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41 results for “Collaborative Cross”
Coastal SEES Collaborative Research: Coastal Sustainability: A cross-site comparison of salt marsh persistence in response to sea-level rise and feedbacks from social adaptations
Coastal ecosystems are often valued for decision-making purposes based on monetized market and non-market values of goods and services, and associated economic impacts. Examples include values of fishery landings, price changes for waterfront homes, and tourism revenues. Monetized quantities such as these do not provide a comprehensive characterization of the values provided by these ecosystems. Human reliance on the goods and services provided by ecosystems and the global decline in the health of many of these ecosystems suggests the need for ecosystem valuation to help inform decision-making and conservation policy. However, traditionally employed economic valuation methods are rarely able to capture the full scope of the benefits ecosystems provide, including benefits provided by "cultural" ecosystem services. Qualitative methods such as focus groups can provide insight on these values not available through quantitative methods alone. This research explores public perceptions of salt marsh value through the use of semi-structured focus groups in marsh-adjacent communities in Massachusetts, Virginia, and Georgia. The data include de-identified focus group transcripts from three 90-minute focus groups held in each state. Initial questions were drawn from the same semi-structured question list in each focus group, with exploratory follow-up questions based on participant responses. Results of text analysis suggest that in case study communities, outdoor experiences in salt marshes inspire serenity in Massachusetts, influence shore identities in Virginia, and promote stewardship cultivation in Georgia. Perceived threats to these benefits, such as the threat of residential development, industrial pollution, and increasing flood risk, together constitute the context for various community responses related to marsh protection. Results supplement information from extant economic valuations and show the importance of utilizing diverse methods to elicit information on soci
Inbred Strain Variant Database (ISVdb): A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders
<p>Data files for the development of a database for storing (and a GUI for retrieving) the imputed variants for 72 Collaborative Cross strains of mice. Files include the inputs for the imputation, as well as the final results. See File_S1_Readme for more details on the included files.</p>
Collaborating to Implement Cross-System Interventions in Child Welfare and Substance Use
ClinicalTrials.gov study NCT03931005. IPD Sharing: NO. Countries: 1. Publications: 2.
Cross-sectoral Collaboration in Multidisciplinary Treatment of Trauma-affected Refugees
ClinicalTrials.gov study NCT04244864. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Identification of candidate risk factor genes for human idelalisib toxicity using a collaborative cross approach
Idelalisib is a phosphatidylinositol 3-kinase inhibitor highly selective for the delta isoform that has shown good efficacy in treating chronic lymphocytic leukemia and follicular lymphoma. In clinical trials, however, idelalisib was associated with rare, but potentially serious liver and lung toxicities. In this study, we used the Collaborative Cross (CC) mouse population to identify genetic factors associated with the drug response that may inform risk management strategies for idelalisib in humans. Eight (8) male mice (4 matched pairs) from 50 CC lines were treated once daily for 14 days by oral gavage with either vehicle or idelalisib at a dose selected to achieve clinically-relevant peak plasma concentrations (150 mg/kg/day). The drug was well tolerated across all CC lines, and there were no observations of overt liver injury. Differences across CC lines were seen in drug concentration in plasma samples collected at the approximate Tmax on study Days 1, 7, and 14. There were also small but statistically significant treatment-induced alterations in plasma total bile acids and microRNA-122, and these may indicate early hepatocellular stress required for immune-mediated hepatotoxicity in humans. Idelalisib treatment further induced significant elevations in the total cell count of terminal bronchoalveolar lavage fluid, which may be analogous to pneumonitis observed in the clinic. Genetic mapping identified loci associated with interim plasma idelalisib concentration and the other three treatment-related endpoints. Thirteen (13) priority candidate quantitative trait genes identified in CC mice may now guide interrogation of risk factors for adverse drug responses associated with idelalisib in humans.
Data from: Candidate risk factors and mechanisms for tolvaptan-induced liver injury are identified using a collaborative cross approach
Clinical trials of tolvaptan showed it to be a promising candidate for the treatment of Autosomal Dominant Polycystic Kidney Disease (ADPKD) but also revealed potential for idiosyncratic drug-induced liver injury (DILI) in this patient population. To identify risk factors and mechanisms underlying tolvaptan DILI, 8 mice in each of 45 strains of the genetically diverse Collaborative Cross (CC) mouse population were treated with a single oral dose of either tolvaptan or vehicle. Significant elevations in plasma alanine aminotransferase (ALT) were observed in tolvaptan-treated animals in 3 of the 45 strains. Genetic mapping coupled with transcriptomic analysis in the liver was used to identify several candidate susceptibility genes including epoxide hydrolase 2, interferon regulatory factor 3, and mitochondrial fission factor. Gene pathway analysis revealed that oxidative stress and immune response pathways were activated in response to tolvaptan treatment across all strains, but genes involved in regulation of bile acid homeostasis were most associated with tolvaptan-induced elevations in ALT. Secretory leukocyte peptidase inhibitor (Slpi) mRNA was also induced in the susceptible strains and was associated with increased plasma levels of Slpi protein, suggesting a potential serum marker for DILI susceptibility. In summary, tolvaptan induced signs of oxidative stress, mitochondrial dysfunction, and innate immune response in all strains, but variation in bile acid homeostasis was most associated with susceptibility to the liver response. This CC study has indicated potential mechanisms underlying tolvaptan DILI and biomarkers of susceptibility that may be useful in managing the risk of DILI in ADPKD patients.
Data from: Human-relevant mechanisms and risk factors for TAK-875-induced liver injury identified via a gene pathway-based approach in collaborative cross mice
<p>Development of TAK-875 was discontinued when a small number of serious drug-induced liver injury (DILI) cases were observed in Phase 3 clinical trials. Subsequent studies have identified hepatocellular oxidative stress, mitochondrial dysfunction, altered bile acid homeostasis, and immune response as mechanisms of TAK-875 DILI and the contribution of genetic risk factors in oxidative response and mitochondrial pathways to the toxicity susceptibility observed in patients. We tested the hypothesis that a novel preclinical approach based on gene pathway analysis in the livers of Collaborative Cross mice could be used to identify human-relevant mechanisms of toxicity and genetic risk factors at the level of the hepatocyte as reported in a human genome-wide association study. Eight (8) male mice (4 matched pairs) from each of 45 Collaborative Cross lines were treated with a single oral (gavage) dose of either vehicle or 600 mg/kg TAK-875. As expected, liver injury was not detected histologically and few changes in plasma biomarkers of hepatotoxicity were observed. However, gene expression profiling in the liver identified hundreds of transcripts responsive to TAK-875 treatment across all strains reflecting alterations in immune response and bile acid homeostasis and the interaction of treatment and strain reflecting oxidative stress and mitochondrial dysfunction. Fold-change expression values were then used to develop pathway-based phenotypes for genetic mapping which identified candidate risk factor genes for TAK-875 toxicity susceptibility at the level of the hepatocyte. Taken together, these findings support our hypothesis that a gene pathway-based approach using Collaborative Cross mice could inform sensitive strains, human-relevant mechanisms of toxicity, and genetic risk factors for TAK-875 DILI. This novel preclinical approach may be helpful in understanding, predicting, and ultimately preventing clinical DILI for other drugs.</p>
A Cross-specialty Collaboration Platform for Mucopolysaccharidosis Confirmative Diagnosis
ClinicalTrials.gov study NCT03017677. IPD Sharing: NO. Countries: 0. Publications: 5.
Data from: Human-relevant mechanisms and risk factors for TAK-875-induced liver injury identified via a gene pathway-based approach in collaborative cross mice
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Data from: Candidate risk factors and mechanisms for tolvaptan-induced liver injury are identified using a collaborative cross approach
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Data from: Genetic structure of phenotypic robustness in the Collaborative Cross mouse diallel panel
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Data from: Identification of candidate risk factor genes for human idelalisib toxicity using a collaborative cross approach
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Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala
GEO Series GSE288772. Mus musculus. 200 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic Profiling of Collaborative Cross Founder Mouse Embryonic Fibroblasts stimulated with Type I, II and III Interferons
GEO Series GSE53057. Mus musculus. 71 samples. Type: Expression profiling by array.
Hepatic transcriptional profiles reveals the role of diet and genetic variation on cardiometabolic traits in progenitor strains of the Collaborative Cross mouse
GEO Series GSE159992. Mus musculus. 48 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic profiling of non-alcoholic fatty liver induced by a high-fat and high-sucrose diet in the genetically diverse Collaborative Cross mice.
GEO Series GSE149863. Mus musculus. 120 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic Profiling of Primary Osteoblast from a panel of Collaborative Cross mice
GEO Series GSE134081. Mus musculus. 96 samples. Type: Expression profiling by high throughput sequencing.
Dissecting the Effect of Genetic Variation on the Hepatic Expression of Drug Disposition Genes across the Collaborative Cross Mouse Strains
GEO Series GSE77715. Mus musculus. 55 samples. Type: Expression profiling by high throughput sequencing.
Identifying protective host signatures to West Nile Virus infection in the collaborative cross [spleen]
GEO Series GSE86000. Mus musculus. 95 samples. Type: Expression profiling by array; Other.
Genome Wide Identification of SARS-CoV Susceptibility Loci Using the Collaborative Cross
GEO Series GSE64660. Mus musculus. 21 samples. Type: Expression profiling by array.
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.