A personalized platform identifies trametinib plus zoledronate for a patient with KRAS-mutant metastatic colorectal cancer.

Colorectal cancer remains a leading source of cancer mortality worldwide. Initial response is often followed by emergent resistance that is poorly responsive to targeted therapies, reflecting currently undruggable cancer drivers such as and overall genomic complexity. Here, we report a novel approach to developing a personalized therapy for a patient with treatment-resistant metastatic KRAS-mutant colorectal cancer.

A transcriptomic model to predict increase in fibrous cap thickness in response to high-dose statin treatment: Validation by serial intracoronary OCT imaging.

Background: Fibrous cap thickness (FCT), best measured by intravascular optical coherence tomography (OCT), is the most important determinant of plaque rupture in the coronary arteries. Statin treatment increases FCT and thus reduces the likelihood of acute coronary events. However, substantial statin-related FCT increase occurs in only a subset of patients.

ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques.

Motivation: Study of brain images of rodent animals is the most straightforward way to understand brain functions and neural basis of physiological functions. An important step in brain image analysis is to precisely assign signal labels to specified brain regions through matching brain images to standardized brain reference atlases. However, no significant effort has been made to match different types of brain images to atlas images due to influence of artifact operation during slice preparation, relatively low resolution of images and large structural variations in individual brains.

Computational deconvolution of synovial tissue cellular composition: presence of adipocytes in synovial tissue decreased during arthritis pathogenesis and progression.

Osteoarthritis (OA) and rheumatoid arthritis (RA) are the most common forms of arthritis. The synovial tissue is the major site of inflammation of OA and RA and consists of diverse cells. Synovial tissue cell composition changes during arthritis pathogenesis and progression have not been systematically characterized and may provide critical insights into disease processes.

Publisher Correction: Gene expression imputation across multiple brain regions provides insights into schizophrenia risk.

In the HTML version of the article originally published, the author group 'The Schizophrenia Working Group of the Psychiatric Genomics Consortium' was displayed incorrectly. The error has been corrected in the HTML version of the article.

Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities.

One-third of the world's population carries (), the infectious agent that causes tuberculosis (TB), and every 17 s someone dies of TB. After infection, can live dormant for decades in a granuloma structure arising from the host immune response, and cholesterol is important for this persistence of . Current treatments require long-duration drug regimens with many associated toxicities, which are compounded by the high doses required.

Plasma FGF-19 Levels are Increased in Patients with Post-Bariatric Hypoglycemia.

Background: Hypoglycemia is an increasingly recognized complication of bariatric surgery. Mechanisms contributing to glucose lowering remain incompletely understood. We aimed to identify differentially abundant plasma proteins in patients with post-bariatric hypoglycemia (PBH) after Roux-en-Y gastric bypass (RYGB), compared to asymptomatic post-RYGB.

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to access for biological researchers due to the need for data processing using complex computational pipelines.

Detecting virus-specific effects on post-infection temporal gene expression.

Background: Different types of viruses have different envelope proteins, and may have their shared or distinctive host-virus interactions which result in various post-infection effects in humans and animals. These effects often do not appear at once but take time to unfold. To characterize the virus-specific effects, we applied a Multivariate Polynomial Time-dependent Genetic Association (MPTGA) method, previously proposed for detecting differences in temporal gene expression traits, to test for the differences in mouse lung transcriptome response to infection of different subtypes of influenza A viruses.

Gene expression imputation across multiple brain regions provides insights into schizophrenia risk.

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility.

Microbial Adjuncts for Food Allergen Immunotherapy.

Purpose Of Review: Food allergen immunotherapy may benefit from adjunct therapies to enhance safety and efficacy. We review preclinical studies investigating the effects of probiotics and other microbial-based interventions on oral tolerance, describe the human clinical trial evidence thus far for microbial adjuncts, and discuss steps for translating research findings in this area to clinical therapy.

Recent Findings: Murine studies support that microbial-based interventions confer protection against sensitization and may augment treatment efficacy for food allergy.

ORE identifies extreme expression effects enriched for rare variants.

Motivation: Non-coding rare variants (RVs) may contribute to Mendelian disorders but have been challenging to study due to small sample sizes, genetic heterogeneity and uncertainty about relevant non-coding features. Previous studies identified RVs associated with expression outliers, but varying outlier definitions were employed and no comprehensive open-source software was developed.

Results: We developed Outlier-RV Enrichment (ORE) to identify biologically-meaningful non-coding RVs.

Parkinson's Disease is Associated with Dysregulations of a Dopamine-Modulated Gene Network Relevant to Sleep and Affective Neurobehaviors in the Striatum.

In addition to the characteristic motor symptoms, Parkinson's disease (PD) often involves a constellation of sleep and mood symptoms. However, the mechanisms underlying these comorbidities are largely unknown. We have previously reconstructed gene networks in the striatum of a population of (C57BL/6J x A/J) F2 mice and associated the networks to sleep and affective phenotypes, providing a resource for integrated analyses to investigate perturbed sleep and affective functions at the gene network level.

Erectile Dysfunction Is Highly Prevalent in Men With Newly Diagnosed Inflammatory Bowel Disease.

Background And Aims: Cross-sectional studies on sexual function in men with inflammatory bowel disease (IBD) yield mixed results. Using a prospective incidence cohort, we aimed to describe sexual function at baseline and over time and to identify factors associated with impaired sexual function in men with IBD.

Methods: Men 18 years and older enrolled between April 2008 and January 2013 in the Ocean State Crohn's and Colitis Area Registry (OSCCAR) with a minimum of 2 years of follow-up were eligible for study.

Improved Pre-miRNAs Identification Through Mutual Information of Pre-miRNA Sequences and Structures.

Playing critical roles as post-transcriptional regulators, microRNAs (miRNAs) are a family of short non-coding RNAs that are derived from longer transcripts called precursor miRNAs (pre-miRNAs). Experimental methods to identify pre-miRNAs are expensive and time-consuming, which presents the need for computational alternatives. In recent years, the accuracy of computational methods to predict pre-miRNAs has been increasing significantly.

Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images.

Multiparametric magnetic resonance imaging (mpMRI) has become increasingly important for the clinical assessment of prostate cancer (PCa), but its interpretation is generally variable due to its relatively subjective nature. Radiomics and classification methods have shown potential for improving the accuracy and objectivity of mpMRI-based PCa assessment. However, these studies are limited to a small number of classification methods, evaluation using the AUC score only, and a non-rigorous assessment of all possible combinations of radiomics and classification methods.

A Longitudinal Study of Sexual Function in Women With Newly Diagnosed Inflammatory Bowel Disease.

Background: The literature provides conflicting data on sexual function in women with inflammatory bowel disease (IBD). We aim to describe sexual function at baseline and over time in a prospective inception cohort of adult women with IBD.

Methods: Women age 18 years or older enrolled in the Ocean State Crohn's & Colitis Area Registry (OSCCAR) with 2 years of prospective follow-up were included in the study.

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose a novel ensemble learning framework, ensembleCNV, to detect and genotype CNVs using single nucleotide polymorphism (SNP) array data. EnsembleCNV (a) identifies and eliminates batch effects at raw data level; (b) assembles individual CNV calls into CNV regions (CNVRs) from multiple existing callers with complementary strengths by a heuristic algorithm; (c) re-genotypes each CNVR with local likelihood model adjusted by global information across multiple CNVRs; (d) refines CNVR boundaries by local correlation structure in copy number intensities; (e) provides direct CNV genotyping accompanied with confidence score, directly accessible for downstream quality control and association analysis.

The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription.

Oligodendrocyte (OLG)-related abnormalities have been broadly observed in schizophrenia (SZ); however, the etiology of these abnormalities remains unknown. As SZ is broadly believed to be a developmental disorder, the etiology of the myelin abnormalities in SZ may be related to OLG fate specification during development. Noncoding RNAs (ncRNAs) are an important part of multifaceted transcriptional complexes participating in neurogenic commitment and regulation of postmitotic cell function.

The Role of S1P and the Related Signaling Pathway in the Development of Tissue Fibrosis.

Tissue fibrosis, including pulmonary fibrosis, hepatic fibrosis, and cardiac fibrosis, is an important stage in the development of many diseases. It can lead to structural damage and dysfunction and even severe carcinogenesis or death. There is currently no effective method for the treatment of fibrosis.