A biomimetic algorithm for the improved detection of microarray features,

One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface

'Extremotaxis': Computing with a bacterial-inspired algorithm

We present a general-purpose optimization algorithm inspired by “run-and-tumble”, the biased random walk chemotactic swimming strategy used by the bacterium Escherichia coli to locate regions of high nutrient concentration The method uses particles (corresponding to bacteria) that swim through the variable space (corresponding to the attractant concentration profile). By constantly performing temporal comparisons, the particles drift towards the minimum or maximum of the function of interest. We illustrate the use of our method with four examples. We also present a discrete version of the algorithm. The new algorithm is expected to be useful in combinatorial optimization problems involving many variables, where the functional landscape is apparently stochastic and has local minima, but preserves some derivative structure at intermediate scales

Verificação, avaliação e processamento das informações do programa de melhoramento de trigo para acesso e consulta por meio de bancos de dados relacional e grafo.

Editores técnicos: Joseani Mesquita Antunes, Ana Lídia Variani Bonato, Márcia Barrocas Moreira Pimentel

Parallel Mapper

The construction of Mapper has emerged in the last decade as a powerful and effective topological data analysis tool that approximates and generalizes other topological summaries, such as the Reeb graph, the contour tree, split, and joint trees. In this paper, we study the parallel analysis of the construction of Mapper. We give a provably correct parallel algorithm to execute Mapper on multiple processors and discuss the performance results that compare our approach to a reference sequential Mapper implementation. We report the performance experiments that demonstrate the efficiency of our method

Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch

The bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. This has previously been understood in terms of the classic two-state, concerted model of allosteric regulation. Here, we used high-resolution optical microscopy to observe switching of single motors and uncover the stochastic multistate nature of the switch. Our observations are in detailed quantitative agreement with a recent general model of allosteric cooperativity that exhibits conformational spread—the stochastic growth and shrinkage of domains of adjacent subunits sharing a particular conformational state. We expect that conformational spread will be important in explaining cooperativity in other large signaling complexes

Embedded software developments in KM3NeT phase I

TheKM3NeT collaboration has already produced more than one thousand acquisition boards, used for building two deep-sea neutrino detectors at the bottom of the Mediterranean Sea, with the aim of instrumenting a volume of several cubic kilometers with light sensors to detect the Cherenkov radiation produced in neutrino interactions. The so-called digital optical modules, house the PMTs and the acquisition and control electronics of the module, the central logic board, which includes a Xilinx FPGA and embedded soft processor. The present work presents the architecture and functionalities of the software embedded in the soft processor of the central logic board

Measurement of the atmospheric muon flux with the NEMO Phase-1 detector

The NEMO Collaboration installed and operated an underwater detector including prototypes of the critical elements of a possible underwater km3 neutrino telescope: a four-floor tower (called Mini-Tower) and a Junction Box. The detector was developed to test some of the main systems of the km3 detector, including the data transmission, the power distribution, the timing calibration and the acoustic positioning systems as well as to verify the capabilities of a single tridimensional detection structure to reconstruct muon tracks. We present results of the analysis of the data collected with the NEMO Mini-Tower. The position of photomultiplier tubes (PMTs) is determined through the acoustic position system. Signals detected with PMTs are used to reconstruct the tracks of atmospheric muons. The angular distribution of atmospheric muons was measured and results compared with Monte Carlo simulations.Comment: Astrop. Phys., accepte

Measurement of the atmospheric muon depth intensity relation with the NEMO Phase-2 tower

The results of the analysis of the data collected with the NEMO Phase-2 tower, deployed at 3500 m depth about 80 km off-shore Capo Passero (Italy), are presented. Cherenkov photons detected with the photomultipliers tubes were used to reconstruct the tracks of atmospheric muons. Their zenith-angle distribution was measured and the results compared with Monte Carlo simulations. An evaluation of the systematic effects due to uncertainties on environmental and detector parameters is also included. The associated depth intensity relation was evaluated and compared with previous measurements and theoretical predictions. With the present analysis, the muon depth intensity relation has been measured up to 13 km of water equivalent.Comment: submitted to Astroparticle Physic

Physical Conditions in the Foreground Gas of Reflection Nebulae: NGC 2023, vdB 102, and NGC 7023

High resolution optical spectra of HD 37903 and HD 147009, which illuminate the reflection nebulae, NGC 2023 and vdB 102, were obtained for comparison with our results for HD 200775 and NGC 7023. Ground-based measurements of the molecules, CH, C$_2$, and CN, and the atoms, Na I and K I, were analyzed to extract physical conditions in the foreground cloud. Estimates of the gas density, gas temperature and flux of ultraviolet radiation were derived and were compared with the results from infrared and radio studies of the main molecular cloud. The conditions are similar to those found in studies of diffuse clouds. The foreground material is less dense than the gas in the molecular cloud behind the star(s). The gas temperature was set at 40 K, the temperature determined for the foreground gas in NGC 7023. The flux of ultraviolet radiation was found to be less intense than in the molecular material behind the star(s). The column densities of Na I and K I were reproduced reasonably well when the extinction curve for the specific line of sight was adopted. We obtained NEWSIPS data from the IUE archive for HD 37903 and HD 200775. The ultraviolet data on C I and CO allow extraction of the physical conditions by alternate methods. General agreement among the various diagnostics was found, leading to self-consistent pictures of the foreground photodissociation regions. An Appendix describes checks on the usefulness of IUE NEWSIPS data for interstellar studies. (Abridged)Comment: 65 pages, 18 tables, 14 figures, Accepted for publication in ApJ

NEMO: A Project for a km3^3 Underwater Detector for Astrophysical Neutrinos in the Mediterranean Sea

The status of the project is described: the activity on long term characterization of water optical and oceanographic parameters at the Capo Passero site candidate for the Mediterranean km$^3$ neutrino telescope; the feasibility study; the physics performances and underwater technology for the km$^3$; the activity on NEMO Phase 1, a technological demonstrator that has been deployed at 2000 m depth 25 km offshore Catania; the realization of an underwater infrastructure at 3500 m depth at the candidate site (NEMO Phase 2).Comment: Proceeding of ISCRA 2006, Erice 20-27 June 200