Territoriality and male-biased sexual size dimorphism in Argia reclusa (Odonata: Zygoptera)

In Odonata, many species present sexual size dimorphism (SSD), which can be associated with male territoriality in Zygoptera. We hypothesized that in the territorial damselfly Argia reclusa, male-male competition can favor large males, and consequently, drive selection pressures to generate male-biased SSD. The study was performed at a small stream in southeastern Brazil. Males were marked, and we measured body size and assessed the quality of territories. We tested if larger territorial males (a) defended the best territories (those with more male intrusions and visiting females), (b) won more fights, and (c) mated more. Couples were collected and measured to show the occurrence of sexual size dimorphism. Results indicated that males are larger than females, and that territorial males were larger than non-territorial males. Larger territorial males won more fights and defended the best territories. There was no difference between the mating success of large territorial and small non-territorial males. Although our findings suggest that male territoriality may play a significant role on the evolution of sexual size dimorphism in A. reclusa, we suggest that other factors should also be considered to explain the evolution of SSD in damselflies, since non-territorial males are also capable of acquiring mates.

Seismites as a tool in the palaeoenvironmental reconstruction of fluvial deposits: The Cambrian Guarda Velha Formation, southern Brazil

Soft-sediment deformation (SSD) is widely described in the literature, but there is no clear consensus regarding its origin and significance. Existing models for SSD in fluvial sediments do not clearly demonstrate a relationship between the structures, preserved facies expression, and larger-scale depositional architecture. In this study several types of SSD structures are recorded in Cambrian fluvial deposits and these occur interbedded with undeformed strata throughout the entire stratigraphic interval. The random distribution of these features in relation to primary facies types and fluvial forms indicates that they have neither a direct nor indirect relationship with any depositional processes or bedform type. We propose that the relationship of SSD at the bed-set-scale to larger-scale depositional architecture, combined with tectono-stratigraphic analysis allows the determination of both short-term fluvial hydraulic conditions in ancient stream systems, such as the nature of the flow regime responsible for depositing ancient fluvial stream successions, and the long-term subsidence rates, in the form of mean recurrence interval of the seismic events responsible for triggering the generation of SSD in tectonically active basins. (c) 2012 Elsevier B.V. All rights reserved.

Pavement and alignment design of a new rural road in the province of Bologna

This thesis aims to give a general view of pavement types all over the world, by showing the different characteristics of each one and its different life steps starting from construction, passing by maintenance and arriving until recycling phase. The flexible pavement took the main part of this work because it has been used in the last part of this thesis to design a project of a rural road. This project is located in the province of Bologna-Italy (‘Comune di Argelato’, 26 km in the north of Bologna), and has 5677, 81 m of length. A pavement design was made using the program BISAR 3.0 and a fatigue life study was made, also, in order to estimate the number of loads (in terms of heavy vehicles axle) to cause road’s failure . An alignment design was made for this project and a safety study was established in order to check if the available sight distance at curves respects the safety norms or not, by comparing it to the stopping sight distance. Different technical sheets are demonstrated and several cases are discussed in order to clarify the main design principles and underline the main hazardous cases to be avoided especially at intersection. This latter, its type’s choice depends on several factors in order to make the suitable design according to the environmental data. At this part of the road, the safety is a primordial point due to the high accident rate in this zone. For this reason, different safety aspects are discussed especially at roundabouts, signalized intersections, and also some other common intersection types. The design and the safety norms are taken with reference to AASHTO (American Association of State Highway and Transportation Officials), ACT (Transportation Association of Canada), and also according to Italian norms (Decreto Ministeriale delle Starde).

Monte Carlo dose calculation improvements for low energy electron beams using eMC

The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm(2) of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d(max) and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm(2) at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose calculation for 4 and 6 MeV electron beams of Varian linear accelerators.

Benefits of low-frequency attenuation of baha® in single-sided sensorineural deafness

To investigate the effect of low-frequency attenuation of Bone-Anchored Hearing Aids (Bahas) in users with single-sided sensorineural deafness (SSD). The underlying notion is that low-frequency sounds up to approximately 1500 Hz reach the contralateral ear without significant attenuation and that Bahas tend to show more distortion at lower frequencies. Furthermore, to transmit low frequencies, higher moving masses are needed when compared with high frequencies.

Effects of erythropoietin on erythrocyte deformability in non-transfused preterm infants

AIM: Suppression of erythropoiesis due to low plasma erythropoietin levels is an important factor in the development of anaemia of prematurity. Premature infants may therefore be treated with recombinant human erythropoietin (rhEPO). This prospective, randomised and controlled study was designed to find out whether rhEPO treatment improves erythrocyte deformability in preterm infants. METHODS: Sixteen infants were treated with rhEPO (250 IU/kg three times weekly) a total of 15 times beginning on day of life 5 whereas fifteen infants served as controls. Haemoglobin concentration, haematocrit, reticulocyte count, ferritin level and erythrocyte deformability were measured on days 5, 14, 28, 42 and 63. Erythrocyte elongation was determined as an indicator of erythrocyte deformability using a shear stress diffractometer (Rheodyn SSD) at shear forces of 0.3 to 60 Pa. RESULTS: Haemoglobin concentration was significantly higher on days 28 and 42 and reticulocyte percentage on day 28 in the rhEPO group compared to the controls. Serum ferritin was lower in the rhEPO group on day 28. Erythrocyte deformability was significantly increased on days 28 and 42 in the infants receiving rhEPO. We found a strong relationship between erythrocyte elongation and reticulocyte count. CONCLUSION: RhEPO markedly increases the erythropoiesis in preterm infants in the critical first weeks of life and the anaemia of prematurity is obviously reduced. The erythrocyte deformability improved under rhEPO treatment. Erythrocyte deformability was significantly related to the reticulocyte count indicating that the improvement of erythrocyte deformability was due to the formation of well-deformable young erythrocytes.

Testing the GlaaS algorithm for dose measurements on low- and high-energy photon beams using an amorphous silicon portal imager

The GLAaS algorithm for pretreatment intensity modulation radiation therapy absolute dose verification based on the use of amorphous silicon detectors, as described in Nicolini et al. [G. Nicolini, A. Fogliata, E. Vanetti, A. Clivio, and L. Cozzi, Med. Phys. 33, 2839-2851 (2006)], was tested under a variety of experimental conditions to investigate its robustness, the possibility of using it in different clinics and its performance. GLAaS was therefore tested on a low-energy Varian Clinac (6 MV) equipped with an amorphous silicon Portal Vision PV-aS500 with electronic readout IAS2 and on a high-energy Clinac (6 and 15 MV) equipped with a PV-aS1000 and IAS3 electronics. Tests were performed for three calibration conditions: A: adding buildup on the top of the cassette such that SDD-SSD = d(max) and comparing measurements with corresponding doses computed at d(max), B: without adding any buildup on the top of the cassette and considering only the intrinsic water-equivalent thickness of the electronic portal imaging devices device (0.8 cm), and C: without adding any buildup on the top of the cassette but comparing measurements against doses computed at d(max). This procedure is similar to that usually applied when in vivo dosimetry is performed with solid state diodes without sufficient buildup material. Quantitatively, the gamma index (gamma), as described by Low et al. [D. A. Low, W. B. Harms, S. Mutic, and J. A. Purdy, Med. Phys. 25, 656-660 (1998)], was assessed. The gamma index was computed for a distance to agreement (DTA) of 3 mm. The dose difference deltaD was considered as 2%, 3%, and 4%. As a measure of the quality of results, the fraction of field area with gamma larger than 1 (%FA) was scored. Results over a set of 50 test samples (including fields from head and neck, breast, prostate, anal canal, and brain cases) and from the long-term routine usage, demonstrated the robustness and stability of GLAaS. In general, the mean values of %FA remain below 3% for deltaD equal or larger than 3%, while they are slightly larger for deltaD = 2% with %FA in the range from 3% to 8%. Since its introduction in routine practice, 1453 fields have been verified with GLAaS at the authors' institute (6 MV beam). Using a DTA of 3 mm and a deltaD of 4% the authors obtained %FA = 0.9 +/- 1.1 for the entire data set while, stratifying according to the dose calculation algorithm, they observed: %FA = 0.7 +/- 0.9 for fields computed with the analytical anisotropic algorithm and %FA = 2.4 +/- 1.3 for pencil-beam based fields with a statistically significant difference between the two groups. If data are stratified according to field splitting, they observed %FA = 0.8 +/- 1.0 for split fields and 1.0 +/- 1.2 for nonsplit fields without any significant difference.

Influence of directionality and maximal power output on speech understanding with bone anchored hearing implants in single sided deafness

Bone-anchored hearing implants (BAHI) are routinely used to alleviate the effects of the acoustic head shadow in single-sided sensorineural deafness (SSD). In this study, the influence of the directional microphone setting and the maximum power output of the BAHI sound processor on speech understanding in noise in a laboratory setting were investigated. Eight adult BAHI users with SSD participated in this pilot study. Speech understanding in noise was measured using a new Slovak speech-in-noise test in two different spatial settings, either with noise coming from the front and noise from the side of the BAHI (S90N0) or vice versa (S0N90). In both spatial settings, speech understanding was measured without a BAHI, with a Baha BP100 in omnidirectional mode, with a BP100 in directional mode, with a BP110 power in omnidirectional and with a BP110 power in directional mode. In spatial setting S90N0, speech understanding in noise with either sound processor and in either directional mode was improved by 2.2-2.8 dB (p = 0.004-0.016). In spatial setting S0N90, speech understanding in noise was reduced by either BAHI, but was significantly better by 1.0-1.8 dB, if the directional microphone system was activated (p = 0.046), when compared to the omnidirectional setting. With the limited number of subjects in this study, no statistically significant differences were found between the two sound processors.

Abundance and biomass of in- and epibenthic invertebrate macrofauna in the German Bight from 1969 to 2000

In order to examine the long-term development of offshore macrozoobenthic soft-bottom communities of the German Bight, four representative permanent stations (MZB-SSd, -FSd, -Slt, -WB) have been sampled continuously since 1969. Inter-annual variability and possible long-term trends were analysed based on spring-time samples from 1969 until 2000. This is part of the ecological long-term series of the AWI and is supplemented by periodic large-scale mapping of the benthos. The main factors influencing the development of the benthic communities are biological interactions, climate, food supply (eutrophication) and the disturbance regime. The most frequent disturbances are sediment relocations during strong storms or by bottom trawling, while occasional oxygen deficiencies and extremely cold winters are important disturbance events working on a much larger scale. Benthic communities at the sampling stations show a large inter-annual variability combined with a variation on a roughly decadal scale. In accordance with large-scale system shifts reported for the North Sea, benthic community transitions occurred between roughly the 1970ies, 80ies and 90ies. The transitions between periods are not distinctly marked by strong changes but rather reflected in gradual changes of the species composition and dominance structure.

Registry of all samples from the Tara Oceans Expedition (2009-2013)

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. Data sets in this collection provide methodological and environmental context to all samples collected during the Tara Oceans Expedition (2009-2013).

Microinformática en entornos profesionales : instalación, configuración, mantenimiento y reparación

Los sistemas microinformáticos se componen principalmente de hardware y software, con el paso del tiempo el hardware se degrada, se deteriora y en ocasiones se avería. El software evoluciona, requiere un mantenimiento, de actualización y en ocasiones falla teniendo que ser reparado o reinstalado. A nivel hardware se analizan los principales componentes que integran y que son comunes en gran parte estos sistemas, tanto en equipos de sobre mesa como portátiles, independientes del sistema operativo, además de los principales periféricos, también se analizan y recomiendan algunas herramientas necesarias para realizar el montaje, mantenimiento y reparación de estos equipos. Los principales componentes hardware internos son la placa base, memoria RAM, procesador, disco duro, carcasa, fuente de alimentación y tarjeta gráfica. Los periféricos más destacados son el monitor, teclado, ratón, impresora y escáner. Se ha incluido un apartado donde se detallan los distintos tipos de BIOS y los principales parámetros de configuración. Para todos estos componentes, tanto internos como periféricos, se ha realizado un análisis de las características que ofrecen y los detalles en los que se debe prestar especial atención en el momento de seleccionar uno frente a otro. En los casos que existen diferentes tecnologías se ha hecho una comparativa entre ambas, destacando las ventajas y los inconvenientes de unas frente a otras para que sea el usuario final quien decida cual se ajusta mejor a sus necesidades en función de las prestaciones y el coste. Un ejemplo son las impresoras de inyección de tinta frente a las laser o los discos duros mecánicos en comparación con y los discos de estado sólido (SSD). Todos estos componentes están relacionados, interconectados y dependen unos de otros, se ha dedicado un capítulo exclusivamente para estudiar cómo se ensamblan estos componentes, resaltando los principales fallos que se suelen cometer o producir y se han indicado unas serie tareas de mantenimiento preventivo que se pueden realizar para prolongar la vida útil del equipo y evitar averías por mal uso. Los mantenimientos se pueden clasificar como predictivo, perfectivo, adaptativo, preventivo y correctivo. Se ha puesto el foco principalmente en dos tipos de mantenimiento, el preventivo descrito anteriormente y en el correctivo, tanto software como hardware. El mantenimiento correctivo está enfocado al análisis, localización, diagnóstico y reparación de fallos y averías hardware y software. Se describen los principales fallos que se producen en cada componente, cómo se manifiestan o qué síntomas presentan para poder realizar pruebas específicas que diagnostiquen y acoten el fallo. En los casos que es posible la reparación se detallan las instrucciones a seguir, en otro caso se recomienda la sustitución de la pieza o componente. Se ha incluido un apartado dedicado a la virtualización, una tecnología en auge que resulta muy útil para realizar pruebas de software, reduciendo tiempos y costes en las pruebas. Otro aspecto interesante de la virtualización es que se utiliza para montar diferentes servidores virtuales sobre un único servidor físico, lo cual representa un importante ahorro en hardware y costes de mantenimiento, como por ejemplo el consumo eléctrico. A nivel software se realiza un estudio detallado de los principales problemas de seguridad y vulnerabilidades a los que está expuesto un sistema microinformático enumerando y describiendo el comportamiento de los distintos tipos de elementos maliciosos que pueden infectar un equipo, las precauciones que se deben tomar para minimizar los riesgos y las utilidades que se pueden ejecutar para prevenir o limpiar un equipo en caso de infección. Los mantenimientos y asistencias técnicas, en especial las de tipo software, no siempre precisan de la atención presencial de un técnico cualificado, por ello se ha dedicado un capítulo a las herramientas de asistencia remota que se pueden utilizar en este ámbito. Se describen algunas de las más populares y utilizadas en el mercado, su funcionamiento, características y requerimientos. De esta forma el usuario puede ser atendido de una forma rápida, minimizando los tiempos de respuesta y reduciendo los costes. ABSTRACT Microcomputer systems are basically made up of pieces of hardware and software, as time pass, there’s a degradation of the hardware pieces and sometimes failures of them. The software evolves, new versions appears and requires maintenance, upgrades and sometimes also fails having to be repaired or reinstalled. The most important hardware components in a microcomputer system are analyzed in this document for a laptop or a desktop, with independency of the operating system they run. In addition to this, the main peripherals and devices are also analyzed and a recommendation about the most proper tools necessary for maintenance and repair this kind of equipment is given as well. The main internal hardware components are: motherboard, RAM memory, microprocessor, hard drive, housing box, power supply and graphics card. The most important peripherals are: monitor, keyboard, mouse, printer and scanner. A section has been also included where different types of BIOS and main settings are listed with the basic setup parameters in each case. For all these internal components and peripherals, an analysis of their features has been done. Also an indication of the details in which special attention must be payed when choosing more than one at the same time is given. In those cases where different technologies are available, a comparison among them has been done, highlighting the advantages and disadvantages of selecting one or another to guide the end user to decide which one best fits his needs in terms of performance and costs. As an example, the inkjet vs the laser printers technologies has been faced, or also the mechanical hard disks vs the new solid state drives (SSD). All these components are interconnected and are dependent one to each other, a special chapter has been included in order to study how they must be assembled, emphasizing the most often mistakes and faults that can appear during that process, indicating different tasks that can be done as preventive maintenance to enlarge the life of the equipment and to prevent damage because of a wrong use. The different maintenances can be classified as: predictive, perfective, adaptive, preventive and corrective. The main focus is on the preventive maintains, described above, and in the corrective one, in software and hardware. Corrective maintenance is focused on the analysis, localization, diagnosis and repair of hardware and software failures and breakdowns. The most typical failures that can occur are described, also how they can be detected or the specific symptoms of each one in order to apply different technics or specific tests to diagnose and delimit the failure. In those cases where the reparation is possible, instructions to do so are given, otherwise, the replacement of the component is recommended. A complete section about virtualization has also been included. Virtualization is a state of the art technology that is very useful especially for testing software purposes, reducing time and costs during the tests. Another interesting aspect of virtualization is the possibility to have different virtual servers on a single physical server, which represents a significant savings in hardware inversion and maintenance costs, such as electricity consumption. In the software area, a detailed study has been done about security problems and vulnerabilities a microcomputer system is exposed, listing and describing the behavior of different types of malicious elements that can infect a computer, the precautions to be taken to minimize the risks and the tools that can be used to prevent or clean a computer system in case of infection. The software maintenance and technical assistance not always requires the physical presence of a qualified technician to solve the possible problems, that’s why a complete chapter about the remote support tools that can be used to do so has been also included. Some of the most popular ones used in the market are described with their characteristics and requirements. Using this kind of technology, final users can be served quickly, minimizing response times and reducing costs.

Role of tyrosine phosphorylation of a cellular protein in adeno-associated virus 2-mediated transgene expression

The adeno-associated virus 2 (AAV), a single-stranded DNA-containing, nonpathogenic human parvovirus, has gained attention as a potentially useful vector for human gene therapy. However, the single-stranded nature of the viral genome significantly impacts upon the transduction efficiency, because the second-strand viral DNA synthesis is the rate-limiting step. We hypothesized that a host-cell protein interacts with the single-stranded D sequence within the inverted terminal repeat structure of the AAV genome and prevents the viral second-strand DNA synthesis. Indeed, a cellular protein has been identified that interacts specifically and preferentially with the D sequence at the 3′ end of the AAV genome. This protein, designated the single-stranded D-sequence-binding protein (ssD-BP), is phosphorylated at tyrosine residues and blocks AAV-mediated transgene expression in infected cells by inhibiting the leading strand viral DNA synthesis. Inhibition of cellular protein tyrosine kinases by genistein results in dephosphorylation of the ssD-BP, leading not only to significant augmentation of transgene expression from recombinant AAV but also to autonomous replication of the wild-type AAV genome. Dephosphorylation of the ssD-BP also correlates with adenovirus infection, or expression of the adenovirus E4orf6 protein, which is known to induce AAV DNA replication and gene expression. Thus, phosphorylation state of the ssD-BP appears to play a crucial role in the life cycle of AAV and may prove to be an important determinant in the successful use of AAV-based vectors in human gene therapy.

Atenuação de vibrações em pás de helicópteros utilizando circuito piezelétrico semi-passivo

O uso de materiais inteligentes em problemas de controle de vibração tem sido investigado em diversas pesquisas ao longo dos últimos anos. Apesar de que diferentes materiais inteligentes estão disponíveis, o piezelétrico tem recebido grande atenção devido à facilidade de uso como sensores, atuadores, ou ambos simultaneamente. As principais técnicas de controle usando materiais piezoelétricos são os ativos e passivos. Circuitos piezelétricos passivos são ajustados para uma frequência específica e, portanto, a largura de banda efetiva é pequena. Embora os sistemas ativos possam apresentar um bom desempenho no controle de vibração, a quantidade de energia externa e hardware adicionado são questões importantes. As técnicas SSD (Synchronized Switch Damping) foram desenvolvidas como uma alternativa aos controladores passivos e controladores ativos de vibração. Elas podem ser técnicas semi-ativas ou semi-passivas que introduzem um tratamento não linear na tensão elétrica proveniente do material piezelétrico e induz um aumento na conversão de energia mecânica para energia elétrica e, consequentemente, um aumento no efeito de amortecimento. Neste trabalho, o controle piezoelétrico semi-passivo de uma pá piezelétrica engastada é apresentado e comparado com outros controladores. O modelo não linear electromecânico de uma pá com piezocerâmicas incorporados é determinado com base no método variacional-assintótico (VAM). O sistema rotativo acoplado não linear é resolvido no domínio do tempo, utilizando um método de integração alfa-generalizado afim de garantir a estabilidade numérica. As simulações são realizadas para uma vasta gama de velocidades de rotação. Em primeiro lugar, um conjunto de resistências (variando desde a condição de curto-circuito para a condição de circuito aberto) é considerada. O efeito da resistência ótima (que resulta em máximo amortecimento) sobre o comportamento do sistema é investigado para o aumento da velocidade de rotação. Mais tarde, a técnica SSDS é utilizada para amortecer as oscilações da pá com o aumento da velocidade de rotação. Os resultados mostram que a técnica SSDS pode ser um método útil para o controle de vibrações de vigas rotativas não lineares, tais como pás de helicóptero.

Simulación de Sucesos Discretos. Prácticas en casos reales con R. Competición de estudiantes de simulación

La Simulación de Sucesos Discretos (SSD)es una metodología que permite aplicar los procedimientos de simulación estocástica, para representar un sistema en el que las variables aleatorias que lo componen están relacionadas entre si. En esta monografía se recogen distintos casos reales en los que puede aplicarse SSD junto con su implementación en R y resultados finales.

Desempenho comparativo do BLAST e do mpiBLAST

Em Bioinformática são frequentes problemas cujo tratamento necessita de considerável poder de processamento/cálculo e/ou grande capacidade de armazenamento de dados e elevada largura de banda no acesso aos mesmos (de forma não comprometer a eficiência do seu processamento). Um exemplo deste tipo de problemas é a busca de regiões de similaridade em sequências de amino-ácidos de proteínas, ou em sequências de nucleótidos de DNA, por comparação com uma dada sequência fornecida (query sequence). Neste âmbito, a ferramenta computacional porventura mais conhecida e usada é o BLAST (Basic Local Alignment Search Tool) [1]. Donde, qualquer incremento no desempenho desta ferramenta tem impacto considerável (desde logo positivo) na atividade de quem a utiliza regularmente (seja para investigação, seja para fins comerciais). Precisamente, desde que o BLAST foi inicialmente introduzido, foram surgindo diversas versões, com desempenho melhorado, nomeadamente através da aplicação de técnicas de paralelização às várias fases do algoritmo (e. g., partição e distribuição das bases de dados a pesquisar, segmentação das queries, etc. ), capazes de tirar partido de diferentes ambientes computacionais de execução paralela, como: máquinas multi-core (BLAST+ 2), clusters de nós multi-core (mpiBLAST3J e, mais recentemente, co-processadores aceleradores como GPUs" ou FPGAs. É também possível usar as ferramentas da família BLAST através de um interface/sítio WEB5, que permite, de forma expedita, a pesquisa de uma variedade de bases de dados conhecidas (e em permanente atualização), com tempos de resposta suficientemente pequenos para a maioria dos utilizadores, graças aos recursos computacionais de elevado desempenho que sustentam o seu backend. Ainda assim, esta forma de utilização do BLAST poderá não ser a melhor opção em algumas situações, como por exemplo quando as bases de dados a pesquisar ainda não são de domínio público, ou, sendo-o, não estão disponíveis no referido sitio WEB. Adicionalmente, a utilização do referido sitio como ferramenta de trabalho regular pressupõe a sua disponibilidade permanente (dependente de terceiros) e uma largura de banda de qualidade suficiente, do lado do cliente, para uma interacção eficiente com o mesmo. Por estas razões, poderá ter interesse (ou ser mesmo necessário) implantar uma infra-estrutura BLAST local, capaz de albergar as bases de dados pertinentes e de suportar a sua pesquisa da forma mais eficiente possível, tudo isto levando em conta eventuais constrangimentos financeiros que limitam o tipo de hardware usado na implementação dessa infra-estrutura. Neste contexto, foi realizado um estudo comparativo de diversas versões do BLAST, numa infra-estrutura de computação paralela do IPB, baseada em componentes commodity: um cluster de 8 nós (virtuais, sob VMWare ESXi) de computação (com CPU Í7-4790K 4GHz, 32GB RAM e 128GB SSD) e um nó dotado de uma GPU (CPU Í7-2600 3.8GHz, 32GB RAM, 128 GB SSD, 1 TB HD, NVIDIA GTX 580). Assim, o foco principal incidiu na avaliação do desempenho do BLAST original e do mpiBLAST, dado que são fornecidos de base na distribuição Linux em que assenta o cluster [6]. Complementarmente, avaliou-se também o BLAST+ e o gpuBLAST no nó dotado de GPU. A avaliação contemplou diversas configurações de recursos, incluindo diferentes números de nós utilizados e diferentes plataformas de armazenamento das bases de dados (HD, SSD, NFS). As bases de dados pesquisadas correspondem a um subconjunto representativo das disponíveis no sitio WEB do BLAST, cobrindo uma variedade de dimensões (desde algumas dezenas de MBytes, até à centena de GBytes) e contendo quer sequências de amino-ácidos (env_nr e nr), quer de nucleótidos (drosohp. nt, env_nt, mito. nt, nt e patnt). Para as pesquisas foram 'usadas sequências arbitrárias de 568 letras em formato FASTA, e adoptadas as opções por omissão dos vários aplicativos BLAST. Salvo menção em contrário, os tempos de execução considerados nas comparações e no cálculo de speedups são relativos à primeira execução de uma pesquisa, não sendo assim beneficiados por qualquer efeito de cache; esta opção assume um cenário real em que não é habitual que uma mesma query seja executada várias vezes seguidas (embora possa ser re-executada, mais tarde). As principais conclusões do estudo comparativo realizado foram as seguintes: - e necessário acautelar, à priori, recursos de armazenamento com capacidade suficiente para albergar as bases de dados nas suas várias versões (originais/compactadas, descompactadas e formatadas); no nosso cenário de teste a coexistência de todas estas versões consumiu 600GBytes; - o tempo de preparação (formataçâo) das bases de dados para posterior pesquisa pode ser considerável; no nosso cenário experimental, a formatação das bases de dados mais pesadas (nr, env_nt e nt) demorou entre 30m a 40m (para o BLAST), e entre 45m a 55m (para o mpiBLAST); - embora economicamente mais onerosos, a utilização de discos de estado sólido, em alternativa a discos rígidos tradicionais, permite melhorar o tempo da formatação das bases de dados; no entanto, os benefícios registados (à volta de 9%) ficam bastante aquém do inicialmente esperado; - o tempo de execução do BLAST é fortemente penalizado quando as bases de dados são acedidas através da rede, via NFS; neste caso, nem sequer compensa usar vários cores; quando as bases de dados são locais e estão em SSD, o tempo de execução melhora bastante, em especial com a utilização de vários cores; neste caso, com 4 cores, o speedup chega a atingir 3.5 (sendo o ideal 4) para a pesquisa de BDs de proteínas, mas não passa de 1.8 para a pesquisa de BDs de nucleótidos; - o tempo de execução do mpiBLAST é muito prejudicado quando os fragmentos das bases de dados ainda não se encontram nos nós do cluster, tendo que ser distribuídos previamente à pesquisa propriamente dita; após a distribuição, a repetição das mesmas queries beneficia de speedups de 14 a 70; porém, como a mesma base de dados poderá ser usada para responder a diferentes queries, então não é necessário repetir a mesma query para amortizar o esforço de distribuição; - no cenário de teste, a utilização do mpiBLAST com 32+2 cores, face ao BLAST com 4 cores, traduz-se em speedups que, conforme a base de dados pesquisada (e previamente distribuída), variam entre 2 a 5, valores aquém do máximo teórico de 6.5 (34/4), mas ainda assim demonstradores de que, havendo essa possibilidade, compensa realizar as pesquisas em cluster; explorar vários cores) e com o gpuBLAST, realizada no nó com GPU (representativo de uma workstation típica), permite aferir qual a melhor opção no caso de não serem possíveis pesquisas em cluster; as observações realizadas indicam que não há diferenças significativas entre o BLAST e o BLAST+; adicionalmente, o desempenho do gpuBLAST foi sempre pior (aproximadmente em 50%) que o do BLAST e BLAST+, o que pode encontrar explicação na longevidade do modelo da GPU usada; - finalmente, a comparação da melhor opção no nosso cenário de teste, representada pelo uso do mpiBLAST, com o recurso a pesquisa online, no site do BLAST5, revela que o mpiBLAST apresenta um desempenho bastante competitivo com o BLAST online, chegando a ser claramente superior se se considerarem os tempos do mpiBLAST tirando partido de efeitos de cache; esta assunção acaba por se justa, Já que BLAST online também rentabiliza o mesmo tipo de efeitos; no entanto, com tempos de pequisa tão reduzidos (< 30s), só é defensável a utilização do mpiBLAST numa infra-estrutura local se o objetivo for a pesquisa de Bds não pesquisáveis via BLAS+ online.