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Biomedical subjects

S Hazout

Publications and source records attributed to S Hazout.

At least 19 recordsLinked to original sources
PubMed1992

Searching for geometric molecular shape complementarity using bidimensional surface profiles.

The study presented herein is a bidimensional approach to the complementarity of two molecular surfaces. From two chosen sections we have established a methodology of generating the optimal matching of two shapes. Our approach consists in describing two molecular surface sections by a shape vector (the angular profile), in finding their matching patterns by comparison of the two profiles, and in optimizing the relative locations of the two sections in two-dimensional space, using rotations and translations defined by geometric characteristics. The set of optimal configurations are successively displayed on a screen. Satisfying results have been obtained for the matching of the complex kallikreine A-trypsin pancreatic bovin 2. This efficient method could be used as a preprocessing for a tridimensional shape complementarity approach between two molecular surfaces.

Animals↗
PubMed1992

A method for delineating structurally homogeneous regions in protein sequences.

A homogeneous region in a protein sequence is a set of contiguous residues that share common features, concerning physico-chemical, structural and mutational information. This paper presents a method for identifying such homogeneous regions. From a profile describing a given type of biological information along the sequence, the algorithm allows the segmentation of the sequence by optimizing a criterion characterized by two user-defined control parameters: the 'homogenizing degree' of the regions and the 'site neighbourhood' size. We apply the method to the envelope proteins of the human immunodeficiency virus HIV-1, for the identification of homogeneous regions in a hydrophobicity profile and the delineation of variable and conserved regions in a variability profile.

Algorithms↗
PubMed1992

[Familial Alzheimer's disease in France: results of a preliminary survey].

This study concerns French families with Alzheimer's disease (13 families, with 37 diseased individuals). The incidence of female patients is higher than that of males. Variance of the age of onset is less important for intra-familial than inter-familial cases. The mean duration of the disease is shorter for early onset forms. One of these families was retained for molecular genetics studies.

Age Factors↗
PubMed1991

FORME: an interactive package for protein backbone deformation.

The FORME package presented herein is designed for modeling purposes: It allows interactive deformation of the protein backbone. General formalism on transformations is introduced and the operators of stretching inside an "acceptance area" and stretching with end-block invariance (i.e., governed by a translational moving) are described. A discussion is presented on the choice of strategy to achieve an interactive deformation tool. Perspectives about complex transformations are presented.

Computer Graphics↗
PubMed1991

A new approach to the rapid determination of protein side chain conformations.

Two efficient algorithms have been developed which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation. Both these approaches are based on the assumption that each side chain can be represented by a small number of rotameric states. These states have been obtained by a dynamic cluster analysis of a large data base of known crystallographic structures. Successful applications of these algorithms to the prediction of known protein conformations are presented.

Algorithms↗
PubMed1991

MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences.

This paper presents a method for the multiple alignment of a sequence set. The MASH algorithm uses a non-redundant database of common motifs and an 'alignment priority' criterion that depends on the length and the occurrence frequency of the patterns in the set of sequences. This user-defined criterion allows the determination of the series of the patterns to be aligned. This program is applied to a fragment of envelope gene env gp120 for 20 isolates of the immunodeficiency virus. The multiplicity of alignments obtained by modifying the criterion parameters reveals different aspects of similarity between the sequences.

Algorithms↗
PubMed1991

'Size leap' algorithm: an efficient extraction of the longest common motifs from a molecular sequence set. Application to the DNA sequence reconstruction.

We propose a new method, called 'size leap' algorithm, of search for motifs of maximum size and common to two fragments at least. It allows the creation of a reduced database of motifs from a set of sequences whose size obeys the series of Fibonacci numbers. The convenience lies in the efficiency of the motif extraction. It can be applied in the establishment of overlap regions for DNA sequence reconstruction and multiple alignment of biological sequences. The method of complete DNA sequence reconstruction by extraction of the longest motifs ('anchor motifs') is presented as an application of the size leap algorithm. The details of a reconstruction from three sequenced fragments are given as an example.

Algorithms↗
PubMed1991

Genetic similarity maps and immunoglobulin allotypes of eleven populations from the Pyrenees (France).

The genetic heterogeneity of eleven populations from the Pyrenees (France) based on the polymorphism of the immunoglobulin allotypes is studied by means of a 'genetic similarity map'. The method described here, called 'Mobile Node Method', allows the deformation of a square grid, in which the studied region is represented, by moving the nodes at each step in order to reduce the difference between the geographic and genetic distances. This tool allows the overall quantification of the genetic heterogeneity of a population set and possibly the study of its dynamics. Other maps constructed to complete the interpretation are 'map of moving vectors', 'iso-displacement curves' and 'site displacements'. This study identified an overall genetic homogeneity among the Pyrenean populations and several local genetic heterogeneities in different regions.

France↗
PubMed1991

The p49/TaqI Y-specific DNA haplotypes in Australian aborigines.

The TaqI/p49 Y-specific RFLPs were studied in 59 Australian aborigines. A new haplotype was found (not present in Caucasians and Africans, number XXV). In the revised genealogy of haplotypes, Australian haplotypes appear to occupy an intermediate position between African Pygmies and Papua haplotypic repartitions, while the most common Australian haplotypes (haplotype III, 25% of the subjects) is apparently derived from them.

Australia↗
PubMed1990

The p49/TaqI Y-specific polymorphisms in three groups of Indians.

The TaqI/p49 Y-specific RFLPs were studied in 98 Indians coming from 3 locations in the country. A new allele (G0) and five new haplotypes (XX-XXIV) were found, not present in Caucasians and in Africans. In the genealogy of haplotypes, the new Indian haplotypes appear grouped together, and all Indian haplotypes occupy an intermediate position between Caucasian and African haplotypes.

Alleles↗
PubMed1989

Y chromosome DNA polymorphisms in two African populations.

Y chromosome-specific DNA polymorphisms were detected using probe p49f after restriction with TaqI enzyme on samples coming from two African populations: Bantus and Pygmies. All the main TaqI alleles at five Y loci already found in Caucasians are also found in these two populations; 12 of the 16 Caucasian haplotypes were found in these two African populations, and two new haplotypes are Pygmy specific. A proposed phylogeny of the various haplotypes that was derived by using the parsimony criterion established that haplotypes XIII and XVIII, respectively the most frequent one and only one present in Pygmies, are probably ancestral.

Alleles↗
PubMed1988

Modelling the 1985 influenza epidemic in France.

The Rvachev-Baroyan-Longini model is a space-time predictive model of the spread of influenza epidemics. It has been applied to 128 cities of the USSR, and more recently, to forecasting the spread of the pandemic of 1968-1969 throughout 52 large cities. It is a deterministic, mass-action, space and time continuous model. The model has been applied to the simulation of the influenza epidemic of 1984-1985 in the 22 French Metropolitan districts and results are presented. Estimates of the parameters of the model were made using the French Communicable Diseases Network data. These parameters are the contact rate, a, (estimate = 0.55) which is the number of people with whom an infectious individual will make contact daily sufficient to pass infection and the infectious period, 1/b, estimated as 2.49 days. The mean annual railroad passenger traffic from district i to district j varies from 0 to 1,991,000 persons depending on the districts. The computer spread of the epidemic is presented on weekly maps. Results are also presented on district charts, giving the size of district epidemics and the time of peak of the epidemic. The precision of the computer fittings was judged satisfactory by the calculated size of peak differing from the real one by less than 100 per cent, in 17 out of 18 districts, and by the calculated time of peak differing from the observed by less than two weeks in 14 out of 18 districts. Although precision could be improved with more detailed information about passenger traffic, the French use of the model has been satisfactory.

Computer Simulation↗
PubMed1988

Restriction map construction using a 'complete sentences compatibility' algorithm.

We have developed a new algorithm 'Complete sentences compatibility' (CSC) which uses single and double digestion fragments to rapidly determine restriction maps of circular DNA. From possible combinations of fragments of each simple digestion, which we call 'sentences of decomposition', we construct a restriction map which combines the sentences while taking into account compatibility rules. The algorithm can also deal with experimental errors of fragment weight and can suggest solutions that account for non-readable bands (fragments of zero length or multiple bands) on the gel. Because experiments using pairs of restrictive enzymes often result in multiple solutions, a complementary algorithm tries to reduce the number of proposed solutions by establishing consensus maps. The restriction map construction algorithm was tested on real cases, some containing more than fifteen fragments. Execution times range from 1-10 s on an IBM PC compatible microcomputer.

Algorithms↗
PubMed1987

The algorithm of the cockshafer walk: a movement automaton applied to the construction of the integrated optical density profile of prometaphase chromosomes.

We present an algorithm designed to obtain the optical density profile of prometaphase chromosomes. Our movement automation (the cockshafer) is able to move along the median axis of the chromosome. The criterion used to maintain the correct movement direction lies on the distances from the automaton position to the side boundaries (lengths of the cockshafer antennae). The automaton movements are regulated by rules defined in a decision repertory. This new method does not use a transformation of the image and does not require any prior knowledge of the shape of the chromosome to be sampled.

Algorithms↗
PubMed1987

Evolution of immunoglobulin allotypes and phylogeny of apes.

Serum samples from 72 Pan troglodytes, 5 Pan paniscus, 22 Gorilla gorilla, 23 Pongo pygmaeus abelii, 5 Pongo pygmaeus pygmaeus, 2 hybrids P.p. abelii X P.p. pygmaeus and 13 Hylobates lar were tested for Gm(1, 2, 3, 5, 6, 10, 11, 13, 14, 15, 16, 17, 21, 24, 28), Km(1) and Bm(1, 2, 3, 4, 5, 6, 7, 8) immunoglobulin allotypes by the classical hemagglutination inhibition method. The distribution of the various alleles and phenotypes makes it possible to distinguish each species or subspecies. Common chimpanzees have the richest polymorphism. Pygmy chimpanzees share common phenotypes with gorillas. Bornean and Sumatran orangutans have their own patterns of polymorphism, as do gibbons. Our principal component plot and dendrogram are compatible with the traditional classification of Hominoidea [e.g. Simpson, Bull. Am. Mus. nat. Hist. 85: 1-350, 1945] in 3 families: Hominidae, Pongidae and Hylobatidae.

Animals↗
PubMed1986

[Towards a genealogy of chromosome Y].

Taq I restriction polymorphisms of the 49 f genomic probe are used to establish a possible filiation of the Y chromosome in human populations. Relationships between alleles at the five polymorphic loci revealed by the probe allow the description of 17 haplotypes. Simulations are used to construct a plausible genealogy of these various haplotypes, on the basis of a limited set of basic hypotheses concerning polymorphic alleles evolution.

Biological Evolution↗