Finite Size Effects in Separable Recurrent Neural Networks

We perform a systematic analytical study of finite size effects in separable recurrent neural network models with sequential dynamics, away from saturation. We find two types of finite size effects: thermal fluctuations, and disorder-induced `frozen' corrections to the mean-field laws. The finite size effects are described by equations that correspond to a time-dependent Ornstein-Uhlenbeck process. We show how the theory can be used to understand and quantify various finite size phenomena in recurrent neural networks, with and without detailed balance.Comment: 24 pages LaTex, with 4 postscript figures include

Dynamical Replica Theory for Disordered Spin Systems

We present a new method to solve the dynamics of disordered spin systems on finite time-scales. It involves a closed driven diffusion equation for the joint spin-field distribution, with time-dependent coefficients described by a dynamical replica theory which, in the case of detailed balance, incorporates equilibrium replica theory as a stationary state. The theory is exact in various limits. We apply our theory to both the symmetric- and the non-symmetric Sherrington-Kirkpatrick spin-glass, and show that it describes the (numerical) experiments very well.Comment: 7 pages RevTex, 4 figures, for PR

An initial event in insect innate immune response: structural and biological studies of interactions between β-1,3-glucan and the N-terminal domain of β-1,3-glucan recognition protein

In response to invading microorganisms, insect β-1,3-glucan recognition protein (βGRP), a soluble receptor in the hemolymph, binds to the surfaces of bacteria and fungi and activates serine protease cascades that promote destruction of pathogens by means of melanization or expression of antimicrobial peptides. Here we report on the NMR solution structure of the N-terminal domain of βGRP (N-βGRP) from Indian meal moth (Plodia interpunctella), which is sufficient to activate the prophenoloxidase (proPO) pathway resulting in melanin formation. NMR and isothermal calorimetric titrations of N-βGRP with laminarihexaose, a glucose hexamer containing β-1,3 links, suggest a weak binding of the ligand. However, addition of laminarin, a glucose polysaccharide (~ 6 kDa) containing β-1,3 and β-1,6 links that activates the proPO pathway, to N-βGRP results in the loss of NMR cross-peaks from the backbone 15N-1H groups of the protein, suggesting the formation of a large complex. Analytical ultra centrifugation (AUC) studies of formation of N-βGRP:laminarin complex show that ligand-binding induces sel-fassociation of the protein:carbohydrate complex into a macro structure, likely containing six protein and three laminarin molecules (~ 102 kDa). The macro complex is quite stable, as it does not undergo dissociation upon dilution to sub-micromolar concentrations. The structural model thus derived from the present studies for N-βGRP:laminarin complex in solution differs from the one in which a single N-βGRP molecule has been proposed to bind to a triple helical form of laminarin on the basis of an X-ray crystallographic structure of N-βGRP:laminarihexaose complex [Kanagawa, M., Satoh, T., Ikeda, A., Adachi, Y., Ohno, N., and Yamaguchi, Y. (2011) J. Biol. Chem. 286, 29158-29165]. AUC studies and phenoloxidase activation measurements carried out with the designed mutants of N-βGRP indicate that electrostatic interactions involving Asp45, Arg54, and Asp68 between the ligand-bound protein molecules contribute in part to the stability of N-βGRP:laminarin macro complex and that a decreased stability is accompanied by a reduced activation of the proPO pathway. Increased β-1,6 branching in laminarin also results in destabilization of the macro complex. These novel findings suggest that ligand-induced self-association of βGRP:β-1,3-glucan complex may form a platform on a microbial surface for recruitment of downstream proteases, as a means of amplification of the initial signal of pathogen recognition for the activation of the proPO pathway

Chaos in neural networks with a nonmonotonic transfer function

Time evolution of diluted neural networks with a nonmonotonic transfer function is analitically described by flow equations for macroscopic variables. The macroscopic dynamics shows a rich variety of behaviours: fixed-point, periodicity and chaos. We examine in detail the structure of the strange attractor and in particular we study the main features of the stable and unstable manifolds, the hyperbolicity of the attractor and the existence of homoclinic intersections. We also discuss the problem of the robustness of the chaos and we prove that in the present model chaotic behaviour is fragile (chaotic regions are densely intercalated with periodicity windows), according to a recently discussed conjecture. Finally we perform an analysis of the microscopic behaviour and in particular we examine the occurrence of damage spreading by studying the time evolution of two almost identical initial configurations. We show that for any choice of the parameters the two initial states remain microscopically distinct.Comment: 12 pages, 11 figures. Accepted for publication in Physical Review E. Originally submitted to the neuro-sys archive which was never publicly announced (was 9905001

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Effect of N′-nitrosodimethylamine on red blood cell rheology and proteomic profiles of brain in male albino rats

We investigated the effects of N'-nitrosodimethylamine (NDMA) induced toxicity on red blood cell rheology in male rats and identified bands in proteomic profiles of brain which can be used as novel markers. Polyacrylamide gel electrophoresis (PAGE) profiles exhibited constitutive as well as induced expression of the polypeptides. Remarkably, the molecular weight range of the polypeptides (8–150 kDa) corresponded to that of the family of heat shock proteins. Our results revealed significant changes in blood parameters and showed the presence of acanthocytes, tear drop cells, spicules and cobot rings in the treated categories. Lactate dehydrogenase and esterase zymograms displayed a shift to anaerobic metabolism generating hypoxia-like conditions. This study strongly suggests that NDMA treatment causes acute toxicity leading to cell membrane destruction and alters protein profiles in rats. It is therefore recommended that caution should be exercised in using NDMA to avoid risks, and if at all necessary strategies should be designed to combat such conditions

Dynamical replica analysis of processes on finitely connected random graphs II: Dynamics in the Griffiths phase of the diluted Ising ferromagnet

We study the Glauber dynamics of Ising spin models with random bonds, on finitely connected random graphs. We generalize a recent dynamical replica theory with which to predict the evolution of the joint spin-field distribution, to include random graphs with arbitrary degree distributions. The theory is applied to Ising ferromagnets on randomly diluted Bethe lattices, where we study the evolution of the magnetization and the internal energy. It predicts a prominent slowing down of the flow in the Griffiths phase, it suggests a further dynamical transition at lower temperatures within the Griffiths phase, and it is verified quantitatively by the results of Monte Carlo simulations.Comment: 30 pages, 4 figures, submitted to J.Phys.

Report of the US Long Baseline Neutrino Experiment Study.

This report provides the results of an extensive and important study of the potential for a U.S. scientific program that will extend our knowledge of neutrino oscillations well beyond what can be anticipated from ongoing and planned experiments worldwide. The program examined here has the potential to provide the U.S. particle physics community with world leading experimental capability in this intensely interesting and active field of fundamental research. Furthermore, this capability is not likely to be challenged anywhere else in the world for at least two decades into the future. The present study was initially commissioned in April 2006 by top research officers of Brookhaven National Laboratory and Fermilab and, as the study evolved, it also provides responses to questions formulated and addressed to the study group by the Neutrino Scientific Advisory Committee (NuSAG) of the U.S. DOE and NSF. The participants in the study, its Charge and history, plus the study results and conclusions are provided in this report and its appendices. A summary of the conclusions is provided in the Executive Summary