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Stability and change in male fertility patterns by cognitive ability across 32 birth cohorts
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Data from: Variations in regional white matter volumetry and microstructure during the post-adolescence period: a cross-sectional study of a cohort of 1,713 university students
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Data from: Single-cell peripheral immunoprofiling of Lewy body and Parkinson’s disease in a multi-site cohort
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Heel and cord blood datasets for Bangladesh and Zambia cohorts
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Data from: The MRi-Share database: Brain imaging in a cross-sectional cohort of 1,870 university students
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Effects of Tamoxifen on the Reproductive System of Females with Breast Cancer – an Ultrasound-based Cohort study
<p>This data represent an ultrasound-based cohort study conducted in three oncology centers. The studied groups included a total of ‎‎255 patients, 140 premenopausal (PreM) and 115 postmenopausal (PostM) female patients with ER-positive BC using TMX adjuvant hormonal treatment in ‎a dose of 20 mg/day for at least three months after surgery and adjuvant ‎chemo/radiotherapy.‎ The study conducted at the three main oncology centers in Baghdad. The collected data includes: age of the patient, menopausal status, co-morbid chronic illness such as hypertension, diabetes mellitus, etc, and used medications.an ultrasound-based cohort study conducted in three oncology centers. The studied groups included a total of ‎‎255 patients, 140 premenopausal (PreM) and 115 postmenopausal (PostM) female patients with ER-positive BC using TMX adjuvant hormonal treatment in ‎a dose of 20 mg/day for at least three months after surgery and adjuvant ‎chemo/radiotherapy.‎ The study conducted at the three main oncology centers in Baghdad. The collected data includes: age of the patient, menopausal status, co-morbid chronic illness such as hypertension, diabetes mellitus, etc, and used medications.</p>
Dataset for airway managed by emergency physicians or anaesthesiologists in trauma patients: A retrospective cohort analysis of outcomes
<p>This data is generated for a registry-based unmatched cohort study. We identified trauma patients requiring intubation during resuscitation in the emergency department of Queen Elizabeth Hospital, Hong Kong. Then extracted relevant trauma related parameters and outcome data from the trauma registry of the hospital and patients’ health records.<br> The hospital trauma registry captures any patients who met trauma resuscitation team activation criteria, who were triaged as critical or emergency in the ED, who died (excluding death prior to arrival to ED) and were admitted to intensive care units (ICU)/high dependency units (HDU). Injury and outcome data were prospectively collected and entered into the registry.</p>
Maternal and cohort effects modulate offspring responses to multiple stressors
Current concerns about climate change has led to intensive research attempting to understand how climate driven stressors affect the performance of organisms, in particular on offspring of many invertebrate and fish. Although stressors are likely to act on several stages of the life cycle, little is known about their action across life phases, for instance how multiple stressors experienced simultaneously in the maternal environment can modulate the responses to the same stressors operating in the offspring environment. Here, we study how performance of offspring of a marine invertebrate (shore crab Carcinus maenas) in response to two stressors (temperature and salinity) changes if the same stressors are experienced at the time of embryogenesis in cohorts of mothers breeding eggs at different seasons. On average, offspring responses were antagonistic: high temperature mitigated the negative effects of low salinity on survival. However, the magnitude of the response was modulated by the temperature and salinity conditions experienced by egg-carrying mothers. Performance also varied among cohorts, suggesting a role for genetic variation, and/or maternal conditions prior to fertilisation. We speculate that similar maternal effects may occur in other brooding organisms, as a consequence of anthropogenic modification of the environment.
Outcomes and adverse events of pre- and extensively drug-resistant tuberculosis patients in Kinshasa, Democratique Republic of the Congo: retrospective cohort study
<p><strong>Abstract</strong></p> <p><strong>Background</strong>: Extensively drug-resistant tuberculosis (XDR TB) is a very serious form of tuberculosis that is burdened with a heavy mortality toll, especially before the advent of new TB drugs. The Democratic Republic of the Congo (DRC) is among the countries most affected by this new epidemic.</p> <p><strong>Methods:</strong> A retrospective analysis was performed of the records of all patients with pre- and extensively drug-resistant tuberculosis hospitalized from January 1, 2015 to December 31, 2017 and monitored for at least 6 months to one year after the end of their treatment in Kinshasa; an individualized therapeutic regimen with bedaquiline for 20 months was built for each patient. The adverse effects were systematically monitored.</p> <p><strong>Results:</strong> Of the 40 laboratory-confirmed patients, 32 (80%) patients started treatment, including 29 preXRB and 3 XDR TB patients. In the eligible group, 3 patients (9.4%) had HIV-TB coinfections. The therapeutic success rate was 53.2%, and the mortality rate was 46.8% (15/32); there were no relapses, failures or losses to follow-up. All coinfected HIV–TB patients died during treatment. The cumulative patient survival rate was 62.5% at 3 months, 53.1% at 6 months and 53.1% at 20 months. The most common adverse events were vomiting, Skin rash, anemia and peripheral neuropathy.</p> <p><strong>Conclusion: </strong>Bedaquiline based treatment improves patient survival in the DRC despite the still high mortality rate. The new anti-tuberculosis<br> drugs are a real hope for the management of Drug Resistant tuberculosis patient and other new therapeutic combinations may improve favorable outcomes.</p>
Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource
Objectives: To analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area. Setting: Retrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018. Participants: Including one eye per patient, 3357 eyes/patients (61% female). Extraction criteria were ≥ 1 ranibizumab or aflibercept injection, entry of "AMD" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database. Main outcome measures: Primary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain. Results: Mean VA gain at one-year and two years were +5.5 (95%CI:5.0,6.0) and +4.9 (95%CI:4.2,5.6) letters respectively. Fifty-four percent of eyes gained ≥5 letters at two years, 63% had stable VA (±≤14 letters), forty-four percent of eyes maintained good VA (≥70 letters). Patients received a mean of 7.7 (95%CI:7.6,7.8) injections during year one and 13.0 (95%CI:12.8,13.2) injections over two years. Younger age, lower baseline VA, and more injections were associated with higher VA gain at two years. Conclusion: This study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.
Code list used to generate cohorts in ICD-10 CCI US validation study
<p>Code list used to generate cohorts in validating the Charlson comorbidity index (CCI) for ICD-10 in the United States.</p>
A comparative assessment of the dentoskeletal effects of clear aligners versus miniplate-supported posterior intrusion with fixed appliances in adult anterior open bite patients. A multi-centre, retrospective cohort study.
<p>In this retrospective study, the aim was to evaluate the dentoskeletal effects of clear aligner treatment (Invisalign®) versus miniplate-supported posterior intrusion (MSPI) in adults with anterior open bite.</p>
Return to work following diagnosis of low-grade glioma: A nationwide matched cohort study
<p>Objective: Return-to-work (RTW) following diagnosis of infiltrative low-grade gliomas (LGG) is unknown. </p> <p>Methods: Swedish patients with histopathological verified WHO grade II diffuse glioma diagnosed between 2005-2015 were included. Data were acquired from several Swedish registries. A total of 381 patients aged 18-60 were eligible. A matched control population (n=1900) was acquired. Individual data on sick leave, compensations, comorbidity, and treatments assigned were assessed. Predictors were explored using multivariable logistic regression. </p> <p>Results: One year before surgery/index date, 88 % of cases were working compared to 91 % of controls. The proportion of controls working remained constant, while patients had a rapid increase in sick leave approximately six months prior to surgery. After one and two years respectively, 52 % and 63 % of the patients were working. Predictors for no-RTW after one year were previous sick leave (OR 0.92, 95 % CI 0.88-0.96, p <0.001), older age (OR 0.96, 95 % CI 0.94-0.99, p=0.005) and lower functional level (OR 0.64 95% CI, 0.45-0.91 p=0.01). Patients receiving adjuvant treatment were less likely to RTW within the first year. At two years, biopsy (as opposed to resection), female sex and co-morbidity were also unfavorable, while age and adjuvant treatment were no longer significant. </p> <p>Conclusions: Approximately half of the patients RTW within the first year. Lower functional status, previous sick leave, older age, and adjuvant treatment were risk factors for no-RTW at one year after surgery. Female sex, co-morbidity, and biopsy only were also unfavorable for RTW at two years.</p>
Genetic variants beyond amyloid and tau associated cognitive decline: a cohort study
<p>Objective: To identify single nucleotide polymorphisms (SNPs) associated with cognitive decline independent of amyloid &[beta] (A&[beta]) and tau pathology in Alzheimer's disease (AD). Methods: Discovery and replication datasets consisting of 414 subjects (94 cognitively normal control [CN), 185 with mild cognitive impairment [MCI], and 135 AD) and 72 subjects (22 CN, 39 MCI, and 11 AD), respectively, were obtained from the Alzheimer's Disease Neuroimaging Initiative database. Genome-wide association analysis was conducted to identify SNPs associated with individual cognitive function (measured using the MMSE and ADAS-cog) while controlling for the level of A&[beta] and tau (measured as CSF p-tau/A&[beta]1-42). Gene ontology analysis was performed on SNP associated genes.</p> <p>Results: We identified one significant (rs55906536, &[beta]=-1.91,standard error 0.34, P =4.07×10<sup>-8</sup>) and four suggestive variants on chromosome 6, which were associated with poorer cognitive function. Congruent results were found in the replication data. A structural equation model showed that the identified SNP deteriorated cognitive function partially through cortical thinning of the brain in a region-specific manner. Furthermore, a bioinformatics analysis showed that the identified SNPs were associated with genes related to glutathione metabolism.</p> <p>Conclusions: In this study, we identified SNPs related to cognitive decline, in a manner which could not be explained by A&[beta] and tau levels. Our findings provide insight into the complexity of AD pathogenesis and support the growing literature on the role of glutathione in AD. This study suggests anti-oxidative agents may serve therapeutic for AD subjects with the identified SNPs.</p>
USP8 and TP53 drivers are associated with CNV in a corticotroph adenoma cohort enriched for aggressive tumors
<p><b>Context:</b> Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropic hormone (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown.</p> <p><b>Objective</b><strong>:</strong> To investigate genomic drivers of corticotroph tumors at risk for aggressive behavior.</p> <p><b>Design:</b> Whole-exome sequencing of patient-matched corticotroph tumor and normal DNA from a patient cohort enriched for tumors at risk for aggressive behavior.</p> <p><b>Setting:</b> Tertiary care center.</p> <p><b>Patients:</b> 27 corticotroph tumors from 22 patients analyzed. 12 tumors were macroadenomas, of which 6 were silent ACTH tumors, 2 were Crooke's cell tumors, and 1 was a corticotroph carcinoma.</p> <p><b>Intervention:</b> Whole-exome sequencing.</p> <p><b>Main outcome measure:</b> Somatic mutation genomic biomarkers.</p> <p><b>Results:</b> We found recurrent somatic mutations in USP8 and TP53 genes, both with higher allelic fractions than other somatic mutations. These mutations were mutually exclusive, with TP53 mutations occurring only in USP8-wildtype (WT) tumors, indicating they may be independent driver genes. USP8-WT tumors were characterized by extensive somatic copy number variation compared to USP8-mutated tumors. Independent of molecular driver status, we found an association between invasiveness, macroadenomas, and aneuploidy.</p> <p><b>Conclusions: </b>Our data suggest that corticotroph tumors may be categorized into a USP8-mutated, genome-stable subtype versus a USP8-WT, genome-disrupted subtype, the latter of which has a TP53-mutated subtype with high level of chromosome instability. These findings could help identify high risk corticotroph tumors, namely those with widespread CNV, that may need closer monitoring and more aggressive treatment.</p>
Implementation and adherence of routine pertussis vaccination (DTP) in a low-resource urban birth cohort
<p><strong>Introduction</strong>: Reliable information on rates of up-to-date coverage and timely administration of routine childhood immunizations is critical for guiding public health efforts worldwide, yet prospective observation of vaccination programs within individual communities is rare. Here we provide a longitudinal analysis of the directly-observed administration of a 3-dose primary vaccination series to infants in a low-resource community in Lusaka, Zambia.</p> <p><strong>Methods</strong>: Throughout 2015, we recruited a longitudinal birth cohort of mother/infant pairs (initial enrollment, 1,981 pairs; attending, 1,497 pairs) from the peri-urban informal settlement of Chawama compound, located in Lusaka, Zambia. We prospectively monitored the administration of scheduled Diphtheria-Tetanus-Pertussis (DTP) vaccinations across the first 14-18 weeks of life. We analyzed study attendance and vaccine coverage, both overall and stratified by age group. We employed Kaplan-Meier analyses to estimate delays in age-appropriate administration of vaccine doses. We also assessed schedule timing violations, including early and compressed dose administration.</p> <p><strong>Results</strong>: At study completion, first dose (DTP1) rates were high (92.9% of attending), whereas third dose completion (DTP3) rates were far lower (61.9%). Missed vaccinations and study dropout both contributed to the low DTP3 completion rates. DTP1 was administered very late (at or after 10 weeks) to 61 infants (4.1%). DPT1 was administered too early to 64 infants (4.3%), and 77 (5.1%) received consecutive doses below the minimum recommended spacing of 28 days.</p> <p><strong>Conclusions</strong>: We observe substantial individual variation in the timing of early childhood DTP doses, though following this birth cohort proved challenging. Our results indicate that timely administration of both DTP1 and DPT3 remains a challenge in this community. These directly-observed, individual-based results provide an important counterpoint to more course-grained, survey-based national and province estimates of up-to-date vaccine coverage. This study also highlights the challenges of vaccine hesitancy and sub-optimal utilization of (no-cost) healthcare services in a low-resource urban setting.</p>
Data from: Association between total dose of ritodrine hydrochloride and pulmonary edema in twin pregnancy: a retrospective cohort study in Japan
Objective Pulmonary edema is recognized as a severe side effect of ritodrine hydrochloride. Recently, the number of twin pregnancies has been increasing. Few studies have reported the association between total dose of ritodrine hydrochloride prior to delivery and pulmonary edema in twin pregnancy. We aimed to examine this association and determine the optimal cutoff threshold of total ritodrine hydrochloride dose to predict the incidence of pulmonary edema in twin pregnancy, based on obstetric records. Design Retrospective cohort study. Setting Yamanashi Prefectural Central Hospital, Japan Participants Two hundred twenty-six women with twin pregnancy who delivered at Yamanashi Prefectural Central Hospital between September 2009 and November 2016 Methods The obstetric records of the participants were analyzed. We defined one unit of ritodrine hydrochloride as 72 mg per 24 h continuous transfusion at 50 µg/min to calculate the dose of ritodrine used for tocolysis. Outcome measures Multivariable logistic regression analysis was performed to examine the association between total dose of ritodrine hydrochloride used for threatened preterm labor and pulmonary edema, while controlling for potential confounding factors. Then, a receiver-operating characteristic curve was used to determine the optimal cutoff of total ritodrine dose to predict pulmonary edema incidence. Results Mean maternal age was 32 (range, 18-46) years; 143 participants were nulliparous (63.3%), 109 had (48.2%) term deliveries, and 194 (85.8%) had cesarean deliveries. The overall incidence of pulmonary edema was 13.7% (31/226). Multivariable analysis showed that the total dose of ritodrine was significantly associated with pulmonary edema (adjusted odds ratio 1.02; 95% confidence interval, 1.004-1.03). The best cut-off point to predict the incidence of pulmonary edema was 26 units (1872 mg) (sensitivity, 61.3%; specificity, 87.8%). Conclusion Our results suggest that consideration of the total dose of ritodrine hydrochloride is helpful in the management of patients with threatened preterm labor in twin pregnancy.
Employment status and sick-leave following obesity surgery: a five-year prospective cohort study
<p>This is a dataset (SPSS, sav. file) related to the study "Employment status and sick-leave following obesity surgery: a five-year prospective cohort study". If anyone wants the file in a different format, contact the uploader (see the link on the right side).</p>
Dataset STI screening German HIV-1 seroconverter cohort
<p>The Stata file contains the raw data of a project in the scope of the German HIV-1 seroconverter cohort, run by the Robert Koch Institute, Berlin, Germany. The data covers anonymous sociodemographic and clinical information of the patients as well as results of a serologocal screening on coinfection with hepatitis B, hepatitis C and syphilis.</p>
Early Onset TAAD cohort logR Ratio and B allele frequency data
<p>Recurrent Rare Genomic Copy Number Variants and Bicuspid Aortic Valve Are Enriched in Early Onset Thoracic Aortic Aneurysms and Dissections</p> <p>Abstract:</p> <p>Thoracic Aortic Aneurysms and Dissections (TAAD) are a major cause of death in the United States. The spectrum of TAAD ranges from genetic disorders, such as Marfan syndrome, to sporadic isolated disease of unknown cause. We hypothesized that genomic copy number variants (CNVs) contribute causally to early onset TAAD (ETAAD). We conducted a genome-wide SNP array analysis of ETAAD patients of European descent who were enrolled in the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC). Genotyping was performed on the Illumina Omni-Express platform, using PennCNV, Nexus and CNVPartition for CNV detection. ETAAD patients (n = 108, 100% European American, 28% female, average age 20 years, 55% with bicuspid aortic valves) were compared to 7013 dbGAP controls without a history of vascular disease using downsampled Omni 2.5 data. For comparison, 805 sporadic TAAD patients with late onset aortic disease (STAAD cohort) and 192 affected probands from families with at least two affected relatives (FTAAD cohort) from our institution were screened for additional CNVs at these loci with SNP arrays. We identified 47 recurrent CNV regions in the ETAAD, FTAAD and STAAD groups that were absent or extremely rare in controls. Nine rare CNVs that were either very large (>1 Mb) or shared by ETAAD and STAAD or FTAAD patients were also identified. Four rare CNVs involved genes that cause arterial aneurysms when mutated. The largest and most prevalent of the recurrent CNVs were at Xq28 (two duplications and two deletions) and 17q25.1 (three duplications). The percentage of individuals harboring rare CNVs was significantly greater in the ETAAD cohort (32%) than in the FTAAD (23%) or STAAD (17%) cohorts. We identified multiple loci affected by rare CNVs in one-third of ETAAD patients, confirming the genetic heterogeneity of TAAD. Alterations of candidate genes at these loci may contribute to the pathogenesis of TAAD.</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.