Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Terbium(III) and dysprosium(III) 8-connected 3D networks containing 2,5-thiophenedicarboxylate anion: Crystal structures and photoluminescence studies

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Gene flow networks among American Aedes aegypti populations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Determination and statistical treatment of short-circuit currents for faults on the lines of networks of 440 kV CESP system

The distribution of short-circuit current is investigated by means of two methods, one direct and the other analytic; both methods consider uniform probability distribution of line faults. In the direct method, the procedure consists of calculating fault currents at equidistant points along the line, starting from one of the end points and considering the other end open. The magnitude of the current is classified according to Brazilian standards (regulation NBR-7118). The analytic method assumes that the distribution of short-circuit currents through the busbar and the distribution of the line length connected to it are known, as well as the independence of values. The method is designed to determine the probability that fault currents through a line will surpass the pre-established magnitude, thus generating frequency distribution curves of short-circuit currents along the lines.

Minimal cross-subsidies approach for loss allocation in distribution networks with open access

Open access philosophy applied by regulatory agencies may lead to a scenario where captive consumers will solely face the responsibility on distribution network's losses even with Independent Energy Producers (also known as Distributed Generation) and Independent Energy Consumers connected to the system. This work proposes the utilization of a loss allocation method in distribution systems where open access is allowed, in which cross-subsidies, that appear due to the influence the generators have over the system losses, are minimized. Thus, guaranteeing to some extent the efficiency and transparency of the economic signals of the market. Results obtained through the Zbus loss allocation method adapted for distribution networks are processed in such a way that the corresponding allocation to the generation buses is divided among the consumer buses, while still considering consumers spatial characteristics. © 2007 IEEE.

Voltage regulator modeling for the three-phase power flow in distribution networks

In this paper a three-phase power flow for electrical distribution systems considering different models of voltage regulators is presented. A voltage regulator (VR) is an equipment that maintains the voltage level in a predefined value in a distribution line in spite of the load variations within its nominal power. Three different types of connections are analyzed: 1) wye-connected regulators, 2) open delta-connected regulators and 3) closed delta-connected regulators. To calculate the power flow, the three-phase backward/forward sweep algorithm is used. The methodology is tested on the IEEE 34 bus distribution system. ©2008 IEEE.

Comparing support vector machines and artificial neural networks in the recognition of steering angle for driving of mobile robots through paths in plantations

The use of mobile robots turns out to be interesting in activities where the action of human specialist is difficult or dangerous. Mobile robots are often used for the exploration in areas of difficult access, such as rescue operations and space missions, to avoid human experts exposition to risky situations. Mobile robots are also used in agriculture for planting tasks as well as for keeping the application of pesticides within minimal amounts to mitigate environmental pollution. In this paper we present the development of a system to control the navigation of an autonomous mobile robot through tracks in plantations. Track images are used to control robot direction by pre-processing them to extract image features. Such features are then submitted to a support vector machine and an artificial neural network in order to find out the most appropriate route. A comparison of the two approaches was performed to ascertain the one presenting the best outcome. The overall goal of the project to which this work is connected is to develop a real time robot control system to be embedded into a hardware platform. In this paper we report the software implementation of a support vector machine and of an artificial neural network, which so far presented respectively around 93% and 90% accuracy in predicting the appropriate route. (C) 2013 The Authors. Published by Elsevier B.V. Selection and peer review under responsibility of the organizers of the 2013 International Conference on Computational Science

Pruning methods to MLP neural networks considering proportional apparent error rate for classification problems with unbalanced data

This article deals with classification problems involving unequal probabilities in each class and discusses metrics to systems that use multilayer perceptrons neural networks (MLP) for the task of classifying new patterns. In addition we propose three new pruning methods that were compared to other seven existing methods in the literature for MLP networks. All pruning algorithms presented in this paper have been modified by the authors to do pruning of neurons, in order to produce fully connected MLP networks but being small in its intermediary layer. Experiments were carried out involving the E. coli unbalanced classification problem and ten pruning methods. The proposed methods had obtained good results, actually, better results than another pruning methods previously defined at the MLP neural network area. (C) 2014 Elsevier Ltd. All rights reserved.

A Time-domain Harmonic Power-Flow Analysis in Electrical Energy Distribution Networks, Using Norton Models for Non-linear Loading

The purpose of this paper is to present the application of a three-phase harmonic propagation analysis time-domain tool, using the Norton model to approach the modeling of non-linear loads, making the harmonics currents flow more appropriate to the operation analysis and to the influence of mitigation elements analysis. This software makes it possible to obtain results closer to the real distribution network, considering voltages unbalances, currents imbalances and the application of mitigation elements for harmonic distortions. In this scenario, a real case study with network data and equipments connected to the network will be presented, as well as the modeling of non-linear loads based on real data obtained from some PCCs (Points of Common Coupling) of interests for a distribution company.

A nature-inspired approach to speed up optimum-path forest clustering and its application to intrusion detection in computer networks

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Integration of wireless sensor networks to the internet of things using a 6LoWPAN Gateway

The Internet of Things is a new paradigm where smart embedded devices and systems are connected to the Internet. In this context, Wireless Sensor Networks (WSN) are becoming an important alternative for sensing and actuating critical applications like industrial automation, remote patient monitoring and domotics. The IEEE 802.15.4 protocol has been adopted as a standard for WSN and the 6LoWPAN protocol has been proposed to overcome the challenges of integrating WSN and Internet protocols. In this paper, the mechanisms of header compression and fragmentation of IPv6 datagrams proposed in the 6LoWPAN standard were evaluated through field experiments using a gateway prototype and IEEE 802.15.4 nodes.