A hydro-elastic model of hydrocephalus

We combine elements of poroelasticity and of fluid mechanics to construct a mathematical model of the human brain and ventricular system. The model is used to study hydrocephalus, a pathological condition in which the normal flow of the cerebrospinal fluid is disturbed, causing the brain to become deformed. Our model extends recent work in this area by including flow through the aqueduct, by incorporating boundary conditions which we believe more accurately represent the anatomy of the brain and by including time dependence. This enables us to construct a quantitative model of the onset, development and treatment of this condition. We formulate and solve the governing equations and boundary conditions for this model and give results which are relevant to clinical observations

A User Satisfaction Study of the London Congestion Charging e-Service

This research seeks to measure citizen satisfaction with the electronic London Congestion Charging (LCC) payment system offered by Transport For London (TFL) in the United Kingdom (UK). The paper reports on the findings of a survey of 500 users of the TFL LCC online payment system. Satisfaction is measured using the four dimensions from the COBRA framework 0that comprise the cost, opportunity, benefits and risk assessment constructs. The results show that most citizens using the LCC electronic service are satisfied with the service and that the service meets their essential needs. The paper also presents the results of qualitative feedback obtained from the participants that can be used to determine the areas that need further improvement in the current electronic LCC electronic-service (e-service) system and potential influences on user satisfaction

Error Correction and de novo Genome Assembly of DNA Sequencing Data

The ability to obtain the genetic code of any species has caused a revolution in biological sciences. Current technologies are capable of sequencing short pieces of DNA with very high quality. These short pieces of DNA determint the sequence of bases in the genome of any species. This information is key in understanding many of the aspects of how life functions. The accuracy of sequencing is extremely important since the differences between individuals of the same species are caused by very few changes. All sequencing technologies make errors, and before the data can be used for downstream applications it is usually best to correct the errors first. I present an error correction program called RACER that is an error correction program that aims to correct substitution sequencing errors. There are many substitution error correction programs available for DNA sequencing technologies, so it is important for biologists to know which program is best to use for their sequencing technology. I present a comprehensive survey of substitution error correction programs for DNA sequencing data to address this issue. I also present two programs to evaluate the performance of error correcting programs. Since the current dominant platform in the market can only obtain small pieces of DNA, software is needed to assemble these pieces to determine the full sequence of the sampled genome. Current genome assembly programs are not capable of assembling the entire genome of most species due to the repetitive nature of genomes and the uneven coverage of the sampled genome. I present a genome assembly program called SAGE2 that improves upon the current state-of-the-art

Error Correction in Next Generation DNA Sequencing Data

Motivation: High throughput Next Generation Sequencing (NGS) technologies can sequence the genome of a species quickly and cheaply. Errors that are introduced by NGS technologies limit the full potential of the applications that rely on their data. Current techniques used to correct these errors are not sufficient, and a more efficient and accurate program is needed to correct errors. Results: We have designed and implemented RACER (Rapid Accurate Correction of Errors in Reads), an error correction program that targets the Illumina genome sequencer, which is currently the dominant NGS technology. RACER combines advanced data structures with an intricate analysis of data to achieve high performance. It has been implemented in C++ and OpenMP for parallelization. We have performed extensive testing on a variety of real data sets to compare RACER with the current leading programs. RACER performs better than all the current technologies in time, space, and accuracy. RACER corrects up to twice more errors than all other parallel programs, while being one order of magnitude faster. We hope RACER will become a very useful tool for many applications that use NGS data

Thermalization of gluon matter including gg<->ggg interactions

Within a pQCD inspired kinetic parton cascade we simulate the space time evolution of gluons which are produced initially in a heavy ion collision at RHIC energy. The inelastic gluonic interactions $gg \leftrightarrow ggg$ do play an important role: For various initial conditions it is found that thermalization and the close to ideal fluid dynamical behaviour sets in at very early times. Special emphasis is put on color glass condensate initial conditions and the `bottom up thermalization' scenario. Off-equilibrium $3\to 2$ processes make up the very beginning of the evolution leading to an initial decrease in gluon number and a temporary avalanche of the gluon momentum distribution to higher transversal momenta.Comment: 6 pages, 8 figures, Talk given at International Conference on Strong and Electroweak Matter (SEWM 2006), BNL, New York, May 200

A multi-layer phase field model for extracting multiple near-circular objects

This paper proposes a functional that assigns low `energy' to sets of subsets of the image domain consisting of a number of possibly overlapping near-circular regions of approximately a given radius: a `gas of circles'. The model can be used as a prior for object extraction whenever the objects conform to the `gas of circles' geometry, e.g. cells in biological images. Configurations are represented by a multi-layer phase field. Each layer has an associated function, regions being defined by thresholding. Intra-layer interactions assign low energy to configurations consisting of non-overlapping near-circular regions, while overlapping regions are represented in separate layers. Inter-layer interactions penalize overlaps. Here we present a theoretical and experimental analysis of the model

Thickness Dependent Growth of Epitaxial Iron Silicide Nanoobjects on Si (001)

Strain-induced, self-assembled iron silicide nanostructures were grown on Si(001) substrate by conventional Fe evaporation and subsequent annealing. The initial Fe thickness was in the 0.1-6.0 nm range and the annealing temperature was 850 °C. The formed phases and structures were characterized by reflection high energy electron diffraction, and scanning electron microscopy. The electrical characteristics were investigated by I-V and C-V measurements, and by DLTS. The samples show silicide nanostructure formation in the whole thickness range. The shape of the nanostructures varied from rod like to triangular and quadratic depending on the initial Fe thickness. The size distribution of the formed iron silicide nanoobjects was not homogeneous, but they were oriented in square directions on Si(001). Higher thickness resulted in increased particles size. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/3518

The mitochondrial permeability transition pore components

The mitochondrial permeability transition pore (MPTP) is a non-specific channel in the inner mitochondrial membrane (IMM) that opens following ischaemia and reperfusion due to the presence of various stimuli, such as oxidative stress, elevated phosphate concentration, and adenine nucleotide depletion. MPTP opening causes the mitochondria to swell and become dysfunctional. This results in cell death, especially by necrosis, due to the loss of oxidative phosphorylation and the subsequent drop in adenosine triphosphate levels. In search of the identity of the pore numerous studies have been done by several research groups in the last three decades. For many years a widely accepted hypothesis prevailed suggesting the involvement of the adenine nucleotide translocase (ANT) and voltage-dependent anion channel (VDAC) as core proteins of the MPTP. Recent genetic studies, however, contradict this hypothesis and ascribe only a regulatory role to the ANT. Furthermore, there is now sufficient evidence to conclude that VDAC plays no role in mitochondrial permeability transition. In a recent study it was suggested that the mitochondrial phosphate carrier (PiC) may fulfil a role as a pore component. According to a proposed model MPTP is formed as a consequence of a conformational change in the PiC, triggered by calcium binding. Opening of the pore may be enhanced through interactions with the ANT in the “c” conformation and cyclophilin-D, a mitochondrial matrix protein