Bayesian modeling of recombination events in bacterial populations

Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/ mnf//mate/jc/software/brat.html

A multiscale method for optimising surface topography in elastohydrodynamic lubrication (EHL) using metamodels

The frictional performance of a bearing is of significant interest in any mechanical system where there are lubricated surfaces under load and in relative motion. Surface topography plays a major role in determining the coefficient of friction for the bearing because the size of the fluid film and topography are of a comparable order. The problem of optimising topography for such a system is complicated by the separation in scales between the size of the lubricated domain and that of the topography, which is of at least one order of magnitude or more smaller. This paper introduces a multiscale method for optimising the small scale topography for improved frictional performance of the large scale bearing. The approach fully couples the elastohydrodynamic lubrication at both scales between pressure generated in the lubricant and deformation of the bounding surfaces. Homogenised small scale data is used to inform the large scale model and is represented using Moving Least Squares metamodels calibrated by cross validation. An optimal topography for a minimum coefficient of friction for the bearing is identified and comparisons made of local minima in the response, where very different topographies with similar frictional performance are observed. Comparisons of the optimal topography with the smooth surface model demonstrated the complexity of capturing the non-linear effect of topography and the necessity of the multiscale method in capturing this. Deviations from the smooth surface model were quantified by the metamodel coefficients and showed how topographies with a similar frictional performance have very different characteristics

Botulinum toxin type-A in the prophylactic treatment of medication-overuse headache: a multicenter, double-blind, randomized, placebo-controlled, parallel group study

Medication-overuse headache (MOH) represents a severely disabling condition, with a low response to prophylactic treatments. Recently, consistent evidences have emerged in favor of botulinum toxin type-A (onabotulinum toxin A) as prophylactic treatment in chronic migraine. In a 12-week double-blind, parallel group, placebo-controlled study, we tested the efficacy and safety of onabotulinum toxin A as prophylactic treatment for MOH. A total of 68 patients were randomized (1:1) to onabotulinum toxin A (n = 33) or placebo (n = 35) treatment and received 16 intramuscular injections. The primary efficacy end point was mean change from baseline in the frequency of headache days for the 28-day period ending with week 12. No significant differences between onabotulinum toxin A and placebo treatment were detected in the primary (headache days) end point (12.0 vs. 15.9; p = 0.81). A significant reduction was recorded in the secondary end point, mean acute pain drug consumption at 12 weeks in onabotulinum toxin A-treated patients when compared with those with placebo (12.1 vs. 18.0; p = 0.03). When we considered the subgroup of patients with pericranial muscle tenderness, we recorded a significant improvement in those treated with onabotulinum toxin A compared to placebo treated in both primary (headache days) and secondary end points (acute pain drug consumption, days with drug consumption), as well as in pain intensity and disability measures (HIT-6 and MIDAS) at 12 weeks. Onabotulinum toxin A was safe and well tolerated, with few treatment-related adverse events. Few subjects discontinued due to adverse events. Our data identified the presence of pericranial muscle tenderness as predictor of response to onabotulinum toxin A in patients with complicated form of migraine such as MOH, the presence of pericranial muscle tenderness and support it as prophylactic treatment in these patients

Boundary Conditions for Elastohydrodynamics of Circular Point Contacts

The paper presents the solution of an elastohydrodynamic point contact condition using inlet and outlet lubricant entrainment with partial counter-flow. The inlet and outlet boundaries are determined using potential flow analysis for the pure rolling of contiguous surfaces. This shows that Swift–Stieber boundary conditions best conform to the observed partial counter-flow at the inlet conjunction, satisfying the compatibility condition. For the outlet region, the same is true when Prandtl–Hopkins boundary conditions are employed. Using these boundary conditions, the predictions conform closely to the measured pressure distribution using a deposited pressure-sensitive micro-transducer in a ball-to-flat race contact. Furthermore, the predicted conjunctional shape closely conforms to the often observed characteristic keyhole conjunction through optical interferometry. The combined numerical–experimental analysis with realistic boundary conditions described here has not hitherto been reported in the literature

Continuously Adjustable, Molecular-Sieving "Gate" on 5A Zeolite for Distinguishing Small Organic Molecules by Size

Zeolites/molecular sieves with uniform, molecular-sized pores are important for many adsorption-based separation processes. Pore size gaps, however, exist in the current zeolite family. This leads to a great challenge of separating molecules with size differences at ~0.01 nm level. Here, we report a novel concept, pore misalignment, to form a continuously adjustable, molecular-sieving “gate” at the 5A zeolite pore entrance without sacrificing the internal capacity. Misalignment of the micropores of the alumina coating with the 5A zeolite pores was related with and facilely adjusted by the coating thickness. For the first time, organic molecules with sub-0.01 nm size differences were effectively distinguished via appropriate misalignment. This novel concept may have great potential to fill the pore size gaps of the zeolite family and realize size-selective adsorption separation

Italian guidelines for primary headaches: 2012 revised version

The first edition of the Italian diagnostic and therapeutic guidelines for primary headaches in adults was published in J Headache Pain 2(Suppl. 1):105–190 (2001). Ten years later, the guideline committee of the Italian Society for the Study of Headaches (SISC) decided it was time to update therapeutic guidelines. A literature search was carried out on Medline database, and all articles on primary headache treatments in English, German, French and Italian published from February 2001 to December 2011 were taken into account. Only randomized controlled trials (RCT) and meta-analyses were analysed for each drug. If RCT were lacking, open studies and case series were also examined. According to the previous edition, four levels of recommendation were defined on the basis of levels of evidence, scientific strength of evidence and clinical effectiveness. Recommendations for symptomatic and prophylactic treatment of migraine and cluster headache were therefore revised with respect to previous 2001 guidelines and a section was dedicated to non-pharmacological treatment. This article reports a summary of the revised version published in extenso in an Italian version