Teracluster LSSC-II - Its Designing Principles and Applications in Large Scale Numerical Simulations

The teracluster LSSC-II installed at the State Key Laboratory of Scientific and Engineering Computing, Chinese Academy of Sciences is one of the most powerful PC clusters in China. It has a peek performance of 2Tflops. With a Linpack performance of 1.04Tflops, it is ranked at the 43rd place in the 20th TOP500 List (November 2002), 51st place in the 21st TOP500 List (June 2003), and the 82nd place in the 22nd TOP500 List (November 2003) with a new Linpack performance of 1.3Tflops. In this paper, we present some design principles of this cluster, as well as its applications in some largescale numerical simulations.

Mechanical control of floating aquatic weed: Kainji Lake experience

The paper describes the uniqueness and invasiveness of water hyacinth (Eichhornia crassipes) on Lake Kainji (Nigeria). The mechanical blocking device design concept based on the Kainji Lake flooding regime is also highlighted. Water hyacinth coverage, that was over 23% at high water in level in 1994, was reduced to 0.75% in the same period in 2000. Although this feat cannot be wholly ascribed to mechanical control effort alone, the first year of the device's full operation more than 1.04 million kg of fresh weight of water hyacinth were trapped, collected and deposited in two separate dumping pits, each at about 1 km off the shoreline of either side of the Lake. On further analysis over a period of one year of uncleared inflow of water hyacinth indicated the effectiveness of the bloom. Recommendations are advanced for the use of such local but highly technical knowledge to control floating water hyacinth that is vastly taking over the intricate network of Nigerian water systems and within the West African sub-region

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Automatically exposing OpenLifeData via SADI semantic Web Services

Background: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. Results: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. Conclusions: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Uma proposta para introdução de noções de Cálculo no ensino médio

A presente dissertação tem o objetivo de propor a reinclusão de elementos de Cálculo no ensino médio, pois no passado o Cálculo fazia parte do currículo e foi abolido após uma reforma no ensino da matemática. O trabalho apresenta os resultados de um levantamento estatístico sobre os índices de reprovação na disciplina Cálculo Diferencial e Integral I nos períodos mais recentes da Universidade do Estado do Rio de Janeiro (UERJ) e, também, uma pesquisa quantitativa com quarenta professores de matemática com o objetivo de analisar a viabilidade do projeto e os problemas a serem enfrentados. Por fim, a dissertação conta com uma série de atividades comentadas sobre o tema de limites, que é o foco do trabalho. Tais atividades podem ser incluídas já no 1 ano do ensino médio, paralelamente ao conteúdo de funções, e visam proporcionar aos estudantes o contato com elementos de Cálculo em uma linguagem acessível, e orientar o professor nesta tarefa

Educação Médica para controle do câncer: avaliação de egressos de um curso de Medicina e a contribuição das ligas acadêmicas como mais uma estratégia de ensino

O câncer ganha cada vez mais destaque como problema de saúde pública. Desta forma, diversas estratégias somam-se com objetivo de reduzir a morbi-mortalidade associada a este conjunto de doenças. Para o pleno sucesso das políticas de controle, o profissional de saúde, em especial o médico, assume papel fundamental. Contudo, depara-se com a deficiência encontrada nos currículos das escolas médicas (EM), principalmente no que tange ao ensino de ações desenvolvidas dentro da atenção primária em saúde. No Brasil, diversos projetos genericamente denominados de Ligas Acadêmicas (LA) têm ganhado destaque como propostas para ensino, enquanto atividades extracurriculares, através da iniciativa discente. Esta dissertação tem como objetivos: (1) avaliar a capacitação de alunos de Medicina quanto a conhecimentos e práticas para prevenção, rastreamento e diagnóstico precoce das neoplasias mais frequentes no Brasil e (2) avaliar a repercussão e as propostas das LA como complementação de ensino. Foi realizada a adaptação transcultural de um questionário autopreenchível utilizado em estudos norte-americanos como instrumento para coleta de dados. Os dados foram obtidos de alunos do último ano de uma universidade pública no Rio de Janeiro. Dos 78 alunos elegíveis, 74 participaram do estudo. Destes, 87% consideram que o estudo de câncer no currículo é insuficiente. Apenas 4% souberam informar corretamente as neoplasias com protocolo de rastreamento recomendados no Brasil. Os resultados mostram que o treinamento em habilidades para o controle do câncer é fraco: quanto ao aconselhamento de pacientes, 30% receberam treinamento para orientar a cessação do tabagismo e um percentual ainda menor (15%) chegam ao final do curso sem terem sido treinados para avaliar a história nutricional dos pacientes. Em relação ao exame físico, quase 60% nunca foram treinados a realizar o exame clínico da pele, 50% terminam a graduação sem terem executado um preventivo ginecológico e quase 20% sem realizar o exame clínico das mamas. Já em relação a autopercepção, os alunos sentem-se muito mais preparados a aconselhar pacientes quanto a hábitos para prevenção do câncer. Outras variáveis estudadas (gênero, sistema de ingresso no vestibular e familiares/pessoas próximas com câncer) não afetaram o desempenho dos alunos nas dimensões avaliadas (treinamento, prática e autopercepção). Para avaliar o efeito graduação, foi utilizado um grupo controle formado por alunos do primeiro ano (n=77). Houve ganho significativo nas dimensões treinamento e prática quando comparamos os dois grupos e, numa proporção bem menor, na dimensão autopercepção. Para avaliação das LA, foi realizado um levantamento de todas as EM no Brasil que iniciaram suas atividades antes do ano de 2010 e, após relação nominal, foram identificadas aquelas com LA e com LA relacionada ao estudo do câncer. Contudo, o verdadeiro impacto destes projetos só pode ser entendido com uma análise qualitativa dos mesmos. Observa-se que, nas LA, os alunos são estimulados a desenvolver habilidades pouco abordadas nos currículos tradicionais, fundamentais para a formação profissional, como gestão, liderança, empreendedorismo, inovação, extensão universitária e construção da cidadania.

Part I: Binders & technologies - Basic principles

The first three reports in this series (Parts I, II and III) deals with binders and technologies used in stabilisation/ solidification (S/S) practice and research in the UK. This first part covers 'basic principles'while the second covers 'research' and the third 'applications'. The purpose of this work, which forms part of the Network STARNET on stabilisation/solidification treatment and remediation, is to identify the knowledge gaps and future research needs in this field. This paper describes the details and basic principles of available binders and technologies in the UK. The introduction in the report includes background on S/S, legislation aspects, overview of STARNET and its activities and details of commonly used binder selection criteria. The report is then divided into two main sections. The first covers binders and includes cement, blastfurnace slag, pulverised fuel ash, lime, natural and organophilic clays, bitumen, waste binders and concludes with proprietary binders. The second part details implementation processes for S/S treatment systems starting with ex-situ treatment systems, such as plant processing, direct mixing and in-drum processing and finishes with in-situ treatment processes, such as mechanical mixing and pressure mixing. © 2005 Taylor & Francis Group.

Development of a servo-hydraulic earthquake actuator for the Cambridge Turner beam centrifuge

Dynamic centrifuge modelling has been carried out at Cambridge since the late 1970s. Over this period, three different mechanical earthquake actuators were developed. In this paper the development of a new servo-hydraulic earthquake actuator is described. The basic design principles are explained along with the need to carry out these designs to match the existing services and systems of the 35 year old Turner beam centrifuge at Cambridge. In addition, some of the features of the Turner beam centrifuge are exploited in the design of this new earthquake actuator. The paper also explains the mechanical fabrication of the actuator and the control systems that were developed in order to generate real earthquake motions. Finally, the performance of this new servo-hydraulic earthquake actuator is presented and assessed based on a wide range of earthquake input motions.

Facets of prior experience and the effectiveness of inclusive design

Research in inclusive design has shown the importance of prior experience for the usability of interactive products. Prior experience, however, is an ill-defined and inconsistently used construct. A number of different definitions and operationalisations of experience exist, but the differing power of these operationalisations to predict the usability of products for older users has rarely been investigated systematically. This study seeks to fill that gap. It is argued that the construct of experience has at least three components. It is proposed that two of these components, exposure and competence, are directly relevant for the current discussion about prior experience in inclusive design and that they can predict to different degrees the usability of a product for older users. In an empirical study, these facets of expertise are each operationalised on three levels of specificity and their impact on usability is assessed. The results show that measures of competence predict usability variables more strongly than measures of exposure and that levels of medium and high specificity are the best predictors. The application of inclusive design principles to a redesigned version of a ticket vending machine-although not resulting in a difference of overall usability-changed the impact of prior experience on usability measures implying an enhanced inclusiveness of the redesign with regard to prior experience. The implications of these findings for the effectiveness of inclusive design for older users are discussed. © 2013 Springer-Verlag Berlin Heidelberg.

The limits of inclusive design in the current design practice

The adoption of inclusive design principles and methods in the design practice is meant to support the equity of use of everyday products by as many people as possible independently of their age, physical, sensorial and cognitive capabilities. Although the intention is highly valuable, inclusive design approaches have not been widely applied in industrial context. This paper analyses the findings of an empirical research conducted with industrial designers and product managers. The research indicates some of the hindrances to the adoption of inclusive design, such as the current way the market is considered and targeted, and; the way the designers are driven by the project's brief and budget to orient their research strategy and activities. The paper proposes a way to improve the current industrial mode by strategically supplying clients, designers or both together with information about inclusivity. © 2013 Taylor & Francis Group.

Robotics education: A case study in soft-bodied locomotion

Locomotion has been one of the frequently used case studies in hands-on curricula in robotics education. Students are usually instructed to construct their own wheeled or legged robots from modular robot kits. In the development process of a robot students tend to emphasize on the programming part and consequently, neglect the design of the robot's body. However, the morphology of a robot (i.e. its body shape and material properties) plays an important role especially in dynamic tasks such as locomotion. In this paper we introduce a case study of a tutorial on soft-robotics where students were encouraged to focus solely on the morphology of a robot to achieve stable and fast locomotion. The students should experience the influence material properties exert on the performance of a robot and consequently, extract design principles. This tutorial was held in the context of the 2012 Summer School on Soft Robotics at ETH Zurich, which was one of the world's first courses specialized in the emerging field. We describe the tutorial set-up, the used hardware and software, the students assessment criteria as well as the results. Based on the high creativity and diversity of the robots built by the students, we conclude that the concept of this tutorial has great potentials for both education and research. © 2013 IEEE.

PRINCIPLES FOR STRUCTURE GENERATION OF ORGANIC ISOMERS FROM MOLECULAR FORMULA

An expert system for the elucidation of the structure of organic compounds (ESESOC) has been developed. The heart of the ESESOC is formed by the structure generator as an integral part, which receives the specific type of information (molecular formula, s