A transient assay for recombination demonstrates that Arabidopsis SNM1 and XRCC3 enhance non-homologous recombination

Replacement of endogenous genes by homologous recombination is rare in plants; the majority of genetic modifications are the result of transforming DNA molecules undergoing random genomic insertion by way of non-homologous recombination. Factors that affect chromatin remodeling and DNA repair are thought to have the potential to enhance the frequency of homologous recombination in plants. Conventional tools to study the frequencies of genetic recombination often rely on stable transformation-based approaches, with these systems being rarely capable of high-throughput or combinatorial analysis. We developed a series of vectors that use chemiluminescent (LUC and REN) reporter genes to assay the relative frequency of homologous and non-homologous recombination in plants. These transient assay vectors were used to screen 14 candidategenes for their effects on recombination frequencies in Nicotiana benthamiana plants. Over-expression of Arabidopsis genes with sequence similarity to SNM1 from yeast and XRCC3 from humans enhanced the frequency of non-homologous recombination when assayed using two different donor vectors. Transient N. benthamiana leaf systems were also used in an alternative assay for preliminary measurements of homologous recombination frequencies, which were found to be enhanced by over-expression of RAD52, MIM and RAD51 from yeast, as well as CHR24 from Arabidopsis. The findings for the assays described here are in line with previous studies that analyzed recombination frequencies using stable transformation. The assays we report have revealed functions in non-homologous recombination for the Arabidopsis SNM1 and XRCC3 genes, so the suppression of these genes' expression offers a potential means to enhance the gene targeting frequency in plants. Furthermore, our findings also indicate that plant gene targeting frequencies could be enhanced by over-expression of RAD52, MIM, CHR24, and RAD51 genes.

Authenticating Multicast Streams in Lossy Channels Using Threshold Techniques

We first classify the state-of-the-art stream authentication problem in the multicast environment and group them into Signing and MAC approaches. A new approach for authenticating digital streams using Threshold Techniques is introduced. The new approach main advantages are in tolerating packet loss, up to a threshold number, and having a minimum space overhead. It is most suitable for multicast applications running over lossy, unreliable communication channels while, in same time, are pertain the security requirements. We use linear equations based on Lagrange polynomial interpolation and Combinatorial Design methods.

Broadcast anti-jamming systems

In a traditional anti-jamming system a transmitter who wants to send a signal to a single receiver spreads the signal power over a wide frequency spectrum with the aim of stopping a jammer from blocking the transmission. In this paper, we consider the case that there are multiple receivers and the transmitter wants to broadcast a message to all receivers such that colluding groups of receivers cannot jam the reception of any other receiver. We propose efficient coding methods that achieve this goal and link this problem to well-known problems in combinatorics. We also link a generalisation of this problem to the Key Distribution Pattern problem studied in combinatorial cryptography.

Efficient one-time proxy signatures

One-time proxy signatures are one-time signatures for which a primary signer can delegate his or her signing capability to a proxy signer. In this work we propose two one-time proxy signature schemes with different security properties. Unlike other existing one-time proxy signatures that are constructed from public key cryptography, our proposed schemes are based one-way functions without trapdoors and so they inherit the communication and computation efficiency from the traditional one-time signatures. Although from a verifier point of view, signatures generated by the proxy are indistinguishable from those created by the primary signer, a trusted authority can be equipped with an algorithm that allows the authority to settle disputes between the signers. In our constructions, we use a combination of one-time signatures, oblivious transfer protocols and certain combinatorial objects. We characterise these new combinatorial objects and present constructions for them.

Made-to-order nanocarbons through deterministic plasma nanotechnology

Through a combinatorial approach involving experimental measurement and plasma modelling, it is shown that a high degree of control over diamond-like nanocarbon film sp3/sp2 ratio (and hence film properties) may be exercised, starting at the level of electrons (through modification of the plasma electron energy distribution function). Hydrogenated amorphous carbon nanoparticle films with high percentages of diamond-like bonds are grown using a middle-frequency (2 MHz) inductively coupled Ar + CH4 plasma. The sp3 fractions measured by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy in the thin films are explained qualitatively using sp3/sp2 ratios 1) derived from calculated sp3 and sp2 hybridized precursor species densities in a global plasma discharge model and 2) measured experimentally. It is shown that at high discharge power and lower CH4 concentrations, the sp3/sp2 fraction is higher. Our results suggest that a combination of predictive modeling and experimental studies is instrumental to achieve deterministically grown made-to-order diamond-like nanocarbons suitable for a variety of applications spanning from nano-magnetic resonance imaging to spin-flip quantum information devices. This deterministic approach can be extended to graphene, carbon nanotips, nanodiamond and other nanocarbon materials for a variety of applications

Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma

Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.

On secure multi-party computation in black-box groups

We study the natural problem of secure n-party computation (in the passive, computationally unbounded attack model) of the n-product function f G (x 1,...,x n ) = x 1 ·x 2 ⋯ x n in an arbitrary finite group (G,·), where the input of party P i is x i  ∈ G for i = 1,...,n. For flexibility, we are interested in protocols for f G which require only black-box access to the group G (i.e. the only computations performed by players in the protocol are a group operation, a group inverse, or sampling a uniformly random group element). Our results are as follows. First, on the negative side, we show that if (G,·) is non-abelian and n ≥ 4, then no ⌈n/2⌉-private protocol for computing f G exists. Second, on the positive side, we initiate an approach for construction of black-box protocols for f G based on k-of-k threshold secret sharing schemes, which are efficiently implementable over any black-box group G. We reduce the problem of constructing such protocols to a combinatorial colouring problem in planar graphs. We then give two constructions for such graph colourings. Our first colouring construction gives a protocol with optimal collusion resistance t < n/2, but has exponential communication complexity O(n*2t+1^2/t) group elements (this construction easily extends to general adversary structures). Our second probabilistic colouring construction gives a protocol with (close to optimal) collusion resistance t < n/μ for a graph-related constant μ ≤ 2.948, and has efficient communication complexity O(n*t^2) group elements. Furthermore, we believe that our results can be improved by further study of the associated combinatorial problems.

Threshold MACs

The power of sharing computation in a cryptosystem is crucial in several real-life applications of cryptography. Cryptographic primitives and tasks to which threshold cryptosystems have been applied include variants of digital signature, identification, public-key encryption and block ciphers etc. It is desirable to extend the domain of cryptographic primitives which threshold cryptography can be applied to. This paper studies threshold message authentication codes (threshold MACs). Threshold cryptosystems usually use algebraically homomorphic properties of the underlying cryptographic primitives. A typical approach to construct a threshold cryptographic scheme is to combine a (linear) secret sharing scheme with an algebraically homomorphic cryptographic primitive. The lack of algebraic properties of MACs rules out such an approach to share MACs. In this paper, we propose a method of obtaining a threshold MAC using a combinatorial approach. Our method is generic in the sense that it is applicable to any secure conventional MAC by making use of certain combinatorial objects, such as cover-free families and their variants. We discuss the issues of anonymity in threshold cryptography, a subject that has not been addressed previously in the literature in the field, and we show that there are trade-offis between the anonymity and efficiency of threshold MACs.

A Memetic Algorithm for the location-based continuously operating reference stations placement problem in Network Real-Time Kinematic

Network Real-Time Kinematic (NRTK) is a technology that can provide centimeter-level accuracy positioning services in real time, and it is enabled by a network of Continuously Operating Reference Stations (CORS). The location-oriented CORS placement problem is an important problem in the design of a NRTK as it will directly affect not only the installation and operational cost of the NRTK, but also the quality of positioning services provided by the NRTK. This paper presents a Memetic Algorithm (MA) for the location-oriented CORS placement problem, which hybridizes the powerful explorative search capacity of a genetic algorithm and the efficient and effective exploitative search capacity of a local optimization. Experimental results have shown that the MA has better performance than existing approaches. In this paper we also conduct an empirical study about the scalability of the MA, effectiveness of the hybridization technique and selection of crossover operator in the MA.

Further development of discrete computational techniques for calculation of restricted diffusion propagators in porous media

Magnetic resonance is a well-established tool for structural characterisation of porous media. Features of pore-space morphology can be inferred from NMR diffusion-diffraction plots or the time-dependence of the apparent diffusion coefficient. Diffusion NMR signal attenuation can be computed from the restricted diffusion propagator, which describes the distribution of diffusing particles for a given starting position and diffusion time. We present two techniques for efficient evaluation of restricted diffusion propagators for use in NMR porous-media characterisation. The first is the Lattice Path Count (LPC). Its physical essence is that the restricted diffusion propagator connecting points A and B in time t is proportional to the number of distinct length-t paths from A to B. By using a discrete lattice, the number of such paths can be counted exactly. The second technique is the Markov transition matrix (MTM). The matrix represents the probabilities of jumps between every pair of lattice nodes within a single timestep. The propagator for an arbitrary diffusion time can be calculated as the appropriate matrix power. For periodic geometries, the transition matrix needs to be defined only for a single unit cell. This makes MTM ideally suited for periodic systems. Both LPC and MTM are closely related to existing computational techniques: LPC, to combinatorial techniques; and MTM, to the Fokker-Planck master equation. The relationship between LPC, MTM and other computational techniques is briefly discussed in the paper. Both LPC and MTM perform favourably compared to Monte Carlo sampling, yielding highly accurate and almost noiseless restricted diffusion propagators. Initial tests indicate that their computational performance is comparable to that of finite element methods. Both LPC and MTM can be applied to complicated pore-space geometries with no analytic solution. We discuss the new methods in the context of diffusion propagator calculation in porous materials and model biological tissues.

Spatial governance: The metalanguage of spatiotemporal information and its infrastructure

‘Spatial governance’ involves a large number of situations where knowledge of place and time is important in achieving acceptable organisational outcomes. This paper argues that spatial governance calls for information-intensive activity in three main areas. The first establishes ‘authority’ in a legal entity to decide issues regarding resources within a territorial jurisdiction. The second involves planning the future use of resources. It engages a language of design, purpose, modeling, visualization, expectations and risk. The third involves monitoring of outcomes to see if expectations are met; and whether changes to authority and planning regimes need to be made in the light of experience. This engages a language of observing, recording, accounting, auditing, statistical indicators and accountability. ‘Authority’, ‘planning’ and ‘monitoring’ regimes can be constructed using a relatively small number of elements, in much the same way that a large number of words with recognisable meanings can be created using a relatively few standardised letters of the alphabet. Words can combine in a similar process of combinatorial explosion to create any message that can be imagined. Similarly, combining authority, planning and monitoring regimes can create a metalanguage of ‘spatial governance’ to give purpose, meaning and value to any spatiotemporal information system that can be imagined, described, interpreted and understood.

A new approach to the cloud-based heterogeneous MapReduce placement problem

Guaranteeing Quality of Service (QoS) with minimum computation cost is the most important objective of cloud-based MapReduce computations. Minimizing the total computation cost of cloud-based MapReduce computations is done through MapReduce placement optimization. MapReduce placement optimization approaches can be classified into two categories: homogeneous MapReduce placement optimization and heterogeneous MapReduce placement optimization. It is generally believed that heterogeneous MapReduce placement optimization is more effective than homogeneous MapReduce placement optimization in reducing the total running cost of cloud-based MapReduce computations. This paper proposes a new approach to the heterogeneous MapReduce placement optimization problem. In this new approach, the heterogeneous MapReduce placement optimization problem is transformed into a constrained combinatorial optimization problem and is solved by an innovative constructive algorithm. Experimental results show that the running cost of the cloud-based MapReduce computation platform using this new approach is 24:3%-44:0% lower than that using the most popular homogeneous MapReduce placement approach, and 2:0%-36:2% lower than that using the heterogeneous MapReduce placement approach not considering the spare resources from the existing MapReduce computations. The experimental results have also demonstrated the good scalability of this new approach.

Balancing exploration and exploitation in particle swarm optimization on search tasking

In this study we present a combinatorial optimization method based on particle swarm optimization and local search algorithm on the multi-robot search system. Under this method, in order to create a balance between exploration and exploitation and guarantee the global convergence, at each iteration step if the distance between target and the robot become less than specific measure then a local search algorithm is performed. The local search encourages the particle to explore the local region beyond to reach the target in lesser search time. Experimental results obtained in a simulated environment show that biological and sociological inspiration could be useful to meet the challenges of robotic applications that can be described as optimization problems.

Phagotopes derived by antibody screening of phage-displayed random peptide libraries vary in immunoreactivity: Studies using an exemplary monoclonal antibody, CII-C1, to type II collagen

Antibody screening of phage-displayed random peptide libraries to identify mimotopes of conformational epitopes is promising. However, because interpretations can be difficult, an exemplary system has been used in the present study to investigate whether variation in the peptide sequences of selected phagotopes corresponded with variation in immunoreactivity. The phagotopes, derived using a well-characterized monoclonal antibody, CII-C1, to a known conformational epitope on type II collagen, C1, were tested by direct and inhibition ELISA for reactivity with CII-C1. A multiple sequence alignment algorithm, PILEUP, was used to sort the peptides expressed by the phagotopes into clusters. A model was prepared of the C1 epitope on type II collagen. The 12 selected phagotopes reacted with CII-C1 by both direct ELISA (titres from < 100-11 200) and inhibition ELISA (20-100% inhibition); the reactivity varied according to the peptide sequence and assay format. The differences in reactivity between the phagotopes were mostly in accord with the alignment, by PILEUP, of the peptide sequences. The finding that the phagotopes functionally mimicked the C1 epitope on collagen was validated in that amino acids RRL at the amino terminal of many of the peptides were topographically demonstrable on the model of the C1 epitope. Notably, one phagotope that expressed the widely divergent peptide C-IAPKRHNSA-C also mimicked the C1 epitope, as judged by reactivity in each of the assays used: these included cross-inhibition of CII-C1 reactivity with each of the other phagotopes and inhibition by a synthetic peptide corresponding to that expressed by the most frequently selected phagotope, RRLPFGSQM. Thus, it has been demonstrated that multiple phage-displayed peptides can mimic the same epitope and that observed immunoreactivity of selected phagotopes with the selecting mAb can depend on the primary sequence of the expressed peptide and also on the assay format used.

Estimates on the coverage of parameter space using populations of models

In this paper we provide estimates for the coverage of parameter space when using Latin Hypercube Sampling, which forms the basis of building so-called populations of models. The estimates are obtained using combinatorial counting arguments to determine how many trials, k, are needed in order to obtain specified parameter space coverage for a given value of the discretisation size n. In the case of two dimensions, we show that if the ratio (Ø) of trials to discretisation size is greater than 1, then as n becomes moderately large the fractional coverage behaves as 1-exp-ø. We compare these estimates with simulation results obtained from an implementation of Latin Hypercube Sampling using MATLAB.