Reduction of CPR artifacts in the ventricular fibrillation ECG by coherent line removal

Background  

Interruption of cardiopulmonary resuscitation (CPR) impairs the perfusion of the fibrillating heart, worsening the chance for successful defibrillation. Therefore ECG-analysis during ongoing chest compression could provide a considerable progress in comparison with standard analysis techniques working only during "hands-off" intervals.     

Movies of cellular and sub-cellular motion by digital holographic microscopy

Background  

Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy.     

Scarless and site-directed mutagenesis in <Emphasis Type="Italic">Salmonella enteritidis</Emphasis>chromosome

Background  

A variety of techniques have been described which introduce scarless, site-specific chromosomal mutations. These techniques can be applied to make point mutations or gene deletions as well as insert heterologous DNA into bacterial vectors for vaccine development. Most methods use a multi-step approach that requires cloning and/or designing repeat sequences to facilitate homologous recombination. We have modified previously published techniques to develop a simple, efficient PCR-based method for scarless insertion of DNA into Salmonella enteritidis chromosome.     

Structural and RNAi characterization of the German cockroach lipophorin receptor,and the evolutionary relationships of lipoprotein receptors

Background  

Lipophorin receptors (LpRs) have been described in a number of insects, but functional studies have been reported only in locusts and mosquitoes. The aim of the present work was to characterize the LpR of the cockroach Blattella germanica, not only molecularly but also functionally using RNAi techniques, and to place LpRs in a phylogenetical context among lipoprotein receptors.     

Image fusion for dynamic contrast enhanced magnetic resonance imaging

Background  

Multivariate imaging techniques such as dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) have been shown to provide valuable information for medical diagnosis. Even though these techniques provide new information, integrating and evaluating the much wider range of information is a challenging task for the human observer. This task may be assisted with the use of image fusion algorithms.     

A comparison on effects of normalisations in the detection of differentially expressed genes

Background  

Various normalisation techniques have been developed in the context of microarray analysis to try to correct expression measurements for experimental bias and random fluctuations. Major techniques include: total intensity normalisation; intensity dependent normalisation; and variance stabilising normalisation. The aim of this paper is to discuss the impact of normalisation techniques for two-channel array technology on the process of identification of differentially expressed genes.     

Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling

Background  

A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering coefficient, and shortest path length were previously proposed for this purpose. However, there is still a pressing need to investigate another topological measure that can better describe the functional importance of network nodes. In this respect, we considered a feedback loop which is ubiquitously found in various biological networks.     

Mixed infections with <Emphasis Type="Italic">Chlamydia</Emphasis> and porcine epidemic diarrhea virus - a new <Emphasis Type="Italic">in vitro</Emphasis> model of chlamydial persistence

Background  

Chlamydiae induce persistent infections, which have been associated with a wide range of chronic diseases in humans and animals. Mixed infections with Chlamydia and porcine epidemic diarrhea virus (PEDV) may result in generation of persistent chlamydial infections. To test this hypothesis, an in vitro model of dual infection with cell culture-adapted PEDV and Chlamydia abortus or Chlamydia pecorum in Vero cells was established.     

Estimation of current density distribution under electrodes for external defibrillation

Background  

Transthoracic defibrillation is the most common life-saving technique for the restoration of the heart rhythm of cardiac arrest victims. The procedure requires adequate application of large electrodes on the patient chest, to ensure low-resistance electrical contact. The current density distribution under the electrodes is non-uniform, leading to muscle contraction and pain, or risks of burning. The recent introduction of automatic external defibrillators and even wearable defibrillators, presents new demanding requirements for the structure of electrodes.     

VitAL: Viterbi Algorithm for de novo Peptide Design

Background

Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use of peptide drugs enables a partial solution to the toxicity problem. There has been a wide interest in peptide design, but the design techniques of a specific and selective peptide inhibitor against a protein target have not yet been established.

Methodology/Principal Findings

A novel de novo peptide design approach is developed to block activities of disease related protein targets. No prior training, based on known peptides, is necessary. The method sequentially generates the peptide by docking its residues pair by pair along a chosen path on a protein. The binding site on the protein is determined via the coarse grained Gaussian Network Model. A binding path is determined. The best fitting peptide is constructed by generating all possible peptide pairs at each point along the path and determining the binding energies between these pairs and the specific location on the protein using AutoDock. The Markov based partition function for all possible choices of the peptides along the path is generated by a matrix multiplication scheme. The best fitting peptide for the given surface is obtained by a Hidden Markov model using Viterbi decoding. The suitability of the conformations of the peptides that result upon binding on the surface are included in the algorithm by considering the intrinsic Ramachandran potentials.

Conclusions/Significance

The model is tested on known protein-peptide inhibitor complexes. The present algorithm predicts peptides that have better binding energies than those of the existing ones. Finally, a heptapeptide is designed for a protein that has excellent binding affinity according to AutoDock results.     

Using hexamers to predict cis-regulatory motifs in Drosophila

Background  

Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered.     

Fast quantitative determination of microbial rhamnolipids from cultivation broths by ATR-FTIR Spectroscopy

Background  

Vibrational spectroscopic techniques are becoming increasingly important and popular because they have the potential to provide rapid and convenient solutions to routine analytical problems. Using these techniques, a variety of substances can be characterized, identified and also quantified rapidly.     

A previously unidentified <Emphasis Type="Italic">Chorioptes</Emphasis> species infesting outer ear canals of moose (<Emphasis Type="Italic">Alces alces</Emphasis>): characterization of the mite and the pathology of infestation

Background  

During the past decade, Chorioptes mites occupying the outer ear canals have been a common finding at routine necropsies of moose (Alces alces) in Sweden, but neither the taxonomy of the mites nor lesions from the infestation have been investigated. In this study, the mites are characterized by morphological and molecular techniques, and the histopathology of the skin of the outer ear canal is described.     

Evaluation of normalization methods for cDNA microarray data by <Emphasis Type="Italic">k</Emphasis>-NN classification

Background  

Non-biological factors give rise to unwanted variations in cDNA microarray data. There are many normalization methods designed to remove such variations. However, to date there have been few published systematic evaluations of these techniques for removing variations arising from dye biases in the context of downstream, higher-order analytical tasks such as classification.     

Cardiac arrhythmia classification using autoregressive modeling

Background  

Computer-assisted arrhythmia recognition is critical for the management of cardiac disorders. Various techniques have been utilized to classify arrhythmias. Generally, these techniques classify two or three arrhythmias or have significantly large processing times. A simpler autoregressive modeling (AR) technique is proposed to classify normal sinus rhythm (NSR) and various cardiac arrhythmias including atrial premature contraction (APC), premature ventricular contraction (PVC), superventricular tachycardia (SVT), ventricular tachycardia (VT) and ventricular fibrillation (VF).     

Direct visualization of hemolymph flow in the heart of a grasshopper (Schistocerca americana)

Background  

Hemolymph flow patterns in opaque insects have never been directly visualized due to the lack of an appropriate imaging technique. The required spatial and temporal resolutions, together with the lack of contrast between the hemolymph and the surrounding soft tissue, are major challenges. Previously, indirect techniques have been used to infer insect heart motion and hemolymph flow, but such methods fail to reveal fine-scale kinematics of heartbeat and details of intra-heart flow patterns.     

Comparison of LPS-stimulated release of cytokines in punch versus transwell tissue culture systems of human gestational membranes

Background  

Cytokine signaling within the amnionic, chorionic and decidual extraplacental gestational membranes plays an important role in membrane rupture and the timing of birth. The predominant in vitro explant culture system for evaluating cytokine induction in human gestational membranes has been the free-floating biopsy punch culture. Punch systems have been used to investigate the impact of various toxicants, pharmaceuticals and genetic variation on expression of pro-inflammatory cytokines. More recently, a dual compartment transwell culture system has been developed that more closely mimics the intrauterine compartment. The current study compares these two systems with respect to release of pro- and anti-inflammatory cytokines in response to lipopolysaccharide (LPS), a model stimulant.