Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
448
datasets available to search
ShareScore release 0.9.0
Dataset results
448 results for “Infection risk”
Public dataset for Antibiotic Prophylaxis for Surgical Site Infections as a Risk Factor for Infection with Clostridium difficile
<p>This is the minimal publicly available dataset for the manuscript titled "Antibiotic Prophylaxis for Surgical Site Infections as a Risk Factor for Infection with Clostridium difficile". We have also included the data dictionary. </p>
Data and code for 'Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk'
<p>This repository provides all data and R code from the analysis presented in the following paper:</p> <p>Turner, A., Heard, G., Hall, A., Wassens, S. (in review). Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk.</p> <p>The data are provided as a series of .csv files, R script and two zip folders of R packages (Surv_mod and VB_mod)</p> <p>1. <strong>Skeleto_dat_ready_Jan2021.csv</strong> Data from frog surveys conducted by Anna Turner</p> <p>2. <strong>Geoffs_data.csv</strong> Data from frog surveys conducted by Geoff Heard</p> <p>3. <strong>Environmental_variables_skeleto.csv</strong> Environmental data collected during surveys </p> <p>4. <strong>sk.dat_July21.csv</strong> Collated data from Anna and Geoff - created by 'Data_collation_for_analysis_2.R' ready for analysis</p> <p>5. <strong>Variables_that_are_highly_correlated_with_each_other_season_wide.csv</strong> Testing for correlation</p> <p>6. <strong>Model_structure_skeleto_2.csv </strong>creates model structure for analysis</p> <p>7. <strong>Model_selection_statistics_June_21.csv </strong>Output from model</p> <p>R code is provided seperately for each of the following components:</p> <p>1. <strong>Data_collation_for_analysis_2.R</strong> Collating data from Anna and Geoffs datasets</p> <p>2. <strong>Skeleto_analysis_5.R - </strong>First uses regression modelling to explore factors correlated with variation in age</p> <p> - Following Scheele et al. (2016) regression models with a poisson distribution</p> <p> - Use bayesian non-linear regression to fit the Von Bertalanffy growth model to size-at-age data</p> <p> - Plots male and female growth curves</p> <p> - Uses catch curve approach to estimate survival from best fitting regression model following Scroggie (2012) but with bayesian implementation</p>
Diet and SARS-Cov-2 Infection Risk: A Retrospective Observational Study
<p>Dataset, Analysis, Regression and Description.</p> <p>From mid-summer 2020 to January 2022, based on phase 2 to 3 of a self-reported questionnaire survey, we asked 15851 families across Iran about their diet and their COVID-19 disease. The results showed that some diets increased the risk of SARS-Cov-2 Apparent Infection Risk and some reduced it.</p> <p>The results show that the risk of reporting SARS-CoV-2 apparent infection in the second group was 12 times higher than the Third group. <strong>The two-tailed P value is less than 0.0001</strong>. Also, the risk of reporting SARS-CoV-2 apparent infection in the first group was 9 times higher than the Third group. <strong>The two-tailed P value is less than 0.0001</strong>. By conventional criteria, these differences are considered to be extremely statistically significant.</p>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Health records
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for infection, inflammation, and allergy related traits in 487,297 individuals</p>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Serology
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for quantitative antibody responses in 9611 individuals and results for a meta-analysis of UK Biobank and CoLaus/PsyCoLaus antibody responses.</p> <p> </p>
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 Double-Edged Sword: Parental care increases risk of offspring infection by a maternally-vectored parasite
<p>Parental care can protect offspring from predators but can also create opportunities for parents to vector parasites to their offspring. We hypothesized that the risk of infection by maternally-vectored parasites would increase with the frequency of mother-offspring contact. Ammophila spp. wasps (Hymenoptera: Sphecidae) build nests in which they rear single offspring. Ammophila species exhibit varied offspring provisioning behaviors: some species enter the nest once to provision a single, large caterpillar, whereas others enter the nest repeatedly to provision with many smaller caterpillars. We hypothesized that each nest visit increases the risk of offspring parasitism by Paraxenos lugubris (Strepsiptera: Xenidae), whose infectious stages ride on the mother wasp (phoresy) to reach the vulnerable Ammophila offspring. We quantified parasitism risk by external examination of museum-curated Ammophila specimens—the anterior portion of P. lugubris protrudes between the adult host's abdominal sclerites and reflects infection during the larval stage. As predicted, Ammophila species that receive larger numbers of provisions incur greater risks of parasitism, with nest provisioning behavior explaining ca. 90% of the interspecific variation in mean parasitism. These findings demonstrate that parental care can augment, rather than reduce, risk of parasite transmission to offspring.</p>
Timescale reverses the relationship between host density and infection risk
Host density shapes infection risk through two opposing phenomena. First, when infective stages are subdivided among multiple hosts, greater host densities decrease infection risk through "safety in numbers". Hosts, however, represent resources for parasites, and greater host availability also fuels parasite reproduction. Hence, host density increases infection risk through "density-dependent transmission". Theory proposes that these phenomena are not disparate outcomes but occur over different timescales. That is, higher host densities may reduce short-term infection risk, but because they support parasite reproduction, may increase long-term risk. We tested this theory in a zooplankton-disease system with laboratory experiments and field observations. Supporting theory, we found that negative density-risk relationships ('safety in numbers') sometimes emerged over short timescales, but these relationships reversed to 'density-dependent transmission' within two generations. By allowing parasite numerical responses to play out, time can shift the consequences of host density, from reduced immediate risk to amplified future risk.
High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling - Datasets
<p>Datasets and notebooks used in the publication High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling</p>
Fig. 1 in Anthropozoonotic significance, risk factors and spatial distribution of Giardia spp. infections in quenda (Isoodon obesulus) in the greater Perth region, Western Australia
Fig. 1. Geographical distribution of Giardia spp. infection in Perth quenda. Quenda were mapped using the GPS position of the location at which they were trapped. GPS points are jittered, and icons for uninfected quenda are 50% transparent, to improve visualisation of the relative distribution of Giardia spp. infection. By Kulldorff's spatial scan statistic, the circle in the north-west region represents a cluster of relatively decreased Giardia spp. infection risk in Perth quenda (OR of infection <0.001, compared to quenda trapped elsewhere in Perth; p <0.001).
Fig. 3 in Comparison of the modified agglutination test and real-time PCR for detection of Toxoplasma gondii exposure in feral cats from Phillip Island, Australia, and risk factors associated with infection
Fig. 3. Predicted lines of fit for the multivariable logistic regression model plotted as probability of Toxoplasma gondii qPCR positivity in feral cats on Phillip Island (Victoria) versus body weight for each season. Dashed lines show 95% confidence intervals.
Fig. 1 in Comparison of the modified agglutination test and real-time PCR for detection of Toxoplasma gondii exposure in feral cats from Phillip Island, Australia, and risk factors associated with infection
Fig. 1. Location and Toxoplasma gondii infection status, as detected by real-time PCR (qPCR), of feral cats trapped on Phillip Island (Victoria) from July 2016 to December 2017. Map shows the distribution of different location types (Park, Agricultural, Residential) used in multivariable regression analysis. A circular spread of points around a location marked with 'x' indicates multiple animals were sampled at the same site (i.e. same GPS coordinates). Red = T. gondii qPCR positive, white = T. gondii qPCR negative. Map created using Quantum GIS, version 3.8. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1 in Sero-prevalence and risk factors of Toxoplasma gondii infection in wild cervids in Denmark
Fig. 1. The geographical distribution of wild cervids included in the study and the number of animals tested positive for antibodies against Toxoplasma gondii in the hunting season 2017–2018 in Denmark (n = 428). Shown by region and proportion of species sampled (roe deer, fallow deer or red deer) in each region. Pie charts indicate proportion of samples from each cervid species. Note Sika deer was only sampled in Mid-Jutland (n = 14), and hence not included in the map. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Risk factors for treatment failure in women with uncomplicated lower urinary tract infection
<p><strong>Origin :</strong></p> <p>This dataset represent a sub-population of a previous clinical trial. </p> <blockquote> <p><a href="https://pubmed.ncbi.nlm.nih.gov/29710295/">Huttner A, Kowalczyk A, Harbarth S, et al.. Effect of 5-Day Nitrofurantoin vs Single-Dose Fosfomycin on Clinical Resolution of Uncomplicated Lower Urinary Tract Infection in Women: A Randomized Clinical Trial. JAMA. 2018;319(17):1781-1789. DOI: 10.1001/jama.2018.3627.</a></p> </blockquote> <p> </p> <p><strong>Databases : </strong></p> <ul> <li>1st database : women included in the nested cohort study (n=350)</li> <li>2nd database : women with microbiologically conformed UTI (n=279)</li> <li>3d database : women with <em>E.coli</em> related UTI (n=185)</li> </ul> <p><strong>Important : </strong></p> <ul> <li>Data from Tel Aviv have been removed from this dataset, and might be shared by the corresponding author upon reasonable request at the following address (romainmartischang@gmail.com).</li> </ul> <p><strong>Codebook : </strong></p> <ul> <li>v1_XXX; 0/1 : All symptoms present at baseline</li> <li>v1dipstick : Negative (0), nitrites (1), leukocytes esterase (2), both (3), not done (4)</li> <li>centre : recruitment centre (CHE or POL)</li> <li>rfscore : risk factor for carrying a resistant bacteria as defined in the initial trial</li> <li>treatment : nitrofurantoin (0) vs fosfomycin (1)</li> <li>dm : diabetes mellitus </li> <li>case2 : bacteriological failure at 28 days as defined in the initial trial</li> <li>case1 : clinical failure at 28 days as defined in the initial trial</li> <li>recur14 : bacteriological failure at 14 days as defined in the initial trial</li> <li>fail14 : clinical failure at 14 days as defined in the initial trial</li> <li>v1pathogen[1-3] : pathogen present at baseline</li> </ul>
Data and R code from: Haemosporidian infections influence risk-taking behaviours in young male blackcaps Sylvia atricapilla
<p>This repository contains all data and code necessary to reproduce the results and figures of the paper:</p> <p>Remacha, C., Ramírez, A., Arriero, E. and Pérez-Tris, J. 2023. Haemosporidian infections influence risk-taking behaviours in young male blackcaps <em>Sylvia atricapilla</em>. Animal Behaviour, 196, 113-126. <a href="https://doi.org/10.1016/j.anbehav.2022.12.001">https://doi.org/10.1016/j.anbehav.2022.12.001</a></p> <p>The repository contains a readme file (README_SYAT_MS_ANIBEH_Scripts.txt) with a description of the code and the data. The code is organised in eight R script files. Instructions to run the code are provided in the readme file. The data are organised in two separate files. One file (SYAT_MS_BH_ANIBEHdata.txt) contains data of exploratory and antipredatory behaviours of 43 young male blackcaps. The other one (SYAT_MS_BH_BIOL_ANIBEHdata.txt) contains biological and experimental attributes of the same individuals: status and intensity of parasite infection, experimental treatment, morphology and body mass.</p>
Study of a Candidate Clostridium Difficile Toxoid Vaccine in Subjects at Risk for C. Difficile Infection
ClinicalTrials.gov study NCT01887912. IPD Sharing: YES. Countries: 26. Publications: 1.
Data from: Crowding reduces per-capita parasite infection risk in a butterfly host
Open the record for dataset details and reuse information.
Timescale reverses the relationship between host density and infection risk
Open the record for dataset details and reuse information.
A Double-Edged Sword: Parental care increases risk of offspring infection by a maternally-vectored parasite
Open the record for dataset details and reuse information.
A specific IL6 polymorphic genotype modulates the risk of T. cruzi parasitemia while IL18, IL17A and IL1B variant profiles and HIV infection protect against cardiomyopathy in Chagas disease
<p><strong>Background:</strong> Chagas disease caused by Trypanosoma cruzi (T. cruzi) affects approximately six million individuals worldwide. Clinical manifestations are expected to occur due to the parasite persistence and host immune response. Herein we investigated potential associations between IL1B, IL6, IL17A or IL18 polymorphism profiles and cardiomyopathy or T. cruzi parasitemia, as well as the impact of HIV infection on cardiopathy.</p> <p><strong>Methods:</strong> 206 patients and 90 control individuals were analyzed. IL1B rs1143627 T>C, IL6 rs1800795 C>G, IL17A rs2275913 G>A, IL18 rs187238 C>G, and IL18 rs1946518 C>A SNVs were analyzed by real-time PCR and T. cruzi parasitemia by PCR.</p> <p><strong>Results: </strong>Our data revealed association between a cytokine gene polymorphism and parasitemia never previously reported. The IL6 rs1800795 CG genotype lowered the risk of positive parasitemia (OR=0.45, 95% CI 0.24–0.86, P=0.015). Original findings included associations between IL17A rs2275913 AA and IL18 s1946518 AA genotypes with decreased risk of developing cardiomyopathy (OR=0.27, 95% CI 0.07-0.97, P=0.044; and OR=0.35, 95% CI 0.14-0.87, P=0.023, respectively). IL18 rs1946518 AA and IL1B rs1143627 TC were associated with reduced risk for cardiomyopathy severity, including NYHA (New York Heart Association) class≥ 2 (OR=0.21, 95% CI 0.06-0.68, P=0.009; and OR=0.48, 95% CI 0.24-0.95, P=0.036, respectively) and LVEF (Left Ventricular Ejection Fraction) <45% for IL18 rs1946518 AA (OR=0.22, 95% CI 0.05-0.89, P=0.034). A novel, unexpected protective effect of HIV infection against development/progression of cardiomyopathy was identified, based on a lower risk of developing cardiopathy (OR=0.48, 95% CI 0.23‐0.96, P=0.039), NYHA class≥2 (OR=0.15, 95% CI 0.06‐0.39, P<0.001) and LVEF<45% (OR=0.03, 95% CI 0.00‐0.25, P=0.001). Digestive involvement was negatively associated with NYHA ≥2 and LVEF<45% (OR=0.20, 95% CI 0.09‐0.47, P<0.001; and OR=0.24, 95% CI 0.09-0.62, P=0.004, respectively).</p> <p><strong>Conclusions: </strong>Our data support a protective role of IL17A AA, IL18 AA and IL1B TC genotypes against development/progression of cardiomyopathy and a modulatory effect of the IL6 CG genotype on the risk of parasitemia in Chagas disease. Notably, HIV infection was shown to protect against development/progression of cardiopathy, potentially associated with a synergistic effect of HIV and HAART, attenuating a Th1-mediated response in the myocardium. This proposed hypothesis requires confirmation, however, in larger and more comprehensive future studies.</p>
ScienceDex guides
Understand access before you commit
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.