Electronically nonadiabatic decomposition mechanisms of clusters of zinc and dimethylnitramine

Electronically nonadiabatic decomposition mechanisms of dimethylnitramine (DMNA) in presence of zinc metal clusters are explored. Complete active space self-consistent field (CASSCF) calculation is employed for DMNA-Zn and ONIOM (Our own N-layered integrated molecular orbital and molecular mechanics) methodology is coupled with CASSCF methodology for DMNA-Zn-10 cluster. Present computational results show that DMNA-Zn clusters undergo electronically nonadiabatic reactions, rendering nitro-nitrite isomerization followed by NO elimination. The overall reactions are also found to be highly exothermic in nature. This is the first report on electronically nonadiabatic decomposition pathways of DMNA-Zn-n neutral clusters. (C) 2014 Elsevier B.V. All rights reserved.

Use of Mycobacterium smegmatis Deficient in ADP-Ribosyltransferase as Surrogate for Mycobacterium tuberculosis in Drug Testing and Mutation Analysis

Rifampicin (Rif) is a first line drug used for tuberculosis treatment. However, the emergence of drug resistant strains has necessitated synthesis and testing of newer analogs of Rif. Mycobacterium smegmatis is often used as a surrogate for M. tuberculosis. However, the presence of an ADP ribosyltransferase (Arr) in M. smegmatis inactivates Rif, rendering it impractical for screening of Rif analogs or other compounds when used in conjunction with them (Rif/Rif analogs). Rifampicin is also used in studying the role of various DNA repair enzymes by analyzing mutations in RpoB (a subunit of RNA polymerase) causing Rif resistance. These analyses use high concentrations of Rif when M. smegmatis is used as model. Here, we have generated M. smegmatis strains by deleting arr (Delta arr). The M. smegmatis Delta arr strains show minimum inhibitory concentration (MIC) for Rif which is similar to that for M. tuberculosis. The MICs for isoniazid, pyrazinamide, ethambutol, ciprofloxacin and streptomycin were essentially unaltered for M. smegmatis Delta arr. The growth profiles and mutation spectrum of Delta arr and, Delta arr combined with Delta udgB (udgB encodes a DNA repair enzyme that excises uracil) strains were similar to their counterparts wild-type for arr. However, the mutation spectrum of Delta fpg Delta arr strain differed somewhat from that of the Delta fpg strain (fpg encodes a DNA repair enzyme that excises 8-oxo-G). Our studies suggest M. smegmatis Delta arr strain as an ideal model system in drug testing and mutation spectrum determination in DNA repair studies.

Li2MnO3: a rare red-coloured manganese(IV) oxide exhibiting tunable red-yellow-green emission

An experimental assessment of Li2MnO3 has been conducted, in conjunction with related Mn(IV) oxides, to investigate its red colour and photoluminescence. Optical absorption spectra revealed strong band gap absorption, with a sharp edge at similar to 610 nm and a transparent region between similar to 610 and similar to 650 nm, giving rise to the red colour of this compound. Octahedral Mn(IV) ligand field transitions have been observed in the excitation spectra of Li2MnO3, corresponding both to Mn(IV) at ideal sites and displaced in Li sites in the rock salt-based layered structure of Li2MnO3. Optical excitation at ligand field transition energies produces tunable emission in the red-yellow-green region, rendering Li2MnO3 a unique Mn(IV) oxide. The honeycomb-ordered LiMn6] units in its structure are probably the origin of both the absorption and the photoluminescent properties of Li2MnO3.

Weakly corrected numerical solutions to stochastically driven nonlinear dynamical systems

A method to weakly correct the solutions of stochastically driven nonlinear dynamical systems, herein numerically approximated through the Eule-Maruyama (EM) time-marching map, is proposed. An essential feature of the method is a change of measures that aims at rendering the EM-approximated solution measurable with respect to the filtration generated by an appropriately defined error process. Using Ito's formula and adopting a Monte Carlo (MC) setup, it is shown that the correction term may be additively applied to the realizations of the numerically integrated trajectories. Numerical evidence, presently gathered via applications of the proposed method to a few nonlinear mechanical oscillators and a semi-discrete form of a 1-D Burger's equation, lends credence to the remarkably improved numerical accuracy of the corrected solutions even with relatively large time step sizes. (C) 2015 Elsevier Inc. All rights reserved.

Autoregulation of topoisomerase I expression by supercoiling sensitive transcription

The opposing catalytic activities of topoisomerase I (TopoI/relaxase) and DNA gyrase (supercoiling enzyme) ensure homeostatic maintenance of bacterial chromosome supercoiling. Earlier studies in Es-cherichia coli suggested that the alteration in DNA supercoiling affects the DNA gyrase and TopoI expression. Although, the role of DNA elements around the promoters were proposed in regulation of gyrase, the molecular mechanism of supercoiling mediated control of TopoI expression is not yet understood. Here, we describe the regulation of TopoI expression from Mycobacterium tuberculosis and Mycobac-terium smegmatis by a mechanism termed Supercoiling Sensitive Transcription (SST). In both the organisms, topoI promoter(s) exhibited reduced activity in response to chromosome relaxation suggesting that SST is intrinsic to topoI promoter(s). We elucidate the role of promoter architecture and high transcriptional activity of upstream genes in topoI regulation. Analysis of the promoter(s) revealed the presence of suboptimal spacing between the -35 and -10 elements, rendering them supercoiling sensitive. Accordingly, upon chromosome relaxation, RNA polymerase occupancy was decreased on the topoI promoter region implicating the role of DNA topology in SST of topoI. We propose that negative supercoiling induced DNA twisting/writhing align the -35 and -10 elements to facilitate the optimal transcription of topoI.

Implication of scaling hierarchy associated with nonequilibrium: field and particulate

The advent of nanotechnology has necessitated a better understanding of how material microstructure changes at the atomic level would affect the macroscopic properties that control the performance. Such a challenge has uncovered many phenomena that were not previously understood and taken for granted. Among them are the basic foundation of dislocation theories which are now known to be inadequate. Simplifying assumptions invoked at the macroscale may not be applicable at the micro- and/or nanoscale. There are implications of scaling hierrachy associated with in-homegeneity and nonequilibrium. of physical systems. What is taken to be homogeneous and equilibrium at the macroscale may not be so when the physical size of the material is reduced to microns. These fundamental issues cannot be dispensed at will for the sake of convenience because they could alter the outcome of predictions. Even more unsatisfying is the lack of consistency in modeling physical systems. This could translate to the inability for identifying the relevant manufacturing parameters and rendering the end product unpractical because of high cost. Advanced composite and ceramic materials are cases in point. Discussed are potential pitfalls for applying models at both the atomic and continuum levels. No encouragement is made to unravel the truth of nature. Let it be partiuclates, a smooth continuum or a combination of both. The present trend of development in scaling tends to seek for different characteristic lengths of material microstructures with or without the influence of time effects. Much will be learned from atomistic simulation models to show how results could differ as boundary conditions and scales are changed. Quantum mechanics, continuum and cosmological models provide evidence that no general approach is in sight. Of immediate interest is perhaps the establishment of greater precision in terminology so as to better communicate results involving multiscale physical events.

Effects of underwater explosions on oysters, crabs and fish: a preliminary report.

Investigation on the effects of explosive shock on marine life. Necessary that the "commercial" effects, the actual damage to commercially important stocks of fish and shellfish, be evaluated. Equally important are the "biological" effects, the immediate physical effects of shock waves on animals and the indirect effects on future stocks. Indirect effects might include the diversion of migratory stocks from an area, or actual damage to the habitat, rendering it unfit for sedentary or non-migratory native species. Interruption of the food chains in an area by destruction of forge forms or vegetation. (PDF contains 43 pages)

Designing of Portlet-basedWeb Portals

166 p.

Extracting material response from simple mechanical tests on hardening-softening-hardening viscoplastic solids

Compliant foams are usually characterized by a wide range of desirable mechanical properties. These properties include viscoelasticity at different temperatures, energy absorption, recoverability under cyclic loading, impact resistance, and thermal, electrical, acoustic and radiation-resistance. Some foams contain nano-sized features and are used in small-scale devices. This implies that the characteristic dimensions of foams span multiple length scales, rendering modeling their mechanical properties difficult. Continuum mechanics-based models capture some salient experimental features like the linear elastic regime, followed by non-linear plateau stress regime. However, they lack mesostructural physical details. This makes them incapable of accurately predicting local peaks in stress and strain distributions, which significantly affect the deformation paths. Atomistic methods are capable of capturing the physical origins of deformation at smaller scales, but suffer from impractical computational intensity. Capturing deformation at the so-called meso-scale, which is capable of describing the phenomenon at a continuum level, but with some physical insights, requires developing new theoretical approaches.

A fundamental question that motivates the modeling of foams is ‘how to extract the intrinsic material response from simple mechanical test data, such as stress vs. strain response?’ A 3D model was developed to simulate the mechanical response of foam-type materials. The novelty of this model includes unique features such as the hardening-softening-hardening material response, strain rate-dependence, and plastically compressible solids with plastic non-normality. Suggestive links from atomistic simulations of foams were borrowed to formulate a physically informed hardening material input function. Motivated by a model that qualitatively captured the response of foam-type vertically aligned carbon nanotube (VACNT) pillars under uniaxial compression [2011,“Analysis of Uniaxial Compression of Vertically Aligned Carbon Nanotubes,” J. Mech.Phys. Solids, 59, pp. 2227–2237, Erratum 60, 1753–1756 (2012)], the property space exploration was advanced to three types of simple mechanical tests: 1) uniaxial compression, 2) uniaxial tension, and 3) nanoindentation with a conical and a flat-punch tip. The simulations attempt to explain some of the salient features in experimental data, like
1) The initial linear elastic response.
2) One or more nonlinear instabilities, yielding, and hardening.

The model-inherent relationships between the material properties and the overall stress-strain behavior were validated against the available experimental data. The material properties include the gradient in stiffness along the height, plastic and elastic compressibility, and hardening. Each of these tests was evaluated in terms of their efficiency in extracting material properties. The uniaxial simulation results proved to be a combination of structural and material influences. Out of all deformation paths, flat-punch indentation proved to be superior since it is the most sensitive in capturing the material properties.

Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites

G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family’s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.

Condições de trabalho e saúde dos trabalhadores de enfermagem que atuam em clínica médica

Trata-se de um estudo descritivo cujo objeto é a saúde dos trabalhadores de enfermagem e sua relação com as condições de trabalho em enfermarias de clínica médica, desenvolvido em um Hospital Universitário na cidade do Rio de Janeiro. Os objetivos orientaram para: caracterizar o perfil profissional dos trabalhadores de enfermagem; identificar, na perspectiva dos trabalhadores de enfermagem, as condições de trabalho e os fatores de risco à saúde existentes nas enfermarias de clínica médica; analisar os problemas de saúde identificados pelo trabalhador de enfermagem e a sua relação com as condições de trabalho por ele descrita em enfermarias de clínica médica. A pesquisa foi realizada no período de 2004 a 2005. O referencial teórico fundamentou-se nos estudos de especialistas das áreas de ergonomia, saúde do trabalhador e riscos no trabalho de enfermagem. A população foi de 41 trabalhadores de enfermagem que atuam nas unidades especializadas de clínica médica, sendo 73,2% de servidores públicos e 26,8% de prestadores de serviço temporário e bolsistas; a faixa etária predominante é de 40 a 49 anos; 73% são do sexo feminino; 90% com dupla e tripla jornada, com carga horária semanal de mais de 50 horas. Os riscos ocupacionais percebidos foram: manutenção de posturas inadequadas, esforço físico que produz fadiga, ritmo de trabalho acelerado, manipulação de cargas pesadas, risco de contrair infecção, temperatura inadequada, falta de materiais e insumos e iluminação insuficiente. Os problemas de saúde relacionados com as condições de trabalho foram: distúrbios osteomusculares, varizes e estresse. Os trabalhadores se interessam pela prevenção de riscos ocupacionais, porém não participam na instituição, da elaboração das políticas e estratégias na área de saúde do trabalhador. Com os resultados deste estudo e o respaldo da literatura, pode-se concluir que os problemas de saúde e condições de trabalho estão inter-relacionados; que a carga horária excessiva devido a dupla e tripla jornada, acrescido do cuidado com os filhos, idosos e afazeres domésticos, sem a prática regular de cuidados com sua saúde, tornam esses sujeitos mais vulneráveis a problemas de saúde.

Memórias da equipe de enfermagem na primeira década da epidemia da Aids

Na década de 80 dramáticas ocorrências atingiram o país e o mundo na área da saúde com a descoberta da Síndrome da Imunodeficiência Adquirida (Aids) síndrome, causada pelo Vírus da Imunodeficiência Humana (HIV). O objetivo deste estudo foi descrever as representações sociais do HIV/Aids e as memórias sociais do cuidado de enfermagem construídas na década de 80 pela equipe de enfermagem. Optou-se por uma abordagem qualitativa, embasada na teoria de representações sociais e nos conceitos do campo da memória social. Os sujeitos do estudo foram 20 profissionais de enfermagem de serviços ambulatoriais e/ou da atenção básica, atuantes em 11 instituições públicas de saúde da cidade do Rio de Janeiro que possuem o Programa Nacional de DST/Aids. A coleta de dados foi realizada através de entrevista semiestruturada e questionário de caracterização sócio profissional. A análise dos dados deu-se em duas etapas, a primeira atraves da técnica de análise de conteúdo temática destinada a identificar nos depoimentos dos entrevistados os conteúdos discursivos relativos a década de 80. Posteriormente os trechos selecionados foram submetidos à análise lexical pelo software Alceste 4.10. Obteve-se três classes temáticas que abordaram: As percepções e as ações do cuidado de enfermagem na década de 80; Os primeiros contatos profissionais e pessoais com HIV/Aids e A mídia e a construção das representações sociais do HIV/Aids. Na primeira classe os profissionais de enfermagem relatam as memórias referentes aos cuidados prestados na década de 80, descrevendo como esse cuidado era prestado, o medo da contaminação e os profissionais que atuavam na prestação de serviços. Na classe 2 os sujeitos resgatam as primeiras vivências com as pessoas com HIV/Aids e os sentimentos experimentados neste primeiro contato. As características físicas, os aspectos emocionais, a introdução do AZT e o abandono familiar são elementos destacados. Na classe 3 são relatas as memórias referentes ao início da epidemia de HIV/Aids, com destaque para as ancoragens representacionais do surgimento do vírus, tendo especialmente o macaco como hospedeiro. Os meios de comunicação surgiram como formadores das memórias do início da epidemia, veiculando imagens, como a do cantor Cazuza, fortemente citado pelos sujeitos. Conclui-se que este estudo permitiu compreender, através das memórias e das representações, como se constituiu a atuação dos profissionais no início da epidemia, assim como a permanência de elementos simbólicos até hoje nas representações sociais do HIV/Aids.

Efeito da terapia farmacológica anti-hipertensiva sobre densidade capilar e função endotelial microcirculatória

Hipertensos têm rarefação capilar e disfunção endotelial microcirculatória, tornando-se mais vulneráveis a lesões em órgãos-alvo. O estudo buscou avaliar o efeito de seis meses de tratamento farmacológico sobre densidade capilar e reatividade microvascular a estímulos fisiológicos e farmacológicos em hipertensos de baixo risco cardiovascular. Secundariamente testou-se a existência de diversidade nas respostas a diferentes estratégias anti-hipertensivas. Foram recrutados 44 pacientes, com 46,71,3 anos e 20 normotensos com 48,01,6 anos. Avaliaram-se dados antropométricos e laboratoriais e dosaram-se no soro o fator de crescimento vascular endotelial (VEGF), receptor Flt-1 para VEGF e óxido nítrico (NO). A contagem capilar foi por microscopia intravital, captando-se imagens da microcirculação no dorso da falange do dedo médio e contando os capilares com programa específico. Repetia-se o procedimento após hiperemia reativa pós-oclusiva (HRPO) para avaliar o recrutamento capilar. A reatividade vascular foi testada por fluxometria Laser Doppler, iontoforese de acetilcolina (Ach), HRPO e hiperemia térmica local (HTL). Os pacientes foram distribuídos aleatoriamente para dois grupos de tratamento: succinato de metoprolol titulado a 100 mg diários ou olmesartana medoxomila titulada a 40 mg diários, empregando-se, se necessário, a hidroclorotiazida. Os controles seguiram o mesmo protocolo inicial e após seis meses todos os testes foram repetidos nos hipertensos. As variáveis clínicas e laboratoriais basais eram semelhantes em comparação aos controles e entre os dois grupos de tratamento. Após seis meses, havia pequenas diferenças entre os grupos na relação cintura-quadril e HDL. A densidade capilar antes do tratamento era significativamente menor que no grupo controle (71,31,5 vs 80,61,8 cap/mm2 p<0,001 e HRPO 71,71,5 vs 79,52,6 cap/mm2 p<0,05) e, com o tratamento, aumentou para 75,41,1 cap/mm2 (p<0,01) no estado basal e para 76,81,1 cap/mm2 à HRPO (p<0,05). À reatividade vascular, a condutância vascular cutânea (CVC) em unidades de perfusão (UP)/mmHg era similar à HTL nos controles e hipertensos e aumentou com o tratamento nos dois subgrupos (metoprolol:1,730,2 a 1,900,2 p<0,001 e olmesartana:1,490,1 a 1,870,1 p<0,001). A CVC máxima à HRPO era menor nos hipertensos: 0,30(0,22-0,39) que nos controles: 0,39(0,31-0,49) com p<0,001. Após tratamento, aumentou para 0,41(0,29-0,51) com p<0,001. O aumento foi significativo apenas no grupo olmesartana (0,290,02 a 0,420,04 p<0,001). A diferença entre o tempo para atingir o fluxo máximo à HRPO aumentou no grupo metoprolol após tratamento 3,0 (-0,3 a 8,8) segundos versus olmesartana 0,4 (-2,1 a 2,4) segundos p<0,001. À iontoforese, a área sob a curva de fluxo (AUC) era similar nos grupos e aumentou com o tratamento, de 6087(3857-9137) para 7296(5577-10921) UP/s p=0,04. O VEGF e receptor não diferiam dos controles nem sofreram variações. A concentração de NO era maior nos hipertensos que nos controles: 64,9 (46,8-117,6) vs 50,7 (42-57,5) M/dl p=0,02 e não variou com tratamento. Em conclusão, hipertensos de baixo risco têm menor densidade e menor recrutamento capilar e ambos aumentam com tratamento. Apresentam também disfunção endotelial microcirculatória que melhora com a terapia.

Implementação de Visualização de Dados Tridimensionais de Malhas Irregulares no Processador Cell Broadband Engine.

A renderização de volume direta tornou-se uma técnica popular para visualização volumétrica de dados extraídos de fontes como simulações científicas, funções analíticas, scanners médicos, entre outras. Algoritmos de renderização de volume, como o raycasting, produzem imagens de alta qualidade. O seu uso, contudo, é limitado devido à alta demanda de processamento computacional e o alto uso de memória. Nesse trabalho, propomos uma nova implementação do algoritmo de raycasting que aproveita a arquitetura altamente paralela do processador Cell Broadband Engine, com seus 9 núcleos heterogêneos, que permitem renderização eficiente em malhas irregulares de dados. O poder computacional do processador Cell BE demanda um modelo de programação diferente. Aplicações precisam ser reescritas para explorar o potencial completo do processador Cell, que requer o uso de multithreading e código vetorizado. Em nossa abordagem, enfrentamos esse problema distribuindo a computação de cada raio incidente nas faces visíveis do volume entre os núcleos do processador, e vetorizando as operações da integral de iluminação em cada um. Os resultados experimentais mostram que podemos obter bons speedups reduzindo o tempo total de renderização de forma significativa.