Stochastic arrays and learning networks

This thesis presents a study of stochastic arrays and learning networks. These arrays will be shown to consist of simple elements utilising probabilistic coding techniques which may interact with a random and noisy environment to produce useful results. Such networks have generated considerable interest since it is possible to design large parallel self-organising arrays of these elements which are trained by example rather than explicit instruction. Once the learning process has been completed, they then have the potential ability to form generalisations, perform global optimisation of traditionally difficult problems such as routing and incorporate an associative memory capability which can enable such tasks as image recognition and reconstruction to be performed, even when given a partial or noisy view of the target. Since the method of operation of such elements is thought to emulate the basic properties of the neurons of the brain, these arrays have been termed neural 'networks. The research demonstrates the use of stochastic elements for digital signal processing by presenting a novel systolic array, utilising a simple, replicated cell structure, which is shown to perform the operations of Cyclic Correlation and the Discrete Fourier Transform on inherently random and noisy probabilistic single bit inputs. This work is then extended into the field of stochastic learning automata and to neural networks by examining the Associative Reward-Punish (A(_R-P)) pattern recognising learning automaton. The thesis concludes that all the networks described may potentially be generalised to simple variations of one standard probabilistic element utilising stochastic coding, whose properties resemble those of biological neurons. A novel study is presented which describes how a powerful deterministic algorithm, previously considered to be biologically unviable due to its nature, may be represented in this way. It is expected that combinations of these methods may lead to a series of useful hybrid techniques for training networks. The nature of the element generalisation is particularly important as it reveals the potential for encoding successful algorithms in cheap, simple hardware with single bit interconnections. No claim is made that the particular algorithms described are those actually utilised by the brain, only to demonstrate that those properties observed of biological neurons are capable of endowing collective computational ability and that actual biological algorithms may perhaps then become apparent when viewed in this light

Colliding Black Holes: The Close Limit

The problem of the mutual attraction and joining of two black holes is of importance as both a source of gravitational waves and as a testbed of numerical relativity. If the holes start out close enough that they are initially surrounded by a common horizon, the problem can be viewed as a perturbation of a single black hole. We take initial data due to Misner for close black holes, apply perturbation theory and evolve the data with the Zerilli equation. The computed gravitational radiation agrees with and extends the results of full numerical computations.Comment: 4 pages, Revtex, 3 postscript figures included, CGPG-94/2-

Late-Time Behavior of Stellar Collapse and Explosions: II. Nonlinear Evolution

Problem with the figures should be corrected. Apparently a broken uuencoder was the cause.Comment: 23pp, RevTex, 15 figures (included), NSF-ITP-93-8

Formation of a rotating hole from a close limit head-on collision

Realistic black hole collisions result in a rapidly rotating Kerr hole, but simulations to date have focused on nonrotating final holes. Using a new solution of the Einstein initial value equations we present here waveforms and radiation for an axisymmetric Kerr-hole-forming collision starting from small initial separation (the ``close limit'' approximation) of two identical rotating holes. Several new features are present in the results: (i) In the limit of small separation, the waveform is linear (not quadratic) in the separation. (ii) The waveforms show damped oscillations mixing quasinormal ringing of different multipoles.Comment: 4 pages, 4 figures, submitted to PR

Black Hole Spectroscopy: Testing General Relativity through Gravitational Wave Observations

Assuming that general relativity is the correct theory of gravity in the strong field limit, can gravitational wave observations distinguish between black hole and other compact object sources? Alternatively, can gravitational wave observations provide a test of one of the fundamental predictions of general relativity? Here we describe a definitive test of the hypothesis that observations of damped, sinusoidal gravitational waves originated from a black hole or, alternatively, that nature respects the general relativistic no-hair theorem. For astrophysical black holes, which have a negligible charge-to-mass ratio, the black hole quasi-normal mode spectrum is characterized entirely by the black hole mass and angular momentum and is unique to black holes. In a different theory of gravity, or if the observed radiation arises from a different source (e.g., a neutron star, strange matter or boson star), the spectrum will be inconsistent with that predicted for general relativistic black holes. We give a statistical characterization of the consistency between the noisy observation and the theoretical predictions of general relativity, together with a numerical example.Comment: 19 pages, 7 figure

Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis

<p>Abstract</p> <p>Background</p> <p>Expansion of aquaculture is seriously limited by reductions in fish oil (FO) supply for aquafeeds. Terrestrial alternatives such as vegetable oils (VO) have been investigated and recently a strategy combining genetic selection with changes in diet formulations has been proposed to meet growing demands for aquaculture products. This study investigates the influence of genotype on transcriptomic responses to sustainable feeds in Atlantic salmon.</p> <p>Results</p> <p>A microarray analysis was performed to investigate the liver transcriptome of two family groups selected according to their estimated breeding values (EBVs) for flesh lipid content, 'Lean' or 'Fat', fed diets containing either FO or a VO blend. Diet principally affected metabolism genes, mainly of lipid and carbohydrate, followed by immune response genes. Genotype had a much lower impact on metabolism-related genes and affected mostly signalling pathways. Replacement of dietary FO by VO caused an up-regulation of long-chain polyunsaturated fatty acid biosynthesis, but there was a clear genotype effect as fatty acyl elongase (elovl2) was only up-regulated and desaturases (Δ5 fad and Δ6 fad) showed a higher magnitude of response in Lean fish, which was reflected in liver fatty acid composition. Fatty acid synthase (FAS) was also up-regulated by VO and the effect was independent of genotype. Genetic background of the fish clearly affected regulation of lipid metabolism, as PPARα and PPARβ were down-regulated by the VO diet only in Lean fish, while in Fat salmon SREBP-1 expression was up-regulated by VO. In addition, all three genes had a lower expression in the Lean family group than in the Fat, when fed VO. Differences in muscle adiposity between family groups may have been caused by higher levels of hepatic fatty acid and glycerophospholipid synthesis in the Fat fish, as indicated by the expression of FAS, 1-acyl-sn-glycerol-3-phosphate acyltransferase and lipid phosphate phosphohydrolase 2.</p> <p>Conclusions</p> <p>This study has identified metabolic pathways and key regulators that may respond differently to alternative plant-based feeds depending on genotype. Further studies are required but data suggest that it will be possible to identify families better adapted to alternative diet formulations that might be appropriate for future genetic selection programmes.</p

A widespread family of bacterial cell wall assembly proteins

Teichoic acids and acidic capsular polysaccharides are major anionic cell wall polymers (APs) in many bacteria, with various critical cell functions, including maintenance of cell shape and structural integrity, charge and cation homeostasis, and multiple aspects of pathogenesis. We have identified the widespread LytR–Cps2A–Psr (LCP) protein family, of previously unknown function, as novel enzymes required for AP synthesis. Structural and biochemical analysis of several LCP proteins suggest that they carry out the final step of transferring APs from their lipid-linked precursor to cell wall peptidoglycan (PG). In Bacillus subtilis, LCP proteins are found in association with the MreB cytoskeleton, suggesting that MreB proteins coordinate the insertion of the major polymers, PG and AP, into the cell wall

Histological basis of laminar MRI patterns in high resolution images of fixed human auditory cortex

Functional magnetic resonance imaging (fMRI) studies of the auditory region of the temporal lobe would benefit from the availability of image contrast that allowed direct identification of the primary auditory cortex, as this region cannot be accurately located using gyral landmarks alone. Previous work has suggested that the primary area can be identified in magnetic resonance (MR) images because of its relatively high myelin content. However, MR images are also affected by the iron content of the tissue and in this study we sought to confirm that different MR image contrasts did correlate with the myelin content in the grey matter and were not primarily affected by iron content as is the case in the primary visual and somatosensory areas. By imaging blocks of fixed post-mortem cortex in a 7 Tesla scanner and then sectioning them for histological staining we sought to assess the relative contribution of myelin and iron to the grey matter contrast in the auditory region. Evaluating the image contrast in T2*-weighted images and quantitative R2* maps showed a reasonably high correlation between the myelin density of the grey matter and the intensity of the MR images. The correlation with T1-weighted phase sensitive inversion recovery (PSIR) images was better than with the previous two image types, and there were clearly differentiated borders between adjacent cortical areas in these images. A significant amount of iron was present in the auditory region, but did not seem to contribute to the laminar pattern of the cortical grey matter in MR images. Similar levels of iron were present in the grey and white matter and although iron was present in fibres within the grey matter, these fibres were fairly uniformly distributed across the cortex. Thus we conclude that T1- and T2*-weighted imaging sequences do demonstrate the relatively high myelin levels that are characteristic of the deep layers in primary auditory cortex and allow it and some of the surrounding areas to be reliably distinguished

Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet

Background: Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutritional value, particularly in marine fish species, which exhibit low capacity for biosynthesis of long-chain poly-unsaturated fatty acids (LC-PUFA). The main objective of the present study was to analyse the effects of a plant-based diet on the hepatic transcriptome of European sea bass (Dicentrarchus labrax). Results: We report the first results obtained using a transcriptomic approach on the liver of two half-sibfamilies of the European sea bass that exhibit similar growth rates when fed a fish-based diet (FD), but significantly different growth rates when fed an all-plant diet (VD). Overall gene expression was analysed using oligo DNA microarrays (GPL9663). Statistical analysis identified 582 unique annotated genes differentially expressed between groups of fish fed the two diets, 199 genes regulated by genetic factors, and 72 genes that exhibited diet-family interactions. The expression of several genes involved in the LC-PUFA and cholesterol biosynthetic pathways was found to be up-regulated in fish fed VD, suggesting a stimulation of the lipogenic pathways. No significant diet-family interaction for the regulation of LC-PUFA biosynthesis pathways could be detected by microarray analysis. This result was in agreement with LC-PUFA profiles, which were found to be similar in the flesh of the two half-sibfamilies. In addition, the combination of our transcriptomic data with an analysis of plasmatic immune parameters revealed a stimulation of complement activity associated with an immunodeficiency in the fish fed VD, and different inflammatory status between the two half-sibfamilies. Biological processes related to protein catabolism, amino acid transaminations, RNA splicing and blood coagulation were also found to be regulated by diet, while the expression of genes involved in protein and ATP synthesis differed between the half-sibfamilies. Conclusions: Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies