Protease footprinting reveals a surface on transcription factor TFIIB that serves as an interface for activators and coactivators.

Transcriptional stimulation by the model activator GAL4-VP16 (a chimeric protein consisting of the DNA-binding domain of the yeast activator GAL4 and the acidic activation domain of the herpes simplex virus protein VP16) involves a series of poorly understood protein-protein interactions between the VP16 activation domain and components of the RNA polymerase II general transcription machinery. One of these interactions is the VP16-mediated binding and recruitment of transcription factor TFIIB. However, TATA box-binding protein (TBP)-associated factors (TAFs), or coactivators, are required for this interaction to culminate in productive transcription complex assembly, and one such TAF, Drosophila TAF40, reportedly forms a ternary complex with VP16 and TFIIB. Due to TFIIB's central role in gene activation, we sought to directly visualize the surfaces of this protein that mediate formation of the ternary complex. We developed an approach called protease footprinting in which the broad-specificity proteases chymotrypsin and alkaline protease were used to probe binding of 32P-end-labeled TFIIB to GAL4-VP16 or TAF40. Analysis of the cleavage products revealed two regions of TFIIB protected by VP16 from protease attack, one of which overlapped with a region protected by TAF40. The close proximity of the VP16 and TAF40 binding sites on the surface of TFIIB suggests that this region could act as a regulatory interface mediating the effects of activators and coactivators on transcription complex assembly.

Estudo fenomenológico e numérico do escoamento estratificado óleo-água ondulado e com mistura na interface

Escoamentos bifásicos estão presentes em diversos processos naturais e industriais, como na indústria de petróleo. Podem apresentar-se em diferentes configurações topológicas, ou, padrões de escoamento, entre eles o escoamento estratificado ondulado e o estratificado com mistura na interface. Os escoamentos bifásicos estratificados óleo-água têm sido utilizados como uma forma conveniente de evitar a formação de emulsões de água em óleo em oleodutos e possuem uma ocorrência comum em poços de petróleo direcionais. Quando a onda interfacial ultrapassa determinado limite geométrico e cinemático, surge o fenômeno do entranhamento de gotas, representado por misturas entre as fases junto à interface que promovem um aumento na queda de pressão. Modelos têm sido apresentados pela literatura na tentativa de descrever o fenômeno do entranhamento de gotas. Neste trabalho é apresentada uma nova proposta de modelagem matemática unidimensional para o entranhamento de gotas com o objetivo de melhorar a previsão dos parâmetros envolvidos, em especial, da fração volumétrica de óleo e da queda de pressão bifásica. Também foi utilizada simulação numérica computacional, CFD (Computational Fluid Dynamics), com o uso de software comercial para obtenção dos valores dos parâmetros do escoamento estratificado ondulado óleo-água (fração volumétrica de óleo, queda de pressão, amplitude e comprimento da onda interfacial). Os resultados da modelagem fenomenológica para entranhamento e os de CFD foram comparados com bancos de dados experimentais. Os resultados em CFD mostram concordância com os resultados experimentais, tanto na análise qualitativa das propriedades geométricas das ondas interfaciais, quanto na comparação direta com os dados para fração volumétrica e queda de pressão. Os resultados numéricos da modelagem fenomenológica para fatores de entranhamento apresentam boa concordância com dados da literatura.

Dependência de exercício físico em academias de ginástica e sua interface com suplementação e imagem corporal

O Brasil é o segundo país no mundo em número de academias de ginástica, contando atualmente com cerca de 30 mil unidades. Apesar da transição no modelo de gestão e filosofia das academias do fitness para o wellness, muitas ainda propagam em seus ambientes o culto ao corpo magro e atlético, dietas sem fundamentação nutricional e consumo descontrolado de suplementos. Crescem as evidências de que uma parcela significativa dos frequentadores de academias desenvolve um comprometimento exacerbado à prática de exercícios físicos, gerando até uma dependência patológica. O objetivo foi determinar a associação entre dependência de exercício físico (DEF), consumo de suplementos e insatisfação da imagem corporal em frequentadores de academias. Para tanto foi empregada a Escala de Comprometimento com Exercício Físico (CEF) em uma amostra de 227 frequentadores, maiores de 19 anos, de ambos os sexo em três academias. Foi realizada entrevista individual com emprego de anamnese nutricional para determinar o perfil de consumo suplementar, avaliação antropométrica, da imagem corporal, do compromisso ao exercício físico assim como de participação na academia. A frequência de DEF nas academias foi de 66% e sendo que as chances estimadas deste ser consumidor de suplementos de 4,53. Os indivíduos dependentes de exercício físico são jovens, com maior chance de pertencer ao sexo masculino, frequentar a academia > 5 vezes por semana, consumir mais de um tipo de suplemento e praticar musculação. A frequência de insatisfação com a imagem corporal foi alta tanto entre homens (50,9%) como mulheres (78,4%).

Fénix: a flexible information exchange data model for natural language processing

In this paper we describe Fénix, a data model for exchanging information between Natural Language Processing applications. The format proposed is intended to be flexible enough to cover both current and future data structures employed in the field of Computational Linguistics. The Fénix architecture is divided into four separate layers: conceptual, logical, persistence and physical. This division provides a simple interface to abstract the users from low-level implementation details, such as programming languages and data storage employed, allowing them to focus in the concepts and processes to be modelled. The Fénix architecture is accompanied by a set of programming libraries to facilitate the access and manipulation of the structures created in this framework. We will also show how this architecture has been already successfully applied in different research projects.

Analysis of Lead-Acid batteries with a third-order dynamical model

Electrical energy storage is a really important issue nowadays. As electricity is not easy to be directly stored, it can be stored in other forms and converted back to electricity when needed. As a consequence, storage technologies for electricity can be classified by the form of storage, and in particular we focus on electrochemical energy storage systems, better known as electrochemical batteries. Largely the more widespread batteries are the Lead-Acid ones, in the two main types known as flooded and valve-regulated. Batteries need to be present in many important applications such as in renewable energy systems and in motor vehicles. Consequently, in order to simulate these complex electrical systems, reliable battery models are needed. Although there exist some models developed by experts of chemistry, they are too complex and not expressed in terms of electrical networks. Thus, they are not convenient for a practical use by electrical engineers, who need to interface these models with other electrical systems models, usually described by means of electrical circuits. There are many techniques available in literature by which a battery can be modeled. Starting from the Thevenin based electrical model, it can be adapted to be more reliable for Lead-Acid battery type, with the addition of a parasitic reaction branch and a parallel network. The third-order formulation of this model can be chosen, being a trustworthy general-purpose model, characterized by a good ratio between accuracy and complexity. Considering the equivalent circuit network, all the useful equations describing the battery model are discussed, and then implemented one by one in Matlab/Simulink. The model has been finally validated, and then used to simulate the battery behaviour in different typical conditions.

Diagnostic motor vehicle inspection demonstration projects, program engineering support. Volume 9 - appendix H: vehicle designs that facilitate or hinder inspection and repair and interchangeability and interface capability of test equipment and vehicles. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Edge-to-edge matching model for predicting orientation relationships and habit planes-the improvements

The edge-to-edge matching model has been further developed along with the Cu/Cr system as an example. The conditions for zigzag atom rows to be matching directions are included and the critical value of interatomic spacing misfit along matching directions and the critical value of d-value mismatch between matching planes are proposed in the new version of the model. (c) 2005 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Inflatable rescue boat-related injuries in Queensland surf lifesavers: The epidemiology - biomechanics interface

The objective was to describe the relationship between epidemiological and biomechanical factors in the causal pathway of inflatable rescue boat (IRB)-related injuries in Australian surf lifesavers; to develop epidemiological and biomechanical methodologies and measurement instruments that identify and measure the risk factors, for use in future epidemiological studies. Epidemiological and biomechanical models of injury causation were combined. Host, agent and environmental factors that influenced total available force for transfer to host were specified. Measurement instruments for each of the specified risk factors were developed. Instruments were piloted in a volunteer sample of surf lifesavers. Participant characteristics were recorded using demographic questionnaires; IRB operating techniques were recorded using a custom-made on-board camera (Grand RF-Guard) and images of operating techniques were coded by two independent observers. Ground reaction forces transmitted to the host through the lifesaver's feet at the time of wave impact were measured using a custom-built piezoelectric force platform. The demographic questionnaire was found practical; the on-board camera functioned successfully within the target environment. Agreement between independent coders of IRB operating technique images was significant (p < 0.001) with Kappa values ranging from 0.5 to 0.7. Biomechanical instruments performed successfully in the target environment. Peak biomechanical forces were 415.6N (left foot) and 252.9N (right foot). This study defines the relationship between epidemiological and biomechanical factors in modifying the risk of IRB-related injury in a population of surf lifesavers. Preliminary feasibility of combining epidemiological and biomechanical information has been demonstrated. Further testing of the proposed model and measurement instruments is required.

Selective transport of attached particles across the pulp-froth interface

A technique for determining the recovery of attached particles across the froth phase in flotation that relies on measuring the rate at which bubble-particle aggregates enter the froth is used to investigate the selectivity of attached particles across the froth phase. Combining these measurements with those of other techniques for determining the froth recovery of attached particles provides an insight into the different sub-processes of particle rejection in the froth phase. The results of experiments conducted in a 3 m(3) Outokumpu tank cell show that the detachment of particles from aggregates in the froth phase occurs largely at the pulp-froth interface. In particular it is shown that the pulp-froth interface selectively detaches particles from aggregates according to their physical attributes. (C) 2005 Elsevier Ltd. All rights reserved.

Biocompatible properties of surgical mesh using an animal model

To study the biocompatibility of surgical meshes for use in pelvic reconstructive surgery using an animal model. Eight different types of mesh: Atrium, Dexon, Gynemesh, IVS tape, Prolene, SPARC tape, TVT tape and Vypro II, were implanted into the abdominal walls of rats for 3 months' duration. Explanted meshes were assessed, using light microscopy, for parameters of rejection and incorporation. Type 1 (Atrium, Gynemesh, Prolene, SPARC and TVT) and type 3 (Vypro II, Dexon and IVS) meshes demonstrated different biocompatible properties. Inflammatory cellular response and fibrosis at the interface of mesh and host tissue was most marked with Vypro II and IVS. All type 1 meshes displayed similar cellular responses despite markedly different mesh architecture. The inflammatory response and fibrous reaction in the non-absorbable type 3 meshes tested (IVS and Vypro II) was more marked than the type 1 meshes. The increased inflammatory and fibrotic response may be because of the multifilamentous polypropylene components of these meshes. Material and filament composition of mesh is the main factor in determining cellular response.

Application of edge-to-edge matching model to understand the in-plane texture of TiSi2 (C49) thin films on (001)(Si) surface

The edge-to-edge matching model, which was originally developed for predicting crystallographic features in diffusional phase transformations in solids, has been used to understand the formation of in-plane textures in TiSi2 (C49) thin films on Si single crystal (001)si surface. The model predicts all the four previously reported orientation relationships between C49 and Si substrate based on the actual atom matching across the interface and the basic crystallographic data only. The model has strong potential to be used to develop new thin film materials. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Effect of solute on the growth rate and the constitutional undercooling ahead of the advancing interface during solidification of an alloy and the implications for nucleation

A framework is presented for modeling the nucleation in the constitutionally supercooled liquid ahead of the advancing solid/liquid interface. The effects of temperature gradient, imposed velocity, slope of liquidus, and initial concentration have been taken into account in this model by considering the effect of interface retardation, which is caused by solute buildup at the interface. Furthermore, the effect of solute concentration on the chemical driving force for nucleation has been considered in this model. The model is used for describing the nucleation of Al-Si and Al-Cu alloys. It was found that the solute of Si has a significant impact on the chemical driving force for nucleation in AI-Si alloys whereas Cu has almost no effect in Al-Cu alloys.

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface

Hydrophobins are small (similar to 100 aa) proteins that have an important role in the growth and development of mycelial fungi. They are surface active and, after secretion by the fungi, self-assemble into amphipathic membranes at hydrophobic/hydrophilic interfaces, reversing the hydrophobicity of the surface. In this study, molecular dynamics simulation techniques have been used to model the process by which a specific class I hydrophobin, SC3, binds to a range of hydrophobic/ hydrophilic interfaces. The structure of SC3 used in this investigation was modeled based on the crystal structure of the class II hydrophobin HFBII using the assumption that the disulfide pairings of the eight conserved cysteine residues are maintained. The proposed model for SC3 in aqueous solution is compact and globular containing primarily P-strand and coil structures. The behavior of this model of SC3 was investigated at an air/water, an oil/water, and a hydrophobic solid/water interface. It was found that SC3 preferentially binds to the interfaces via the loop region between the third and fourth cysteine residues and that binding is associated with an increase in a-helix formation in qualitative agreement with experiment. Based on a combination of the available experiment data and the current simulation studies, we propose a possible model for SC3 self-assembly on a hydrophobic solid/water interface.

RANKL protein is expressed at the pannus-bone interface at sites of articular bone erosion in rheumatoid arthritis

Objectives. Receptor activator of NF-kappa B ligand (RANKL) and osteoprotegerin (OPG) have been demonstrated to be critical regulators of osteoclast generation and activity. In addition, RANKL has been implicated as an important mediator of bone erosion in rheumatoid arthritis (RA). However, the expression of RANKL and OPG at sites of pannus invasion into bone has not been examined. The present study was undertaken to further elucidate the contribution of this cytokine system to osteoclastogenesis and subsequent bone erosion in RA by examining the pattern of protein expression for RANKL, OPG and the receptor activator of NF-kappa B (RANK) in RA at sites of articular bone erosion. Methods. Tissues from 20 surgical procedures from 17 patients with RA were collected as discarded materials. Six samples contained only synovium or tenosynovium remote from bone, four samples contained pannus-bone interface with adjacent synovium and 10 samples contained both synovium remote from bone and pannu-bone interface with adjacent synovium. Immunohistochemistry was used to characterize the cellular pattern of RANKL, RANK and OPG protein expression immediately adjacent to and remote from sites of bone erosion. Results. Cellular expression of RANKL protein was relatively restricted in the bone microenvironment; staining was focal and confined largely to sites of osteoclast-mediated erosion at the pannus-bone interface and at sites of subchondral bone erosion. RANK-expressing osteoclast precursor cells were also present in these sites. OPG protein expression was observed in numerous cells in synovium remote from bone but was more limited at sites of bone erosion, especially in regions associated with RANKL expression. Conclusions. The pattern of RANKL and OPG expression and the presence of RANK-expressing osteoclast precursor cells at sites of bone erosion in RA contributes to the generation of a local microenvironment that favours osteoclast differentiation and activity. These data provide further evidence implicating RANKL in the pathogenesis of arthritis-induced joint destruction.

Scattering and tangential momentum accommodation at a 2D adsorbate-solid interface

We calculate tangential momentum coefficients for the exchange of momentum between molecules in transport and the internal surface of a membrane pore, modelled as a simple atomic structure. We introduce a local specular reflection (LSR) hypothesis, which states that impinging molecules undergo mirror-like reflection in a plane tangent to a surface atom at the point of impact. As a consequence, the components of the velocity, parallel to the direction of flow will (in general) change on impact. The overall effect is a loss of tangential momentum, since more is lost in the upstream direction than is gained in the downstream direction. The loss of tangential momentum is greater when the size ratio of fluid to solid atom is small, allowing more steeply inclined impact planes to become accessible to the fluid phase molecules. (c) 2005 Elsevier B.V. All rights reserved.