Caracterização molecular de bastonetes Gram positivos irregulares e actinomicetos aeróbios obtidos de espécimes clínicos, de ensaios de esterilidade e de áreas limpas

Os bastonetes Gram positivos irregulares (BGPIs) compõem um grupo de espécies bacterianas com ampla diversidade fenotípica e que podem estar presente no meio ambiente, na microbiota humana e de animais. A identificação acurada de BGPIs em nível de gênero e espécie empregando métodos bioquímicos convencionais é bastante limitada, sendo recomendado, portanto, o uso de técnicas moleculares. No presente estudo, foram identificadas amostras de BGPIs oriundas de espécimes clínicos de humanos, de produtos farmacêuticos e de áreas limpas através da análise de sequencias do gene 16S rRNA e de outros genes conservados (housekeeping genes). Os resultados obtidos pelo sequenciamento dos genes 16S rRNA e rpoB demonstraram C. striatum multi-resistente (MDR) como responsável por surto epidêmico em ambiente hospitalar da cidade do Rio de Janeiro. Quinze cepas de C. striatum foram isoladas em cultura pura a partir de secreção traqueal de pacientes adultos submetidos a procedimentos de entubação endotraqueal. A análise por eletroforese em gel de campo pulsado (PFGE) indicou a presença de quatro perfis moleculares, incluindo dois clones relacionados com cepas MDR (PFGE I e II). Os dados demonstram a predominância de PFGE I entre cepas MDR isoladas de unidades de terapia intensiva e enfermarias cirúrgicas. Uma potencial ligação causal entre a morte e a infecção por C. striatum MDR (PFGE tipos I e II) foi observada em cinco casos. Adicionalmente, acreditamos que este seja o primeiro estudo de identificação de espécies de Nocardia relacionadas com infecções humanas pela análise da sequencia multilocus (MLSA) no Brasil. Diferente dos dados observados na literatura (1970 a 2013) e obtidos pelos testes fenotípicos convencionais, a caracterização molecular de quatro lócus (gyrB-16S-secA1-hsp65) permitiu a identificação das espécies N. nova, N. cyriacigeorgica, N. asiatica e N. exalbida/gamkensis relacionadas com quadros de nocardiose em humanos. Cepas de N. nova isoladas de diferentes materiais clínicos de um único paciente apresentaram padrões de susceptibilidade antimicrobianos idênticos e dois perfis PFGE, indicando a possibilidade de quadros de co-infecção por N. nova em humanos. Em outra etapa da investigação, amostras de BGPIs obtidos de ambientes de salas limpas que não puderam ser identificadas por critérios convencionais foram submetidas a análise da sequência do gene 16S rRNA e caracterizadas 95,83% em nível de gênero e 35,42% em espécies. Para gêneros mais encontrados no estudo, foram analisados os genes rpoB e recA de dezessete cepas de Microbacterium e utilizado o MLSA para a identificação de sete cepas identificadas como Streptomyces. Os ensaios permitiram a identificação de três cepas de Microbacterium e de uma única amostra de Streptomyces ao nível de espécie. A análise da sequencia do gene rpoB também se mostrou eficaz na identificação de espécies de cepas de Corynebacterium. Finalmente, para as cepas ambientais pertencentes à classe Actinobacteria os dados morfológicos, bioquímicos e genotípicos permitiram documentar a cepa 3117BRRJ como representante de uma nova espécie do gênero Nocardioides, para o qual o nome Nocardioides brasiliensis sp. nov. e as cepas 3712BRRJ e 3371BRRJ como representante de um novo gênero e espécie para o qual o nome Guaraldella brasiliensis nov. foi proposto.

Inflação em sistemas com fluidos de radiação com viscosidade e dissipação e análise de estabilidade

Este trabalho apresenta um estudo da estabilidade das equações da inflação morna com um fluido de radiação viscoso. A viscosidade do fluido é proveniente do constante decaimento de partículas neste, devido à dissipação do campo escalar da inflação, o ínflaton.Esta viscosidade, que pode ser volumar ou laminar, é tratada em termos de teorias termodinâmicas fora do equilíbrio. Este estudo se limita às equações de fundo da inflação morna, de modo que somente a viscosidade volumar tem um efeito significativo, sendo a viscosidade laminar importante somente no contexto de perturbações cosmológicas. A descrição da viscosidade em termos de uma termodinâmica fora do equilíbrio, porém, não pode ser realizada univocamente, pois a única informação que temos sobre processos irreversíveis é a segunda lei da termodinâmica. Portanto, parte-se em busca de teorias que estejam de acordo com esta lei e que, por argumentos plausíveis, sejam capazes de descrever o comportamento dos fluxos dissipativos próximo ao equilíbrio. O objetivo deste trabalho é estudar a estabilidade da inflação morna viscosa para teorias causais e não causais para o fluido de radiação com viscosidade, de forma que se possa observar o impacto da viscosidade no regime inflacionário e a relevância de se passar a considerar a causalidade. Para o fluido de radiação, as teorias consideradas são a teoria não causal de Eckart e as teorias causais de Israel-Stewart e de Denicol et al (hidrodinâmica dissipativa causal não linear). Obtém-se que as teorias causais, como era de se esperar, além de serem, por definição, consistentes no tocante à finitude da velocidade de propagação dos fluxos dissipativos, tornam o sistema dinâmico estável para valores de viscosidade mais distantes do equilíbrio. Observa-se também, nitidamente, que a teoria de Denicol et al é a mais robusta nesse sentido. Este trabalho, portanto, visa dar continuidade ao estudo dos efeitos não-isentrópicos na inflação, já que, além da dissipação do ínflaton na inflação morna, o impacto da viscosidade tem despertado bastante interesse.

Métodos e técnicas de Design Centrado no Usuário: um levantamento a partir da usabilidade de produtos do CTIC/Fiocruz

A relação causal entre métodos de projeto e a usabilidade de produtos de comunicação e informação foi o tema desse estudo que buscou identificar o estado da arte sobre um processo de projeto que resulte em mais usabilidade na web. A partir dessa identificação, avaliou-se as melhorias que poderiam ser adotadas nos processos de desenvolvimento de interfaces utilizados por uma equipe específica da Fundação Oswaldo Cruz (CTIC - Fiocruz). Entendeu-se que um método de projeto deve estar atualizado em relação aos conhecimentos de áreas como a Ergonomia, a Interação Humano-computador e o Design de Interação. Para isso, adotou-se a hipótese de que o processo de projeto deve combinar três aspectos: a) um significativo envolvimento do usuário ao longo do processo; b) o uso de sucessivas iterações para configurar o produto e c) uma combinação mínima de técnicas relacionadas a objetivos específicos de cada fase de uma abordagem de Design Centrado no Usuário. Para contribuir com o desenvolvimento de métodos e técnicas que melhorem a usabilidade, descreveu-se as características dos métodos registrados na literatura e praticados por profissionais externos à Fundação Oswaldo Cruz (Fiocruz). A partir dessas informações, o estudo direcionou-se para o segundo objetivo específico: identificar melhorias nos métodos e técnicas aplicáveis no caso do CTIC Fiocruz. Através da combinação da revisão de literatura e da pesquisa de campo foram produzidas informações sobre tipos de fluxo dos métodos, tipos de envolvimento dos usuários, quantidade e gravidade de problemas de usabilidade observadas pelos profissionais e a validade de base geral de método para diferentes produtos. A primeira rodada de entrevista foi realizada para melhor entender o contexto da hipótese e a relação entre suas variáveis. A segunda rodada identificou as características do processo de projeto utilizado no CTIC. A partir dessas informações, aplicou-se duas técnicas com profissionais externos. Um questionário on-line foi utilizado para levantar informações bem específicas, em sua maioria de características quantitativas. A última técnica aplicada foi um card sorting on-line que apresentou um caso de projeto em que os profissionais indicaram quais técnicas seriam utilizadas diante de dois cenários diferentes: um mais favorável e outro restritivo. A análise demonstrou que a maioria dos profissionais acredita que os problemas de usabilidade são consequência da falta de determinadas abordagens e técnicas. Por isso, esses profissionais combinam fluxos iterativos com um significativo envolvimento do usuário no processo. Foram sugeridas melhorias para o método utilizado no CTIC sintetizadas através de um processo de Design Centrado no Usuário como ponto de partida que aplica o conceito tradicional de usabilidade (performance). Assim que possível, esse processo deve ser aperfeiçoado ao incluir o conceito de experiência do usuário que considera também os aspectos emocionais e hedonômicos na interação.

Temporal trends (2000–2011) and influences on fishery-independent catch rates for loggerhead sea turtles (Caretta caretta) at an important coastal foraging region in the southeastern United States

Seasonal trawling was conducted randomly in coastal (depths of 4.6–17 m) waters from St. Augustine, Florida, (29.9°N) to Winyah Bay, South Carolina (33.1°N), during 2000–03, 2008–09, and 2011 to assess annual trends in the relative abundance of sea turtles. A total of 1262 loggerhead sea turtles (Caretta caretta) were captured in 23% (951) of 4207 sampling events. Capture rates (overall and among prevalent 5-cm size classes) were analyzed through the use of a generalized linear model with log link function for the 4097 events that had complete observations for all 25 model parameters. Final models explained 6.6% (70.1–75.0 cm minimum straight-line carapace length [SCLmin]) to 14.9% (75.1–80.0 cm SCLmin) of deviance in the data set. Sampling year, geographic subregion, and distance from shore were retained as significant terms in all final models, and these terms collectively accounted for 6.2% of overall model deviance (range: 4.5–11.7% of variance among 5-cm size classes). We retained 18 parameters only in a subset of final models: 4 as exclusively significant terms, 5 as a mixture of significant or nonsignificant terms, and 9 as exclusively nonsignificant terms. Four parameters also were dropped completely from all final models. The generalized linear model proved appropriate for monitoring trends for this data set that was laden with zero values for catches and was compiled for a globally protected species. Because we could not account for much model deviance, metrics other than those examined in our study may better explain catch variability and, once elucidated, their inclusion in the generalized linear model should improve model fits.

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Long-term monitoring of habitats and reef fish found inside and outside the U.S. Virgin Islands Coral Reef National Monument: a comparative assessment

The primary objective of this study was to assess the efficacy of the Virgin Islands Coral Reef National Monument (VICR), a marine protected area in St John, US Virgin Islands. Surveys of habitat and fishes inside and outside of VICR were conducted in 2003-2008. Areas outside the VICR had significantly more scleractinian corals, greater habitat complexity, and greater species richness and density of reef fishes than areas inside., Areas inside and outside the VICR exhibited significant decreases in percent scleractinian coral coverage over the study period. A contrasting trend of increasing macroalgal cover was also observed. No clear effect of the severe 2005 coral bleaching event was observed suggesting other causal factors. No obvious trends in the fish community were observed across the study period. The significant decline in habitat condition, coupled with the initial incorporation of some of the more degraded reefs into the marine protected area may result in a longer time period necessary to detect positive changes in the St. John coral reef ecosystem and associated reef fish abundance and community structure.

Radiocarbon record of solar variability and Holocene climatic change in coastal southern California

EXTRACT (SEE PDF FOR FULL ABSTRACT): Pollen analysis and 5 radiocarbon dates for a 687-cm core provide a detailed chronology of environmental change for San Joaquin Marsh at the head of Newport Bay, Orange County, California. Sediment deposition kept pace with sea level rise during the mid-Holocene, but after 4500 years BP, sea water regularly reached the coring site, and salt marsh was the local vegetation. Brief periods of dominance by fresh-water vegetation 3800, 2800, 2300 and after 560 years BP correlate global cooling events and (except the 3800-year BP event) with carbon-14 production anomalies. The coincidence of climate change and carbon-14 anomalies support a causal connection with solar variability, but regardless of the causal mechanism(s) the delta-carbon-14 curves provide a chronology for global, high-frequency climatic change comparable to that of Milankovitch cyclicity for longer time scales.

Near and distant connection of atmospheric systems to ocean temperature change in the coastal California Current region

In studying hydrosphere, atmosphere, and biosphere interactions, it is useful to focus on specific subsystem processes and energy exchanges (forcing). Since subsystem scales range over ten orders of magnitude, it may be difficult to focus research on scales that will yield useful results in terms of establishing causal and predictive connections between more easily and less easily observed subsystems. In an effort to find pertinent scales, we have begun empirical investigations into relationships between atmospheric, oceanic, and biological systems having spatial scales exceeding 10^3 kilometers and temporal scales of six months or more.

Manipulation of chromosomes in fish: review of various techniques and their implications in aquaculture

Human ingenuity has made it possible to advent the chromosome manipulation techniques to produce individuals with differing genomic status in a number of fish using various causal agents such as physical shocks (temperature or hydrostatic pressure), chemical (endomitotics) and anesthetic treatments either to suppress the second meiotic division shortly after fertilization of eggs or to prevent the first mitotic division shortly prior to mitotic cleavage formation. This results in the induction of polyploidy (triploidy and tetraploidy), gynogenesis (both meiotic and mitotic leading to clonal lines) and androgenesis in fish population. The rationale for the induction of such ploidy in fish has been its potential for generating sterile individuals, rapidly inbred lines and masculinized fish, which could be of benefit to fish farming and aquaculture. In this paper, these are critically reviewed and the implication of recently developed chromosome manipulation techniques to various fin fishes is discussed.

Network structure preserving model reduction with weak a priori structural information

This paper extends a state projection method for structure preserving model reduction to situations where only a weaker notion of system structure is available. This weaker notion of structure, identifying the causal relationship between manifest variables of the system, is especially relevant is settings such as systems biology, where a clear partition of state variables into distinct subsystems may be unknown, or not even exist. The resulting technique, like similar approaches, does not provide theoretical performance guarantees, so an extensive computational study is conducted, and it is observed to work fairly well in practice. Moreover, conditions characterizing structurally minimal realizations and sufficient conditions characterizing edge loss resulting from the reduction process, are presented. ©2009 IEEE.

Integrated online speaker clustering and adaptation

For many applications, it is necessary to produce speech transcriptions in a causal fashion. To produce high quality transcripts, speaker adaptation is often used. This requires online speaker clustering and incremental adaptation techniques to be developed. This paper presents an integrated approach to online speaker clustering and adaptation which allows efficient clustering of speakers using the same accumulated statistics that are normally used for adaptation. Using a consistent criterion for both clustering and adaptation should yield gains for both stages. The proposed approach is evaluated on a meetings transcription task using audio from multiple distant microphones. Consistent gains over standard clustering and adaptation were obtained. Copyright © 2011 ISCA.

A structured modelling approach to simulating dynamic behaviours in complex organisations

This article reports a case study application of a systematic approach to modelling complex organisations, centred on simulation modelling (SM). The approach leads to populated instances of complementary model types, in ways that systematically capture, validate and facilitate various uses of organisational understandings, knowledge and data normally distributed amongst multiple knowledge holders. The model-driven approach to decision making enables improved manufacturing responsiveness. Literature on modelling technologies relevant to manufacturing systems organisation design and change is presented, as is literature on production planning and control. This provides a rationale for the development of a new modelling methodology which combines the use of enterprise, causal loop and SM. Subsequently, this article describes how in the case of a specific manufacturing enterprise the combined modelling techniques have informed the choice of alternative production planning and control policies. An example enterprise model of a capacitor manufacturing company is illustrated as derivative causal-loop models that structure and enable the design and use of a general purpose simulation model.

Unified modelling in support of organization design and change

The aim of this research is to provide a unified modelling-based method to help with the evaluation of organization design and change decisions. Relevant literature regarding model-driven organization design and change is described. This helps identify the requirements for a new modelling methodology. Such a methodology is developed and described. The three phases of the developed method include the following. First, the use of CIMOSA-based multi-perspective enterprise modelling to understand and capture the most enduring characteristics of process-oriented organizations and externalize various types of requirement knowledge about any target organization. Second, the use of causal loop diagrams to identify dynamic causal impacts and effects related to the issues and constraints on the organization under study. Third, the use of simulation modelling to quantify the effects of each issue in terms of organizational performance. The design and case study application of a unified modelling method based on CIMOSA (computer integrated manufacturing open systems architecture) enterprise modelling, causal loop diagrams, and simulation modelling, is explored to illustrate its potential to support systematic organization design and change. Further application of the proposed methodology in various company and industry sectors, especially in manufacturing sectors, would be helpful to illustrate complementary uses and relative benefits and drawbacks of the methodology in different types of organization. The proposed unified modelling-based method provides a systematic way of enabling key aspects of organization design and change. The case company, its relevant data, and developed models help to explore and validate the proposed method. The application of CIMOSA-based unified modelling method and integrated application of these three modelling techniques within a single solution space constitutes an advance on previous best practice. Also, the purpose and application domain of the proposed method offers an addition to knowledge. © IMechE 2009.

Dynamical structure function identifiability conditions enabling signal structure reconstruction

Networks of controlled dynamical systems exhibit a variety of interconnection patterns that could be interpreted as the structure of the system. One such interpretation of system structure is a system's signal structure, characterized as the open-loop causal dependencies among manifest variables and represented by its dynamical structure function. Although this notion of structure is among the weakest available, previous work has shown that if no a priori structural information is known about the system, not even the Boolean structure of the dynamical structure function is identifiable. Consequently, one method previously suggested for obtaining the necessary a priori structural information is to leverage knowledge about target specificity of the controlled inputs. This work extends these results to demonstrate precisely the a priori structural information that is both necessary and sufficient to reconstruct the network from input-output data. This extension is important because it significantly broadens the applicability of the identifiability conditions, enabling the design of network reconstruction experiments that were previously impossible due to practical constraints on the types of actuation mechanisms available to the engineer or scientist. The work is motivated by the proteomics problem of reconstructing the Per-Arnt-Sim Kinase pathway used in the metabolism of sugars. © 2012 IEEE.

Integrating design attributes, knowledge and uncertainty in aerospace sector

The delivery of integrated product and service solutions is growing in the aerospace industry, driven by the potential of increasing profits. Such solutions require a life cycle view at the design phase in order to support the delivery of the equipment. The influence of uncertainty associated with design for services is increasingly a challenge due to information and knowledge constraints. There is a lack of frameworks that aim to define and quantify relationship between information and knowledge with uncertainty. Driven by this gap, the paper presents a framework to illustrate the link between uncertainty and knowledge within the design context for services in the aerospace industry. The paper combines industrial interaction and literature review to initially define the design attributes, the associated knowledge requirements and the uncertainties experienced. The framework is then applied in three cases through development of causal loop models (CLMs), which are validated by industrial and academic experts. The concepts and inter-linkages are developed with the intention of developing a software prototype. Future recommendations are also included. © 2014 CIRP.