On Optimization Modulo Theories, MaxSMT and Sorting Networks

Optimization Modulo Theories (OMT) is an extension of SMT which allows for finding models that optimize given objectives. (Partial weighted) MaxSMT --or equivalently OMT with Pseudo-Boolean objective functions, OMT+PB-- is a very-relevant strict subcase of OMT. We classify existing approaches for MaxSMT or OMT+PB in two groups: MaxSAT-based approaches exploit the efficiency of state-of-the-art MAXSAT solvers, but they are specific-purpose and not always applicable; OMT-based approaches are general-purpose, but they suffer from intrinsic inefficiencies on MaxSMT/OMT+PB problems. We identify a major source of such inefficiencies, and we address it by enhancing OMT by means of bidirectional sorting networks. We implemented this idea on top of the OptiMathSAT OMT solver. We run an extensive empirical evaluation on a variety of problems, comparing MaxSAT-based and OMT-based techniques, with and without sorting networks, implemented on top of OptiMathSAT and {\nu}Z. The results support the effectiveness of this idea, and provide interesting insights about the different approaches.Comment: 17 pages, submitted at Tacas 1

The Structure of β-Carbonic Anhydrase from the Carboxysomal Shell Reveals a Distinct Subclass with One Active Site for the Price of Two

CsoSCA (formerly CsoS3) is a bacterial carbonic anhydrase localized in the shell of a cellular microcompartment called the carboxysome, where it converts HCO-3 to CO2 for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (RuBisCO). CsoSCA lacks significant sequence similarity to any of the four known classes of carbonic anhydrase (α, β, γ, or δ), and so it was initially classified as belonging to a new class, ϵ. The crystal structure of CsoSCA from Halothiobacillus neapolitanus reveals that it is actually a representative member of a new subclass of β-carbonic anhydrases, distinguished by a lack of active site pairing. Whereas a typical β-carbonic anhydrase maintains a pair of active sites organized within a two-fold symmetric homodimer or pair of fused, homologous domains, the two domains in CsoSCA have diverged to the point that only one domain in the pair retains a viable active site. We suggest that this defunct and somewhat diminished domain has evolved a new function, specific to its carboxysomal environment. Despite the level of sequence divergence that separates CsoSCA from the other two subclasses of β-carbonic anhydrases, there is a remarkable level of structural similarity among active site regions, which suggests a common catalytic mechanism for the interconversion of HCO-3 and CO2. Crystal packing analysis suggests that CsoSCA exists within the carboxysome shell either as a homodimer or as extended filaments

Electrospray Ionization Mass Spectrometry Fingerprinting Of Propolis.

Crude ethanolic extracts of propolis, a natural resin, have been directly analysed using electrospray ionization mass (ESI-MS) and tandem mass spectrometry (ESI-MS/MS) in the negative ion mode. European, North American and African samples have been analyzed, but emphasis has been given to Brazilian propolis which displays diverse and region-dependent chemical composition. ESI-MS provides characteristic fingerprint mass spectra, with propolis samples being divided into well-defined groups directly related to their geographical origins. Chemometric multivariate analysis statistically demonstrates the reliability of the ESI-MS fingerprinting method for propolis. On-line ESI-MS/MS tandem mass spectrometry of characteristic [M - H](-) ion markers provides an additional dimension of fingerprinting selectivity, while structurally characterizing the ESI-MS marker components of propolis. By comparison with standards, eight such markers have been identified: para-coumaric acid, 3-methoxy-4-hydroxycinnamaldehyde, 2,2-dimethyl-6-carboxyethenyl-2H-1-benzopyran, 3-prenyl-4-hydroxycinnamic acid, chrysin, pinocembrin, 3,5-diprenyl-4-hydroxycinnamic acid and dicaffeoylquinic acid. The negative mode ESI-MS fingerprinting method is capable of discerning distinct composition patterns to typify, to screen the sample origin and to reveal characteristic details of the more polar and acidic chemical components of propolis samples from different regions of the world.129739-4

Charge redistribution at Pd surfaces: ab initio grounds for tight-binding interatomic potentials

A simplified tight-binding description of the electronic structure is often necessary for complex studies of surfaces of transition metal compounds. This requires a self-consistent parametrization of the charge redistribution, which is not obvious for late transition series elements (such as Pd, Cu, Au), for which not only d but also s-p electrons have to be taken into account. We show here, with the help of an ab initio FP-LMTO approach, that for these elements the electronic charge is unchanged from bulk to the surface, not only per site but also per orbital. This implies different level shifts for each orbital in order to achieve this orbital neutrality rule. Our results invalidate any neutrality rule which would allow charge redistribution between orbitals to ensure a common rigid shift for all of them. Moreover, in the case of Pd, the power law which governs the variation of band energy with respect to coordination number, is found to differ significantly from the usual tight-binding square root.Comment: 6 pages, 2 figures, Latex; Phys.Rev. B 56 (1997

Structural Analysis of CsoS1A and the Protein Shell of the \u3ci\u3eHalothiobacillus neapolitanus\u3c/i\u3e Carboxysome

The carboxysome is a bacterial organelle that functions to enhance the efficiency of CO2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/ oxygenase (RuBisCO) and carbonic anhydrase. The outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. Here we describe the structure of the shell protein CsoS1A from the chemoautotrophic bacterium Halothiobacillus neapolitanus. The CsoS1A protein forms hexameric units that pack tightly together to form a molecular layer, which is perforated by narrow pores. Sulfate ions, soaked into crystals of CsoS1A, are observed in the pores of the molecular layer, supporting the idea that the pores could be the conduit for negatively charged metabolites such as bicarbonate, which must cross the shell. The problem of diffusion across a semiporous protein shell is discussed, with the conclusion that the shell is sufficiently porous to allow adequate transport of small molecules. The molecular layer formed by CsoS1A is similar to the recently observed layers formed by cyanobacterial carboxysome shell proteins. This similarity supports the argument that the layers observed represent the natural structure of the facets of the carboxysome shell. Insights into carboxysome function are provided by comparisons of the carboxysome shell to viral capsids, and a comparison of its pores to the pores of transmembrane protein channels

Analytical methods applied to diverse types of Brazilian propolis

Propolis is a bee product, composed mainly of plant resins and beeswax, therefore its chemical composition varies due to the geographic and plant origins of these resins, as well as the species of bee. Brazil is an important supplier of propolis on the world market and, although green colored propolis from the southeast is the most known and studied, several other types of propolis from Apis mellifera and native stingless bees (also called cerumen) can be found. Propolis is usually consumed as an extract, so the type of solvent and extractive procedures employed further affect its composition. Methods used for the extraction; analysis the percentage of resins, wax and insoluble material in crude propolis; determination of phenolic, flavonoid, amino acid and heavy metal contents are reviewed herein. Different chromatographic methods applied to the separation, identification and quantification of Brazilian propolis components and their relative strengths are discussed; as well as direct insertion mass spectrometry fingerprinting

A Global Health Research Checklist for clinicians.

Global health research has become a priority in most international medical projects. However, it is a difficult endeavor, especially for a busy clinician. Navigating the ethics, methods, and local partnerships is essential yet daunting.To date, there are no guidelines published to help clinicians initiate and complete successful global health research projects. This Global Health Research Checklist was developed to be used by clinicians or other health professionals for developing, implementing, and completing a successful research project in an international and often low-resource setting. It consists of five sections: Objective, Methodology, Institutional Review Board and Ethics, Culture and partnerships, and Logistics. We used individual experiences and published literature to develop and emphasize the key concepts. The checklist was trialed in two workshops and adjusted based on participants\u27 feedback