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3,585 results for “Population study”
Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [CANE]
GEO Series GSE83225. Canis lupus familiaris. 4 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
scRNA-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wann
GEO Series GSE179707. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Plasma microRNA ratios associated with breast cancer detection: results from a nested case-control study in an Italian population-based mammography screening cohort
GEO Series GSE210329. Homo sapiens. 131 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Village In a Dish: A Model System for Population-scale hiPSC Studies [scRNA-Seq]
GEO Series GSE225278. Homo sapiens. 19 samples. Type: Expression profiling by high throughput sequencing.
Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [COO]
GEO Series GSE83151. Canis lupus familiaris. 51 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
A study of genetic variants associated with skin traits in the Vietnamese population
GEO Series GSE248483. Homo sapiens. 96 samples. Type: SNP genotyping by SNP array.
An eQTL study in the Japanese population [gene expression_1]
GEO Series GSE42227. Homo sapiens. 24 samples. Type: Expression profiling by array.
Genome wide DNA methylation profiling of United Kingdom Ovarian Cancer Population Study (UKOPS)
GEO Series GSE19711. Homo sapiens. 540 samples. Type: Methylation profiling by array.
CSF pQTL study in the Japanese population [genotyping Q35]
GEO Series GSE83709. Homo sapiens. 64 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
TCR-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wannab
GEO Series GSE179708. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
Village In a Dish: A Model System for Population-scale hiPSC Studies [Affymetrix]
GEO Series GSE224950. Homo sapiens. 20 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Data from: Genome-wide association study for tobiano spotting coat color in Korean Jeju × Thoroughbred horse population
Korean Jeju horse features a small to medium frame size and stature having varieties of coat colors including grey, milky, spotted and bay1. Crossbreeding with Thoroughbred has been a long tradition in Korea to have intermediate frame size horse suitable for racing, leisure activities and meat production2. Tobiano white-spotting pattern is preferred by many horse breeders and owners which is inherited as an autosomal dominant trait1,3. Polymorphisms in proto-oncogene receptor tyrosine kinase (KIT) gene were strongly associated with tobiano and sabino coat color pattern in American and European horse breeds3,5. In addition, ECA3 inversion locus near KIT gene also significantly associated with tobiano spotting pattern in horses4,5. Here, we report SNPs and harbored genes associated with tobiano coat color in a crossbred horse population through genome-wide SNP association analysis. In this study, coat color patterns of 142 crossbred horses (Jeju indigenous horse × Thoroughbred) were verified according to previously described methods3,5 and coded as "0" or "1" (Figure S1). Genomic DNA was extracted from blood samples using DNeasy 96 blood DNA extraction Kit (QIAGEN, USA). Genotyping was performed using Equine SNP 50K BeadChip (Illumina, San Diego, USA) at AGBD, NIAS, Korea. A total of 45,204 SNPs passed the set quality control criteria as minor allele frequency (MAF<0.01), missing genotype (GENO>0.10) and Hardy-Weinberg equilibrium (HWE<0.0001) in 142 individuals. Finally, a set of 16,223 independent SNPs were generated through –indep –pairwise 25 5 0.25 pruning6. Genome wide association study revealed 18 Bonferroni adjusted SNPs located on chromosome 3 (ECA3) significantly associated with tobiano coat color in the studied population (Figure 1, Table S1). These SNPs broadly plotted on 40 Mbp region (from 39 to 79 Mbp) of ECA3 which might be due to high LD among the significant SNPs. The most significant association was found between ECA3 inversion locus (77657979 bp) and tobiano pattern (P< 5.56×10-17) while the second highest association was detected with SNP rs68555258 (48853535 bp; P< 4.04×10-12, Table S1). Apart from this, genotypes of ECA3 inversion locus by pyrosequencing matched perfectly in our study (Table S2). All tobiano horses (n = 37) were heterozygous for inversion locus (+/To) while solid-colored horses (n = 103) were homozygous (+/+). ECA3 inversion is located 70 kbp downstream from KIT gene which possessed causal variants for tobiano pattern in horse5,6. The Biomart and Variant Effect Predictor tools in Ensembl Genome Browser (http://www.ensembl.org/index.html) identified several significant SNPs harboring genes of which GPRIN3, ARHGAP24, SCFD2, RASSL11B and WDFY3 are noticeable (Table S3). Based on our genome wide association and inversion locus genotyping results, it is suggested that ECA3 inversion locus variant is either causative or completely linked with causative variants for tobiano coat color in this crossbred horse population. Moreover, a set of putative mutations in other genes might be in high LD with causative variants that could be explored for functional annotations associated with tobiano coat color pattern in horse population.
Data from: Ectopic fat obesity presents the greatest risk for incident type 2 diabetes: a population-based longitudinal study
Objectives: Obesity is a risk factor for type 2 diabetes mellitus. Among obesity, visceral fat obesity, and ectopic fat obesity, it has been unclear which has the greatest effect on incident diabetes. Methods: In this historical cohort study of 8430 men and 7034 women, we investigated the effect of obesity phenotypes on incident diabetes. Obesity, visceral fat obesity, and ectopic fat obesity were defined as body mass index ≥25 kg/m2, waist circumference ≥90 cm in men or ≥80 cm in women, and having fatty liver diagnosed by abdominal ultrasonography, respectively. We divided the participants into eight groups according to the presence or absence of the three obesity phenotypes. Results: During the median 5.8 years follow-up for men and 5.1 years follow-up for women, 286 men and 87 women developed diabetes. Compared to the non-obese group, the hazard ratios (HRs) of incident diabetes in the only-obesity, only-visceral fat obesity, only-ectopic fat obesity groups, and with all-three types of obesity group were 1.85 (95%CI 1.06–3.26, p = 0.05) in men and 1.79 (0.24–13.21, p = 0.60) in women, 3.41 (2.51–4.64, p < 0.001) in men and 2.30 (0.87–6.05, p = 0.12) in women, 4.74 (1.91–11.70, p < 0.001) in men and 13.99 (7.23–27.09, p < 0.001) in women and 10.5 (8.02–13.8, p < 0.001) in men and 30.0 (18.0–50.0, p < 0.001) in women. Moreover, the risk of incident diabetes of the groups with ectopic fat obesity were almost higher than that of the four groups without ectopic fat obesity. Conclusion: Ectopic fat obesity presented the greatest risk of incident type 2 diabetes.
Data from: The majority of the pre-antiretroviral population who were lost to follow-up stopped their care in Freetown, Sierra Leone: a 12-month prospective cohort study starting with HIV diagnosis
Background: The heterogeneity of the pre-antiretroviral (pre-ART) population calls for more granular depictions of the cascade of HIV care. Methods: We studied a prospective cohort of persons newly diagnosed with HIV infection from a single center in Freetown, Sierra Leone, over a 12-month period and then traced those persons who were lost to follow-up (LTFU) during pre-ART care (before ART initiation). ART eligibility was based on a CD4 cell count result of < 350 mm/cells and/or WHO clinical stage 3 or 4. Persons who attended an appointment in the final three months were considered to be retained in care. Adherence to ART was measured using pharmacy refill dates. "Effective HIV care" was defined as completion of the cascade of care at 12-months regardless of whether patients are on ART. Tracing outcomes were obtained for those who were LTFU during pre-ART care. Results: 408 persons newly diagnosed with HIV infection were screened, 338 were enrolled, and 255 persons were staged for ART. ART-ineligible persons had higher retention rates than ART-eligible persons (59.6% vs 41.8%, p=0.03). 77 (22.8%) of 338 persons received effective HIV care. Most attrition (61.9%) occurred with persons during pre-ART care. 123 of 138 persons (89.1%) who were LTFU prior to ART initiation were found, and 91 of those 123 (74.0%) were alive. Of the 74 persons who were alive and described their engagement in care, 40 (54.1%) stopped care. Nearly half (42.5%) of those 40 stopped after assessment of ART-eligibility but before ART initiation. The main limitation of this study was the lack of tracing outcomes for those lost during ART care. Conclusions: The majority of the pre-ART LTFU population stopped their care, particularly after ART-eligibility but before ART initiation. Interventions to hasten ART initiation and retain this at-risk group may have significant downstream impact on effective HIV care.
A Multi-Centric Novel Coronavirus (COVID-19) Population-Based Age-Stratified Sero-Epidemiological Study (In Urban, Rural and Tribal Communities at Selected Centers in India: A Prospective Study)
<p>Results of population-based age stratified seroepidemiological investigation in India</p>
Large-Population based Deep Learning Models in Classifying Primary Bone Tumors and Bone Infections based on Radiographs: a Retrospective and Multi-reader Multi-center Study
<p>This retrospective multicenter study collected patients via consecutive sampling between 2013 and 2022 from two cohorts: training cohort (from the Second Xiangya Hospital of Central South University) and testing cohort (from Xiangya Hospital of Central South University and Hunan Children's Hospital of Central South University). These lesions were identified to have bone involvement through pre-operative radiographs and were histologically diagnosed following biopsy or surgery. <br>(i) For the inclusion criteria, lesions were confirmed and diagnosed as PBTs according to the 2020 World Health Organization (WHO) system for the classification for tumors of bone 1 while bone infections were confirmed and proven by histology and (or) bacterial culture. The other vital inclusion criteria are evident as well as available clinical information and pre-operative radiographs. <br>(ii) The screening criteria: (a) radiographs were from patients diagnosed between 2013 and 2022 (b) in selected three hospitals; (c) radiographs with robust quality for reliable assessments of the bone lesions and (d) all of these radiographs were pre-operative. <br>Clinical characteristics like age, gender, and the location of the lesion of interest and so on were obtained from the patients' electronic medical records after data desensitization and standardization.<br>Radiographs were kept and downloaded as Digital Imaging and Communications in Medicine (DICOM) files from the picture archiving and communication system (PACS) at their original sizes and resolutions. All of these radiograph images have undergone desensitization processing of disengaging patient protected health information from DICOM data to meet the relevant legal criteria and requirements of US (HIPAA) as well as European (GDPR). Delineating the region of interest (ROI) was performed by two proficient radiologists. ROIs were meticulously outlined via Click 2 Crop (version 5.2.2) (https://click-2-crop.en.softonic.com/) to closely segment pertinent entities present in each PBT or bone infection. The smallest rectangular box that can completely cover the ROI was manually annotated as the boundary box by senior seniority radiologist to ensure accuracy. Afterwards, the annotated ROIs were used as ground truth for the model development process.</p>
Data from: Identifying consistent allele frequency differences in studies of stratified populations
1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used ,which means that underlying assumptions about the data are frequently violated. 2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re-analyse a published dataset. 3. The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re-scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect. 4. Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs.
Figure 3 from: Kotze D, Brandmayr P, Casale A, Dauffy-Richard E, Dekoninck W, Koivula M, Lovei G, Mossakowski D, Noordijk J, Paarmann W, Pizzoloto R, Saska P, Schwerk A, Serrano J, Szyszko J, Taboada Palomares A, Turin H, Venn S, Vermeulen R, Zetto Brandmayr T (2011) Forty years of carabid beetle research in Europe – from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation. ZooKeys 100: 55-148. https://doi.org/10.3897/zookeys.100.1523
Figure 3 - Examples of pitfall trap placements across a forest edge.
Figure 4 from: Kotze D, Brandmayr P, Casale A, Dauffy-Richard E, Dekoninck W, Koivula M, Lovei G, Mossakowski D, Noordijk J, Paarmann W, Pizzoloto R, Saska P, Schwerk A, Serrano J, Szyszko J, Taboada Palomares A, Turin H, Venn S, Vermeulen R, Zetto Brandmayr T (2011) Forty years of carabid beetle research in Europe – from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation. ZooKeys 100: 55-148. https://doi.org/10.3897/zookeys.100.1523
Figure 4 - Cylindera germanica (Photo by Jinze Noordijk)
Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study [questionnaire]
<p>Assessment of general population knowledge, attitude, and practice on safe unused and expired drugs disposal: a cross-sectional study [questionnaire]</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.