Computing with Noise - Phase Transitions in Boolean Formulas

Computing circuits composed of noisy logical gates and their ability to represent arbitrary Boolean functions with a given level of error are investigated within a statistical mechanics setting. Bounds on their performance, derived in the information theory literature for specific gates, are straightforwardly retrieved, generalized and identified as the corresponding typical-case phase transitions. This framework paves the way for obtaining new results on error-rates, function-depth and sensitivity, and their dependence on the gate-type and noise model used.Comment: 10 pages, 2 figure

The grand canonical ABC model: a reflection asymmetric mean field Potts model

We investigate the phase diagram of a three-component system of particles on a one-dimensional filled lattice, or equivalently of a one-dimensional three-state Potts model, with reflection asymmetric mean field interactions. The three types of particles are designated as $A$, $B$, and $C$. The system is described by a grand canonical ensemble with temperature $T$ and chemical potentials $T\lambda_A$, $T\lambda_B$, and $T\lambda_C$. We find that for $\lambda_A=\lambda_B=\lambda_C$ the system undergoes a phase transition from a uniform density to a continuum of phases at a critical temperature $\hat T_c=(2\pi/\sqrt3)^{-1}$. For other values of the chemical potentials the system has a unique equilibrium state. As is the case for the canonical ensemble for this $ABC$ model, the grand canonical ensemble is the stationary measure satisfying detailed balance for a natural dynamics. We note that $\hat T_c=3T_c$, where $T_c$ is the critical temperature for a similar transition in the canonical ensemble at fixed equal densities $r_A=r_B=r_C=1/3$.Comment: 24 pages, 3 figure

Clinical use of Whole Genome Sequencing for Mycobacterium tuberculosis

Drug resistant tuberculosis (TB) remains a major challenge to global health and to healthcare in the UK. In 2014, England recorded 6520 cases of TB of which 1.4% were multi-drug resistant (MDR-TB). Extensively drug resistant TB (XDR-TB) occurs at a much lower rate, but the impact on the patient and hospital is severe. Current diagnostic methods such as drug susceptibility testing and targeted molecular tests are slow to return or examine only a limited number of target regions respectively. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen thus improving patient outcome and reducing overall healthcare costs. Whole genome sequencing has been shown to provide a rapid and comprehensive view of the genotype of the organism and thus enable reliable prediction of the drug susceptibility phenotype within a clinically relevant time frame. In addition it provides the highest resolution when investigating transmission events in possible outbreak scenarios. However, robust software and database tools need to be developed for the full potential to be realized in this specialized area of medicine

Identification of sortase A (SrtA) substrates in Streptococcus uberis: evidence for an additional hexapeptide (LPXXXD) sorting motif

Sortase (a transamidase) has been shown to be responsible for the covalent attachment of proteins to the bacterial cell wall. Anchoring is effected on secreted proteins containing a specific cell wall motif toward their C-terminus; that for sortase A (SrtA) in Gram-positive bacteria often incorporates the sequence LPXTG. Such surface proteins are often characterized as virulence determinants and play important roles during the establishment and persistence of infection. Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis, which impacts on animal health and welfare and the economics of milk production. Comparison of stringently produced cell wall fractions from S. uberis and an isogenic mutant strain lacking SrtA permitted identification of 9 proteins likely to be covalently anchored at the cell surface. Analysis of these sequences implied the presence of two anchoring motifs for S. uberis, the classical LPXTG motif and an additional LPXXXD motif

Novel draw solution for forward osmosis based solar desalination

Forward osmosis (FO) is an emerging technology for water desalination which requires no external force for its operation. The performance of FO for water desalination is dependent on draw solution (DS) that must provide high osmosis pressure, minimum reverse flux and efficient separation of water. This work proposes an innovative concept of energy efficient material as DS having two functions, i.e. high osmotic pressure and efficient absorption of solar energy for the regeneration phase. The potassium functionalised carbon nanofibers (K/CNF) which are highly solar absorptive, are engineered and suspended in triethylene glycol (TEG) aqueous solution with different concentrations to act as a novel DS. The TEG-K/CNF is fully characterised for morphological appearance and thermophysical characteristics before using in FO experiments. It is found that the osmotic pressure and water flux of the novel DS are directly dependent on the concentration of K/CNF and TEG. The draw solution is re-concentrated by evaporating the water aided by the highly solar absorptive K/CNF under simulated solar flux. The vapours are condensed and the quality of product water is found to be comparable with potable water standard. The novel concept proposed in this study has the potential to be used in arid areas where solar energy is abundant to fulfil the potable water needs

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing