Vacancy clustering and diffusion in silicon: Kinetic lattice Monte Carlo simulations

Diffusion and clustering of lattice vacancies in silicon as a function of temperature, concentration, and interaction range are investigated by Kinetic Lattice Monte Carlo simulations. It is found that higher temperatures lead to larger clusters with shorter lifetimes on average, which grow by attracting free vacancies, while clusters at lower temperatures grow by aggregation of smaller clusters. Long interaction ranges produce enhanced diffusivity and fewer clusters. Greater vacancy concentrations lead to more clusters, with fewer free vacancies, but the size of the clusters is largely independent of concentration. Vacancy diffusivity is shown to obey power law behavior over time, and the exponent of this law is shown to increase with concentration, at fixed temperature, and decrease with temperature, at fixed concentration.Comment: 14 pages, 12 figures. To appear in Physical Review

Multigradient field-active contour model for multilayer boundary detection of ultrasound rectal wall image

Extraction and reconstruction of rectal wall structures from an ultrasound image is helpful for surgeons in rectal clinical diagnosis and 3-D reconstruction of rectal structures from ultrasound images. The primary task is to extract the boundary of the muscular layers on the rectal wall. However, due to the low SNR from ultrasound imaging and the thin muscular layer structure of the rectum, this boundary detection task remains a challenge. An active contour model is an effective high-level model, which has been used successfully to aid the tasks of object representation and recognition in many image-processing applications. We present a novel multigradient field active contour algorithm with an extended ability for multiple-object detection, which overcomes some limitations of ordinary active contour models—"snakes." The core part in the algorithm is the proposal of multigradient vector fields, which are used to replace image forces in kinetic function for alternative constraints on the deformation of active contour, thereby partially solving the initialization limitation of active contour for rectal wall boundary detection. An adaptive expanding force is also added to the model to help the active contour go through the homogenous region in the image. The efficacy of the model is explained and tested on the boundary detection of a ring-shaped image, a synthetic image, and an ultrasound image. The experimental results show that the proposed multigradient field-active contour is feasible for multilayer boundary detection of rectal wal

A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases

Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework, implemented in a user-friendly software package, named KGGSeq (http://statgenpro.psychiatry.hku.hk/kggseq), will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes

Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity

The design of synthetic gene networks requires an extensive genetic toolbox to control the activities and levels of protein components to achieve desired cellular functions. Recently, a novel class of RNA-based control modules, which act through post-transcriptional processing of transcripts by directed RNase III (Rnt1p) cleavage, were shown to provide predictable control over gene expression and unique properties for manipulating biological networks. Here, we increase the regulatory range of the Rnt1p control elements, by modifying a critical region for enzyme binding to its hairpin substrates, the binding stability box (BSB). We used a high throughput, cell-based selection strategy to screen a BSB library for sequences that exhibit low fluorescence and thus high Rnt1p processing efficiencies. Sixteen unique BSBs were identified that cover a range of protein expression levels, due to the ability of the sequences to affect the hairpin cleavage rate and to form active cleavable complexes with Rnt1p. We further demonstrated that the activity of synthetic Rnt1p hairpins can be rationally programmed by combining the synthetic BSBs with a set of sequences located within a different region of the hairpin that directly modulate cleavage rates, providing a modular assembly strategy for this class of RNA-based control elements

The association between survey timing and patient-reported experiences with hospitals: results of a national postal survey

<p>Abstract</p> <p>Background</p> <p>Research on the effect of survey timing on patient-reported experiences and patient satisfaction with health services has produced contradictory results. The objective of this study was thus to assess the association between survey timing and patient-reported experiences with hospitals.</p> <p>Methods</p> <p>Secondary analyses of a national inpatient experience survey including 63 hospitals in the 5 health regions in Norway during the autumn of 2006. 10,912 (45%) patients answered a postal questionnaire after their discharge from hospital. Non-respondents were sent a reminder after 4 weeks. Multilevel linear regression analysis was used to assess the association between survey timing and patient-reported experiences, both bivariate analysis and multivariate analysis controlling for other predictors of patient experiences.</p> <p>Results</p> <p>Multivariate multilevel regression analysis revealed that survey time was significantly and negatively related to three of six patient-reported experience scales: doctor services (Beta = -0.424, <it>p</it>< 0.05), information about examinations (Beta = -0.566, <it>p </it>< 0.05) and organization (Beta = -0.528, <it>p </it>< 0.05). Patient age, self-perceived health and type of admission were significantly related to all patient-reported experience scales (better experiences with higher age, better health and routine admission), and all other predictors had at least one significant association with patient-reported experiences.</p> <p>Conclusions</p> <p>Survey time was significantly and negatively related to three of the six scales for patient-reported experiences with hospitals. Large differences in survey time across hospitals could be problematic for between-hospital comparisons, implying that survey time should be considered as a potential adjustment factor. More research is needed on this topic, including studies with other population groups, other data collection modes and a longer time span.</p

Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats

Biological factors that influence the host range and spillover of Ebola virus (EBOV) and other filoviruses remain enigmatic. While filoviruses infect diverse mammalian cell lines, we report that cells from African straw-colored fruit bats (Eidolon helvum) are refractory to EBOV infection. This could be explained by a single amino acid change in the filovirus receptor, NPC1, which greatly reduces the affinity of EBOV-NPC1 interaction. We found signatures of positive selection in bat NPC1 concentrated at the virus-receptor interface, with the strongest signal at the same residue that controls EBOV infection in Eidolon helvum cells. Our work identifies NPC1 as a genetic determinant of filovirus susceptibility in bats, and suggests that some NPC1 variations reflect host adaptations to reduce filovirus replication and virulence. A single viral mutation afforded escape from receptor control, revealing a pathway for compensatory viral evolution and a potential avenue for expansion of filovirus host range in nature

MHC immunoevasins: protecting the pathogen reservoir in infection

Alteration of antigen recognition by T cells as result of insufficient major histocompatibility complex (MHC)-dependent antigen-presenting function has been observed in many cases of infections, particularly in in vitro systems. To hide themselves from an efficient immune response, pathogens may act on MHC-related functions at three levels: (i) by limiting the number of potential antigens that can be presented to naive T cells; (ii) by synthesizing proteins which directly affect MHC cell-surface expression; and (iii) by altering the normal intracellular pathway of peptide loading on MHC. Here, we review examples of pathogens' action on each single step of MHC function and we suggest that the result of these often synergistic actions is both a limitation of the priming of naive T cells and, more importantly, a protection of the pathogen's reservoir from the attack of primed T cells. The above mechanisms may also generate a skewing effect on immune effector mechanisms, which helps preserving the reservoir of infection from sterilization by the immune system