Best practices in measuring algorithm performance for dynamic optimization problems

Dynamic optimization problems (DOPs) have attracted considerable attention due to the wide range of problems they can be applied to. Lots of efforts have been expended in modeling dynamic situations, proposing algorithms, and analyzing the results (too often in a visual way). Numeric performance measurements and their statistical validation have been however barely used in the literature. Most of works in DOPs report only the best-of-generation fitness, due to its simplicity of computation. Although this measure indicates the best algorithm in terms of fitness, it does not provide any details about the actual strength and weakness of each algorithm. In this article, we conduct a comparative study among algorithms of different search modes via several performance measures to demonstrate their relative advantages. We discuss the role of using different performance measures in drawing balanced conclusions about algorithms for DOPs.     

Dealing with hardware heterogeneity: a new parallel search model

In this article we present Ethane, a parallel heterogeneous metaheuristic model specifically designed for its execution on heterogeneous hardware environments. With Ethane we propose a hybrid parallel search algorithm inspired in the structure of the chemical compound of the same name, implementing a heterogeneous island model based in the structure of the chemical bonds of the ethane compound. Here we also shape a schema for describing a complete family of parallel heterogeneous metaheuristics inspired by the structure of hydrocarbons in nature, HydroCM (HydroCarbon inspired Metaheuristics), establishing a resemblance between atoms and computers, and between chemical bonds and communication links. Our goal is to gracefully match computers of different computing power to algorithms of different behavior (genetic algorithm and simulated annealing in this study), all them collaborating to solve the same problem. In addition to the nice natural metaphor we will show that Ethane, though simple, can solve search problems in a faster and more robust way than well-known panmictic and distributed algorithms very popular in the literature, as well as can achieve a better exploration/exploitation balance during the search process.     

Tart Cherries and health: Current knowledge and need for a better understanding of the fate of phytochemicals in the human gastrointestinal tract

Tart cherries are increasingly popular due to purported health benefits. This Prunus cesarus species is cultivated worldwide, and its market has increased significantly in the last two decades due to improvements in agricultural practices and food processing technology. Tart cherries are rich in polyphenols, with a very specific profile combining anthocyanins and flavonols (berries-like) and chlorogenic acid (coffee-like). Tart cherries have been suggested to exert several potentially beneficial health effects including: lowering blood pressure, modulating blood glucose, enhancing cognitive function, protecting against oxidative stress and reducing inflammation. Studies focusing on tart cherry consumption have demonstrated particular benefits in recovery from exercise-induced muscle damage and diabetes associated parameters. However, the bioconversion of tart cherry polyphenols by resident colonic microbiota has never been considered, considerably reducing the impact of in vitro studies that have relied on fruit polyphenol extracts. In vitro and in vivo gut microbiota and metabolome studies are necessary to reinforce health claims linked to tart cherries consumption.     

Effect of Trichoderma asperellum on Wheat Plants’ Biochemical and Molecular Responses,and Yield under Different Water Stress Conditions

Eight Trichoderma strains were evaluated for their potential to protect wheat seedlings against severe (no irrigation within two weeks) water stress (WS). Considering the plant fresh weight and phenotype, T. asperellum T140, which displays 1-aminocyclopropane-1-carboxylic acid deaminase activity and which is able to produce several phytohormones, was selected. The molecular and biochemical results obtained from 4-week-old wheat seedlings linked T140 application with a downregulation in the WS-response genes, a decrease in antioxidant activities, and a drop in the proline content, as well as low levels of hydrogen peroxide and malondialdehyde in response to severe WS. All of these responses are indicative of T140-primed seedlings having a higher tolerance to drought than those that are left untreated. A greenhouse assay performed under high nitrogen fertilization served to explore the long-term effects of T140 on wheat plants subjected to moderate (halved irrigation) WS. Even though all of the plants showed acclimation to moderate WS regardless of T140 application, there was a positive effect exerted by T. asperellum on the level of tolerance of the wheat plants to this stress. Strain T140 modulated the expression of a plant ABA-dependent WS marker and produced increased plant superoxide dismutase activity, which would explain the positive effect of Trichoderma on increasing crop yields under moderate WS conditions. The results demonstrate the effectiveness of T. asperellum T140 as a biostimulant for wheat plants under WS conditions, making them more tolerant to drought.     

Yttrium incorporation in Cr2AlC: On the metastable phase formation and decomposition of (Cr,Y)2AlC MAX phase thin films

Herein we report on the synthesis of a metastable (Cr,Y)₂AlC MAX phase solid solution by co-sputtering from a composite Cr–Al–C and elemental Y target, at room temperature, followed by annealing. However, direct high-temperature synthesis resulted in multiphase films, as evidenced by X-ray diffraction analyses, room-temperature depositions, followed by annealing to 760°C led to the formation of phase pure (Cr,Y)₂AlC by diffusion. Higher annealing temperatures caused a decomposition of the metastable phase into Cr₂AlC, Y₅Al₃, and Cr-carbides. In contrast to pure Cr₂AlC, the Y-containing phase crystallizes directly in the MAX phase structure instead of first forming a disordered solid solution. Furthermore, the crystallization temperature was shown to be Y-content dependent and was increased by ∼200°C for 5 at.% Y compared to Cr₂AlC. Calculations predicting the metastable phase formation of (Cr,Y)₂AlC and its decomposition are in excellent agreement with the experimental findings.     

Identification of Hck Inhibitors As Hits for the Development of Antileukemia and Anti‐HIV Agents

Hematopoietic cell kinase (Hck) is a member of the Src family of non‐receptor protein tyrosine kinases. High levels of Hck are associated with drug resistance in chronic myeloid leukemia. Furthermore, Hck activity has been connected with HIV‐1. Herein, structure‐based drug design efforts were aimed at identifying novel Hck inhibitors. First, an in‐house library of pyrazolo[3,4‐d]pyrimidine derivatives, which were previously shown to be dual Abl and c‐Src inhibitors, was analyzed by docking studies within the ATP binding site of Hck to select the best candidates to be tested in a cell‐free assay. Next, the same computational protocol was applied to screen a database of commercially available compounds. As a result, most of the selected compounds were found active against Hck, with K_i values ranging from 0.14 to 18.4 μM , confirming the suitability of the computational approach adopted. Furthermore, selected compounds showed an interesting antiproliferative activity profile against the human leukemia cell line KU‐812, and one compound was found to block HIV‐1 replication at sub‐toxic concentrations.     

Biodegradable composites with improved barrier properties and transparency from the impregnation of PLA to bacterial cellulose membranes

Poly(lactic acid) (PLA) was impregnated in bacterial cellulose (BC) membranes. BC/PLA films were prepared by solvent casting and mechanical, optical and barrier properties, and biodegradation process were investigated. The transparency of processed films was higher than that of neat BC and increased with PLA content. Moreover, the incorporation of PLA to BC enhanced significantly the water vapor barrier properties of the BC membranes. The bionanocomposites contained a high percentage of cellulose due to the impregnation method that leads to the film with a BC content of 94%, which practically maintains the excellent mechanical properties of BC. However, when increasing the PLA content in the bionanocomposites the mechanical properties decreased slightly with respect to BC. Biodegradation under real soil conditions was determined indirectly through the study of the visual degradation and disintegration, demonstrating that the bionanocomposites were degraded faster than the neat PLA. The successful production of BC/PLA bionanocomposites suggested the possible application of them for active food packaging. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 43669.     

Regulation of Phosphatidic Acid Levels in <Emphasis Type="Italic">Trypanosoma cruzi</Emphasis>

Lipid kinases and phosphatases play essential roles in signal transduction processes involved in cytoskeletal rearrangement, membrane trafficking, and cellular differentiation. Phosphatidic acid (PtdOH) is an important mediator lipid in eukaryotic cells, but little is known regarding its regulation in the parasite Trypanosoma cruzi, an agent of Chagas disease. In order to clarify the relationship between PtdOH metabolism and developmental stages of T. cruzi, epimastigotes in culture were subjected to hyperosmotic stress (~1,000 mOsm/L), mimicking the environment in the rectum of vector triatomine bugs. These experimental conditions resulted in differentiation to an intermediate form between epimastigotes and trypomastigotes. Morphological changes of epimastigotes were correlated with an increase in PtdOH mass accomplished by increased enzyme activity of diacylglycerol kinase (DAGK, E.C. 2.7.1.107) and concomitant decreased activity of phosphatidate phosphatases type 1 and type 2 (PAP1, PAP2, E.C. 3.1.3.4). Our results indicate progressive increases of PtdOH levels during the differentiation process, and suggest that the regulation of PtdOH metabolism is an important mechanism in the transition from T. cruzi epimastigote to intermediate form.