EASEA: specification and execution of evolutionary algorithms on GPGPU

EASEA is a framework designed to help non-expert programmers to optimize their problems by evolutionary computation. It allows to generate code targeted for standard CPU architectures, GPGPU-equipped machines as well as distributed memory clusters. In this paper, EASEA is presented by its underlying algorithms and by some example problems. Achievable speedups are also shown onto different NVIDIA GPGPUs cards for different optimization algorithm families.     

Broken symmetries and thermodynamic limit in quantum antiferromagnets

We study how the Néel order breaks the symmetries of the hamiltonian in quantum antiferromagnet. The construction of a quantum wave packet that mimics the classical groundstate implies the existence of an extensive number of states: 1) with an energy scale much smaller than the spin-waves excitations (magnons); 2) with well defined symmetries.For the case of the triangular lattice, we find that all necessary properties to obtain a Néel state are well verified, already on periodic samples as small as 21 spins. For this system, this is a new and strong evidence of Néel order in the thermodynamic limit.     

Structural studies on γ-MnO2 by transmission electron microscopy

Single-crystal electron diffraction patterns were obtained on five specimens of -MnO₂: one natural, two electrolytical (EMD) and two chemical (CMD) samples. EMDs are best described by the orthorhombic structure proposed by De Wolff which is derived from the ramsdellite structure. A CMD prepared from MnCO₃ fits the hexagonal cell of -MnO₂. Flaky grains from the natural sample and fibres from a CMD prepared from Mn(NO₃)₂ are hexagonal with a new cell:a 0.494,c 0.539 nm. No simple relation between chemical composition, morphology and structure could be found.     

Hyperhomocysteinemia and Cardiovascular Disease: Is the Adenosinergic System the Missing Link?

The influence of hyperhomocysteinemia (HHCy) on cardiovascular disease (CVD) remains unclear. HHCy is associated with inflammation and atherosclerosis, and it is an independent risk factor for CVD, stroke and myocardial infarction. However, homocysteine (HCy)-lowering therapy does not affect the inflammatory state of CVD patients, and it has little influence on cardiovascular risk. The HCy degradation product hydrogen sulfide (H₂S) is a cardioprotector. Previous research proposed a positive role of H₂S in the cardiovascular system, and we discuss some recent data suggesting that HHCy worsens CVD by increasing the production of H₂S, which decreases the expression of adenosine A_2A receptors on the surface of immune and cardiovascular cells to cause inflammation and ischemia, respectively.     

The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway.     

Cardiac Oxidative Signaling and Physiological Hypertrophy in the Na/K-ATPase α1s/sα2s/s Mouse Model of High Affinity for Cardiotonic Steroids

The Na/K-ATPase is the specific receptor for cardiotonic steroids (CTS) such as ouabain and digoxin. At pharmacological concentrations used in the treatment of cardiac conditions, CTS inhibit the ion-pumping function of Na/K-ATPase. At much lower concentrations, in the range of those reported for endogenous CTS in the blood, they stimulate hypertrophic growth of cultured cardiac myocytes through initiation of a Na/K-ATPase-mediated and reactive oxygen species (ROS)-dependent signaling. To examine a possible effect of endogenous concentrations of CTS on cardiac structure and function in vivo, we compared mice expressing the naturally resistant Na/K-ATPase α1 and age-matched mice genetically engineered to express a mutated Na/K-ATPase α1 with high affinity for CTS. In this model, total cardiac Na/K-ATPase activity, α1, α2, and β1 protein content remained unchanged, and the cardiac Na/K-ATPase dose–response curve to ouabain shifted to the left as expected. In males aged 3–6 months, increased α1 sensitivity to CTS resulted in a significant increase in cardiac carbonylated protein content, suggesting that ROS production was elevated. A moderate but significant increase of about 15% of the heart-weight-to-tibia-length ratio accompanied by an increase in the myocyte cross-sectional area was detected. Echocardiographic analyses did not reveal any change in cardiac function, and there was no fibrosis or re-expression of the fetal gene program. RNA sequencing analysis indicated that pathways related to energy metabolism were upregulated, while those related to extracellular matrix organization were downregulated. Consistent with a functional role of the latter, an angiotensin-II challenge that triggered fibrosis in the α1^r/rα2^s/s mouse failed to do so in the α1^s/sα2^s/s. Taken together, these results are indicative of a link between circulating CTS, Na/K-ATPase α1, ROS, and physiological cardiac hypertrophy in mice under baseline laboratory conditions.     

PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction

Peptidoglycan recognition proteins (PGRPs) are ubiquitous among animals and play pivotal functions in insect immunity. Non-catalytic PGRPs are involved in the activation of immune pathways by binding to the peptidoglycan (PGN), whereas amidase PGRPs are capable of cleaving the PGN into non-immunogenic compounds. Drosophila PGRP-LB belongs to the amidase PGRPs and downregulates the immune deficiency (IMD) pathway by cleaving meso-2,6-diaminopimelic (meso-DAP or DAP)-type PGN. While the recognition process is well analyzed for the non-catalytic PGRPs, little is known about the enzymatic mechanism for the amidase PGRPs, despite their essential function in immune homeostasis. Here, we analyzed the specific activity of different isoforms of Drosophila PGRP-LB towards various PGN substrates to understand their specificity and role in Drosophila immunity. We show that these isoforms have similar activity towards the different compounds. To analyze the mechanism of the amidase activity, we performed site directed mutagenesis and solved the X-ray structures of wild-type Drosophila PGRP-LB and its mutants, with one of these structures presenting a protein complexed with the tracheal cytotoxin (TCT), a muropeptide derived from the PGN. Only the Y78F mutation abolished the PGN cleavage while other mutations reduced the activity solely. Together, our findings suggest the dynamic role of the residue Y78 in the amidase mechanism by nucleophilic attack through a water molecule to the carbonyl group of the amide function destabilized by Zn²⁺.     

Oxidation of hafnium carbide and hafnium carbide with additions of tantalum and praseodymium

The oxidation behavior of HfC, HfC-25 wt. % TaC, and HfC-7 wt.% PrC₂ has been studied between 1200–2200° C. Parabolic growth of the oxide layer has been observed for both HfC and HfC-TaC over the entire temperature range. A break in the temperature dependence of the oxidation kinetics occurs around 1600°C. At lower temperatures, the kinetics are limited by gaseous diffusion via pores in the oxide. Above 1800°C, gaseous diffusion through pores becomes less important as scale-growth kinetics are dominated by bulk (ambipolar) diffusion of oxygen and electrons through the oxide.     

Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

A new short-path distillation system applied to the reduction of cholesterol in butter and lard

A molecular distillation plant, built particularly to increase the separation efficiency and to obtain safer working conditions, was tested to remove cholesterol from anhydrous butter and lard. A preliminary experiment was carried out with butter to evaluate the fractionation obtained at temperatures between 190 and 250°C and residual pressures between 10⁻³ and 10⁻⁴ torr. A second experiment was carried out at 185°C and at the maximum operational vacuum, evaluating the fractionation achieved within a time scale between 30 and 180 min. Cholesterol was almost completely removed during the second hour with minimal loss of low-molecular weight triglycerides. An experiment was carried out with lard at 250°C and maximum achievable operational vacuum (10⁻⁴ Torr), lasting approximately 6 h, and cholesterol was removed almost completely during the second hour without significant modifications in the triglyceride composition. This situation remained constant throughout the duration of the test.