Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Silylation of layered double hydroxides via an induced hydrolysis method

A series of layered double hydroxides (LDHs) based composites were synthesized by using induced hydrolysis silylation method (IHS), surfactant precursor method, in-situ coprecipitation method, and direct silylation method. Their structures, morphologies, bonding modes and thermal stabilities can be readily adjusted by changing the parameters during preparation and drying processing of the LDHs. The characterization results show that the direct silylation reaction cannot occur between the dried LDHs and 3-aminopropyltriethoxysilane (APS) in an ethanol medium. However, the condensation reaction can proceed with heating process between adsorbed APS and LDHs plates. While using wet state substrates with and without surfactant and ethanol as the solvent, the silylation process can be induced by hydrolysis of APS on the surface of LDHs plates. Surfactants improve the hydrophobicity of the LDHs during the process of nucleation and crystallization, resulting in fluffy shaped crystals; meanwhile, they occupy the surface –OH positions and leave less “free –OH” available for the silylation reaction, favoring formation of silylated products with a higher population in the hydrolyzed bidentate (T2) and tridentate (T3) bonding forms. These bonding characteristics lead to spherical aggregates and tightly bonded particles. All silylated products show higher thermal stability than those of pristine LDHs.

A mass-conservative control volume-finite element method for solving Richards’ equation in heterogeneous porous media

We present a mass-conservative vertex-centred finite volume method for efficiently solving the mixed form of Richards’ equation in heterogeneous porous media. The spatial discretisation is particularly well-suited to heterogeneous media because it produces consistent flux approximations at quadrature points where material properties are continuous. Combined with the method of lines, the spatial discretisation gives a set of differential algebraic equations amenable to solution using higher-order implicit solvers. We investigate the solution of the mixed form using a Jacobian-free inexact Newton solver, which requires the solution of an extra variable for each node in the mesh compared to the pressure-head form. By exploiting the structure of the Jacobian for the mixed form, the size of the preconditioner is reduced to that for the pressure-head form, and there is minimal computational overhead for solving the mixed form. The proposed formulation is tested on two challenging test problems. The solutions from the new formulation offer conservation of mass at least one order of magnitude more accurate than a pressure head formulation, and the higher-order temporal integration significantly improves both the mass balance and computational efficiency of the solution.

Developing a research method to test a new first-order decision making model for the procurement of public sector major infrastructure

Given global demand for new infrastructure, governments face substantial challenges in funding new infrastructure and simultaneously delivering Value for Money (VfM). The paper begins with an update on a key development in a new early/first-order procurement decision making model that deploys production cost/benefit theory and theories concerning transaction costs from the New Institutional Economics, in order to identify a procurement mode that is likely to deliver the best ratio of production costs and transaction costs to production benefits, and therefore deliver superior VfM relative to alternative procurement modes. In doing so, the new procurement model is also able to address the uncertainty concerning the relative merits of Public-Private Partnerships (PPP) and non-PPP procurement approaches. The main aim of the paper is to develop competition as a dependent variable/proxy for VfM and a hypothesis (overarching proposition), as well as developing a research method to test the new procurement model. Competition reflects both production costs and benefits (absolute level of competition) and transaction costs (level of realised competition) and is a key proxy for VfM. Using competition as a proxy for VfM, the overarching proposition is given as: When the actual procurement mode matches the predicted (theoretical) procurement mode (informed by the new procurement model), then actual competition is expected to match potential competition (based on actual capacity). To collect data to test this proposition, the research method that is developed in this paper combines a survey and case study approach. More specifically, data collection instruments for the surveys to collect data on actual procurement, actual competition and potential competition are outlined. Finally, plans for analysing this survey data are briefly mentioned, along with noting the planned use of analytical pattern matching in deploying the new procurement model and in order to develop the predicted (theoretical) procurement mode.

Semantic modeling method for configurable enterprise information systems

Business practices vary from one company to another and business practices often need to be changed due to changes of business environments. To satisfy different business practices, enterprise systems need to be customized. To keep up with ongoing business practice changes, enterprise systems need to be adapted. Because of rigidity and complexity, the customization and adaption of enterprise systems often takes excessive time with potential failures and budget shortfall. Moreover, enterprise systems often drag business behind because they cannot be rapidly adapted to support business practice changes. Extensive literature has addressed this issue by identifying success or failure factors, implementation approaches, and project management strategies. Those efforts were aimed at learning lessons from post implementation experiences to help future projects. This research looks into this issue from a different angle. It attempts to address this issue by delivering a systematic method for developing flexible enterprise systems which can be easily tailored for different business practices or rapidly adapted when business practices change. First, this research examines the role of system models in the context of enterprise system development; and the relationship of system models with software programs in the contexts of computer aided software engineering (CASE), model driven architecture (MDA) and workflow management system (WfMS). Then, by applying the analogical reasoning method, this research initiates a concept of model driven enterprise systems. The novelty of model driven enterprise systems is that it extracts system models from software programs and makes system models able to stay independent of software programs. In the paradigm of model driven enterprise systems, system models act as instructors to guide and control the behavior of software programs. Software programs function by interpreting instructions in system models. This mechanism exposes the opportunity to tailor such a system by changing system models. To make this true, system models should be represented in a language which can be easily understood by human beings and can also be effectively interpreted by computers. In this research, various semantic representations are investigated to support model driven enterprise systems. The significance of this research is 1) the transplantation of the successful structure for flexibility in modern machines and WfMS to enterprise systems; and 2) the advancement of MDA by extending the role of system models from guiding system development to controlling system behaviors. This research contributes to the area relevant to enterprise systems from three perspectives: 1) a new paradigm of enterprise systems, in which enterprise systems consist of two essential elements: system models and software programs. These two elements are loosely coupled and can exist independently; 2) semantic representations, which can effectively represent business entities, entity relationships, business logic and information processing logic in a semantic manner. Semantic representations are the key enabling techniques of model driven enterprise systems; and 3) a brand new role of system models; traditionally the role of system models is to guide developers to write system source code. This research promotes the role of system models to control the behaviors of enterprise.