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Background: Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB). Methods: All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development. Results: The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides ``Motif search'' and ``GBrowse''. The HIGDB is freely accessible through the URL:http://bioserverl.physicslisc.ernetin/HIGDB/. Discussion: The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae. (C) 2014 Elsevier Ltd. All rights reserved.

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On 15-16 January 2005, three offshore species of cetaceans (33 short-finned pilot whales, Globicephala macrorhynchus, one minke whale, Balaenoptera acutorostrata, and two dwarf sperm whales, Kogia sima) stranded alive on the beaches of North Carolina. The pilot whales stranded near Oregon Inlet, the minke whale in northern North Carolina, and the dwarf sperm whales near Cape Hatteras. Live strandings of three species in one weekend was unique in North Carolina and qualified as an Unusual Mortality Event. Gross necropsies were conducted on 16-17 January 2005 on 27 pilot whales, two dwarf sperm whales, and the minke whale. Samples were collected for clinical pathology, parasitology, gross pathology, histopathology, microbiology and serology. There was variation in the number of animals sampled for each collection type, however, due to carcasses washing off the beach or degradation in carcass condition during the course of the response. Comprehensive histologic examination was conducted on 16 pilot whales, both dwarf sperm whales, and the minke whale. Limited organ or only head tissue suites were obtained from nine pilot whales. Histologic examination of tissues began in February 2005 and concluded in December 2005 when final sampling was concluded. Neither the pilot whales nor dwarf sperm whales were emaciated although none had recently ingested prey in their stomachs. The minke whale was emaciated; it was likely a dependent calf that became separated from the female. Most serum biochemistry abnormalities appear to have resulted from the stranding and indicated deteriorating condition from being on land for an extended period. Three pilot whales had clinical evidence of pre-existing systemic inflammation, which was supported by histopathologic findings. Although gross and histologic lesions involving all organ systems were noted, consistent lesions were not observed across species. Verminous pterygoid sinusitis and healed fishery interactions were seen in pilot whales but neither of these changes were causes of debilitation or death. In three pilot whales and one dwarf sperm whale there was evidence of clinically significant disease in postcranial tissues which led to chronic debilitation. Cardiovascular disease was present in one pilot whale and one dwarf sperm whale; musculoskeletal disease and intra-abdominal granulomas were present in two pilot whales. These lesions were possible, but not definitive, causal factors in the stranding. Remaining lesions were incidental or post-stranding. The minke whale and three of five tested pilot whales had positive morbillivirus titers (≥1:8 with one at >1:256), but there was no histologic evidence of active viral infection. Parasites (nematodes, cestodes, and trematodes) were collected from 26 pilot whales and two dwarf sperm whales. Sites of collection included stomach, nasal/pterygoid, peribullar sinuses, blubber, and abdominal cavity. Parasite species, locations and loads were within normal limits for free-ranging cetaceans and were not considered causative for the stranding event. Gas emboli lesions which were considered consistent with or diagnostic of sonarassociated strandings of beaked whales or small cetaceans were not found in the whales stranded as part of UMESE0501Sp. Twenty-five heads were examined with nine specific anatomic locations of interest: extramandibular fat, intramandibular fat, auditory meatus, peribullar acoustic fat, peribullar soft tissue, peribullar sinus, pterygoid sinus, melon, and brain. The common finding in all examined heads was verminous pterygoid sinusitis. Intramandibular adipose tissue reddening, typically adjacent to the vascular plexus, was observed in some individuals and could represent localized hemorrhage resulting from vascular rete rupture, hypostatic congestion, or erythrocyte rupture during the freeze/thaw cycle. One cetacean had peracute to acute subdural hemorrhage that likely occurred from thrashing on the beach post-stranding, although its occurrence prior to stranding cannot be excluded. Information provided to NMFS by the U.S. Navy indicated routine tactical mid-frequency sonar operations from individual surface vessels over relatively short durations and small spatial scales within the area and time period investigated. No marine mammals were detected by marine mammal observers on operational vessels; standard operating procedure for surface naval vessels operating mid-frequency sonar is the use of trained visual lookouts using high-powered binoculars. Sound propagation modeling using information provided to NMFS indicated that acoustic conditions in the vicinity likely depended heavily on position of the receivers (e.g., range, bearing, depth) relative to that of the sources. Absent explicit information on the location of animals meant that it was not possible to estimate received acoustic exposures from active sonar transmissions. Nonetheless, the event was associated in time and space with naval activity using mid-frequency active sonar. It also had a number of features in common (e.g., the “atypical” distribution of strandings involving multiple offshore species, all stranding alive, and without evidence of common infectious or other disease process) with other sonar-related cetacean mass stranding events. Given that this event was the only stranding of offshore species to occur within a 2-3 day period in the region on record (i.e., a very rare event), and given the occurrence of the event simultaneously in time and space with a naval exercise using active sonar, the association between the naval sonar activity and the location and timing of the event could be a causal rather than a coincidental relationship. However, evidence supporting a definitive association is lacking, and, in particular, there are differences in operational/environmental characteristics between this event and previous events where sonar has apparently played a role in marine mammal strandings. This does not preclude behavorial avoidance of noise exposure. No harmful algal blooms were present along the Atlantic coast south of the Chesapeake Bay during the months prior to the event. Environmental conditions, including strong winds, changes in upwelling- to downwelling-favorable conditions, and gently sloping bathymetry, were consistent with conditions which have been correlated with other mass strandings. In summary, we did not find commonality in gross and histologic lesions that would indicate a single cause for this stranding event. Three pilot whales and one dwarf sperm whale had debilitating conditions identified that could have contributed to stranding, one pilot whale had a debilitating condition (subdural hemorrhage) that could have been present prior to or resulting from stranding. While the pilot and dwarf sperm whale strandings may have had a common cause, the minke whale stranding was probably just coincidental. On the basis of examination of physical evidence in the affected whales, however, we cannot definitively conclude that there was or was not a causal link between anthropogenic sonar activity or environmental conditions (or a combination of these factors) and the strandings. Overall, the cause of UMESE0501Sp in North Carolina is not and likely will not be definitively known. (PDF contains 240 pages)

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An investigation was conducted into the deaths of more than 220 bottlenose dolphins (Tursiops truncatus) that occurred within the coastal bay ecosystem of mid-Texas between January and May 1992. The high mortality rate was unusual in that it was limited to a relatively small geographical area, occurred primarily within an inshore bay system separated from the Gulf of Mexico by barrier islands, and coincided with deaths of other taxa including birds and fish. Factors examined to determine the potential causes of the dolphin mortalities included microbial pathogens, natural biotoxins, industrial pollutants, other environmental contaminants, and direct human interactions. Emphasis was placed on nonpoint source pesticide runoff from agricultural areas, which had resulted from record rainfall that occurred during the period of increased mortality. Analytical results from sediment, water, and biota indicated that biotoxins, trace metals, and industrial chemical contamination were not likely causative factors in this mortality event. Elevated concentrations of pesticides (atrazine and aldicarb) were detected in surface water samples from bays within the region, and bay salinities were reduced to <10 ppt from December 1991 through April 1992 due to record rainfall and freshwater runoff exceeding any levels since 1939. Prolonged exposure to low salinity could have played a significant role in the unusual mortalities because low salinity exposure may cause disruption of the permeability barrier in dolphin skin. The lack of established toxicity data for marine mammals, particularly dermal absorption and bioaccumulation, precludes accurate toxicological interpretation of results beyond a simple comparison to terrestrial mammalian models. Results clearly indicated that significant periods of agricultural runoff and accompanying low salinities co-occurred with the unusual mortality event in Texas, but no definitive cause of the mortalities was determined. (PDF file contains 25 pages.)

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The development of techniques for oncogenomic analyses such as array comparative genomic hybridization, messenger RNA expression arrays and mutational screens have come to the fore in modern cancer research. Studies utilizing these techniques are able to highlight panels of genes that are altered in cancer. However, these candidate cancer genes must then be scrutinized to reveal whether they contribute to oncogenesis or are coincidental and non-causative. We present a computational method for the prioritization of candidate (i) proto-oncogenes and (ii) tumour suppressor genes from oncogenomic experiments. We constructed computational classifiers using different combinations of sequence and functional data including sequence conservation, protein domains and interactions, and regulatory data. We found that these classifiers are able to distinguish between known cancer genes and other human genes. Furthermore, the classifiers also discriminate candidate cancer genes from a recent mutational screen from other human genes. We provide a web-based facility through which cancer biologists may access our results and we propose computational cancer gene classification as a useful method of prioritizing candidate cancer genes identified in oncogenomic studies.

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This thesis examines foundational questions in behavioral economics—also called psychology and economics—and the neural foundations of varied sources of utility. We have three primary aims: First, to provide the field of behavioral economics with psychological theories of behavior that are derived from neuroscience and to use those theories to identify novel evidence for behavioral biases. Second, we provide neural and micro foundations of behavioral preferences that give rise to well-documented empirical phenomena in behavioral economics. Finally, we show how a deep understanding of the neural foundations of these behavioral preferences can feed back into our theories of social preferences and reference-dependent utility.

The first chapter focuses on classical conditioning and its application in identifying the psychological underpinnings of a pricing phenomenon. We return to classical conditioning again in the third chapter where we use fMRI to identify varied sources of utility—here, reference dependent versus direct utility—and cross-validate our interpretation with a conditioning experiment. The second chapter engages social preferences and, more broadly, causative utility (wherein the decision-maker derives utility from making or avoiding particular choices).

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More than thirty years after the discovery that Human Immunodeficiency Virus (HIV) was the causative agent of Acquired Immunodeficiency Syndrome (AIDS), the disease remains pandemic as long as no effective universal vaccine is found. Over 34 million individuals in the world are infected with the virus, and the vast majority of them have no access to the antiretroviral therapies that have largely reduced HIV to a chronic disease in the developed world. The first chapter of this thesis introduces the history of the virus. The key to the infectious mechanism of the virus lies in its envelope glycoprotein (Env), a trimeric spike on the viral surface that utilizes host T cell receptors for entry. Though HIV-1 Env is immunogenic, most infected patients do not mount an effective neutralizing antibody response against it. Broadly-neutralizing anti-Env antibodies (bNAbs) present in the serum of a minority of infected individuals are usually sufficient to prevent the progression to full blown AIDS. Thus, the molecular details of these bNAbs as well as the antibody-antigen interface are of prime interest for structural studies, as insight gained would contribute to the design of a more effective immunogen and potential vaccine candidate. The second chapter of this thesis describes the low-resolution crystal structure of one such antibody, 2G12 dimer, which targets a high mannose epitope on the surface of Env. Patients infected with HIV-2, a related virus with ~35% sequence identity in the Env region, can generally mount a robust antibody response sufficient for viral control for reasons still unknown. The final two chapters of this thesis focus on the first reported structural studies of HIV-2 Env, the molecular details of which may inform HIV-1 therapy and immunogen design.

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Parasitic and infectious diseases of fish, of wide distribution in fish-rearing ponds, retard to a significant extent the development of fish culture in the Ukraine. One of the diseases of fish attracting attention in connection with the general distribution of its causative agent, the fungus Saprolegnia parasitica Coker, in water-bodies of various types, appears to be dermatomycosis. The aim of this investigation is to study the conditions favouring the development of S. parasitica. Among the studied factors were water temperature and oxygen content.

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Oração sem sujeito é toda e qualquer oração destituída de SN sujeito, exceto nos casos em que tal SN encontra-se em elipse. Sua manifestação na língua pode se dar tanto em termos pessoais quanto impessoais. Estas incluem ocorrências essenciais, aqui chamadas de fenomenológicas e acidentais, denominadas impessoalizadas. Já aquelas se apresentam nos casos de indeterminação de agente por omissão do SN sujeito, tradicionalmente alcunhados casos de sujeito indeterminado e por meio do processo de ergativização em sua versão secundária, aquele que atua sobre verbos não causativos e tem sido porta de entrada à concretização de orações destituídas de SN sujeito no português brasileiro. Objetivamos neste trabalho a descrição de todas as estruturas apontadas, em termos de seus comportamentos morfossintáticos na língua, pois compreendemos que descrever a oração sem sujeito portuguesa é identificar contextos morfossintáticos de dispensa, em distintos graus, do SN sujeito. Para tanto, valemo-nos de um enfoque prototípico da língua, através do qual dialogamos com a natureza escalar de nosso objeto de estudo

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Neste trabalho utilizou-se a técnica fluorescência de raios X usando radiação síncrotron (SR-TXRF) para estudar, quantitativamente, o transporte de cloro, potássio e cálcio na hemolinfa, urina e túbulos de Malpighi (TM) em ninfas de quinto estágio do Rhodnius prolixus (R. prolixus), considerando a excreção destes elementos em diferentes dias após o repasto sanguíneo. R. prolixus é um dos principais vetores do Trypanosoma cruzi, agente causador da doença de Chagas. R. prolixus fornece um sistema modelo particularmente útil porque seus TMs tanto secretam quanto reabsorvem íons a taxas elevadas. Os TMs filtram a hemolinfa e secretam um líquido que é muitas vezes comparado com a urina primária em vertebrados. Os resultados obtidos mostram que a concentração de potássio na urina é substancialmente maior do que na hemolinfa. A concentração de cloro na hemolinfa é menor do que na urina, mas a diferença não é tão marcada como no caso do potássio. No caso do Rhodnius é razoável interpretar a elevada concentração de potássio na urina como adaptativo para o problema de excreção imediato do inseto. A concentração de cálcio nos TMs é substancialmente maior em comparação com os valores encontrados na hemolinfa e urina. Este resultado mostra que o cálcio é retido no corpo do R. prolixus e pouco eliminado. Os resultados obtidos estão coerentes com a literatura. Avaliou-se também o efeito no transporte de Cl, K e Ca após um repasto de sangue de coelho contaminado com HgCl2 de modo a avaliar o efeito da presença deste metal tóxico no balanço iônico nos fluidos de excreção urina e hemolinfa e também pelo principal órgão de transporte, os túbulos de Malpighi. As excreções de Cl e K pela urina são afetadas pela ingestão. Este resultado é esperado levando-se em consideração a ingestão de excesso de Cl através do HgCl2. O transporte de Cl, K e Ca na hemolinfa do Rhodnius prolixus não é afetada pela ingestão de HgCl2. Nos túbulos de Malpighi, as altas concentrações de Ca obtidas foram comparáveis àquelas encontradas nos insetos controle. Pode-se concluir que SR-TXRF é um método muito promissor para análises diretas, rápidas e confiáveis para a quantificação simultânea de elementos envolvidos na regulação do transporte e em todo o sistema excretor de insetos. Além disso, o estudo do transporte e a excreção de elementos no inseto Rhodnius prolixus abrem oportunidade para a maior compreensão de efeitos da poluição em espécies de invertebrados.

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O presente trabalho teve como objetivo descrever o fenômeno da adesão nas igrejas neopentecostais a partir da psicologia social, mais especificamente, da teoria das representações sociais. Desta maneira, nós procuramos identificar os elementos constitutivos das práticas religiosas decorrentes de um determinado grupo religioso neopentecostal correlacionando-os àss representações sociais. Destarte, este trabalho identificou e analisou o processo de utilização do senso comum religioso pela comunidade neopentecostal Igreja Mundial do Poder de Deus, como instrumento gerador de adesão, considerando-se os fatores emocionais pertinentes ao senso comum do grupo como força motivadora de adesão à igreja referida. Deste modo, chegamos a quatro temas básicos que nos possibilitaram identificar as representações sociais construídas na interatividade da igreja. Os temas foram: oferta de milagres e feitos extraordinários; a singularidade da Igreja Mundial do Poder de Deus; a batalha entre o bem e o mal; o líder espiritual e sua relação com os adeptos de sua comunidade. As representações sociais identificadas foram: representação social da igreja como lugar de bênçãos e feitos extraordinários; representação social dos demônios; representação social do divino; representação social do ungido de Deus. Tendo em vista as representações identificadas e analisadas, o que se conclui é que, na igreja pesquisada, o senso comum - enquanto significações circulantes entre os membros desta igreja - aliado a fatores emocionais que lhe são pertinentes, se constitui como fator causativo de adesão, na medida em que os sujeitos percebem que as soluções para suas demandas e males são ofertadas, pela igreja, de maneira identificada com os significados já presentes neste senso comum.

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O trabalho aqui apresentado teve como objetivo, avaliar o método de Eaton (1975) aplicado ao cálculo de pressão de poros das formações rochosas em subsuperfície, utilizando dados de perfis de poços no que diz respeito a porosidade, tais como, o Tempo de Transito da onda compressional, Resistividade, Densidade e Neutrão. Posteriormente foi avaliado o resultado alcançado por esta técnica e confrontado com o dado obtido pelo registro de pressão real da formação, adquirido pela ferramenta de perfilagem MDT. Distribuídos em 6 poços perfurados na porção sul da Bacia de Campos, o intervalo cronoestratigráfico estudado está compreendido no período geológico Terciário, e os registros de pressão real da formação foram adquiridos nos reservatórios turbidíticos da Formação Carapebus (Eoceno). Apesar de existir um mecanismo causador de anomalia de pressão na bacia (Desequilíbrio de Compactação Difícil migração dos fluidos ao longo do tempo geológico) devido ao forte aporte sedimentar sustentado pelo soerguimento da Serra do Mar no Eoceno, os resultados encontrados não apontaram qualquer tipo de alteração nas respostas dos perfis utilizados, onde a referência foi a assinatura do perfil sônico em um trend normal de compactação compreendido por rochas argilosas dentro do intervalo cronoestratigráfico estudado. O presente trabalho atesta que a boa calibração do trend de ompactação normal em rochas argilosas, juntamente com a similaridade entre o resultado obtido pelo cálculo da pressão de poros a partir do perfil sônico, e os valores reais registrados diretamente na formação, pela ferramenta de registro de pressões (MDT), comprovam a aplicabilidade do método de Eaton (1975) para o cálculo de geopressões a partir de um conjunto básico de perfis de poços tais como: Raios Gama, Resistividade, Velocidade Acústica, Densidade e Neutrão

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In the Florida Panhandle region, bottlenose dolphins (Tursiops truncatus) have been highly susceptible to large-scale unusual mortality events (UMEs) that may have been the result of exposure to blooms of the dinoflagellate Karenia brevis and its neurotoxin, brevetoxin (PbTx). Between 1999 and 2006, three bottlenose dolphin UMEs occurred in the Florida Panhandle region. The primary objective of this study was to determine if these mortality events were due to brevetoxicosis. Analysis of over 850 samples from 105 bottlenose dolphins and associated prey items were analyzed for algal toxins and have provided details on tissue distribution, pathways of trophic transfer, and spatial-temporal trends for each mortality event. In 1999/2000, 152 dolphins died following extensive K. brevis blooms and brevetoxin was detected in 52% of animals tested at concentrations up to 500 ng/g. In 2004, 105 bottlenose dolphins died in the absence of an identifiable K. brevis bloom; however, 100% of the tested animals were positive for brevetoxin at concentrations up to 29,126 ng/mL. Dolphin stomach contents frequently consisted of brevetoxin-contaminated menhaden. In addition, another potentially toxigenic algal species, Pseudo-nitzschia, was present and low levels of the neurotoxin domoic acid (DA) were detected in nearly all tested animals (89%). In 2005/2006, 90 bottlenose dolphins died that were initially coincident with high densities of K. brevis. Most (93%) of the tested animals were positive for brevetoxin at concentrations up to 2,724 ng/mL. No DA was detected in these animals despite the presence of an intense DA-producing Pseudo-nitzschia bloom. In contrast to the absence or very low levels of brevetoxins measured in live dolphins, and those stranding in the absence of a K. brevis bloom, these data, taken together with the absence of any other obvious pathology, provide strong evidence that brevetoxin was the causative agent involved in these bottlenose dolphin mortality events.

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Limited information currently exists on the recovery periods of bleached corals as well as the spatial extent, causative factors, and the overall impact of bleaching on coral reef ecosystems. During October, 2005, widespread coral bleaching was observed within Buck Island Reef National Monument (BUIS) St. Croix, USVI. The bleaching event was preceded by 10 weeks of higher than average water temperatures (28.9-30.1°C). Random transects (100 square meters) over hard bottom habitats (N=94) revealed that approximately 51% of live coral cover was bleached. Nineteen of 23 coral species within 16 genera and two hydrocoral species exhibited signs of bleaching; species-specific bleaching patterns were variable throughout the study area. Coral cover for Montastraea annularisand species of the genus Agariciawere the most affected, while other species exhibited variability to bleaching. Although a weak but significant negative relationship (r2=0.10, P=0.0220) was observed, bleaching was evident at all depths (1.5-28 m). Bleaching was spatially autocorrelated (P=0.001) and hot-spot analysis identified a cluster of high bleaching stations northeast of Buck Island. Bleaching was significantly reduced within all depth zones and habitat types upon subsequent monitoring during April (15%) and October (3%) 2006.

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The artisanal fish preservation methods in Uganda are characterized by extreme operating conditions. Consequently, vital nutritional components diminish in value and quantity which renders fish consumer nutritionally insecure. To establish the magnitude of nutritional loss, duplicate samples of Mukene Rastrineobola argentea were collected from Kiyindi landing site on L. Victoria and Moone landing site on L. Kyoga. Each set of duplicate samples was divided into five portions and kept on ice. For each preservation method a portion was processed into respective products at Food Bioscience and Agri-Business Laboratories aside from the control (fresh) sample. Both preserved and control samples were analysed for nutrient loss at Department of Chemistry, Makerere University using AOAC methods. The composition of fatty acids was determined by methanolysis gas chromatography and Mass spectrophotometry of the resultant methyl esters. The results indicate that nutrients of all preserved samples did not vary significantly from the control except for some fatty acids. The Eicosapentaenoic acid (EPA) in fresh samples declined from 6.72% to 1.08% in deep-fried samples constituting 83.93% nutrient loss. The sum ratio w3:w6 as well as EPA: DHA (Docosahexaenoic) ratio in fried samples also varied significantly (p<0.5) lower than 0.668 and 0.20 for the average of either preservation methods and experts recommended ratio respectively. Further research has been recommended to ascertain the causative factor, since Mukene frying is being promoted in the Great lakes region as alternative method to sun-drying. In conclusion, regular consumers of fried Mukene do not benefit much from the nutritional and health attributes of Omega 3 and 6.