Development and validation of molecular markers for characterization of Boehmeria nivea var. nivea and Boehmeria nivea var. tenacissima

<p>Abstract</p> <p>Background</p> <p>The root of <it>Boehmeria </it>spp (ramie) is a hepatoprotective Chinese herbal medicine. Medicinal properties vary between <it>Boehmeria nivea </it>var. <it>nivea </it>and <it>Boehmeria nivea </it>var. <it>tenacissima</it>, which are local species found in Taiwan. As commercial preparations may use either species, there is a need for a rapid and simple assay to identify variants for quality control.</p> <p>Methods</p> <p>Four methods were developed and tested for their applicability in differentiating the two species. These methods were random amplified polymorphic DNA (RAPD); sequence characterized amplified regions (SCAR); single nucleotide polymorphisms (SNP) and cleaved amplified polymorphic sequences (CAPS).</p> <p>Results</p> <p>Three RAPD markers were developed that produced unique bands in <it>B. nivea </it>var. <it>tenacissima </it>and <it>B. nivea </it>var. <it>nivea</it>. Based on sequenced RAPD bands, one SCAR marker was developed that produced a single DNA band in <it>B. nivea </it>var. <it>nivea</it>. Two SNP markers differentiated between <it>B. nivea </it>var. <it>nivea </it>and <it>B. nivea </it>var. <it>tenacissima </it>based on single nucleotide substitutions. A pair of CAPS oligonucleotides was developed by amplifying a 0.55-kb DNA fragment that exhibited species-specific digestion patterns with restriction enzymes <it>Alf </it>III and <it>Nde </it>I. Consistent results were obtained with all the four markers on all tested <it>Boehmeria </it>lines.</p> <p>Conclusion</p> <p>The present study demonstrates the use of the RAPD, SCAR, SNP and CAPS markers for rapid identification of two closely related <it>Boehmeria </it>species.</p

Non-integrability of Self-dual Yang-Mills-Higgs System

We examine integrability of self-dual Yang-Mills system in the Higgs phase, with taking simpler cases of vortices and domain walls. We show that the vortex equations and the domain-wall equations do not have Painleve property. This fact suggests that these equations are not integrable.Comment: 15 pages, no figures, v2: references added, v3: typos corrected, the final version to appear in NP

An RBF-based reparameterization method for constrained texture mapping

Texture mapping has long been used in computer graphics to enhance the realism of virtual scenes. However, to match the 3D model feature points with the corresponding pixels in a texture image, surface parameterization must satisfy specific positional constraints. However, despite numerous research efforts, the construction of a mathematically robust, foldover‐free parameterization that is subject to positional constraints continues to be a challenge. In the present paper, this foldover problem is addressed by developing radial basis function (RBF) based reparameterization. Given initial 2D embedding of a 3D surface, the proposed method can reparameterize 2D embedding into a foldover ‐free 2D mesh, satisfying a set of user‐specified constraint points. In addition, this approach is mesh‐free. Therefore, generating smooth texture mapping results is possible without extra smoothing optimization

Evaluation of the United States National Air Quality Forecast Capability experimental real-time predictions in 2010 using Air Quality System ozone and NO₂ measurements

The National Air Quality Forecast Capability (NAQFC) project provides the US with operational and experimental real-time ozone predictions using two different versions of the three-dimensional Community Multi-scale Air Quality (CMAQ) modeling system. Routine evaluation using near-real-time AIRNow ozone measurements through 2011 showed better performance of the operational ozone predictions. In this work, quality-controlled and -assured Air Quality System (AQS) ozone and nitrogen dioxide (NO₂) observations are used to evaluate the experimental predictions in 2010. It is found that both ozone and NO₂ are overestimated over the contiguous US (CONUS), with annual biases of +5.6 and +5.1 ppbv, respectively. The annual root mean square errors (RMSEs) are 15.4 ppbv for ozone and 13.4 ppbv for NO₂. For both species the overpredictions are most pronounced in the summer. The locations of the AQS monitoring sites are also utilized to stratify comparisons by the degree of urbanization. Comparisons for six predefined US regions show the highest annual biases for ozone predictions in Southeast (+10.5 ppbv) and for NO₂ in the Lower Middle (+8.1 ppbv) and Pacific Coast (+7.1 ppbv) regions. The spatial distributions of the NO₂ biases in August show distinctively high values in the Los Angeles, Houston, and New Orleans areas. In addition to the standard statistics metrics, daily maximum eight-hour ozone categorical statistics are calculated using the current US ambient air quality standard (75 ppbv) and another lower threshold (70 ppbv). Using the 75 ppbv standard, the hit rate and proportion of correct over CONUS for the entire year are 0.64 and 0.96, respectively. Summertime biases show distinctive weekly patterns for ozone and NO₂. Diurnal comparisons show that ozone overestimation is most severe in the morning, from 07:00 to 10:00 local time. For NO₂, the morning predictions agree with the AQS observations reasonably well, but nighttime concentrations are overpredicted by around 100%

Anti-microbial Activity of Urine after Ingestion of Cranberry: A Pilot Study

We explore the anti-microbial activity of urine specimens after the ingestion of a commercial cranberry preparation. Twenty subjects without urinary infection, off antibiotics and all supplements or vitamins were recruited. The study was conducted in two phases: in phase 1, subjects collected the first morning urine prior to ingesting 900 mg of cranberry and then at 2, 4 and 6 h. In phase 2, subjects collected urine on 2 consecutive days: on Day 1 no cranberry was ingested (control specimens), on Day 2, cranberry was ingested. The pH of all urine specimens were adjusted to the same pH as that of the first morning urine specimen. Aliquots of each specimen were independently inoculated with Escherichia coli, Klebsiella pneumoniae or Candida albicans. After incubation, colony forming units/ml (CFU ml−1) in the control specimen was compared with CFU ml−1 in specimens collected 2, 4 and 6 h later. Specimens showing ≥50% reduction in CFU ml−1 were considered as having ‘activity’ against the strains tested. In phase 1, 7/20 (35%) subjects had anti-microbial activity against E. coli, 13/20 (65%) against K. pneumoniae and 9/20 (45%) against C. albicans in specimens collected 2–6 h after ingestion of cranberry. In phase 2, 6/9 (67%) of the subjects had activity against K. pneumoniae. This pilot study demonstrates weak anti-microbial activity in urine specimens after ingestion of a single dose of commercial cranberry. Anti-microbial activity was noted only against K. pneumoniae 2–6 h after ingestion of the cranberry preparation

Disturbance spreading in incommensurate and quasiperiodic systems

The propagation of an initially localized excitation in one dimensional incommensurate, quasiperiodic and random systems is investigated numerically. It is discovered that the time evolution of variances $\sigma^2(t)$ of atom displacements depends on the initial condition. For the initial condition with nonzero momentum, $\sigma^2(t)$ goes as $t^\alpha$ with $\alpha=1$ and 0 for incommensurate Frenkel-Kontorova (FK) model at $V$ below and above $V_c$ respectively; and $\alpha=1$ for uniform, quasiperiodic and random chains. It is also found that $\alpha=1-\beta$ with $\beta$ the exponent of distribution function of frequency at zero frequency, i.e., $\rho(\omega)\sim \omega^{\beta}$ (as $\omega\to 0$). For the initial condition with zero momentum, $\alpha=0$ for all systems studied. The underlying physical meaning of this diffusive behavior is discussed.Comment: 8 Revtex Pages, 5 PS figures included, to appear in Phys. Rev. B April 200

1/2, 1/4 and 1/8 BPS Equations in SUSY Yang-Mills-Higgs Systems -- Field Theoretical Brane Configurations --

We systematically classify 1/2, 1/4 and 1/8 BPS equations in SUSY gauge theories in d=6, 5, 4, 3 and 2 with eight supercharges, with gauge groups and matter contents being arbitrary. Instantons (strings) and vortices (3-branes) are only allowed 1/2 BPS solitons in d=6 with N=1 SUSY. We find two 1/4 BPS equations and the unique 1/8 BPS equation in d=6 by considering configurations made of these field theory branes. All known BPS equations are rederived while several new 1/4 and 1/8 BPS equations are found in dimension less than six by dimensional reductions.Comment: 41 pages, no figures, v2: 49 pages, no figures, typos corrected, references added, the final version in NP

WNP: A Novel Algorithm for Gene Products Annotation from Weighted Functional Networks

Predicting the biological function of all the genes of an organism is one of the fundamental goals of computational system biology. In the last decade, high-throughput experimental methods for studying the functional interactions between gene products (GPs) have been combined with computational approaches based on Bayesian networks for data integration. The result of these computational approaches is an interaction network with weighted links representing connectivity likelihood between two functionally related GPs. The weighted network generated by these computational approaches can be used to predict annotations for functionally uncharacterized GPs. Here we introduce Weighted Network Predictor (WNP), a novel algorithm for function prediction of biologically uncharacterized GPs. Tests conducted on simulated data show that WNP outperforms other 5 state-of-the-art methods in terms of both specificity and sensitivity and that it is able to better exploit and propagate the functional and topological information of the network. We apply our method to Saccharomyces cerevisiae yeast and Arabidopsis thaliana networks and we predict Gene Ontology function for about 500 and 10000 uncharacterized GPs respectively

Domain Walls and Flux Tubes in N=2 SQCD: D-Brane Prototypes

This paper could have been entitled "D branes and strings from flesh and blood." We study field theoretic prototypes of D branes/strings. To this end we consider (2+1)-dimensional domain walls in (3+1)-dimensional N=2 SQCD with SU(2) gauge group and two quark flavors in the fundamental representation. This theory is perturbed by a small mass term of the adjoint matter which, in the leading order in the mass parameter, does not break N=2 supersymmetry, and reduces to a (generalized) Fayet-Iliopoulos term in the effective low-energy N=2 SQED. We find 1/2 BPS-saturated domain wall solution interpolating between two quark vacua at weak coupling, and show that this domain wall localizes a U(1) gauge field. To make contact with the brane/string picture we consider the Abrikosov-Nielsen-Olesen magnetic flux tube in one of two quark vacua and demonstrate that it can end on the domain wall. We find an explicit 1/4 BPS-saturated solution for the wall/flux tube junction. We verify that the end point of the flux tube on the wall plays the role of an electric charge in the dual (2+1)-dimensional SQED living on the wall. Flow to N=1 theory is discussed. Our results lead us to a conjecture regarding the notorious "missing wall" in the solution of Kaplunovsky et al.Comment: 41 pages, 5 figures, Sect. 9.3 expanded, typos correcte