Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region

The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip®) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genom

Survival Probability of a Local Excitation in a Non-Markovian Environment: Survival Collapse, Zeno and Anti-Zeno effects

The decay dynamics of a local excitation interacting with a non-Markovian environment, modeled by a semi-infinite tight-binding chain, is exactly evaluated. We identify distinctive regimes for the dynamics. Sequentially: (i) early quadratic decay of the initial-state survival probability, up to a spreading time $t_{S}$, (ii) exponential decay described by a self-consistent Fermi Golden Rule, and (iii) asymptotic behavior governed by quantum diffusion through the return processes and leading to an inverse power law decay. At this last cross-over time $t_{R}$ a survival collapse becomes possible. This could reduce the survival probability by several orders of magnitude. The cross-overs times $t_{S}$ and $t_{R}$ allow to assess the range of applicability of the Fermi Golden Rule and give the conditions for the observation of the Zeno and Anti-Zeno effect

Characteristics of improvements in balance control using vibro-tactile biofeedback of trunk sway for multiple sclerosis patients

Background and aims: Previously, we determined that training with vibrotactile feedback (VTfb) of trunk sway improves MS patients’ balance impairment. Here, we posed 5 questions: 1) How many weeks of VTfb training are required to obtain the best short-term carry over effect (CoE) with VTfb? 2) How long does the CoE last once VTfb training terminates? 3) Is the benefit similar for stance and gait? 4) Is position or velocity based VTfb more effective in reducing trunk sway? 5) Do patients’ subjective assessments of balance control improve? Methods: Balance control of 16 MS patients was measured with gyroscopes at the lower trunk. The gyroscopes drove directionally active VTfb in a head-band. Patients trained twice per week with VTfb for 4 weeks to determine when balance control with and without VTfb stopped improving. Thereafter, weekly assessments without VTfb over 4 weeks and at 6 months determined when CoEs ended. Results: A 20% improvement in balance to normal levels occurred with VTfb. Short term CoEs improved from 15 to 20% (p ≤0.001). Medium term (1–4 weeks) CoEs were constant at 19% (p ≤0.001). At 6 months improvement was not significant, 9%. Most improvement was for lateral sway. Equal improvement occurred when angle position or velocity drove VTfb. Subjectively, balance improvements peaked after 3 weeks of training (32%, p ≤0.05). Conclusions: 3–4 weeks VTfb training yields clinically relevant sway reductions and subjective improvements for MS patients during stance and gait. The CoEs lasted at least 1 month. Velocity-based VTfb was equally effective as position-based VTf

Large-eddy simulation of the lid-driven cubic cavity flow by the spectral element method

This paper presents the large-eddy simulation of the lid-driven cubic cavity flow by the spectral element method (SEM) using the dynamic model. Two spectral filtering techniques suitable for these simulations have been implemented. Numerical results for Reynolds number $\text{Re}=12'000$ are showing very good agreement with other experimental and DNS results found in the literature

Risks, alternative knowledge strategies and democratic legitimacy: the conflict over co-incineration of hazardous industrial waste in Portugal.

The decision to incinerate hazardous industrial waste in cement plants (the socalled ‘co-incineration’ process) gave rise to one of the most heated environmental conflicts ever to take place in Portugal. The bitterest period was between 1997 and 2002, after the government had made a decision. Strong protests by residents, environmental organizations, opposition parties, and some members of the scientific community forced the government to backtrack and to seek scientific legitimacy for the process through scientific expertise. The experts ratified the government’s decision, stating that the risks involved were socially acceptable. The conflict persisted over a decade and ended up clearing the way for a more sustainable method over which there was broad social consensus – a multifunctional method which makes it possible to treat, recover and regenerate most wastes. Focusing the analysis on this conflict, this paper has three aims: (1) to discuss the implications of the fact that expertise was ‘confiscated’ after the government had committed itself to the decision to implement co-incineration and by way of a reaction to the atmosphere of tension and protest; (2) to analyse the uses of the notions of ‘risk’ and ‘uncertainty’ in scientific reports from both experts and counter-experts’ committees, and their different assumptions about controllability and criteria for considering certain practices to be sufficiently safe for the public; and (3) to show how the existence of different technical scientific and political attitudes (one more closely tied to government and the corporate interests of the cement plants, the other closer to the environmental values of reuse and recycling and respect for the risk perception of residents who challenged the facilities) is closely bound up with problems of democratic legitimacy. This conflict showed how adopting more sustainable and lower-risk policies implies a broader view of democratic legitimacy, one which involves both civic movements and citizens themselves

Second harmonic generation and birefringence of some ternary pnictide semiconductors

A first-principles study of the birefringence and the frequency dependent second harmonic generation (SHG) coefficients of the ternary pnictide semiconductors with formula ABC$_2$ (A = Zn, Cd; B = Si, Ge; C = As, P) with the chalcopyrite structures was carried out. We show that a simple empirical observation that a smaller value of the gap is correlated with larger value of SHG is qualitatively true. However, simple inverse power scaling laws between gaps and SHG were not found. Instead, the real value of the nonlinear response is a result of a very delicate balance between different intraband and interband terms.Comment: 13 pages, 12 figure

Non-destructive, dynamic detectors for Bose-Einstein condensates

We propose and analyze a series of non-destructive, dynamic detectors for Bose-Einstein condensates based on photo-detectors operating at the shot noise limit. These detectors are compatible with real time feedback to the condensate. The signal to noise ratio of different detection schemes are compared subject to the constraint of minimal heating due to photon absorption and spontaneous emission. This constraint leads to different optimal operating points for interference-based schemes. We find the somewhat counter-intuitive result that without the presence of a cavity, interferometry causes as much destruction as absorption for optically thin clouds. For optically thick clouds, cavity-free interferometry is superior to absorption, but it still cannot be made arbitrarily non-destructive . We propose a cavity-based measurement of atomic density which can in principle be made arbitrarily non-destructive for a given signal to noise ratio

BAFFR activates PI3K/AKT signaling in human naive but not in switched memory B cells through direct interactions with B cell antigen receptors.

Binding of BAFF to BAFFR activates in mature B cells PI3K/AKT signaling regulating protein synthesis, metabolic fitness, and survival. In humans, naive and memory B cells express the same levels of BAFFR, but only memory B cells seem to survive without BAFF. Here, we show that BAFF activates PI3K/AKT only in naive B cells and changes the expression of genes regulating migration, proliferation, growth, and survival. BAFF-induced PI3K/AKT activation requires direct interactions between BAFFR and the B cell antigen receptor (BCR) components CD79A and CD79B and is enhanced by the AKT coactivator TCL1A. Compared to memory B cells, naive B cells express more surface BCRs, which interact better with BAFFR than IgG or IgA, thus allowing stronger responses to BAFF. As ablation of BAFFR in naive and memory B cells causes cell death independent of BAFF-induced signaling, BAFFR seems to act also as an intrinsic factor for B cell survival

Infrared Behavior of Three-Point Functions in Landau Gauge Yang-Mills Theory

Analytic solutions for the three-gluon and ghost-gluon vertices in Landau gauge Yang-Mills theory at low momenta are presented in terms of hypergeometric series. They do not only show the expected scaling behavior but also additional kinematic divergences when only one momentum goes to zero. These singularities, which have also been proposed previously, induce a strong dependence on the kinematics in many dressing functions. The results are generalized to two and three dimensions and a range of values for the ghost propagator's infrared exponent kappa.Comment: 21 pages, 29 figures; numerical data of the infrared dressing functions can be obtained from the authors v2: a few minor changes, corresponds to version appearing in EPJ