Structure-function studies of the plant cyclotides: The role of a circular protein backbone

The traditional idea of proteins as linear chains of amino acids is being challenged with the discovery of miniproteins that contain a circular backbone. The cyclotide family is the largest group of circular proteins and is characterized by an amide-circularized protein backbone and six conserved cysteine residues. These conserved cysteines are paired to form a knotted network of disulfide bonds. The combination of the circular backbone and a cystine knot, known as the cyclic cystine knot (CCK) motif, confers exceptional stability upon the cyclotides. This review discusses the role of the circular backbone based on studies of both the oxidative folding of kalata B1, the prototypical cyclotide, and a comparison of the structure and activity of kalata B1 and its acyclic permutants.

The cross-entropy method for network reliability estimation

Consider a network of unreliable links, modelling for example a communication network. Estimating the reliability of the network-expressed as the probability that certain nodes in the network are connected-is a computationally difficult task. In this paper we study how the Cross-Entropy method can be used to obtain more efficient network reliability estimation procedures. Three techniques of estimation are considered: Crude Monte Carlo and the more sophisticated Permutation Monte Carlo and Merge Process. We show that the Cross-Entropy method yields a speed-up over all three techniques.

A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays

Motivation: An important problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. We provide a straightforward and easily implemented method for estimating the posterior probability that an individual gene is null. The problem can be expressed in a two-component mixture framework, using an empirical Bayes approach. Current methods of implementing this approach either have some limitations due to the minimal assumptions made or with more specific assumptions are computationally intensive. Results: By converting to a z-score the value of the test statistic used to test the significance of each gene, we propose a simple two-component normal mixture that models adequately the distribution of this score. The usefulness of our approach is demonstrated on three real datasets.

Do simple intransitive finger movements consistently activate frontoparietal mirror neuron areas in humans?

The posterior inferior frontal gyrus (pIFG) and anterior inferior parietal lobule (aIPL) form the core regions of the human “mirror neuron system” that matches an observed movement onto its internal motor representation. We used event-related functional MRI to examine whether simple intransitive finger movements evoke “mirror activity” in the pIFG and aIPL. In separate sessions, participants either merely observed visuospatial stimuli or responded to them as quickly as possible with a spatially compatible finger movement. A picture of a relaxed hand with static dots on the tip of the index and little finger was continuously presented as high-level baseline. Four types of stimuli were presented in a pseudorandom order: a color change of a dot, a moving finger, a moving dot, or a simultaneous finger-dot movement. Dot movements were spatially and kinematically matched to finger movements. Participants were faster at imitating a finger movement than performing the same movement in response to a moving dot or a color change of a dot. Though imitative responses were facilitated, fMRI revealed no additional “mirror activity” in the pIFG and aIPL during the observation or imitation of finger movements as opposed to observing or responding to a moving dot. Mere observation of a finger movement alone failed to induce significant activation of the pIFG and aIPL. The lack of a signature of “mirror neuron activity” in the inferior frontoparietal cortex is presumably due to specific features of the task which may have favored stimulus–response mapping based on common spatial coding. We propose that the responsiveness of human frontoparietal mirror neuron areas to simple intransitive movements critically depends on the experimental context.

Reduction of nonlinear intrachannel effects by channel asymmetry in transmission lines with strong bit overlapping

We have examined the statistics of simulated bit-error rates in optical transmission systems with strong patterning effects and have found strong correlation between the probability of marks in a pseudorandom pattern and the error-free transmission distance. We discuss how a reduced density of marks can be achieved by preencoding optical data.

Network effects, network structure and consumer interaction in mobile telecommunications in Europe and Asia

This paper estimates the importance of (tariff-mediated) network effects and the impact of a consumer's social network on her choice of mobile phone provider. The study uses network data obtained from surveys of students in several European and Asian countries. We use the Quadratic Assignment Procedure, a non-parametric permutation test, to adjust for the particular error structure of network data. We find that respondents strongly coordinate their choice of mobile phone providers, but only if their provider induces network effects. This suggests that this coordination depends on network effects rather than on information contagion or pressure to conform to the social environment.

On a New Approach to Williamson's Generalization of Pólya's Enumeration Theorem

Pólya’s fundamental enumeration theorem and some results from Williamson’s generalized setup of it are proved in terms of Schur- Macdonald’s theory (S-MT) of “invariant matrices”. Given a permutation group W ≤ Sd and a one-dimensional character χ of W , the polynomial functor Fχ corresponding via S-MT to the induced monomial representation Uχ = ind|Sdv/W (χ) of Sd , is studied. It turns out that the characteristic ch(Fχ ) is the weighted inventory of some set J(χ) of W -orbits in the integer-valued hypercube [0, ∞)d . The elements of J(χ) can be distinguished among all W -orbits by a maximum property. The identity ch(Fχ ) = ch(Uχ ) of both characteristics is a consequence of S-MT, and is equivalent to a result of Williamson. Pólya’s theorem can be obtained from the above identity by the specialization χ = 1W , where 1W is the unit character of W.

Realization of an Optimal Schedule for the Two-machine Flow-Shop with Interval Job Processing Times

Non-preemptive two-machine flow-shop scheduling problem with uncertain processing times of n jobs is studied. In an uncertain version of a scheduling problem, there may not exist a unique schedule that remains optimal for all possible realizations of the job processing times. We find necessary and sufficient conditions (Theorem 1) when there exists a dominant permutation that is optimal for all possible realizations of the job processing times. Our computational studies show the percentage of the problems solvable under these conditions for the cases of randomly generated instances with n ≤ 100 . We also show how to use additional information about the processing times of the completed jobs during optimal realization of a schedule (Theorems 2 – 4). Computational studies for randomly generated instances with n ≤ 50 show the percentage of the two- machine flow-shop scheduling problems solvable under the sufficient conditions given in Theorems 2 – 4.

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.

On Solving the Maximum Betweenness Problem Using Genetic Algorithms

In this paper a genetic algorithm (GA) is applied on Maximum Betweennes Problem (MBP). The maximum of the objective function is obtained by finding a permutation which satisfies a maximal number of betweenness constraints. Every permutation considered is genetically coded with an integer representation. Standard operators are used in the GA. Instances in the experimental results are randomly generated. For smaller dimensions, optimal solutions of MBP are obtained by total enumeration. For those instances, the GA reached all optimal solutions except one. The GA also obtained results for larger instances of up to 50 elements and 1000 triples. The running time of execution and finding optimal results is quite short.

Dickson Polynomials that are Permutations

2000 Mathematics Subject Classification: 11T06, 13P10.

Mathematical Modeling of the Weaving Structure Design

Красимир Йорджев, Христина Костадинова - В работата се разглежда една релация на еквивалентност в множеството от всички квадратни бинарни матрици. Обсъдена е комбинаторната задача за намиране мощността и елементите на фактормножеството относно тази релация. Разгледана е и възможността за получаване на някои специални елементи на това фактормножество. Предложен е алгоритъм за решаване на поставените задачи. Получените в статията резултати намират приложение при описанието топологията на различните тъкачни структури.

On some Finite-Dimensional Representations of Artin Braid Group

Валентин В. Илиев - Авторът изучава някои хомоморфни образи G на групата на Артин на плитките върху n нишки в крайни симетрични групи. Получените пермутационни групи G са разширения на симетричната група върху n букви чрез подходяща абелева група. Разширенията G зависят от един целочислен параметър q ≥ 1 и се разцепват тогава и само тогава, когато 4 не дели q. В случая на нечетно q са намерени всички крайномерни неприводими представяния на G, а те от своя страна генерират безкрайна редица от неприводими представяния на групата на плитките.

Zolotarev's proof of Gauss reciprocity and Jacobi symbols

2000 Mathematics Subject Classification: Primary 11A15.

Polynomial automorphisms over finite fields: Mimicking tame maps by the Derksen group

2010 Mathematics Subject Classification: 14L99, 14R10, 20B27.