Application of particle swarm optimization to understand the mechanism of action of allosteric inhibitors of the enzyme HSD17β13.

Understanding a drug candidate's mechanism of action is crucial for its further development. However, kinetic schemes are often complex and multi-parametric, especially for proteins in oligomerization equilibria. Here, we demonstrate the use of particle swarm optimization (PSO) as a method to select between different sets of parameters that are too far apart in the parameter space to be found by conventional approaches.

Both Traditional and Stair Climbing-based HIIT Cardiac Rehabilitation Induce Beneficial Muscle Adaptations.

Purpose: There is a lack of knowledge as to how different exercise-based cardiac rehabilitation programming affects skeletal muscle adaptations in coronary artery disease (CAD) patients. We first characterized the skeletal muscle from adults with CAD compared with a group of age- and sex-matched healthy adults. We then determined the effects of a traditional moderate-intensity continuous exercise program (TRAD) or a stair climbing-based high-intensity interval training program (STAIR) on skeletal muscle metabolism in CAD.

MMiRNA-Viewer, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network.

Background: Although there are many studies on the characteristics of miRNA-mRNA interactions using miRNA and mRNA sequencing data, the complexity of the change of the correlation coefficients and expression values of the miRNA-mRNA pairs between tumor and normal samples is still not resolved, and this hinders the potential clinical applications. There is an urgent need to develop innovative methodologies and tools that can characterize and visualize functional consequences of cancer risk gene and miRNA pairs while analyzing the tumor and normal samples simultaneously.

Results: We developed an innovative bioinformatics tool for visualizing functional annotation of miRNA-mRNA pairs in a network, known as MMiRNA-Viewer.

Sample descriptors linked to metagenomic sequencing data from human and animal enteric samples from Vietnam.

There is still limited information on the diversity of viruses co-circulating in humans and animals. Here, we report data obtained from a large field collection of enteric samples taken from humans, pigs, rodents and other mammal hosts in Vietnam between 2012 and 2016. Each of 2100 stool or rectal swab samples was subjected to virally-enriched agnostic metagenomic sequencing; the short read sequence data are accessible from the European Nucleotide Archive (ENA).

Activation of coagulation and endothelium with concurrent impairment of anticoagulant mechanisms in patients with typhoid fever.

Objectives: Typhoid fever caused by Salmonella Typhi remains a major burden worldwide. Gastrointestinal bleeding can be seen in up to 10 percent of patients and may be fatal. The coagulopathy, which may be the driver of this severe complication in patients with typhoid fever, however is ill defined.

Transcranial Magnetic Stimulation with Intermittent Theta Burst Stimulation Alters Corticospinal Output in Patients with Chronic Incomplete Spinal Cord Injury.

Intermittent theta burst stimulation (iTBS) is intended primarily to alter corticospinal excitability, creating an attractive opportunity to alter neural output following incomplete spinal cord injury (SCI). This study is the first to assess the effects of iTBS in SCI. Eight individuals with chronic incomplete SCI were studied.

Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer.

Background: MicroRNAs (miRNA) are short nucleotides that interact with their target genes through 3' untranslated regions (UTRs). The Cancer Genome Atlas (TCGA) harbors an increasing amount of cancer genome data for both tumor and normal samples. However, there are few visualization tools focusing on concurrently displaying important relationships and attributes between miRNAs and mRNAs of both cancer tumor and normal samples.

Correlating bladder cancer risk genes with their targeting microRNAs using MMiRNA-Tar.

The Cancer Genome Atlas (TCGA) (http://cancergenome.nih.gov) is a valuable data resource focused on an increasing number of well-characterized cancer genomes.

Spontaneous resolution of postoperative chylothorax following surgery for persistent right aortic arch in two dogs.

Two young dogs underwent surgical management of a persistent right aortic arch (PRAA) and developed chylothorax postoperatively. In both cases, the surgical procedure and anesthetic recovery were uncomplicated and routine. Following surgery, both patients appeared bright, alert, responsive, and previous signs of regurgitation had resolved.

Diagnostic grade wireless ECG monitoring.

In remote monitoring of Electrocardiogram (ECG), it is very important to ensure that the diagnostic integrity of signals is not compromised by sensing artifacts and channel errors. It is also important for the sensors to be extremely power efficient to enable wearable form factors and long battery life. We present an application of Compressive Sensing (CS) as an error mitigation scheme at the application layer for wearable, wireless sensors in diagnostic grade remote monitoring of ECG.

Expression of Staphylococcus epidermidis SdrG increases following exposure to an in vivo environment.

SdrG is a surface-associated fibrinogen binding protein present in most strains of Staphylococcus epidermidis. Surface expression of SdrG was not detected by flow cytometry or immunofluorescence microscopy on S. epidermidis 0-47 grown in nutrient broth or in the presence of human serum.

Stent grafts for thoracic aortic pathology: single-center experience in Western Australia.

The purpose of this article is to report a single-center experience in treating thoracic aortic pathology with stent grafts. This is a retrospective review of cases done within a period of 30 months. Between January 2002 and May 2004, 12 patients were treated in our institution with thoracic stent grafts (n = 12) for various clinical conditions.

Identification of immunogenic and serum binding proteins of Staphylococcus epidermidis.

Staphylococcus epidermidis is a commensal of human skin and a leading cause of nosocomial bloodstream infections. Limited information is available about S. epidermidis proteins that are expressed upon transition to the bloodstream or those involved in host-pathogen interactions.

Integrated gene and species phylogenies from unaligned whole genome protein sequences.

Motivation: Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments.