Cascade atom in high-Q cavity: The spectrum for non-Markovian decay

The spontaneous emission spectrum for a three level cascade configuration atom in a single mode high-Q cavity coupled to a zero temperature reservoir of continuum external modes is determined from the atom-cavity mode master equation using the quantum regression theorem. Initially the atom is in its upper state and the cavity mode empty of photons. Following Glauber, the spectrum is defined via the response of a detector atom. Spectra are calculated for the detector located inside the cavity (case A), outside the cavity end mirror (Case B-end emission), or placed for emission out the side of the cavity (Case C). The spectra for case A and case B are found to be essentially the same. In all the cases the predicted lineshapes are free of instrumental effects and only due to cavity decay. Spectra are presented for intermediate and strong coupling regime situations (where both atomic transitions are resonant with the cavity frequency), for cases of non-zero cavity detuning, and for cases where the two atomic transition frequencies differ. The spectral features for Cases B(A) and C are qualitatively similar, with six spectral peaks for resonance cases and eight for detuned cases. These general features of the spectra can be understood via the dressed atom model. However, Case B and C spectra differ in detail, with the latter exhibiting a deep spectral hole at the cavity frequency due to quantum interference effects.Comment: 29 pages, 14 figures; v2: very minor correction to two equations, thicker lines in some figure

High caseload of childhood tuberculosis in hospitals on Java Island, Indonesia: a cross sectional study

Background Childhood tuberculosis (TB) has been neglected in the fight against TB. Despite implementation of Directly Observed Treatment Shortcourse (DOTS) program in public and private hospitals in Indonesia since 2000, the burden of childhood TB in hospitals was largely unknown. The goals of this study were to document the caseload and types of childhood TB in the 0-4 and 5-14 year age groups diagnosed in DOTS hospitals on Java Island, Indonesia. Methods Cross-sectional study of TB cases recorded in inpatient and outpatient registers of 32 hospitals. Cases were analyzed by hospital characteristics, age groups, and types of TB. The number of cases reported in the outpatient unit was compared with that recorded in the TB register. Results Of 5,877 TB cases in the inpatient unit and 15,694 in the outpatient unit, 11% (648) and 27% (4,173) respectively were children. Most of the childhood TB cases were under five years old (56% and 53% in the inpatient and outpatient clinics respectively). The proportion of smear positive TB was twice as high in the inpatient compared to the outpatient units (15.6% vs 8.1%). Extra-pulmonary TB accounted for 15% and 6% of TB cases in inpatient and outpatient clinics respectively. Among children recorded in hospitals only 1.6% were reported to the National TB Program. Conclusion In response to the high caseload and gross under-reporting of childhood TB cases, the National TB Program should give higher priority for childhood TB case management in designated DOTS hospitals. In addition, an international guidance on childhood TB recording and reporting and improved diagnostics and standardized classification is require

Information transmission in oscillatory neural activity

Periodic neural activity not locked to the stimulus or to motor responses is usually ignored. Here, we present new tools for modeling and quantifying the information transmission based on periodic neural activity that occurs with quasi-random phase relative to the stimulus. We propose a model to reproduce characteristic features of oscillatory spike trains, such as histograms of inter-spike intervals and phase locking of spikes to an oscillatory influence. The proposed model is based on an inhomogeneous Gamma process governed by a density function that is a product of the usual stimulus-dependent rate and a quasi-periodic function. Further, we present an analysis method generalizing the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the information content in such data. We demonstrate these tools on recordings from relay cells in the lateral geniculate nucleus of the cat.Comment: 18 pages, 8 figures, to appear in Biological Cybernetic

Universal Resistances of the Quantum RC circuit

We examine the concept of universal quantized resistance in the AC regime through the fully coherent quantum RC circuit comprising a cavity (dot) capacitively coupled to a gate and connected via a single spin-polarized channel to a reservoir lead. As a result of quantum effects such as the Coulomb interaction in the cavity and global phase coherence, we show that the charge relaxation resistance $R_q$ is identical for weak and large transmissions and it changes from $h/2e^2$ to $h/e^2$ when the frequency (times $\hbar$) exceeds the level spacing of the cavity; $h$ is the Planck constant and $e$ the electron charge. For large cavities, we formulate a correspondence between the charge relaxation resistance $h/e^2$ and the Korringa-Shiba relation of the Kondo model. Furthermore, we introduce a general class of models, for which the charge relaxation resistance is universal. Our results emphasize that the charge relaxation resistance is a key observable to understand the dynamics of strongly correlated systems.Comment: 12 pages, 3 figure

FLORA: a novel method to predict protein function from structure in diverse superfamilies

Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues

Newtonian flow inside carbon nanotube with permeable boundary taking into account van der Waals forces

Here, water flow inside large radii semi-infinite carbon nanotubes is investigated. Permeable wall taking into account the molecular interactions between water and a nanotube, and the slip boundary condition will be considered. Furthermore, interactions among molecules are approximated by the continuum approximation. Incompressible and Newtonian fluid is assumed, and the Navier-Stokes equations, after certain assumptions, transformations and derivations, can be reduced into two first integral equations. In conjunction with the asymptotic expansion technique, we are able to derive the radial and axial velocities analytically, capturing the effect of the water leakage, where both mild and exceptionally large leakages will be considered. The radial velocity obeys the prescribed boundary condition at the (im)permeable wall. Through the mean of the radial forces, the sufficiently large leakages will enhance the radial velocity at the center of the tube. On the other hand, unlike the classical laminar flow, the axial velocity attains its maximum at the wall due to the coupling effect with the radial forces as water is being pushed into the proximity of the inner wall. In addition, the axial velocity and the flux with the consideration of the suck-in forces, induced by the tubes’ entry turn out to be one order higher than that without the suck-in forces. All the aforementioned considerations might partially resolve the mysteriously high water penetration through nanotubes. Axial velocity also drops with the tube’s length when the water leakage is permitted and the suck-in forces will ease the decline rate of the axial velocity. The present mathematical framework can be directly employed into the water flow inside other porous nano-materials, where large water leakage is permitted and therefore are of huge practical impact on ultra-filtration and environmental protection

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

Ras proteins regulate signaling cascades crucial for cell proliferation and differentiation by switching between GTP- and GDP-bound conformations. Distinct Ras isoforms have unique physiological functions with individual isoforms associated with different cancers and developmental diseases. Given the small structural differences among isoforms and mutants, it is currently unclear how these functional differences and aberrant properties arise. Here we investigate whether the subtle differences among isoforms and mutants are associated with detectable dynamical differences. Extensive molecular dynamics simulations reveal that wild-type K-Ras and mutant H-Ras A59G are intrinsically more dynamic than wild-type H-Ras. The crucial switch 1 and switch 2 regions along with loop 3, helix 3, and loop 7 contribute to this enhanced flexibility. Removing the gamma-phosphate of the bound GTP from the structure of A59G led to a spontaneous GTP-to-GDP conformational transition in a 20-ns unbiased simulation. The switch 1 and 2 regions exhibit enhanced flexibility and correlated motion when compared to non-transitioning wild-type H-Ras over a similar timeframe. Correlated motions between loop 3 and helix 5 of wild-type H-Ras are absent in the mutant A59G reflecting the enhanced dynamics of the loop 3 region. Taken together with earlier findings, these results suggest the existence of a lower energetic barrier between GTP and GDP states of the mutant. Molecular dynamics simulations combined with principal component analysis of available Ras crystallographic structures can be used to discriminate ligand- and sequence-based dynamic perturbations with potential functional implications. Furthermore, the identification of specific conformations associated with distinct Ras isoforms and mutants provides useful information for efforts that attempt to selectively interfere with the aberrant functions of these species

Reduction in Phencyclidine Induced Sensorimotor Gating Deficits in the Rat Following Increased System Xc − Activity in the Medial Prefrontal Cortex

Rationale: Aspects of schizophrenia, including deficits in sensorimotor gating, have been linked to glutamate dysfunction and/or oxidative stress in the prefrontal cortex. System xc −, a cystine–glutamate antiporter, is a poorly understood mechanism that contributes to both cellular antioxidant capacity and glutamate homeostasis. Objectives: Our goal was to determine whether increased system xc − activity within the prefrontal cortex would normalize a rodent measure of sensorimotor gating. Methods: In situ hybridization was used to map messenger RNA (mRNA) expression of xCT, the active subunit of system xc −, in the prefrontal cortex. Prepulse inhibition was used to measure sensorimotor gating; deficits in prepulse inhibition were produced using phencyclidine (0.3–3 mg/kg, sc). N-Acetylcysteine (10–100 μM) and the system xc − inhibitor (S)-4-carboxyphenylglycine (CPG, 0.5 μM) were used to increase and decrease system xc − activity, respectively. The uptake of 14C-cystine into tissue punches obtained from the prefrontal cortex was used to assay system xc − activity. Results: The expression of xCT mRNA in the prefrontal cortex was most prominent in a lateral band spanning primarily the prelimbic cortex. Although phencyclidine did not alter the uptake of 14C-cystine in prefrontal cortical tissue punches, intraprefrontal cortical infusion of N-acetylcysteine (10–100 μM) significantly reduced phencyclidine- (1.5 mg/kg, sc) induced deficits in prepulse inhibition. N-Acetylcysteine was without effect when coinfused with CPG (0.5 μM), indicating an involvement of system xc −. Conclusions: These results indicate that phencyclidine disrupts sensorimotor gating through system xc − independent mechanisms, but that increasing cystine–glutamate exchange in the prefrontal cortex is sufficient to reduce behavioral deficits produced by phencyclidine

Exploring the uncertainties of early detection results: model-based interpretation of mayo lung project

Background: The Mayo Lung Project (MLP), a randomized controlled clinical trial of lung cancer screening conducted between 1971 and 1986 among male smokers aged 45 or above, demonstrated an increase in lung cancer survival since the time of diagnosis, but no reduction in lung cancer mortality. Whether this result necessarily indicates a lack of mortality benefit for screening remains controversial. A number of hypotheses have been proposed to explain the observed outcome, including over-diagnosis, screening sensitivity, and population heterogeneity (initial difference in lung cancer risks between the two trial arms). This study is intended to provide model-based testing for some of these important arguments.Method: Using a micro-simulation model, the MISCAN-lung model, we explore the possible influence of screening sensitivity, systematic error, over-diagnosis and population heterogeneity.Results: Calibrating screening sensitivity, systematic error, or over-diagnosis does not noticeably improve the fit of the model, whereas calibrating population heterogeneity helps the model predict lung cancer incidence better.Conclusions: Our conclusion is that the hypothesized imperfection in screening sensitivity, systematic error, and over-diagnosis do not in themselves explain the observed trial results. Model fit improvement achieved by accounting for population heterogeneity suggests a higher risk of cancer incidence in the intervention group as compared with the control group