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Distinct phenotype of CD4 + T cells driving celiac disease identified in multiple autoimmune conditions

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TLDR
It is found that gluten-specific CD4+ T cells in the blood and intestines of patients with celiac disease display a surprisingly rare phenotype, suggesting a way to characterize CD4 + T cells specific for disease-driving antigens in multiple autoimmune conditions.
Abstract
Combining HLA-DQ-gluten tetramers with mass cytometry and RNA sequencing analysis, we find that gluten-specific CD4+ T cells in the blood and intestines of patients with celiac disease display a surprisingly rare phenotype. Cells with this phenotype are also elevated in patients with systemic sclerosis and systemic lupus erythematosus, suggesting a way to characterize CD4+ T cells specific for disease-driving antigens in multiple autoimmune conditions.

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Pathway paradigms revealed from the genetics of inflammatory bowel disease.

TL;DR: IBD is described as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system and future prospects for disease-subtype classification and therapeutic intervention are discussed.
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Autoimmunity and organ damage in systemic lupus erythematosus

TL;DR: Tsokos reviews how the genetic, epigenetic and microbial environments influence innate and adaptive immune cells to drive immunopathology and organ damage in systemic lupus erythematosus.
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Maternal Immunological Adaptation During Normal Pregnancy

TL;DR: What is known about the immunological changes that occur during a normal pregnancy is described and strategies to prevent maternal fatalities due to infections and optimize maternal vaccination to best protect the mother-fetus dyad and the infant after birth are described.
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Immune monitoring using mass cytometry and related high-dimensional imaging approaches.

TL;DR: The underlying technologies for high-dimensional immune monitoring and aspects necessary for their successful implementation are introduced, including study design principles, analytical tools and future developments for the field of rheumatology.
References
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal Article

Visualizing Data using t-SNE

TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
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Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus.

TL;DR: In 1992, Piette and colleagues suggested that the ACR revised criteria be reevaluated in light of the above discoveries, and the presence and clinical associations or antiphospholipid antibodies in patients with SLE was suggested.
Journal ArticleDOI

Salmon provides fast and bias-aware quantification of transcript expression

TL;DR: Salmon is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.
Journal ArticleDOI

2013 classification criteria for systemic sclerosis: an American college of rheumatology/European league against rheumatism collaborative initiative

Frank H J van den Hoogen, +46 more
TL;DR: The ACR/EULAR classification criteria for SSc performed better than the 1980 ACR criteria and should allow for more patients to be classified correctly as having the disease.
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