Detection of HIV-1 RNA by nucleic acid sequence-based amplification combined with fluorescence correlation spectroscopy

Nucleic acid sequence-based amplification (NASBA) has proved to be an ultrasensitive method for HIV-1 diagnosis in plasma even in the primary HIV infection stage. This technique was combined with fluorescence correlation spectroscopy (FCS) which enables online detection of the HIV-1 RNA molecules amplified by NASBA. A fluorescently labeled DNA probe at nanomolar concentration was introduced into the NASBA reaction mixture and hybridizing to a distinct sequence of the amplified RNA molecule. The specific hybridization and extension of this probe during amplification reaction, resulting in an increase of its diffusion time, was monitored online by FCS. As a consequence, after having reached a critical concentration of 0.1–1 nM (threshold for unaided FCS detection), the number of amplified RNA molecules in the further course of reaction could be determined. Evaluation of the hybridization/extension kinetics allowed an estimation of the initial HIV-1 RNA concentration that was present at the beginning of amplification. The value of initial HIV-1 RNA number enables discrimination between positive and false-positive samples (caused for instance by carryover contamination)—this possibility of discrimination is an essential necessity for all diagnostic methods using amplification systems (PCR as well as NASBA). Quantitation of HIV-1 RNA in plasma by combination of NASBA with FCS may also be useful in assessing the efficacy of anti-HIV agents, especially in the early infection stage when standard ELISA antibody tests often display negative results.

How the owl resolves auditory coding ambiguity

The barn owl (Tyto alba) uses interaural time difference (ITD) cues to localize sounds in the horizontal plane. Low-order binaural auditory neurons with sharp frequency tuning act as narrow-band coincidence detectors; such neurons respond equally well to sounds with a particular ITD and its phase equivalents and are said to be phase ambiguous. Higher-order neurons with broad frequency tuning are unambiguously selective for single ITDs in response to broad-band sounds and show little or no response to phase equivalents. Selectivity for single ITDs is thought to arise from the convergence of parallel, narrow-band frequency channels that originate in the cochlea. ITD tuning to variable bandwidth stimuli was measured in higher-order neurons of the owl’s inferior colliculus to examine the rules that govern the relationship between frequency channel convergence and the resolution of phase ambiguity. Ambiguity decreased as stimulus bandwidth increased, reaching a minimum at 2–3 kHz. Two independent mechanisms appear to contribute to the elimination of ambiguity: one suppressive and one facilitative. The integration of information carried by parallel, distributed processing channels is a common theme of sensory processing that spans both modality and species boundaries. The principles underlying the resolution of phase ambiguity and frequency channel convergence in the owl may have implications for other sensory systems, such as electrolocation in electric fish and the computation of binocular disparity in the avian and mammalian visual systems.

The nucleocapsid protein specifically anneals tRNALys-3 onto a noncomplementary primer binding site within the HIV-1 RNA genome in vitro

HIV type 1 (HIV-1) specifically uses host cell tRNALys-3 as a primer for reverse transcription. The 3′ 18 nucleotides of this tRNA are complementary to a region on the HIV RNA genome known as the primer binding site (PBS). HIV-1 has a strong preference for maintaining a lysine-specific PBS in vivo, and viral genomes with mutated PBS sequences quickly revert to be complementary to tRNALys-3. To investigate the mechanism for the observed PBS reversion events in vitro, we examined the capability of the nucleocapsid protein (NC) to anneal various tRNA primer sequences onto either complementary or noncomplementary PBSs. We show that NC can anneal different full-length tRNAs onto viral RNA transcripts derived from the HIV-1 MAL or HXB2 isolates, provided that the PBS is complementary to the tRNA used. In contrast, NC promotes specific annealing of only tRNALys-3 onto an RNA template (HXB2) whose PBS sequence has been mutated to be complementary to the 3′ 18 nt of human tRNAPro. Moreover, HIV-1 reverse transcriptase extends this binary complex from the proline-specific PBS. The formation of the noncomplementary binary complex does not occur when a chimeric tRNALys/Pro containing proline-specific D and anticodon domains is used as the primer. Thus, elements outside the acceptor-TΨC domains of tRNALys-3 play an important role in preferential primer use in vitro. Our results support the hypothesis that mutant PBS reversion is a result of tRNALys-3 annealing onto and extension from a PBS that specifies an alternate host cell tRNA.

Functional organization of the hippocampal memory system

In humans declarative or explicit memory is supported by the hippocampus and related structures of the medial temporal lobe working in concert with the cerebral cortex. This paper reviews our progress in developing an animal model for studies of cortical–hippocampal interactions in memory processing. Our findings support the view that the cortex maintains various forms of memory representation and that hippocampal structures extend the persistence and mediate the organization of these codings. Specifically, the parahippocampal region, through direct and reciprocal interconnections with the cortex, is sufficient to support the convergence and extended persistence of cortical codings. The hippocampus itself is critical to the organization cortical representations in terms of relationships among items in memory and in the flexible memory expression that is the hallmark of declarative memory.

A high-resolution physical map of human chromosome 11.

The development of a highly reliable physical map with landmark sites spaced an average of 100 kbp apart has been a central goal of the Human Genome Project. We have approached the physical mapping of human chromosome 11 with this goal as a primary target. We have focused on strategies that would utilize yeast artificial chromosome (YAC) technology, thus permitting long-range coverage of hundreds of kilobases of genomic DNA, yet we sought to minimize the ambiguities inherent in the use of this technology, particularly the occurrence of chimeric genomic DNA clones. This was achieved through the development of a chromosome 11-specific YAC library from a human somatic cell hybrid line that has retained chromosome 11 as its sole human component.To maximize the efficiency of YAC contig assembly and extension, we have employed an Alu-PCR-based hybridization screening system. This system eliminates many of the more costly and time-consuming steps associated with sequence tagged site content mapping such as sequencing, primer production, and hierarchical screening, resulting in greater efficiency with increased throughput and reduced cost. Using these approaches, we have achieved YAC coverage for >90% of human chromosome 11, with an average intermarker distance of <100 kbp. Cytogenetic localization has been determined for each contig by fluorescent in situ hybridization and/or sequence tagged site content. The YAC contigs that we have generated should provide a robust framework to move forward to sequence-ready templates for the sequencing efforts of the Human Genome Project as well as more focused positional cloning on chromosome 11.

Método de estimativa de torque da articulação do joelho baseada em EMG

Este trabalho apresenta um método de estimativa de torque do joelho baseado em sinais eletromiográficos (EMG) durante terapia de reabilitação robótica. Os EMGs, adquiridos de cinco músculos envolvidos no movimento de flexão e extensão do joelho, são processados para encontrar as ativações musculares. Em seguida, mediante um modelo simples de contração muscular, são calculadas as forças e, usando a geometria da articulação, o torque do joelho. As funções de ativação e contração musculares possuem parâmetros limitados que devem ser calibrados para cada usuário, sendo o ajuste feito mediante a minimização do erro entre o torque estimado e o torque medido na articulação usando a dinâmica inversa. São comparados dois métodos iterativos para funções não-lineares como técnicas de otimização restrita para a calibração dos parâmetros: Gradiente Descendente e Quasi-Newton. O processamento de sinais, calibração de parâmetros e cálculo de torque estimado foram desenvolvidos no software MATLAB®; o cálculo de torque medido foi feito no software OpenSim com sua ferramenta de dinâmica inversa.

Análise da composição, abundância e distribuição da comunidade fitoplanctônica nos reservatórios do sistema em cascata do Médio e Baixo rio Tietê/SP

Com a finalidade de atender a demanda energética, muitos reservatórios foram construídos no Brasil e, notadamente na região Sudeste, as construções das barragens não somente atenderam aos usos múltiplos (geração de energia, irrigação, lazer e abastecimento público), como também foram elementos propulsores da economia regional, contribuindo para a expansão das atividades industriais e rurais, bem como, um desordenado crescimento urbano. Em conseqüência da falta de planejamento, áreas naturais foram desmatadas, sendo substituídas por formas de plantio inadequadas e por projetos de especulação imobiliária não condizentes com a sustentabilidade ambiental. No decorrer das últimas décadas, os impactos aumentaram em magnitude e extensão, ocasionando sérios problemas aos recursos hídricos, culminando em conflitos pelo uso da água. Dentro deste contexto, destaca-se o rio Tietê, o qual percorre importantes cidades e extensas áreas rurais no Estado de São Paulo, sendo que, neste longo percurso, recebe a contribuição de diversos tributários (poluídos ou não) e efluentes urbanos, industriais e aqueles derivados de fontes não pontuais, além do processo de fragmentação que foi instalado a partir da construção de inúmeras barragens. De forma conjunta, todos os fatores promoveram alterações significativas no sistema e, procurando avaliar a situação atual dos reservatórios, desenvolveu-se uma pesquisa direcionada à análise da composição, densidade e distribuição da comunidade fitoplanctônica e sua relação com as variáveis limnológicas, climatológicas e hidrodinâmicas dos reservatórios da Barra Bonita, Bariri, Ibitinga, Promissão, Nova Avanhandava, Três Irmãos, além dos rios Tietê e Piracicaba e parte do rio Paraná (reservatório de Jupiá e a Jusante do reservatório de Ilha Solteira). Para tanto, foram realizadas coletas nos meses de fevereiro, maio, julho e outubro de 2000 e os resultados obtidos demonstram uma elevada concentração de nutrientes, com redução na seqüência dos reservatórios, além da variabilidade temporal, com efeito significativo da precipitação no transporte de materiais, promovendo alterações no estado trófico de cada sistema. A disponibilidade de nutrientes, transparência da água, vazão e tempo de residência, associados aos fatores climatológicos, foram elementos importantes no estabelecimento das populações, influenciando a composição, densidade e distribuição da comunidade fitoplanctônica, a qual apresentou maior dominância das classes Cyanophyceae e Chlorophyceae, com maior contribuição em densidade e riqueza de espécies, respectivamente.

The role of the social environment in non-suicidal self-injury among LGBTQ youth: A mixed methods study

Non-suicidal self-injury (NSSI), such as cutting and burning, is a widespread social problem among lesbian, gay, bisexual, transgender, queer, and questioning (LGBTQ) youth. Extant research indicates that this population is more than twice as likely to engage in NSSI than heterosexual and cisgender (non-transgender) youth. Despite the scope of this social problem, it remains relatively unexamined in the literature. Research on other risk behaviors among LGBTQ youth indicates that experiencing homophobia and transphobia in key social contexts such as families, schools, and peer relationships contributes to health disparities among this group. Consequently, the aims of this study were to examine: (1) the relationship between LGBTQ youth's social environments and their NSSI behavior, and (2) whether/how specific aspects of the social environment contribute to an understanding of NSSI among LGBTQ youth. This study was conducted using an exploratory, sequential mixed methods design with two phases. The first phase of the study involved analysis of transcripts from interviews conducted with 44 LGBTQ youth recruited from a community-based organization. In this phase, five qualitative themes were identified: (1) Violence; (2) Misconceptions, Stigma, and Shame; (3) Negotiating LGBTQ Identity; (4) Invisibility and Isolation; and (5) Peer Relationships. Results from the qualitative phase were used to identify key variables and specify statistical models in the second, quantitative, phase of the study, using secondary data from a survey of 252 LGBTQ youth. The qualitative phase revealed how LGBTQ youth, themselves, described the role of the social environment in their NSSI behavior, while the quantitative phase was used to determine whether the qualitative findings could be used to predict engagement in NSSI among a larger sample of LGBTQ youth. The quantitative analyses found that certain social-environmental factors such as experiencing physical abuse at home, feeling unsafe at school, and greater openness about sexual orientation significantly predicted the likelihood of engaging in NSSI among LGBTQ youth. Furthermore, depression partially mediated the relationships between family physical abuse and NSSI and feeling unsafe at school and NSSI. The qualitative and quantitative results were compared in the interpretation phase to explore areas of convergence and incongruence. Overall, this study's findings indicate that social-environmental factors are salient to understanding NSSI among LGBTQ youth. The particular social contexts in which LGBTQ youth live significantly influence their engagement in this risk behavior. These findings can inform the development of culturally relevant NSSI interventions that address the social realities of LGBTQ youth's lives.

Compactação e elevação da vida útil de transformadores de distribuição empregando óleo vegetal isolante.

A busca no aumento da vida útil dos transformadores de distribuição, redução dos custos de manutenção e mitigação de falhas, leva ao desenvolvimento de novos materiais e critérios de exploração diferenciados desses ativos. Esta pesquisa apresenta o desenvolvimento de um novo transformador de distribuição compacto e mais eficiente utilizando óleo vegetal isolante totalmente biodegradável. Além de biodegradável, o óleo vegetal utilizado possui menor agressividade ambiental e maior capacidade térmica aumentando, a capacidade de carregamento do transformador sem comprometer a sua vida útil. A fim de atestar essa menor agressividade em relação ao óleo mineral, ensaios foram efetuados em um equipamento que permaneceu 12 anos em operação. O equipamento foi totalmente desmontado para análise e coleta de amostras de papel e óleo vegetal isolante. As análises visam comprovar a menor agressividade em relação ao óleo mineral, apresentadas na revisão bibliográfica. A menor agressividade torna possível a proposição de uma nova filosofia de planejamento de redes de distribuição utilizando uma quantidade menor dos novos transformadores para uma mesma carga, tornando-a mais compacta e eficiente.

Multi-objective adaptive evolutionary strategy for tuning compilations

Tuning compilations is the process of adjusting the values of a compiler options to improve some features of the final application. In this paper, a strategy based on the use of a genetic algorithm and a multi-objective scheme is proposed to deal with this task. Unlike previous works, we try to take advantage of the knowledge of this domain to provide a problem-specific genetic operation that improves both the speed of convergence and the quality of the results. The evaluation of the strategy is carried out by means of a case of study aimed to improve the performance of the well-known web server Apache. Experimental results show that a 7.5% of overall improvement can be achieved. Furthermore, the adaptive approach has shown an ability to markedly speed-up the convergence of the original strategy.

Difference schemes for numerical solutions of lagging models of heat conduction

Non-Fourier models of heat conduction are increasingly being considered in the modeling of microscale heat transfer in engineering and biomedical heat transfer problems. The dual-phase-lagging model, incorporating time lags in the heat flux and the temperature gradient, and some of its particular cases and approximations, result in heat conduction modeling equations in the form of delayed or hyperbolic partial differential equations. In this work, the application of difference schemes for the numerical solution of lagging models of heat conduction is considered. Numerical schemes for some DPL approximations are developed, characterizing their properties of convergence and stability. Examples of numerical computations are included.

Difference schemes for time-dependent heat conduction models with delay

Different non-Fourier models of heat conduction, that incorporate time lags in the heat flux and/or the temperature gradient, have been increasingly considered in the last years to model microscale heat transfer problems in engineering. Numerical schemes to obtain approximate solutions of constant coefficients lagging models of heat conduction have already been proposed. In this work, an explicit finite difference scheme for a model with coefficients variable in time is developed, and their properties of convergence and stability are studied. Numerical computations showing examples of applications of the scheme are presented.

A compact difference scheme for numerical solutions of second order dual-phase-lagging models of microscale heat transfer

Dual-phase-lagging (DPL) models constitute a family of non-Fourier models of heat conduction that allow for the presence of time lags in the heat flux and the temperature gradient. These lags may need to be considered when modeling microscale heat transfer, and thus DPL models have found application in the last years in a wide range of theoretical and technical heat transfer problems. Consequently, analytical solutions and methods for computing numerical approximations have been proposed for particular DPL models in different settings. In this work, a compact difference scheme for second order DPL models is developed, providing higher order precision than a previously proposed method. The scheme is shown to be unconditionally stable and convergent, and its accuracy is illustrated with numerical examples.

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Mode of access: Internet.

Windbreaks for Illinois farmsteads.

"In cooperation with University of Illinois. College of Agriculture. Agricultural Experiment Station and Extension Service in Agriculture and Home Economics."