CD206+ Trem2+ macrophage accumulation in the murine knee joint after injury is associated with protection against post-traumatic osteoarthritis in MRL/MpJ mice.

Post-traumatic osteoarthritis (PTOA) is a painful joint disease characterized by the degradation of bone, cartilage, and other connective tissues in the joint. PTOA is initiated by trauma to joint-stabilizing tissues, such as the anterior cruciate ligament, medial meniscus, or by intra-articular fractures. In humans, ~50% of joint injuries progress to PTOA, while the rest spontaneously resolve.

Spatiotemporal analysis of lung immune dynamics in lethal infection.

Coccidioidomycosis, or Valley fever, is a lung disease caused by inhalation of fungi, prevalent in the Southwestern United States, Mexico, and parts of Central and South America. Annually, the United States reports 10,000-20,000 cases, although those numbers are expected to increase as climate change expands the fungal geographic range. While 60% of infections are asymptomatic, 40% symptomatic infections are often misdiagnosed due to similarities with bronchitis or pneumonia.

Boosting Single-Cell RNA Sequencing Analysis with Simple Neural Attention.

A limitation of current deep learning (DL) approaches for single-cell RNA sequencing (scRNAseq) analysis is the lack of interpretability. Moreover, existing pipelines are designed and trained for specific tasks used disjointly for different stages of analysis. We present scANNA, a novel interpretable DL model for scRNAseq studies that leverages neural attention to learn gene associations.

ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders.

Motivation: Single-cell RNA sequencing (scRNAseq) technologies allow for measurements of gene expression at a single-cell resolution. This provides researchers with a tremendous advantage for detecting heterogeneity, delineating cellular maps or identifying rare subpopulations. However, a critical complication remains: the low number of single-cell observations due to limitations by rarity of subpopulation, tissue degradation or cost.

CD8 follicular T cells localize throughout the follicle during germinal center reactions and maintain cytolytic and helper properties.

Follicular CXCR5+ PD-1+ CD8 T cells (CD8 Tfc) arise in multiple models of systemic autoimmunity yet their functional contribution to disease remains in debate. Here we define the follicular localization and functional interactions of CD8 Tfc with B cells during autoimmune disease. The absence of functional T regulatory cells in autoimmunity allows for CD8 Tfc development that then expands with lymphoproliferation.

Glutaredoxin represses transcriptional and developmental responses to nitrate in roots.

Glutaredoxins (GRXs) are small oxidoreductase enzymes that can reduce disulfide bonds in target proteins. The class III GRX gene family is unique to land plants, and has 21 class III GRXs, which remain largely uncharacterized. About 80% of class III GRXs are transcriptionally regulated by nitrate, and several recent studies have suggested roles for these GRXs in nitrogen signaling.