PRIVATIZATION AND TRANSITION ISSUES IN RUSSIAN AGRICULTURE

Agricultural and Food Policy,

A biochemical and biophysical study on cell division proteins from Staphylococcus aureus and biofilm proteins from Bacillus subtilis.

PhD ThesisPart I Cell division in bacteria is tightly regulated by a multiprotein complex called the divisome. Proteins in the divisome couple cell division and growth, ensuring that a single copy of the chromosome is present in each resulting daughter cell, and preventing more than one instance of division from occurring at any one time. This thesis concerns a combination of biophysical and biochemical techniques used to study the cell division proteins DivIVA, Stk1 and GpsB from Staphylococcus aureus. A model of the solution molecular envelope of DivIVA is derived by small-angle X-ray scattering and compared to a previously proposed model of the protein from Bacillus subtilis. The molecular mechanisms of DivIVA oligomerization are probed through use of size-exclusion chromatography coupled multi-angle light scattering on various truncations of the protein. The structure of the N-terminal domain of S. aureus GpsB is solved and used to rationalise the interaction between GpsB and PBP4. Attempts are made to determine an interaction network between the cell division proteins and members of the peptidoglycan and wall-teichoic acid synthesis machinery by several biochemical and biophysical assays. Part II Biofilms are communities of sessile bacteria that form on a wide variety of natural and manmade surfaces, sometimes at a detriment to human health. Bacteria in biofilms are held together by a viscous extracellular matrix consisting of polysaccharides, lipids, proteins, and extracellular DNA (eDNA). Species of Bacillus are known to secrete two structurally similar endonucleases, Nuclease A and B (NucA & NucB), into their environment as a means of taking up eDNA either to enhance their genetic diversity, or for metabolic purposes, respectively. As a mechanism of protection from self-induced genome degradation, NucA is co-expressed with a proposed inhibitor, Nin. A combination of biophysical/chemical techniques are used to probe the interaction between NucA/B and Nin from Bacillus subtilis. In vitro studies show that NucA and NucB bind to Nin and that Nin inhibits their endonuclease activity. The affinity of the interactions between NucA or NucB and Nin are probed and found to be sub-nanomolar. The structures of NucA/NucB in complex with Nin are solved by X-ray crystallography, revealing the mechanism of inhibition by Nin, and allowing for the calculated dismantling of the complexes by site-directed mutagenesis

Fundamental properties and applications of quasi-local black hole horizons

The traditional description of black holes in terms of event horizons is inadequate for many physical applications, especially when studying black holes in non-stationary spacetimes. In these cases, it is often more useful to use the quasi-local notions of trapped and marginally trapped surfaces, which lead naturally to the framework of trapping, isolated, and dynamical horizons. This framework allows us to analyze diverse facets of black holes in a unified manner and to significantly generalize several results in black hole physics. It also leads to a number of applications in mathematical general relativity, numerical relativity, astrophysics, and quantum gravity. In this review, I will discuss the basic ideas and recent developments in this framework, and summarize some of its applications with an emphasis on numerical relativity.Comment: 14 pages, 2 figures. Based on a talk presented at the 18th International Conference on General Relativity and Gravitation, 8-13 July 2007, Sydney, Australi

An excited-state approach within full configuration interaction quantum Monte Carlo.

We present a new approach to calculate excited states with the full configuration interaction quantum Monte Carlo (FCIQMC) method. The approach uses a Gram-Schmidt procedure, instantaneously applied to the stochastically evolving distributions of walkers, to orthogonalize higher energy states against lower energy ones. It can thus be used to study several of the lowest-energy states of a system within the same symmetry. This additional step is particularly simple and computationally inexpensive, requiring only a small change to the underlying FCIQMC algorithm. No trial wave functions or partitioning of the space is needed. The approach should allow excited states to be studied for systems similar to those accessible to the ground-state method due to a comparable computational cost. As a first application, we consider the carbon dimer in basis sets up to quadruple-zeta quality and compare to existing results where available.N.S.B. gratefully acknowledges Trinity College, Cambridge for funding. G.H.B. gratefully acknowledges the Royal Society for funding via a university research fellowship. This work has been supported by the EPSRC under grant no. EP/J003867/1.This is the accepted manuscript. The final version is available at http://scitation.aip.org/content/aip/journal/jcp/143/13/10.1063/1.4932595

A comparison between quantum chemistry and quantum Monte Carlo techniques for the adsorption of water on the (001) LiH surface

We present a comprehensive benchmark study of the adsorption energy of a single water molecule on the (001) LiH surface using periodic coupled cluster and quantum Monte Carlo theories. We benchmark and compare different implementations of quantum chemical wave function based theories in order to verify the reliability of the predicted adsorption energies and the employed approximations. Furthermore we compare the predicted adsorption energies to those obtained employing widely-used van der Waals density-functionals. Our findings show that quantum chemical approaches are becoming a robust and reliable tool for condensed phase electronic structure calculations, providing an additional tool that can also help in potentially improving currently available van der Waals density-functionals

An automated pattern recognition system for the quantification of inflammatory cells in hepatitis-C-infected liver biopsies

This paper presents an automated system for the quantification of inflammatory cells in hepatitis-C-infected liver biopsies. Initially, features are extracted from colour-corrected biopsy images at positions of interest identified by adaptive thresholding and clump decomposition. A sequential floating search method and principal component analysis are used to reduce dimensionality. Manually annotated training images allow supervised training. The performance of Gaussian parametric and mixture models is compared when used to classify regions as either inflammatory or healthy. The system is optimized using a response surface method that maximises the area under the receiver operating characteristic curve. This system is then tested on images previously ranked by a number of observers with varying levels of expertise. These results are compared to the automated system using Spearman rank correlation. Results show that this system can rank 15 test images, with varying degrees of inflammation, in strong agreement with five expert pathologists

Outcome determinism in measurement-based quantum computation with qudits

In measurement-based quantum computing (MBQC), computation is carried out by a sequence of measurements and corrections on an entangled state. Flow, and related concepts, are powerful techniques for characterising the dependence of the corrections on previous measurement outcomes. We introduce flow-based methods for MBQC with qudit graph states, which we call Z d -flow, when the local dimension is an odd prime. Our main results are a proof that Z d -flow is a necessary and sufficient condition for a strong form of outcome determinism. Along the way, we find a suitable generalisation of the concept of measurement planes to this setting and characterise the allowed measurements in a qudit MBQC. We also provide a polynomial-time algorithm for finding an optimal Z d -flow whenever one exists

Adolescent bullying and sleep difficulties

This study evaluated whether adolescents who report having been bullied, being bullies, or report both being a bully and being bullied experience more sleep difficulties than children uninvolved in bullying. The study drew upon cognitive theories of insomnia, investigating whether the extent to which young people report worrying about bullying can moderate associations between victimization and sleep difficulties. Participants were 5420 adolescents who completed a self-report questionnaire. Pure Victims (OR = 1.72: 95% CI [1.07 – 2.75]), Pure Bullies (OR = 1.80: 95% CI [1.16 – 2.81]), and Bully-Victims (OR = 2.90: 95% CI [1.17 – 4.92]) were all more likely to experience sleep difficulties when compared to uninvolved young people. The extent to which young people reported worrying about being bullied did not moderate the links between victimization and sleep difficulties. In this way, bullying is clearly related to sleep difficulties among adolescents but the conceptual reach of the cognitive model of insomnia in this domain is questioned

Area-preserving parameterizations for spherical ellipses

We present new methods for uniformly sampling the solid angle subtended by a disk. To achieve this, we devise two novel area-preserving mappings from the unit square $[0,1]^2$ to a spherical ellipse (i.e. the projection of the disk onto the unit sphere). These mappings allow for low-variance stratified sampling of direct illumination from disk-shaped light sources. We discuss how to efficiently incorporate our methods into a production renderer and demonstrate the quality of our maps, showing significantly lower variance than previous work