The multiple pheromone ant clustering algorithm and its application to real world domains

The Multiple Pheromone Ant Clustering Algorithm (MPACA) models the collective behaviour of ants to find clusters in data and to assign objects to the most appropriate class. It is an ant colony optimisation approach that uses pheromones to mark paths linking objects that are similar and potentially members of the same cluster or class. Its novelty is in the way it uses separate pheromones for each descriptive attribute of the object rather than a single pheromone representing the whole object. Ants that encounter other ants frequently enough can combine the attribute values they are detecting, which enables the MPACA to learn influential variable interactions. This paper applies the model to real-world data from two domains. One is logistics, focusing on resource allocation rather than the more traditional vehicle-routing problem. The other is mental-health risk assessment. The task for the MPACA in each domain was to predict class membership where the classes for the logistics domain were the levels of demand on haulage company resources and the mental-health classes were levels of suicide risk. Results on these noisy real-world data were promising, demonstrating the ability of the MPACA to find patterns in the data with accuracy comparable to more traditional linear regression models. © 2013 Polish Information Processing Society.

Close contact fluctuations:the seeding of signalling domains in the immunological synapse

We analyse the size and density of thermally induced regions of close contact in cell : cell contact interfaces within a harmonic potential approximation, estimating these regions to be below one-tenth of a micron across. Our calculations indicate that as the distance between the close contact threshold depth and the mean membrane-membrane separation increases, the density of close contact patches decreases exponentially while there is only a minimal variation in their mean size. The technique developed can be used to calculate the probability of first crossing in reflection symmetry violating systems. © Europhysics Letters Association.

A procedure for the temperature reconstruction in corner domains from Cauchy data

An iterative procedure is proposed for the reconstruction of a stationary temperature field from Cauchy data given on a part of the boundary of a bounded plane domain where the boundary is smooth except for a finite number of corner points. In each step, a series of mixed well-posed boundary value problems are solved for the heat operator and its adjoint. Convergence is proved in a weighted L2-space. Numerical results are included which show that the procedure gives accurate and stable approximations in relatively few iterations.

Cardiac dysfunction and cell damage across clinical stages of severity in growth-restricted fetuses

Objective - The purpose of this study was to assess cardiac function and cell damage in intrauterine growth-restricted (IUGR) fetuses across clinical Doppler stages of deterioration. Study Design - One hundred twenty appropriate-for-gestational-age and 81 IUGR fetuses were classified in stages 1/2/3 according umbilical artery present/absent/reversed end-diastolic blood flow, respectively. Cardiac function was assessed by modified-myocardial performance index, early-to-late diastolic filling ratios, cardiac output, and cord blood B-type natriuretic peptide; myocardial cell damage was assessed by heart fatty acid–binding protein, troponin-I, and high-sensitivity C-reactive protein. Results - Modified-myocardial performance index, blood B-type natriuretic peptide, and early-to-late diastolic filling ratios were increased in a stage-dependent manner in IUGR fetuses, compared with appropriate-for-gestational-age fetuses. Heart fatty acid–binding protein levels were higher in IUGR fetuses at stage 3, compared with control fetuses. Cardiac output, troponin-I, and high-sensitivity C-reactive protein did not increase in IUGR fetuses at any stage. Conclusion - IUGR fetuses showed signs of cardiac dysfunction from early stages. Cardiac dysfunction deteriorates further with the progression of fetal compromise, together with the appearance of biochemical signs of cell damage.

Communication between the nucleotide binding domains of P-glycoprotein occurs via conformational changes that involve residue 508

Our aim is to provide molecular understanding of the mechanisms underlying the (i) interaction between the two nucleotide binding domains (NBDs) and (ii) coupling between NBDs and transmembrane domains within P-glycoprotein (Pgp) during a transport cycle. To facilitate this, we have introduced a number of unique cysteine residues at surface exposed positions (E393C, S452C, I500C, N508C, and K578C) in the N-terminal NBD of Pgp, which had previously been engineered to remove endogenous cysteines. Positions of the mutations were designed using a model based on crystallographic features of prokaryotic NBDs. The single cysteine mutants were expressed in insect cells using recombinant baculovirus and the proteins purified by metal affinity chromatography by virtue of a polyhistidine tag. None of the introduced cysteine residues perturbed the function of Pgp as judged by the characteristics of drug stimulated ATP hydrolysis. The role of residues at each of the introduced sites in the catalytic cycle of Pgp was investigated by the effect of covalent conjugation with N-ethyl-maleimide (NEM). All but one mutation (K578C) was accessible to labeling with [3H]-NEM. However, perturbation of ATPase activity was only observed for the derivitized N508C isoform. The principle functional manifestation was a marked inhibition of the "basal" rate of ATP hydrolysis. Neither the extent nor potency to which a range of drugs could affect the ATPase activity were altered in the NEM conjugated N508C isoform. The results imply that the accessibility of residue 508, located in the alpha-helical subdomain of NBD1 in Pgp, is altered by the conformational changes that occur during ATP hydrolysis.

Effects of lipoic acid and dihydrolipoic acid on total erythrocytic thiols under conditions of restricted glucose in vitro

The effects of lipoic acid and dihydrolipoic acid were explored on total thiol maintenance in diabetic and non-diabetic human erythrocytes in vitro over 22 hr in a 37°C incubation system with no added glucose. Over 18-22.5 hr after treatment in both non-diabetic and diabetic cells, lipoic acid (1 mM) was associated with greater loss of cellular thiols than dihydrolipoic acid (1 mM), compared to respective control values. At 0.1 mM, in non-diabetic cells, although lipoic acid-treated cells' thiol levels were significantly lower than control, there was no significant difference between dihydrolipoic acid-treated cells and control cells regarding thiol levels. In addition, at 0.1 mM, dihydrolipoic acid-treated diabetic cells showed a reduction in thiol levels compared to control. At 0.01 mM, lipoic acid-treated cells had significantly lower measured thiol levels compared with diabetic cells exposed to dihydrolipoic acid, whereas in non-diabetic cells, dihydrolipoic acid-treated erythrocytic thiol levels were significantly greater than those treated with lipoic acid, although there were no other significant differences between the groups. At 22.5 hr, control values of methaemoglobin rose to 6.4 ± 1.1% in diabetic cells and 3.6 ± 2.1% in non-diabetic cells. Lipoic acid (1 mM) showed greater methaemoglobin formation in diabetic rather than non-diabetic cells (13.6 ± 1.5% versus 11.6 ± 1.5%), whereas dihydrolipoic acid-treated diabetic and non-diabetic cells were less potent in methaemoglobin generation (8.5 ± 2.4% and 8.4 ± 1.4%, respectively). These studies suggest that in certain circumstances such as hypoglycaemia, lipoic acid administration may actually be detrimental to cellular oxidant protection status. © 2006 The Authors.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

Site-restricted web searches for data collection in regional dialectology

This article presents a new method for data collection in regional dialectology based on site-restricted web searches. The method measures the usage and determines the distribution of lexical variants across a region of interest using common web search engines, such as Google or Bing. The method involves estimating the proportions of the variants of a lexical alternation variable over a series of cities by counting the number of webpages that contain the variants on newspaper websites originating from these cities through site-restricted web searches. The method is evaluated by mapping the 26 variants of 10 lexical variables with known distributions in American English. In almost all cases, the maps based on site-restricted web searches align closely with traditional dialect maps based on data gathered through questionnaires, demonstrating the accuracy of this method for the observation of regional linguistic variation. However, unlike collecting dialect data using traditional methods, which is a relatively slow process, the use of site-restricted web searches allows for dialect data to be collected from across a region as large as the United States in a matter of days.

Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

Domains with Complicated Structures and Their Ontologies

The article defines the class of domains with complicated structures, gives the definition of multilevel ontologies and determines the method for developing such ontologies.

Learning higher-level features with convolutional restricted Boltzmann machines for sentiment analysis

In recent years, learning word vector representations has attracted much interest in Natural Language Processing. Word representations or embeddings learned using unsupervised methods help addressing the problem of traditional bag-of-word approaches which fail to capture contextual semantics. In this paper we go beyond the vector representations at the word level and propose a novel framework that learns higher-level feature representations of n-grams, phrases and sentences using a deep neural network built from stacked Convolutional Restricted Boltzmann Machines (CRBMs). These representations have been shown to map syntactically and semantically related n-grams to closeby locations in the hidden feature space. We have experimented to additionally incorporate these higher-level features into supervised classifier training for two sentiment analysis tasks: subjectivity classification and sentiment classification. Our results have demonstrated the success of our proposed framework with 4% improvement in accuracy observed for subjectivity classification and improved the results achieved for sentiment classification over models trained without our higher level features.

Groups with Restricted Conjugacy Classes

Let F C 0 be the class of all finite groups, and for each nonnegative integer n define by induction the group class FC^(n+1) consisting of all groups G such that for every element x the factor group G/CG ( ^G ) has the property FC^n . Thus FC^1 -groups are precisely groups with finite conjugacy classes, and the class FC^n obviously contains all finite groups and all nilpotent groups with class at most n. In this paper the known theory of FC-groups is taken as a model, and it is shown that many properties of FC-groups have an analogue in the class of FC^n -groups.

Description Reduction for Restricted Sets of (0,1) Matrices

* The research is supported partly by INTAS: 04-77-7173 project, http://www.intas.be

Numerical solution of parabolic Cauchy problems in planar corner domains

An iterative method for the parabolic Cauchy problem in planar domains having a finite number of corners is implemented based on boundary integral equations. At each iteration, mixed well-posed problems are solved for the same parabolic operator. The presence of corner points renders singularities of the solutions to these mixed problems, and this is handled with the use of weight functions together with, in the numerical implementation, mesh grading near the corners. The mixed problems are reformulated in terms of boundary integrals obtained via discretization of the time-derivative to obtain an elliptic system of partial differential equations. To numerically solve these integral equations a Nyström method with super-algebraic convergence order is employed. Numerical results are presented showing the feasibility of the proposed approach. © 2014 IMACS.

Methodology for Language Analysis and Generation in Closed Domains: Pharmaceutical Leaflet

The best results in the application of computer science systems to automatic translation are obtained in word processing when texts pertain to specific thematic areas, with structures well defined and a concise and limited lexicon. In this article we present a plan of systematic work for the analysis and generation of language applied to the field of pharmaceutical leaflet, a type of document characterized by format rigidity and precision in the use of lexicon. We propose a solution based in the use of one interlingua as language pivot between source and target languages; we are considering Spanish and Arab languages in this case of application.