Finite temperature molecular dynamics study of unstable stacking fault free energies in silicon

We calculate the free energies of unstable stacking fault (USF) configurations on the glide and shuffle slip planes in silicon as a function of temperature, using the recently developed Environment Dependent Interatomic Potential (EDIP). We employ the molecular dynamics (MD) adiabatic switching method with appropriate periodic boundary conditions and restrictions to atomic motion that guarantee stability and include volume relaxation of the USF configurations perpendicular to the slip plane. Our MD results using the EDIP model agree fairly well with earlier first-principles estimates for the transition from shuffle to glide plane dominance as a function of temperature. We use these results to make contact to brittle-ductile transition models.Comment: 6 pages revtex, 4 figs, 16 refs, to appear in Phys. Rev.

Analysis of cyt0kine gene expression in stimulated T cells of small children by semi-quantitative PCR

Only limited amounts of peripheral blood samples can be obtained from small children. Therefore, a polymerase chain reaction (PCR) aided analysis of cytokine gene expression by PBMC or T cells is a valuable tool. We present a combination of procedures to obtain an accurate estimation of the expression of the cytokines IL-4 and IFN-γ. This can be performed on T cells purified from blood samples of up to 5 ml in volume from children aged 0–4 years with allergic asthma and atopic dermatitis. This procedure includes multiple sampling of PCR products to determine the linear phase of the PCR; inter-experiment correction using a helper T-cell clone, expressing both IL-4 and IFN-γ; interpatient correction by comparing the expression of a housekeeping gene (HPRT); and finally the development of specific software to analyse densitometric data obtained by scanning photographs of agarose gels, separating PCR products. In this way it is possible to study cytokine gene expression from a very small amount of material

Temperature effects on dislocation core energies in silicon and germanium

Temperature effects on the energetics of the 90-degree partial dislocation in silicon and germanium are investigated, using non-equilibrium methods to estimate free energies, coupled with Monte Carlo simulations. Atomic interactions are described by Tersoff and EDIP interatomic potentials. Our results indicate that the vibrational entropy has the effect of increasing the difference in free energy between the two possible reconstructions of the 90-degree partial, namely, the single-period and the double-period geometries. This effect further increases the energetic stability of the double-period reconstruction at high temperatures. The results also indicate that anharmonic effects may play an important role in determining the structural properties of these defects in the high-temperature regime.Comment: 8 pages in two-column physical-review format with six figure

Pyrimidine biosynthesis is not an essential function for trypanosoma brucei bloodstream forms

<p>Background: African trypanosomes are capable of both pyrimidine biosynthesis and salvage of preformed pyrimidines from the host, but it is unknown whether either process is essential to the parasite.</p> <p>Methodology/Principal Findings: Pyrimidine requirements for growth were investigated using strictly pyrimidine-free media, with or without single added pyrimidine sources. Growth rates of wild-type bloodstream form Trypanosoma brucei brucei were unchanged in pyrimidine-free medium. The essentiality of the de novo pyrimidine biosynthesis pathway was studied by knocking out the PYR6-5 locus that produces a fusion product of orotate phosphoribosyltransferase (OPRT) and Orotidine Monophosphate Decarboxylase (OMPDCase). The pyrimidine auxotroph was dependent on a suitable extracellular pyrimidine source. Pyrimidine starvation was rapidly lethal and non-reversible, causing incomplete DNA content in new cells. The phenotype could be rescued by addition of uracil; supplementation with uridine, 2′deoxyuridine, and cytidine allowed a diminished growth rate and density. PYR6-5−/− trypanosomes were more sensitive to pyrimidine antimetabolites and displayed increased uracil transport rates and uridine phosphorylase activity. Pyrimidine auxotrophs were able to infect mice although the infection developed much more slowly than infection with the parental, prototrophic trypanosome line.</p> <p>Conclusions/Significance: Pyrimidine salvage was not an essential function for bloodstream T. b. brucei. However, trypanosomes lacking de novo pyrimidine biosynthesis are completely dependent on an extracellular pyrimidine source, strongly preferring uracil, and display reduced infectivity. As T. brucei are able to salvage sufficient pyrimidines from the host environment, the pyrimidine biosynthesis pathway is not a viable drug target, although any interruption of pyrimidine supply was lethal.</p&gt

Population-based mammography screening below age 50: balancing radiation-induced vs prevented breast cancer deaths

Introduction:Exposure to ionizing radiation at mammography screening may cause breast cancer. Because the radiation risk increases with lower exposure age, advancing the lower age limit may affect the balance between screening benefits and risks. The present study explores the benefit-risk ratio of screening before age 50.Methods:The benefits of biennial mammography screening, starting at various ages between 40 and 50, and continuing up to age 74 were examined using micro-simulation. In contrast with previous studies that commonly used excess relative risk models, we assessed the radiation risks using the latest BEIR-VII excess abso

Fusion of 3D QCA and IVUS/OCT

The combination/fusion of quantitative coronary angiography (QCA) and intravascular ultrasound (IVUS)/optical coherence tomography (OCT) depends to a great extend on the co-registration of X-ray angiography (XA) and IVUS/OCT. In this work a new and robust three-dimensional (3D) segmentation and registration approach is presented and validated. The approach starts with standard QCA of the vessel of interest in the two angiographic views (either biplane or two monoplane views). Next, the vessel of interest is reconstructed in 3D and registered with the corresponding IVUS/OCT pullback series by a distance mapping algorithm. The accuracy of the registration was retrospectively evaluated on 12 silicone phantoms with coronary stents implanted, and on 24 patients who underwent both coronary angiography and IVUS examinations of the left anterior descending artery. Stent borders or sidebranches were used as markers for the validation. While the most proximal marker was set as the baseline position for the distance mapping algorithm, the subsequent markers were used to evaluate the registration error. The correlation between the registration error and the distance from the evaluated marker to the baseline position was analyzed. The XA-IVUS registration error for the 12 phantoms was 0.03 ± 0.32 mm (P = 0.75). One OCT pullback series was excluded from the phantom study, since it did not cover the distal stent border. The XA-OCT registration error for the remaining 11 phantoms was 0.05 ± 0.25 mm (P = 0.49). For the in vivo validation, two patients were excluded due to insufficient image quality for the analysis. In total 78 sidebranches were identified from the remaining 22 patients and the registration error was evaluated on 56 markers. The registration error was 0.03 ± 0.45 mm (P = 0.67). The error was not correlated to the distance between the evaluated marker and the baseline position (P = 0.73). In conclusion, the new XA-IVUS/OCT co-registration approach is a straightforward and reliable solution to combine X-ray angiography and IVUS/OCT imaging for the assessment of the extent of coronary artery disease. It provides the interventional cardiologist with detailed information about vessel size and plaque size at every position along the vessel of interest, making this a suitable tool during the actual intervention

Multiple marker mapping of quantitative trait loci of Finnish dairy cattle by regression

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Efficiency of free energy calculations of spin lattices by spectral quantum algorithms

Quantum algorithms are well-suited to calculate estimates of the energy spectra for spin lattice systems. These algorithms are based on the efficient calculation of the discrete Fourier components of the density of states. The efficiency of these algorithms in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size.Comment: 9 pages, 4 figures; corrected typographical and minor mathematical error

Fast-Neutron Activation of Long-Lived Isotopes in Enriched Ge

We measured the production of \nuc{57}{Co}, \nuc{54}{Mn}, \nuc{68}{Ge}, \nuc{65}{Zn}, and \nuc{60}{Co} in a sample of Ge enriched in isotope 76 due to high-energy neutron interactions. These isotopes, especially \nuc{68}{Ge}, are critical in understanding background in Ge detectors used for double-beta decay experiments. They are produced by cosmogenic-neutron interactions in the detectors while they reside on the Earth's surface. These production rates were measured at neutron energies of a few hundred MeV. We compared the measured production to that predicted by cross-section calculations based on CEM03.02. The cross section calculations over-predict our measurements by approximately a factor of three depending on isotope. We then use the measured cosmic-ray neutron flux, our measurements, and the CEM03.02 cross sections to predict the cosmogenic production rate of these isotopes. The uncertainty in extrapolating the cross section model to higher energies dominates the total uncertainty in the cosmogenic production rate.Comment: Revised after feedback and further work on extrapolating cross sections to higher energies in order to estimate cosmic production rates. Also a numerical error was found and fixed in the estimate of the Co-57 production rat