Optimizing T cell inflamed signature through a combination biomarker approach for predicting immunotherapy response in NSCLC.

The introduction of anti-PD-1/PD-L1 therapies revolutionized treatment for advanced non-small cell lung cancer (NSCLC), yet response rates remain modest, underscoring the need for predictive biomarkers. While a T cell inflamed gene expression profile (GEP) has predicted anti-PD-1 response in various cancers, it failed in a large NSCLC cohort from the Stand Up To Cancer-Mark (SU2C-MARK) Foundation. Re-analysis revealed that while the T cell inflamed GEP alone was not predictive, its performance improved significantly when combined with gene signatures of myeloid cell markers.

A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).

Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.

Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library.

Background: The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features.

Results: Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features.

DynOmics to identify delays and co-expression patterns across time course experiments.

Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time.

The effect of microbial colonization on the host proteome varies by gastrointestinal location.

Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum and proximal colon under three colonization states: germ-free (GF), monocolonized with Bacteroides thetaiotaomicron and conventionally raised (CR). Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal (GI) tract.

A Linear Mixed Model Spline Framework for Analysing Time Course 'Omics' Data.

Time course 'omics' experiments are becoming increasingly important to study system-wide dynamic regulation. Despite their high information content, analysis remains challenging. 'Omics' technologies capture quantitative measurements on tens of thousands of molecules.

A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum).

Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars.

Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity.

Sibling family practices: guidelines for healthy boundaries.

A questionnaire was given to 500 mental health and child welfare professionals asking for maximum acceptable ages for siblings to engage jointly in certain family practices related to hygiene, affection, and privacy. A large proportion of respondents felt it was never acceptable for siblings to take showers together (40%), kiss on the mouth (37%), or toilet together (32%). Some significant differences occurred based on the gender of the older sibling within sets of same gender or mixed gender pairs, with older brothers being acceptable up to lower ages than older sisters.