Numerical Study of Wave Propagation in Uniaxially Anisotropic Lorentzian Backward Wave Slabs

The propagation and refraction of a cylindrical wave created by a line current through a slab of backward wave medium, also called left-handed medium, is numerically studied with FDTD. The slab is assumed to be uniaxially anisotropic. Several sets of constitutive parameters are considered and comparisons with theoretical results are made. Electric field distributions are studied inside and behind the slab. It is found that the shape of the wavefronts and the regions of real and complex wave vectors are in agreement with theoretical results.Comment: 6 pages, figure

Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck

Towards gravitationally assisted negative refraction of light by vacuum

Propagation of electromagnetic plane waves in some directions in gravitationally affected vacuum over limited ranges of spacetime can be such that the phase velocity vector casts a negative projection on the time-averaged Poynting vector. This conclusion suggests, inter alia, gravitationally assisted negative refraction by vacuum.Comment: 6 page

Condensed matter and AdS/CFT

I review two classes of strong coupling problems in condensed matter physics, and describe insights gained by application of the AdS/CFT correspondence. The first class concerns non-zero temperature dynamics and transport in the vicinity of quantum critical points described by relativistic field theories. I describe how relativistic structures arise in models of physical interest, present results for their quantum critical crossover functions and magneto-thermoelectric hydrodynamics. The second class concerns symmetry breaking transitions of two-dimensional systems in the presence of gapless electronic excitations at isolated points or along lines (i.e. Fermi surfaces) in the Brillouin zone. I describe the scaling structure of a recent theory of the Ising-nematic transition in metals, and discuss its possible connection to theories of Fermi surfaces obtained from simple AdS duals.Comment: 39 pages, 12 figures; Lectures at the 5th Aegean summer school, "From gravity to thermal gauge theories: the AdS/CFT correspondence", and the De Sitter Lecture Series in Theoretical Physics 2009, University of Groninge

The Nonabelian Debye Mass at Next-to-Leading Order

It is shown that after a resummation of leading high-temperature contributions, a complete and gauge-independent result for the nonabelian Debye screening mass at next-to-leading order can be extracted from the static gluon propagator. In contrast to previous, incomplete results, the correction to the Debye mass is found to be logarithmically sensitive to the nonperturbative magnetic mass and positive, in accordance with recent high-statistics results from lattice calculations.Comment: 8 pages, REVTEX v3.0, BI-TP 93/42 (minor corrections in text and references

Approximate string matching with reduced alphabet

Peer reviewe

Low free 25-hydroxyvitamin D and high vitamin D binding protein and parathyroid hormone in obese Caucasians. A complex association with bone?

BackgroundStudies have shown altered vitamin D metabolism in obesity. We assessed differences between obese and normal-weight subjects in total, free, and bioavailable 25-hydroxyvitamin D (25(OH) D, 25(OH) D-Free, and 25(OH) D-Bio, respectively), vitamin D binding protein (DBP), parathyroid hormone (PTH) and bone traits.Methods595 37-47-year-old healthy Finnish men and women stratified by BMI were examined in this cross-sectional study. Background characteristic and intakes of vitamin D and calcium were collected. The concentrations of 25(OH) D, PTH, DBP, albumin and bone turnover markers were determined from blood. 25(OH) D-Free and 25(OH) D-Bio were calculated. pQCT was performed at radius and tibia.ResultsMean +/- SE (ANCOVA) 25(OH) D-Free (10.8 +/- 0.6 vs 12.9 +/- 0.4 nmol/L; P = 0.008) and 25(OH) DBio (4.1 +/- 0.3 vs 5.1 +/- 0.1 nmol/L; P = 0.003) were lower in obese than in normal-weight women. In men, 25(OH) D (48.0 +/- 2.4 vs 56.4 +/- 2.0 nmol/L, P = 0.003), 25(OH) D-Free (10.3 +/- 0.7 vs 12.5 +/- 0.6 pmol/L; P = 0.044) and 25(OH) D-Bio (4.2 +/- 0.3 vs 5.1 +/- 0.2 nmol/L; P = 0.032) were lower in obese. Similarly in all subjects, 25(OH) D, 25(OH) D-Free and 25(OH) D-Bio were lower in obese (P<0.001). DBP (399 +/- 12 vs 356 +/- 7mg/L, P = 0.008) and PTH (62.2 +/- 3.0 vs 53.3 +/- 1.9 ng/L; P = 0.045) were higher in obese than in normal-weight women. In all subjects, PTH and DBP were higher in obese (P = 0.047 and P = 0.004, respectively). In obese women, 25(OH) D was negatively associated with distal radius trabecular density (R-2 = 0.089, P = 0.009) and tibial shaft cortical strength index (CSI) (R-2 = 0.146, P = 0.004). 25(OH) D-Free was negatively associated with distal radius CSI (R-2 = 0.070, P = 0.049), radial shaft cortical density (CorD) (R-2 = 0.050, P = 0.045), and tibial shaft CSI (R-2 = 0.113, P = 0.012). 25(OH) D-Bio was negatively associated with distal radius CSI (R-2 = 0.072, P = 0.045), radial shaft CorD (R-2 = 0.059, P = 0.032), and tibial shaft CSI (R-2 = 0.093, P = 0.024).ConclusionsThe associations between BMI and 25(OH) D, 25(OH) D-Free, and 25(OH) D-Bio, DBP, and PTH suggest that obese subjects may differ from normal-weight subjects in vitamin D metabolism. BMI associated positively with trabecular bone traits and CSI in our study, and slightly negatively with cortical bone traits. Surprisingly, there was a negative association of free and bioavailable 25(OH) D and some of the bone traits in obese women

Fast index based algorithms and software for matching position specific scoring matrices

BACKGROUND: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task. RESULTS: We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of PSSMs in large databases. Our approach preprocesses the search space, e.g., a complete genome or a set of protein sequences, and builds an enhanced suffix array that is stored on file. This allows the searching of a database with a PSSM in sublinear expected time. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows the efficient computation of a matrix similarity threshold for a PSSM, given an E-value or a p-value. Our method is based on dynamic programming and, in contrast to other methods, it employs lazy evaluation of the dynamic programming matrix. We evaluated algorithm ESAsearch with nucleotide PSSMs and with amino acid PSSMs. Compared to the best previous methods, ESAsearch shows speedups of a factor between 17 and 275 for nucleotide PSSMs, and speedups up to factor 1.8 for amino acid PSSMs. Comparisons with the most widely used programs even show speedups by a factor of at least 3.8. Alphabet reduction yields an additional speedup factor of 2 on amino acid sequences compared to results achieved with the 20 symbol standard alphabet. The lazy evaluation method is also much faster than previous methods, with speedups of a factor between 3 and 330. CONCLUSION: Our analysis of ESAsearch reveals sublinear runtime in the expected case, and linear runtime in the worst case for sequences not shorter than | [Formula: see text] |(m )+ m - 1, where m is the length of the PSSM and [Formula: see text] a finite alphabet. In practice, ESAsearch shows superior performance over the most widely used programs, especially for DNA sequences. The new algorithm for accurate on-the-fly calculations of thresholds has the potential to replace formerly used approximation approaches. Beyond the algorithmic contributions, we provide a robust, well documented, and easy to use software package, implementing the ideas and algorithms presented in this manuscript

Hand Grip Strength: age and gender stratified normative data in a population-based study

Extent: 5p.Background: The North West Adelaide Health Study is a representative longitudinal cohort study of people originally aged 18 years and over. The aim of this study was to describe normative data for hand grip strength in a community-based Australian population. Secondary aims were to investigate the relationship between body mass index (BMI) and hand grip strength, and to compare Australian data with international hand grip strength norms. Methods: The sample was randomly selected and recruited by telephone interview. Overall, 3 206 (81% of those recruited) participants returned to the clinic during the second stage (2004-2006) which specifically focused on the collection of information relating to musculoskeletal conditions. Results: Following the exclusion of 435 participants who had hand pain and/or arthritis, 1366 men and 1312 women participants provided hand grip strength measurement. The study population was relatively young, with 41.5% under 40 years; and their mean BMI was 28.1 kg/m2 (SD 5.5). Higher hand grip strength was weakly related to higher BMI in adults under the age of 30 and over the age of 70, but inversely related to higher BMI between these ages. Australian norms from this sample had amongst the lowest of the hand grip strength of the internationally published norms, except those from underweight populations. Conclusions: This population demonstrated higher BMI and lower grip strength in younger participants than much of the international published, population data. A complete exploration of the relationship between BMI and hand grip strength was not fully explored as there were very few participants with BMI in the underweight range. The age and gender grip strength values are lower in younger adults than those reported in international literature.Nicola M Massy-Westropp, Tiffany K Gill, Anne W Taylor, Richard W Bohannon and Catherine L Hil

Novel Coronin7 interactions with Cdc42 and N-WASP regulate actin organization and Golgi morphology

YesThe contribution of the actin cytoskeleton to the unique architecture of the Golgi complex is manifold. An important player in this process is Coronin7 (CRN7), a Golgi-resident protein that stabilizes F-actin assembly at the trans-Golgi network (TGN) thereby facilitating anterograde trafficking. Here, we establish that CRN7-mediated association of F-actin with the Golgi apparatus is distinctly modulated via the small Rho GTPase Cdc42 and N-WASP. We identify N-WASP as a novel interaction partner of CRN7 and demonstrate that CRN7 restricts spurious F-actin reorganizations by repressing N-WASP ‘hyperactivity’ upon constitutive Cdc42 activation. Loss of CRN7 leads to increased cellular F-actin content and causes a concomitant disruption of the Golgi structure. CRN7 harbours a Cdc42- and Rac-interactive binding (CRIB) motif in its tandem β-propellers and binds selectively to GDP-bound Cdc42N17 mutant. We speculate that CRN7 can act as a cofactor for active Cdc42 generation. Mutation of CRIB motif residues that abrogate Cdc42 binding to CRN7 also fail to rescue the cellular defects in fibroblasts derived from CRN7 KO mice. Cdc42N17 overexpression partially rescued the KO phenotypes whereas N-WASP overexpression failed to do so. We conclude that CRN7 spatiotemporally influences F-actin organization and Golgi integrity in a Cdc42- and N-WASP-dependent manner.This work was supported by SFB 670 and DFG NO 113/22. K.B. was supported by a fellowship from the NRW International Graduate School “From Embryo to Old Age: the Cell Biology and Genetics of Health and Disease” (IGSDHD), Cologne