Programmable active pixel sensor to investigate neural interactions within the retina

Detection of the visual scene by the eye and the resultant neural interactions of the retina-brain system give us our perception of sight. We have developed an Active Pixel Sensor (APS) to be used as a tool for both furthering understanding of these interactions via experimentation with the retina and to make developments towards a realisable retinal prosthesis. The sensor consists of 469 pixels in a hexagonal array. The pixels are interconnected by a programmable neural network to mimic lateral interactions between retinal cells. Outputs from the sensor are in the form of biphasic current pulse trains suitable to stimulate retinal cells via a biocompatible array. The APS will be described with initial characterisation and test results

The influence of paternal height and weight on birth-weight

Analysis of 5,989 couples, for whom fathers' and mothers' heights and weights were recorded, showed that paternal height had a significant influence (p less than 0.0007) on birth-weight while paternal body mass index (Quetelets Index) had no significant effect (p greater than 0.05). Depending upon mother's height, the average effect of father's height (ranging from 165 cm to 184 cm) on birth-weight was up to 152 g, with a greater effect where the mother was taller (up to 235 g) and a lesser effect where the mother was shorter (confirming the effect of maternal constraint). The significance of these findings lies more with the need to consider this effect as an important variable in statistical analysis involving birth-weight than in its immediate obstetrical implications

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

A Comprehensive Workflow for General-Purpose Neural Modeling with Highly Configurable Neuromorphic Hardware Systems

In this paper we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware-experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results

6D supergravity without tensor multiplets

We systematically investigate the finite set of possible gauge groups and matter content for N = 1 supergravity theories in six dimensions with no tensor multiplets, focusing on nonabelian gauge groups which are a product of SU(N) factors. We identify a number of models which obey all known low-energy consistency conditions, but which have no known string theory realization. Many of these models contain novel matter representations, suggesting possible new string theory constructions. Many of the most exotic matter structures arise in models which precisely saturate the gravitational anomaly bound on the number of hypermultiplets. Such models have a rigid symmetry structure, in the sense that there are no moduli which leave the full gauge group unbroken.Comment: 31 pages, latex; v2, v3: minor corrections, references adde

5d quivers and their AdS(6) duals

We consider an infinite class of 5d supersymmetric gauge theories involving products of symplectic and unitary groups that arise from D4-branes at orbifold singularities in Type I' string theory. The theories are argued to be dual to warped AdS(6)x S4/Zn backgrounds in massive Type IIA supergravity. In particular, this demonstrates the existence of supersymmetric 5d fixed points of quiver type. We analyze the spectrum of gauge fields and charged states in the supergravity dual, and find a precise agreement with the symmetries and charged operators in the quiver theories. We also comment on other brane objects in the supergravity dual and their interpretation in the field theories.Comment: 29 pages, 15 figure

Size and shape constancy in consumer virtual reality

With the increase in popularity of consumer virtual reality headsets, for research and other applications, it is important to understand the accuracy of 3D perception in VR. We investigated the perceptual accuracy of near-field virtual distances using a size and shape constancy task, in two commercially available devices. Participants wore either the HTC Vive or the Oculus Rift and adjusted the size of a virtual stimulus to match the geometric qualities (size and depth) of a physical stimulus they were able to refer to haptically. The judgments participants made allowed for an indirect measure of their perception of the egocentric, virtual distance to the stimuli. The data show under-constancy and are consistent with research from carefully calibrated psychophysical techniques. There was no difference in the degree of constancy found in the two headsets. We conclude that consumer virtual reality headsets provide a sufficiently high degree of accuracy in distance perception, to allow them to be used confidently in future experimental vision science, and other research applications in psychology

<i>Trypanosoma brucei rhodesiense</i> transmitted by a single tsetse fly bite in vervet monkeys as a model of human African trypanosomiasis

Sleeping sickness is caused by a species of trypanosome blood parasite that is transmitted by tsetse flies. To understand better how infection with this parasite leads to disease, we provide here the most detailed description yet of the course of infection and disease onset in vervet monkeys. One infected tsetse fly was allowed to feed on each host individual, and in all cases infections were successful. The characteristics of infection and disease were similar in all hosts, but the rate of progression varied considerably. Parasites were first detected in the blood 4-10 days after infection, showing that migration of parasites from the site of fly bite was very rapid. Anaemia was a key feature of disease, with a reduction in the numbers and average size of red blood cells and associated decline in numbers of platelets and white blood cells. One to six weeks after infection, parasites were observed in the cerebrospinal fluid (CSF), indicating that they had moved from the blood into the brain; this was associated with a white cell infiltration. This study shows that fly-transmitted infection in vervets accurately mimics human disease and provides a robust model to understand better how sleeping sickness develops

Cholesterol and the risk of grade-specific prostate cancer incidence: evidence from two large prospective cohort studies with up to 37 years' follow up

&lt;b&gt;Background&lt;/b&gt; High cholesterol may be a modifiable risk factor for prostate cancer but results have been inconsistent and subject to potential "reverse causality" where undetected disease modifies cholesterol prior to diagnosis.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; We conducted a prospective cohort study of 12,926 men who were enrolled in the Midspan studies between 1970 and 1976 and followed up to 31st December 2007. We used Cox-Proportional Hazards Models to evaluate the association between baseline plasma cholesterol and Gleason grade-specific prostate cancer incidence. We excluded cancers detected within at least 5 years of cholesterol assay.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; 650 men developed prostate cancer in up to 37 years' follow-up. Baseline plasma cholesterol was positively associated with hazard of high grade (Gleason score[greater than or equal to]8) prostate cancer incidence (n=119). The association was greatest among men in the 4th highest quintile for cholesterol, 6.1 to &#60;6.69 mmol/l, Hazard Ratio 2.28, 95% CI 1.27 to 4.10, compared with the baseline of &#60;5.05 mmol/l. This association remained significant after adjustment for body mass index, smoking and socioeconomic status.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; Men with higher cholesterol are at greater risk of developing high-grade prostate cancer but not overall risk of prostate cancer. Interventions to minimise metabolic risk factors may have a role in reducing incidence of aggressive prostate cancer

Proceedings of the Salford Postgraduate Annual Research Conference (SPARC) 2011

These proceedings bring together a selection of papers from the 2011 Salford Postgraduate Annual Research Conference(SPARC). It includes papers from PhD students in the arts and social sciences, business, computing, science and engineering, education, environment, built environment and health sciences. Contributions from Salford researchers are published here alongside papers from students at the Universities of Anglia Ruskin, Birmingham City, Chester,De Montfort, Exeter, Leeds, Liverpool, Liverpool John Moores and Manchester