Vemurafenib and concomitant stereotactic radiation for the treatment of melanoma with spinal metastases: A case report

A 56-year-old man with BRAFV600E melanoma and spinal metastases treated with vemurafenib and stereotactic radiation showed a partial response without neurological, skin or mucosal toxicity, 8 months after completion of this combination. This case suggests that stereotactic radiation spares normal tissues and might be safer than conventional fractionated radiation with vemurafenib.     

Perhydrolase-nanotube paint composites with sporicidal and antiviral activity

AcT (perhydrolase) containing paint composites were prepared leading to broad-spectrum decontamination. AcT was immobilized onto multi-walled carbon nanotubes (MWNTs) and then incorporated into latex-based paints to form catalytic coatings. These AcT-based paint composites showed a 6-log reduction in the viability of spores of Bacillus cereus and Bacillus anthracis (Sterne) within 60 min. The paint composites also showed >4-log reduction in the titer of influenza virus (X-31) within 10 min (initially challenged with 10⁷ PFU/mL). AcT-based paint composites were also tested using various perhydrolase acyl donor substrates, including propylene glycol diacetate (PGD), glyceryl triacetate, and ethyl acetate, with PGD observed to be the best among the substrates tested for generation of peracetic acid and killing of bacillus spores. The operational stability of paint composites was also studied at different relative humidities and temperatures to simulate real-life operation.     

Transient fluorescence signals from pyrene labeled pike nerves during action potential possible implications for membrane fluidity changes

Pike olfactory nerves labeled with pyrene and illuminated at 340 nm showed a highly resolved monomer fluorescence emission and a broad excimer emission band at longer wavelength. The excimer formation being controlled by lateral diffusion in the membrane lipids, the ratio of both maxima emission amplitudes is a fluidity parameter and was found to depend on temperature. When these nerves were stimulated, this ratio (F) underwent a small transient decrease ($\text{Δ}\text{F}\text{F}$ range = 10^?3 to 10^?4), synchronous with the propagated impulse. These findings may be interpreted as a transient decreased fluidity of the membrane lipids during excitation     

Pathway analysis of microarray data via regression.

Pathway analysis of microarray data evaluates gene expression profiles of a priori defined biological pathways in association with a phenotype of interest. We propose a unified pathway-analysis method that can be used for diverse phenotypes including binary, multiclass, continuous, count, rate, and censored survival phenotypes. The proposed method also allows covariate adjustments and correlation in the phenotype variable that is encountered in longitudinal, cluster-sampled, and paired designs. These are accomplished by combining the regression-based test statistic for each individual gene in a pathway of interest into a pathway-level test statistic. Applications of the proposed method are illustrated with two real pathway-analysis examples: one evaluating relapse-associated gene expression involving a matched-pair binary phenotype in children with acute lymphoblastic leukemia; and the other investigating gene expression in breast cancer tissues in relation to patients' survival (a censored survival phenotype). Implementations for various phenotypes are available in R. Additionally, an Excel Add-in for a user-friendly interface is currently being developed.     

Comparative study of different methods for detection of toxic and other enzymatic factors in Vibrio cholerae strains

The purpose of this work was to characterize the toxin profile and the presence of other virulence factors involved in the pathogenesis and biology of 13 V. cholerae O1 (11 clinical cases and 2 waters) and 6 V. cholerae non O1 strains (4 clinical cases and 2 waters) using genetic (PCR), immunological (RPLA), biochemical (NAD degradation, haemolysis, Kanagawa phenomenon, caseinase, lecithinase, mucinase, amylase, esculine hydrolysis) and cell culture (Vero E6, HEp-2) assays. The results indicated a concordance between PCR-RPLA (84%), PCR-NAD (73%) and RPLA-NAD (84%) methods. The sensitivity of RPLA and NAD degradation methods were comparable to PCR in detecting CT in Vibrio cholerae O1 strains. Although NAD degradation method was not exclusively specific for the CT detection, it proved its usefulness in screening certain virulent, CT-negative clones of V. cholerae. The cytotoxic effect on Vero E6 cells, enzyme production (Kanagawa haemolysins, lecithinase, caseinase, esculine hydrolysis) as well as adherence ability on inert substrate proved to be much more constant in V. cholerae non O1 (CT- negative) than in V. cholerae O1 (CT-positive). All V. cholerae non O1 strains isolated in diarrheal cases were Kanagawa positive. This complex of virulence factors detected in V. cholerae non O1 strains could probably contribute during interepidemic periods to human-to-human transmission and to greater resistance as compared to O1 strains in the environment.     

A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis

Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing -mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown) organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.     

Improving gene set analysis of microarray data by SAM-GS

Background  

Gene-set analysis evaluates the expression of biological pathways, or a priori defined gene sets, rather than that of individual genes, in association with a binary phenotype, and is of great biologic interest in many DNA microarray studies. Gene Set Enrichment Analysis (GSEA) has been applied widely as a tool for gene-set analyses. We describe here some critical problems with GSEA and propose an alternative method by extending the individual-gene analysis method, Significance Analysis of Microarray (SAM), to gene-set analyses (SAM-GS).     

Influence of temporal lobe lesions on photic-evoked responses in occipital visual areas.

In 20 patients with temporal lobe lesions and 10 controls, the averaged photic-evoked responses (APERs) and their dispersion pattern (DP) were investigated in inion-vertex-lead and bilaterally in inion-parietal leads (I-P3 and I-P4). The patients with temporal lobe lesions, regardless of lesion location in temporal areas, displayed either absence of APER (the whole APER or only the initial components) or a latency increase without amplitude changes. The DP was generally abnormal. The role of the temporal lobe in the organization of APER in visual areas is discussed.