Compact cancer biomarkers discovery using a swarm intelligence feature selection algorithm

Biomarker discovery is a typical application from functional genomics. Due to the large number of genes studied simultaneously in microarray data, feature selection is a key step. Swarm intelligence has emerged as a solution for the feature selection problem. However, swarm intelligence settings for feature selection fail to select small features subsets. We have proposed a swarm intelligence feature selection algorithm based on the initialization and update of only a subset of particles in the swarm. In this study, we tested our algorithm in 11 microarray datasets for brain, leukemia, lung, prostate, and others. We show that the proposed swarm intelligence algorithm successfully increase the classification accuracy and decrease the number of selected features compared to other swarm intelligence methods.     

Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015

We describe binding free energy calculations in the D3R Grand Challenge 2015 for blind prediction of the binding affinities of 180 ligands to Hsp90. The present D3R challenge was built around experimental datasets involving Heat shock protein (Hsp) 90, an ATP-dependent molecular chaperone which is an important anticancer drug target. The Hsp90 ATP binding site is known to be a challenging target for accurate calculations of ligand binding affinities because of the ligand-dependent conformational changes in the binding site, the presence of ordered waters and the broad chemical diversity of ligands that can bind at this site. Our primary focus here is to distinguish binders from nonbinders. Large scale absolute binding free energy calculations that cover over 3000 protein–ligand complexes were performed using the BEDAM method starting from docked structures generated by Glide docking. Although the ligand dataset in this study resembles an intermediate to late stage lead optimization project while the BEDAM method is mainly developed for early stage virtual screening of hit molecules, the BEDAM binding free energy scoring has resulted in a moderate enrichment of ligand screening against this challenging drug target. Results show that, using a statistical mechanics based free energy method like BEDAM starting from docked poses offers better enrichment than classical docking scoring functions and rescoring methods like Prime MM-GBSA for the Hsp90 data set in this blind challenge. Importantly, among the three methods tested here, only the mean value of the BEDAM binding free energy scores is able to separate the large group of binders from the small group of nonbinders with a gap of 2.4 kcal/mol. None of the three methods that we have tested provided accurate ranking of the affinities of the 147 active compounds. We discuss the possible sources of errors in the binding free energy calculations. The study suggests that BEDAM can be used strategically to discriminate binders from nonbinders in virtual screening and to more accurately predict the ligand binding modes prior to the more computationally expensive FEP calculations of binding affinity.     

Studies of Protonation of Some Aminopolycarboxylates by Carbon-13 NMR Spectroscopy

¹³C nmr chemical shifts are used to evaluate successive protonations of the aminopolycarboxylate systems diethylenetriaminepentaacetic acid (DTPA) and triethylenetetraminehexaacetic acid (TTHA).     

Orbital pair theory of N.M.R. shielding

A simple correction accounting for the effect of truncating the atomic orbital basis on the calculation of N.M.R. shielding is proposed. This correction is obtained from the expression for the magnetic shielding as a sum of orbital pair contributions: a spurious term that vanishes only if a complete basis is used appears in this expression. It is demonstrated both theoretically and numerically (using the example of PH₃) that removing this term from the results obtained with a truncated basis improves significantly the agreement with the experimental values. As a by-product the gauge dependence of the numerical results is much reduced. The additional computing time is negligible.     

Polymerization of Cyclic Imino Ethers. X. Kinetics,Chain Transfer,and Repolymerization

The main conclusions in studies on polymerization catalysts and the nature of chain transfer in the polymerization of cyclic imino ethers were that there is extensive chain transfer in the 2-alkyl oxazolines to produce polymer with a reactive end. Toward the end of polymerization, these chain-transferred molecules repolymerize back on the active center producing a multibranched star polymer. A theory for the data was developed.     

Electrical control of the direction of spin accumulation

We are able to continuously change the direction of polarization of spin accumulation in a nonmagnetic metal by varying the currents injected by two ferromagnetic spin injectors. From measurements made at a distance from the injection area, we find a cosvarphi variation of the spin signal. This confirms that the angle of polarization of the nonlocal spin polarization with respect to the magnetization of the fixed spin detector is continuously varied as we change the injection currents. We give an explanation for the origin of this simple cosvarphi variation of the spin signal.     

Magnetic-field effects on the size of vortices below the surface of NbSe2 detected using low energy beta-NMR

A low energy radioactive beam of polarized 8Li has been used to observe the vortex lattice near the surface of superconducting NbSe2. The inhomogeneous magnetic-field distribution associated with the vortex lattice was measured using depth-resolved beta-detected NMR. Below Tc, one observes the characteristic line shape for a triangular vortex lattice which depends on the magnetic penetration depth and vortex core radius. The size of the vortex core varies strongly with the magnetic field. In particular, in a low field of 10.8 mT, the core radius is much larger than the coherence length. The possible origin of these giant vortices is discussed.     

Effects produced by metal-coated near-field probes on the performance of silicon waveguides and resonators

We study the effects of metal-coated fiber near-field probes on the performance of nanophotonic devices. Employing a heterodyne near-field scanning optical microscope and analyzing transmission characteristics, we find that a metal-coated probe can typically introduce a 3 dB intensity loss and a 0.2 rad phase shift during characterization of a straight waveguide made in a silicon-on-insulator system. In resonant nanophotonic structures such as a 5 mum radius microring resonator, we demonstrate that the probe induces a 1 nm shift in resonant wavelength and decreases the resonator quality factor, Q, from 1100 to 480.