coronal suture fusion (brachycephaly and anterior plagiocephaly), and a control model (normocephaly and positional plagiocephaly). Each of the models is available in an .h5 file. We also include 100 mesh instances as a .ply file in a zip file. The model's statistical information can be incorporated into the [Liverpool-York child head model (Dai et al. 2019)](https://doi.org/10.1007/s11263-019-01260-7) as it uses the same vertex order and IDs (starting from index 0). If you want to synthesize new models, take a look a the demo.py file. For information about the hierarchy in the h5-file, take a look at documentation.md.</p>
The supplemental data for the paper: "Methodology of generation of CFD meshes and 4D shape reconstruction of coronary arteries from patient-specific dynamic CT"
<p>The supplemental data for the paper: "Methodology of generation of CFD meshes and 4D shape reconstruction of coronary arteries from patient-specific dynamic CT"</p><p>A video file (minimum play resolution is HD to see the mesh) showing the movement of the LCA throughout the heart cycle and .STL files for 10--100% (increment of 10\%) of the heart cycle phase.</p>
Short tandem repeat expansions in LRP12 are absent in familial and sporadic amyotrophic lateral sclerosis patients of European ancestry
<p>In patients of Asian ancestry, a heterozygous CGG repeat expansion of >100 units in <i>LRP12</i> is the cause of oculopharyngodistal myopathy type 1 (OPDM1), and has been associated with amyotrophic lateral sclerosis (ALS) when repeat lengths are between 61-100 units, although with unusually long disease duration and without significant upper motor neuron involvement. This study investigated if <i>LRP12</i> CGG tandem repeats were expanded in ALS patients of European ancestry. We screened whole-genome sequencing data from 608 sporadic ALS patients, 35 familial ALS probands, and 4,703 neurologically normal controls for the <i>LRP12</i> CGG expansion using ExpansionHunter v4. All individuals had <i>LRP12 </i>CGG repeat lengths between 3-25 units. Our results suggest that <i>LRP12 </i>CGG repeat expansions may only be present in ALS patients of Asian ancestry with atypical clinical presentations.</p>
The Mexican dataset of an rTMS clinical trial on cocaine use disorder patients: SUDMEX TMS
<p>The SUDMEX_TMS dataset is the result of a longitudinal clinical trial of cocaine use disorder patients that were treated with rTMS at 5-Hz on the left dorsolateral prefrontal cortex (lDLPFC) for a 2 week double-blind acute phase and an open-label maintenance phase that included clinical, cognitive and MRI data acquisition. The design was a double-blind placebo-controlled randomized controlled trial with parallel groups (acute phase). The study was done at the National Institute of Psychiatry .</p> <p>Each patient had more than one clinical and MRI session or time point from baseline (T0), 2 weeks (T1), 3 months (T2), 6 months (T3) and some patients had 12 months (T4). The T14 time point was only for patients in the Sham group who decided to continue the clinical trial with open-label rTMS. The T14 refers to 2 weeks after T1 (4 weeks after T0).</p> <p>The MRI sequences were: 1) T1-weighted, 2) rsfMRI 10 min, 3) HARDI-DWI multishell (next release).</p> <p>The data set is curated and organized by test and item for each experimental phase and also has a dictionary to define the variables measured.</p> <p> </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>
Single-cell RNA-seq profiles of lung adenocarcinoma patients and tumor-bearing mice
<p>single-cell RNA sequencing (scRNA-seq) profiles from eight patients with lung adenocarcinoma (LUAD) and four samples of tumor tissues from tumor bearing mice were performed. By integrating other scRNA-seq data and clinical information, we identified activated adaptive immune responses in older patients, reflected by enriched dysfunctional T cell signature scores and immune checkpoint molecules. Our study shows increased efficacy of immune checkpoint blockade therapy in older patients, addressing the prominent role of age when considering immunotherapy.</p>
16S rRNA Sequencing Data of Fecal Microbiota in an Italian Cohort of Patients with CDKL5 Deficiency Disorder
<h3>Summary of the study </h3> <p>CDKL5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by global developmental delay, early-onset seizures, intellectual disability, visual and motor impairments, distinct from Rett Syndrome (RTT) due to the absence of a clear regression period. Gastrointestinal (GI) disturbances and signs of subclinical immune dysregulation are common in CDD patients, yet the underlying causes are unknown. Recent studies hint at a possible link between neurological disorders and gut microbiota, an unexplored area in CDD. In this groundbreaking study, we examined fecal microbiota in CDD patients and their healthy relatives, revealing differences in bacterial diversity and composition. We further investigated microbiota changes based on various factors, including the severity of GI issues, seizure frequency, sleep disorders, food intake type, neuro-behavioral features (assessed through the RTT Behaviour Questionnaire – RSBQ), and ambulation capacity. </p> <p>Our findings suggest a potential connection between CDD, microbiota, and symptom severity. This study represents the first exploration of the gut-microbiota-brain axis in CDD patients, contributing to the growing body of research on the role of gut microbiota in neurodevelopmental disorders. It opens doors to potential interventions targeting intestinal microbes to enhance the well-being of individuals with CDD.</p> <h3>Mehods</h3> <p>The Dataset represent the raw data (.fastq) obtained from the sequencing of the fecal samples from 17 Italian Patients with CDD, and 17 Healthy Relatives (i.e. siblings or mother), collected at a single time-point.</p> <p>Samples from Patients affected by CDD are called CDD, samples from Healthy Relatives are called HC-CDD (i.e. healthy controls of patients affected by CDD). For details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted from fecal samples using the QIAmp Powerfexal DNA Kit (Qiagen, Germany) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Germany).</p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). </p>
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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.