Multiplex PCR system to track authorized and unauthorized genetically modified soybean events in food and feed

A diverse range of genetic elements has been used to develop genetically modified organisms (GMOs) over the last 18 years. Screening methods that target few elements, such as the Cauliflower Mosaic Virus 35S promoter (P-35S) and Agrobacterium tumefaciens nopaline terminator (T-nos), are not sufficient to screen GMOs. In the present study, a multiplex PCR system for all globally commercialized GM soybean events was developed to easily trace the events. For this purpose, screening elements of 24 GM soybean events were investigated and 9 screening targets were selected and divided into three individual triplex PCR systems: P-35S, ribulose-1,5-bisphosphate carboxylase small subunit promoter of Arabidopsis thaliana, T-nos, T-35S, pea E9 terminator, open reading frame 23 terminator of A. tumefaciens, proteinase inhibitor II terminator of potato, acetohydroxy acid synthase large subunit terminator of A. thaliana, and the revealed 3′ flanking sequences of DP-305423-1. The specificity of the assays was confirmed using thirteen GM soybean events as the respective positive/negative controls. The limit of detection of each multiplex set, as determined using certified reference materials of specific GM events, ranged from 0.03 to 0.5%, depending upon target. Furthermore, 26 food samples that contained soybean ingredients, which were purchased from the USA, China, Japan, and Korea, were analyzed, 17 of which contained one or more GM soybean events. These results suggest that the developed screening method can be used to efficiently track and identify 24 GM soybean events in food and feed.     

Deliberately Losing Control of C−H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism

Combined photochemical arylation, “nuisance effect” (S_NAr) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein–ligand structure determination. Reactions were deliberately allowed to run “out of control” in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with S_NAr processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.     

A novel methodology for the rapid identification of the water diffusion coefficients of composite materials

The paper presents a novel methodology for the rapid identification of the water diffusion coefficients of composite materials. The methodology consists in employing a numerical parametric Proper Generalized Decomposition (PGD) method allowing incorporating the diffusion coefficients among the number of degrees of freedom. Compared to classical identification schemes, often based on Finite Element Method (FEM) iterations, the proposed method allows achieving consistent CPU time gain. The method is general and can be applied when diffusion anomalies take place or when diffusion–reaction coupling must be taken into account, moreover can deal with anisotropic materials. However, for the scope of illustration, in the present case, it is applied to the simple case of “classical diffusion” (Fick’s model with constant boundary conditions) and concerns isotropic materials.     

Synthesis of electrically conducting composite adsorbents for wastewater treatment using adsorption & electrochemical regeneration

Electrically conducting adsorbent materials called Nyex™ 1000 & 2000 have already been reported with comparatively low adsorption capacity for various organic, biologically non-degradable and toxic compounds. Two composite adsorbents called CA₁ & CA₂ were synthesized using synthetic graphite-carbon black and expanded graphite-carbon black respectively. The aim of developing the new adsorbents was to increase the adsorption capacity along with good electrical properties. The developed adsorbents were characterized using N₂ adsorption for specific surface area, Boehm surface titration for surface chemistry, bed electrical conductivity, laser size analyzer for average particle size, and scanning electron microscope (SEM) for particle morphology and shape. Then both the composite adsorbents were tested for the adsorption of acid violet 17 followed by an electrochemical regeneration. The adsorption study revealed that both the adsorbents had almost similar kinetic behavior with a significant increase in adsorption capacity for acid violet 17 (300 & 26 mg g⁻¹ respectively) when compared with the adsorption capacity of previously developed electrically conducting materials called Nyex™ 1000 & 2000 (3.5 and 9 mg g⁻¹ respectively). The composite adsorbent CA₂ was successfully electrochemically regenerated by passing an electric charge of 138 C g⁻¹ at a current density of 14 mA cm⁻² for a treatment time of 60 min, whereas, the composite adsorbent CA₁ could not be regenerated successfully. The regeneration efficiencies of CA₂ were obtained at around 120% during five adsorption–regeneration cycles. The amount of actual charge passed of 138 C g⁻¹ for achieving 100% regeneration efficiency was found to be similar with stoichiometrically calculated amount of charge. The amount of electrical energy required to oxidize each mg of adsorbed acid violet onto CA₂ (24 J mg⁻¹) was found to be significantly lower to that of Nyex™ 1000 & 2000 adsorbents (52 J mg⁻¹ & 32 J mg⁻¹ respectively).     

Modified cuckoo optimization algorithm (MCOA) to solve graph coloring problem

In recent years, various heuristic optimization methods have been developed. Many of these methods are inspired by swarm behaviors in nature, such as particle swarm optimization (PSO), firefly algorithm (FA) and cuckoo optimization algorithm (COA). Recently introduced COA, has proven its excellent capabilities, such as faster convergence and better global minimum achievement. In this paper a new approach for solving graph coloring problem based on COA was presented. Since COA at first was presented for solving continuous optimization problems, in this paper we use the COA for the graph coloring problem, we need a discrete COA. Hence, to apply COA to discrete search space, the standard arithmetic operators such as addition, subtraction and multiplication existent in COA migration operator based on the distance's theory needs to be redefined in the discrete space. Redefinition of the concept of the difference between the two habitats as the list of differential movements, COA is equipped with a means of solving the discrete nature of the non-permutation. A set of graph coloring benchmark problems are solved and its performance is compared with some well-known heuristic search methods. The obtained results confirm the high performance of the proposed method.     

Tractability frontiers of the partner units configuration problem

The partner units problem (PUP) is an acknowledged hard benchmark problem for the Logic Programming community with various industrial application fields like surveillance, electrical engineering, computer networks or railway safety systems. Although it is already known for a while that the PUP is NP-complete in its general form, complexity for subproblems reflecting the real problems in industrial fields remained widely unclear so far. In this article we provide all missing complexity results. For the subclass of the PUP that belongs to the complexity class P we present a polynomial-time algorithm and give in-depth algorithmic complexity results.     

2011 CAV award announcement

The 2011 CAV (Computer-Aided Verification) Award was presented on July 17, 2011 at the 23rd annual CAV conference in Snowbird, Utah to Thomas Ball and Sriram Rajamani of Microsoft Research for their contributions to software model checking, specifically the development of the SLAM/SDV software model checker, which successfully demonstrated computer-aided verification techniques on real programs.     

Relay pursuit of a maneuvering target using dynamic Voronoi diagrams

This paper addresses the problem of the pursuit of a maneuvering target by a group of pursuers distributed in the plane. This pursuit problem is solved by associating it with a Voronoi-like partitioning problem that characterizes the set of initial positions from which the target can be intercepted by a given pursuer faster than any other pursuer from the same group. In the formulation of this partitioning problem, the target does not necessarily travel along prescribed trajectories, as it is typically assumed in the literature, but, instead, it can apply an “evading” strategy in an effort to delay or, if possible, escape capture. We characterize an approximate solution to this problem by associating it with a standard Voronoi partitioning problem. Subsequently, we propose a relay pursuit strategy, that is, a special group pursuit scheme such that, at each instant of time, only one pursuer is assigned the task of capturing the maneuvering target. During the course of the relay pursuit, the pursuer–target assignment changes dynamically with time based on the (time varying) proximity relations between the pursuers and the target. This proximity information is encoded in the solution of the Voronoi-like partitioning problem. Simulation results are presented to highlight the theoretical developments.     

Algorithmic probabilistic game semantics

We present a detailed account of a translation from probabilistic call-by-value programs with procedures to Rabin’s probabilistic automata. The translation is fully abstract in that programs exhibit the same computational behaviour if and only if the corresponding automata are language-equivalent. Since probabilistic language equivalence is decidable, we can apply the translation to analyse the behaviour of probabilistic programs and protocols. We illustrate our approach on a number of case studies.