Dual gene set enrichment analysis (dualGSEA); an R function that enables more robust biological discovery and pre-clinical model alignment from transcriptomics data.

Gene set enrichment analysis (GSEA) tools can identify biological insights within gene expression-based studies. Although their statistical performance has been compared, the downstream biological implications that arise when choosing between the range of pairwise or single sample forms of GSEA methods remain understudied. We compare the statistical and biological results obtained from various pre-ranking methods/options for pairwise GSEA, followed by a stand-alone comparison of GSEA, single sample GSEA (ssGSEA) and gene set variation analysis (GSVA).

Outcomes in infective endocarditis among adults with CHD: a comparative national study.

Background: Given increased survival for adults with CHD, we aim to determine outcome differences of infective endocarditis compared to patients with structurally normal hearts in the general population.

Methods: We conducted a retrospective cross-sectional study identifying infective endocarditis hospitalisations in patients 18 years and older from the National Inpatient Sample database between 2001 and 2016 using International Classification of Disease diagnosis and procedure codes. Weighting was used to create national annual estimates indexed to the United States population, and multivariable logistic regression analysis determined variable associations.

Formal Methods for Establishing Simulation Interoperability for Military Health System Applications.

Introduction: Advancements in information technology have facilitated information exchange practices within the Military Health System (MHS), enabling "systems of systems" approaches that broaden and coordinate the set of capabilities available to enhance patient outcomes. This is applicable for MHS modeling and simulation (M&S) applications as well. Learning from successful approaches applied in current interoperability solutions used in the military helps to ensure interoperability practices yield trusted compositions of simulations.

Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer.

Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5 stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1 stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease.

β-Catenin Drives Butyrophilin-like Molecule Loss and γδ T-cell Exclusion in Colon Cancer.

Intraepithelial lymphocytes (IEL) expressing γδ T-cell receptors (γδTCR) play key roles in elimination of colon cancer. However, the precise mechanisms by which progressing cancer cells evade immunosurveillance by these innate T cells are unknown. Here, we investigated how loss of the Apc tumor suppressor in gut tissue could enable nascent cancer cells to escape immunosurveillance by cytotoxic γδIELs.

MmCMS: mouse models' consensus molecular subtypes of colorectal cancer.

Background: Colorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1-4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach.

Recurrent Rash in an 11-Year-Old Boy With Pericardial and Pleural Effusions.

An 11-year-old, previously healthy boy presented to the emergency center (EC) for acute respiratory distress in the setting of 5 months of recurrent and worsening rash with progressive fatigue, shortness of breath, chest pain, and cough. At the onset of his rash, he and his younger brothers were diagnosed with roseola. Although his brothers' symptoms resolved, the patient's rash recurred, prompting his primary care provider to prescribe amoxicillin.

Antihistamines for motion sickness.

Background: Motion sickness is a syndrome that occurs as a result of passive body movement in response to actual motion, or the illusion of motion when exposed to virtual and moving visual environments. The most common symptoms are nausea and vomiting. Antihistamines have been used in the management of motion sickness for decades, however studies have shown conflicting results regarding their efficacy.

Biological Misinterpretation of Transcriptional Signatures in Tumor Samples Can Unknowingly Undermine Mechanistic Understanding and Faithful Alignment with Preclinical Data.

Purpose: Precise mechanism-based gene expression signatures (GES) have been developed in appropriate in vitro and in vivo model systems, to identify important cancer-related signaling processes. However, some GESs originally developed to represent specific disease processes, primarily with an epithelial cell focus, are being applied to heterogeneous tumor samples where the expression of the genes in the signature may no longer be epithelial-specific. Therefore, unknowingly, even small changes in tumor stroma percentage can directly influence GESs, undermining the intended mechanistic signaling.

Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer.

Objective: Stroma-rich tumours represent a poor prognostic subtype in stage II/III colon cancer (CC), with high relapse rates and limited response to standard adjuvant chemotherapy.

Design: To address the lack of efficacious therapeutic options for patients with stroma-rich CC, we stratified our human tumour cohorts according to stromal content, enabling identification of the biology underpinning relapse and potential therapeutic vulnerabilities specifically within stroma-rich tumours that could be exploited clinically. Following human tumour-based discovery and independent clinical validation, we use a series of and stroma-rich models to test and validate the therapeutic potential of elevating the biology associated with reduced relapse in human tumours.

A Multisite Retrospective Review of Direct Oral Anticoagulants Compared to Warfarin in Adult Fontan Patients.

Purpose: Direct oral anticoagulants (DOACs) are not recommended in adult Fontan patients (Level of Evidence C). We hypothesized that DOACs are comparable to warfarin and do not increase thrombotic and embolic complications (TEs) or clinically significant bleeds.

Methods: We reviewed the medical records of adult Fontan patients on DOACs or warfarin at three major medical centers.

Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2,3,4,5-Tetrahydrobenzo[F][1,4]oxazepines as Potential New Trypanocidal Agents.

African and American trypanosomiases are estimated to affect several million people across the world, with effective treatments distinctly lacking. New, ideally oral, treatments with higher efficacy against these diseases are desperately needed. Peroxisomal import matrix (PEX) proteins represent a very interesting target for structure- and ligand-based drug design.

Endovascular Repair of a Descending Thoracic Aortic Aneurysm in a Pediatric Patient with Tuberous Sclerosis: A Case Report and Review of the Literature.

Aortic aneurysm in children is rare, but has been described in the tuberous sclerosis complex (TSC) population. While surgical repair has been utilized as the primary means of intervention, we present the first known case reporting exclusion of a descending thoracic aortic aneurysm with percutaneous covered stent implantation in a pediatric patient with TSC. A review of the literature is also included herein.

Sizing Up Fontan Failure: Association with Increasing Weight in Adulthood.

Obesity has become increasingly recognized in adults with Fontan palliation, yet the relationship between weight changes in adulthood and Fontan failure is not clearly defined. We hypothesize that increasing weight in adulthood among Fontan patients is associated with the development of Fontan failure. Single-center data from adults with Fontan palliation who were not in Fontan failure at their first clinic visit in adulthood and who received ongoing care were retrospectively collected.

HeartMate 3 in a ccTGA patient.

A 49-year-old female with congenitally corrected (or levo-) transposition of the great arteries complicated by nonischemic cardiomyopathy presented for worsening heart failure despite guideline-directed medical therapy and was found to be in cardiogenic shock. She successfully underwent ventricular assist device placement with a HeartMate III to her systemic right ventricle as a bridge to transplantation.

Sizing heart transplant donors in adults with congenital heart disease.

Objective: Optimal donor sizing for heart transplantation (HT) in adults with congenital heart disease (CHD) remains unclear, given the propensity for pulmonary hypertension related to shunting, staged repairs, and periods of pulmonary overcirculation. We studied HT outcomes related to donor size matching in the adult CHD population.

Methods: We conducted a retrospective cohort analysis of patients with CHD undergoing HT in the United States from January 1, 2000, to December 31, 2015.

Shape Similarity by Fractal Dimensionality: An Application in the de novo Design of (-)-Englerin A Mimetics.

Molecular shape and pharmacological function are interconnected. To capture shape, the fractal dimensionality concept was employed, providing a natural similarity measure for the virtual screening of de novo generated small molecules mimicking the structurally complex natural product (-)-englerin A. Two of the top-ranking designs were synthesized and tested for their ability to modulate transient receptor potential (TRP) cation channels which are cellular targets of (-)-englerin A.

Sensitivity of musculoskeletal model-based lumbar spinal loading estimates to type of kinematic input and passive stiffness properties.

The study investigated the potential for obtaining more accurate spine joint reaction force (JRF) estimates from musculoskeletal models by incorporating dynamic stereo X-ray imaging (DSX)-based in vivo lumbar vertebral rotational and translational kinematics compared to generic, rhythm (RHY)-based kinematics, while also observing the influence of accompanying inputs: intervertebral segment stiffness and neutral state. A full-body OpenSim® musculoskeletal model, constructed by combining existing lower- and upper-body models, was driven based on one volunteer's (female; age 25; 60.8 kg; 176 cm) anthropometrics and kinematics from a series of upright standing and straight-legged dynamic lifting tasks.

Heart transplantation and in-hospital outcomes in adult congenital heart disease patients with Fontan: A decade nationwide analysis from 2004 to 2014.

Introduction: Treatment of adult congenital heart disease patients who require advanced therapies remains challenging due to high perioperative and wait-list mortality and limited donors. Patients palliated with Fontan are at the highest risk of early mortality due to multiorgan involvement and few centers able to safely transplant them. We sought to evaluate the early outcomes of heart transplants in these adult Fontan patients.

A Dynamic Radiographic Imaging Study of Lumbar Intervertebral Disc Morphometry and Deformation In Vivo.

Intervertebral discs are important structural components of the spine but also are significant sources of morbidity, especially for the "low back" lumbar region. Mechanical damage to, or degeneration of, the lumbar discs can diminish their structural integrity and elicit debilitating low back pain. Advancement of reparative or regenerative means to treat damaged or degenerated discs is hindered by a lack of basic understanding of the disc load-deformation characteristics in vivo.

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery.

Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides opportunities for the discovery and development of innovative drugs. Various machine learning approaches have recently (re)emerged, some of which may be considered instances of domain-specific AI which have been successfully employed for drug discovery and design. This review provides a comprehensive portrayal of these machine learning techniques and of their applications in medicinal chemistry.

More than the heart: Hepatic, renal, and cardiac dysfunction in adult Fontan patients.

Setting: Fontan-associated liver disease universally affects adults with single ventricle heart disease. Chronic kidney disease is also highly prevalent in adult Fontan patients. In this study, we evaluate the relationship of Fontan hemodynamics invasively and noninvasively with extra-cardiac dysfunction as measured by MELD and MELD-XI.