Compositional Constraints Research Articles

Time-Based Web Service Composition

This article describes how incorporating temporal constraints in web service composition results in more complex models and makes the verification of temporal consistency during the modeling and execution crucial. This article proposes a model named H-Service-Net based on the time petri net model to control and manage temporal consistency; the model also supports time constraints and exception handling. First, this approach proposes a modular approach for modeling composition using Extend Time Unit System, Allen's interval algebra, and comparison operators in a time petri net model to consider all types of temporal constraints. Subsequently, this article presents algorithms on checking temporal consistency and mechanism for exception handling and validating the system in an implementation tool (H-Service-Editor) based on the proposed approach that uses BizTalk Server 2013 to evaluate the implementation of temporal constraints and timeout exception handling. Finally, an exhaustive performance experiment is presented to assess the scalability of the authors' approach.

The analyses of relationships among nucleotide, synonymous codon and amino acid usages for E2 gene of bovine viral diarrhea virus

In this study, the systemic analyses of nucleotide, codon and amino acid usages for E2 gene of bovine viral diarrhea virus (BVDV) were carried out for estimating its genetic features. The nucleotide usage pattern at the first codon position was strongly influenced by the overall nucleotide composition, while the nucleotide usage patterns at the second and third codon positions seemed to have little link to the overall nucleotide composition. The result indicated that the mutation pressure from nucleotide composition constraint was not the single evolutionary force for genetic features of BVDV E2 gene. Just 18 out of 59 synonymous codons were similar with synonymous codon usage patterns for E2 gene between BVDV1 and BVDV2, while all synonymous codons which contain CpG dinucleotides were selected at the low level by E2 gene, suggesting that this gene suppressed the usages of codons containing CpG dinucleotides to regulate E2 gene replicate and transcript efficiently and avoid immune response from infected hosts. Amino acid usage patterns of E2 protein were generally different between BVDV1 and BVDV2. The patterns of synonymous codon and amino acid usages for E2 gene might be caused by the equilibrium of evolutionary forces from virus and host. Our work gave new investigations into the role of host origin in the formations of synonymous codon/amino acid usages and the evolutionary trend of BVDV E2 gene. The genetic characteristics that codon/amino acid usages of E2 gene adapted to the internal environment of individual animals might assist in understanding the changes of genetics and antigenicity for newly emerging BVDV.

Parallel processing on Big Data in the context of Machine Learning and Hadoop Ecosystem: A Survey

Emergent Big Data applications have become gradually more essential. In reality, a lot of institutes, businesses and in general entire society from diverse segments depend more and more on information take out from enormous quantity of raw information, statistics and numbers. On the other hand, in Big Data perspective, customary information methods and policies are not as much of capable. They prove a time-consuming receptiveness and are short of quantifiability, measurability, presentation and accurateness. To solve the composite Big Data constraints and difficulties, a large amount effort has been carried out. As an effect, different categories of packages, distributions and technologies have been developed. In this paper an evaluation is done, this studies recent technologies developed for Big Data. It aims to assist to choose and adopt the exact combination of diverse Big Data technologies according to their technological, scientific needs and particular applications requirements. It provides not only a worldwide sight of most important Big Data technologies but also relationship according to special organizational, classifications levels such as Information Storage Level, Information Processing Level, Information Querying Level, Information Access Level and Management Level. It classifies and talks about main tools and its features, advantages, restrictions and treatments.

Fake Plate Vehicle Auditing Based on Composite Constraints in Internet of Things Environment

Accordance to the real application demands, this paper proposes a fake plate vehicle auditing method based on composite constrains strategy, a corresponding simulated IOT (internet of things) environment was created and uses liner matrix, Base64 encryption and grid monitoring technology and puts forward a real-time detecting algorithm for fake plate vehicles. The developed real system not only shows the superiority on its speed, detection accuracy and visualization, it also be good at realizing the vehicle’s real-time position and predicting the possible traveling trajectory.

Codon usage vis-a-vis start and stop codon context analysis of three dicot species

To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly A-ending and/or T-ending codons. GC3s directly mimic theusage pattern of global GC content. Relative synonymous codon usage analysis suggests that the high usage frequency of A/T over G/C mononucleotide containing codons in AT-rich dicot genome is due to compositional constraint as a factor of codon usage bias. Odds ratio analysis identified the dinucleotides TpG, TpC, GpA, CpA and CpT as over-represented, where, CpG and TpA as under-represented dinucleotides. The results of (NcExp-NcObs)/NcExp plot suggests that selection pressure other than mutation played a significant role in influencing the pattern of codon usage in these dicots. PR2 analysis revealed the significant role of selection pressure on codon usage. Analysis of varience on codon usage at start and stop site showed variation in codon selection in these sites. This study provides evidence that the dicot genes were subjected to compositional selection pressure.

Compositional dynamics and codon usage pattern of BRCA1 gene across nine mammalian species

The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T –ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals. The codon usage bias in BRCA1 and AARS genes is low. The codon CGC encoding arginine amino acid and the codon TTA encoding leucine were uniformly distributed in BRCA1 and AARS genes, respectively in mammals including human. Natural selection might have played a major role while mutation pressure might have played a minor role in shaping the codon usage pattern of BRCA1 and AARS genes.

English

Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous codons (GC3s), codon adaptation index, hydrophobicity, aromaticity of conceptually translated gene products were calculated using the Codon W 1.4.2 program. HPV preferentially used codons ending with A/U. By comparing relative synonymous codon usage of the HPV genome and human genome, the codon usage of HPV was almost entirely different from that of humans. Statistical significant of the separation between codons ending with A/U and G/C on the first axis was shown by the principal component analysis. The greater number of the effective number of codon values against the value of GC3s was below the expected values. The correlation between effective number of codon values and both aromaticity and hydrophobicity showed significant high negative correlation. These results showed that composition constraint is likely the key element for codon usage in the HPV genome.   Key words: Principal component analysis, composition constraints, papilloma virus, codon usage.

Plasmodium parasites of birds have the most AT-rich genes of eukaryotes.

The genomic architecture of organisms, including nucleotide composition, can be highly variable, even among closely-related species. To better understand the causes leading to structural variation in genomes, information on distinct and diverse genomic features is needed. Malaria parasites are known for encompassing a wide range of genomic GC-content and it has long been thought that Plasmodium falciparum, the virulent malaria parasite of humans, has the most AT-biased eukaryotic genome. Here, I perform comparative genomic analyses of the most AT-rich eukaryotes sequenced to date, and show that the avian malaria parasites Plasmodium gallinaceum, P. ashfordi, and P. relictum have the most extreme coding sequences in terms of AT-bias. Their mean GC-content is 21.21, 21.22 and 21.60 %, respectively, which is considerably lower than the transcriptome of P. falciparum (23.79 %) and other eukaryotes. This information enables a better understanding of genome evolution and raises the question of how certain organisms are able to prosper despite severe compositional constraints.

Effects of lattice constraint on structures and electronic properties of BAlN and BGaN alloys: A first-principles study

Structures and electronic properties of BxAl1−xN and BxGa1−xN alloys are investigated on the basis of density functional calculations. We find that the wurtzite structure is stabilized over a wide range of alloy composition, and lattice constraint by the substrate affects the relative stability of the wurtzite and graphitic hexagonal structures. We also reveal that BxAl1−xN with wurtzite structure possesses a direct bandgap owing to lattice constraint by AlN, whereas BxGa1−xN, without lattice constraint, has a direct bandgap over a wide range of B compositions. The results suggest that the structural and electronic properties of BxAl1−xN and BxGa1−xN can be controlled by varying the alloy composition and lattice constraint.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

Constraints of texture and composition of clinopyroxene phenocrysts of Holocene volcanic rocks on a magmatic plumbing system beneath Tengchong, SW China

Understanding processes of magma replenishment in a magma plumbing system is essential to predict eruption potential of a dormant volcano. In this study, we present new petrologic and thermobarometric data for youngest lava flows from the Holocene Heikongshan volcano in the Tengchong area, SW China. Clinopyroxene phenocrysts from the trachytic lava flows display various textural/compositional zoning styles (i.e., normal, reverse and oscillatory). Such zoning patterns are indicative of an open magmatic plumbing system with multiphase magma replenishment and mixing, which were likely a key drive of the volcanic eruptions. Thermobarometric calculations of these zoned clinopyroxene phenocrysts yield crystallization pressures of 3.8–7.1 kbar (peak at 4.5–7.0 kbar), corresponding to a magma chamber at depths of 14–21 km. The calculated depths are consistent with the large low-resistivity body at 12–30 km beneath the Heikongshan volcano, implying that the magmatic plumbing system may still be active. Recent earthquakes in the Tengchong area suggest that the regional strike-slip faulting are still active, and may trigger future volcanic eruptions if the magma chamber(s) beneath the Tengchong volcanic field is disturbed, in spite of the volcanic quiescence since 1609 CE.

Prevalence and genetic features of hepatitis E virus in swine, in Gansu, China.

The prevalence of hepatitis E virus (HEV) in domestic swine threats the public health, due to the risk of zoonotic transmission. In this study, we investigated the prevalence and genetic features of HEV in swine, in Gansu, which is geographically an important province in China. 377 fecal samples were collected from pig farms in Gansu province of China and tested for HEV RNA by RT-PCR. The prevalence rate is about 23% in pig farms of Gansu province. By RT-nPCR, 5' and 3' RACE methods, a whole genome with 7,284 nt in length, termed as swCH189, was obtained and investigated by nucleotide, codon and amino acid usage analyses. Phylogenetic tree analysis classified swCH189 strain into genotype 4e. Although this subtype has never been reported in the local population, genotype 4 is known as zoonotic and more pathogenic than other genotypes. According to the synonymous codon usage patterns of the three open reading frames (ORFs) of swCH189, compositional constraint mainly influences usage patterns of synonymous codons with A-end, while natural selections dominate in usage patterns of synonymous codons with G, C and U-ends. Genetic diversities of each ORFs, in respect to codon and amino acid usage patterns, are closely related to other members of genotype 4 in general, but with distinct features. Thus, the prevalence rate and the genetic features of HEV determined by this study are important for the prevention of zoonotic transmission of HEV from swine to human in this region as well as in China.

On the structure of superbasic (MgO)n sites solvated in a faujasite zeolite.

We report the synthesis and characterisation of a HY/MgO zeolite/oxide nanocomposite material with high crystallinity and highly dispersed, highly basic MgO sites. Preparation was optimized in order to preserve sample crystallinity, to avoid the formation of mesoporosity and to minimize the formation of separate Mg-containing phases. These features were checked by means of electron microscopy, X-ray powder diffraction, porosimetry and IR spectroscopy. A highly dispersed material was obtained, comprising nanoclusters of magnesium oxide and hydroxide hosted by the microporous zeolite framework. The location and structure of the Mg-containing clusters have been studied by means of a combination of Rietveld refinement of XRPD data and high quality quantum mechanical simulations. The refinement has shown the presence of magnesium and oxygen atoms in the double six-membered ring cages, consistent with the presence of mononuclear Mg moieties. However, the composition and IR spectroscopy demonstrate that other Mg species must exist, likely located in the zeolite pores. In order to propose candidate structures for these species, several hypothetic periodic models of the material were built by placing (MgO)n clusters in different locations of the zeolite structure, taking into account the material composition and other constraints imposed by the experimental observations. Periodic structures with P1 symmetry were optimized at the B3LYP-D*/DZVP level with the CRYSTAL code and classified according to their stability. Two families of possible sites were identified: highly solvated (MgO)n units in narrow cavities and less coordinated clusters in the supercages. The stability of these clusters appears to be regulated by the ability of Mg2+ and O2- ions to interact with the pore walls and by the formation of Mg-OH species as result of the reaction of Mg-O couples with remaining acidic protons. The reactivity of four representative models with CO2 has been simulated at the B3LYP-D*/TZVP level. CO2 forms very stable linear end-on adducts with low coordinated Mg ions in most cases. Isolated sites give rise to bridge bidentate complexes in agreement with previous spectroscopic observations. The formation of hydrogen-carbonates is observed only on specific sites, through a process having a low adsorption energy because of the high deformation of the adsorption site.

Bank Interest Rate Margin, Portfolio Composition and Institutional Constraints

The objective of this paper is to empirically determine the factors that impact bank interest margins in China. We use relevant banking data for the period 1998-2015. Importantly, we examine, how the composition of assets and liabilities impacts interest margins. To our knowledge this aspect has not been explored. We also consider the impact of institutional environment and market structure changes. We found that the market pricing mechanism in interest rate hasn’t taken off yet despite the long-term reform by the Chinese government. Borrowing and lending rate are twisted. Foreign banks incorporated in China and the institutional settings represented by them have yet to exert any positive affect interest rate margins in China.

Alkan’s Petits Préludes for organ

Stylistic and pitch-related data derived from the score of Alkan’s Petits Préludes for organ are analyzed using nonparametric correlations and multidimensional scaling, and the results used to reconstruct his compositional process. The reconstruction is then verified by comparing it to an existing cognitive model of musical composition and Alkan’s use of multiple compositional constraints discussed as an example of a strategy employed by master composers to reduce their problem space. The tidy fit of the reconstruction to the model and the agreement of the evidence with a number of previous findings and hypotheses concerning the cognitive processes underlying musical composition strongly suggests that the model and similar analyses of musical variables could be applied to works by other composers and used as a basis for or an adjunct to musicological and psychological studies of the compositional process, particularly when limited to a post hoc analysis or by a finite dataset.

Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus.

The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.

Optimization of pre-concentration, entrainer recycle and pressure selection for the extractive distillation of acetonitrile-water with ethylene glycol

We optimize the extractive distillation process for separating the acetonitrile – water azeotropic mixture with ethylene glycol by using a multi-objective genetic algorithm for minimizing under purity constraints the total cost, the energy consumption and the separation efficiency. For the first time we have shown the interest of five aspects by considering them simultaneously (1) the pre-concentration column has been included and (2) there is no need to set a distillate composition constraint (like being at the azeotropic composition) in the pre-concentration column. (3) The operating pressure should be lower than 1 atm because it enhances the relative volatility for 1.0-1a class system. (4) A closed loop optimization must be run, to handle the effect of impurity in the entrainer recycle since too much impurity limits the main product recovery and purity from the extractive column. (5) All three columns process must be optimized together rather than sequentially and with multiple objectives. The studied system belongs to class 1.0-1a and the impurity of the recycled entrainer has strong effect on the purity of acetonitrile product. Overall, 17 variables are optimized; column trays, all feed locations, refluxes, entrainer flow rate and all distillate products; under purity constraints for the acetonitrile and water product and for the entrainer recycle impurity. Among nearly 400 designs satisfying the purity specifications, the design case 3 shows an energy consumption and TAC reduced by more than 20% than a literature reference case, thanks to smaller entrainer flow rate, a reduction of 32 trays and lower operating pressures. The best design is a trade-off between first a feasibility governed by thermodynamics through composition profiles and relative volatility maps and second process cost and energy demands.

PRIMASS visits Hilda and Cybele groups

The Cybele and Hilda dynamical groups delimit the outer edge of the asteroid belt. Their compositional distribution is a key element to constrain evolutionary models of the Solar System. In this paper, we present a compositional analysis of these populations using spectroscopic observations, SDSS and NEOWISE data. As part of the PRIMASS (Primitive Asteroids Spectroscopic Survey), we acquired visible spectra of 18 objects in Hilda or Cybele groups with the Goodman High Throughput Spectrometer at the 4.1 m SOAR telescope and 20 near-IR spectra of Hilda objects with Near Infrared Camera Spectrograph at the 3.56 m TNG. The sample is enlarged with spectra taken from the literature in order to increase our statistical analysis. The spectra were inspected for aqueous alteration bands and other spectral features that can be linked to compositional constraints. The analysis shows a continuous distribution of compositions from the main-belt to the Cybele, Hilda and Trojan regions. We also identify a population in the Trojans group not present in Hilda or Cybele objects.

Codon usage of HIV regulatory genes is not determined by nucleotide composition.

Codon usage bias can be a result of either mutational bias or selection for translational efficiency and/or accuracy. Previous data has suggested that nucleotide composition constraint was the main determinant of HIV codon usage, and that nucleotide composition and codon usage were different between the regulatory genes, tat and rev, and other viral genes. It is not clear whether translational selection contributed to the codon usage difference and how nucleotide composition and translational selection interact to determine HIV codon usage. In this study, a model of codon bias due to GC composition with modification for the A-rich third codon position was used to calculate predicted HIV codon frequencies based on its nucleotide composition. The predicted codon usage of each gene was compared with the actual codon frequency. The predicted codon usage based on GC composition matched well with the actual codon frequencies for the structural genes (gag, pol and env). However, the codon usage of the regulatory genes (tat and rev) could not be predicted. Codon usage of the regulatory genes was also relatively unbiased showing the highest effective number of codons (ENC). Moreover, the codon adaptation index (CAI) of the regulatory genes showed better adaptation to human codons when compared to other HIV genes. Therefore, the early expressed genes responsible for regulation of the replication cycle, tat and rev, were more similar to humans in terms of codon usage and GC content than other HIV genes. This may help these genes to be expressed efficiently during the early stages of infection.

Whole-rock and mineral compositional constraints on the magmatic evolution of the Ni-Cu-(PGE) sulfide ore-bearing Kevitsa intrusion, northern Finland

The ~2.06Ga mafic-ultramafic Kevitsa intrusion is located in the Central Lapland greenstone belt. The lower ultramafic part of the intrusion hosts a large disseminated Ni-Cu-(PGE) sulfide deposit with Ni tenors ranging widely from <4wt% (uneconomic false ore and contact mineralization) to 4–7wt% (regular ore) and up to 40wt% (Ni-PGE ore). The stratigraphy of the ultramafic cumulates is divided into the basal pyroxenite–gabbro (Basal series), olivine pyroxenite (OLPX), pyroxenite, and plagioclase-bearing (ol) websterite (pOLWB), of which the latter occurs together with minor microgabbros in the ore-bearing domain of the intrusion. Around the ore domain, the ultramafic cumulate succession records a simple lithological stratigraphy and modest and predictable variations in whole-rock and mineral compositions. The ore-bearing domain, in contrast, is characterized by a complex internal architecture, variations in whole-rock and mineral compositions, and the presence of numerous inclusions and xenoliths.The OLPXs are mainly composed of cumulus olivine (Fo77–89) and clinopyroxene (Mg#81–92) with variable amounts of oikocrystic orthopyroxene (Mg#79–84). They comprise the bulk of the ultramafic cumulates and are the dominant host rocks to the sulfide ore. The host rocks to the regular and false ore type are mineralogically and compositionally similar (Fo~80–83, mostly) and show mildly LREE-enriched REE patterns (CeN/YbN~2), characteristic for the bulk of the Kevitsa ultramafic cumulates. The abundance of orthopyroxene and magnetite is lowest in the host rocks to the Ni-PGE ore type, being in line with the mineral compositions of the silicates, which are the most primitive in the intrusion. However, it contrasts with the LREE-enriched nature of the ore type (CeN/YbN~7), indicating significant involvement of crustal material in the magma.The contrasting intrusive stratigraphy in the different parts of the intrusion likely reflects different emplacement histories. It is proposed that the Kevitsa magma chamber was initially filled by stable continuous flow (“single” input) of basaltic magma followed by differentiation in an at least nearly closed system. In the following stage, new magma pulses were repeatedly emplaced into the interior of the intrusion in a dynamic (open) system forming the sulfide ore bodies. To gain the peculiar compositional and mineralogical characteristics of the Ni-PGE ore type, the related magma probably interacted with different country rocks en route to the Kevitsa magma chamber.