Multiplexed DNA-mediated electrochemistry

The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of π-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the π-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA π-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.

First, Methylene Blue (MB′) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB′ was reduced through DNA-mediated charge transport. The redox signal intensity for MB′-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB′ on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.

Next, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening π-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA. Further gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.

Finally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.

Atom localization via interference of dark resonances

A scheme of atom localization based on the interference of resonance of double-dark states is proposed, in which the atom interacts with a classical standing-wave field. It is found that the localization property is significantly improved due to the interaction of double-dark resonances. It is realized that the atom is localized just at the nodes of the standing-wave field with higher precision. Moreover, an improvement by a factor of 2 in the detecting probability of a single atom within the subwavelength domain can be achieved by adjusting the probe-field detuning. This scheme shows more advantages than other schemes of atom localization.

Energy Supply and the Sustainability of Endogenous Growth

29 p.

Random propagation in complex systems : nonlinear matrix recursions and epidemic spread

This dissertation studies long-term behavior of random Riccati recursions and mathematical epidemic model. Riccati recursions are derived from Kalman filtering. The error covariance matrix of Kalman filtering satisfies Riccati recursions. Convergence condition of time-invariant Riccati recursions are well-studied by researchers. We focus on time-varying case, and assume that regressor matrix is random and identical and independently distributed according to given distribution whose probability distribution function is continuous, supported on whole space, and decaying faster than any polynomial. We study the geometric convergence of the probability distribution. We also study the global dynamics of the epidemic spread over complex networks for various models. For instance, in the discrete-time Markov chain model, each node is either healthy or infected at any given time. In this setting, the number of the state increases exponentially as the size of the network increases. The Markov chain has a unique stationary distribution where all the nodes are healthy with probability 1. Since the probability distribution of Markov chain defined on finite state converges to the stationary distribution, this Markov chain model concludes that epidemic disease dies out after long enough time. To analyze the Markov chain model, we study nonlinear epidemic model whose state at any given time is the vector obtained from the marginal probability of infection of each node in the network at that time. Convergence to the origin in the epidemic map implies the extinction of epidemics. The nonlinear model is upper-bounded by linearizing the model at the origin. As a result, the origin is the globally stable unique fixed point of the nonlinear model if the linear upper bound is stable. The nonlinear model has a second fixed point when the linear upper bound is unstable. We work on stability analysis of the second fixed point for both discrete-time and continuous-time models. Returning back to the Markov chain model, we claim that the stability of linear upper bound for nonlinear model is strongly related with the extinction time of the Markov chain. We show that stable linear upper bound is sufficient condition of fast extinction and the probability of survival is bounded by nonlinear epidemic map.

Valuation of wind energy projects: A real options approach

27 p.

体布拉格光栅外腔半导体激光器光谱特性研究

用体布拉格光栅(VBG)作为反馈元件与瓦级半导体激光器(LD)以及快轴准直柱透镜构成一个可以将半导体激光器的工作波长稳定在体布拉格光栅布拉格波长处的外腔激光器。测量了体布拉格光栅外腔激光器的波长稳定性与其工作电流、热汇温度、激光束准直装置等因素的关系。分析了波长稳定效果与半导体激光器增益谱特性、外腔结构参量等因素的关系。研究表明,在相同的工作电流、热汇温度下,当准直柱透镜直径为0.4 mm时的波长稳定效果较好;在此情况下,当热汇温度控制在30 ℃,工作电流从0.5 A增加到1.5 A的测量范围内,以及当工

连续工作的体布拉格光栅外腔半导体激光器的温度特性

对体布拉格光栅(VBG)作为波长选择元件的外腔半导体激光器的波长锁定进行了实验研究,报道了连续运转输出功率达43.5 W的半导体激光器阵列的体布拉格光栅波长锁定实验结果,给出了不同热沉温度下的稳定的波长锁定结果,说明采用体布拉格光栅外腔将减小半导体激光器的温控压力。实验中发现,随着注入电流的增大,输出激光功率逐渐增强,锁定的激射波长向长波长方向偏移。在输出功率为34.5 W时,波长红移约0.56 nm。这一移动与实验测量的体布拉格光栅的温度特性相吻合。连续和高占空比运行、高输出功率情况下,在器件的设计和使用时应该考虑这一效应。

Origem e composição da matéria orgânica sedimentar na margem continental próximo a Cabo Frio (RJ), porção sul da Bacia de Campos, costa sudeste do Brasil

Lipídios como marcadores moleculares (ácidos graxos, esterois e n- alcoois) e COT foram analisados em 48 amostras de sedimento superficial (0-2 cm) em dois períodos (inverno de 2008/2009 e verão de 2009) ao longo de 12 isóbatas em 2 transectos (25 a 3000 m) na principal região de ressurgência da costa sudeste do Brasil, onde a influência do aporte fluvial é mínima. O objetivo foi (i) avaliar as fontes, transporte e regiões de acúmulo da matéria orgânica (MO) (ii) identificar a fração da MO potencialmente disponível para os orgânismos bentônicos. Este estudo faz parte do Projeto Habitats Heterogeneidade Ambiental da Bacia de Campos coordenado pelo CENPES/PETROBRAS. Lipídios derivados da produção primária (0.058 - 3.1 mg gCOT-1) e secundária (0.015 - 2.2 mg gCOT-1) representaram a maior fração da MO sedimentar, enquanto lipídios derivados de fontes alóctonas (0.043 - 0.40 mg gCOT-1) e bactérias (<0.01 - 0.43 mg gCOT-1) foram menos representativos. O padrão de transporte e acúmulo da MO no sedimento depende da associação entre fatores físicos (hidrodinâmicos) e biológicos (resposta a ressurgência), e não é influenciado sazonalmente como observado em dados prévios na mesma região. Verificou-se que regiões restritas da plataforma continental apresentam acúmulo de MO lábil e esse material é exportado para regiões do talude (400 a 1000 m de profundidade), o que representa uma fonte importante de MO biodisponível para a comunidade bentônica desta região.

Analysis of dispersion compensation for position-dependence in externally modulated CATV lightwave systems by using chirped fiber grating

The dispersion compensation characteristics of the chirped fiber grating (CFG) for different dispersion compensation positions are analyzed in externally modulated cable television (CATV) lightwave system and the analytic expression of the composite second order (CSO) distortion is derived. The analyses give a reasonable explanation for the position-dependent effect of CFG dispersion compensator, which was found in practical systems. Moreover, the theoretical result is also verified by an experiment. It is believed that the theory will be helpful in designing optical CATV fiber links with nodes at proper positions both for intensity amplification and dispersion compensation.

Design and evaluation of an optical switching node

[EN]For a good development of elastic optical networks, the design of flexible optical switching nodes is required. This work analyses the previously proposed flexible architectures and, based on the most appropriate, which is the Architecture on Demand (AoD), proposes a specific configuration of the node that includes spatial and spectral switching and the wavelength conversion functionality with a low blocking probability and the minimum amount of modules; the characteristics of the traffic that the designed node is able to cope with are specified in the last chapter. An evaluation of the designed node is also done, and, compared to the other architectures, it is shown that the Architecture on Demand gives better results than others and that it has a higher potential for future developments.

Avaliação do potencial anti-inflamatório agudo e crônico e imunossupressor do extrato etanólico de Pterodon polygalaeflorus através de estudos in vivo e in vitro

O gênero Pterodon pertence à família das Papilonaceas e inclui cinco espécies nativas do Brasil: P. pubescens Benth., P. emarginatus Vog., P. apparicioi Pedersoli e P. abruptus Benth., sendo a espécie objeto deste estudo a P. polygalaeflorus Benth.. Seus frutos são livremente comercializados em mercados da flora medicinal e utilizados pela medicina popular devido a propriedades anti-reumática, analgésica, antiinflamatória, dentre outros efeitos associados a esses frutos. O principal uso popular está relacionado ao efeito antiartrítico que parece se encontrar na fração oleosa do fruto. O objetivo deste trabalho foi avaliar o extrato etanólico de Pterodon polygalaeflorus (EEPpg) quanto ao seu potencial antiinflamatório crônico através do modelo de artrite induzida por colágeno (CIA) e seu efeito sobre os linfócitos in vitro, bem como sobre a expansão de células MAC-1+ induzida por adjuvante completo de Freund (AFC). A caracterização química do EEPpg foi realizada por cromatografia em camada delgada (TLC), cromatografia líquida de alta performance (HPLC) e cromatografia gasosa acoplada a espectrômetro de massa (GC-MS), através dos quais uma gama de compostos, incluindo terpenóides de polaridades variadas e flavonóides, foram observados. No modelo de CIA, o EEPpg reduziu significativamente parâmetros associados ao desenvolvimento e progressão da doença e à severidade da doença , inibindo em até 99% o seu desenvolvimento e levando a ausência de sinais clínicos evidentes após tratamento com as menores doses do extrato (0,01 mg/kg e 0,001 mg/kg). O tratamento com EEPpg também reduziu características histopatológicas típicas de articulações de animais com CIA, que também são observadas na artrite reumatóide. O EEPpg reduziu significativamente o peso dos linfonodos dos camundongos, bem como o número absoluto de segmentados, monócitos e linfócitos no sangue. In vitro, O EEPpg mostrou uma atividade anti-proliferativa dos esplenócitos estimulados com concanavalina A (Con A) ou lipopolissacarídeo (LPS) analisada através do ensaio de redução do sal de tetrazólio MTT, corroborada pelo seu efeito sobre o ciclo celular de linfócitos estimulados com Con A, onde o EEPpg nas concentrações de 5, 10 e 20 μg/mL reduziu significativamente, de maneira concentração-dependente, o número de células nas fases S+G2/M e aumentou na fase G0/G1 do ciclo celular. O efeito anti-proliferativo do EEPpg parece também estar associado ao aumento da apoptose dos linfócitos após estimulação com Con A, com aumento estatisticamente significativo no percentual de células mortas por apoptose nas maiores concentrações . O EEPpg inibiu a expansão de células Mac-1+ induzida por AFC no baço, porém não no peritônio. Esse resultado sugere um efeito inibidor do EEPpg sobre a migração celular para as articulações artríticas. Esses resultados contribuem para a validação do uso popular de P. polygalaeflorus contra doenças relacionadas a processos inflamatórios e imunes, sobretudo na artrite reumatóide, antes nunca demonstrado.

Total cross section measurements for ^3He(^3He, 2p)^4He at low energies

Precise measurements of the total reaction cross section for ³He(³He,2p)⁴He He have been made in the range of center-of-mass energies between 1100 keV and 80 keV. A differentially pumped gas target modified to operate with a limited quantity of the target gas was employed to minimize the uncertainties in the primary energy and energy straggle. Beam integration inside the target gas was carried out by a calorimetric device which measures the total energy spent in a heat sink rather than the total charge in a Faraday cup. Proton energy spectra have been obtained using a counter telescope consisting of a gas proportional counter and a surface barrier detector and angular distributions of these protons have been measured at seven bombarding energies. Cross section factors, S(E), have been calculated from the total cross sections and fitted to a linear function of energy over different ranges of energy. For E_cm < 500 keV

S(E_cm) = S₀ + S₁ E_cm

where S₀ = (5.0 ^+0.6_-0.4) MeV - barns and S₁ = (-1.8 ± 0.5) barns.

Oxygen relationships in intermittent sand filtration of wastewaters

A model for some of the many physical-chemical and biological processes in intermittent sand filtration of wastewaters is described and an expression for oxygen transfer is formulated.

The model assumes that aerobic bacterial activity within the sand or soil matrix is limited, mostly by oxygen deficiency, while the surface is ponded with wastewater. Atmospheric oxygen reenters into the soil after infiltration ends. Aerobic activity is resumed, but the extent of penetration of oxygen is limited and some depths may be always anaerobic. These assumptions lead to the conclusion that the percolate shows large variations with respect to the concentration of certain contaminants, with some portions showing little change in a specific contaminant. Analyses of soil moisture in field studies and of effluent from laboratory sand columns substantiated the model.

The oxygen content of the system at sufficiently long times after addition of wastes can be described by a quasi-steady-state diffusion equation including a term for an oxygen sink. Measurements of oxygen content during laboratory and field studies show that the oxygen profile changes only slightly up to two days after the quasi-steady state is attained.

Results of these hypotheses and experimental verification can be applied in the operation of existing facilities and in the interpretation of data from pilot plant-studies.

Aplicabilidade da Norma Regulamentadora 32: visão dos trabalhadores de enfermagem de um hospital público do RJ

Pesquisa de natureza descritiva e abordagem quantitativa de dados sobre a Aplicabilidade da Norma Regulamentadora-32 (NR 32) do Ministério do Trabalho e Emprego (MTE), visando mobilizar os trabalhadores de enfermagem para reduzir a exposição aos riscos inerentes do trabalho em estabelecimentos de saúde. Problema de pesquisa: Quais os fatores que interferem na implantação da Norma Regulamentadora-32 nas enfermarias de um Hospital Público Estadual do Rio de Janeiro, na visão dos trabalhadores de enfermagem? Teve como objetivo geral analisar os fatores que interferem na aplicabilidade da NR 32 pela enfermagem, em um hospital público do Rio de Janeiro. A população foi composta de 138 trabalhadores de enfermagem das enfermarias de clínica médica, cirúrgica e ortopédica. Utilizou-se para a coleta de dados um questionário estruturado com perguntas fechadas. Os dados foram coletados no período de 28 de janeiro a 14 de fevereiro de 2009, e analisados através do Programa Statical Package for the Social Sciences (SPSS) versão 13 for Windows e Microsoft Office Excel 2003. Os resultados apontaram que os trabalhadores de enfermagem desse hospital estão, em sua maioria, na faixa etária de 30-49 anos, com pelo menos 1 ano de atuação no mesmo setor e formaram-se há 15 anos ou mais, além disso, 68,1% são estatutários. Constatou-se que há recomendações da NR-32 e precauções-padrão não são seguidas pelos participantes da pesquisa. Os fatores que interferem no cumprimento da atual legislação vão desde o desconhecimento dos riscos ocupacionais e comportamento dos trabalhadores, até a falta de uma ação efetiva de Educação Continuada e da Comissão de Controle de Infecção Hospitalar (CCIH). Destacaram-se, entre outros, o uso de adornos (51,8%); calçado aberto (48,9%); alimentação no posto de trabalho (46,3%); uso da pia para outras finalidades (44,9%), reencape ou desconexão manual de agulhas (36,4%); sair do local de trabalho com uniforme ou Equipamento de Proteção Individual - EPI (21%); limite de recipiente de descarte de perfurocortantes não respeitado (11,8%), falta de uso de EPI quando auxilia no exame com Raios-X (32,6%) e na manipulação de quimioterápicos (7,8%). A instituição não fornece uniformes nem calçados. Outros fatores institucionais foram a falta de equipamentos, a falta de um política de prevenção e promoção da saúde, inexistência de serviço de saúde ocupacional e instalações físicas inadequadas. Tal descumprimento expõe, de forma excessiva, os trabalhadores de enfermagem aos mais variados fatores de riscos ocupacionais, podendo refletir na sua saúde e no processo de trabalho. Recomenda-se um trabalho efetivo e integrado dos Programas de Educação Continuada e CCIH para esclarecimento dos trabalhadores de enfermagem, e implantação do Serviço de Saúde do Trabalhador. Sugere-se aos gestores expandirem este estudo para os demais setores das unidades hospitalares e outras instituições públicas de saúde para o conhecimento da situação de trabalho, bem como a criação de espaços de discussão para a busca de soluções dos problemas com a participação dos trabalhadores.

Impact of polarized illumination on high NA imaging in ArF immersion lithography at 45 nm node

Immersion lithography has been considered as the mainstream technology to extend the feasibility of optical lithography to further technology nodes. Using proper polarized illumination in an immersion lithographic tool is a powerful means to enhance the image quality and process capability for high numerical aperture (NA) imaging. In this paper, the impact of polarized illumination on high NA imaging in ArF immersion lithography for 45 nm dense lines and semi-dense lines is studied by PROLITH simulation. The normalized image log slope (NILS) and exposure defocus (ED) window are simulated under various polarized illumination modes, and the impact of polarized illumination on image quality and process latitude is analyzed. (C) 2007 Elsevier GmbH. All rights reserved.