Large Scale Structures a Gradient Lines: the case of the Trkal Flow

A specific asymptotic expansion at large Reynolds numbers (R)for the long wavelength perturbation of a non stationary anisotropic helical solution of the force less Navier-Stokes equations (Trkal solutions) is effectively constructed of the Beltrami type terms through multi scaling analysis. The asymptotic procedure is proved to be valid for one specific value of the scaling parameter,namely for the square root of the Reynolds number (R).As a result large scale structures arise as gradient lines of the energy determined by the initial conditions for two anisotropic Beltrami flows of the same helicity.The same intitial conditions determine the boundaries of the vortex-velocity tubes, containing both streamlines and vortex linesComment: 27 pages, 2 figure

Topological current of point defects and its bifurcation

From the topological properties of a three dimensional vector order parameter, the topological current of point defects is obtained. One shows that the charge of point defects is determined by Hopf indices and Brouwer degrees. The evolution of point defects is also studied. One concludes that there exist crucial cases of branch processes in the evolution of point defects when the Jacobian $D(\frac \phi x)=0$.Comment: revtex,14 pages,no figur

Direct mass measurements of 19B, 22C, 29F, 31Ne, 34Na and other light exotic nuclei

We report on direct time-of-flight based mass measurements of 16 light neutron-rich nuclei. These include the first determination of the masses of the Borromean drip-line nuclei $^{19}$B, $^{22}$C and $^{29}$F as well as that of $^{34}$Na. In addition, the most precise determinations to date for $^{23}$N and $^{31}$Ne are reported. Coupled with recent interaction cross-section measurements, the present results support the occurrence of a two-neutron halo in $^{22}$C, with a dominant $\nu2s_{1/2}^2$ configuration, and a single-neutron halo in $^{31}$Ne with the valence neutron occupying predominantly the 2$p_{3/2}$ orbital. Despite a very low two-neutron separation energy the development of a halo in $^{19}$B is hindered by the 1$d_{5/2}^2$ character of the valence neutrons.Comment: 5 page

Direct observation of free excitons in luminescence spectra of xenon clusters

Luminescence of surface and free bulk excitons is detected in xenon for the first time for substrate-free rare-gas clusters. Xenon clusters were produced by the method of gas condensation in a supersonic jet emitted into vacuum. Optical study was accompanied by electron diffraction measurements to determine the structure of clusters.Comment: The more complete version of the paper is to be published in 'Low Temperature Physics' (2007

Degree of entanglement for two qubits

In this paper, we present a measure to quantify the degree of entanglement for two qubits in a pure state.Comment: 5 page

MAYA: An active-target detector for binary reactions with exotic beams

International audienceWith recent improvements in the production of radioactive beams in facilities such as SPIRAL at GANIL, a larger area of the nuclear chart is now accessible for experimentation. For these usually low-intensity and low-energy secondary beams, we have developed the new MAYA detector based on the active-target concept. This device allows to use a relatively thick target without loss of resolution by using the detection gas as target material. Dedicated 3D tracking, particle identification, energy loss and range measurements allow complete kinematic reconstruction of reactions taking place inside MAYA

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

We previously modeled the in vivo evolution of human immunodeficiency virus-1 (HIV-1) under drug selective pressure from cross-sectional viral sequences. These fitness landscapes (FLs) were made by using first a Bayesian network (BN) to map epistatic substitutions, followed by scaling the fitness landscape based on an HIV evolution simulator trying to evolve the sequences from treatment naïve patients into sequences from patients failing treatment. In this study, we compared four FLs trained with different sequence populations. Epistatic interactions were learned from three different cross-sectional BNs, trained with sequence from patients experienced with indinavir (BNT), all protease inhibitors (PIs) (BNP) or all PI except indinavir (BND). Scaling the fitness landscape was done using cross-sectional data from drug naïve and indinavir experienced patients (Fcross using BNT) and using longitudinal sequences from patients failing indinavir (FlongT using BNT, FlongP using BNP, FlongD using BND). Evaluation to predict the failing sequence and therapy outcome was performed on independent sequences of patients on indinavir. Parameters included estimated fitness (LogF), the number of generations (GF) or mutations (MF) to reach the fitness threshold (average fitness when a major resistance mutation appeared), the number of generations (GR) or mutations (MR) to reach a major resistance mutation and compared to genotypic susceptibility score (GSS) from Rega and HIVdb algorithms. In pairwise FL comparisons we found significant correlation between fitness values for individual sequences, and this correlation improved after correcting for the subtype. Furthermore, FLs could predict the failing sequence under indinavir-containing combinations. At 12 and 48 weeks, all parameters from all FLs and indinavir GSS (both for Rega and HIVdb) were predictive of therapy outcome, except MR for FlongT and FlongP. The fitness landscapes have similar predictive power for treatment response under indinavir-containing regimen as standard rules-based algorithms, and additionally allow predicting genetic evolution under indinavir selective pressure

The development of computational biology in South Africa: successes achieved and lessons learnt

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt