A Standardised Benchmark for Assessing the Performance of Fixed Radius Near Neighbours

Many agent based models require agents to have an awareness of their local peers. The handling of these fixed radius near neighbours (FRNNs) is often a limiting factor of performance. However without a standardised metric to assess the handling of FRNNs, contributions to the field lack the rigorous appraisal necessary to expose their relative benefits. This paper presents a standardised specification of a multi agent based benchmark model. The benchmark model provides a means for the objective assessment of FRNNs performance, through the comparison of implementations. Results collected from implementations of the benchmark model under three agent based modelling frameworks show the 64-bit floating point performance of each framework to scale linearly with agent population, in contrast the GPU accelerated framework’s 32- bit floating point performance only became linear after maximal device utilisation around 100,000 agent

Extracellular free water and glutathione in first-episode psychosis-a multimodal investigation of an inflammatory model for psychosis.

Evidence has been accumulating for an immune-based component to the etiology of psychotic disorders. Advancements in diffusion magnetic resonance imaging (MRI) have enabled estimation of extracellular free water (FW), a putative biomarker of neuroinflammation. Furthermore, inflammatory processes may be associated with altered brain levels of metabolites, such as glutathione (GSH). Consequently, we sought to test the hypotheses that FW is increased and associated with decreased GSH in patients with first-episode schizophrenia (SZ) compared with healthy controls (HC). SZ (n = 36) and HC (n = 40) subjects underwent a multi-shell diffusion MRI scan on a Siemens 3T scanner. 1H-MR spectroscopy data were acquired using a GSH-optimized MEGA-PRESS editing sequence and GSH/creatine ratios were calculated for DLPFC (SZ: n = 33, HC: n = 37) and visual cortex (SZ: n = 29, HC: n = 35) voxels. Symptoms and functioning were measured using the SANS, SAPS, BPRS, and GSF/GRF. SZ demonstrated significantly elevated FW in whole-brain gray (p = .001) but not white matter (p = .060). There was no significant difference between groups in GSH in either voxel. However, there was a significant negative correlation between DLPFC GSH and both whole-brain and DLPFC-specific gray matter FW in SZ (r = -.48 and -.47, respectively; both p < .05), while this relationship was nonsignificant in HC and in both groups in the visual cortex. These data illustrate an important relationship between a metabolite known to be important for immune function-GSH-and the diffusion extracellular FW measure, which provides additional support for these measures as neuroinflammatory biomarkers that could potentially provide tractable treatment targets to guide pharmacological intervention

The impact of the Lombard effect on audio and visual speech recognition systems

When producing speech in noisy backgrounds talkers reflexively adapt their speaking style in ways that increase speech-in-noise intelligibility. This adaptation, known as the Lombard effect, is likely to have an adverse effect on the performance of automatic speech recognition systems that have not been designed to anticipate it. However, previous studies of this impact have used very small amounts of data and recognition systems that lack modern adaptation strategies. This paper aims to rectify this by using a new audio-visual Lombard corpus containing speech from 54 different speakers – significantly larger than any previously available – and modern state-of-the-art speech recognition techniques. The paper is organised as three speech-in-noise recognition studies. The first examines the case in which a system is presented with Lombard speech having been exclusively trained on normal speech. It was found that the Lombard mismatch caused a significant decrease in performance even if the level of the Lombard speech was normalised to match the level of normal speech. However, the size of the mismatch was highly speaker-dependent thus explaining conflicting results presented in previous smaller studies. The second study compares systems trained in matched conditions (i.e., training and testing with the same speaking style). Here the Lombard speech affords a large increase in recognition performance. Part of this is due to the greater energy leading to a reduction in noise masking, but performance improvements persist even after the effect of signal-to-noise level difference is compensated. An analysis across speakers shows that the Lombard speech energy is spectro-temporally distributed in a way that reduces energetic masking, and this reduction in masking is associated with an increase in recognition performance. The final study repeats the first two using a recognition system training on visual speech. In the visual domain, performance differences are not confounded by differences in noise masking. It was found that in matched-conditions Lombard speech supports better recognition performance than normal speech. The benefit was consistently present across all speakers but to a varying degree. Surprisingly, the Lombard benefit was observed to a small degree even when training on mismatched non-Lombard visual speech, i.e., the increased clarity of the Lombard speech outweighed the impact of the mismatch. The paper presents two generally applicable conclusions: i) systems that are designed to operate in noise will benefit from being trained on well-matched Lombard speech data, ii) the results of speech recognition evaluations that employ artificial speech and noise mixing need to be treated with caution: they are overly-optimistic to the extent that they ignore a significant source of mismatch but at the same time overly-pessimistic in that they do not anticipate the potential increased intelligibility of the Lombard speaking style

Enhancing breadth of knowledge within multidisciplinary doctoral research: reflections from the Cambridge Generic Nutrition Training course for non-nutritionist postgraduates and professionals

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The spectral transmission of ocular media suggests ultraviolet sensitivity is widespread among mammals

Although ultraviolet (UV) sensitivity is widespread among animals it is considered rare in mammals, being restricted to the few species that have a visual pigment maximally sensitive (λmax) below 400 nm. However, even animals without such a pigment will be UV-sensitive if they have ocular media that transmit these wavelengths, as all visual pigments absorb significant amounts of UV if the energy level is sufficient. Although it is known that lenses of diurnal sciurid rodents, tree shrews and primates prevent UV from reaching the retina, the degree of UV transmission by ocular media of most other mammals without a visual pigment with λmax in the UV is unknown. We examined lenses of 38 mammalian species from 25 families in nine orders and observed large diversity in the degree of short-wavelength transmission. All species whose lenses removed short wavelengths had retinae specialized for high spatial resolution and relatively high cone numbers, suggesting that UV removal is primarily linked to increased acuity. Other mammals, however, such as hedgehogs, dogs, cats, ferrets and okapis had lenses transmitting significant amounts of UVA (315–400 nm), suggesting that they will be UV-sensitive even without a specific UV visual pigment

Host pathogen interactions in relation to management of light leaf spot disease (caused by Pyrenopeziza brassicae) on Brassica species

Light leaf spot, caused by Pyrenopeziza brassicae, is currently the most damaging disease problem in oilseed rape in the UK. According to recent survey data, the severity of epidemics has increased progressively across the UK, with current yield losses of up to £160M per annum in England and more severe epidemics in Scotland. Light leaf spot is a polycyclic disease with primary inoculum consisting of air-borne ascospores produced on diseased debris from the previous cropping season. Splash-dispersed conidia produced on diseased leaves are the main component of the secondary inoculum. P. brassicae is also able to infect and cause considerable yield losses on vegetable brassicas, especially Brussels sprouts. There may be spread of light leaf spot among different brassica species. Since they have a wide host range, Pyrenopeziza brassicae populations are likely to have considerable genetic diversity and there is evidence suggesting population variations between different regions, which need further study. Available disease-management tools are not sufficient to provide adequate control of the disease. There is a need to identify new sources of resistance, which can be integrated with fungicide applications to achieve sustainable management of light leaf spot. Several major resistance genes and quantitative trait loci have been identified in previous studies, but rapid improvements in the understanding of molecular mechanisms underpinning B. napus – P. brassicae interactions can be expected through exploitation of novel genetic and genomic information for brassicas and extracellular fungal pathogens.Peer reviewe

Organisational participation and women - an attitude problem?

Employee participation is a dynamic and contested area of organisational behaviour, attracting continuing academic, practitioner and policy interest and debate. This chapter focuses on organisational participation and women

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data

The Seychelles archipelago is unique among isolated oceanic islands because it features an endemic radiation of caecilian amphibians (Gymnophiona). In order to develop population genetics resources for this system, we identified microsatellite loci using unassembled Illumina MiSeq data generated from a genomic library of Grandisonia alternans, a species that occurs on multiple islands in the archipelago. Applying a recently described method (PALFINDER) we identified 8001 microsatellite loci that were potentially informative for population genetics analyses. Of these markers, we screened 60 loci using five individuals, directly sequenced several amplicons to confirm their identity, and then used eight loci to score allele sizes in 64 G. alternans individuals originating from five islands. A number of these individuals were sampled using non-lethal methods, demonstrating the efficacy of non-destructive molecular sampling in amphibian research. Although two loci satisfied our criteria as diploid, neutrally evolving loci with the statistical power to detect population structure, our success in identifying reliable loci was very low. Additionally, we discovered some issues with primer redundancy and differences between Illumina and Sanger sequences that suggest some Illumina-inferred loci are invalid. We investigated cross-species utility for eight loci and found most could be successfully amplified, sequenced and aligned across other species and genera of caecilians from the Seychelles. Thus, our study in part supported the validity of using PALFINDER with unassembled reads for microsatellite discovery within and across species, but importantly identified major limitations to applying this approach to small datasets (ca. 1 million reads) and loci with small tandem repeat sizes