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Yoram Louzoun

Publications and source records attributed to Yoram Louzoun.

18 recordsLinked to original sources
PubMed2006

The emergence of goals in a self-organizing network: a non-mentalist model of intentional actions.

A model of intentional actions is presented through the operation of two connected neural networks. A deterministic causal recurrent network relates a random initial state to an ordered final state. A perceptron-like, feed-forward network provides a memory mechanism that links the final states to the original initial states. A non-supervised learning mechanism that selects which final states are defined as goals to be retrieved together with initial states leading to them. Causal sequences of states are transformed into procedures directed towards the achievements of goals. We propose a mechanism through which goals and their achievement in goal-directed actions can be emerging properties of self-organizing networks, not initially endowed with intentionality. This allows for a monist, non-mentalist description which does not need to resort to intentional mental states as causes of intentional actions. Cognitive, neurophysiological and philosophical implications are discussed.

Animals↗
PubMed2006

Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome.

Attempts to develop peptide vaccines, based on a limited number of peptides face two problems: HLA polymorphism and the high mutation rate of viral epitopes. We have developed a new genomic method that ensures maximal coverage and thus maximal applicability of the peptide vaccine. The same method also promises a large number of epitopes per HLA to prevent escape via mutations. Our design can be applied swiftly in order to face rapidly emerging viral diseases. We use a genomic scan of all candidate peptides and join them optimally. For a given virus, we use algorithms computing: peptide cleavage probability, transfer through TAP and MHC binding for a large number of HLA alleles. The resulting peptide libraries are pruned for peptides that are not conserved or are too similar to self peptides. We then use a genetic algorithm to produce an optimal protein composed of peptides from this list properly ordered for cleavage. The selected peptides represent an optimal combination to cover all HLA alleles and all viral proteins. We have applied this method to HCV and found that some HCV proteins (mainly envelope proteins) represent much less peptide than expected. A more detailed analysis of the peptide variability shows a balance between the attempts of the immune system to detect less mutating peptides, and the attempts of viruses to mutate peptides and avoid detection by the immune system. In order to show the applicability of our method, we have further used it on HIV-I, Influenza H3N2 and the Avian Flu Viruses.

Amino Acid Sequence↗
PubMed2006

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.

MOTIVATION: B cells responding to antigenic stimulation can fine-tune their binding properties through a process of affinity maturation composed of somatic hypermutation, affinity-selection and clonal expansion. The mutation rate of the B cell receptor DNA sequence, and the effect of these mutations on affinity and specificity, are of critical importance for understanding immune and autoimmune processes. Unbiased estimates of these properties are currently lacking due to the short time-scales involved and the small numbers of sequences available. RESULTS: We have developed a bioinformatic method based on a maximum likelihood analysis of phylogenetic lineage trees to estimate the parameters of a B cell clonal expansion model, which includes somatic hypermutation with the possibility of lethal mutations. Lineage trees are created from clonally related B cell receptor DNA sequences. Important links between tree shapes and underlying model parameters are identified using mutual information. Parameters are estimated using a likelihood function based on the joint distribution of several tree shapes, without requiring a priori knowledge of the number of generations in the clone (which is not available for rapidly dividing populations in vivo). A systematic validation on synthetic trees produced by a mutating birth-death process simulation shows that our estimates are precise and robust to several underlying assumptions. These methods are applied to experimental data from autoimmune mice to demonstrate the existence of hypermutating B cells in an unexpected location in the spleen.

Algorithms↗
PubMed2006

Catalyst-induced growth with limited catalyst lifespan and competition.

Spatially extended catalyst-induced growth processes are studied. This type of processes exists in all domains of biology, ranging from ecology (nutrients and growth), through immunology (antigens and lymphocytes) to molecular biology (signaling molecules initiating signaling cascades). The extinction-proliferation transition is considered for a system containing discrete catalysts (A) that induces the proliferation of a discrete reactant (B). The realization of this model on an infinite capacity d-dimensional discrete lattice for immortal catalysts has been previously considered (the AB model). It was shown that the adaptation of the reactants to the diffusive noise induced by stochastic fluctuations of catalyst density yields proliferation even if the average environmental conditions lead to extinction. This model is extended here to include more realistic situations, like finite lifespan of the catalysts and finite carrying capacity of the reactants. By using a combination of Monte Carlo simulation, percolation-theory-based estimations and an analytic perturbative analysis, the asymptotic behavior of these systems is studied. In both cases studied, it turns out that the overall survival of the reactant population at the long run is based on the size and shape of a typical single colony, related to the localized proliferation around spatio-temporal catalyst density fluctuations. If the density of these colonies (based on the lifetime of the spatial fluctuation and the carrying capacity of the medium) is large enough, i.e. above the percolation threshold, the reactant population survives even in (on average) hostile environment. This model provides a new insight on the population dynamics in chemical, biological and ecological systems.

Animals↗
PubMed2006

Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW.

UNLABELLED: We study two kinds of networks: genetic regulatory networks and the World Wide Web. We systematically test microscopic mechanisms to find the set of such mechanisms that optimally explain each networks' specific properties. In the first case we formulate a model including mainly random unbiased gene duplications and mutations. In the second case, the basic moves are website generation and rapid surf-induced link creation (/destruction). The different types of mechanisms reproduce the appropriate observed network properties. We use those to show that different kinds of networks have strongly system-dependent macroscopic experimental features. The diverging properties result from dissimilar node and link basic dynamics. The main non-uniform properties include the clustering coefficient, small-scale motifs frequency, time correlations, centrality and the connectivity of outgoing links. Some other features are generic such as the large-scale connectivity distribution of incoming links (scale-free) and the network diameter (small-worlds). The common properties are just the general hallmark of autocatalysis (self-enhancing processes), while the specific properties hinge on the specific elementary mechanisms. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.

Animals↗
PubMed2005

T-cell epitope repertoire as predicted from human and viral genomes.

During thymic education, strongly self-reactive T cells are selected against, while weakly self-reactive cells are positively selected. However, the probability of an antigen being self derived and the number of self-peptides have never been properly defined. We merge algorithms for: cleavage prediction, TAP binding probability estimates and MHC binding properties to estimate the number and distribution of all MHC binding peptides. We show that the number of self-peptides with a high affinity to a given human MHC-I molecule is between 200 and almost 200,000 and is much less than the estimated total number of peptide sequences. This result suggests that MHC molecules are selected through evolution in order to reduce the number of self-peptides presented. The number of viral peptides presented is also low and varies between zero and a few hundred per virus for a given HLA allele. These low numbers explain the need for multiple alleles within an individual. We show that six codominantly expressed MHC-I alleles are sufficient to present at least one or two peptides per virus for the vast majority of viruses. Viruses can escape detection either by using peptides that cannot be presented on MHC molecules or by using peptides whose presented segments overlap significantly with self. Most viral families (such as influenza, HIV, Hepatitis and HPV) present as many peptides as predicted from their genome length, and overlap minimally with the human self-peptide repertoire. However, a few latent viruses, such as herpes and adenovirus share considerable peptide sequence homology with their human hosts.

Antigens, Viral↗
PubMed2004

Editing anti-DNA B cells by Vlambdax.

Receptor editing is performed by replacement of Vkappa genes that contribute to autoreactivity. In addition, the Ckappa locus can be deleted by Vkappa rearrangement to intronic or 3' of Ckappa RS sequences (also referred to as kappa deletion elements). B cells that delete the Ckappa can then express lambda light chains. However, the lambda locus, either of man or mouse, does not allow V gene replacement. Nor does it appear to be deleted. Therefore, editing of autoreactive lambda B cells may require alternative pathways. We have found that in anti-DNA heavy chain transgenic mice (tgs) VH3H9/56R, B cells that express anti-DNA receptors comprised of lambda1 in association with an anti-DNA heavy chain often coexpress a kappa chain that prevents DNA binding. We speculate that such isotypically included cells may have low anti-DNA receptor densities, a feature that may lead to self-tolerance. Here we describe a mechanism of preventing DNA binding by expression of a rarely used member of the Vlambda family, Vlambdax. The lambdax B cells of the tgs also express CD25 and may represent B cells that have exhausted light chain editing possibilities.

Animals↗
PubMed2004

Functional connectivity of the prefrontal cortex and the amygdala in posttraumatic stress disorder.

BACKGROUND: Persistent, intrusive re-experiencing in posttraumatic stress disorder (PTSD) is commonly construed as a failure of cingulate inhibition (i.e., extinction) over a hyperresponsive amygdala, based primarily on animal research of fear conditioning and the finding of cingulate hypoperfusion in PTSD. METHODS: We examined functional connectivity in patients with PTSD and healthy trauma survivors during repeated symptom provocation using H(2)O(15) positron emission tomography. RESULTS: Memory retrieval networks (right prefrontal cortex, hippocampus, and visual cortex) were common to both groups. Networks supporting autonomic and emotional control and preparatory motor action (amygdala, anterior cingulate, subcallosal gyrus, and premotor cortex) differed between the two groups and became progressively disparate with successive presentations of the traumatic script. Patterns of effective connectivity demonstrated the predominance of direct influences of the amygdala on visual cortex, subcallosal gyrus, and anterior cingulate in PTSD but not in control subjects. There was little evidence for failure of inhibition of cingulate or subcallosal cortex over the amygdala. CONCLUSIONS: These patterns might represent excessive influences of the amygdala over regions involved in autonomic, and higher-order visual memory processing in PTSD. The present data suggest that inferences of direct correspondence between animal studies and pathophysiology of PTSD should be made with caution.

Adult↗
PubMed2003

Cerebral blood flow in chronic symptomatic mild traumatic brain injury.

Patients with mild traumatic brain injury (MTBI) challenge physicians' skills and test their patience. Their manifold symptomatology is often not supported by objective neurological findings. We sought to compare regional cerebral blood flow (rCBF) between symptomatic subjects with longstanding MTBI and healthy controls, and to examine the correspondence between neuropsychological deficit and rCBF compromise. Twenty-eight clinically symptomatic male subjects with MTBI and twenty matched controls underwent neuropsychological testing and Tc-99m-HMPAO brain SPECT imaging. Neuropsychological test data were used to categorize subjects into sub-groups according to the presumed location of lesions based on their neurobehavioral deficits. Image subtraction comparisons were made between controls, all MTBI subjects and sub-groups. MTBI patients demonstrated regions of hypoperfusion in frontal, pre-frontal and temporal cortices, and sub-cortical structures. Hypoperfusion in 'frontal', 'left posterior' and to a lesser extent 'sub-cortical' sub-groups was concordant with neuropsychological localization. This was not the case for the 'right posterior' group, where no concordance was found. The rCBF is reduced in symptomatic patients with longstanding MTBI and unremarkable structural brain imaging. Although group analysis is appropriate for the generation of statistically significant differences, the clinical application of brain SPECT imaging in MTBI calls for a capability to associate clinical examination, neuropsychological assessment and cerebral perfusion at the individual subject level. Such competence is still to be attained.

Adult↗
PubMed2003

Resting regional cerebral perfusion in recent posttraumatic stress disorder.

BACKGROUND: Brain imaging research in posttraumatic stress disorder has been largely performed on patients with chronic disease, often heavily medicated, with current or past alcohol and substance abuse. Additionally, virtually only activation brain imaging paradigms have been done in posttraumatic stress disorder, whereas in other mental disorders both resting and activation studies have been performed. METHODS: Twenty-eight (11 posttraumatic stress disorder) trauma survivors underwent resting state hexamethylpropyleneamineoxime single photon emission computed tomography and magnetic resonance imaging 6 months after trauma. Eleven nontraumatized subjects served as healthy controls. RESULTS: Regional cerebral blood flow in the cerebellum was higher in posttraumatic stress disorder than in both control groups. Regional cerebral blood flow in right precentral, superior temporal, and fusiform gyri in posttraumatic stress disorder was higher than in healthy controls. Cerebellar and extrastriate regional cerebral blood flow were positively correlated with continuous measures of depression and posttraumatic stress disorder. Cortisol level in posttraumatic stress disorder was negatively correlated with medial temporal lobe perfusion. Anterior cingulate perfusion and cortisol level were positively correlated in posttraumatic stress disorder and negatively correlated in trauma survivors without posttraumatic stress disorder. CONCLUSIONS: Recent posttraumatic stress disorder is accompanied by elevated regional cerebral blood flow, particularly in the cerebellum. This warrants attention because the cerebellum is often used as a reference region in regional cerebral blood flow studies. The inverse correlation between plasma cortisol and medial temporal lobe perfusion may herald hippocampal damage.

Adult↗
PubMed2003

Estimating hypermutation rates from clonal tree data.

To understand the mechanisms underlying the varying patterns of mutations that occur during immune and autoimmune responses, estimates of the somatic hypermutation rate are critical. However, despite its significance, precise estimates of the mutation rate do not currently exist. Microdissection studies of mutating B cell clones provide an opportunity to measure this rate more accurately than previously possible. Each microdissection provides a number of clonally related sequences that, through the analysis of shared mutations, can be genealogically related to each other. The shape of these clonal trees is influenced by many processes, including the hypermutation rate. We have developed two different methods to estimate the mutation rate based on these data. These methods are applied to two sets of experimental data, one from an autoimmune response and one from the antihapten response to (4-hydroxy-3-nitrophenyl)acetyl (NP). Comparable mutation rates are estimated for both responses, 0.7-0.9 x 10(-3) and 0.9-1.1 x 10(-3) bp(-1) division(-1) for the autoimmune and NP responses, respectively. In addition to comparing the results of the two procedures, we investigate the effect on our estimate of assumptions, such as the fraction of lethal mutations.

Animals↗
PubMed2003

Cerebral blood flow in depressed patients: a methodological comparison of statistical parametric mapping and region of interest analyses.

Functional brain imaging has assumed a leading role in neuropsychiatric research. However, findings reported for mental disorders often vary. Whether this reflects diversity in pathophysiology or heterogeneity of imaging techniques and data-analytic procedures is still unknown. This study compares region of interest (ROI) and statistical parametric mapping (SPM) analyses of a Tc99m-HMPAO single photon emission computed tomography (SPECT) imaging study of 23 depressed and 21 control subjects. Reduced regional cerebral blood flow (rCBF) was demonstrated by both methods in the right parietal and occipital lobes, but additional regions were identified only on ROI analysis (left temporal) and only on SPM analysis (left parietal). To investigate the contribution of SPM spatial normalization to these discrepancies, further ROI analyses were performed, applying the original ROI templates to normalized images, and applying regions identified by SPM to the original images. This study demonstrated considerable overlap in findings of SPM and ROI analyses. Differences between these methods may be mostly related to subjective placement of ROIs in ROI analysis, and standardized warping inherent in normalization in SPM. Given the advantages and drawbacks of each procedure, the choice of methodology should be determined in accordance with the study design, and complementary use of both methods may be considered.

Adult↗
PubMed2003

The importance of thermodynamic equilibrium for high throughput gene expression arrays.

We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm for choosing a probe set with high specificity for targeted genes under equilibrium conditions. The algorithm as well as existing methods is used to select probes from the full Saccharomyces cerevisiae genome, and these probe sets, along with a randomly selected set, are used to simulate array experiments and identify sources of error. Inasmuch as specificity and sensitivity are maximum at thermodynamic equilibrium, we are particularly interested in the factors that affect the approach to equilibrium. These are analyzed later in the article, where we develop and apply a rapidly executable method to simulate the kinetics of hybridization on a solid phase support. Although the difference between solution phase and solid phase hybridization is of little consequence for specificity and sensitivity when equilibrium is achieved, the kinetics of hybridization has a pronounced effect on both. We first use the model to estimate the effects of diffusion, crosshybridization, relaxation time, and target concentration on the hybridization kinetics, and then investigate the effects of the most important kinetic parameters on specificity. We find even when using probe sets that have high specificity at equilibrium that substantial crosshybridization is present under nonequilibrium conditions. Although those complexes that differ from perfect complementarity by more than a single base do not contribute to sources of error at equilibrium, they slow the approach to equilibrium dramatically and confound interpretation of the data when they dissociate on a time scale comparable to the time of the experiment. For the best probe set, our simulation shows that steady-state behavior is obtained in a relaxation time of approximately 12-15 h for experimental target concentrations approximately (10(-13) - 10(-14))M, but the time is greater for lower target concentrations in the range (10(-15)-10(-16))M. The result points to an asymmetry in the accuracy with which up- and downregulated genes are identified.

Algorithms↗
PubMed2003

Proliferation and competition in discrete biological systems.

We study the emergence of collective spatio-temporal objects in biological systems by representing individually the elementary interactions between their microscopic components. We use the immune system as a prototype for such interactions. The results of this detailed explicit analysis are compared with the traditional procedure of representing the collective dynamics in terms of densities that obey partial differential equations. The simulations show even for very simple elementary reactions the spontaneous emergence of localized complex structures, from microscopic noise. In turn the effective dynamics of these structures affects the average behaviour of the system in a very decisive way: systems which would according to the differential equations approximation die, display in reality a very lively behaviour. As the optimal modelling method we propose a mixture of microscopic simulation systems describing each reaction separately, and continuous methods describing the average behaviour of the agents.

Adaptation, Physiological↗
PubMed2003

Dynamical analysis of a degenerate primary and secondary humoral immune response.

Lymphocyte receptor response to antigen is degenerate. Each receptor can have a high affinity to more than one antigen. The optimal level of degeneracy was previously modeled using different methods; all showing that the degeneracy level should be inversely proportional to the probability that an antigen belongs to the self repertoire. Here we develop a new formalism, reproducing the results of previous models, which enables us to study the relation between receptor degeneracy and the pathogen-immune cell interaction dynamics, in primary and secondary response. We begin by developing a general formalism and reproducing the results obtained by Nemazee: (1) that an optimal immune system will have a capacity which is inversely proportional to the fraction of self-antigens and (2) that the number of self-reactive cells that the body destroys is tuned by this capacity optimization to be 63%. We then use our extended framework to relate the minimal number of B cell precursor required to mount an immune response to the naive B cell production rate. Finally, we analyze the dynamics of the interaction between the immune system and a pathogen and show that memory cells may be used as the first line of defense, while newly created cells are used later to refine the immune response.

Animals↗
PubMed2003

World-size global markets lead to economic instability.

Economic and cultural globalization is one of the most important processes humankind has been undergoing lately. This process is assumed to be leading the world into a wealthy society with a better life. However, the current trend of globalization is not unprecedented in human history, and has had some severe consequences in the past. By applying a quantitative analysis through a microscopic representation we show that globalization, besides being unfair (with respect to wealth distribution), is also unstable and potentially dangerous as one event may lead to a collapse of the system. It is proposed that the optimal solution in controlling the unwanted aspects and enhancing the advantageous ones lies in limiting competition to large subregions, rather than making it worldwide.

Internationality↗
PubMed2002

Analysis of B cell receptor production and rearrangement. Part I. Light chain rearrangement.

A probabilistic model of allelic exclusion fails to explain the status of receptor genes and the receptor phenotype of most B cells. A large proportion of B cells have incompletely rearranged H and/or L chain genes (e.g. kappa0/kappa+) and most B cells express only one receptor. These properties seem to require deterministic features of B cell development such as special mechanisms that stop rearrangement. However, receptor editing has revealed that rearrangement-stop is not stable and that multi-receptor lymphocytes make up a significant fraction of certain B and T cell populations. Consequently we have revived the purely probabilistic approach in a model that now includes receptor editing and allows for some multi-receptor B cells. We find that this model can explain the observed properties of B cells when the frequency of self-reactive B cells is high. Indeed, as we illustrate for anti-DNA, this is the case. Hence the probabilistic model has life and assiduous use of the model suggests unexpected but not unrealistic features of lymphocyte development.

Algorithms↗