An evolutionary tree represents the relationship among a group of species, DNA or protein sequences, and play fundamental roles in biological lineage research. A high quality tree construction relies heavily on optimal multiple sequence alignment (MSA), which aligns three or more sequence simultaneously to derive the similarity. On the other hand, a good tree can also be used to guide the MSA process. Due to the high computational cost to conduct both the MSA and tree construction, parallel approaches are exploited to utilize the enormous amount of computing power and memory housed in a supercomputer or Linux cluster. In this paper, first of all, a divide and conquer based parallel algorithm is designed and implemented to perform optimal three sequence alignment using reduced memory cost. Secondly, all internal nodes of a phylogenetic tree resulting from a parallel Maximum-likelihood inference software are labeled using the parallel MSA. Such tree node labeling process is carried out from top down and is also parallelized to fully utilize the numerous cores and nodes in a high performance computing facility.

Faculty of Science School of Geography Archaeology and Enviromental Science 0406606f wglenny@nmsa.org.za / The analysis of micromammal remains from the MSA deposits at Sibudu Cave, KwaZulu-Natal, constitutes the first in-depth study of the micromammal assemblage at this site. This study highlights the usefulness of taphonomic analyses and micromammal assemblages in the reconstruction of past environments. Little digestive etching suggests that Tyto alba, Tyto capensis and Asio capensis, are the most likely nocturnal raptors responsible for the accumulation of the assemblage. The environmental information from the Sibudu micromammal assemblage showed similarities with other proxy site data from charcoal, seed and macrofaunal analyses. These studies indicate that the immediate environment around Sibudu Cave was very similar at 53.4 ± 3.2 kyr (OSL) and 35.2 ± 1.8 kyr (OSL), consisting of a complex mosaic environment, dominated by open savannah grassland with a small woodland and riverine element.

Diplomová práce se zabývá hodnocením způsobilosti pracovního zařízení. V teoretické části jsou popsány metody hodnocení procesů/výrobních zařízení, metoda DOE a hodnocení způsobilosti měřících systémů. V teoretické části je popsána vlastní analýza - aplikace v praxi.

Submitted by CARLOS ANTÓNIO MATOS null (cmatos62@yahoo.com.br) on 2017-05-23T17:44:16Z No. of bitstreams: 1 Tese_Carlos_Antonio_Mato_2017.pdf: 2145169 bytes, checksum: a2aa0c6111ab05dde2597a7a07b2c0a7 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-05-23T18:34:48Z (GMT) No. of bitstreams: 1 matos_ca_me_jabo.pdf: 2145169 bytes, checksum: a2aa0c6111ab05dde2597a7a07b2c0a7 (MD5) / Made available in DSpace on 2017-05-23T18:34:48Z (GMT). No. of bitstreams: 1 matos_ca_me_jabo.pdf: 2145169 bytes, checksum: a2aa0c6111ab05dde2597a7a07b2c0a7 (MD5) Previous issue date: 2017-04-19 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / A babesiose é uma doença infecciosa economicamente importante que afeta o gado bovino em todo o mundo, endêmica e importante causa de morbidade e mortalidade em bovinos no Brasil. A doença é causada por Babesia bigemina e B. bovis, protozoários parasitas intraeritrocíticos do filo Apicomplexa, agentes de enorme importância econômica em regiões tropicais e subtropicais. Merozoitos de B. bovis possuem em sua superfície, pelo menos, cinco glico-proteínas, que pertencem à família de antígenos variáveis de superfície do merozoíto (VMSA). A família VMSA de B. bovis inclui os genes msa-1, msa-2a1, msa-2a2, msa-2b e msa-2c. Estes antígenos são altamente imunogênicos e contêm epítopos sensíveis à neutralização e, por conseguinte, têm sido considerados como antígenos candidatos para o desenvolvimento de vacinas de subunidades contra B. bovis. No entanto, estes antígenos de superfície são geneticamente diversificados entre diferentes isolados de B. bovis, O que resulta em diferenças antigénicas entre vários isolados de B. bovis. A fim de avaliar a resposta imune humoral contra B. bovis e a diversidade genética de antígenos de superfície de merozoítos de B. bovis, amostras de soro e DNA de sangue de 30 bezerras, sendo 15 da Fazenda Pesagro, Seropédica, Rio de Janeiro, e outras 15 da Fazenda Germânia, Taiaçu, São Paulo, foram obtidas trimestralmente, desde o nascimento até aos 12 meses de idade. Os Anticorpos IgG para B. bovis foram detectados pelos testes de Imunofluorescência Indireta (RIFI) e Ensaio de Imunoadsorção Enzimático Indireto (IELISA). A Reação em Cadeia da Polimerase (PCR) foi utilizada com o objetivo de avaliar a diversidade genética de B. bovis, com base em genes que codificam antígenos de superfície de merozoítos (MSAs). Os resultados da sorologia demonstram que, a partir dos seis meses de idade, todas as bezerras foram soropositivas para B. bovis. Entre as 150 amostras de DNA testadas para a presença de três fragmentos de genes de msa de B. bovis, amplicons positivos foram obtidos em 14 amostras para msa-1, 24 para msa-2b e 34 para msa-2c de bezerras da Fazenda Pesagro e em 9 amostras para msa-1, 28 para msa-2b e 34 para msa-2c em amostras de bezerras da Fazenda Germânia. O sequenciamento foi realizado pelo método de Sanger para os fragmentos de genes msa-2b (n = 3), msa- 2c (n = 5) de Seropédica e msa-1 (n = 2), msa-2b (n = 5), msa-2c (n = 5) de Taiaçu. A análise filogenética foi realizada pelo método de Máxima verossimilhança e modelos GTR + G, GTR + G + I e GTR + G+ I para MSA-1, MSA-2b e MSA-2c, respectivamente. As sequências de MSAs dos genes msa-2b e msa-2c de Seropédica posicionaram-se em dois clados, enquanto que as sequências de MSAs dos genes msa-1 e msa-2b de Taiaçu posicionaram-se em dois clados, e sequências do gene msa-2c agruparam-se em um único clado. Os resultados da sorologia mostram que foi atingida a estabilidade endêmica em ambas as fazendas. Com base nas sequências do gene msa-2b, amplificadas no presente estudo, e a análise filogenética, pode-se afirmar que as amostras de B. bovis das fazendas Pesagro e Germânia dividem-se em dois grupos genotipicos, havendo um genótipo compartilhado por ambas as fazendas. / Babesiosis, an economically important infectious disease that affects cattle worldwide, is endemic and important cause of morbidity and mortality of cattle in Brazil. The disease is caused by Babesia bigemina and B. bovis, apicomplexan intraerythrocytic protozoa parasites, which are agents of huge economic importance in tropical and subtropical regions. B. bovis merozoites present at least five (glyco-) proteins on their surfaces, which belong to a family of variable merozoite surface antigens (VMSA). The members of the VMSA family consist of merozoite surface antigen msa-1, msa-2a1, msa-2a2, msa-2b, and msa-2c. These antigens are highly immunogenic and contain neutralization-sensitive epitopes, and therefore have been considered as candidate antigens for developing subunit vaccines against B. bovis. However, these surface antigens are genetically diverse among different isolates of B. bovis, which results in antigenic differences among various B. bovis isolates. In order to evaluate the humoral immune response against B. bovis and genetic diversity of merozoite surface antigens of B. bovis, serum and DNA blood samples of 30 dairy calves, 15 from Seropedica, state of Rio de Janeiro, and the other 15 from a herd located in Taiaçu, state of São Paulo were obtained quarterly, since the birth up to 12 months of age. IgG antibodies to B. bovis were detected by Indirect Fluorescent Antibody Test (IFAT) and Enzyme-Linked Immunoadsorbent Assay (ELISA) tests. Polymerase Chain Reaction (PCR) was used aiming to assess the genetic diversity of B. bovis, based on genes that encode merozoite surface antigens (MSAs). The serology results demonstrate that up to six months of age all calves were seropositive to B. bovis. Among the 150 DNA blood samples tested for the presence of three B. bovis-msa gene fragments, positive amplicons were obtained in 14 samples for msa-1, 24 samples for msa-2b and 34 for msa-2c from calves of Pesagro herd, 9 samples for msa-1, 28 for msa-2b and 34 for msa-2c from calves of Germânia herd. Sequencing, by Sanger method, was performed for msa-2b (n=3), and msa-2c (n=5), genes fragments of Seropedica and msa-1(n=2), msa-2b (n=5), and msa-2c (n=5), genes fragments of Taiaçu. The phylogenetic analysis was performed by Maximum Likelihood method and models GTR+G, GTR+G+I and GTR+G+I for MSA-1, MSA-2b and MSA-2c, respectively. The Seropedica MSAs sequences namely msa-2b and msa-2c were positioned in two clades, and a Taiaçu MSAs sequence, that is msa-1 and msa-2b, were positioned in two clades, while msa-2c sequences were all grouped in only one clade. Serology results show that endemic stability has been achieved in both farms. Based on the msa-2b gene sequences amplified in the present study, and the phylogenetic analysis, it can be stated that the B. bovis samples from the Pesagro and Germânia farms are classified into two genotypic groups, having one genotype shared by both farms.

Inom dagens samhälle är de flesta mobilenheter uppkopplade till en basstation. Mycket information förväntas kunna överföras från telefonen till basstationen utan några störningar för användaren. Detta kan underlättas genom att använda en bitfelskorrigerare exempelvis Min Sum Algoritmen (MSA), för att avkoda Low-Density Parity-Check (LDPC) koder. Algoritmen fungerar genom att utföra fyra moment: initialisering, radoperation, kolumnoperation och beslutsoperation. Istället för att utföra momenten på en Central Processing Unit (CPU), effektiviseras processen genom att utnyttja Graphics Processing Units (GPU) möjlighet till parallellisering. Optimeringen för detta sker genom Compute Unified Device Architecture (CUDA). Resultatet visar på en effektivisering på 89% vad gäller exekveringstid för bitfelskorrigering genom att använda GPU:er istället för CPU:er. / In today's society, most mobile devices are connected to a base station. A lot of information is expected to be able to be transferred from the phone to the base station without any interference for the user. This can be facilitated by using a bit error corrector such as the Min-Sum Algorithm (MSA), to decode Low-Density Parity-Check (LDPC) codes. The algorithm works by performing four steps: initialization, row operation, column operation, and decision operation. Instead of performing the steps on a Central Processing Unit (CPU), the process is made more efficient by utilizing the Graphics Processing Unit's (GPU) ability to parallelize. The optimization is done by using CUDA. The result shows an 89% efficiency improvement in execution time for bit error correction by using GPUs instead of CPUs.

1 Assesment of land use influence on landscape naturalness Abstract Human activities are putting an increasing pressure on natural areas. Complex understanding and evaluation of human impact on the environment is considered to be a key tool to preserve natural balance. Biodiversity was chosen as proxy for naturalness as it has been recognized as one of the main components of environmental stability. Several different indices has been developed to assess human-induced changes in biodiversity. In this study, mean abundance of original species relative to their abundance in undisturbed ecosystems (MSA) is used as an indicator for current state of naturalness. Indicator MSA is built on simple cause-effect relationships between environmental drivers and biodiversity impacts, based on state-of-the-art knowledge. Drivers considered are landcover change, land-use intensity, fragmentation and infrastructure development. As most of biodiversity indices, MSA illustrate prevailingly poor condition of nature as a result of human induced pressures, especially land cover change. Considering constantly increasing population and economic development human pressure grow is likely to continue during the coming decades with irreversible loss in the diversity of life on the Earth. Keywords: Mean species abundance (MSA) - land...

L'objectif de cette thèse est d'étudier la décontamination en ions de solutions aqueuses par les oxydes échangeurs d'ions en s'intéressant plus particulièrement à l'adsorption du strontium par le nonatitanate de sodium. Le but est de développer un modèle prédictif qui tienne compte des phénomènes physico-chimiques mis en jeu et des écarts à l'idéalité dans la solution, mais également dans le matériau. Pour cela, le calcul des coefficients d'activité des ions en solution a été calculé à partir d'une approche basée sur la théorie MSA (Mean Spherical Approximation) où les phénomènes spécifiques d'association ont été pris en compte. Cela a permis de calculer les coefficients d'activité des ions dans les mélanges ternaires. La validité des lois de mélange de Zdanovskii-Stokes-Robinson et McKay-Perring a également été précisée. Deux modèles d'activité, représentant les interactions à longues distances et à courtes distances, ont été utilisés pour l'étude des ions dans le solide. Les isothermes d'adsorption à différentes concentrations ont alors été modélisées. Une étude pH-métrique a également été conduite sur le nonatitanate de sodium afin de déterminer la constante d'hydrolyse ainsi que le taux d'hydrolyse du solide. Une étude structurale et morphologique a permis de mettre en évidence qu'avec des solutions très acides le nonatitanate de sodium se dissout et précipite de nouveau sous différentes formes cristallographiques du TiO2. / The objective of this thesis is to study the ionics decontamination of aqueous solutions by ionic oxide exchangers with a particular focus on the strontium adsorption by the sodium nonatitanate. The goal is to develop a predictive model takes into account the phenomena involved, and the deviations to the ideality into the solution but also in the material.The activity coefficients of the ions in solution have been calculated from an approach based on the MSA theory (Mean Spherical Approximation), where the specific association phenomenons have been taken into account. This allowed for calculating the ionic activity coefficients in the ternary mixtures. The validity of mixture laws of Zdanovskii-Stokes-Robinson and McKay-Perring has been also specified. Two activity models, which represent the long and the short-range interactions, have been used for the ionic studied in the solid. The adsorption isotherms at various concentrations have been hence modeled.A pH-metric study has also been performed on the sodium nonatitanate in order to determine the hydrolysis constant as well as the solid hydrolysis rate. A structural and morphologic study allowed for highlighting that for highly acidic solutions the sodium nonatitanate is dissolved and precipitated again under different crystallographic forms of the TiO2.

This thesis is focused on the design and implementation of binary low-density parity-check (LDPC) code decoders for high-speed modern communication systems. The basic of LDPC codes and the performance and bottlenecks, in terms of complexity and hardware efficiency, of the main soft-decision and hard-decision decoding algorithms (such as Min-Sum, Optimized 2-bit Min-Sum and Reliability-based iterative Majority-Logic) are analyzed. The complexity and performance of those algorithms are improved to allow efficient hardware architectures. A new decoding algorithm called One-Minimum Min-Sum is proposed. It reduces considerably the complexity of the check node update equations of the Min-Sum algorithm. The second minimum is estimated from the first minimum value by a means of a linear approximation that allows a dynamic adjustment. The Optimized 2-bit Min-Sum algorithm is modified to initialize it with the complete LLR values and to introduce the extrinsic information in the messages sent from the variable nodes. Its variable node equation is reformulated to reduce its complexity. Both algorithms were tested for the (2048,1723) RS-based LDPC code and (16129,15372) LDPC code using an FPGA-based hardware emulator. They exhibit BER performance very close to Min-Sum algorithm and do not introduce early error-floor. In order to show the hardware advantages of the proposed algorithms, hardware decoders were implemented in a 90 nm CMOS process and FPGA devices based on two types of architectures: full-parallel and partial-parallel one with horizontal layered schedule. The results show that the decoders are more area-time efficient than other published decoders and that the low-complexity of the Modified Optimized 2-bit Min-Sum allows the implementation of 10 Gbps decoders in current FPGA devices. Finally, a new hard-decision decoding algorithm, the Historical-Extrinsic Reliability-Based Iterative Decoder, is presented. This algorithm introduces the new idea of considering hard-decision votes as soft-decision to compute the extrinsic information of previous iterations. It is suitable for high-rate codes and improves the BER performance of the previous RBI-MLGD algorithms, with similar complexity. / Esta tesis se ha centrado en el diseño e implementación de decodificadores binarios basados en códigos de comprobación de paridad de baja densidad (LDPC) válidos para los sistemas de comunicación modernos de alta velocidad. Los conceptos básicos de códigos LDPC, sus prestaciones y cuellos de botella, en términos de complejidad y eficiencia hardware, fueron analizados para los principales algoritmos de decisión soft y decisión hard (como Min-Sum, Optimized 2-bit Min-Sum y Reliability-based iterative Majority-Logic). La complejidad y prestaciones de estos algoritmos se han mejorado para conseguir arquitecturas hardware eficientes. Se ha propuesto un nuevo algoritmo de decodificación llamado One-Minimum Min-Sum. Éste reduce considerablemente la complejidad de las ecuaciones de actualización del nodo de comprobación del algoritmo Min-Sum. El segundo mínimo se ha estimado a partir del valor del primer mínimo por medio de una aproximación lineal, la cuál permite un ajuste dinámico. El algoritmo Optimized 2-bit Min-Sum se ha modificado para ser inicializado con los valores LLR e introducir la información extrínseca en los mensajes enviados desde los nodos variables. La ecuación del nodo variable de este algoritmo ha sido reformulada para reducir su complejidad. Ambos algoritmos fueron probados para el código (2048,1723) RS-based LDPC y para el código (16129,15372) LDPC utilizando un emulador hardware implementado en un dispositivo FPGA. Éstos han alcanzado unas prestaciones de BER muy cercanas a las del algoritmo Min-Sum evitando, además, la aparición temprana del fenómeno denominado suelo del error. Con el objetivo de mostrar las ventajas hardware de los algoritmos propuestos, los decodificadores se implementaron en hardware utilizando tecnología CMOS de 90 nm y en dispositivos FPGA basados en dos tipos de arquitecturas: completamente paralela y parcialmente paralela utilizando el método de actualización por capas horizontales. Los resultados muestran que los decodificadores propuestos e implementados son más eficientes en área-tiempo que otros decodificadores publicados y que la baja complejidad del algoritmo Modified Optimized 2-bit Min-Sum permite la implementación de decodificadores en los dispositivos FPGA actuales consiguiendo una tasa de 10 Gbps. Finalmente, se ha presentado un nuevo algoritmo de decodificación de decisión hard, el Historical-Extrinsic Reliability-Based Iterative Decoder. Este algoritmo introduce la nueva idea de considerar los votos de decisión hard como decisión soft para calcular la información extrínseca de iteracions anteriores. Este algoritmo es adecuado para códigos de alta velocidad y mejora el rendimiento BER de los algoritmos RBI-MLGD anteriores, con una complejidad similar. / Aquesta tesi s'ha centrat en el disseny i implementació de descodificadors binaris basats en codis de comprovació de paritat de baixa densitat (LDPC) vàlids per als sistemes de comunicació moderns d'alta velocitat. Els conceptes bàsics de codis LDPC, les seues prestacions i colls de botella, en termes de complexitat i eficiència hardware, van ser analitzats pels principals algoritmes de decisió soft i decisió hard (com el Min-Sum, Optimized 2-bit Min-Sum y Reliability-based iterative Majority-Logic). La complexitat i prestacions d'aquests algoritmes s'han millorat per aconseguir arquitectures hardware eficients. S'ha proposat un nou algoritme de descodificació anomenat One-Minimum Min-Sum. Aquest redueix considerablement la complexitat de les equacions d'actualització del node de comprovació del algoritme Min-Sum. El segon mínim s'ha estimat a partir del valor del primer mínim per mitjà d'una aproximació lineal, la qual permet un ajust dinàmic. L'algoritme Optimized 2-bit Min-Sum s'ha modificat per ser inicialitzat amb els valors LLR i introduir la informació extrínseca en els missatges enviats des dels nodes variables. L'equació del node variable d'aquest algoritme ha sigut reformulada per reduir la seva complexitat. Tots dos algoritmes van ser provats per al codi (2048,1723) RS-based LDPC i per al codi (16129,15372) LDPC utilitzant un emulador hardware implementat en un dispositiu FPGA. Aquests han aconseguit unes prestacions BER molt properes a les del algoritme Min-Sum evitant, a més, l'aparició primerenca del fenomen denominat sòl de l'error. Per tal de mostrar els avantatges hardware dels algoritmes proposats, els descodificadors es varen implementar en hardware utilitzan una tecnologia CMOS d'uns 90 nm i en dispositius FPGA basats en dos tipus d'arquitectures: completament paral·lela i parcialment paral·lela utilitzant el mètode d'actualització per capes horitzontals. Els resultats mostren que els descodificadors proposats i implementats són més eficients en àrea-temps que altres descodificadors publicats i que la baixa complexitat del algoritme Modified Optimized 2-bit Min-Sum permet la implementació de decodificadors en els dispositius FPGA actuals obtenint una taxa de 10 Gbps. Finalment, s'ha presentat un nou algoritme de descodificació de decisió hard, el Historical-Extrinsic Reliability-Based Iterative Decoder. Aquest algoritme presenta la nova idea de considerar els vots de decisió hard com decisió soft per calcular la informació extrínseca d'iteracions anteriors. Aquest algoritme és adequat per als codis d'alta taxa i millora el rendiment BER dels algoritmes RBI-MLGD anteriors, amb una complexitat similar. / Català Pérez, JM. (2017). Design and implementation of decoders for error correction in high-speed communication systems [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86152 / TESIS

<p>Detta projekt är ett första utkast för företagets eventuella satsning på en ny modell inom segmentet jakt. Projektet innefattar en förundersökning som visar att det finns en stor brist i användningen av hörselskydd bland jägare, trots att många både medvetna om riskerna och i många fall dessutom redan fått en försämrad hörsel på grund av jakten. Ett trendbrott kan dock ses då allt fler faktiskt har börjat använda skydden under de senaste 10 åren, fortfarande en alldeles för liten del av dem totala gruppen jägare. Som tillverkare av hörselskydd kan man här se en potentiell marknad. Ett trendbrott bland en grupp människor som mer än gärna lägger lite extra pengar på senaste tekniken där fortfarande endast cirka 40 % av gruppen använder produkten borde ses som en god affärsmarknad.</p><p>Genomförd användarstudie har gett ett gott underlag för vidare produktutveckling och slutligen modellframtagning.</p> / <p>This project is a first draft for the company´s possible investment at a new model within the hunting segment. The project has included a fundamental investigation that shown that there is a big burst in the use of hearing protection equipment among the hunters today. Despite that many both is well aware about the risks and in many cases already got a deteriorated hearing because of the hunting. A break in that trend can however be seen because of a increasing use of protection during the last 10 years, still a far to small group of people. As producers of earmuffs can one here see a potential market. A break of trend among a group of people that more then gladly pays a little more money to get the last technology and still just approximately 40 % of the group uses earmuffs. That must be a good business concept.</p><p>A user studie has been implemented that has given a good basis for further development and finally a mock-up production.</p>

This thesis investigates the effect that variation in employment between industries has had on the depth of recession faced by Metropolitan Statistical Areas (MSAs) in the United States. This analysis is limited to the previous two national recessions. I use regression analysis to find that increases in variation in employment has a significant effect on the maximum increase in unemployment rate in MSAs after controlling for relevant MSA characteristics. In this framework I also find that increases in education could mitigate the negative effects of this variation. I include several other measures of depth of recession including the fall in economic conditions and length for real GDP to recover to its pre-recession levels. I find that the measure of variation is significant in explaining falls in the economic conditions, but not so in explaining the length it takes for each MSA to recover its real GDP.