Online Permutation Routing in Partitioned Optical Passive Star Networks

This paper establishes the state of the art in both deterministic and randomized online permutation routing in the POPS network. Indeed, we show that any permutation can be routed online on a POPS network either with $O(\frac{d}{g}\log g)$ deterministic slots, or, with high probability, with $5c\lceil d/g\rceil+o(d/g)+O(\log\log g)$ randomized slots, where constant $c=\exp (1+e^{-1})\approx 3.927$. When $d=\Theta(g)$, that we claim to be the "interesting" case, the randomized algorithm is exponentially faster than any other algorithm in the literature, both deterministic and randomized ones. This is true in practice as well. Indeed, experiments show that it outperforms its rivals even starting from as small a network as a POPS(2,2), and the gap grows exponentially with the size of the network. We can also show that, under proper hypothesis, no deterministic algorithm can asymptotically match its performance

Routing Permutations in Partitioned Optical Passive Star Networks

It is shown that a POPS network with g groups and d processors per group can efficiently route any permutation among the n=dg processors. The number of slots used is optimal in the worst case, and is at most the double of the optimum for all permutations p such that p(i)i for all i.Comment: 8 pages, 3 figure

Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference

Some Simple Distributed Algorithms for Sparse Networks

We give simple, deterministic, distributed algorithms for computing maximal matchings, maximal independent sets and colourings. We show that edge colourings with at most 2D-1 colours, and maximal matchings can be computed within O(log^* n + D) deterministic rounds, where D is the maximum degree of the network. We also show how to find maximal independent sets and (D+1)-vertex colourings within O(log^* n + D^2) deterministic rounds. All hidden constants are very small and the algorithms are very simple

Multifractal Characterization of Protein Contact Networks

The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the characteristic exponents and the multifractal spectrum can be further analyzed to discover important insights about the underlying dynamical process. In this paper, we employ multifractal analysis techniques in the study of protein contact networks. To this end, initially a network is mapped to three different time series, each of which is generated by a stationary unbiased random walk. To capture the peculiarities of the networks at different levels, we accordingly consider three observables at each vertex: the degree, the clustering coefficient, and the closeness centrality. To compare the results with suitable references, we consider also instances of three well-known network models and two typical time series with pure monofractal and multifractal properties. The first result of notable interest is that time series associated to proteins contact networks exhibit long-range correlations (strong persistence), which are consistent with signals in-between the typical monofractal and multifractal behavior. Successively, a suitable embedding of the multifractal spectra allows to focus on ensemble properties, which in turn gives us the possibility to make further observations regarding the considered networks. In particular, we highlight the different role that small and large fluctuations of the considered observables play in the characterization of the network topology

A generative model for protein contact networks

In this paper we present a generative model for protein contact networks. The soundness of the proposed model is investigated by focusing primarily on mesoscopic properties elaborated from the spectra of the graph Laplacian. To complement the analysis, we study also classical topological descriptors, such as statistics of the shortest paths and the important feature of modularity. Our experiments show that the proposed model results in a considerable improvement with respect to two suitably chosen generative mechanisms, mimicking with better approximation real protein contact networks in terms of diffusion properties elaborated from the Laplacian spectra. However, as well as the other considered models, it does not reproduce with sufficient accuracy the shortest paths structure. To compensate this drawback, we designed a second step involving a targeted edge reconfiguration process. The ensemble of reconfigured networks denotes improvements that are statistically significant. As a byproduct of our study, we demonstrate that modularity, a well-known property of proteins, does not entirely explain the actual network architecture characterizing protein contact networks. In fact, we conclude that modularity, intended as a quantification of an underlying community structure, should be considered as an emergent property of the structural organization of proteins. Interestingly, such a property is suitably optimized in protein contact networks together with the feature of path efficiency.Comment: 18 pages, 67 reference

Region-Based PDEs for Cells Counting and Segmentation in 3D+Time Images of Vertebrate Early Embryogenesis

This paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage

Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins

In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological descriptors, such as the modularity and statistics of the shortest paths, and different interpretations in terms of diffusion provided by the discrete heat kernel, which is elaborated from the normalized graph Laplacians. A principal component analysis shows high discrimination among the network types, either by considering the topological and heat kernel based vector characterizations. Furthermore, a canonical correlation analysis demonstrates the strong agreement among those two characterizations, providing thus an important justification in terms of interpretability for the heat kernel. Finally, and most importantly, the focused analysis of the heat kernel provides a way to yield insights on the fact that proteins have to satisfy specific structural design constraints that the other considered networks do not need to obey. Notably, the heat trace decay of an ensemble of varying-size proteins denotes subdiffusion, a peculiar property of proteins

Colour coded

This 300 word publication to be published by the Society of Dyers and Colourists (SDC) is a collection of the best papers from a 4-year European project that has considered colour from the perspective of both the arts and sciences.The notion of art and science and the crossovers between the two resulted in application and funding for cross disciplinary research to host a series of training events between 2006 and 2010 Marie Curie Conferences & Training Courses (SCF) Call Identifier: FP6-Mobility-4, Euros 532,363.80 CREATE – Colour Research for European Advanced Technology Employment. The research crossovers between the fields of art, science and technology was also a subject that was initiated through Bristol’s Festival if Ideas events in May 2009. The author coordinated and chaired an event during which the C.P Snow lecture “On Two Cultures’ (1959) was re-presented by Actor Simon Cook and then a lecture made by Raymond Tallis on the notion of the Polymath. The CREATE project has a worldwide impact for researchers, academics and scientists. Between January and October 2009, the site has received 221, 414 visits. The most popular route into the site is via the welcome page. The main groups of visitors originate in the UK (including Northern Ireland), Italy, France, Finland, Norway, Hungary, USA, Finland and Spain. A basic percentage breakdown of the traffic over ten months indicates: USA -15%; UK - 16%; Italy - 13%; France -12%; Hungary - 10%; Spain - 6%; Finland - 9%; Norway - 5%. The remaining approximate 14% of visitors are from other countries including Belgium, The Netherlands and Germany (approx 3%). A discussion group has been initiated by the author as part of the CREATE project to facilitate an ongoing dialogue between artists and scientists. http://createcolour.ning.com/group/artandscience www.create.uwe.ac.uk.Related papers to this research: A report on the CREATE Italian event: Colour in cultural heritage.C. Parraman, A. Rizzi, ‘Developing the CREATE network in Europe’, in Colour in Art, Design and Nature, Edinburgh, 24 October 2008.C. Parraman, “Mixing and describing colour”. CREATE (Training event 1), France, 2008