Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.

Aquatic weed automatic classification using machine learning techniques

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

Bronze Bug Thaumastocoris Peregrinus Carpintero and Dellapé (Hemiptera: Thaumastocoridae) on Eucalyptus in Brazil and its Distribution

The bronze bug Thaumastocoris peregrinus Carpintero & Dellape (Hemiptera: Thaumastocoridae) was detected infesting Eucalyptus trees in Brazil in 2008, in the states of São Paulo, Rio Grande do Sul and Minas Gerais and in 2009 was found in the state of Espirito Santo, Mato Grosso do Sul, Rio de Janeiro and Parana. Details about geographical spread, means of introduction, impact in Eucalyptus plantations and natural enemies observed in the field are discussed.

Automatic detection of thermal damage in grinding process by artificial neural network

Esse trabalho tem por objetivo o desenvolvimento de um sistema inteligente para detecção da queima no processo de retificação tangencial plana através da utilização de uma rede neural perceptron multi camadas, treinada para generalizar o processo e, conseqüentemente, obter o limiar de queima. em geral, a ocorrência da queima no processo de retificação pode ser detectada pelos parâmetros DPO e FKS. Porém esses parâmetros não são eficientes nas condições de usinagem usadas nesse trabalho. Os sinais de emissão acústica e potência elétrica do motor de acionamento do rebolo são variáveis de entrada e a variável de saída é a ocorrência da queima. No trabalho experimental, foram empregados um tipo de aço (ABNT 1045 temperado) e um tipo de rebolo denominado TARGA, modelo ART 3TG80.3 NVHB.

Power performance evaluation of an electric home fan with triac-based automatic speed control system

In order to provide a low cost system of thermal comfort, a common model of home fan, 40 cm diameter size, had its manual four-button control system replaced by an automatic speed control. The new control system has a temperature sensor feeding a microcontroller that, by using an optic coupling, DIAC or TRIAC-based circuit, varies the RMS value of the fan motor input voltage and its speed, according to the room temperature. Over a wide range of velocity, the fan net power and the motor fan input power were measured working under both control system. The temperature of the motor stator and the voltage waveforms were observed too. Measured values analysis showed that the TRIAC-based control system makes the fan motor work at a very low power factor and efficiency values. The worst case is at low velocity range where the higher fan motor stator temperatures were registered. The poor power factor and efficiency and the harmonics signals inserted in the motor input voltage wave by the TRIAC commutation procedure are correlated.

A Beam Search Method to Solve the Problem of Assignment Cells to Switches in a Cellular Mobile Network

Assigning cells to switches in a cellular mobile network is known as an NP-hard optimization problem. This means that the alternative for the solution of this type of problem is the use of heuristic methods, because they allow the discovery of a good solution in a very satisfactory computational time. This paper proposes a Beam Search method to solve the problem of assignment cell in cellular mobile networks. Some modifications in this algorithm are also presented, which allows its parallel application. Computational results obtained from several tests confirm the effectiveness of this approach and provide good solutions for large scale problems.

Automatic dimming multi-lamp fluorescent management system with active input power factor corrector stage

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

Stability analysis of power systems described with detailed models by automatic method

The power system stability analysis is approached taking into explicit account the dynamic performance of generators internal voltages and control devices. The proposed method is not a direct method in the usual sense since conclusion for stability or instability is not exclusively based on energy function considerations but it is automatic since the conclusion is achieved without an analyst intervention. The stability test accounts for the nonconservative nature of the system with control devices such as the automatic voltage regulator (AVR) and automatic generation control (AGC) in contrast with the well-known direct methods. An energy function is derived for the system with machines forth-order model, AVR and AGC and it is used to start the analysis procedure and to point out criticalities. The conclusive analysis itself is made by means of a method based on the definition of a region surrounding the equilibrium point where the system net torque is equilibrium restorative. This region is named positive synchronization region (PSR). Since the definition of the PSR boundaries have no dependence on modelling approximation, the PSR test conduces to reliable results. (C) 2008 Elsevier Ltd. All rights reserved.

Productive performance of Nile tilapia (Oreochromis niloticus) fed at different frequencies and periods with automatic dispenser

Avaliou-se o desempenho de tilápias-do-nilo (Oreochromis niloticus) produzidas em tanque-rede, providas de dispensadores automáticos de ração, alimentadas em diferentes frequências - uma vez por hora e a cada duas horas - e períodos - durante o dia, à noite ou ambos. Dezoito tanques-rede de 1.0m³ foram colocados em um tanque de 2000m² com dois metros de profundidade e renovação de água de 5%. Cento e setenta tilápias, com peso inicial de 16.0±4.9g foram distribuídas em cada tanque-rede de 1m³ e a taxa alimentar foi ajustada a cada 21 dias junto com as biometrias. As medidas foram coletadas de março a julho (outono e inverno). Observou-se diferença significativa para peso final (P<0.05) entre os tratamentos. O aumento da frequência alimentar melhorou o desempenho produtivo de tilápias-do-nilo produzidas em tanque-rede e permitiu melhor manejo alimentar. A melhor conversão alimentar para alta frequência, 24 vezes dia-1, pode resultar em uma economia de até 360kg de ração por tonelada de peixe produzido, melhorando a sustentabilidade econômica para produção de tilápia e sugerindo menor poluição ambiental.

CIE L*a*b*: comparison of digital images obtained photographically by manual and automatic modes

The aim of this study was to analyze the color alterations performed by the CIE L*a*b* system in the digital imaging of shade guide tabs, which were obtained photographically according to the automatic and manual modes. This study also sought to examine the observers' agreement in quantifying the coordinates. Four Vita Lumin Vaccum shade guide tabs were used: A3.5, B1, B3 and C4. An EOS Canon digital camera was used to record the digital images of the shade tabs, and the images were processed using Adobe Photoshop software. A total of 80 observations (five replicates of each shade according to two observers in two modes, specifically, automatic and manual) were obtained, leading to color values of L*, a* and b*. The color difference (AE) between the modes was calculated and classified as either clinically acceptable or unacceptable. The results indicated that there was agreement between the two observers in obtaining the L*, a* and b* values related to all guides. However, the B1, B3, and C4 shade tabs had AE values classified as clinically acceptable (Delta E = 0.44, Delta E = 2.04 and Delta E = 2.69, respectively). The A3.5 shade tab had a AE value classified as clinically unacceptable (Delta E = 4.17), as it presented higher values for luminosity in the automatic mode (L* = 54.0) than in the manual mode (L* = 50.6). It was concluded that the B1, B3 and C4 shade tabs can be used at any of the modes in digital camera (manual or automatic), which was a different finding from that observed for the A3.5 shade tab.

Assignment of chromosome rearrangements between X chromosomes of human and cattle by laser microdissection and Zoo-FISH

Cross-species fluorescence in-situ hybridization (Zoo-FISH) was performed on cattle metaphase spreads using Homo sapiens X chromosome (HSAX) painting probes specific for the p- and q-arms to identify the cytogenetic location of a chromosome breakpoint between HSAX and the Bos taurus X chromosome (BTAX). The existence of a breakpoint is strongly suggested by recent radiation hybrid and FISH mapping results. Hybridization probes were generated by microdissection of HSAX p- and q-arms using the contact-free technology of Laser Microdissection and Pressure Catapulting (LMPC), amplification of the isolated chromosome material by DOP-PCR, and labelling of the PCR products with digoxigenin in a secondary PCR. Independent Zoo-FISH of the two painting probes on bovine metaphase chromosomes (detected by antidigoxigenin-fluorescein) resulted in clear hybridization signals on BTAX. A breakpoint was identified between HSAXp and HSAXq on BTAX, and narrowed down between the G-bands BTAXq25 and BTAXq26. The assumed centromere transposition between HSAX and BTAX associated with the rearranged chromosome segments is supported by cytogenetic assignments of the genes BGN and G6PD to BTAX.

Edge detection and noise removal by use of a partial differential equation with automatic selection of parameters

This work deals with noise removal by the use of an edge preserving method whose parameters are automatically estimated, for any application, by simply providing information about the standard deviation noise level we wish to eliminate. The desired noiseless image u(x), in a Partial Differential Equation based model, can be viewed as the solution of an evolutionary differential equation u t(x) = F(u xx, u x, u, x, t) which means that the true solution will be reached when t ® ¥. In practical applications we should stop the time ''t'' at some moment during this evolutionary process. This work presents a sufficient condition, related to time t and to the standard deviation s of the noise we desire to remove, which gives a constant T such that u(x, T) is a good approximation of u(x). The approach here focused on edge preservation during the noise elimination process as its main characteristic. The balance between edge points and interior points is carried out by a function g which depends on the initial noisy image u(x, t0), the standard deviation of the noise we want to eliminate and a constant k. The k parameter estimation is also presented in this work therefore making, the proposed model automatic. The model's feasibility and the choice of the optimal time scale is evident through out the various experimental results.