T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Monotonic continuous-time random walks with drift and stochastic reset events

In this paper we consider a stochastic process that may experience random reset events which suddenly bring the system to the starting value and analyze the relevant statistical magnitudes. We focus our attention on monotonic continuous-time random walks with a constant drift: The process increases between the reset events, either by the effect of the random jumps, or by the action of the deterministic drift. As a result of all these combined factors interesting properties emerge, like the existence (for any drift strength) of a stationary transition probability density function, or the faculty of the model to reproduce power-law-like behavior. General formulas for two extreme statistics, the survival probability, and the mean exit time, are also derived. To corroborate in an independent way the results of the paper, Monte Carlo methods were used. These numerical estimations are in full agreement with the analytical predictions.

Association between resistin levels and cardiovascular disease events in older adults: The health, aging and body composition study.

OBJECTIVE: Prospective data on the association between resistin levels and cardiovascular disease (CVD) events are sparse with conflicting results. METHODS: We studied 3044 aged 70-79 years from the Health, Aging, and Body Composition Study. CVD events were defined as coronary heart disease (CHD) or stroke events. «Hard » CHD events were defined as CHD death or myocardial infarction. We estimated hazard ratio (HR) and 95% confidence intervals (CI) according to the quartiles of serum resistin concentrations and adjusted for clinical variables, and then further adjusted for metabolic disease (body mass index, fasting plasma glucose, abdominal visceral and subcutaneous adipose tissue, leptin, adiponectin, insulin) and inflammation (C-reactive protein, interleukin-6, tumor necrosis factors-α). RESULTS: During a median follow-up of 10.1 years, 559 patients had « hard » CHD events, 884 CHD events and 1106 CVD Events. Unadjusted incidence rate for CVD events was 36.6 (95% CI 32.1-41.1) per 1000 persons-year in the lowest quartile and 54.0 per 1000 persons-year in the highest quartile (95% CI 48.2-59.8, P for trend < 0.001). In the multivariate models adjusted for clinical variables, HRs for the highest vs. lowest quartile of resistin was 1.52 (95% CI 1.20-1.93, P < 0.001) for « Hard » CHD events, 1.41 (95% CI 1.16-1.70, P = 0.001) for CHD events and 1.35 (95% CI 1.14-1.59, P = 0.002) for CVD events. Further adjustment for metabolic disease slightly reduced the associations while adjustment for inflammation markedly reduced the associations. CONCLUSIONS: In older adults, higher resistin levels are associated with CVD events independently of clinical risk factors and metabolic disease markers, but markedly attenuated by inflammation.

Transpolar voltage and polar cap flux during the substorm cycle and steady convection events

Transpolar voltages observed during traversals of the polar cap by the Defense Meteorological Satellite Program (DMSP) F-13 spacecraft during 2001 are analyzed using the expanding-contracting polar cap model of ionospheric convection. Each of the 10,216 passes is classified by its substorm phase or as a steady convection event (SCE) by inspection of the AE indices. For all phases, we detect a contribution to the transpolar voltage by reconnection in both the dayside magnetopause and in the crosstail current sheet. Detection of the IMF influence is 97% certain during quiet intervals and >99% certain during substorm/SCE growth phases but falls to 75% in substorm expansion phases: It is only 27% during SCEs. Detection of the influence of the nightside voltage is only 19% certain during growth phases, rising during expansion phases to a peak of 96% in recovery phases: During SCEs, it is >99%. The voltage during SCEs is dominated by the nightside, not the dayside, reconnection. On average, substorm expansion phases halt the growth phase rise in polar cap flux rather than reversing it. The main destruction of the excess open flux takes place during the 6- to 10-hour interval after the recovery phase (as seen in AE) and at a rate which is relatively independent of polar cap flux because the NENL has by then retreated to the far tail. The best estimate of the voltage associated with viscous-like transfer of closed field lines into the tail is around 10 kV.

Changes in race-specific virulence in pseudomonas syringae pv. phaseolicola are Associated with a chimeric transposable element and rare deletion events in a plasmid-borne pathogenicity island

Virulence for bean and soybean is determined by effector genes in a plasmid-borne pathogenicity island (PAI) in race 7 strain 1449B of Pseudomonas syringae pv. phaseolicola. One of the effector genes, avrPphF, confers either pathogenicity, virulence, or avirulence depending on the plant host and is absent from races 2, 3, 4, 6, and 8 of this pathogen. Analysis of cosmid clones and comparison of DNA sequences showed that the absence of avrPphF from strain 1448A is due to deletion of a continuous 9.5-kb fragment. The remainder of the PAI is well conserved in strains 1448A and 1449B. The left junction of the deleted region consists of a chimeric transposable element generated from the fusion of homologs of IS1492 from Pseudomonas putida and IS1090 from Ralstonia eutropha. The borders of the deletion were conserved in 66 P. syringae pv. phaseolicola strains isolated in different countries and representing the five races lacking avrPphF. However, six strains isolated in Spain had a 10.5-kb deletion that extended 1 kb further from the right junction. The perfect conservation of the 28-nucleotide right repeat of the IS1090 homolog in the two deletion types and in the other 47 insertions of the IS1090 homolog in the 1448A genome strongly suggests that the avrPphF deletions were mediated by the activity of the chimeric mobile element. Our data strongly support a clonal origin for the races of P. syringae pv. phaseolicola lacking avrPphF.

Can valuation factors be prescribed? The case of collective enfranchisement and leasehold extension of flats in England and Wales

Recent concerns over the valuation process in collective leasehold enfranchisement and lease extension cases have culminated in new legislation. To underpin this, the Government (Department of Environment Transport and the Regions (DETR)) commissioned new research, which examined whether the valuation of the freehold in such cases could be simplified through the prescription of either yield or marriage value/relativity. This paper, which is based on that research, examines whether it is possible or desirable to prescribe such factors in the valuation process. Market, settlement and Local Valuation Tribunal (LVT) decisions are analysed, and the basis of 'relativity charts' used in practice is critically examined. Ultimately the imperfect nature of the market in freehold investment sales and leasehold vacant possession sales means that recommendations must rest on an analysis of LVT data. New relativity curves are developed from this data and used in conjunction with an alternative approach to valuation yields (based on other investment assets). However, the paper concludes that although the prescription of yields and relativity is possible, it is not fully defensible because of problems in determining risk premia; that the evidential basis for relativity consists of LVT decisions; and that a formula approach would tend to 'lead' the market as a whole.

Longitudinal investigation of the role of temperament and stressful life events in childhood anxiety

The current study investigated the longitudinal relationships between BI, life events, and anxiety in a sample of 102 behaviourally inhibited (BI) and 100 uninhibited (BUI) children aged 3 to 4 years. Children’s parents completed questionnaires on BI, stressful life events, and anxiety symptoms, and were administered a diagnostic interview three times in a 5-year period. In line with our hypotheses, negative life events, and negative behaviour- dependent life events (i.e. life events that are related to the children’s own behaviours) in particular, and the impact of negative life events, were predictive of increases in subsequent anxiety symptoms, the likelihood of having an anxiety disorder, and increased number of anxiety diagnoses over the five year follow-up period. Experiencing more positive, behaviour-independent life events decreased the risk of being diagnosed with an anxiety disorder. Furthermore, differences were found in life events between BI and BUI children. That is, BI children experienced fewer positive and specifically positive behaviour-dependent life events, and the impact of these positive life events was also lower in BI children than in BUI children. However, BI did not interact with life events in the prediction of anxiety problems as hypothesized. Therefore, this study seems to indicate that BI and life events act as additive risk factors in the development of anxiety problems.

Low-altitude signatures of the cusp and flux transfer events

The usual interpretation of a flux transfer event (FTE) at the magnetopause, in terms of time-dependent and possibly patchy reconnection, demands that it generate an ionospheric signature. Recent ground-based observations have revealed that auroral transients in the cusp/cleft region have all the characteristics required of FTE effects. However, signatures in the major available dataset, namely that from low-altitude polar-orbiting satellites, have not yet been identified. In this paper, we consider a cusp pass of the DE-2 spacecraft during strongly southward IMF. The particle detectors show magnetosheath ion injection signatures. However, the satellite motion and convection are opposed, and we discuss how the observed falling energy dispersion of the precipitating ions can have arisen from a static, moving or growing source. The spatial scale of the source is typical of an FTE. A simple model of the ionospheric signature of an FTE reproduces the observed electric and magnetic field perturbations. Precipitating electrons of peak energy ∼100eV are found to lie on the predicted boundary of the newly-opened tube, very similar to those found on the edges of FTEs at the magnetopause. The injected ions are within this boundary and their dispersion is consistent with its growth as reconnection proceeds. The reconnection potential and the potential of the induced ionospheric motion are found to be the same (≃25kV). The scanning imager on DE-1 shows a localised transient auroral feature around DE-2 at this time, similar to the recent optical/radar observations of FTEs.

Inferences about pressures and vertical extension of cloud layers from POLDER3/PARASOL measurements in the oxygen A-band

We present new inferences about cloud vertical structures from multidirectionnal measurements in the oxygen A-band. The analysis of collocated data provided by instruments onboard satellite platforms within the A-Train, as well as simulations have shown that for monolayered clouds, the cloud oxygen pressure PO2PO2 derived from the POLDER3 instrument was sensitive to the cloud vertical structure in two ways: First, PO2PO2 is actually close to the pressure of the geometrical middle of cloud and we propose a method to correct it to get the cloud top pressure (CTP), and then to obtain the cloud geometrical extent. Second, for the liquid water clouds, the angular standard deviation σPO2σPO2 of PO2PO2 is correlated with the geometrical extent of cloud layers, which makes possible a second estimation of the cloud geometrical thickness. The determination of the vertical location of cloud layers from passive measurements, eventually completed from other observations, would be useful in many applications for which cloud macrophysical properties are needed

On Approximate KKT Condition and its Extension to Continuous Variational Inequalities

In this work, we introduce a necessary sequential Approximate-Karush-Kuhn-Tucker (AKKT) condition for a point to be a solution of a continuous variational inequality, and we prove its relation with the Approximate Gradient Projection condition (AGP) of Garciga-Otero and Svaiter. We also prove that a slight variation of the AKKT condition is sufficient for a convex problem, either for variational inequalities or optimization. Sequential necessary conditions are more suitable to iterative methods than usual punctual conditions relying on constraint qualifications. The AKKT property holds at a solution independently of the fulfillment of a constraint qualification, but when a weak one holds, we can guarantee the validity of the KKT conditions.