Behavioral simulation and synthesis of biological neuron systems using synthesizable VHDL

Neurons are complex biological entities which form the basis of nervous systems. Insight can be gained into neuron behavior through the use of computer models and as a result many such models have been developed. However, there exists a trade-off between biological accuracy and simulation time with the most realistic results requiring extensive computation. To address this issue, a novel approach is described in this paper that allows complex models of real biological systems to be simulated at a speed greater than real time and with excellent accuracy. The approach is based on a specially developed neuron model VHDL library which allows complex neuron systems to be implemented on field programmable gate array (FPGA) hardware. The locomotion system of the nematode Caenorhabditis elegans is used as a case study and the measured results show that the real time FPGA based implementation performs 288 times faster than traditional ModelSim simulations for the same accuracy

Chitinase and Fizz family members are a generalized feature of nematode infection with selective Upregulation of Ym1 and F10.1 by antigen-presenting cells

Ym1 and Fizz1 are secreted proteins that have been identified in a variety of Th2-mediated inflammatory settings. We originally found Ym1 and Fizz1 as highly expressed macrophage genes in a Brugia malayi infection model. Here, we show that their expression is a generalized feature of nematode infection and that they are induced at the site of infection with both the tissue nematode Litomosoides sigmodontis and the gastrointestinal nematode Nippostrongylus brasiliensis. At the sites of infection with N. brasiliensis, we also observed induction of other chitinase and Fizz family members (ChaFFs): acidic mammalian chitinase (AMCase) and Fizz2. The high expression of both Ym1 and AMCase in the lungs of infected mice suggests that abundant chitinase production is an important feature of Th2 immune responses in the lung. In addition to expression of ChaFFs in the tissues, Ym1 and Fizz1 expression was observed in the lymph nodes. Expression both in vitro and in vivo was restricted to antigen-presenting cells, with the highest expression in B cells and macrophages. ChaFFs may therefore be important effector or wound-repair molecules at the site of nematode infection, with potential regulatory roles for Ym1 and Fizz1 in the draining lymph nodes

Reliability-Based Design of Solid and Nail-jointed I-Section of Nigerian-Grown African Birch (Anogeissus leiocarpus) Timber Column

The Nigerian-grown African birch timber was used to assemble I- section specimens which were tested in the laboratory for their compressive strengths. Solid square sections of the same specie were similarly tested for an apt comparison of results. A structural reliability analysis was carried out for these two sections to ascertain their performance as structural timber columns using statistical parameters that were determined for the deterministic design of the timber column. A FORTRAN-based program was also developed and used for the reliability analysis of the Nigerian-grown African birch columns designed to ascertain their level of safety using First-Order Reliability Method (FORM). The ‘I’- section was found unsafe to bear the design load unlike its corresponding solid section. An identified I- section of (100 x 400mm) was found adequate (with Pf =1.22 x 10-02) whose compressive resistance corresponds to (200 x 100mm) of the solid section (with Pf =7.76 x 10-02) which is practically half the dimension of the I-section. This shows that the solid section has a capacity twice that of the ‘I’- section of equal dimensions. However, considering the minimum dimension of the of the two sections capable of supporting the design load, the ‘I’- section is more economical than the solid section since it offers a less effective area of 11,200mm2 compared to the solid section with an effective area of 20,000mm2 . The ‘I’-section also showed a higher capacity to bear the Euler load with greater lengths than the solid section because of its greater radius of gyration and rigidity value and would be rather preferable for long columns than the solid section. Considering the limited availability of larger dimensions of solid sections, the built-up I- section would be more relevant where large sized sections are required.Keywords: Solid section, Compressive capacity, Built-up sections, Reliability, Probability of failure (Pf

Investigating hookworm genomes by comparative analysis of two Ancylostoma species

Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics

The Effect of Large Amplitude Fluctuations in the Ginzburg-Landau Phase Transition

The lattice Ginzburg-Landau model in d=3 and d=2 is simulated, for different values of the coherence length $\xi$ in units of the lattice spacing $a$, using a Monte Carlo method. The energy, specific heat, vortex density $v$, helicity modulus $\Gamma_\mu$ and mean square amplitude are measured to map the phase diagram on the plane $T-\xi$. When amplitude fluctuations, controlled by the parameter $\xi$, become large ($\xi \sim 1$) a proliferation of vortex excitations occurs changing the phase transition from continuous to first order.Comment: 4 pages, 5 postscript (eps) figure

Dimensionality of spin modulations in 1/8-doped lanthanum cuprates from the perspective of NQR and muSR experiments

We investigate the dimensionality of inhomogeneous spin modulation patterns in the cuprate family of high-temperature superconductors with particular focus on 1/8-doped lanthanum cuprates. We compare one-dimensional stripe modulation pattern with two-dimensional checkerboard of spin vortices in the context of nuclear quadrupole resonance(NQR) and muon spin rotation(muSR) experiments. In addition, we also consider the third pattern, a two-dimensional superposition of spin spirals. Overall, we have found that none of the above patterns leads to a consistent interpretation of the two types of experiments considered. This, in particular, implies that the spin vortex checkerboard cannot be ruled out on the basis of available NQR/muSR experimental results.Comment: 6 pages, 2 figure

An investigation of the efficacy of a polyvalent mastitis vaccine using different vaccination regimens under field conditions in the United Kingdom

Vaccination can play a useful role in mastitis control programs, although there is a relative dearth of large, well-controlled field efficacy studies. This paper presents the findings on the use of a commercially available vaccine (Startvac, Hipra UK Ltd., Nottingham, UK) on commercial units under UK field conditions. In total, 3,130 cows were recruited from 7 farms and were randomly allocated, within farm, to 1 of 3 groups. The first group received the vaccine following the label regimen, the second group was vaccinated every 90 d following an initial vaccination course, and the third group was left unvaccinated to act as controls. Vaccine efficacy was assessed in the first 120 d of lactation. Data were available for analysis from 1,696 lactations in 1,549 cows. In total, 779 cases of clinical mastitis occurred in the 3 study groups, and we detected no significant difference in the incidence or prevalence of clinical or subclinical mastitis between any of the 3 groups. Mastitis vaccination following the label regimen was associated with a significant reduction in the severity of clinical cases. Cows in this group were at significantly decreased odds of developing clinical mastitis presenting with more than just milk changes [odds ratio: 0.58; 95% confidence interval (CI): 0.35–0.98]. Similarly, each additional vaccination resulted in a cow being at decreased odds of developing clinical mastitis presenting with more than just milk changes (odds ratio: 0.87; 95% CI: 0.77–0.98). Although no cows were culled because of severe mastitis in either of the vaccinated groups, we detected no significant difference in the mastitis-related culling rate between groups. Analysis of milk production data demonstrated that, on average, cows on the label regimen produced a higher volume of milk (231 L; 95% CI: 104.1–357.4) and more milk solids (12.36 kg; 95% CI: 3.12–21.60) than unvaccinated cows in the first 120 d of lactation. Conservative analysis suggested that a return on investment of 2.57:1 could be expected under UK conditions based on increased milk yield alone

Reflections and Experiences of a Co-Researcher involved in a Renal Research Study

Background Patient and Public Involvement (PPI) is seen as a prerequisite for health research. However, current Patient and public involvement literature has noted a paucity of recording of patient and public involvement within research studies. There have been calls for more recordings and reflections, specifically on impact. Renal medicine has also had similar criticisms and any reflections on patient and public involvement has usually been from the viewpoint of the researcher. Roles of patient and public involvement can vary greatly from sitting on an Advisory Group to analysing data. Different PPI roles have been described within studies; one being a co-researcher. However, the role of the co-researcher is largely undefined and appears to vary from study to study. Methods The aims of this paper are to share one first time co-researcher's reflections on the impact of PPI within a mixed methods (non-clinical trial) renal research study. A retrospective, reflective approach was taken using data available to the co-researcher as part of the day-to-day research activity. Electronic correspondence and documents such as meeting notes, minutes, interview thematic analysis and comments on documents were re-examined. The co-researcher led on writing this paper. Results This paper offers a broad definition of the role of the co-researcher. The co-researcher reflects on undertaking and leading on the thematic analysis of interview transcripts, something she had not previously done before. The co-researcher identified a number of key themes; the differences in time and responsibility between being a coresearcher and an Advisory Group member; how the role evolved and involvement activities could match the co-researchers strengths (and the need for flexibility); the need for training and support and lastly, the time commitment. It was also noted that it is preferable that a co-researcher needs to be involved from the very beginning of the grant application. Conclusions The reflections, voices and views of those undertaking PPI has been largely underrepresented in the literature. The role of co-researcher was seen to be rewarding but demanding, requiring a large time commitment. It is hoped that the learning from sharing this experience will encourage others to undertake this role, and encourage researchers to reflect on the needs of those involved.Peer reviewedFinal Published versio

A forage-only diet alters the metabolic response of horses in training

Most athletic horses are fed a high-starch diet despite the risk of health problems. Replacing starch concentrate with high-energy forage would alleviate these health problems, but could result in a shift in major substrates for muscle energy supply from glucose to short-chain fatty acids (SCFA) due to more hindgut fermentation of fibre. Dietary fat inclusion has previously been shown to promote aerobic energy supply during exercise, but the contribution of SCFA to exercise metabolism has received little attention. This study compared metabolic response with exercise and lactate threshold (VLa4) in horses fed a forage-only diet (F) and a more traditional high-starch, low-energy forage diet (forage–concentrate diet - FC). The hypothesis was that diet F would increase plasma acetate concentration and increase VLa4 compared with diet FC. Six Standardbred geldings in race training were used in a 29-day change-over experiment. Plasma acetate, non-esterified fatty acids (NEFA), lactate, glucose and insulin concentrations and venous pH were measured in samples collected before, during and after a treadmill exercise test (ET, day 25) and muscle glycogen concentrations before and after ET. Plasma acetate concentration was higher before and after exercise in horses on diet F compared with diet FC, and there was a tendency ( P50.09) for increased VLa4 on diet F. Venous pH and plasma glucose concentrations during exercise were higher in horses on diet F than diet FC, as was plasma NEFA on the day after ET. Plasma insulin and muscle glycogen concentrations were lower for diet F, but glycogen utilisation was similar for the two diets. The results show that a high-energy, forage-only diet alters the metabolic response to exercise and, with the exception of lowered glycogen stores, appears to have positive rather than negative effects on performance traits