flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.

Summary: flowDensity facilitates reproducible, high-throughput analysis of flow cytometry data by automating a predefined manual gating approach. The algorithm is based on a sequential bivariate gating approach that generates a set of predefined cell populations. It chooses the best cut-off for individual markers using characteristics of the density distribution.

Laminin α4 deficient mice exhibit decreased capacity for adipose tissue expansion and weight gain.

Obesity is a global epidemic that contributes to the increasing medical burdens related to type 2 diabetes, cardiovascular disease and cancer. A better understanding of the mechanisms regulating adipose tissue expansion could lead to therapeutics that eliminate or reduce obesity-associated morbidity and mortality. The extracellular matrix (ECM) has been shown to regulate the development and function of numerous tissues and organs.

A highly charged region in the middle domain of plant endoplasmic reticulum (ER)-localized heat-shock protein 90 is required for resistance to tunicamycin or high calcium-induced ER stresses.

Heat-shock protein 90 (HSP90) is a highly conserved molecular chaperone that is involved in modulating a multitude of cellular processes under both physiological and stress conditions. In Arabidopsis, there are seven HSP90 isoforms (HSP90.1-HSP90.

Evaluation of the osteogenic potential of growth factor-rich demineralized bone matrix in vivo.

Background: The study evaluates the osteogenic properties and biocompatibility of growth factor-rich demineralized bone matrix (GDBM) by comparing with cancellous mineralized bone matrix (CMBM) and anorganic bovine bone matrix (ABBM).

Methods: Thirty-six Sprague-Dawley rats were used (n = 6/group/time point). To assess biocompatibility and osteoinductivity, the respective bone matrices were randomly placed in subcutaneous pouches for 7 and 28 days and evaluated by histology and osteopontin expression.

The alteration of inflammatory markers and apoptosis on chronic prostatitis induced by estrogen and androgen.

Purpose: The age-related decline of the testosterone-to-estrogen (T-to-E2) ratio in serum is associated with the increased prevalence of prostatic inflammation. The goal of the study was to induce prostatic inflammation with E2 and androgen treatment and to explore the inflammatory markers and apoptosis on prostatitis.

Methods: Castrated SD rats were treated with E2 and different doses of androgens to achieve an elevated concentration of E2 and a wide range of the androgen-to-E2 ratio in serum.

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulation protocol [Huber and Kim, , , 97-110] to generate equilibrium trajectory ensembles and extract nonequilibrium subsets for computing kinetic quantities.

Identification of factors that predict outpatient utilisation of a Plastic Dressing Clinic. A retrospective review of 287 paediatric burn cases.

Introduction: This study investigated aetiology of burn cases presenting to the Royal Hospital for Sick Children in Edinburgh to identify factors that influence the number of outpatient visits patients make to the Plastic Dressing Clinic (PDC) following discharge.

Methods: A retrospective review was performed of all paediatric burn cases presenting between January 2009 and July 2012. Information gathered included patient demographics, burn aetiology, details of inpatient admission and outpatient PDC attendance.

Tonsillectomy for periodic fever, aphthous stomatitis, pharyngitis and cervical adenitis syndrome (PFAPA).

Background: Periodic fever, aphthous stomatitis, pharyngitis and cervical adenitis (PFAPA) syndrome is a rare clinical syndrome of unknown cause usually identified in children. Tonsillectomy is considered a potential treatment option for this syndrome. This is an update of a Cochrane review first published in 2010.

SeqControl: process control for DNA sequencing.

As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality.

Fluoxetine a novel anti-hepatitis C virus agent via ROS-, JNK-, and PPARβ/γ-dependent pathways.

More than 20% of chronic hepatitis C (CHC) patients receiving interferon-alpha (IFN-α)-based anti-hepatitis C virus (HCV) therapy experienced significant depression, which was relieved by treatment with fluoxetine. However, whether and how fluoxetine affected directly the anti-HCV therapy remained unclear. Here, we demonstrated that fluoxetine inhibited HCV infection and blocked the production of reactive oxygen species (ROS) and lipid accumulation in Huh7.

N-Phenacylthiazolium bromide inhibits the advanced glycation end product (AGE)-AGE receptor axis to modulate experimental periodontitis in rats.

Background: Advanced glycation end products (AGEs) are involved in the inflammatory process and are considered to be etiologic factors of diabetic periodontitis. The purpose of this study is to investigate the capability of N-phenacylthiazolium bromide (PTB), a glycated cross-link breaker, in the modulation of periodontitis in various disease phases.

Methods: Mitogenesis and cytotoxicity of human periodontal ligament cells (hPDLCs) undergoing PTB treatment were evaluated in vitro.

Impaired Nef function is associated with early control of HIV-1 viremia.

Unlabelled: Host and viral factors influence the HIV-1 infection course. Reduced Nef function has been observed in HIV-1 controllers during the chronic phase, but the kinetics and mechanisms of Nef attenuation in such individuals remain unclear. We examined plasma RNA-derived Nef clones from 10 recently infected individuals who subsequently suppressed viremia to less than 2,000 RNA copies/ml within 1 year postinfection (acute controllers) and 50 recently infected individuals who did not control viremia (acute progressors).

Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia.

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments.

Role of SIRT1 in Streptococcus pneumoniae-induced human β-defensin-2 and interleukin-8 expression in A549 cell.

Streptococcus pneumoniae is an important pathogen of pneumonia in human. Human alveolar epithelium acts as an effective barrier and is an active participant in host defense against invasion of bacterial by production of various mediators. Sirtuin 1 (SIRT1), the prototypic class III histone deacetylase, is involved in the molecular control of lifespans and immune responses.

Elucidating diphosphoinositol polyphosphate function with nonhydrolyzable analogues.

The diphosphoinositol polyphosphates (PP-IPs) represent a novel class of high-energy phosphate-containing messengers which control a wide variety of cellular processes. It is thought that PP-IPs exert their pleiotropic effects as allosteric regulators and through pyrophosphorylation of protein substrates. However, most details of PP-IP signaling have remained elusive because of a paucity of suitable tools.

Customized, automated stimulus location choice for assessment of visual field defects.

Purpose: To introduce a perimetric algorithm (gradient-oriented automated natural neighbor approach [GOANNA]) that automatically chooses spatial test locations to improve characterization of visual field (VF) loss without increasing test times.

Methods: Computer simulations were undertaken to assess the performance of GOANNA. GOANNA was run on a 3° grid of 150 locations, and was compared with a zippy estimation by sequential testing (ZEST) thresholding strategy for locations in the 24-2 test pattern, with the remaining 98 locations being interpolated.

Successful treatment of liver abscess secondary to foreign body penetration of the alimentary tract: a case report and literature review.

Hepatic abscess caused by foreign body penetration of the alimentary tract is rare. We report a case of gastric antrum penetration due to a toothpick complicated by liver abscess formation. A 41-year-old man was admitted to our hospital with the chief complaint of upper abdominal pain for 2 mo.

Protective effect of curcumin on acute airway inflammation of allergic asthma in mice through Notch1-GATA3 signaling pathway.

Curcumin, a natural product derived from the plant Curcuma longa, has been found to have anti-inflammatory, antineoplastic and antifibrosis effects. It has been reported that curcumin attenuates allergic airway inflammation in mice through inhibiting NF-κB and its downstream transcription factor GATA3. It also has been proved the antineoplastic effect of curcumin through down-regulating Notch1 receptor and its downstream nuclear transcription factor NF-κB levels.

Evaluating the strength of salt bridges: a comparison of current biomolecular force fields.

Recent advances in computer hardware and software have made rigorous evaluation of current biomolecular force fields using microsecond-scale simulations possible. Force fields differ in their treatment of electrostatic interactions, including the formation of salt bridges in proteins. Here we conducted an extensive evaluation of salt bridge interactions in the latest AMBER, CHARMM, and OPLS force fields, using microsecond-scale molecular dynamics simulations of amino acid analogues in explicit solvent.

Morphological and genetic variations of the freshwater leech, Hirudinaria spp., in Peninsular Malaysia.

In this study the genetic diversity of local freshwater leeches (Hirudinaria spp.) was inferred using mtDNA COI gene analysis and compared with the gross external variations of 26 freshwater leech specimens obtained from the wild and leech farms. Based on a neighbor-joining tree generated from 516 COI base sequences, four distinct clades of Hirudinaria were seen with interspecific genetic divergence in the range of 7.

Replacement versus repair of defective restorations in adults: amalgam.

Background: Amalgam is a common filling material for posterior teeth, as with any restoration amalgams have a finite life-span. Traditionally replacement was the ideal approach to treat defective amalgam restorations, however, repair offers an alternative more conservative approach where restorations are only partially defective. Repairing a restoration has the potential of taking less time and may sometimes be performed without the use of local anaesthesia hence it may be less distressing for a patient when compared with replacement.

Replacement versus repair of defective restorations in adults: resin composite.

Background: Composite filling materials have been increasingly used for the restoration of posterior teeth in recent years as a tooth-coloured alternative to amalgam. As with any filling material composites have a finite life-span. Traditionally, replacement was the ideal approach to treat defective composite restorations, however, repairing composites offers an alternative more conservative approach to the tooth structure where restorations are partly still serviceable.

Application of quantitative estimates of fecal hemoglobin concentration for risk prediction of colorectal neoplasia.

Aim: To determine the role of the fecal immunochemical test (FIT), used to evaluate fecal hemoglobin concentration, in the prediction of histological grade and risk of colorectal tumors.

Methods: We enrolled 17881 individuals who attended the two-step colorectal cancer screening program in a single hospital between January 2010 and October 2011. Colonoscopy was recommended to the participants with an FIT of ≥ 12 ngHb/mL buffer.

Comparison of acetabular version angle measurements between prone and reformatted supine computed tomography images.

Purpose: To compare acetabular version angle measurements of CT scans in the prone and reformatted supine positions. CT acetabular version angle measurements have previously been done in the prone position to correct for pelvic tilt. With the advent of multidetector CT, recent studies have evaluated acetabular version angles measured in the supine position.

Zinc status alters growth and oxidative stress responses in rat hepatoma cells.

Zinc deficiency and excess influence cellular homeostasis and are believed to modulate apoptosis. Zinc also regulates cell growth and proliferation. Understanding of the role of zinc in the mechanisms associated with these changes is limited because of its diverse, complex, and cell-specific effects.