Cell recognition based on topological sparse coding for microscopy imaging of focused ultrasound treatment.

Background: Ultrasound is considered a reliable, widely available, non-invasive, and inexpensive imaging technique for assessing and detecting the development phases of cancer; both in vivo and ex vivo, and for understanding the effects on cell cycle and viability after ultrasound treatment.

Methods: Based on the topological continuity characteristics, and that adjacent points or areas represent similar features, we propose a topological penalized convex objective function of sparse coding, to recognize similar cell phases.

Results: This method introduces new features using a deep learning method of sparse coding with topological continuity characteristics.

Self-Assembly of Asymmetrically Interacting ABC Star Triblock Copolymer Melts.

The phase behavior of asymmetrically interacting ABC star triblock copolymer melts is investigated by the self-consistent field theory (SCFT). Motivated by the experimental systems, in this study, we focus on the systems in which the Flory-Huggins interaction parameters satisfy χAC > χ BC ≈ χAB. Using various initialization strategies, a large number of periodic structures have been obtained in our calculations.

Is high high-density lipoprotein cholesterol beneficial for premature coronary heart disease? A meta-analysis.

Aims: To clarify the association between premature coronary heart disease of patients ≤55 years and high-density lipoprotein cholesterol (HDL-C) plasma levels.

Methods: Searches were performed between 2002 and 2013 using PubMed, Web of Science, Science Direct, and Google Scholar. The original articles selected published premature coronary heart disease diagnosed by World Health Organization criteria or via angiograph both in males and females ≤55 years and with plasma HDL-C levels in both the case and control groups.

A Dietary Intervention in Urban African Americans: Results of the "Five Plus Nuts and Beans" Randomized Trial.

Introduction: Unhealthy diets, often low in potassium, likely contribute to racial disparities in blood pressure. We tested the effectiveness of providing weekly dietary advice, assistance with selection of higher potassium grocery items, and a $30 per week food allowance on blood pressure and other outcomes in African American adults with hypertension.

Design: We conducted an 8-week RCT with two parallel arms between May 2012 and November 2013.

High speed BLASTN: an accelerated MegaBLAST search tool.

Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST.

Division time-based amplifiers for stochastic gene expression.

While cell-to-cell variability is a phenotypic consequence of gene expression noise, sources of this noise may be complex - apart from intrinsic sources such as the random birth/death of mRNA and stochastic switching between promoter states, there are also extrinsic sources of noise such as cell division where division times are either constant or random. However, how this time-based division affects gene expression as well as how it contributes to cell-to-cell variability remains unexplored. Using a computational model combined with experimental data, we show that the cell-cycle length defined as the difference between two sequential division times can significantly impact the expression dynamics.

Roles of factorial noise in inducing bimodal gene expression.

Some gene regulatory systems can exhibit bimodal distributions of mRNA or protein although the deterministic counterparts are monostable. This noise-induced bimodality is an interesting phenomenon and has important biological implications, but it is unclear how different sources of expression noise (each source creates so-called factorial noise that is defined as a component of the total noise) contribute separately to this stochastic bimodality. Here we consider a minimal model of gene regulation, which is monostable in the deterministic case.

Azathioprine plus corticosteroid treatment in Chinese patients with neuromyelitis optica.

We investigated the efficacy of azathioprine (AZA) plus long-term low dose corticosteroids in Chinese patients with neuromyelitis optica (NMO) and neuromyelitis optica spectrum disorders (NMOSD) at the Center for Demyelinating Diseases, South China. We prospectively enrolled patients between June 2010 and June 2014. Annualized relapse rate (ARR), expanded disability status scale (EDSS) score and modified Rankin Scale (mRS) were analyzed retrospectively.

The effect of body-mind relaxation meditation induction on major depressive disorder: A resting-state fMRI study.

Background: Meditation has been increasingly evaluated as an important complementary therapeutic tool for the treatment of depression. The present study employed resting-state functional magnetic resonance imaging (rs-fMRI) to examine the effect of body-mind relaxation meditation induction (BMRMI) on the brain activity of depressed patients and to investigate possible mechanisms of action for this complex intervention.

Method: 21 major depressive disorder patients (MDDs) and 24 age and gender-matched healthy controls (HCs) received rs-fMRI scans at baseline and after listening to a selection of audio designed to induce body-mind relaxation meditation.

Effects of promoter leakage on dynamics of gene expression.

Background: Quantitative analysis of simple molecular networks is an important step forward understanding fundamental intracellular processes. As network motifs occurring recurrently in complex biological networks, gene auto-regulatory circuits have been extensively studied but gene expression dynamics remain to be fully understood, e.g.

The Relationship Among Genetic Heritability, Environmental Effects, and Autism Spectrum Disorders: 37 Pairs of Ascertained Twin Study.

Autism spectrum disorders (ASD) comprise a heterogeneous group of neurodevelopmental disorders that have strong heritability. To better understand the heritable factors in twins with clinically diagnosed ASD and to discuss the relationship between social impairments and genetic and environmental factors. In last 13 years, over 12,000 cases of ASD were diagnosed in the children's development and behavior center, the authors review 37 pairs of these twins, in each pair, and at least 1 twin had been diagnosed with an ASD, and found that the concordance rate was 80% [95% confidence interval (CI) 51.

Modified momentum exchange method for fluid-particle interactions in the lattice Boltzmann method.

In this paper, a modified momentum exchange method for fluid-particle interactions is proposed based on the finite-volume lattice Boltzmann method. The idea of the improvement is to remove the restriction that the boundary points must be set as the midpoints of the grid lines or the intersection of the grid lines with the solid boundaries. The particle surface is represented by a set of arc (area) elements, and the interior fluid is used which the geometric conservation law is naturally satisfied.

An exploitation-competition system with negative effect of prey on its predator.

This paper considers an exploitation-competition system in which exploitation is the dominant interaction when the prey is at low density, while competition is dominant when the prey is at high density due to its negative effect on the predator. The two-species system is characterized by differential equations, which are the combination of Lotka-Volterra competitive and predator-prey models. Global dynamics of the model demonstrate some basic properties of exploitation-competition systems: (i) When the growth rate of prey is extremely small, the prey cannot promote the growth of predator.

Body mass index (BMI) is associated with microalbuminuria in Chinese hypertensive patients.

There is no general consensus on possible factors associated with microalbuminuria in hypertensive patients nor any reported study about this issue in Chinese patients. To examine this issues, 944 hypertensive patients were enrolled in a study based on a cross-sectional survey conducted in Southern China. Multivariate regression analyses were performed to identify the factors related with the presence of microalbuminuria and urinary excretion of albumin.

Dynamical analysis of mCAT2 gene models with CTN-RNA nuclear retention.

As an experimentally well-studied nuclear-retained RNA, CTN-RNA plays a significant role in many aspects of mouse cationic amino acid transporter 2 (mCAT2) gene expression, but relevant dynamical mechanisms have not been completely clarified. Here we first show that CTN-RNA nuclear retention can not only reduce pre-mCAT2 RNA noise but also mediate its coding partner noise. Then, by collecting experimental observations, we conjecture a heterodimer formed by two proteins, p54(nrb) and PSP1, named p54(nrb)-PSP1, by which CTN-RNA can positively regulate the expression of nuclear mCAT2 RNA.

Persistence of pollination mutualisms in the presence of ants.

This paper considers plant-pollinator-ant systems in which the plant-pollinator interaction is mutualistic but ants have both positive and negative effects on plants. The ants also interfere with pollinators by preventing them from accessing plants. While a Beddington-DeAngelis (BD) formula can describe the plant-pollinator interaction, the formula is extended in this paper to characterize the pollination mutualism under the ant interference.

Feedback-induced counterintuitive correlations of gene expression noise with bursting kinetics.

Previous studies showed that a higher frequency of bursting results in lower expression noise whereas a larger size of bursting leads to higher expression noise. Here, we show counterintuitive correlations of expression noise with bursting kinetics due to the effect of feedback. Specifically, in the case of increasing the negative feedback strength but keeping the mean expression fixed, both the mean burst frequency and the mean burst size are invariant if the off-switching rate decreases, but expression noise is reduced; or the mean burst frequency is invariant and the burst size decreases if the transcription rate increases, but expression noise is amplified.

Pathway-based analysis tools for complex diseases: a review.

Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehensive understanding of the molecular mechanisms underlying complex diseases.

Population dynamics of intraguild predation in a lattice gas system.

In the system of intraguild predation (IGP) we are concerned with, species that are in a predator-prey relationship, also compete for shared resources (space or food). While several models have been established to characterize IGP, mechanisms by which IG prey and IG predator can coexist in IGP systems with spatial competition, have not been shown. This paper considers an IGP model, which is derived from reactions on lattice and has a form similar to that of Lotka-Volterra equations.

On power idealization filter topologies of lattice implication algebras.

The aim of this paper is to introduce power idealization filter topologies with respect to filter topologies and power ideals of lattice implication algebras, and to investigate some properties of power idealization filter topological spaces and their quotient spaces.

An unconditionally stable, positivity-preserving splitting scheme for nonlinear Black-Scholes equation with transaction costs.

This paper deals with the numerical analysis of nonlinear Black-Scholes equation with transaction costs. An unconditionally stable and monotone splitting method, ensuring positive numerical solution and avoiding unstable oscillations, is proposed. This numerical method is based on the LOD-Backward Euler method which allows us to solve the discrete equation explicitly.

Reinitiation enhances reliable transcriptional responses in eukaryotes.

Gene transcription is a noisy process carried out by the transcription machinery recruited to the promoter. Noise reduction is a fundamental requirement for reliable transcriptional responses which in turn are crucial for signal transduction. Compared with the relatively simple transcription initiation in prokaryotes, eukaryotic transcription is more complex partially owing to its additional reinitiation mechanism.

Ideal regularization for learning kernels from labels.

In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels.

A cooperative system of two species with bidirectional interactions.

Cooperation between species is often regarded to mean that the increase of each species promotes the growth of the other. The well-known cooperative model is the Lotka-Volterra equations (LVEs). In the LVEs, population densities of species increase infinitely as the cooperation is strong, which is called the divergence problem.

Alternative-splicing-mediated gene expression.

Alternative splicing (AS) is a fundamental process during gene expression and has been found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels both quantitatively and qualitatively remains to be fully explored. Here, we analyze two common models of gene expression, each incorporating a simple splice mechanism that a pre-mRNA is spliced into two mature mRNA isoforms in a probabilistic manner.