News from FormCalc and LoopTools

The FormCalc package automates the computation of FeynArts amplitudes up to one loop including the generation of a Fortran code for the numerical evaluation of the squared matrix element. Major new or enhanced features in Version 5 are: iterative build-up of essentially arbitrary phase-spaces including cuts, convolution with density functions, and uniform treatment of kinematical variables. The LoopTools library supplies the one-loop integrals necessary for evaluating the squared matrix element. Its most significant extensions in Version 2.2 are the five-point family of integrals, and complex and alternate versions.Comment: 5 pages, to appear in the proceedings of the 7th International Symposium on Radiative Corrections (RADCOR05), Shonan Village, Japan, 200

Static and Dynamic Resource Allocation Effects of Corporate and PersonalTax Integration in the U.S.: A General Equilibrium Approach(Rev)

This paper presents estimates of static and dynamic general equilibrium resource allocation effects for four alternative plans for corporate and personal income tax integration in the U.S. A medium—scale numerical general equilibrium model is used which integrates the U.S. tax system with consumer demand behavior by household and producer behavior by industry. Results indicate that total integration of personal and corporate taxes would yield an annual static efficiency gain of around $4 billion (1973 dollars). Partial integration plans yield less. Dynamic effects are larger, and our analysis indicates that full integration may yield gains whose present value is as large as$400 billion or 0.8% of the discounted present value of the GNP stream to the U.S. economy after correction for population growth. Plans differ in their distributional impacts, although these findings depend on the nature of replacement taxes used to preserve government revenues. The size of dynamic resource allocation effects are sensitive to the choice of the replacement tax, while static gains are reasonably robust.

Novel bioinformatics tools for epitope-based peptide vaccine design

BACKGROUND T-cells are essential in the mediation of immune responses, helping clear bacteria, viruses and cancerous cells. T-cells recognise anomalies in the cellular proteome associated with infection and neoplasms through the T-cell receptor (TCR). The most common TCRs in humans, αβ TCRs, engage processed peptide epitopes presented on the major histocompatibility complex (pMHC). TCR-pMHC interaction is critical to vaccination. In this thesis I will discuss three pieces of software and outcomes derived from them that contribute to epitope-based vaccine design. RESULTS Three pieces of software were developed to help scientists study and understand T-cell responses. The first, STACEI allows users to interrogate the TCR-pMHC crystal structures. The time consuming, error-prone analysis that previously would have to be ran manually, is replaced by a single, flexible package. The second development is the introduction of general-purpose computing on the GPU (GP-GPU) in aiding the prediction of T-cell epitopes by scanning protein datasets using data derived from combinatorial peptide libraries (CPLs). Finally, I introduce RECIPIENT, a reverse vaccinology tool (RV) that combines pangenomic and population genetics methods to predict good vaccine targets across multiple pathogen samples. CONCLUSION Across this thesis, I introduce three different methods that aid the study of T-cells that will hopefully improve future vaccine design. These methods range across data types and methodologies, with methods focusing on mechanistic understanding of the TCR-pMHC binding event; the application of GP-GPU to CPLs and using microbial genomics to aid the study and understanding of antigen-specific T-cell responses. These three methods have a significant potential for further integration, especially the structural methods

Wheat growth responses to soil mechanical impedance are dependent on phosphorus supply

Increased mechanical impedance induced by soil drying or compaction causes reduction in plant growth and crop yield. However, how mechanical impedance interacts with nutrient stress has been largely unknown. Here, we investigated the effect of mechanical impedance on the growth of wheat seedlings under contrasting phosphorus (P) supply in a sand culture system which allows the mechanical impedance to be independent of water and nutrient availability. Two wheat genotypes containing the Rht-B1a (tall) or Rht-B1c (gibberellin-insensitive dwarf) alleles in the Cadenza background were used and their shoot and root traits were determined. Mechanical impedance caused a significant reduction in plant growth under sufficient P supply, including reduced shoot and root biomass, leaf area and total root length. By contrast, under low P supply, mechanical impedance did not affect biomass, tiller number, leaf length, and nodal root number in both wheat genotypes, indicating that the magnitude of the growth restriction imposed by mechanical impedance was dependent on P supply. The interaction effect between mechanical impedance and P level was significant on most plant traits except for axial and lateral root length, suggesting an evident physical and nutritional interaction. Our findings provide valuable insights into the integrated effects of plants in response to both soil physical and nutritional stresses. Understanding the response patterns is critical for optimizing soil tillage and nutrient management in the field

Equilibrium unemployment in a general equilibrium model with taxes

The ratio of unemployed to vacancies has risen sharply in the UK after the recession of 2008/09. How harmful is it for the long run growth, equity and efficiency and what sorts of long run cycles does it generate in the economy? With a dynamic computable general equilibrium model with Pissarides (1979, 2011) and Mortensen and Pissarides (1994) type equilibrium unemployment, impacts of tax-transfer programmes are assessed for the UK. The model contains more desirable structure of households and production sectors and includes more type of shocks in preferences, technology, trade and policy instruments for stochastic analyses than is usual in DSGE models. It assesses growth and cycles as well as equity and efficiency effects of policies simultaneously. Improvements in the matching technology lowers the equilibrium unemployment and raises the long-run growth rate and life time utilities of households and reduces long run cycles. Matching could be made more efficient by influencing the relative price system by optimal set of tax and transfer instruments. Better matching techniques can make transition of job-seekers to employment more efficient so that the intertemporal labour-leisure and consumption-saving decisions have greater impacts on growth and redistribution reducing fluctuations in the economy

Responses of Salmonella biofilms to oxidizing biocides: evidence of spatial clustering

The spatial organization of biofilm bacterial communities can be influenced by several factors, including growth conditions and challenge with antimicrobials. Differential survival of clusters of cells within biofilms has been observed. In this work, we present a variety of methods to identify, quantify and statistically analyse clusters of live cells from images of two Salmonella strains with differential biofilm forming capacity exposed to three oxidizing biocides. With a support vector machine approach, we showed spatial separation between the two strains, and, using statistical testing and high‐performance computing (HPC), we determined conditions which possess an inherent cluster structure. Our results indicate that there is a relationship between biocide potency and inherent biofilm formation capacity with the tendency to select for spatial clusters of survivors. There was no relationship between positions of clusters of live or dead cells within stressed biofilms. This work identifies an approach to robustly quantify clusters of physiologically distinct cells within biofilms and suggests work to understand how clusters form and survive is needed. Significance statement: Control of biofilm growth remains a major challenge and there is considerable uncertainty about how bacteria respond to disinfection within a biofilm and how clustering of cells impacts survival. We have developed a methodological approach to identify and statistically analyse clusters of surviving cells in biofilms after biocide challenge. This approach can be used to understand bacterial behaviour within biofilms under stress and is widely applicable

A self-consistent, multi-variate method for the determination of gas phase rate coefficients, applied to reactions of atmospheric VOCs and the hydroxyl radical

Gas-phase rate coefficients are fundamental to understanding atmospheric chemistry, yet experimental data are not available for the oxidation reactions of many of the thousands of volatile organic compounds (VOCs) observed in the troposphere. Here a new experimental method is reported for the simultaneous study of reactions between multiple different VOCs and OH, the most important daytime atmospheric radical oxidant. This technique is based upon established relative rate concepts but has the advantage of a much higher throughput of target VOCs. By evaluating multiple VOCs in each experiment, and through measurement of the depletion in each VOC after reaction with OH, the OH + VOC reaction rate coefficients can be derived. Results from experiments conducted under controlled laboratory conditions were in good agreement with the available literature for the reaction of nineteen VOCs, prepared in synthetic gas mixtures, with OH. This approach was used to determine a rate coefficient for the reaction of OH with 2,3-dimethylpent-1-ene for the first time; k = 5.7 (±0.3) × 10–11–cm3 molecule−1 s−1. In addition, a further seven VOCs had only two, or fewer, individual OH rate coefficient measurements available in the literature. The results from this work were in good agreement with those measurements. A similar dataset, at an elevated temperature of 323 (±10) K, was used to determine new OH rate coefficients for twelve aromatic, five alkane, five alkene and three monoterpene VOC + OH reactions. In OH relative reactivity experiments that used ambient air at the University of York, a large number of different VOCs were observed, of which 23 were positively identified. 19 OH rate coefficients were derived from these ambient air samples, including ten reactions for which data was previously unavailable at the elevated reaction temperature of T = 323 (±10) K