Find research datasets worth reusing

opencc-by-4.0Jul 2024View details →

Supplementary material for journal article "Challenge dose titration in a Mycobacterium bovis infection model in goats"

Supplementary Figure and Table to Journal article. Figure shows daily rectal temperature of each animal after inoculation. Table 1 shows number and volume of pulmonary lesions for each animal as detected by computed tomography imaging. Table 2 gives details about scoring used at clinical examination.

opencc-by-4.0Aug 2021View details →

Inflammatory Responses in the Placenta upon SARS-CoV-2 Infection Late in Pregnancy - IHC data

SARS-CoV-2 infection during pregnancy does not affect the large majority of neonates but presents an increased risk for adverse pregnancy outcome. The effects of SARS-CoV-2 of its recently identified variants on placental function are not well understood. In this study, we investigated the impact of late gestational SARS-CoV-2 infection on the placenta. This dataset of is comprised of 897 images of classic immunohistochemistry for 3 markers in placenta from COVID-19 patients and controls. A full description of the tissues, markers, and donors is available in the metadata.csv file.

opencc-by-4.0Aug 2021View details →

Data for: Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites

This dataset supports the findings presented in: Manzi, F., Halle, S., Seemann, L., Ben-Ami, F., & Wolinska, J. (2021). Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites. Parasitology, 1-42. doi:10.1017/S0031182021001384

opencc-zeroNov 2022View details →

Data for Few studies of wild animal performance account for parasite infections: a systematic review

Data from a systematic review across eight scientific journals publishing primarily studies in animal behaviour and physiology over a 5-year period to assess the proportion of studies which acknowledge, treat or control for parasite infection in their study design and/or analyses. Wild animals have parasites. This inconvenient truth has far-reaching implications for biologists measuring animal performance traits: infection with parasites can alter host behaviour and physiology in profound and sometimes counterintuitive ways. Yet, to what extent do studies on wild animals take individual infection status into account? We explored whether parasite inclusion differed between studies that are experimental versus observational, conducted in the field vs the laboratory and measure behavioural vs physiological traits. We also investigated the importance of other factors such as the journal, the year of publication, the trait category (e.g. locomotion, reproduction) measured, the vertebrate taxonomic group investigated, and the host climatic zone of origin. Our results show that parasite inclusion was generally lacking across recent studies on wild vertebrates. In over 680 filtered papers, we found that only 21.9% acknowledged the potential effects of infections on animal performance in the text, and only 5.1% of studies treated animals for infection (i.e. parasite control) or considered infection status in the statistical analyses (i.e. parasite analysis). Parasite inclusion, control and analysis were higher in laboratory compared to field studies and higher for physiological studies compared to behavioural studies but did not differ among journals, performance trait categories and taxonomic groups. Overall, our literature review suggests that parasites are sorely under-acknowledged by researchers in recent years despite growing evidence that infections can modify animal performance. Given the ubiquity of parasites in the environment, we encourage scientists to consider individual infection status when assessing performance of wild animals. We also suggest ways for researchers to implement such practices in both experimental and observational studies.

Mice infected with High shedder S. mansoni parasites from cross A - cage 1 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 2/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Mice infected with High shedder S. mansoni parasites from cross A - cage 2 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 3/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Health records

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.  ------------------------------------------------------------------------------------- This dataset contains GWAS summary statistics for infection, inflammation, and allergy related traits in 487,297 individuals

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Serology

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.  ------------------------------------------------------------------------------------- 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.

Mycobacteroides abscessus subp. bolletii strain associated with a persistent infection (genome assembly and annotation dataset)

This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) of a Mycobacteroides abscessus subp. bolletti strain associated with a persistente infection. (genome anotation was performed using Bakta v1.2.2 https://github.com/oschwengers/bakta) The raw sequence reads were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB57933; Run Accession: ERR10554471).

opencc-by-4.0Dec 2022View details →

Antagonism between viral infection and innate immunity at the single-cell level -- Immunostaining Imaging Dataset

This dataset accompanies the article "Antagonism between viral infection and innate immunity at the single-cell level", at the time of submission available as a <a href="https://doi.org/10.1101/2022.11.18.517110">preprint</a>.

Mice infected with High shedder S. mansoni parasites from cross B - cage 1 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 6/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Tagged Twitter timelines for users reporting SARS-CoV-2 infections and related data

Twitter data was collected through the Twitter API v2.0, specifically through the timeline endpoint. Details about the inference of SARS-CoV-2 self-reports and the tagging of the full timeline of each user can be found in the <a href="https://github.com/digitalepidemiologylab/content_changes_paper">GitHub repository</a>. The larger dataset ("preprocessed_data.csv") consists of a total of 8,534,171 tweets posted by 30,856 users from January 1, 2020 to October to September 30, 2021. The raw data from Twitter, including tweet and user IDs, has been removed or anonymized in order to comply with the EPFL guidelines for data sharing. In particular, the date of the tweets was removed, the text of the tweets, URLs and URL domains have been substituted with the "text", "<URL>" and "<URL_DOMAIN>" token respectively. User IDs have been substitued with new IDs in the [0, number of users] range (e.g. U0, U1, ...) . Tweet IDs have been substitued with new IDs in the [0, number of tweets] range (e.g. T0, T1, ...) . In addition to self-explanatory columns about topics, emotions, URL classification and symptoms we tagged, we also share the columns: <ul> <li>pdate: date of the SARS-CoV-2 infection self-report for that user (adjusted with SUTime)</li> <li>effective_date: date of the tweet adjusted with SUTime, when the SUTime columns is available.</li> <li>rel_effective_day(week, month): days (weeks, months) computed with respect to the positivity date (i.e. "pdate" column). Negative numbers refer to tweets posted before the user reported a COVID-19 infection on Twitter.</li> </ul>

Mice infected with Low shedder S. mansoni parasites from cross A - cage 2 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 5/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Mice infected with Low shedder S. mansoni parasites from cross A - cage 1 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 4/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.1 / 2C.2 / 2C.3).

The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.1/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.

Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.4 / 2C.5).

The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.2/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.

Mice infected with High shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 7/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Mice infected with Low shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 9/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.

Mice infected with Low shedder S. mansoni parasites from cross B - cage 1 - Liver histopathology data.

The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 8/11). Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.