An effective procedure for feature subset selection in logistic regression based on information criteria

Computational Optimization and Applications - In this paper, the problem of best subset selection in logistic regression is addressed. In particular, we take into account formulations of the...     

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

Solvated interaction energy (SIE) is an end-point physics-based scoring function for predicting binding affinities from force-field nonbonded interaction terms, continuum solvation, and configurational entropy linear compensation. We tested the SIE function in the Community Structure-Activity Resource (CSAR) scoring challenge consisting of high-resolution cocrystal structures for 343 protein-ligand complexes with high-quality binding affinity data and high diversity with respect to protein targets. Particular emphasis was placed on the sensitivity of SIE predictions to the assignment of protonation and tautomeric states in the complex and the treatment of metal ions near the protein-ligand interface. These were manually curated from an originally distributed CSAR-HiQ data set version, leading to the currently distributed CSAR-NRC-HiQ version. We found that this manual curation was a critical step for accurately testing the performance of the SIE function. The standard SIE parametrization, previously calibrated on an independent data set, predicted absolute binding affinities with a mean-unsigned-error (MUE) of 2.41 kcal/mol for the CSAR-HiQ version, which improved to 1.98 kcal/mol for the upgraded CSAR-NRC-HiQ version. Half-half retraining-testing of SIE parameters on two predefined subsets of CSAR-NRC-HiQ led to only marginal further improvements to an MUE of 1.83 kcal/mol. Hence, we do not recommend altering the current default parameters of SIE at this time. For a sample of SIE outliers, additional calculations by molecular dynamics-based SIE averaging with or without incorporation of ligand strain, by MM-PB(GB)/SA methods with or without entropic estimates, or even by the linear interaction energy (LIE) formalism with an explicit solvent model, did not further improve predictions.     

Comparison of mass transfer models for the numerical prediction of sheet cavitation around a hydrofoil

Cavitating flows, which can occur in a variety of practical cases, can be modelled with a wide range of methods. One strategy consists of using the RANS (Reynolds Averaged Navier Stokes) equations and an additional transport equation for the liquid volume fraction, where mass transfer rate due to cavitation is modelled by a mass transfer model. In this study, we compare three widespread mass transfer models available in literature for the prediction of sheet cavitation around a hydrofoil. These models share the common feature of employing empirical coefficients, to tune the models of condensation and evaporation processes, that can influence the accuracy and stability of the numerical predictions. In order to compare the different mass transfer models fairly and congruently, the empirical coefficients of the different models are first well tuned using an optimization strategy. The resulting well tuned mass transfer models are then compared considering the flow around the NACA66(MOD) and NACA009 hydrofoils. The numerical predictions based on the three different tuned mass transfer models are very close to each other and in agreement with the experimental data. Moreover, the optimization strategy seems to be stable and accurate, and could be extended to additional mass transfer models and further flow problems.     

Use of titanium dioxide photocatalysis on the remediation of model textile wastewaters containing azo dyes

The photocatalytic degradation of two commercial textile azo dyes, namely C.I Reactive Black 5 and C.I Reactive Red 239, has been studied. TiO(2) P25 Degussa was used as catalyst and photodegradation was carried out in aqueous solution under artificial irradiation with a 125 W mercury vapor lamp. The effects of the amount of TiO(2) used, UV-light irradiation time, pH of the solution under treatment, initial concentration of the azo dye and addition of different concentrations of hydrogen peroxide were investigated. The effect of the simultaneous photodegradation of the two azo dyes was also investigated and we observed that the degradation rates achieved in mono and bi-component systems were identical. The repeatability of photocatalytic activity of the photocatalyst was also tested. After five cycles of TiO(2) reuse the rate of colour lost was still 77% of the initial rate. The degradation was followed monitoring the change of azo dye concentration by UV-Vis spectroscopy. Results show that the use of an efficient photocatalyst and the adequate selection of optimal operational parameters may easily lead to a complete decolorization of the aqueous solutions of both azo dyes.     

Charge exchange in collisions of beryllium with its ion

Close-coupling calculations of the resonance and near resonance charge exchange in ion-atom collisions of Be at low and intermediate energies are presented. Accurate ab initio calculations are carried out of the Born-Oppenheimer potentials and the non-adiabatic couplings that are due to the finite nuclear masses and drive the near resonance charge exchange. We show that the near resonance charge exchange cross section follows Wigner's threshold law of inelastic processes for energies below 10(-8) eV and that the zero temperature rate constant for it is 4.5 × 10(-10) cm(3) s(-1). At collision energies much larger than the isotope shift of the ionization potentials of the atoms, we show that the near resonance charge exchange process is equivalent to the resonance charge exchange with cross sections having a logarithmic dependence. We also investigate the perturbation to the charge exchange process due to the non-adiabatic interaction to an electronic excited state. We show that the influence is negligible at low temperatures and still small at intermediate energies despite the presence of resonances.     

Guest-controlled aggregation of cavitand gold nanoparticles and N-methyl pyridinium-terminated PEG

The introduction of a disulfide functionalized tetraphosphonate cavitand on Au nanoparticles promotes the reversible self-assembly of a hybrid network upon addition of a polymeric ditopic guest.     

Structural properties of semilinear SPDEs driven by cylindrical stable processes

We consider a class of semilinear stochastic evolution equations driven by an additive cylindrical stable noise. We investigate structural properties of the solutions like Markov, irreducibility, stochastic continuity, Feller and strong Feller properties, and study integrability of trajectories. The obtained results are applied to semilinear stochastic heat equations with Dirichlet boundary conditions and bounded and Lipschitz nonlinearities.     

Monotonicity constraints and supercritical Neumann problems

We prove the existence of a positive and radially increasing solution for a semilinear Neumann problem on a ball. No growth conditions are imposed on the nonlinearity. The method introduces monotonicity constraints which simplify the existence of a minimizer for the associated functional. Special care must be employed to establish the validity of the Euler equation.     

An exact approach for the Vertex Coloring Problem

Given an undirected graph $G=(V,E)$, the Vertex Coloring Problem (VCP) requires to assign a color to each vertex in such a way that colors on adjacent vertices are different and the number of colors used is minimized. In this paper, we present an exact algorithm for the solution of VCP based on the well-known Set Covering formulation of the problem. We propose a Branch-and-Price algorithm embedding an effective heuristic from the literature and some methods for the solution of the slave problem, as well as two alternative branching schemes. Computational experiments on instances from the literature show the effectiveness of the algorithm, which is able to solve, for the first time to proven optimality, five of the benchmark instances in the literature, and reduce the optimality gap of many others.     

Reaction of singlet oxygen with thioanisole in ionic liquid-acetonitrile binary mixtures

A study of the reaction of thioanisole with singlet oxygen in different ionic liquid-acetonitrile binary mixtures has shown that ILs are able to accelerate the thioanisole sulfoxidation when used as additives. With imidazolium ILs, the maximum efficiency is reached at x(IL) ～ 0.1-0.2, whereas for the pyrrolidinium IL a plateau is reached. These results are discussed in terms of the ILs' tendency to form ionic aggregates and of differences in sulfoxidation reaction mechanism.