Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.

The Complex Unified Evolutionary Approach to the Creation of the Multilevel Distributed Control System of a Gas-transport Company

The objects of a large-scale gas-transport company (GTC) suggest a complex unified evolutionary approach, which covers basic building concepts, up-to-date technologies, models, methods and means that are used in the phases of design, adoption, maintenance and development of the multilevel automated distributed control systems (ADCS).. As a single methodological basis of the suggested approach three basic Concepts, which contain the basic methodological principles and conceptual provisions on the creation of distributed control systems, were worked out: systems of the lower level (ACS of the technological processes based on up-to-date SCADA), of the middle level (ACS of the operative-dispatch production control based on MES-systems) and of the high level (business process control on the basis of complex automated systems ERP).

String Measure Applied to String Self-Organizing Maps and Networks of Evolutionary Processors

* Supported by projects CCG08-UAM TIC-4425-2009 and TEC2007-68065-C03-02

The Production Scheduling in Assembly System with Evolutionary Algorithm

In this paper an evolutionary algorithm is proposed for solving the problem of production scheduling in assembly system. The aim of the paper is to investigate a possibility of the application of evolutionary algorithms in the assembly system of a normally functioning enterprise producing household appliances to make the production graphic schedule.

Temperature management for heterogeneous multi-core FPGAs using adaptive evolutionary multi-objective approaches

Heterogeneous multi-core FPGAs contain different types of cores, which can improve efficiency when used with an effective online task scheduler. However, it is not easy to find the right cores for tasks when there are multiple objectives or dozens of cores. Inappropriate scheduling may cause hot spots which decrease the reliability of the chip. Given that, our research builds a simulating platform to evaluate all kinds of scheduling algorithms on a variety of architectures. On this platform, we provide an online scheduler which uses multi-objective evolutionary algorithm (EA). Comparing the EA and current algorithms such as Predictive Dynamic Thermal Management (PDTM) and Adaptive Temperature Threshold Dynamic Thermal Management (ATDTM), we find some drawbacks in previous work. First, current algorithms are overly dependent on manually set constant parameters. Second, those algorithms neglect optimization for heterogeneous architectures. Third, they use single-objective methods, or use linear weighting method to convert a multi-objective optimization into a single-objective optimization. Unlike other algorithms, the EA is adaptive and does not require resetting parameters when workloads switch from one to another. EAs also improve performance when used on heterogeneous architecture. A efficient Pareto front can be obtained with EAs for the purpose of multiple objectives.

Winners and Losers in the Liberalized Energy Retail Sector in Hungary:A Co-evolutionary Approach

This paper examines the recent history of the Hungarian energy trading market in a co-evolutionary framework. Hungary is characterized by a mixed ownership structure with mainly multinational incumbents in energy retail and distribution, while the wholesale is dominantly owned by state-owned companies. The legal framework also has dual characteristics, with free-market regulation for industrial consumers and a regulated price regime for households. Our research method follows a longitudinal approach from the period of market liberalization in 2008 until 2013. We identified strong relationship between the individual and sector performance of the trading companies and the current political ideology and institutional regime.

Megtakarítási típusok - egy adaptív-evolúciós megközelítés = Types of saving - an adaptive-evolutionary approach

A közgazdaságtanban az ágensalapú modellezés egyik alkalmazási területe a makro ökonómia. Ebben a tanulmányban néhány népszerű megtakarítási szabály létét feltételezve adaptív-evolúciós megközelítésben endogén módon próbálunk következtetni e szabályok relatív életképességére. Három különböző típusú ágenst vezetünk be: egy prudens, egy rövidlátó és egy, a permanensjövedelem-elméletnek megfelelően működőt. Rendkívül erős szelekciós nyomás mellett a prudens típus egyértelműen kiszorítja a másik kettőt. A második legéletképesebbnek a rövidlátó típus tűnik, de már közepes szelekciós nyomásnál sem tűnik el egyik típus sem. Szokásos tőkehatékonyság mellett a prudens típus túlzott beruházási tendenciát visz a gazdaságba, és a gazdaság az aranykori megtakarítási rátánál magasabbat ér el. A hitelkorlátok oldása még nagyobb mértékű túlzott beruházáshoz vezethet, a hitelek mennyiségének növekedése mellett a tőketulajdonosok mintegy "kizsákmányoltatják" magukat azokkal, akiknek nincs tőkejövedelmük. A hosszú távú átlagos fogyasztás szempontjából a három típus kiegyensúlyozott aránya adja a legjobb eredményt, ugyanakkor ez jóval nagyobb ingadozással jár, mint amikor csak prudens típusú háztartások léteznek. ____ Agent-based modelling techniques have been employed for some time in macroeconomics. This paper tests some popular saving rules in an adaptive-evolutionary context of looking at their relative survival values. The three types are prudent, short-sighted, and responsive to the permanent-income hypothesis. It is found that where selection pressure is very high, only the prudent type persists. The second most resilient seems to be the short-sighted type, but all three coexist even at medium levels of selection pressure. When the efficiency of capital approaches the level usually assumed in macroeconomics, the prudent type drives the economy towards excessive accumulation of capital, i. e. a long-term savings rate that exceeds the golden rule. If credit constraints are relaxed, this tendency strengthens as credit grows and capital-owners seem to allow themselves to be exploited" by workers. From the angle of average consumption, the best outcome is obtained from a random distribution of types, although this is accompanied by higher volatility.

History and evolutionary trajectory of the Iranian nuclear program

What actors and processes at what levels of analysis and through what mechanisms have pushed Iran's nuclear program (INP) towards being designated as a proliferation threat (securitization)? What actors and processes at what levels of analysis and through what mechanisms have pushed Iran's nuclear program away from being designated as an existential threat (de-securitization)? What has been the overall balance of power and interaction dynamics of these opposing forces over the last half-century and what is their most likely future trajectory? ^ Iran's nuclear story can be told as the unfolding of constant interaction between state and non-state forces of "nuclear securitization" and "nuclear de-securitization." Tracking the crisscrossing interaction between these different securitizing and de-securitizing actors in a historical context constitutes the central task of this project. ^ A careful tracing of "security events" on different analytical levels reveals the broad contours of the evolutionary trajectory of INP and its possible future path(s). Out of this theoretically conscious historical narrative, one can make informed observations about the overall thrust of INP along the securitization - de-securitization continuum. ^ The main contributions of this work are three fold: First, it brings a fresh theoretical perspective on Iran's proliferation behavior by utilizing the "securitization" theory tracing the initial indications of the threat designation of INP all the way back to the mid 1970s. Second, it gives a solid and thematically grounded historical texture to INP by providing an intimate engagement with the persons, processes, and events of Tehran's nuclear pursuit over half a century. Third, it demonstrates how INP has interacted with and even at times transformed the NPT as the keystone of the non-proliferation regime, and how it has affected and injected urgency to the international discourse on nuclear proliferation specifically in the Middle East.^

Students' Perceptions and Opinions of Unscientific Bias in Evolutionary Curriculum

This is a qualitative study with eighth-grade students assessing their views of bias within the evolution chapters of two Florida state-adopted texts. The students determined that a significant degree of bias exists. The texts fail to develop the scientific "habits-of-mind" as stated in the school district's "science as inquiry" competencies.

Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains

Background The HIV virus is known for its ability to exploit numerous genetic and evolutionary mechanisms to ensure its proliferation, among them, high replication, mutation and recombination rates. Sliding MinPD, a recently introduced computational method [1], was used to investigate the patterns of evolution of serially-sampled HIV-1 sequence data from eight patients with a special focus on the emergence of X4 strains. Unlike other phylogenetic methods, Sliding MinPD combines distance-based inference with a nonparametric bootstrap procedure and automated recombination detection to reconstruct the evolutionary history of longitudinal sequence data. We present serial evolutionary networks as a longitudinal representation of the mutational pathways of a viral population in a within-host environment. The longitudinal representation of the evolutionary networks was complemented with charts of clinical markers to facilitate correlation analysis between pertinent clinical information and the evolutionary relationships. Results Analysis based on the predicted networks suggests the following:: significantly stronger recombination signals (p = 0.003) for the inferred ancestors of the X4 strains, recombination events between different lineages and recombination events between putative reservoir virus and those from a later population, an early star-like topology observed for four of the patients who died of AIDS. A significantly higher number of recombinants were predicted at sampling points that corresponded to peaks in the viral load levels (p = 0.0042). Conclusion Our results indicate that serial evolutionary networks of HIV sequences enable systematic statistical analysis of the implicit relations embedded in the topology of the structure and can greatly facilitate identification of patterns of evolution that can lead to specific hypotheses and new insights. The conclusions of applying our method to empirical HIV data support the conventional wisdom of the new generation HIV treatments, that in order to keep the virus in check, viral loads need to be suppressed to almost undetectable levels.

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda)

Background The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history—phylogeny, divergence times, character evolution and diversification—of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. Results Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224–296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. Conclusions Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation.

An application of evolutionary algorithms for WAG optimisation in the Norne Field

Water-alternating-gas (WAG) is an enhanced oil recovery method combining the improved macroscopic sweep of water flooding with the improved microscopic displacement of gas injection. The optimal design of the WAG parameters is usually based on numerical reservoir simulation via trial and error, limited by the reservoir engineer’s availability. Employing optimisation techniques can guide the simulation runs and reduce the number of function evaluations. In this study, robust evolutionary algorithms are utilized to optimise hydrocarbon WAG performance in the E-segment of the Norne field. The first objective function is selected to be the net present value (NPV) and two global semi-random search strategies, a genetic algorithm (GA) and particle swarm optimisation (PSO) are tested on different case studies with different numbers of controlling variables which are sampled from the set of water and gas injection rates, bottom-hole pressures of the oil production wells, cycle ratio, cycle time, the composition of the injected hydrocarbon gas (miscible/immiscible WAG) and the total WAG period. In progressive experiments, the number of decision-making variables is increased, increasing the problem complexity while potentially improving the efficacy of the WAG process. The second objective function is selected to be the incremental recovery factor (IRF) within a fixed total WAG simulation time and it is optimised using the same optimisation algorithms. The results from the two optimisation techniques are analyzed and their performance, convergence speed and the quality of the optimal solutions found by the algorithms in multiple trials are compared for each experiment. The distinctions between the optimal WAG parameters resulting from NPV and oil recovery optimisation are also examined. This is the first known work optimising over this complete set of WAG variables. The first use of PSO to optimise a WAG project at the field scale is also illustrated. Compared to the reference cases, the best overall values of the objective functions found by GA and PSO were 13.8% and 14.2% higher, respectively, if NPV is optimised over all the above variables, and 14.2% and 16.2% higher, respectively, if IRF is optimised.

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish : Proof of concept for key components of the insulin-like growth factor axis

Acknowledgements This study was funded by a Natural Environment Research Council grant (NERC, project code: NBAF704). FML is funded by a NERC Doctoral Training Grant (Project Reference: NE/L50175X/1). RLS was an undergraduate student at the University of Aberdeen and benefitted from financial support from the School of Biological Sciences. DJM is indebted to Dr. Steven Weiss (University of Graz, Austria), Dr. Takashi Yada (National Research Institute of Fisheries Science, Japan), Dr. Robert Devlin (Fisheries and Oceans Canada, Canada), Prof. Samuel Martin (University of Aberdeen, UK), Mr. Neil Lincoln (Environment Agency, UK) and Prof. Colin Adams/Mr. Stuart Wilson (University of Glasgow, UK) for providing salmonid material or assisting with its sampling. We are grateful to staff at the Centre for Genomics Research (University of Liverpool, UK) (i.e. NERC Biomolecular Analysis Facility – Liverpool; NBAF-Liverpool) for performing sequence capture/Illumina sequencing and providing us with details on associated methods that were incorporated into the manuscript. Finally, we are grateful to the organizers of the Society of Experimental Biology Satellite meeting 'Genome-powered perspectives in integrative physiology and evolutionary biology' (held in Prague, July 2015) for inviting us to contribute to this special edition of Marine Genomics and hosting a really stimulating meeting.