Manipulation Strategies for the Rank Maximal Matching Problem

We consider manipulation strategies for the rank-maximal matching problem. In the rank-maximal matching problem we are given a bipartite graph $G = (A \cup P, E)$ such that $A$ denotes a set of applicants and $P$ a set of posts. Each applicant $a \in A$ has a preference list over the set of his neighbours in $G$, possibly involving ties. Preference lists are represented by ranks on the edges - an edge $(a,p)$ has rank $i$, denoted as $rank(a,p)=i$, if post $p$ belongs to one of $a$'s $i$-th choices. A rank-maximal matching is one in which the maximum number of applicants is matched to their rank one posts and subject to this condition, the maximum number of applicants is matched to their rank two posts, and so on. A rank-maximal matching can be computed in $O(\min(c \sqrt{n},n) m)$ time, where $n$ denotes the number of applicants, $m$ the number of edges and $c$ the maximum rank of an edge in an optimal solution. A central authority matches applicants to posts. It does so using one of the rank-maximal matchings. Since there may be more than one rank- maximal matching of $G$, we assume that the central authority chooses any one of them randomly. Let $a_1$ be a manipulative applicant, who knows the preference lists of all the other applicants and wants to falsify his preference list so that he has a chance of getting better posts than if he were truthful. In the first problem addressed in this paper the manipulative applicant $a_1$ wants to ensure that he is never matched to any post worse than the most preferred among those of rank greater than one and obtainable when he is truthful. In the second problem the manipulator wants to construct such a preference list that the worst post he can become matched to by the central authority is best possible or in other words, $a_1$ wants to minimize the maximal rank of a post he can become matched to

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

Structural and properties of Zn-Al2O3-SiC nano-composite coatings by direct electrolytic process

In this paper, Zn-SiC and Zn-Al2O3-SiC composite coating were fabricated by electrodeposition technique from sulfates bath. The resulting composite coating was carried out by adding Al2O3/SiC particulate to a zinc-containing bath. The properties of the composite coating were investigated by SEM equipped with EDS, XRD, and AFM. The electrochemical behavior of the coating alloy was evaluated in 3.65 % NaCl with linear polarization technique and mechanically examined by durascan microhardness tester. The morphology of the thermal treated coatings at 400 °C in 6 h was viewed with high optical microscope (OPM). The results show hardness, thermal stability, and anti-corrosion properties of Zn-Al2O3-SiC were improved significantly as against Zn- SiC coating matrixes. This was attributed to dispersive strengthening effect and grain induced effort of Al2O3/SiC particulate. The decrease in corrosion and thermal stability at 15 g/L of SiC concentration may be as a result of agglomeration and the superimposed particle in the plating bath

Budesonide/formoterol and formoterol provide similar rapid relief in patients with acute asthma showing refractoriness to salbutamol

BACKGROUND: To compare the efficacy and safety of budesonide/formoterol (Symbicort(®)) with formoterol (Oxis(®)) in the treatment of patients with acute asthma who showed evidence of refractoriness to short-acting β(2)-agonist therapy. METHODS: In a 3 hour, randomized, double-blind study, a total of 115 patients with acute asthma (mean FEV(1 )40% of predicted normal) and a refractory response to salbutamol (mean reversibility 2% of predicted normal after inhalation of 400 μg), were randomized to receive either budesonide/formoterol (320/9 μg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 1280/36 μg]) or formoterol (9 μg, 2 inhalations at t = -5 minutes and 2 inhalations at 0 minutes [total dose 36 μg]). The primary efficacy variable was the average FEV(1 )from the first intake of study medication to the measurement at 90 minutes. Secondary endpoints included changes in FEV(1 )at other timepoints and change in respiratory rate at 180 minutes. Treatment success, treatment failure and patient assessment of the effectiveness of the study medication were also measured. RESULTS: FEV(1 )increased after administration of the study medication in both treatment groups. No statistically significant difference between the treatment groups was apparent for the primary outcome variable, or for any of the other efficacy endpoints. There were no statistically significant between-group differences for treatment success, treatment failure or patient assessment of medication effectiveness. Both treatments were well tolerated. CONCLUSION: Budesonide/formoterol and formoterol provided similarly rapid relief of acute bronchoconstriction in patients with asthma who showed evidence of refractoriness to a short-acting β(2)-agonist

Direct Nitrate Reductase Assay versus Microscopic Observation Drug Susceptibility Test for Rapid Detection of MDR-TB in Uganda

The most common method for detection of drug resistant (DR) TB in resource-limited settings (RLSs) is indirect susceptibility testing on Lowenstein-Jensen medium (LJ) which is very time consuming with results available only after 2–3 months. Effective therapy of DR TB is therefore markedly delayed and patients can transmit resistant strains. Rapid and accurate tests suitable for RLSs in the diagnosis of DR TB are thus highly needed. In this study we compared two direct techniques - Nitrate Reductase Assay (NRA) and Microscopic Observation Drug Susceptibility (MODS) for rapid detection of MDR-TB in a high burden RLS. The sensitivity, specificity, and proportion of interpretable results were studied. Smear positive sputum was collected from 245 consecutive re-treatment TB patients attending a TB clinic in Kampala, Uganda. Samples were processed at the national reference laboratory and tested for susceptibility to rifampicin and isoniazid with direct NRA, direct MODS and the indirect LJ proportion method as reference. A total of 229 specimens were confirmed as M. tuberculosis, of these interpretable results were obtained in 217 (95%) with either the NRA or MODS. Sensitivity, specificity and kappa agreement for MDR-TB diagnosis was 97%, 98% and 0.93 with the NRA; and 87%, 95% and 0.78 with the MODS, respectively. The median time to results was 10, 7 and 64 days with NRA, MODS and the reference technique, respectively. The cost of laboratory supplies per sample was low, around 5 USD, for the rapid tests. The direct NRA and MODS offered rapid detection of resistance almost eight weeks earlier than with the reference method. In the study settings, the direct NRA was highly sensitive and specific. We consider it to have a strong potential for timely detection of MDR-TB in RLS

Understanding the decomposition reaction mechanism of chrysanthemic acid: a computational study

<p>Abstract</p> <p>Background</p> <p>Chrysanthemic acid (<b>CHA</b>) is a major product from the photodecomposition of pyrethrin which is an important class of pesticide compounds.</p> <p>In the following paper, Hybrid density functional theory (DFT) calculations of the potential energy surface (PES) for three possible channels decomposition of chrysanthemic acid <b>(</b>cis-trans isomerization, rearrangement and fragmentation) have been carried at the B3LYP/6-311+G** level of theory. DFT was employed to optimize the geometry parameters of the reactants, transition states, intermediates and products based on detailed potential energy surfaces (PES).</p> <p>Results</p> <p>Our results suggest that all three pathways of <b>CHA </b>are endothermic. DFT calculations revealed that the activation barriers for cis-trans isomerization are low, leading to a thermodynamically favorable process than other two pathways. We also investigated the solvent effect on the PES using the polarizable continuum model (PCM). In addition, time-dependent density functional theory (TDDFT) calculations showed that these reactions occur in the ground state rather than in an excited state.</p> <p>Conclusion</p> <p>The rearrangement process seems to be more favorable than the decomposition of <b>CHA </b>to carbene formation. The solvent effect calculations indicated no changes in the shape of the PES with three continua (water, ethanol and cyclohexane), although the solvents tend to stabilize all of the species.</p

Genome Majority Vote Improves Gene Predictions

Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps

Excess risk of adverse pregnancy outcomes in women with porphyria: a population-based cohort study

The porphyrias comprise a heterogeneous group of rare, primarily hereditary, metabolic diseases caused by a partial deficiency in one of the eight enzymes involved in the heme biosynthesis. Our aim was to assess whether acute or cutaneous porphyria has been associated with excess risks of adverse pregnancy outcomes. A population-based cohort study was designed by record linkage between the Norwegian Porphyria Register, covering 70% of all known porphyria patients in Norway, and the Medical Birth Registry of Norway, based on all births in Norway during 1967–2006. The risks of the adverse pregnancy outcomes preeclampsia, delivery by caesarean section, low birth weight, premature delivery, small for gestational age (SGA), perinatal death, and congenital malformations were compared between porphyric mothers and the rest of the population. The 200 mothers with porphyria had 398 singletons during the study period, whereas the 1,100,391 mothers without porphyria had 2,275,317 singletons. First-time mothers with active acute porphyria had an excess risk of perinatal death [adjusted odds ratio (OR) 4.9, 95% confidence interval (CI) 1.5–16.0], as did mothers with the hereditable form of porphyria cutanea tarda (PCT) (3.0, 1.2–7.7). Sporadic PCT was associated with an excess risk of SGA [adjusted relative risk (RR) 2.0, 1.2–3.4], and for first-time mothers, low birth weight (adjusted OR 3.4, 1.2–10.0) and premature delivery (3.5, 1.2–10.5) in addition. The findings suggest women with porphyria should be monitored closely during pregnancy

The FGGY carbohydrate kinase family : insights into the evolution of functional specificities

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Computational Biology 7 (2011): e1002318, doi:10.1371/journal.pcbi.1002318.Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.This study was funded by NIH and DOE grants