New Paper: Perivascular Localization of Macrophages in the Intestinal Mucosa is Regulated by Nr4a1 and the Microbiome
A review of the critical role of eosinophils as regulators of mucosal homeostatic processes including immune maintenance, organ development and more.
New Paper: Simultaneous SNP Selection and Adjustment for Population Structure in High Dimensional Prediction Models
![Table 1. Simulation study results. Mean (standard deviation) from 200 simulations stratified by the number of causal SNPs (null, 1%), the overlap between causal SNPs and kinship matrix (no overlap, all causal SNPs in kinship), and true heritability (10%, 30%). For all simulations, sample size is n = 1000, the number of covariates is p = 5000, and the number of SNPs used to estimate the kinship matrix is k = 10000. TPR at FPR = 5% is the true positive rate at a fixed false positive rate of 5%. Model Size () is the number of selected variables in the training set using the high-dimensional BIC for ggmix and 10-fold cross validation for lasso and twostep. RMSE is the root mean squared error on the test set. Estimation error is the squared distance between the estimated and true effect sizes. Error variance (σ2) for twostep is estimated from an intercept only LMM with a single random effect and is modeled explicitly in ggmix. For the lasso we use [28] as an estimator for σ2. Heritability (η) for twostep is estimated as from an intercept only LMM with a single random effect where and are the variance components for the random effect and error term, respectively. η is explictly modeled in ggmix. There is no positive way to calculate η for the lasso since we are using a PC adjustment. show less](https://i0.wp.com/www.impactt-microbiome.ca/wp-content/uploads/2020/05/journal.pgen_.1008766.t001.png?fit=800%2C443&ssl=1)
ggmix, general penalized linear mixed effects model with a single random effect for simultaneous SNP selection and adjustment for population structure in high dimensional prediction models.
New Paper: Effect of Chicory Inulin-Type Fructan-Containing Snack Bars on the Human Gut Microbiota in Low Dietary Fiber Consumers in a Randomized Crossover Trial
Effect of chicory inulin-type fructan–containing snack bars on the human gut microbiota in low dietary fiber consumers in a randomized crossover trial.
New Paper: Immunological Roles of Intestinal Mesenchymal Cells
Congratulations to our IMPACTT Director and Platform 1 Lead Dr. Kathy McCoy on this recent publication! Abstract The intestine is continuously exposed to an enormous variety and quantity of antigens and innate immune stimuli derived from both pathogens and harmless materials, such as food and commensal bacteria. Accordingly, the intestinal immune system is uniquely adapted […]
New Paper: Clostridioides difficile Colonization Is Differentially Associated With Gut Microbiome Profiles by Infant Feeding Modality at 3–4 Months of Age
Congratulations to our Platform 2 Lead Dr. Anita Kozyrskyj on this recent publication! Abstract Colonization with Clostridioides difficile occurs in up to half of infants under the age of 3 months, is strongly influenced by feeding modality and is largely asymptomatic. In spite of this, C. difficile‘s presence has been associated with susceptibility to chronic disease later in […]
New Paper: Neutrophils Recirculate Through Lymph Nodes to Survey Tissues for Pathogens
Congratulations to our Platform 1 Co-Lead Dr. Paul Kubes on this recent publication! Abstract The adaptive immune function of lymph nodes is dependent on constant recirculation of lymphocytes. In this article, we identify neutrophils present in the lymph node at steady state, exhibiting the same capacity for recirculation. In germ-free mice, neutrophils still recirculate through […]
