Star p-hub center problem and star p-hub median problem with bounded path lengths

We consider two problems that arise in designing two-level star networks taking into account service quality considerations. Given a set of nodes with pairwise traffic demand and a central hub, we select p hubs and connect them to the central hub with direct links and then we connect each nonhub node to a hub. This results in a star/star network. In the first problem, called the Star p-hub Center Problem, we would like to minimize the length of the longest path in the resulting network. In the second problem, Star p-hub Median Problem with Bounded Path Lengths, the aim is to minimize the total routing cost subject to upper bound constraints on the path lengths. We propose formulations for these problems and report the outcomes of a computational study where we compare the performances of our formulations. © 2012 Elsevier Ltd. All rights reserved

The etiology of neuromuscular fatigue induced by the 5-m shuttle run test in adult soccer players

This study investigated the etiology of neuromuscular fatigue induced by a 5-m shuttle run test (5MSRT) in soccer players. Nineteen adult male amateur soccer players (age: 20.0 ± 2.9 years) participated in the present study. Before and after the 5MSRT, they were instructed to complete a maximal voluntary isometric contraction (MVIC) of the knee extensors (KE) during and after which two electrical stimulations were applied at the femoral nerve. Voluntary activation level (VAL), surface electromyography recordings (sEMG), electrophysiological (Mmax) and potentiated resting twitch (Ptw) responses of the KE were compared between pre- and post-5MSRT. Rating of perception exertion (RPE) was also assessed before, during the test immediately following each sprint repetition and after the test. The distance covered during each sprint significantly decreased as the number of trials performed increased (p<.05). The RPE reported following each sprint significantly increased throughout the test. In addition, MVIC (-9%), sEMG (-23%), VAL (-15%), Ptw (-26%) and Mmax (~22%) of the KE were lowered from pre-to-post 5MSRT (.001 < p < .01). The 5MSRT induced a decrease of repeated-sprint running performance and MVIC of the KE. These decrements were accompanied by lowered VAL, sEMG, Ptw and Mmax values of the KE reflecting the involvement of both the central and peripheral origins in the 5MSRT-induced fatigue. Given the important muscle stress induced by 5MSRT, this strenuous test must be applied with caution, after an inevitable familiarization phase, and not during the competition period to avoid the risk of serious injury

Recovery, assessment, and molecular characterization of minor olive genotypes in Tunisia

Olive is one of the oldest cultivated species in the Mediterranean Basin, including Tunisia, where it has a wide diversity, with more than 200 cultivars, of both wild and feral forms. Many minor cultivars are still present in marginal areas of Tunisia, where they are maintained by farmers in small local groves, but they are poorly characterized and evaluated. In order to recover this neglected germplasm, surveys were conducted in different areas, and 31 genotypes were collected, molecularly characterized with 12 nuclear microsatellite (simple sequence repeat (SSR)) markers, and compared with 26 reference cultivars present in the Tunisian National Olive collection. The analysis revealed an overall high genetic diversity of this olive’s germplasm, but also discovered the presence of synonymies and homonymies among the commercialized varieties. The structure analysis showed the presence of different gene pools in the analyzed germplasm. In particular, the marginal germplasm from Ras Jbal and Azmour is characterized by gene pools not present in commercial (Nurseries) varieties, pointing out the very narrow genetic base of the commercialized olive material in Tunisia, and the need to broaden it to avoid the risk of genetic erosion of this species in this country

Early Life Stress Triggers Persistent Colonic Barrier Dysfunction and Exacerbates Colitis in Adult IL-10−/− Mice:

It has become increasingly evident that disease flares in the human inflammatory bowel diseases (IBD) are influenced by life stress. It is known that life stress can trigger disturbances in intestinal barrier function and activate proinflammatory signaling pathways, which are important contributors to intestinal inflammation and clinical disease; however, the exact mechanisms of stress-induced IBD exacerbations remain to be elucidated. Here we present a model of early life stress-induced exacerbation of colitis in IL-10-/- mice

Linear inequalities among graph invariants: Using GraPHedron to uncover optimal relationships

Optimality of a linear inequality in finitely many graph invariants is defined through a geometric approach. For a fixed number of graph vertices, consider all the tuples of values taken by the invariants on a selected class of graphs. Then form the polytope which is the convex hull of all these tuples. By definition, the optimal linear inequalities correspond to the facets of this polytope. They are finite in number, are logically independent, and generate precisely all the linear inequalities valid on the class of graphs. The computer system GraPHedron, developed by some of the authors, is able to produce experimental data about such inequalities for a "small" number of vertices. It greatly helps in conjecturing optimal linear inequalities, which are then hopefully proved for any number of vertices. Two examples are investigated here for the class of connected graphs. First, all the optimal linear inequalities for the stability number and the number of edges are obtained. To this aim, a problem of Ore (1962) related to the Turán Theorem (1941) is solved. Second, several optimal inequalities are established for three invariants: the maximum degree, the irregularity, and the diameter. © 2008 Wiley Periodicals, Inc

SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences

<p>Abstract</p> <p>Background</p> <p>Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limited to short ones or impose some constraints on the pattern type. Many patterns for binding sites in prokaryotic species are not well characterized but are known to be large, between 16–30 base pairs (bp) and contain at least 2 conserved bases. The length of prokaryotic species promoters (about 400 bp) and our interest in studying a small set of genes that could be a cluster of co-regulated genes from microarray experiments led to the development of a new exhaustive algorithm targeting these large patterns.</p> <p>Results</p> <p>We present Searchpattool, a new method to search for and select the most specific (conservative) frequent patterns. This method does not impose restrictions on the density or the structure of the pattern. The best patterns (motifs) are selected using several statistics, including a new application of a z-score based on the number of matching sequences. We compared Searchpattool against other well known algorithms on a <it>Bacillus subtilis </it>group of 14 input sequences and found that in our experiments Searchpattool always performed the best based on performance scores.</p> <p>Conclusion</p> <p>Searchpattool is a new method for pattern discovery relative to transcription factor binding sites for species or genes with short promoters. It outputs the most specific significant patterns and helps the biologist to choose the best candidates.</p

Systematic Bias in Genomic Classification Due to Contaminating Non-neoplastic Tissue in Breast Tumor Samples

Abstract Background Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. Methods To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Results Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Conclusions Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor