Efficient Implementation of a Synchronous Parallel Push-Relabel Algorithm

Motivated by the observation that FIFO-based push-relabel algorithms are able to outperform highest label-based variants on modern, large maximum flow problem instances, we introduce an efficient implementation of the algorithm that uses coarse-grained parallelism to avoid the problems of existing parallel approaches. We demonstrate good relative and absolute speedups of our algorithm on a set of large graph instances taken from real-world applications. On a modern 40-core machine, our parallel implementation outperforms existing sequential implementations by up to a factor of 12 and other parallel implementations by factors of up to 3

Finding Disjoint Paths on Directed Acyclic Graphs

Given k+1 pairs of vertices (s_1,s_2),(u_1,v_1),...,(u_k,v_k) of a directed acyclic graph, we show that a modified version of a data structure of Suurballe and Tarjan can output, for each pair (u_l,v_l) with 1<=l<=k, a tuple (s_1,t_1,s_2,t_2) with {t_1,t_2}={u_l,v_l} in constant time such that there are two disjoint paths p_1, from s_1 to t_1, and p_2, from s_2 to t_2, if such a tuple exists. Disjoint can mean vertex- as well as edge-disjoint. As an application we show that the presented data structure can be used to improve the previous best known running time O(mn) for the so called 2-disjoint paths problem on directed acyclic graphs to O(m(log(n)/log(2+m/n))+n*log³(n)). In this problem, given four vertices s_1, s_2, t_1, and t_2, we want to construct two disjoint paths p_1, from s_1 to t_1, and p_2, from s_2 to t_2, if such paths exist

Low metabolic activity of biofilm formed by Enterococcus faecalis isolated from healthy humans and wild mallards (Anas platyrhynchos)

It is widely known that Enterococcus faecalis virulence is related to its biofilm formation. Although Enterococci are common commensal organisms of the gastrointestinal tract, the difference between commensal and pathogen strains remain unclear. In this study, we compare the biochemical profile of the biofilms formed by two groups of medical and two groups of commensal strains. The medical strains were isolated as pathogens from infections of urinary tract and other infections (wounds, pus and bedsores), and the commensal strains were taken from faeces of healthy volunteers and faeces of wild mallards (Anas platyrhynchos) living in an urban environment. The properties of biofilms formed by medical and commensal strains differed significantly. Commensal strains showed lower metabolic activity and glucose uptake and higher biofilm biomass than the medical ones. Consistent with glucose uptake experiments, we found that the glucose dehydrogenase gene was more expressed in medical strains. These results indicate that higher metabolic activity and lower protein concentration of E. faecalis cells within biofilms are formed during infections.This work was supported by the Medical University of Gdansk research grant (GUMed W-65) and was financed partly by University of Gdansk research grant (BW 1440-5-0099-7). We are grateful to Katarzyna Zolkos for her help in catching mallards and Magdalena Remisiewicz for correcting the English. Catarina Seabra helped in preparing assays

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

Background: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses