Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes

Understanding the factors responsible for variations in mutation patterns and selection efficacy along chromosomes is a prerequisite for deciphering genome sequences. Population genetics models predict a positive correlation between the efficacy of selection at a given locus and the local rate of recombination because of Hill–Robertson effects. Codon usage is considered one of the most striking examples that support this prediction at the molecular level. In a wide range of species including Caenorhabditis elegans and Drosophila melanogaster, codon usage is essentially shaped by selection acting for translational efficiency. Codon usage bias correlates positively with recombination rate in Drosophila, apparently supporting the hypothesis that selection on codon usage is improved by recombination. Here we present an exhaustive analysis of codon usage in C. elegans and D. melanogaster complete genomes. We show that in both genomes there is a positive correlation between recombination rate and the frequency of optimal codons. However, we demonstrate that in both species, this effect is due to a mutational bias toward G and C bases in regions of high recombination rate, possibly as a direct consequence of the recombination process. The correlation between codon usage bias and recombination rate in these species appears to be essentially determined by recombination-dependent mutational patterns, rather than selective effects. This result highlights that it is necessary to take into account the mutagenic effect of recombination to understand the evolutionary role and impact of recombination.

Multiplex selection technique (MuST): an approach to clone transcription factor binding sites.

We have used a multiplex selection approach to construct a library of DNA-protein interaction sites recognized by many of the DNA-binding proteins present in a cell type. An estimated minimum of two-thirds of the binding sites present in a library prepared from activated Jurkat T cells represent authentic transcription factor binding sites. We used the library for isolation of "optimal" binding site probes that facilitated cloning of a factor and to identify binding activities induced within 2 hr of activation of Jurkat cells. Since a large fraction of the oligonucleotides obtained appear to represent "optimal" binding sites for sequence-specific DNA-binding proteins, it is feasible to construct a catalog of consensus binding sites for DNA-binding proteins in a given cell type. Qualitative and quantitative comparisons of the catalogs of binding site sequences from various cell types could provide valuable insights into the process of differentiation acting at the level of transcriptional control.

Simultaneous synthesis of heat exchanger networks with pressure recovery: optimal integration between heat and work

The optimal integration between heat and work may significantly reduce the energy demand and consequently the process cost. This paper introduces a new mathematical model for the simultaneous synthesis of heat exchanger networks (HENs) in which the pressure levels of the process streams can be adjusted to enhance the heat integration. A superstructure is proposed for the HEN design with pressure recovery, developed via generalized disjunctive programming (GDP) and mixed-integer nonlinear programming (MINLP) formulation. The process conditions (stream temperature and pressure) must be optimized. Furthermore, the approach allows for coupling of the turbines and compressors and selection of the turbines and valves to minimize the total annualized cost, which consists of the operational and capital expenses. The model is tested for its applicability in three case studies, including a cryogenic application. The results indicate that the energy integration reduces the quantity of utilities required, thus decreasing the overall cost.

Optimal Design of a Hybrid Membrane System Combining Reverse and Forward Osmosis for Seawater Desalination

In this work we study Forward Osmosis (FO) as an emerging desalination technology, and its capability to replace totally or partially Reverse Osmosis (RO) in order to reduce the great amount of energy required in the current desalination plants. For this purpose, we propose a superstructure that includes both membrane based desalination technologies, allowing the selection of only one of the technologies or a combination of both of them seeking for the optimal configuration of the network. The optimization problem is solved for a seawater desalination plant with a given fresh water production. The results obtained show that the optimal solution combines both desalination technologies to reduce not only the energy consumption but also the total cost of the desalination process in comparison with the same plant but operating only with RO.

Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli

Translational pausing may occur due to a number of mechanisms, including the presence of non-optimal codons, and it is thought to play a role in the folding of specific polypeptide domains during translation and in the facilitation of signal peptide recognition during see-dependent protein targeting. In this whole genome analysis of Escherichia coli we have found that non-optimal codons in the signal peptide-encoding sequences of secretory genes are overrepresented relative to the mature portions of these genes; this is in addition to their overrepresentation in the 5'-regions of genes encoding non-secretory proteins. We also find increased non-optimal codon usage at the 3' ends of most E. coli genes, in both non-secretory and secretory sequences. Whereas presumptive translational pausing at the 5' and 3' ends of E. coli messenger RNAs may clearly have a general role in translation, we suggest that it also has a specific role in sec-dependent protein export, possibly in facilitating signal peptide recognition. This finding may have important implications for our understanding of how the majority of non-cytoplasmic proteins are targeted, a process that is essential to all biological cells. (C) 2004 Elsevier Inc. All rights reserved.

Integrated project evaluation and selection using multiple-attribute decision-making technique

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again till the statutory regulatory authority approves the project. Moreover, project analysis through above process often results sub-optimal project as financial analysis may eliminate better options, as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system, which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple-attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2005 Elsevier B.V. All rights reserved.

Decision support system for project selection

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical, and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again until the statutory regulatory authority approves the project. Moreover, project analysis through the above process often results in suboptimal projects as financial analysis may eliminate better options as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select an optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2008, IGI Global.

Multiple attribute decision making approach to petroleum pipeline route selection

Petroleum pipelines are the nervous system of the oil industry, as this transports crude oil from sources to refineries and petroleum products from refineries to demand points. Therefore, the efficient operation of these pipelines determines the effectiveness of the entire business. Pipeline route selection plays a major role when designing an effective pipeline system, as the health of the pipeline depends on its terrain. The present practice of route selection for petroleum pipelines is governed by factors such as the shortest distance, constructability, minimal effects on the environment, and approachability. Although this reduces capital expenditure, it often proves to be uneconomical when life cycle costing is considered. This study presents a route selection model with the application of an Analytic Hierarchy Process (AHP), a multiple attribute decision making technique. AHP considers all the above factors along with the operability and maintainability factors interactively. This system has been demonstrated here through a case study of pipeline route selection, from an Indian perspective. A cost-benefit comparison of the shortest route (conventionally selected) and optimal route establishes the effectiveness of the model.

Mathematical modelling and optimal multivariable control of chemical processes

This work reports the developnent of a mathenatical model and distributed, multi variable computer-control for a pilot plant double-effect climbing-film evaporator. A distributed-parameter model of the plant has been developed and the time-domain model transformed into the Laplace domain. The model has been further transformed into an integral domain conforming to an algebraic ring of polynomials, to eliminate the transcendental terms which arise in the Laplace domain due to the distributed nature of the plant model. This has made possible the application of linear control theories to a set of linear-partial differential equations. The models obtained have well tracked the experimental results of the plant. A distributed-computer network has been interfaced with the plant to implement digital controllers in a hierarchical structure. A modern rnultivariable Wiener-Hopf controller has been applled to the plant model. The application has revealed a limitation condition that the plant matrix should be positive-definite along the infinite frequency axis. A new multi variable control theory has emerged fram this study, which avoids the above limitation. The controller has the structure of the modern Wiener-Hopf controller, but with a unique feature enabling a designer to specify the closed-loop poles in advance and to shape the sensitivity matrix as required. In this way, the method treats directly the interaction problems found in the chemical processes with good tracking and regulation performances. Though the ability of the analytical design methods to determine once and for all whether a given set of specifications can be met is one of its chief advantages over the conventional trial-and-error design procedures. However, one disadvantage that offsets to some degree the enormous advantages is the relatively complicated algebra that must be employed in working out all but the simplest problem. Mathematical algorithms and computer software have been developed to treat some of the mathematical operations defined over the integral domain, such as matrix fraction description, spectral factorization, the Bezout identity, and the general manipulation of polynomial matrices. Hence, the design problems of Wiener-Hopf type of controllers and other similar algebraic design methods can be easily solved.

The role of stochasticity in an information-optimal neural population code

In this paper we consider the optimisation of Shannon mutual information (MI) in the context of two model neural systems The first is a stochastic pooling network (population) of McCulloch-Pitts (MP) type neurons (logical threshold units) subject to stochastic forcing; the second is (in a rate coding paradigm) a population of neurons that each displays Poisson statistics (the so called 'Poisson neuron'). The mutual information is optimised as a function of a parameter that characterises the 'noise level'-in the MP array this parameter is the standard deviation of the noise, in the population of Poisson neurons it is the window length used to determine the spike count. In both systems we find that the emergent neural architecture and; hence, code that maximises the MI is strongly influenced by the noise level. Low noise levels leads to a heterogeneous distribution of neural parameters (diversity), whereas, medium to high noise levels result in the clustering of neural parameters into distinct groups that can be interpreted as subpopulations In both cases the number of subpopulations increases with a decrease in noise level. Our results suggest that subpopulations are a generic feature of an information optimal neural population.

Stock selection with full-scale optimization and differential evolution

When composing stock portfolios, managers frequently choose among hundreds of stocks. The stocks' risk properties are analyzed with statistical tools, and managers try to combine these to meet the investors' risk profiles. A recently developed tool for performing such optimization is called full-scale optimization (FSO). This methodology is very flexible for investor preferences, but because of computational limitations it has until now been infeasible to use when many stocks are considered. We apply the artificial intelligence technique of differential evolution to solve FSO-type stock selection problems of 97 assets. Differential evolution finds the optimal solutions by self-learning from randomly drawn candidate solutions. We show that this search technique makes large scale problem computationally feasible and that the solutions retrieved are stable. The study also gives further merit to the FSO technique, as it shows that the solutions suit investor risk profiles better than portfolios retrieved from traditional methods.

Decision support system for pipeline route selection

Presents information on a study which proposed a decision support system (DSS) for a petroleum pipeline route selection with the application of analytical hierarchy process. Factors governing route-selection for cross-country petroleum pipelines; Application of the DSS from an Indian perspective; Cost benefit comparison of the shortest route and the optimal route; Results and findings.

Methods of Regularities Searching Based on Optimal Partitioning

The purpose of discussed optimal valid partitioning (OVP) methods is uncovering of ordinal or continuous explanatory variables effect on outcome variables of different types. The OVP approach is based on searching partitions of explanatory variables space that in the best way separate observations with different levels of outcomes. Partitions of single variables ranges or two-dimensional admissible areas for pairs of variables are searched inside corresponding families. Statistical validity associated with revealed regularities is estimated with the help of permutation test repeating search of optimal partition for each permuted dataset. Method for output regularities selection is discussed that is based on validity evaluating with the help of two types of permutation tests.

A Taxonomy of Big Data for Optimal Predictive Machine Learning and Data Mining

Big data comes in various ways, types, shapes, forms and sizes. Indeed, almost all areas of science, technology, medicine, public health, economics, business, linguistics and social science are bombarded by ever increasing flows of data begging to be analyzed efficiently and effectively. In this paper, we propose a rough idea of a possible taxonomy of big data, along with some of the most commonly used tools for handling each particular category of bigness. The dimensionality p of the input space and the sample size n are usually the main ingredients in the characterization of data bigness. The specific statistical machine learning technique used to handle a particular big data set will depend on which category it falls in within the bigness taxonomy. Large p small n data sets for instance require a different set of tools from the large n small p variety. Among other tools, we discuss Preprocessing, Standardization, Imputation, Projection, Regularization, Penalization, Compression, Reduction, Selection, Kernelization, Hybridization, Parallelization, Aggregation, Randomization, Replication, Sequentialization. Indeed, it is important to emphasize right away that the so-called no free lunch theorem applies here, in the sense that there is no universally superior method that outperforms all other methods on all categories of bigness. It is also important to stress the fact that simplicity in the sense of Ockham’s razor non-plurality principle of parsimony tends to reign supreme when it comes to massive data. We conclude with a comparison of the predictive performance of some of the most commonly used methods on a few data sets.

Dynamic decision-making based on NFR for managing software variability and configuration selection

Due to dynamic variability, identifying the specific conditions under which non-functional requirements (NFRs) are satisfied may be only possible at runtime. Therefore, it is necessary to consider the dynamic treatment of relevant information during the requirements specifications. The associated data can be gathered by monitoring the execution of the application and its underlying environment to support reasoning about how the current application configuration is fulfilling the established requirements. This paper presents a dynamic decision-making infrastructure to support both NFRs representation and monitoring, and to reason about the degree of satisfaction of NFRs during runtime. The infrastructure is composed of: (i) an extended feature model aligned with a domain-specific language for representing NFRs to be monitored at runtime; (ii) a monitoring infrastructure to continuously assess NFRs at runtime; and (iii) a exible decision-making process to select the best available configuration based on the satisfaction degree of the NRFs. The evaluation of the approach has shown that it is able to choose application configurations that well fit user NFRs based on runtime information. The evaluation also revealed that the proposed infrastructure provided consistent indicators regarding the best application configurations that fit user NFRs. Finally, a benefit of our approach is that it allows us to quantify the level of satisfaction with respect to NFRs specification.