A hierarchical multi-label classification ant colony algorithm for protein function prediction

This paper proposes a novel ant colony optimisation (ACO) algorithm tailored for the hierarchical multi-label classification problem of protein function prediction. This problem is a very active research field, given the large increase in the number of uncharacterised proteins available for analysis and the importance of determining their functions in order to improve the current biological knowledge. Since it is known that a protein can perform more than one function and many protein functional-definition schemes are organised in a hierarchical structure, the classification problem in this case is an instance of a hierarchical multi-label problem. In this type of problem, each example may belong to multiple class labels and class labels are organised in a hierarchical structure—either a tree or a directed acyclic graph structure. It presents a more complex problem than conventional flat classification, given that the classification algorithm has to take into account hierarchical relationships between class labels and be able to predict multiple class labels for the same example. The proposed ACO algorithm discovers an ordered list of hierarchical multi-label classification rules. It is evaluated on sixteen challenging bioinformatics data sets involving hundreds or thousands of class labels to be predicted and compared against state-of-the-art decision tree induction algorithms for hierarchical multi-label classification.     

Optical Diagnosis for Thyroid and Parathyroid Tissues—A Review

Abstract

This article presents an overview of optical methodologies to aid the diagnosis and differentiation of thyroid and parathyroid tissues. In particular, we review the several techniques and associated methodologies that allow in vivo and ex vivo optical characterization of thyroid and parathyroid tissues. Emphasis is placed on the research potential of these techniques and whether intrinsic characteristics can provide useful contrast for the diagnosis of human thyroid and parathyroid malignant lesions.     

Growth of tertiary dendritic arms during the transient directional solidification of hypoeutectic Pb–Sb alloys

Despite the importance of a complete characterization of dendritic patterns in castings, the availability of studies on the development of tertiary dendrite arms is scarce in the literature. In the present study, the tip cooling rate, local solidification time, primary and tertiary dendrite arm spacings have been determined in Pb–Sb alloys castings directionally solidified under unsteady-state heat flow conditions. The alloys compositions experimentally examined are widely used in the as-cast condition for the manufacture of positive and negative grids of lead-acid batteries. The initial growth of tertiary dendritic arms from the secondary branches was found to occur only for a Pb–3.5 wt% Sb alloy at cooling rates in the range 0.4–0.2?K/s, with no evidence of this spacing pattern for Pb–Sb alloys having lower solute content. Tertiary dendritic branches have been observed along the entire casting lengths for alloys of the Pb–Sb hypoeutectic range having compositions higher than 4.0 wt% Sb. It is shown that a power function experimental law with a characteristic ?0.55 exponent is able to characterize the tertiary spacing evolution with the solidification cooling rate for alloys compositions ≥4.0 wt% Sb. The only exception was the Pb–3.5 wt% Sb alloy for which λ ₃ exhibited significant lower values when compared with the experimental values obtained for the other Pb–Sb alloys for a same solidification cooling rate.     

Raman spectroscopy of very small Cd1−xCoxS quantum dots grown by a novel protocol: direct observation of acoustic‐optical phonon coupling

Glass‐embedded Cd_1−xCo_xS quantum dots (QDs) with mean radius of R ≈ 1.70 nm were successfully synthesized by a novel protocol on the basis of the melting‐nucleation synthesis route and herein investigated by several experimental techniques. Incorporation of Co²⁺ ions into the QD lattice was evidenced by X‐ray diffraction and magnetic force microscopy results. Optical absorption features with irregular spacing in the ligand field region confirmed that the majority of the incorporated Co²⁺ ions are under influence of a low‐symmetry crystal field located near to the Cd_1−xCo_xS QD surface. Electron paramagnetic resonance data confirmed the presence of Co²⁺ ions in a highly inhomogeneous crystal field environment identified at the interface between the hosting glass matrix (amorphous) and the crystalline QD. The acoustic‐optical phonon coupling in the Cd_1−xCo_xS QDs (x ≠ 0.000) was directly observed by Raman measurements, which have shown a high‐frequency shoulder of the longitudinal optical phonon peak. This effect is tuned by the size‐dependent sp‐d exchange interaction due to the magnetic doping, causing variations in the coupling between electrons and longitudinal optical phonon. Copyright © 2013 John Wiley & Sons, Ltd.     

Structural characterization of MnNi and MnPt antiferromagnetic materials for spintronic applications

MnNi and MnPt become antiferromagnetic (AFM) when annealed at high enough temperatures, for which a face-centered cubic (fcc) to face-centered tetragonal (fct) structural transition occurs. Thus, structural information is essential when optimizing exchange bias in these materials. We performed structural (X-ray diffraction), magnetic (Magneto-Optical Kerr effect) and magneto-transport (magnetoresistance) measurements on MnNi based spin valves subjected to different annealing procedures and MnPt/CoFe bilayers with different MnPt thicknesses. We show that high annealing temperatures can in fact lead to the fct antiferromagnetic phase in both materials, but the annealing procedure is also an important factor on the obtained exchange field values. Also, MnPt/CoFe bilayers allowed us to probe the influence of average AFM-grain size on exchange bias.     

Energy potential and thermogravimetric study of pyrolysis kinetics of biomass wastes

The use of agricultural wastes for energy conversion has been widely studied as renewable and carbon neutral energy sources. This paper aims to evaluate the energetic potential of six agricultural wastes—sugarcane bagasse, bean pods, corn stover, pineapple crown leaves, white cotton and natural coloured cotton stalks, through their characterization and pyrolysis kinetic study. The energetic potential of biomasses was evaluated by ultimate and proximate analysis, higher heating value (HHV), apparent density, and kinetic parameters of conversion and apparent activation energy (E_a) determined by Model-Free kinetics though thermogravimetric analysis data. The results indicate energetic density for dry basis biomasses, such as moisture content less than 7%, volatiles higher than 77% and moderate ash content. The HHVs were higher for the biomass with low O:C ratio. The E_a values increased with increasing O:C ratio and were also influenced by the biomass ash content. Among the studied biomasses, PCL are less explored for energy application, although the results confirm its potential for application in thermochemical processes such as pyrolysis or combustion.

     

Nonlinear modeling and analysis of rotors supported by magnetorheological squeeze film journal bearings

Meccanica - The driver coupled to a driven system through mechanical couplings is very common in rotating machinery. These couplings can present angular and parallel misalignments with more or less...     

Influence of stereoelectronic effects on the 1JC─F spin–spin coupling constant in fluorinated heterocyclic compounds

The Perlin effect and its analog for fluorinated compounds (the fluorine Perlin-like effect) manifest on one-bond C─H (C─F for the fluorine Perlin-like effect) spin–spin coupling constants (SSCCs) in six-membered rings. These effects can be useful to probe the stereochemistry (axial or equatorial) of the C─H and C─F bonds, respectively. The origin of these effects has been debatable in the literature as being due to hyperconjugative interactions, dipolar effects, and induced current density. Accordingly, a variety of model compounds has been used to probe such effects since the cyclohexanone carbonyl group and the endocyclic heteroatom lone pairs play different roles on the above-mentioned effects. Thus, the ¹J_C─F SSCC in fluorinated lactams and lactones were theoretically studied to gain further insight on the nature of the fluorine Perlin-like effect. In addition, because the intramolecular α-effect has recently gained attention for its importance in the reactivity and stereoelectronic interactions in peroxide compounds, some fluorinated 1,2-dioxanes and 1,2-dithianes were studied to evaluate the role of the α-effect on the behavior of ¹J_C─F SSCCs. Differently from fluorinated ketones and ethers, the fluorine Perlin-like effect in the amides and esters cannot be explained by hyperconjugative or dipolar interactions alone, because the resonance in these groups affect the ¹J_C─F values. The O─O and S─S-containing systems exhibit a strong fluorine Perlin-like effect, but unlike the α-effect, this behavior cannot be explained neither by hyperconjugation nor by dipolar interactions alone; the spatial proximity of the C─F and O─O/S─S bonds is proposed to affect the magnitude of the ¹J_C─F SSCC.