Networks from gene expression time series: characterization of correlation patterns

This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real data, and features that are due to the method used for network reconstruction (time correlation).Comment: 10 pages, 3 BMP figures, 1 Table. To appear in Int. J. Bif. Chaos, July 2007, Volume 17, Issue

Detection and whole genome sequencing of CPMMV in common bean resistant to BGMV from Paraná State.

Cowpea mild mottle virus (CPMMV) is a Carlavirus from the family Betaflexiviridae which has a linear single stranded positive sense rna genome of approximately 8,200 nt and infects a wide range of cultivated plants from the Fabaceae family. It is transmitted by the whitefly Bemisia tabaci

Nutrient delivery efficiency of a combined sewer along a lake challenged by incipient eutrophication

Although sewage diversion outside of a lake's watershed is now ordinary practice in the restoration of eutrophic lakes, often the observed recovery is slower than expected and the internal load from the lake anoxic sediments is identified as a possible reason. However, in the case of combined sewer, the quantification of the residual nutrient load discharged from sewer spillways must also be questioned. In this paper, the diversion efficiency of the sewer system along the east coast of Lake Iseo, a prealpine Italian lake where eutrophication effects are still severe, is investigated. To this purpose, a representative part of the sewer system was modelled by PCSWMM and calibrated by using an extensive series of discharge measurements. Water quality monitoring during wet weather periods reveals that the first flush is common in tributary sewers, whereas it is absent along the main collector. Moreover, flow discharges are strongly affected by infiltration waters, which are controlled by the lake water level. The calibrated model, including infiltration modeling, was used to assess the annual overflow volumes and the nutrient load through a continuous 10-year simulation. Simulations were conducted both with regard to the current conditions and to a climate change scenario. Results show that the discharged residual load is at least 7 times larger than the design value, with the water infiltration contributing to 17% to the overflow volume and that non-structural practices could considerably reduce the overall impact of the sewer. This research thus provides important insight into the potential impact of combined sewer overflows on lacustrine environments and addresses effective mitigation measures in similar contexts

A HPC and Grid enabling framework for genetic linkage analysis of SNPs

Understanding the structure, function and development of the human genome is a key factor to improve the quality of life. In order to achieve this goal developing and using a modern ICT infrastructure is essential, and can exploit next generation High Performance Computing (HPC) systems beyond the Petaflop scale in a collaborative and efficient way. The genetic linkage analysis of Single Nucleotide Polymorphism (SNP) markers has recently become a very popular approach for genetic epidemiology and population studies, aiming to discover the genetic correlation in complex diseases. The high computational cost and memory requirements of the major algorithms proposed in the literature make analyses of medium/large data sets very hard on a single CPU. A Grid based facility has hence been set up upon a high-performance infrastructure, the EGEE Grid, in order to create a tool for achieving whole-genome linkage analysis

A HPC and Grid enabling framework for genetic linkage analysis of SNPs

Understanding the structure, function and development of the human genome is a key factor to improve the quality of life. In order to achieve this goal developing and using a modern ICT infrastructure is essential, and can exploit next generation High Performance Computing (HPC) systems beyond the Petaflop scale in a collaborative and efficient way. The genetic linkage analysis of Single Nucleotide Polymorphism (SNP) markers has recently become a very popular approach for genetic epidemiology and population studies, aiming to discover the genetic correlation in complex diseases. The high computational cost and memory requirements of the major algorithms proposed in the literature make analyses of medium/large data sets very hard on a single CPU. A Grid based facility has hence been set up upon a high-performance infrastructure, the EGEE Grid, in order to create a tool for achieving whole-genome linkage analysis

Large-scale modelling of neuronal systems

The brain is, without any doubt, the most complex system of the human body. Its complexity is also due to the extremely high number of neurons, as well as the huge number of synapses connecting them. Each neuron is capable to perform complex tasks, like learning and memorizing a large class of patterns. The simulation of large neuronal systems is challenging for both technological and computational reasons, and can open new perspectives for the comprehension of brain functioning. A well-known and widely accepted model of bidirectional synaptic plasticity, the BCM model, is stated by a differential equation approach based on bistability and selectivity properties. We have modified the BCM model extending it from a single-neuron to a whole-network model. This new model is capable to generate interesting network topologies starting from a small number of local parameters, describing the interaction between incoming and outgoing links from each neuron. We have characterized this model in terms of complex network theory, showing how this learning rule can be a support for network generation

Singularities and closed time-like curves in type IIB 1/2 BPS geometries

We study in detail the moduli space of solutions discovered in LLM relaxing the constraint that guarantees the absence of singularities. The solutions fall into three classes, non-singular, null-singular and time machines with a time-like naked singularity. We study the general features of these metrics and prove that there are actually just two generic classes of space-times - those with null singularities are in the same class as the non-singular metrics. AdS/CFT seems to provide a dual description only for the first of these two types of space-time in terms of a unitary CFT indicating the possible existence of a chronology protection mechanism for this class of geometries.Comment: 34 pages, 7 figures, LaTeX. References adde

BPS R-balls in N=4 SYM on R X S^3, Quantum Hall Analogy and AdS/CFT Holography

In this paper, we propose a new approach to study the BPS dynamics in N=4 supersymmetric U(N) Yang-Mills theory on R X S^3, in order to better understand the emergence of gravity in the gauge theory. Our approach is based on supersymmetric, space-filling Q-balls with R-charge, which we call R-balls. The usual collective coordinate method for non-topological scalar solitons is applied to quantize the half and quarter BPS R-balls. In each case, a different quantization method is also applied to confirm the results from the collective coordinate quantization. For finite N, the half BPS R-balls with a U(1) R-charge have a moduli space which, upon quantization, results in the states of a quantum Hall droplet with filling factor one. These states are known to correspond to the ``sources'' in the Lin-Lunin-Maldacena geometries in IIB supergravity. For large N, we find a new class of quarter BPS R-balls with a non-commutativity parameter. Quantization on the moduli space of such R-balls gives rise to a non-commutative Chern-Simons matrix mechanics, which is known to describe a fractional quantum Hall system. In view of AdS/CFT holography, this demonstrates a profound connection of emergent quantum gravity with non-commutative geometry, of which the quantum Hall effect is a special case.Comment: 42 pages, 2 figures; v3: a new paragraph on counting unbroken susy of NC R-balls and references adde