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11:09 EDT 21st July 2019 | BioPortfolio

Biosciences PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Biosciences articles that have been published worldwide.

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Showing "Biosciences" PubMed Articles 1–25 of 113

Predicting lncRNA-disease associations using network topological similarity based on deep mining heterogeneous networks.

A kind of noncoding RNA with length more than 200 nucleotides named long noncoding RNA (lncRNA) has gained considerable attention in recent decades. Many studies have confirmed that human genome contains many thousands of lncRNAs. LncRNAs play significant roles in many important biological processes, including complex disease diagnosis, prognosis, prevention and treatment. For some important diseases such as cancer, lncRNAs have been novel candidate biomarkers. However, the role of lncRNAs in human diseases...


Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data.

Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstra...

State and Parameter Estimation for a Class of Schistosomiasis Models.

We develop a general framework to estimate the proportion of infected snails and snail-human transmission parameter of a class of models that describes the evolution of schistosomiasis. To do so, we consider simultaneously the dynamics of schistosomiasis, captured by the homogeneous version of the classical MacDonald's model, and the measurable output: the number of female schistosomes per single host. The proposed method consists of designing an auxiliary dynamical system, called observer, whose solutions ...


Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN.

Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of samples, shotgun metagenomic sequencing provides a more detailed analysis of the taxonomic and functional content of samples. Long read technologies, such as developed by Pacific Biosciences or Oxford Nanopore, produce much longer stretches of informative sequence, greatly simplifying the difficult and time-consu...

Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy.

Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and ...

The basic reproduction number, R, in structured populations.

In this paper, we provide a straightforward approach to defining and deriving the key epidemiological quantity, the basic reproduction number, R, for Markovian epidemics in structured populations. The methodology derived is applicable to, and demonstrated on, both SIR and SIS epidemics and allows for population as well as epidemic dynamics. The approach taken is to consider the epidemic process as a multitype process by identifying and classifying the different types of infectious units along with the infec...

Modeling the Effects of Muscle Contraction on the Mechanical Response and Circumferential Stability of Coronary Arteries.

Smooth muscle contraction regulates the size of the blood vessel lumen which directly affects the mechanical response of the vessel. Folding in arteries has been observed in arteries during excessive contraction, known as a coronary artery spasm. The interplay of muscle contraction, geometry, and material responses and their effects on stability can be understood through mathematical models. Here, we consider a three-layer cross-sectional model of a coronary artery with anisotropic properties and intimal th...

Biomathematical Model for Simulating Abnormal Orifice Patterns in Colonic Crypts.

Colonic polyps, which are abnormal growths in the colon, are a major concern in colon cancer diagnosis and prevention. Medical studies evidence that there is a correlation between histopathology and the shapes of the orifices in colonic crypts. We propose a biomathematical model for simulating the appearance of anomalous shapes for the orifices of colonic crypts, associated to an abnormal cell proliferation. It couples a mechanical model that is a mixed elastic/viscoelastic quasi-static model describing the...

Is the addition of higher-order interactions in ecological models increasing the understanding of ecological dynamics?

Recent work has shown that higher-order terms in population dynamics models can increase the stability, promote the diversity, and better explain the dynamics of ecological systems. While it is known that these perceived benefits come from an increasing number of alternative solutions given by the nature of multivariate polynomials, this mathematical advantage has not been formally quantified. Here, we develop a general method to quantify the mathematical advantage of adding higher-order interactions in eco...

A new Michaelis-Menten equation valid everywhere multi-scale dynamics prevails.

The Michaelis-Menten reaction scheme is among the most influential models in the field of biochemistry, since it led to a very popular expression for the rate of an enzyme-catalysed reaction. After the realisation that this expression is valid in a limited region of the parameter space, two additional expressions were later introduced. The range of validity of these three expressions has been studied thoroughly, since the significance of a reliable rate is not based only on the accuracy of its predictive ...

RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale.

RAre DAmage and Repair sequencing (RADAR-seq) is a highly adaptable sequencing method that enables the identification and detection of rare DNA damage events for a wide variety of DNA lesions at single-molecule resolution on a genome-wide scale. In RADAR-seq, DNA lesions are replaced with a patch of modified bases that can be directly detected by Pacific Biosciences Single Molecule Real-Time (SMRT) sequencing. RADAR-seq enables dynamic detection over a wide range of DNA damage frequencies, including low phy...

Microfluidic platform enables live-cell imaging of signaling and transcription combined with multiplexed secretion measurements in the same single cells.

Innate immune cells, including macrophages and dendritic cells, protect the host from pathogenic assaults in part through secretion of a program of cytokines and chemokines (C/Cs). Cell-to-cell variability in C/C secretion appears to contribute to the regulation of the immune response, but the sources of secretion variability are largely unknown. To begin to track the biological sources that control secretion variability, we developed and validated a microfluidic device to integrate live-cell imaging of flu...

Optimal control of a Multi-patch Dengue Model under the Influence of Wolbachia Bacterium.

In this work, a multi-patch model for dengue transmission dynamics including the bacterium Wolbachia is studied and by that the control efforts to minimize the disease spread by host and vector control are investigated. The multi-patch system models the host movement within the patches which coupled via a residence-time budgeting matrix P. Numerical results confirm that the control mechanism embedded in incidence rates of the disease transmission, effectively reduce the spread of the disease.

Drug delivery from microcapsules: how can we estimate the release time?

Predicting the release performance of a drug delivery device is an important challenge in pharmaceutics and biomedical science. In this paper, we consider a multi-layer diffusion model of drug release from a composite spherical microcapsule into an external surrounding medium. Based on this model, we present two approaches for estimating the release time, i.e. the time required for the drug-filled capsule to be depleted. Both approaches make use of temporal moments of the drug concentration at the centre of...

Termite population size estimation based on termite tunnel patterns using a convolutional neural network.

Subterranean termites live in large colonies under the ground where they build an elaborate network of tunnels for foraging. In this study, we explored how the termite population size can be estimated using partial information on tunnel patterns. To achieve this, we used an agent-based model to create tunnel patterns that were characterized by three variables: the number of simulated termites (N), passing probability of two termites encountering one another (P), and distance that termites move soil particle...

Conservation Region Finding for Influenza A Viruses by Machine Learning methods of N-linked Glycosylation Sites and B-cell Epitopes.

Influenza type A, a serious infectious disease of the human respiratory tract, poses an enormous threat to human health worldwide. It leads to high mortality rates in poultry, pigs, and humans. The primary target identity regions for the human immune system are hemagglutinin (HA) and neuraminidase (NA), two surface proteins of the influenza A virus. Research and development of vaccines is highly complex because the influenza A virus evolves rapidly. This study focused on three genetic features of viral surf...

On the Z-type control of backward bifurcations in epidemic models.

We investigate how the Z-type dynamic approach can be applied to control backward bifurcation phenomena in epidemic models. Because of its rich phenomenology, that includes stationary or oscillatory subcritical persistence of the disease, we consider the SIR model introduced by Zhou & Fan in [Nonlinear Analysis: Real World Applications, 13(1), 312-324, 2012] and apply the Z-control approach in the specific case of indirect control of the infective population. We derive the associated Z-controlled model both...

High-coverage, long-read sequencing of Han Chinese trio reference samples.

Single-molecule long-read sequencing datasets were generated for a son-father-mother trio of Han Chinese descent that is part of the Genome in a Bottle (GIAB) consortium portfolio. The dataset was generated using the Pacific Biosciences Sequel System. The son and each parent were sequenced to an average coverage of 60 and 30, respectively, with N50 subread lengths between 16 and 18 kb. Raw reads and reads aligned to both the GRCh37 and GRCh38 are available at the NCBI GIAB ftp site (ftp://ftp-trace.ncbi.n...

Generalized concentration addition for ligands that bind to homodimers.

Concentration addition/dose addition (CA) has proved to be a powerful tool for estimating the combined effect of mixtures that act by similar mechanisms. We earlier proposed generalized concentration addition (GCA) to deal with the inability of CA to estimate effects of mixtures above the level of the least efficacious component. GCA requires specifying mathematical concentration response functions for each mixture component that must be invertible, yielding real numbers. We construct concentration response...

Metabolomic discrimination of the edible mushrooms Kuehneromyces mutabilis and Hypholoma capnoides (Strophariaceae, Agaricales) by NMR spectroscopy.

Two edible, cultivable mushroom species of the family Strophariaceae, Kuehneromyces mutabilis (sheathed woodtuft) and Hypholoma capnoides (conifer tuft), were studied using proton nuclear magnetic resonance metabolomic approach. The variation in the metabolites of the two species and their metabolic behaviour regarding caps and stipes and different collection sites were analysed by multivariate analysis methods. Altogether 169 cap and stipe samples of the mushrooms were investigated. The clearest difference...

Impact of water-soluble zwitterionic Zn(II) phthalocyanines against pathogenic bacteria.

The photodynamic impact of water-soluble zwitterionic zinc phthalocyanines (ZnPc1-4) was studied on pathogenic bacterial strains after specific light exposure (LED 665 nm). The structural differences between the studied ZnPc1-4 are in the positions and the numbers of substitution groups as well as in the bridging atoms (sulfur or oxygen) between substituents and macrocycle. The three peripherally substituted compounds (ZnPc1-3) are tetra-2-(N-propanesulfonic acid)oxypyridine (ZnPc1), tetra-2-(N-propanesulfo...

Numerical optimal control of a size-structured PDE model for metastatic cancer treatment.

In this paper, we propose a unified size-structured PDE model for the growth of metastatic tumors, which extends a well-known coupled ODE-PDE dynamical model developed and studied in the literature. A treatment model based on the proposed unified PDE model is investigated via optimal control theory, where its first-order necessary optimality system characterizing the optimal control is derived. We prove that the uniqueness of the optimal control depends on the chosen objective functional, and the optimal co...

Implementation of Control Strategies for Sterile Insect Techniques.

In this paper, we propose a sex-structured entomological model that serves as a basis for design of control strategies relying on releases of sterile male mosquitoes (Aedes spp) and aiming at elimination of the wild vector population in some target locality. We consider different types of releases (constant and periodic impulsive), providing sufficient conditions to reach elimination. However, the main part of the paper is focused on the study of the periodic impulsive control in different situations. When ...

Do cells use passwords in cell-state transitions? Is cell signaling sometimes encrypted?

Organisms must maintain proper regulation including defense and healing. Life-threatening problems may be caused by pathogens or by a multicellular organism's own cells through cancer or autoimmune disorders. Life evolved solutions to these problems that can be conceptualized through the lens of information security, which is a well-developed field in computer science. Here I argue that taking an information security view of cells is not merely semantics, but useful to explain features of signaling, regulat...

Multivariate spectrofluorimetric detection of lipase isolated from Serratia marcescens in chromatographic fractions.

Lipases are ubiquitous enzymes and widespread in nature. They have been widely purified as one of the most important enzymes in molecular biosciences and biotechnology. In this paper, the extracellular lipase was separated from Serratia marcescens. The separated enzyme was purified partially by ammonium sulfate precipitation, dialysis and gel filtration chromatography. Presence of the lipase in chromatography fractions was assayed by the hydrolysis of paranitrophenyl palmitate (pNPP) as substrate. The excit...


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