1,004 research outputs found
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 GeneChipÂź) 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 , (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 a survival collapse becomes possible. This could
reduce the survival probability by several orders of magnitude. The cross-overs
times and 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 patientsâ 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 patientsâ 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 â€0.001). Medium term (1â4 weeks) CoEs were constant at 19% (p â€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 â€0.05). Conclusions: 3â4 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 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
âco-incinerationâ 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
governmentâs 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 â 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 âconfiscatedâ 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 âriskâ and âuncertaintyâ in scientific reports from both
experts and counter-expertsâ 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 (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
Congruency within rural social networks as an indicator of interpersonal influence on risk judgments: the great stir caused by BSE in a village in northern Germany
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