Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies

With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu

Ordering in voter models on networks: Exact reduction to a single-coordinate diffusion

We study the voter model and related random-copying processes on arbitrarily complex network structures. Through a representation of the dynamics as a particle reaction process, we show that a quantity measuring the degree of order in a finite system is, under certain conditions, exactly governed by a universal diffusion equation. Whenever this reduction occurs, the details of the network structure and random-copying process affect only a single parameter in the diffusion equation. The validity of the reduction can be established with considerably less information than one might expect: it suffices to know just two characteristic timescales within the dynamics of a single pair of reacting particles. We develop methods to identify these timescales, and apply them to deterministic and random network structures. We focus in particular on how the ordering time is affected by degree correlations, since such effects are hard to access by existing theoretical approaches.Comment: 37 pages, 10 figures. Revised version with additional discussion and simulation results to appear in J Phys

Modelling of railway curve squeal including effects of wheel rotation

Railway vehicles negotiating tight curves may emit an intense high-pitch noise. The underlying mechanisms of this squeal noise are still a subject of research. Simulation models are complex since they have to consider the non-linear, transient and high-frequency interaction between wheel and rail. Often simplified models are used for wheel and rail to reduce computational effort, which involves the risk of oversimplifications. This paper focuses on the importance to include a rotating wheel instead of a stationary wheel in the simulation models. Two formulations for a rotating wheel are implemented in a previously published wheel/rail interaction model: a realistic model based on an Eulerian modal coordinate approach and a simplified model based on a rotating load and moving Green's functions. The simulation results for different friction coefficients and values of lateral creepage are compared with results obtained for the stationary wheel. Both approaches for the rotating wheel give almost identical results for the rolling speed considered. Furthermore, it can be concluded that a model of a stationary flexible wheel is sufficient to simulate curve squeal

Реконструкция системы электроснабжения ОАО «СтанкоГомель» в связи с изменением технологического процесса и разработкой энергосберегающих мероприятий

The aim of the present study was to compare an ultrasonically activated instrument (US), monopolar electrosurgery, and bipolar electrosurgery (ES) with respect to heat production, nerve function, and nerve morphology following in vivo application. less thanbrgreater than less thanbrgreater thanThe biceps femoris muscle of anesthetized rats was cut in a standardized manner longitudinally 1 mm adjacent to the sciatic nerve using US shears, a monopolar ES knife, or a bipolar ES scissors. Activation time and temperature were recorded continuously within 1-4 mm of the activation site ipsilateral and contralateral to the nerve with two thermoelectric microsensors. Temperature rise and time delay of reaching the temperature maximum, as an expression of heat spread within tissue, maximum temperature, and thermal dose (equivalent time of exposure at 43A degrees C) were measured and calculated. A total of 49 functional experiments were conducted. The electromyographic (EMG) potential was recorded distally. Nerve dysfunction was defined as more than 10% loss of the evoked EMG amplitude. Forty-eight nerves were coded and submitted to blind histopathological examination, and morphological damage was graded on a 4-grade scale. less thanbrgreater than less thanbrgreater thanThe maximum temperature elevation and the thermal dose were significantly higher for the bipolar ES compared with the US instrument ( = 0.024, = 0.049), and with much less variation of results for the US instrument. The monopolar ES maximum temperature and thermal dose were lower, but a very large variation occurred, probably as a result of more random electrical spread to the ground electrode and muscle motion artifacts. Functional loss was least common in the US group-without being significant-compared to bipolar and monopolar ES. Moderate and severe morphological damage was significantly less common in the US group than in the monopolar ES group ( = 0.041). We found no statistically significant correlation between the highest temperatures and the degree of morphological damage or functional loss less thanbrgreater than less thanbrgreater thanThe temperature elevation depends strongly on the distance to the activated instrument. The bipolar ES scissors generates a higher maximum temperature and thermal dose with a greater variation in than the US. Functional loss and severe morphological damage were uncommon in all groups.Funding Agencies|FORSS|

Nucleation of Stable Superconductivity in YBCO-Films

By means of the linear dynamic conductivity, inductively measured on epitaxial films between 30mHz and 30 MHz, the transition line $T_g (B)$ to generic superconductivity is studied in fields between B=0 and 19T. It follows closely the melting line $T_m (B)$ described recently in terms of a blowout of thermal vortex loops in clean materials. The critical exponents of the correlation length and time near $T_g (B)$, however, seem to be dominated by some intrinsic disorder. Columnar defects produced by heavy-ion irradiation up to field-equivalent-doses of $B_{\phi} = 10T$ lead to a disappointing reduction of $T_g (B \to 0)$ while for $B>B_{\phi}$ the generic line of the pristine film is recovered. These novel results are also discussed in terms of a loop-driven destruction of generic superconductivity.Comment: 11 pages including 7 EPS figures, accepted for publication in the Proceedings of the Spring Meeting of the German Physical Society, Muenster 1999,Festkoerperprobleme/Advances in Solid State Physics 199

Theory of plastic vortex creep

We develop a theory for plastic flux creep in a topologically disordered vortex solid phase in type-II superconductors. We propose a detailed description of the plastic vortex creep of the dislocated, amorphous vortex glass in terms of motion of dislocations driven by a transport current $j$. The {\em plastic barriers} $U_{pl}(j)\propto j^{-\mu}$ show power-law divergence at small drives with exponents $\mu=1$ for single dislocation creep and $\mu = 2/5$ for creep of dislocation bundles. The suppression of the creep rate is a hallmark of the transition from the topologically ordered vortex lattice to an amorphous vortex glass, reflecting a jump in $\mu$ from $\mu = 2/11$, characterizing creep in the topologically ordered vortex lattice near the transition, to its plastic values. The lower creep rates explain the observed increase in apparent critical currents in the dislocated vortex glass.Comment: 4 pages, 1 figur

Abrikosov vortex escape from a columnar defect as a topological electronic transition in vortex core

We study microscopic scenario of vortex escape from a columnar defect under the influence of a transport current. For defect radii smaller than the superconducting coherence length the depinning process is shown to be a consequence of two subsequent topological electronic transitions in a trapped vortex core. The first transition at a critical current $j_L$ is associated with the opening of Fermi surface segments corresponding to the creation of a vortex--antivortex pair bound to the defect. The second transition at a certain current $j_d > j_L$ is caused by merging of different Fermi surface segments, which accompanies the formation of a freely moving vortex.Comment: 5 pages, 4 figure

Clades and clans: a comparison study of two evolutionary models

The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under these two models provides valuable insights into macro-evolutionary processes, and is important in hypothesis testing and Bayesian analyses in phylogenetics. Here we show that these distributions are log-convex, which implies that very large clades or very small clades are more likely to occur under these two models. Moreover, we prove that there exists a critical value $\kappa(n)$ for each $n\geqslant 4$ such that for a given clade with size $k$, the probability that this clade is contained in a random tree with $n$ leaves generated under the YHK model is higher than that under the PDA model if $1<k<\kappa(n)$, and lower if $\kappa(n)<k<n$. Finally, we extend our results to binary unrooted trees, and obtain similar results for the distributions of clan sizes.Comment: 21page

Superconducting Coherence and the Helicity Modulus in Vortex Line Models

We show how commonly used models for vortex lines in three dimensional superconductors can be modified to include k=0 excitations. We construct a formula for the k=0 helicity modulus in terms of fluctuations in the projected area of vortex loops. This gives a convenient criterion for the presence of superconducting coherence. We also present Monte Carlo simulations of a continuum vortex line model for the melting of the Abrikosov vortex lattice in pure YBCO.Comment: 4 pages RevTeX, 2 eps figures included using eps

Co-Variation between Seed Dormancy, Growth Rate and Flowering Time Changes with Latitude in Arabidopsis thaliana

Life-history traits controlling the duration and timing of developmental phases in the life cycle jointly determine fitness. Therefore, life-history traits studied in isolation provide an incomplete view on the relevance of life-cycle variation for adaptation. In this study, we examine genetic variation in traits covering the major life history events of the annual species Arabidopsis thaliana: seed dormancy, vegetative growth rate and flowering time. In a sample of 112 genotypes collected throughout the European range of the species, both seed dormancy and flowering time follow a latitudinal gradient independent of the major population structure gradient. This finding confirms previous studies reporting the adaptive evolution of these two traits. Here, however, we further analyze patterns of co-variation among traits. We observe that co-variation between primary dormancy, vegetative growth rate and flowering time also follows a latitudinal cline. At higher latitudes, vegetative growth rate is positively correlated with primary dormancy and negatively with flowering time. In the South, this trend disappears. Patterns of trait co-variation change, presumably because major environmental gradients shift with latitude. This pattern appears unrelated to population structure, suggesting that changes in the coordinated evolution of major life history traits is adaptive. Our data suggest that A. thaliana provides a good model for the evolution of trade-offs and their genetic basis.<br