529 research outputs found

    X-ray Absorption Near-Edge Structure calculations with pseudopotentials. Application to K-edge in diamond and alpha-quartz

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    We present a reciprocal-space pseudopotential scheme for calculating X-ray absorption near-edge structure (XANES) spectra. The scheme incorporates a recursive method to compute absorption cross section as a continued fraction. The continued fraction formulation of absorption is advantageous in that it permits the treatment of core-hole interaction through large supercells (hundreds of atoms). The method is compared with recently developed Bethe-Salpeter approach. The method is applied to the carbon K-edge in diamond and to the silicon and oxygen K-edges in alpha-quartz for which polarized XANES spectra were measured. Core-hole effects are investigated by varying the size of the supercell, thus leading to information similar to that obtained from cluster size analysis usually performed within multiple scattering calculations.Comment: 11 pages, 4 figure

    Locomotor Adaptation versus Perceptual Adaptation when Stepping Over an Obstacle with a Height Illusion

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    Background During locomotion, vision is used to perceive environmental obstacles that could potentially threaten stability; locomotor action is then modified to avoid these obstacles. Various factors such as lighting and texture can make these environmental obstacles appear larger or smaller than their actual size. It is unclear if gait is adapted based on the actual or perceived height of these environmental obstacles. The purposes of this study were to determine if visually guided action is scaled to visual perception, and to determine if task experience influenced how action is scaled to perception. Methodology/Principal Findings Participants judged the height of two obstacles before and after stepping over each of them 50 times. An illusion made obstacle one appear larger than obstacle two, even though they were identical in size. The influence of task experience was examined by comparing the perception-action relationship during the first five obstacle crossings (1–5) with the last five obstacle crossings (46–50). In the first set of trials, obstacle one was perceived to be 2.0 cm larger than obstacle two and subjects stepped 2.7 cm higher over obstacle one. After walking over the obstacle 50 times, the toe elevation was not different between obstacles, but obstacle one was still perceived as 2.4 cm larger. Conclusions/Significance There was evidence of locomotor adaptation, but no evidence of perceptual adaptation with experience. These findings add to research that demonstrates that while the motor system can be influenced by perception, it can also operate independent of perception

    Residential mobility during pregnancy in the north of England

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    <p>Abstract</p> <p>Background</p> <p>Many epidemiological studies assign exposure to an individual's residence at a single time point, such as birth or death. This approach makes no allowance for migration and may result in exposure error, leading to reduced study power and biased risk estimates. Pregnancy outcomes are less susceptible to this bias, however data from North American populations indicate that pregnant women are a highly mobile group. We assessed mobility in pregnant women in the north of England using data from the Northern Congenital Abnormality Survey (NorCAS).</p> <p>Methods</p> <p>Data were extracted from NorCAS for 1985 to 2003. Eligible cases had a gestational age at delivery of ≥ 24 weeks (a viable delivery) (n = 11 559). We assessed mobility between booking appointment (average gestational age 13 weeks) and delivery for pregnancies where the address at booking appointment and delivery were known. The impacts on mobility of maternal age and area-level socio-economic indicators were explored using standard descriptive statistics. A sensitivity analysis and a small validation exercise were undertaken to assess the impact of missing data on the estimate of mobility.</p> <p>Results</p> <p>Out of 7 919 eligible cases for whom addresses at booking and delivery were known, 705 (8.9% (95% CI 8.3 - 9.5)) moved between booking and delivery; the mean and median moving distance was 9.7 and 1.4 km respectively. Movers were significantly younger (25.4 versus 27.3 years, p < 0.01) and lived in more deprived areas (index of multiple deprivation score 38.3 versus 33.7, p < 0.01) than non movers.</p> <p>Conclusion</p> <p>Mobility in the north of England (9%) is considerably lower than that reported in North America and the only other study from the UK (23%). Consistent with other studies, mobility was related to maternal age and socio-economic status, and the majority of moves were over a relatively short distance. Although this population appears relatively stable, the mobility we have observed may still introduce misclassification or error into an exposure assessment relying solely on postcode at delivery, and migration should still therefore be considered a potential source of bias in future studies.</p

    Evaluation of Glycine max mRNA clusters

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    BACKGROUND: Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternatively spliced transcripts. Several methods have been developed to accomplish this, the most widely available being UniGene, a public domain collection of gene-oriented clusters for over 45 different species created and maintained by NCBI. The goal is for each cluster to represent a unique gene, but currently it is not known how closely the overall results represent that reality. UniGene's build procedure begins with initial mRNA clusters before joining ESTs. UniGene's results for soybean indicate a significant amount of redundancy among some sequences reported to be unique mRNAs. To establish a valid non-redundant known gene set for Glycine max we applied our algorithm to the clustering of only mRNA sequences. The mRNA dataset was run through the algorithm using two different matching stringencies. The resulting cluster compositions were compared to each other and to UniGene. Clusters exhibiting differences among the three methods were analyzed by 1) nucleotide and amino acid alignment and 2) submitting authors conclusions to determine whether members of a single cluster represented the same gene or not. RESULTS: Of the 12 clusters that were examined closely most contained examples of sequences that did not belong in the same cluster. However, neither the two stringencies of PECT nor UniGene had a significantly greater record of accuracy in placing paralogs into separate clusters. CONCLUSION: Our results reveal that, although each method produces some errors, using multiple stringencies for matching or a sequential hierarchical method of increasing stringencies can provide more reliable results and therefore allow greater confidence in the vast majority of clusters that contain only ESTs and no mRNA sequences

    ARPES: A probe of electronic correlations

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    Angle-resolved photoemission spectroscopy (ARPES) is one of the most direct methods of studying the electronic structure of solids. By measuring the kinetic energy and angular distribution of the electrons photoemitted from a sample illuminated with sufficiently high-energy radiation, one can gain information on both the energy and momentum of the electrons propagating inside a material. This is of vital importance in elucidating the connection between electronic, magnetic, and chemical structure of solids, in particular for those complex systems which cannot be appropriately described within the independent-particle picture. Among the various classes of complex systems, of great interest are the transition metal oxides, which have been at the center stage in condensed matter physics for the last four decades. Following a general introduction to the topic, we will lay the theoretical basis needed to understand the pivotal role of ARPES in the study of such systems. After a brief overview on the state-of-the-art capabilities of the technique, we will review some of the most interesting and relevant case studies of the novel physics revealed by ARPES in 3d-, 4d- and 5d-based oxides.Comment: Chapter to appear in "Strongly Correlated Systems: Experimental Techniques", edited by A. Avella and F. Mancini, Springer Series in Solid-State Sciences (2013). A high-resolution version can be found at: http://www.phas.ubc.ca/~quantmat/ARPES/PUBLICATIONS/Reviews/ARPES_Springer.pdf. arXiv admin note: text overlap with arXiv:cond-mat/0307085, arXiv:cond-mat/020850

    Immediate breast reconstruction with a saline implant and AlloDerm, following removal of a Phyllodes tumor

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    <p>Abstract</p> <p>Background</p> <p>Phyllodes tumors are uncommon tumors of the breast that exhibit aggressive growth. While surgical management of the tumor has been reported, a single surgical approach with immediate breast reconstruction using AlloDerm has not been reported.</p> <p>Case presentation</p> <p>A 22-year-old woman presented with a 4 cm mass in the left breast upon initial examination. Although the initial needle biopsy report indicated a fibroadenoma, the final pathologic report revealed a 6.5 cm × 6.4 cm × 6.4 cm benign phyllodes tumor <it>ex vivo</it>. Treatment was a simple nipple-sparing mastectomy coupled with immediate breast reconstruction. After the mastectomy, a subpectoral pocket was created for a saline implant and AlloDerm was stitched to the pectoralis and serratus muscle in the lower-pole of the breast.</p> <p>Conclusions</p> <p>Saline implant with AlloDerm can be used for immediate breast reconstruction post-mastectomy for treatment of a phyllodes tumor.</p

    The Role of Sialyl Glycan Recognition in Host Tissue Tropism of the Avian Parasite Eimeria tenella

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    Eimeria spp. are a highly successful group of intracellular protozoan parasites that develop within intestinal epithelial cells of poultry, causing coccidiosis. As a result of resistance against anticoccidial drugs and the expense of manufacturing live vaccines, it is necessary to understand the relationship between Eimeria and its host more deeply, with a view to developing recombinant vaccines. Eimeria possesses a family of microneme lectins (MICs) that contain microneme adhesive repeat regions (MARR). We show that the major MARR protein from Eimeria tenella, EtMIC3, is deployed at the parasite-host interface during the early stages of invasion. EtMIC3 consists of seven tandem MAR1-type domains, which possess a high specificity for sialylated glycans as shown by cell-based assays and carbohydrate microarray analyses. The restricted tissue staining pattern observed for EtMIC3 in the chicken caecal epithelium indicates that EtMIC3 contributes to guiding the parasite to the site of invasion in the chicken gut. The microarray analyses also reveal a lack of recognition of glycan sequences terminating in the N-glycolyl form of sialic acid by EtMIC3. Thus the parasite is well adapted to the avian host which lacks N-glycolyl neuraminic acid. We provide new structural insight into the MAR1 family of domains and reveal the atomic resolution basis for the sialic acid-based carbohydrate recognition. Finally, a preliminary chicken immunization trial provides evidence that recombinant EtMIC3 protein and EtMIC3 DNA are effective vaccine candidates
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