Accelerating MCMC via Parallel Predictive Prefetching

We present a general framework for accelerating a large class of widely used Markov chain Monte Carlo (MCMC) algorithms. Our approach exploits fast, iterative approximations to the target density to speculatively evaluate many potential future steps of the chain in parallel. The approach can accelerate computation of the target distribution of a Bayesian inference problem, without compromising exactness, by exploiting subsets of data. It takes advantage of whatever parallel resources are available, but produces results exactly equivalent to standard serial execution. In the initial burn-in phase of chain evaluation, it achieves speedup over serial evaluation that is close to linear in the number of available cores

Coulomb blockade effects in driven electron transport

We study numerically the influence of strong Coulomb repulsion on the current through molecular wires that are driven by external electromagnetic fields. The molecule is described by a tight-binding model whose first and last site is coupled to a respective lead. The leads are eliminated within a perturbation theory yielding a master equation for the wire. The decomposition into a Floquet basis enables an efficient treatment of the driving field. For the electronic excitations in bridged molecular wires, we find that strong Coulomb repulsion significantly sharpens resonance peaks which broaden again with increasing temperature. By contrast, Coulomb blockade has only a small influence on effects like non-adiabatic electron pumping and coherent current suppression.Comment: 9 pages, 7 figures. Added a plot for temperature dependence of resonance peaks. Published versio

Educational differences in all-cause mortality by marital status

Using life table measures, we compare educational differentials in all-cause mortality at ages 40 to 70 in Bulgaria to those in Finland and the United States. Specifically, we assess whether the relationship between education and mortality is modified by marital status. Although high education and being married are associated with lower mortality in all three countries, absolute educational differences tend to be smaller among married than unmarried individuals. Absolute differentials by education are largest for Bulgarian men, but in relative terms educational differences are smaller among Bulgarian men than in Finland and the U.S. Among women, Americans experience the largest education-mortality gradients in both relative and absolute terms. Our results indicate a particular need to tackle health hazards among poorly educated men in countries in transition.all-cause mortality, Bulgaria, educational differentials, Finland, life table measures, marital status, USA

Non-equilibrium dynamics of a system with Quantum Frustration

Using flow equations, equilibrium and non-equilibrium dynamics of a two-level system are investigated, which couples via non-commuting components to two independent oscillator baths. In equilibrium the two-level energy splitting is protected when the TLS is coupled symmetrically to both bath. A critical asymmetry angle separates the localized from the delocalized phase. On the other hand, real-time decoherence of a non-equilibrium initial state is for a generic initial state faster for a coupling to two baths than for a single bath.Comment: 22 pages, 9 figure

Bacterial β-peptidyl aminopeptidases: on the hydrolytic degradation of β-peptides

The special chemical and biological features of β-peptides have been investigated intensively during recent years. Many studies emphasize the restricted biodegradability and the high metabolic stability of this class of compounds. β-Peptidyl aminopeptidases form the first family of enzymes that hydrolyze a variety of short β-peptides and β-amino-acid-containing peptides. All representatives of this family were isolated from Gram-negative bacteria. The substrate specificities of the peptidases vary greatly, but the enzymes have common structural properties, and a similar reaction mechanism can be expected. This review gives an overview on the β-peptidyl aminopeptidases with emphasis on their biochemical and structural properties. Their possible physiological function is discussed. Functionally and structurally related enzymes are compared to the β-peptidyl aminopeptidase

Chirality of pollutants—effects on metabolism and fate

In most cases, enantiomers of chiral compounds behave differently in biochemical processes. Therefore, the effects and the environmental fate of the enantiomers of chiral pollutants need to be investigated separately. In this review, the different fates of the enantiomers of chiral phenoxyalkanoic acid herbicides, acetamides, organochlorines, and linear alkylbenzenesulfonates are discussed. The focus lies on biological degradation, which may be enantioselective, in contrast to non-biotic conversions. The data show that it is difficult to predict which enantiomer may be enriched and that accumulation of an enantiomer is dependent on the environmental system, the species, and the organ. Racemization and enantiomerization processes occur and make interpretation of the data even more complex. Enantioselective degradation implies that the enzymes involved in the conversion of such compounds are able to differentiate between the enantiomers. "Enzyme pairs” have evolved which exhibit almost identical overall folding. Only subtle differences in their active site determine their enantioselectivities. At the other extreme, there are examples of non-homologous "enzyme pairs” that have developed through convergent evolution to enantioselectively turn over the enantiomers of a chiral compound. For a better understanding of enantioselective reactions, more detailed studies of enzymes involved in enantioselective degradation need to be performe

Can the UNAIDS 90-90-90 target be achieved? A systematic analysis of national HIV treatment cascades

Background In 2014, the Joint United Nations Programme on HIV and AIDS (UNAIDS) and partners set the ‘90-90-90 targets’; aiming to diagnose 90% of all HIV positive people, provide antiretroviral therapy (ART) for 90% of those diagnosed and achieve viral suppression for 90% of those treated, by 2020. This results in 81% of all HIV positive people on treatment and 73% of all HIV positive people achieving viral suppression. We aimed to analyse how effective national HIV treatment programmes are at meeting these targets, using HIV care continuums or cascades. Methods We searched for HIV treatment cascades for 196 countries in published papers, conference presentations, UNAIDS databases and national reports. Cascades were constructed using reliable, generalisable, recent data from national, cross-sectional and longitudinal study cohorts. Data were collected for four stages; total HIV positive people, diagnosed, on treatment and virally suppressed. The cascades were categorised as complete (four stages) or partial (3 stages), and analysed for ‘break points’ defined as a drop >10% in coverage between consecutive 90-90-90 targets. Results 69 country cascades were analysed (32 complete, 37 partial). Diagnosis (target one—90%) ranged from 87% (the Netherlands) to 11% (Yemen). Treatment coverage (target two—81% on ART) ranged from 71% (Switzerland) to 3% (Afghanistan). Viral suppression (target three—73% virally suppressed) was between 68% (Switzerland) and 7% (China). Conclusions No country analysed met the 90-90-90 targets. Diagnosis was the greatest break point globally, but the most frequent key break point for individual countries was providing ART to those diagnosed. Large disparities were identified between countries. Without commitment to standardised reporting methodologies, international comparisons are complex

Anomalous Silicate Dust Emission in the Type 1 Liner Nucleus of M81

doi:10.1088/0004-637X/716/1/490We report the detection and successful modeling of the unusual 9.7μm Si-O stretching silicate emission feature in the type 1 (i.e., face-on) LINER nucleus of M81. Using the Infrared Spectrograph (IRS) instrument on Spitzer, we determine the feature in the central 230 pc of M81 to be in strong emission, with a peak at ∼10.5μm. This feature is strikingly different in character from the absorption feature of the galactic interstellar medium, and from the silicate absorption or weak emission features typical of galaxies with active star formation. We successfully model the high signal-to-noise ratio IRS spectra with porous silicate dust using laboratory-acquired mineral spectra. We find that the most probable fit uses micron-sized, porous grains of amorphous silicate and amorphous carbon. In addition to silicate dust, there is weak polycyclic aromatic hydrocarbon (PAH) emission present (particularly at 11.3μm, arising from the C-H out-of-plane bending vibration of relatively large PAHs of ∼500-1000 C atoms) whose character reflects the low-excitation active galactic nucleus environment, with some evidence that small PAHs of ∼100-200 C atoms (responsible for the 7.7μm C-C stretching band) in the immediate vicinity of the nucleus have been preferentially destroyed. Analysis of the infrared fine structure lines confirms the LINER character of the M81 nucleus. Four of the infrared H2 rotational lines are detected and fit to an excitation temperature of T ∼ 800 K. Spectral maps of the central 230 pc in the [Ne ii] 12.8μm line, the H2 17μm line, and the 11.3μm PAH C-H bending feature reveal arc- or spiral-like structures extending from the core. We also report on epochal photometric and spectroscopic observations of M81, whose nuclear intensity varies in time across the spectrum due to what is thought to be inefficient, sub-Eddington accretion onto its central black hole. We find that, contrary to the implications of earlier photometry, the nucleus has not varied over a period of two years at these infrared wavelengths to a precision of about 1%.H.A.S. and M.L.N.A. acknowledge partial support from NASA Grant NAG5-10654. A.L., M.K., and M.P.L. are supported in part by Spitzer Theory Programs, a Herschel Theory Program, and NSF grant AST 07-07866. This work is based in part on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under NASA contract 1407. Support for the IRAC instrument was provided by NASA through Contract Number 960541 issued by JPL. CUBISM is a product of the SSC and the IRS team

Limitation of entanglement due to spatial qubit separation

We consider spatially separated qubits coupled to a thermal bosonic field that causes pure dephasing. Our focus is on the entanglement of two Bell states which for vanishing separation are known as robust and fragile entangled states. The reduced two-qubit dynamics is solved exactly and explicitly. Our results allow us to gain information about the robustness of two-qubit decoherence-free subspaces with respect to physical parameters such as temperature, qubit-bath coupling strength and spatial separation of the qubits. Moreover, we clarify the relation between single-qubit coherence and two-qubit entanglement and identify parameter regimes in which the terms robust and fragile are no longer appropriate.Comment: 7 pages, 3 figures; revised version, accepted for publication in Europhys. Let

Survival Probability of a Doorway State in regular and chaotic environments

We calculate survival probability of a special state which couples randomly to a regular or chaotic environment. The environment is modelled by a suitably chosen random matrix ensemble. The exact results exhibit non--perturbative features as revival of probability and non--ergodicity. The role of background complexity and of coupling complexity is discussed as well.Comment: 19 pages 5 Figure