SLIDER: Mining correlated motifs in protein-protein interaction networks

Abstract—Correlated motif mining (CMM) is the problem to find overrepresented pairs of patterns, called motif pairs, in interacting protein sequences. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the method SLIDER which uses local search with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks

Methodology of the biological risk classification of animal pathogens in Belgium

The biological hazards posed by micro-organisms have lead to their categorisation into risk groups and the elaboration of classification lists. Current classification systems rely on criteria defined by the World Health Organization, which cover the severity of the disease the micro-organism might cause, its ability to spread and the availability of prophylaxis or efficient treatment. Animal pathogens are classified according to the definitions of the World Organization of Animal Health, which also consider economic aspects of disease. In Europe, classification is often directly linked to containment measures. The Belgian classification system however, only considers the inherent characteristics of the micro-organism, not its use, making the risk classification independent of containment measures. A common classification list for human and animal pathogens has been developed in Belgium using as comprehensive an approach as possible. Evolution of scientific knowledge will demand regular updating of classification lists. This paper describes the Belgian risk classification system and the methodology that was used for its peer-reviewed revision (with a focus on animal pathogens)

The influence of fatty acids on the expression of virulence genes of Salmonella Typhimurium and the colonization of pigs

Salmonella Typhimurium infections in pigs are a major source of human foodborne salmonellosis. To reduce the number of infected pigs, actdified feed or drinking water can be administrated. A study was carried out to evaluate the use of short-chain fatty acids (SCFA) and medium-chain fatty acids (MCFA) for the control of Salmonella Typhimurium infections in ptgs. Short-chain fatty acids formate, acetate, propionate and butyrate (pH 6, osm 600, cone 1 OmM) and medium-chain fatty acids caproic, caprylic and capric acid (pH6, osm 600, cone 2mM) were used

Secure biometric authentication with improved accuracy

We propose a new hybrid protocol for cryptographically secure biometric authentication. The main advantages of the proposed protocol over previous solutions can be summarised as follows: (1) potential for much better accuracy using different types of biometric signals, including behavioural ones; and (2) improved user privacy, since user identities are not transmitted at any point in the protocol execution. The new protocol takes advantage of state-of-the-art identification classifiers, which provide not only better accuracy, but also the possibility to perform authentication without knowing who the user claims to be. Cryptographic security is based on the Paillier public key encryption scheme

A Formal Study of the Privacy Concerns in Biometric-Based Remote Authentication Schemes

With their increasing popularity in cryptosystems, biometrics have attracted more and more attention from the information security community. However, how to handle the relevant privacy concerns remains to be troublesome. In this paper, we propose a novel security model to formalize the privacy concerns in biometric-based remote authentication schemes. Our security model covers a number of practical privacy concerns such as identity privacy and transaction anonymity, which have not been formally considered in the literature. In addition, we propose a general biometric-based remote authentication scheme and prove its security in our security model

Relation between antimicrobial use and resistance in Belgian pig herds

The aim of this study was to determine the link between the characteristics of antimicrobial therapy and occurrence of antimicrobial resistance in Escherichia coli of clinically healthy pigs exposed to antimicrobial treatments. A total of 918 Escherichia coli isolates were obtained from faecal samples, collected from 50 pig herds at the end of the fattening period and susceptibility was tested towards 15 different antimicrobial agents, using the disk diffusion method

Evolution of antimicrobial resistance of Salmonella isolates from pigs in Belgium

The aim of the present study was to investigate the antimicrobial sensitivity of Salmonella isolates from pigs between 2011 and 2015. In total, 275 Salmonella isolates from samples originating from pigs sent in for diagnostic examination at Animal Health Care Flanders were tested for their sensitivity against different antimicrobials. Except for colistin, where the disk prediffusion test was used, the disk diffusion test was used. E. coli ATCC 25922 was used as reference isolate and the interpretative breakpoints were based on the Clinical and Laboratory Standards Institute

SPI-2 of Salmonella Typhimurium is not necessary for long term colonization of pigs

Unravelling the role of Salmonella virulence factors in the porcine host could greatly contribute to the development of control measures such as vaccination. The virulence genes located on the Salmonella Pathogenicity Island 2 (SPI-2) are indispensable for the induction of systemic disease and persistence in BALB/c mice. The role of this pathogenicity island in the pathogenesis of Salmonella Typhimurium infections in pigs is not documented. Therefore, in the present study, the interactions of a porcine field strain of Salmonella Typhimurium and a non-polar isogenic SPI-2 (D-ssrA) deletion mutant were compared in both in vitro and in vivo models. The ssrA mutant strain displayed decreased SPI-2 expression levels in vitro and was attenuated in a mouse model after oral inoculation. No difference was seen in the expression of SPI-1 related virulence genes. Through flowcytometric analysis, the ssrA mutant strain was found to be moderately attenuated in intracellular replication in porcine macrophages in vitro. In an infection experiment, 2 groups of 10 piglets were orally inoculated with the wild type or the ssrA mutant strain. The infection of the animals inoculated with the ssrA mutant strain followed a similar course as the animals infected with the wild type strain. At days 5 and 28 post inoculation, the animals of both groups were infected to the same extent in the gut and gut-associated lymphoid tissue, as well as in the mternal organs. These results suggest that SPI-2 of Salmonella Typhimurium may not contribute to the colonization of pigs to the same extent as it contributes to the colonization of BALB/c mice