Fastidiosipila sanguinis gen. nov., sp nov., a new Gram-positive, coccus-shaped organism from human blood

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6% O-2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al, Int J Syst Bacteriol 44 (1994), 812-826]. Sequence divergence values of 15% or more were observed between the unidentified bacterium and all other recognized species within this and related rRINIA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp, nov. The type strain of Fastidiosipila sanguinis is CCUG 47711(T) (= CIP 108292(T)).

Atopostipes suicloacale gen. nov., sp. nov., isolated from an underground swine manure storage pit

Phenotypic and molecular genetic studies were performed on an unknown facultative anaerobic, catalase-negative, non-spore-forming, rod-shaped bacterium isolated from a pig manure storage pit. The unknown bacterium was nutritionally fastidious with growth enhanced by the addition of rumen fluid and was phenotypically initially identified as an Eubacterium species. Comparative 16S rRNA gene sequencing studies, however, revealed that the unknown bacterium was phylogenetically distant from Eubacterium limosum (the type species of the genus Eubacterium) and related organisms. Phylogenetically, the unknown species displayed a close association with an uncultured organism from human subgingival plaque and formed an unknown sub-line within a cluster of organisms which includes Alloioccoccus otitis, Alkalibacterium olivoapovliticus, Allofustis seminis, Dolosigranulum pigrum, and related organisms, within the low mol% G + C Gram-positive bacteria. Sequence divergence values of > 8% with all known taxonomically recognised taxa, however, clearly indicates the novel bacterium represents a hitherto unknown genus. Based on both phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig manure be classified in a new genus and species, as Atopostipes suicloacale gen. nov., sp. nov. The type strain of Atopostipes suicloacale is PPC79(T) = NRRL 23919(T) = DSM 15692(T). Crown Copyright (C) 2004 Published by Elsevier Ltd. All rights reserved.

Atopococcus tabaci gen. nov., sp nov., a novel Gram-positive, catalase-negative, coccus-shaped bacterium isolated from tobacco

A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4 alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega 9, C-16:0 and C(18:1)omega 9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allolustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (= CIP 108502(T)).

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on LL-diaminopimelic acid (type LL-Dpm-glycine(1)), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H-4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306(T) = DSM 15745(T)).

Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen

An unknown Gram-positive, catalase-negative, facultatively anaerobic, non-spore-forming, rod-shaped bacterium originating from semen of a pig was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a directly cross-linked cell wall murein based on L-lysine and a DNA G + C content of 39 mol%. Comparative 16S rRNA gene sequencing showed that the unidentified rod-shaped organism formed a hitherto unknown subline related, albeit loosely, to Alkalibacterium olivapovliticus, Alloiococcus otitis, Dolosigranulum pigrum and related organisms, in the low-G + C-content Gram-positive bacteria. However, sequence divergence values of > 11 % from these recognized taxa. clearly indicated that the novel bacterium represents a separate genus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from pig semen be classified as a new genus and species, Allofustis seminis gen. nov., sp. nov. The type strain is strain 01-570-1(T) (=CCUG 45438(T)=CIP 107425(T)).

Cloacibacterium normanense gen. nov., sp nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G + C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T)=CIP 108613(T) =ATCC BAA-825(T) = DSM 15886(T)).

Characterization of some strains from human clinical sources which resemble “Leptotrichia sanguinegens”: description of Sneathia sanguinegens sp. nov., gen. nov.

Three strains of a gram-negative, blood or serum requiring, rod-shaped bacterium recovered from human clinical specimens were characterised by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed the unknown rod-shaped strains are members of the same species as some fastidious isolates recovered from human blood specimens and previously designated "Leptotrichia sanguinegens". Based on phylogenetic and phenotypic evidence, it is proposed that the isolates from human sources be classified in a new genus Sneathia, as Sneathia sanguinegens gen. nov., sp. nov. The type strain of Sneathia sanguinegens is CCUG 41628T.

Pleistovultur nevesi gen. et sp nov (Aves: Vulturidae) and the diversity of condors and vultures in the South American Pleistocene

Pleistovultur nevesi, a new genus and species of a large Vulturidae is described from the Upper Pleistocene or beginning of the Holocene, based on a complete and well preserved right tibiotarsus from the Cuvieri cave deposits, one of the hundreds of caves of the Lagoa Santa region in Minas Gerais state, Brazil. Also described here is a distal half of a left tibiotarsus from Gruta dos Brejoes, a cave in Morro do Chapeu, Bahia state, Brazil, which probably belongs to another not-yet-known genus and species of the Vulturidae. The described material, added to prior literature, is proof of the appreciable diversity of the Vulturidae during the Pleistocene in South America.

On the first terrestrial ostracod of the Superfamily Cytheroidea (Crustacea, Ostracoda): description of Intrepidocythere ibipora n. gen. n. sp from forest leaf litter in Sao Paulo State, Brazil

Of the three superfamilies of Ostracoda present in fresh water, only the Cytheroidea had thus far no records in terrestrial environments. Here, we report on a new genus and species, Intrepidocythere ibipora n. gen. n. sp., of the ostracod superfamily Cytheroidea, from forest leaf litter in Sao Paulo State, Brazil. Judging from morphological similarities, this new genus is believed to be closely related to the genus Elpidium. Possible pathways that led to the colonisation of terrestrial habitats are discussed, and an overview is given on the distribution of the known terrestrial ostracod lineages. The present findings strengthen the idea that terrestrial ostracods are more common than previously thought, at least in tropical areas.

A putative gnetalean gymnosperm Cariria orbiculiconiformis gen. nov et spec. nov from the Early Cretaceous of northern Gondwana

Cariria orbiculiconiformis gen. nov. et spec. nov., a gymnosperm with gnetoid characters is described from the upper Aptian Crato Formation of the Araripe Basin in northeastern Brazil. Gross-morphology and anatomical details have been studied and characters have been discussed in respect to various seed plants. Several of these characters fit best with those of Gnetales and their putative fossil allies. However, the fossil plant cannot be assigned to any known extinct or extant group of seed plants in their current circumscription. Stem gross-morphology, xylotomical characters and epidermal features indicate a gnetophytic relationship, whereas characters of the reproductive organs are rather distinct from those found in extant taxa. The reproductive unit of the new taxon represents a triple organ consisting of two dichasial ovulate structures and one median pollen-producing structure containing smooth, monosulcate, boat-shaped pollen in-situ. Each ovulate structure consists of two distinct pairs of bracts, a sterile one at the base and a fertile one forming a terminal orbicular capsule. Stiff processes found in the apex of the ovulate structure may represent micropylar tubes of seeds, as seen in the Bennettitales-Erdtmanithecales-Gnetales group. C orbiculiconiformis gen. nov. et spec. nov. was ans herbaceous or semi-shrub-like plant that may have been adapted to the r-strategy in a stressful environment. (C) 2011 Elsevier B.V. All rights reserved.

Cearania heterophylla gen. nov et sp nov., a fossil gymnosperm with affinities to the Gnetales from the Early Cretaceous of northern Gondwana

Vegetative and fertile shoots of a shrub-like seed plant from the late Aptian Crato Formation of Brazil are described as Cearania heterophylla Kunzmann, Mohr and Bernardes-de-Oliveira, gen. nov. et sp. nov. Anatomical details of the axes, epidermal features and separate ovulate and pollen producing organs indicate the gymnospermous nature of this plant. The vascular tissue of the axes includes tracheids with bordered pits and fiber tracheids. Vegetative shoots comprising at least three branching orders bear opposite-decussately arranged ovate to lanceolate, dorsiventrally flattened, parallelodromous, rather thick leaves that vary tremendously in size. The amphistomatic leaves bear (brachy-)paracytic stomatal complexes arranged in simple longitudinal files. The ovulate structure is interpreted as a terminally attached single globular ovule/seed surrounded by at least five to six lanceolate bracts. A terminally attached pollen-cone like structure grows on a lateral leafy shoot. The unusual character combination may indicate that the fossils belong to a hitherto unknown group with affinities to ephedroid Gnetales. Sterile shoots formerly often described as Podozamites, Nageiopsis or Lilites that are at least partly congeneric with C. heterophylla Kunzmann, Mohr and Bernardes-de-Oliveira, gen. nov. et sp. nov. had a wide geographic distribution during the Early Cretaceous. (C) 2009 Elsevier B.V. All rights reserved.

Um algoritmo de criptografia de chave pública semanticamente seguro baseado em curvas elípticas

Esta dissertação apresenta o desenvolvimento de um novo algoritmo de criptografia de chave pública. Este algoritmo apresenta duas características que o tornam único, e que foram tomadas como guia para a sua concepção. A primeira característica é que ele é semanticamente seguro. Isto significa que nenhum adversário limitado polinomialmente consegue obter qualquer informação parcial sobre o conteúdo que foi cifrado, nem mesmo decidir se duas cifrações distintas correspondem ou não a um mesmo conteúdo. A segunda característica é que ele depende, para qualquer tamanho de texto claro, de uma única premissa de segurança: que o logaritmo no grupo formado pelos pontos de uma curva elíptica de ordem prima seja computacionalmente intratável. Isto é obtido garantindo-se que todas as diferentes partes do algoritmo sejam redutíveis a este problema. É apresentada também uma forma simples de estendê-lo a fim de que ele apresente segurança contra atacantes ativos, em especial, contra ataques de texto cifrado adaptativos. Para tanto, e a fim de manter a premissa de que a segurança do algoritmo seja unicamente dependente do logaritmo elíptico, é apresentada uma nova função de resumo criptográfico (hash) cuja segurança é baseada no mesmo problema.

Um algoritmo numérico de integração de tempo para estruturas dinâmicas com dissipações : o método generalizado-α

O presente trabalho tem por objetivo estudar e aplicar um método de integração numérica de tempo para estrutras dinâmicas com dissipação de energia. Nessa dissertação tal método é analisado e posteriormente implementado em MATLAB, afim de resolver algumas aplicações em sistemas dinâmicos dotados de massas, molas e amortecedores que são apresentados no primeiro capítulo. Usando o método implementado em MATLAB, também é apresentada uma aplicação para vibrações transversais em cordas axialmente.

Um Algoritmo para indução de árvores e regras de decisão

A classificação é uma das tarefas da Mineração de Dados. Esta consiste na aplicação de algoritmos específicos para produzir uma enumeração particular de padrões. Já a classificação é o processo de gerar uma descrição, ou um modelo, para cada classe a partir de um conjunto de exemplos dados. Os métodos adequados e mais utilizados para induzir estes modelos, ou classificadores, são as árvores de decisão e as regras de classificação. As regras e árvores de decisão são populares, principalmente, por sua simplicidade, flexibilidade e interpretabilidade. Entretanto, como a maioria dos algoritmos de indução particionam recursivamente os dados, o processamento pode tornar-se demorado, e a árvore construída pode ser muito grande e complexa, propensa ao overfitting dos dados, que ocorre quando o modelo aprende detalhadamente ao invés de generalizar. Os conjuntos de dados reais para aplicação em Mineração de Dados são, atualmente, muito grandes, e envolvem vários milhares de registros, sendo necessária, também, uma forma de generalizar estes dados. Este trabalho apresenta um novo modelo de indução de classificadores, em que o principal diferencial do algoritmo proposto é a única passada pelo conjunto de treinamento durante o processo de indução, bem como a sua inspiração proveniente de um Sistema Multiagente. Foi desenvolvido um protótipo, o Midas, que foi validado e avaliado com dados de repositórios. O protótipo também foi aplicado em bases de dados reais, com o objetivo de generalizar as mesmas. Inicialmente, foi estudado e revisado o tema de Descoberta de Conhecimento em Bases de Dados, com ênfase nas técnicas e métodos de Mineração de Dados. Neste trabalho, também são apresentadas, com detalhes, as árvores e regras de decisão, com suas técnicas e algoritmos mais conhecidos. Finalizando, o algoritmo proposto e o protótipo desenvolvido são apresentados, bem como os resultados provenientes da validação e aplicação do mesmo.

Soft IP para criptografia usando o algoritmo Rijndael e implementação em lógica programável

A criptografia assumiu papel de destaque no cotidiano das pessoas, em virtude da necessidade de segurança em inúmeras transações eletrônicas. Em determinadas áreas, a utilização de hardware dedicado à tarefa de criptografia apresenta vantagens em relação à implementação em software, devido principalmente ao ganho de desempenho. Recentemente, o National Institute of Standards and Technology (NIST) publicou o novo padrão norte-americano de criptografia simétrica, chamado de Advanced Encryption Standard (AES). Após um período de aproximadamente 3 anos, no qual várias alternativas foram analisadas, adotou-se o algoritmo Rijndael. Assim, este trabalho apresenta um Soft IP do padrão AES, codificado em VHDL, visando a implementação em FPGA Altera. Todo o projeto foi construído com funções e bibliotecas genéricas, a fim de permitir a posterior implementação sobre outras tecnologias. Foram geradas duas versões: uma priorizando desempenho e outra priorizando a área ocupada nos componentes. Para cada uma das versões, produziu-se um circuito para encriptar e outro para decriptar. O desempenho alcançado em termos de velocidade de processamento superou todos os outros trabalhos publicados na área, sobre a mesma tecnologia. São apresentados os detalhes de implementação, arquiteturas envolvidas e decisões de projeto, bem como todos os resultados. A dissertação contém ainda conceitos básicos de criptografia e uma descrição do algoritmo Rijndael.