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Sample records for molecular architectural approach

  1. Architecture Approach in System Development

    Directory of Open Access Journals (Sweden)

    Ladislav Burita

    2017-01-01

    Full Text Available The purpose of this paper is to describe a practical solution of architecture approach in system development. The software application is the system which optimizes the transport service. The first part of the paper defines the enterprise architecture, its parts and frameworks. Next is explained the NATO Architecture Framework (NAF, a tool for command and control systems development in military environment. The NAF is used for architecture design of the system for optimization of the transport service.

  2. Approaching Environmental Issues in Architecture

    DEFF Research Database (Denmark)

    Petersen, Mads Dines; Knudstrup, Mary-Ann

    2013-01-01

    The research presented here takes its point of departure in the design process with a specific focus on how it is approached when designing energy efficient architecture. This is done through a case-study of a design process in a Danish architectural office. This study shows the importance...

  3. Computer architecture a quantitative approach

    CERN Document Server

    Hennessy, John L

    2019-01-01

    Computer Architecture: A Quantitative Approach, Sixth Edition has been considered essential reading by instructors, students and practitioners of computer design for over 20 years. The sixth edition of this classic textbook is fully revised with the latest developments in processor and system architecture. It now features examples from the RISC-V (RISC Five) instruction set architecture, a modern RISC instruction set developed and designed to be a free and openly adoptable standard. It also includes a new chapter on domain-specific architectures and an updated chapter on warehouse-scale computing that features the first public information on Google's newest WSC. True to its original mission of demystifying computer architecture, this edition continues the longstanding tradition of focusing on areas where the most exciting computing innovation is happening, while always keeping an emphasis on good engineering design.

  4. New architectures for molecular materials

    International Nuclear Information System (INIS)

    Arico, Fabio

    2002-01-01

    synthesis of a novel ruthenium-based [2]-catenane by double ring-closing metathesis using Grubbs' catalyst. The photochemical behaviour of the novel catenane architecture was investigated both to confirm the proposed structure and to explore possible future applications of the catenane as a light-driven molecular machine. (author)

  5. Syntheses, molecular and crystalline architectures, and ...

    Indian Academy of Sciences (India)

    Syntheses, molecular and crystalline architectures, and luminescence behaviour of terephthalate bridged heptacoordinated dinuclear lead(II) complexes containing a pentadentate N-donor Schiff base. SUBHASIS ROYa, SOMNATH CHOUBEYa, SUMITAVA KHANa, KISHALAY BHARa,. PARTHA MITRAb and BARINDRA ...

  6. Molecular basis of angiosperm tree architecture.

    Science.gov (United States)

    Hollender, Courtney A; Dardick, Chris

    2015-04-01

    The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

  7. An architectural approach to level design

    CERN Document Server

    Totten, Christopher W

    2014-01-01

    Explore Level Design through the Lens of Architectural and Spatial Experience TheoryWritten by a game developer and professor trained in architecture, An Architectural Approach to Level Design is one of the first books to integrate architectural and spatial design theory with the field of level design. It explores the principles of level design through the context and history of architecture, providing information useful to both academics and game development professionals.Understand Spatial Design Principles for Game Levels in 2D, 3D, and Multiplayer ApplicationsThe book presents architectura

  8. Ancient Climatic Architectural Design Approach

    Directory of Open Access Journals (Sweden)

    Nasibeh Faghih

    2013-01-01

    Full Text Available Ancient climatic architecture had found out a series of appropriate responses for the best compatibility with the critical climate condition for instance, designing ‘earth sheltered houses’ and ‘courtyard houses’. They could provide human climatic comfort without excessive usage of fossil fuel resources. Owing to the normal thermal conditions in the ground depth, earth sheltered houses can be slightly affected by thermal fluctuations due to being within the earth. In depth further than 6.1 meters, temperature alternation is minute during the year, equaling to average annual temperature of outside. More to the point, courtyard buildings as another traditional design approach, have prepared controlled climatic space based on creating the maximum shade in the summer and maximum solar heat absorption in the winter. The courtyard houses served the multiple functions of lighting to the rooms, acting as a heat absorber in the summer and a radiator in the winter, as well as providing an open space inside for community activities. It must be noted that they divided into summer and winter zones located in south and north of the central courtyard where residents were replaced into them according to changing the seasons. Therefore, Ancient climatic buildings provided better human thermal comfort in comparison with the use contemporary buildings of recent years, except with the air conditioning

  9. Computer Architecture A Quantitative Approach

    CERN Document Server

    Hennessy, John L

    2007-01-01

    The era of seemingly unlimited growth in processor performance is over: single chip architectures can no longer overcome the performance limitations imposed by the power they consume and the heat they generate. Today, Intel and other semiconductor firms are abandoning the single fast processor model in favor of multi-core microprocessors--chips that combine two or more processors in a single package. In the fourth edition of Computer Architecture, the authors focus on this historic shift, increasing their coverage of multiprocessors and exploring the most effective ways of achieving parallelis

  10. Computer Architecture A Quantitative Approach

    CERN Document Server

    Hennessy, John L

    2011-01-01

    The computing world today is in the middle of a revolution: mobile clients and cloud computing have emerged as the dominant paradigms driving programming and hardware innovation today. The Fifth Edition of Computer Architecture focuses on this dramatic shift, exploring the ways in which software and technology in the cloud are accessed by cell phones, tablets, laptops, and other mobile computing devices. Each chapter includes two real-world examples, one mobile and one datacenter, to illustrate this revolutionary change.Updated to cover the mobile computing revolutionEmphasizes the two most im

  11. A Declarative Approach to Architectural Reflection

    DEFF Research Database (Denmark)

    Ingstrup, Mads; Hansen, Klaus Marius

    2005-01-01

    which both creates runtime models of specific distributed architectures and allow for evaluation of AQL queries on these models. We illustrate the viability of the approach in two particular applications of such a model: constraint checking relative to an architectural style, and reasoning about certain......Recent research shows runtime architectural reflection is instrumental in, for instance, building adaptive and flexible systems or checking correspondence between design and implementation. Moreover, experience with computational reflection in various branches of computer science shows...... that the interface through which the meta-information of the running system is accessed, and possibly modified, lies at the heart of designing reflective systems. This paper proposes that such an interface should be like a database: accessed through queries expressed using the concepts with which architecture...

  12. Enterprise architecture approach to mining companies engineering

    Directory of Open Access Journals (Sweden)

    Ilin’ Igor

    2017-01-01

    Full Text Available As Russian economy is still largely oriented on commodities production, there are a lot of cities where mining and commodity-oriented enterprises are the backbone of city economy. The mentioned enterprises mostly define the life quality of citizens in such cities, thus there are high requirements for engineering of city-forming enterprises. The paper describes the enterprise architecture approach for management system engineering of the mining enterprises. The paper contains the model of the mining enterprise architecture, the approach to the development and implementation of an integrated management system based on the concept of enterprise architecture and the structure of information systems and information technology infrastructure of the mining enterprise.

  13. Systemic Approach to Architectural Performance

    Directory of Open Access Journals (Sweden)

    Marie Davidova

    2017-04-01

    Full Text Available First-hand experiences in several design projects that were based on media richness and collaboration are described in this article. Although complex design processes are merely considered as socio-technical systems, they are deeply involved with natural systems. My collaborative research in the field of performance-oriented design combines digital and physical conceptual sketches, simulations and prototyping. GIGA-mapping - is applied to organise the data. The design process uses the most suitable tools, for the subtasks at hand, and the use of media is mixed according to particular requirements. These tools include digital and physical GIGA-mapping, parametric computer aided design (CAD, digital simulation of analyses, as well as sampling and 1:1 prototyping. Also discussed in this article are the methodologies used in several design projects to strategize these tools and the developments and trends in the tools employed.  The paper argues that the digital tools tend to produce similar results through given pre-sets that often do not correspond to real needs. Thus, there is a significant need for mixed methods including prototyping in the creative design process. Media mixing and cooperation across disciplines is unavoidable in the holistic approach to contemporary design. This includes the consideration of diverse biotic and abiotic agents. I argue that physical and digital GIGA-mapping is a crucial tool to use in coping with this complexity. Furthermore, I propose the integration of physical and digital outputs in one GIGA-map and the participation and co-design of biotic and abiotic agents into one rich design research space, which is resulting in an ever-evolving research-design process-result time-based design.

  14. Design of Carborane Molecular Architectures via Electronic Structure Computations

    International Nuclear Information System (INIS)

    Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

    2009-01-01

    Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

  15. Architecture and Landscape. Approaches from archaeology

    Directory of Open Access Journals (Sweden)

    Rebeca Blanco-Rotea

    2017-11-01

    Full Text Available This work proposes a theoretical and conceptual basis for the study of the fortified landscapes of the Galician- Portuguese border in the Modern Age. From this theoretical framework there was designed a research program that studies these landscapes. It proposes an approach to the study of this type of archaeological record from the Landscape Archeology and the Archeology of Architecture, introducing the concepts of built space and Archeology of Built Space.

  16. Modelling Approach In Islamic Architectural Designs

    Directory of Open Access Journals (Sweden)

    Suhaimi Salleh

    2014-06-01

    Full Text Available Architectural designs contribute as one of the main factors that should be considered in minimizing negative impacts in planning and structural development in buildings such as in mosques. In this paper, the ergonomics perspective is revisited which hence focuses on the conditional factors involving organisational, psychological, social and population as a whole. This paper tries to highlight the functional and architectural integration with ecstatic elements in the form of decorative and ornamental outlay as well as incorporating the building structure such as wall, domes and gates. This paper further focuses the mathematical aspects of the architectural designs such as polar equations and the golden ratio. These designs are modelled into mathematical equations of various forms, while the golden ratio in mosque is verified using two techniques namely, the geometric construction and the numerical method. The exemplary designs are taken from theSabah Bandaraya Mosque in Likas, Kota Kinabalu and the Sarawak State Mosque in Kuching,while the Universiti Malaysia Sabah Mosque is used for the Golden Ratio. Results show thatIslamic architectural buildings and designs have long had mathematical concepts and techniques underlying its foundation, hence, a modelling approach is needed to rejuvenate these Islamic designs.

  17. Advanced and secure architectural EHR approaches.

    Science.gov (United States)

    Blobel, Bernd

    2006-01-01

    Electronic Health Records (EHRs) provided as a lifelong patient record advance towards core applications of distributed and co-operating health information systems and health networks. For meeting the challenge of scalable, flexible, portable, secure EHR systems, the underlying EHR architecture must be based on the component paradigm and model driven, separating platform-independent and platform-specific models. Allowing manageable models, real systems must be decomposed and simplified. The resulting modelling approach has to follow the ISO Reference Model - Open Distributing Processing (RM-ODP). The ISO RM-ODP describes any system component from different perspectives. Platform-independent perspectives contain the enterprise view (business process, policies, scenarios, use cases), the information view (classes and associations) and the computational view (composition and decomposition), whereas platform-specific perspectives concern the engineering view (physical distribution and realisation) and the technology view (implementation details from protocols up to education and training) on system components. Those views have to be established for components reflecting aspects of all domains involved in healthcare environments including administrative, legal, medical, technical, etc. Thus, security-related component models reflecting all view mentioned have to be established for enabling both application and communication security services as integral part of the system's architecture. Beside decomposition and simplification of system regarding the different viewpoint on their components, different levels of systems' granularity can be defined hiding internals or focusing on properties of basic components to form a more complex structure. The resulting models describe both structure and behaviour of component-based systems. The described approach has been deployed in different projects defining EHR systems and their underlying architectural principles. In that context

  18. A Formal Approach to Software Architecture

    National Research Council Canada - National Science Library

    Allen, Robert

    1997-01-01

    .... While architectural concepts are often embodied in infrastructure to support specific architectural styles and in the initial conceptualization of a system configuration, the lack of an explicit...

  19. Open architecture design and approach for the Integrated Sensor Architecture (ISA)

    Science.gov (United States)

    Moulton, Christine L.; Krzywicki, Alan T.; Hepp, Jared J.; Harrell, John; Kogut, Michael

    2015-05-01

    Integrated Sensor Architecture (ISA) is designed in response to stovepiped integration approaches. The design, based on the principles of Service Oriented Architectures (SOA) and Open Architectures, addresses the problem of integration, and is not designed for specific sensors or systems. The use of SOA and Open Architecture approaches has led to a flexible, extensible architecture. Using these approaches, and supported with common data formats, open protocol specifications, and Department of Defense Architecture Framework (DoDAF) system architecture documents, an integration-focused architecture has been developed. ISA can help move the Department of Defense (DoD) from costly stovepipe solutions to a more cost-effective plug-and-play design to support interoperability.

  20. Synthesis, molecular and crystalline architectures, and properties of ...

    Indian Academy of Sciences (India)

    The construction1 of coordination compounds of cobalt(II) of different nuclearities is the centre of attrac- tion due to interesting structural and physico-chemical properties.1–5 ... Design SQUID MPMS-XL magnetometer working in the 2–300 K range. ..... Complex 1 adopts a molecular architecture cor- responding to the gross ...

  1. Molecular Architecture of the Yeast Monopolin Complex

    Energy Technology Data Exchange (ETDEWEB)

    Corbett, Kevin D.; Harrison, Stephen C. (Harvard-Med); (UCSD)

    2012-07-30

    The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.

  2. Architectonics: Design of Molecular Architecture for Functional Applications.

    Science.gov (United States)

    Avinash, M B; Govindaraju, Thimmaiah

    2018-02-20

    The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing

  3. A Systems Engineering Approach to Architecture Development

    Science.gov (United States)

    Di Pietro, David A.

    2015-01-01

    Architecture development is often conducted prior to system concept design when there is a need to determine the best-value mix of systems that works collectively in specific scenarios and time frames to accomplish a set of mission area objectives. While multiple architecture frameworks exist, they often require use of unique taxonomies and data structures. In contrast, this paper characterizes architecture development using terminology widely understood within the systems engineering community. Using a notional civil space architecture example, it employs a multi-tier framework to describe the enterprise level architecture and illustrates how results of lower tier, mission area architectures integrate into the enterprise architecture. It also presents practices for conducting effective mission area architecture studies, including establishing the trade space, developing functions and metrics, evaluating the ability of potential design solutions to meet the required functions, and expediting study execution through the use of iterative design cycles

  4. Sustainable architecture approach in designing residential ...

    African Journals Online (AJOL)

    Sustainable architecture has been shaped with vernacular materials based on the vernacular architecture according to climatic conditions, saving energy and responding to needs and social and cultural conditions. In cold region architecture, the buildings are constructed as steps on the hills in the direction of sun and ...

  5. Systems approaches to study root architecture dynamics

    Directory of Open Access Journals (Sweden)

    Candela eCuesta

    2013-12-01

    Full Text Available The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation.Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how lateral roots and thereby root system architecture is established and developed.

  6. An ontology-based approach for modelling architectural styles

    OpenAIRE

    Pahl, Claus; Giesecke, Simon; Hasselbring, Wilhelm

    2007-01-01

    peer-reviewed The conceptual modelling of software architectures is of central importance for the quality of a software system. A rich modelling language is required to integrate the different aspects of architecture modelling, such as architectural styles, structural and behavioural modelling, into a coherent framework.We propose an ontological approach for architectural style modelling based on description logic as an abstract, meta-level modelling instrument. Architect...

  7. Molecular architecture of the yeast Mediator complex

    Science.gov (United States)

    Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

    2015-01-01

    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

  8. Homology modeling, docking studies and molecular dynamic simulations using graphical processing unit architecture to probe the type-11 phosphodiesterase catalytic site: a computational approach for the rational design of selective inhibitors.

    Science.gov (United States)

    Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola

    2013-12-01

    Phosphodiesterase 11 (PDE11) is the latest isoform of the PDEs family to be identified, acting on both cyclic adenosine monophosphate and cyclic guanosine monophosphate. The initial reports of PDE11 found evidence for PDE11 expression in skeletal muscle, prostate, testis, and salivary glands; however, the tissue distribution of PDE11 still remains a topic of active study and some controversy. Given the sequence similarity between PDE11 and PDE5, several PDE5 inhibitors have been shown to cross-react with PDE11. Accordingly, many non-selective inhibitors, such as IBMX, zaprinast, sildenafil, and dipyridamole, have been documented to inhibit PDE11. Only recently, a series of dihydrothieno[3,2-d]pyrimidin-4(3H)-one derivatives proved to be selective toward the PDE11 isoform. In the absence of experimental data about PDE11 X-ray structures, we found interesting to gain a better understanding of the enzyme-inhibitor interactions using in silico simulations. In this work, we describe a computational approach based on homology modeling, docking, and molecular dynamics simulation to derive a predictive 3D model of PDE11. Using a Graphical Processing Unit architecture, it is possible to perform long simulations, find stable interactions involved in the complex, and finally to suggest guideline for the identification and synthesis of potent and selective inhibitors. © 2013 John Wiley & Sons A/S.

  9. A Topology Optimisation Approach to Learning in Architectural Design

    DEFF Research Database (Denmark)

    Mullins, Michael; Kirkegaard, Poul Henning; Jessen, Rasmus Zederkof

    2005-01-01

    describes an attempt to unify analytic and analogical approaches in an architectural education setting, using topology optimization software. It uses as examples recent student projects where the architectural design process based on a topology optimization approach has been investigated. The paper...

  10. One approach to architectural acoustics in education

    Science.gov (United States)

    Jaffe, J. Christopher

    2003-04-01

    In the fall of 1997, Dean Alan Balfour of the School of Architecture at the Rennselaer Polytechnic Institute asked me to introduce an undergraduate 14 credit certificate course entitled ''Sonics in Architecture.`` Subsequently, the program was expanded to include a Master's Degree in Building Science. This paper discusses the trials and tribulations of building a scientific program in a liberal arts school. In addition, the problem of acquiring the research funds needed to provide tuition assistance for graduate students in Architectural Acoustics is reviewed. Information on the curriculum developed for both the lecture and laboratory courses is provided. I will also share my concerns regarding the teaching methods currently prevalent in many schools of architecture today, and how building science professionals might assist in addressing these issues.

  11. Approaching Technical Issues in Architectural Education

    DEFF Research Database (Denmark)

    Pugnale, Alberto; Parigi, Dario

    2012-01-01

    This paper discusses teaching of technical subjects in architecture, presenting two experimental activities, recently organized at Aalborg University - a two week long workshop and a one day long lecture. From the pedagogical point of view, the activities are strategically placed between conventi......This paper discusses teaching of technical subjects in architecture, presenting two experimental activities, recently organized at Aalborg University - a two week long workshop and a one day long lecture. From the pedagogical point of view, the activities are strategically placed between...

  12. The molecular genetic architecture of self-employment.

    Science.gov (United States)

    van der Loos, Matthijs J H M; Rietveld, Cornelius A; Eklund, Niina; Koellinger, Philipp D; Rivadeneira, Fernando; Abecasis, Gonçalo R; Ankra-Badu, Georgina A; Baumeister, Sebastian E; Benjamin, Daniel J; Biffar, Reiner; Blankenberg, Stefan; Boomsma, Dorret I; Cesarini, David; Cucca, Francesco; de Geus, Eco J C; Dedoussis, George; Deloukas, Panos; Dimitriou, Maria; Eiriksdottir, Guðny; Eriksson, Johan; Gieger, Christian; Gudnason, Vilmundur; Höhne, Birgit; Holle, Rolf; Hottenga, Jouke-Jan; Isaacs, Aaron; Järvelin, Marjo-Riitta; Johannesson, Magnus; Kaakinen, Marika; Kähönen, Mika; Kanoni, Stavroula; Laaksonen, Maarit A; Lahti, Jari; Launer, Lenore J; Lehtimäki, Terho; Loitfelder, Marisa; Magnusson, Patrik K E; Naitza, Silvia; Oostra, Ben A; Perola, Markus; Petrovic, Katja; Quaye, Lydia; Raitakari, Olli; Ripatti, Samuli; Scheet, Paul; Schlessinger, David; Schmidt, Carsten O; Schmidt, Helena; Schmidt, Reinhold; Senft, Andrea; Smith, Albert V; Spector, Timothy D; Surakka, Ida; Svento, Rauli; Terracciano, Antonio; Tikkanen, Emmi; van Duijn, Cornelia M; Viikari, Jorma; Völzke, Henry; Wichmann, H-Erich; Wild, Philipp S; Willems, Sara M; Willemsen, Gonneke; van Rooij, Frank J A; Groenen, Patrick J F; Uitterlinden, André G; Hofman, Albert; Thurik, A Roy

    2013-01-01

    Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable-entrepreneurship-that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (σ(g)(2)/σ(P)(2) = 25%, h(2) = 55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with pself-employment in an independent sample (p≥0.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases.

  13. Parametric Approach in Designing Large-Scale Urban Architectural Objects

    Directory of Open Access Journals (Sweden)

    Arne Riekstiņš

    2011-04-01

    Full Text Available When all the disciplines of various science fields converge and develop, new approaches to contemporary architecture arise. The author looks towards approaching digital architecture from parametric viewpoint, revealing its generative capacity, originating from the fields of aeronautical, naval, automobile and product-design industries. The author also goes explicitly through his design cycle workflow for testing the latest methodologies in architectural design. The design process steps involved: extrapolating valuable statistical data about the site into three-dimensional diagrams, defining certain materiality of what is being produced, ways of presenting structural skin and structure simultaneously, contacting the object with the ground, interior program definition of the building with floors and possible spaces, logic of fabrication, CNC milling of the proto-type. The author’s developed tool that is reviewed in this article features enormous performative capacity and is applicable to various architectural design scales.Article in English

  14. Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

    KAUST Repository

    Pahovnik, David; Hadjichristidis, Nikolaos

    2015-01-01

    Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization

  15. The Molecular Genetic Architecture of Self-Employment

    Science.gov (United States)

    van der Loos, Matthijs J. H. M.; Rietveld, Cornelius A.; Eklund, Niina; Koellinger, Philipp D.; Rivadeneira, Fernando; Abecasis, Gonçalo R.; Ankra-Badu, Georgina A.; Baumeister, Sebastian E.; Benjamin, Daniel J.; Biffar, Reiner; Blankenberg, Stefan; Boomsma, Dorret I.; Cesarini, David; Cucca, Francesco; de Geus, Eco J. C.; Dedoussis, George; Deloukas, Panos; Dimitriou, Maria; Eiriksdottir, Guðny; Eriksson, Johan; Gieger, Christian; Gudnason, Vilmundur; Höhne, Birgit; Holle, Rolf; Hottenga, Jouke-Jan; Isaacs, Aaron; Järvelin, Marjo-Riitta; Johannesson, Magnus; Kaakinen, Marika; Kähönen, Mika; Kanoni, Stavroula; Laaksonen, Maarit A.; Lahti, Jari; Launer, Lenore J.; Lehtimäki, Terho; Loitfelder, Marisa; Magnusson, Patrik K. E.; Naitza, Silvia; Oostra, Ben A.; Perola, Markus; Petrovic, Katja; Quaye, Lydia; Raitakari, Olli; Ripatti, Samuli; Scheet, Paul; Schlessinger, David; Schmidt, Carsten O.; Schmidt, Helena; Schmidt, Reinhold; Senft, Andrea; Smith, Albert V.; Spector, Timothy D.; Surakka, Ida; Svento, Rauli; Terracciano, Antonio; Tikkanen, Emmi; van Duijn, Cornelia M.; Viikari, Jorma; Völzke, Henry; Wichmann, H. -Erich; Wild, Philipp S.; Willems, Sara M.; Willemsen, Gonneke; van Rooij, Frank J. A.; Groenen, Patrick J. F.; Uitterlinden, André G.; Hofman, Albert; Thurik, A. Roy

    2013-01-01

    Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable–entrepreneurship–that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (σg 2/σP 2 = 25%, h 2 = 55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with pentrepreneurship reveal significant associations. Finally, SNP-based genetic scores that use results from the meta-analysis capture less than 0.2% of the variance in self-employment in an independent sample (p≥0.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases. PMID:23593239

  16. A relational approach to support software architecture analysis

    NARCIS (Netherlands)

    Feijs, L.M.G.; Krikhaar, R.L.; van Ommering, R.C.

    1998-01-01

    This paper reports on our experience with a relational approach to support the analysis of existing software architectures. The analysis options provide for visualization and view calculation. The approach has been applied for reverse engineering. It is also possible to check concrete designs

  17. Molecular Approaches to Studying Denitrification

    Science.gov (United States)

    Voytek, M. A.

    2001-05-01

    Denitrification is carried out by a diverse array of microbes, mainly as an alternative mode of respiration that allows the organisms to respire using oxidized N compounds instead of oxygen. A common approach in biogeochemistry to the study of the regulation of denitrification is to assess activity by mass balance of substrates and products or direct rate measurements and has intrinsically assumed resource regulation of denitrification. Reported rates can vary significantly even among ecosystems characterized by similar environmental conditions, thus indicating that direct control by abiotic factors often is not sufficient to predict denitrification rates accurately in natural environments. Alternatively, a microbiological approach would proceed with the identification of the organisms responsible and an evaluation of the effect of environmental factors on the biochemical pathways involved. Traditional studies have relied on culturing techniques, such as most probable number enrichments, and have failed to assess the role of the predominately uncultivable members of the microbial community. A combination of biogeochemical measurements and the assessment of the microbial community is necessary and becoming increasingly possible with the development and application of molecular techniques. In order to understand how the composition and physiological behavior of the microbial community affects denitrification rates, we use a suite of molecular techniques developed for phylogenetic and metabolic characterization of denitrifying communities. Molecular tools available for quantifying denitrifying bacteria and assessing their diversity and activity are summarized. Their application is illustrated with examples from marine and freshwater environments. Emerging techniques and their application to ground water studies will be discussed.

  18. Molecular approaches for bacterial azoreductases

    Directory of Open Access Journals (Sweden)

    Montira Leelakriangsak

    2013-12-01

    Full Text Available Azo dyes are the dominant types of synthetic dyes, widely used in textiles, foods, leather, printing, tattooing, cosmetics, and pharmaceutical industries. Many microorganisms are able to decolorize azo dyes, and there is increasing interest in biological waste treatment methods. Bacterial azoreductases can cleave azo linkages (-N=N- in azo dyes, forming aromatic amines. This review mainly focuses on employing molecular approaches, including gene manipulation and recombinant strains, to study bacterial azoreductases. The construction of the recombinant protein by cloning and the overexpression of azoreductase is described. The mechanisms and function of bacterial azoreductases can be studied by other molecular techniques discussed in this review, such as RT-PCR, southern blot analysis, western blot analysis, zymography, and muta-genesis in order to understand bacterial azoreductase properties, function and application. In addition, understanding the regulation of azoreductase gene expression will lead to the systematic use of gene manipulation in bacterial strains for new strategies in future waste remediation technologies.

  19. Molecular architecture of protein-RNA recognition sites.

    Science.gov (United States)

    Barik, Amita; C, Nithin; Pilla, Smita P; Bahadur, Ranjit Prasad

    2015-01-01

    The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.

  20. Calsyntenin-3 molecular architecture and interaction with neurexin 1α.

    Science.gov (United States)

    Lu, Zhuoyang; Wang, Yun; Chen, Fang; Tong, Huimin; Reddy, M V V V Sekhar; Luo, Lin; Seshadrinathan, Suchithra; Zhang, Lei; Holthauzen, Luis Marcelo F; Craig, Ann Marie; Ren, Gang; Rudenko, Gabby

    2014-12-12

    Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca(2+), and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca(2+) and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Machine learning and pattern recognition from surface molecular architectures.

    Science.gov (United States)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Sumpter, Bobby; Kalinin, Sergei

    The ability to utilize molecular assemblies as data storage devices requires capability to identify individual molecular states on a scale of thousands of molecules. We present a novel method of applying machine learning techniques for extraction of positional and rotational information from ultra-high vacuum scanning tunneling microscopy (STM) images and apply it to self-assembled monolayer of π-bowl sumanene molecules on gold. From density functional theory (DFT) simulations, we assume existence of distinct polar and multiple azimuthal rotational states. We use DFT-generated templates in conjunction with Markov Chain Monte Carlo (MCMC) sampler and noise modeling to create synthetic images representative of our model. We extract positional information of each molecule and use nearest neighbor criteria to construct a graph input to Markov Random Field (MRF) model to identify polar rotational states. We train a convolutional Neural Network (cNN) on a synthetic dataset and combine it with MRF model to classify molecules based on their azimuthal rotational state. We demonstrate effectiveness of such approach compared to other methods. Finally, we apply our approach to experimental images and achieve complete rotational class information extraction. This research was sponsored by the Division of Materials Sciences and Engineering, Office of Science, Basic Energy Sciences, US DOE.

  2. Molecular Physiology of Root System Architecture in Model Grasses

    Science.gov (United States)

    Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

    2017-12-01

    Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

  3. Molecular approaches to child psychopathology.

    Science.gov (United States)

    Alsobrook, J P; Pauls, D L

    1998-04-01

    Basic research into the genetics of childhood psychiatric disorders has substantially increased during the last two decades. Specific genetic mutations have been characterized in some developmental disorders (e.g., fragile X syndrome and Prader-Willi syndrome), but thus far identification of etiological gene mutations in psychiatric illnesses has been unsuccessful. Several psychiatric disorders serve as examples of the current state of molecular approaches in child psychopathology. Investigations to date of Gilles de la Tourette's syndrome (GTS) have not resulted in the discovery of a gene of major effect. Some studies have implicated the D2 and D4 dopamine receptors as having a direct role in the etiology of GTS, but other studies have disputed those findings. However, the dopamine D2 receptor may modulate the severity of GTS. Obsessive-compulsive disorder has a reported association with a low-activity allele of the enzyme catechol-O-methyltransferase; however, the low-activity genotype is also seen in a significant proportion of unaffected individuals. For reading disability two distinct phenotypes (phonological awareness and single-word reading) have been linked to separate loci on chromosomes 6 and 15. Attention deficit hyperactivity disorder (ADHD) has a reported association with the dopamine transporter. Findings of a genetic locus for the personality trait of novelty seeking remain controversial.

  4. Comparison of Human Exploration Architecture and Campaign Approaches

    Science.gov (United States)

    Goodliff, Kandyce; Cirillo, William; Mattfeld, Bryan; Stromgren, Chel; Shyface, Hilary

    2015-01-01

    As part of an overall focus on space exploration, National Aeronautics and Space Administration (NASA) continues to evaluate potential approaches for sending humans beyond low Earth orbit (LEO). In addition, various external organizations are studying options for beyond LEO exploration. Recent studies include NASA's Evolvable Mars Campaign and Design Reference Architecture (DRA) 5.0, JPL's Minimal Mars Architecture; the Inspiration Mars mission; the Mars One campaign; and the Global Exploration Roadmap (GER). Each of these potential exploration constructs applies unique methods, architectures, and philosophies for human exploration. It is beneficial to compare potential approaches in order to better understand the range of options available for exploration. Since most of these studies were conducted independently, the approaches, ground rules, and assumptions used to conduct the analysis differ. In addition, the outputs and metrics presented for each construct differ substantially. This paper will describe the results of an effort to compare and contrast the results of these different studies under a common set of metrics. The paper will first present a summary of each of the proposed constructs, including a description of the overall approach and philosophy for exploration. Utilizing a common set of metrics for comparison, the paper will present the results of an evaluation of the potential benefits, critical challenges, and uncertainties associated with each construct. The analysis framework will include a detailed evaluation of key characteristics of each construct. These will include but are not limited to: a description of the technology and capability developments required to enable the construct and the uncertainties associated with these developments; an analysis of significant operational and programmatic risks associated with that construct; and an evaluation of the extent to which exploration is enabled by the construct, including the destinations

  5. Information security architecture an integrated approach to security in the organization

    CERN Document Server

    Killmeyer, Jan

    2000-01-01

    An information security architecture is made up of several components. Each component in the architecture focuses on establishing acceptable levels of control. These controls are then applied to the operating environment of an organization. Functionally, information security architecture combines technical, practical, and cost-effective solutions to provide an adequate and appropriate level of security.Information Security Architecture: An Integrated Approach to Security in the Organization details the five key components of an information security architecture. It provides C-level executives

  6. Architecture

    OpenAIRE

    Clear, Nic

    2014-01-01

    When discussing science fiction’s relationship with architecture, the usual practice is to look at the architecture “in” science fiction—in particular, the architecture in SF films (see Kuhn 75-143) since the spaces of literary SF present obvious difficulties as they have to be imagined. In this essay, that relationship will be reversed: I will instead discuss science fiction “in” architecture, mapping out a number of architectural movements and projects that can be viewed explicitly as scien...

  7. Design of complex architectures using a three dimension approach : the crosswork case

    NARCIS (Netherlands)

    Seguel Pérez, R.E.; Grefen, P.W.P.J.; Eshuis, H.

    2010-01-01

    In this paper, we present a three dimensional design approach of complex information systems architectures. Key element of this approach is the model transformation cube, which consists of three dimensions along which architecture models can be positioned. Industry architecture frameworks to guide

  8. Molecular approaches to Taenia asiatica.

    Science.gov (United States)

    Jeon, Hyeong-Kyu; Eom, Keeseon S

    2013-02-01

    Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

  9. Molecular Approaches to Taenia asiatica

    Science.gov (United States)

    Jeon, Hyeong-Kyu

    2013-01-01

    Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms. PMID:23467738

  10. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Administrator

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree– ..... energy decomposition analysis also performed and which clearly ... through molecular dynamics simulation furnished by. Takeguchi,. 46.

  11. H‐shaped double graft copolymers: Effect of molecular architecture on morphology

    International Nuclear Information System (INIS)

    Lee, Chin; Gido, Samuel P.; Poulos, Yiannis; Hadjichristidis, Nikos; Tan, Nora Beck; Trevino, Samuel F.; Mays, Jimmy W.

    1997-01-01

    The morphologies formed by block copolymers with a double‐graft, H or S 2 IS 2 architecture were investigated using transmission electron microscopy (TEM) and small angle neutron scattering (SANS). Here S and I represent blocks of polystyrene and polyisoprene, respectively. These materials were synthesized using anionic polymerization and chlorosilane linking, and they were characterized using size exclusion chromatography, membrane osmometry, and low‐angle laser light scattering. This characterization work confirmed the desired molecular architectures and narrow molecular weight distributions. The results of morphological characterization indicate that one can understand complex grafting architectures by decomposing them into fundamental building blocks, which are taken as the component single graft structures out of which the larger structure is constructed. We propose rules for dividing structures into these components, which we call constituting block copolymers. The morphological behavior of the more complex architecture is approximately equivalent to that of the constituting block copolymer structure. Through the use of the constituting block copolymers we map the experimentally determined morphological behavior of the H architecture onto the morphology diagram calculated by Milner for miktoarm stars [Macromolecules 27, 2333 (1994)]. Mapping the H architecture onto the morphology diagram in this way produces general agreement between experimental results and the model. However, it is found that in the case of the H architecture, as well as in previously published results for I 2 S and I 3 S miktoarm star materials, that the morphology diagram slightly overestimates the amount of shift in the order‐order transition lines produced by asymmetry in molecular architecture. This overestimation in the theory is attribute to a junction point localization effect which was neglected in Milner’s calculation

  12. Molecular approach of auditory neuropathy.

    Science.gov (United States)

    Silva, Magali Aparecida Orate Menezes da; Piatto, Vânia Belintani; Maniglia, Jose Victor

    2015-01-01

    Mutations in the otoferlin gene are responsible for auditory neuropathy. To investigate the prevalence of mutations in the mutations in the otoferlin gene in patients with and without auditory neuropathy. This original cross-sectional case study evaluated 16 index cases with auditory neuropathy, 13 patients with sensorineural hearing loss, and 20 normal-hearing subjects. DNA was extracted from peripheral blood leukocytes, and the mutations in the otoferlin gene sites were amplified by polymerase chain reaction/restriction fragment length polymorphism. The 16 index cases included nine (56%) females and seven (44%) males. The 13 deaf patients comprised seven (54%) males and six (46%) females. Among the 20 normal-hearing subjects, 13 (65%) were males and seven were (35%) females. Thirteen (81%) index cases had wild-type genotype (AA) and three (19%) had the heterozygous AG genotype for IVS8-2A-G (intron 8) mutation. The 5473C-G (exon 44) mutation was found in a heterozygous state (CG) in seven (44%) index cases and nine (56%) had the wild-type allele (CC). Of these mutants, two (25%) were compound heterozygotes for the mutations found in intron 8 and exon 44. All patients with sensorineural hearing loss and normal-hearing individuals did not have mutations (100%). There are differences at the molecular level in patients with and without auditory neuropathy. Copyright © 2015 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  13. Design health village with the approach of sustainable architecture ...

    African Journals Online (AJOL)

    Journal Home > Vol 8, No 3 (2016) > ... a natural environment and away from the pollution of urban life , traditional medical care, hydrotherapy, sports and ... Keywords: Health; city health; smart; sustainability in architecture; architectural design ...

  14. A Systems Approach to Developing an Affordable Space Ground Transportation Architecture using a Commonality Approach

    Science.gov (United States)

    Garcia, Jerry L.; McCleskey, Carey M.; Bollo, Timothy R.; Rhodes, Russel E.; Robinson, John W.

    2012-01-01

    This paper presents a structured approach for achieving a compatible Ground System (GS) and Flight System (FS) architecture that is affordable, productive and sustainable. This paper is an extension of the paper titled "Approach to an Affordable and Productive Space Transportation System" by McCleskey et al. This paper integrates systems engineering concepts and operationally efficient propulsion system concepts into a structured framework for achieving GS and FS compatibility in the mid-term and long-term time frames. It also presents a functional and quantitative relationship for assessing system compatibility called the Architecture Complexity Index (ACI). This paper: (1) focuses on systems engineering fundamentals as it applies to improving GS and FS compatibility; (2) establishes mid-term and long-term spaceport goals; (3) presents an overview of transitioning a spaceport to an airport model; (4) establishes a framework for defining a ground system architecture; (5) presents the ACI concept; (6) demonstrates the approach by presenting a comparison of different GS architectures; and (7) presents a discussion on the benefits of using this approach with a focus on commonality.

  15. Pulsed recording of anisotropy and holographic polarization gratings in azo-polymethacrylates with different molecular architectures

    DEFF Research Database (Denmark)

    Forcén, Patricia; Oriol, Luis; Alcala, Rafael

    2008-01-01

    Recording of anisotropy and holographic polarization gratings using 532 nm, 4 ns light pulses has been carried out in thin films of polymers with the same azobenzene content (20 wt %) and different molecular architectures. Random and block copolymers comprising azobenzene and methylmethacrylate (...

  16. Branched polyacrylamides : Synthesis and effect of molecular architecture on solution rheology

    NARCIS (Netherlands)

    Wever, D. A. Z.; Picchioni, F.; Broekhuis, A. A.

    2013-01-01

    Linear, star and comb-like polyacrylamides (PAM) have been prepared by atomic transfer radical polymerization (ATRP) in aqueous media at room temperature. The influence of the molecular architecture of PAM on the rheological properties in aqueous solution has been investigated. The well-known theory

  17. The hybrid thermography approach applied to architectural structures

    Science.gov (United States)

    Sfarra, S.; Ambrosini, D.; Paoletti, D.; Nardi, I.; Pasqualoni, G.

    2017-07-01

    This work contains an overview of infrared thermography (IRT) method and its applications relating to the investigation of architectural structures. In this method, the passive approach is usually used in civil engineering, since it provides a panoramic view of the thermal anomalies to be interpreted also thanks to the use of photographs focused on the region of interest (ROI). The active approach, is more suitable for laboratory or indoor inspections, as well as for objects having a small size. The external stress to be applied is thermal, coming from non-natural apparatus such as lamps or hot / cold air jets. In addition, the latter permits to obtain quantitative information related to defects not detectable to the naked eyes. Very recently, the hybrid thermography (HIRT) approach has been introduced to the attention of the scientific panorama. It can be applied when the radiation coming from the sun, directly arrives (i.e., possibly without the shadow cast effect) on a surface exposed to the air. A large number of thermograms must be collected and a post-processing analysis is subsequently applied via advanced algorithms. Therefore, an appraisal of the defect depth can be obtained passing through the calculation of the combined thermal diffusivity of the materials above the defect. The approach is validated herein by working, in a first stage, on a mosaic sample having known defects while, in a second stage, on a Church built in L'Aquila (Italy) and covered with a particular masonry structure called apparecchio aquilano. The results obtained appear promising.

  18. Genetic and Molecular Mechanisms of Quantitative Trait Loci Controlling Maize Inflorescence Architecture.

    Science.gov (United States)

    Li, Manfei; Zhong, Wanshun; Yang, Fang; Zhang, Zuxin

    2018-03-01

    The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging, but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs.

  19. Space and place concepts analysis based on semiology approach in residential architecture

    Directory of Open Access Journals (Sweden)

    Mojtaba Parsaee

    2015-12-01

    Full Text Available Space and place are among the fundamental concepts in architecture about which many discussions have been held and the complexity and importance of these concepts were focused on. This research has introduced an approach to better cognition of the architectural concepts based on theory and method of semiology in linguistics. Hence, at first the research investigates the concepts of space and place and explains their characteristics in architecture. Then, it reviews the semiology theory and explores its concepts and ideas. After obtaining the principles of theory and also the method of semiology, they are redefined in an architectural system based on an adaptive method. Finally, the research offers a conceptual model which is called the semiology approach by considering the architectural system as a system of signs. The approach can be used to decode the content of meanings and forms and analyses of the architectural mechanism in order to obtain its meanings and concepts. In this way and based on this approach, the residential architecture of the traditional city of Bushehr – Iran was analyzed as a case of study and its concepts were extracted. The results of this research demonstrate the effectiveness of this approach in structure detection and identification of an architectural system. Besides, this approach has the capability to be used in processes of sustainable development and also be a basis for deconstruction of architectural texts. The research methods of this study are qualitative based on comparative and descriptive analyses.

  20. Unifying approach for model transformations in the MOF metamodeling architecture

    NARCIS (Netherlands)

    Ivanov, Ivan; van den Berg, Klaas

    2004-01-01

    In the Meta Object Facility (MOF) metamodeling architecture a number of model transformation scenarios can be identified. It could be expected that a metamodeling architecture will be accompanied by a transformation technology supporting the model transformation scenarios in a uniform way. Despite

  1. Unit 1A: General Approach to the Teaching of Architecture

    DEFF Research Database (Denmark)

    Gammelgaard Nielsen, Anders

    2011-01-01

    An ideal course Ever since the founding of the Aar- hus School of Architecture in 1965 there has been a tradition for lively discussion surrounding the content of the architecture program. The discussion has often been con- ducted from ideological or norma- tive positions, with the tendency to st...

  2. Service-Oriented Architecture Approach to MAGTF Logistics Support Systems

    Science.gov (United States)

    2013-09-01

    Support System-Marine Corps IT Information Technology KPI Key Performance Indicators LCE Logistics Command Element ITV In-transit Visibility LCM...building blocks, options, KPI (key performance indicators), design decisions and the corresponding; the physical attributes which is the second attribute... KPI ) that they impact. h. Layer 8 (Information Architecture) The business intelligence layer and information architecture safeguards the inclusion

  3. The molecular architecture of human N-acetylgalactosamine kinase.

    Science.gov (United States)

    Thoden, James B; Holden, Hazel M

    2005-09-23

    Galactokinase plays a key role in normal galactose metabolism by catalyzing the conversion of alpha-d-galactose to galactose 1-phosphate. Within recent years, the three-dimensional structures of human galactokinase and two bacterial forms of the enzyme have been determined. Originally, the gene encoding galactokinase in humans was mapped to chromosome 17. An additional gene, encoding a protein with sequence similarity to galactokinase, was subsequently mapped to chromosome 15. Recent reports have shown that this second gene (GALK2) encodes an enzyme with greater activity against GalNAc than galactose. This enzyme, GalNAc kinase, has been implicated in a salvage pathway for the reutilization of free GalNAc derived from the degradation of complex carbohydrates. Here we report the first structural analysis of a GalNAc kinase. The structure of the human enzyme was solved in the presence of MnAMPPNP and GalNAc or MgATP and GalNAc (which resulted in bound products in the active site). The enzyme displays a distinctly bilobal appearance with its active site wedged between the two domains. The N-terminal region is dominated by a seven-stranded mixed beta-sheet, whereas the C-terminal motif contains two layers of anti-parallel beta-sheet. The overall topology displayed by GalNAc kinase places it into the GHMP superfamily of enzymes, which generally function as small molecule kinases. From this investigation, the geometry of the GalNAc kinase active site before and after catalysis has been revealed, and the determinants of substrate specificity have been defined on a molecular level.

  4. A portable approach for PIC on emerging architectures

    Science.gov (United States)

    Decyk, Viktor

    2016-03-01

    A portable approach for designing Particle-in-Cell (PIC) algorithms on emerging exascale computers, is based on the recognition that 3 distinct programming paradigms are needed. They are: low level vector (SIMD) processing, middle level shared memory parallel programing, and high level distributed memory programming. In addition, there is a memory hierarchy associated with each level. Such algorithms can be initially developed using vectorizing compilers, OpenMP, and MPI. This is the approach recommended by Intel for the Phi processor. These algorithms can then be translated and possibly specialized to other programming models and languages, as needed. For example, the vector processing and shared memory programming might be done with CUDA instead of vectorizing compilers and OpenMP, but generally the algorithm itself is not greatly changed. The UCLA PICKSC web site at http://www.idre.ucla.edu/ contains example open source skeleton codes (mini-apps) illustrating each of these three programming models, individually and in combination. Fortran2003 now supports abstract data types, and design patterns can be used to support a variety of implementations within the same code base. Fortran2003 also supports interoperability with C so that implementations in C languages are also easy to use. Finally, main codes can be translated into dynamic environments such as Python, while still taking advantage of high performing compiled languages. Parallel languages are still evolving with interesting developments in co-Array Fortran, UPC, and OpenACC, among others, and these can also be supported within the same software architecture. Work supported by NSF and DOE Grants.

  5. Design Considerations. An Interior Architectural Design Approach to Interiors

    Science.gov (United States)

    Sawyer, William C.

    1971-01-01

    The State University Construction Fund, utilizing the nation's top professional talents, must design by contract, within fixed budgets and strict time schedules, quality architecture for 32 campuses in New York State. (Author)

  6. Molecular computing towards a novel computing architecture for complex problem solving

    CERN Document Server

    Chang, Weng-Long

    2014-01-01

    This textbook introduces a concise approach to the design of molecular algorithms for students or researchers who are interested in dealing with complex problems. Through numerous examples and exercises, you will understand the main difference of molecular circuits and traditional digital circuits to manipulate the same problem and you will also learn how to design a molecular algorithm of solving any a problem from start to finish. The book starts with an introduction to computational aspects of digital computers and molecular computing, data representation of molecular computing, molecular operations of molecular computing and number representation of molecular computing, and provides many molecular algorithm to construct the parity generator and the parity checker of error-detection codes on digital communication, to encode integers of different formats, single precision and double precision of floating-point numbers, to implement addition and subtraction of unsigned integers, to construct logic operations...

  7. A lightweight approach for designing enterprise architectures using BPMN : an application in hospitals

    NARCIS (Netherlands)

    Barros, O.; Seguel Pérez, R.E.; Quezada, A.; Dijkman, R.; Hofstetter, J.; Koehler, J.

    2011-01-01

    An Enterprise Architecture (EA) comprises different models at different levels of abstraction. Since existing EA design approaches, e.g. MDA, use UML for modeling, the design of the architecture becomes complex and time consuming. In this paper, we present an integrated and lightweight design

  8. Individual Biomarkers Using Molecular Personalized Medicine Approaches.

    Science.gov (United States)

    Zenner, Hans P

    2017-01-01

    Molecular personalized medicine tries to generate individual predictive biomarkers to assist doctors in their decision making. These are thought to improve the efficacy and lower the toxicity of a treatment. The molecular basis of the desired high-precision prediction is modern "omex" technologies providing high-throughput bioanalytical methods. These include genomics and epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, imaging, and functional analyses. In most cases, producing big data also requires a complex biomathematical analysis. Using molecular personalized medicine, the conventional physician's check of biomarker results may no longer be sufficient. By contrast, the physician may need to cooperate with the biomathematician to achieve the desired prediction on the basis of the analysis of individual big data typically produced by omex technologies. Identification of individual biomarkers using molecular personalized medicine approaches is thought to allow a decision-making for the precise use of a targeted therapy, selecting the successful therapeutic tool from a panel of preexisting drugs or medical products. This should avoid the treatment of nonresponders and responders that produces intolerable unwanted effects. © 2017 S. Karger AG, Basel.

  9. Software representation methodology for agile application development: An architectural approach

    Directory of Open Access Journals (Sweden)

    Alejandro Paolo Daza Corredor

    2016-06-01

    Full Text Available The generation of Web applications represents the execution of repetitive tasks, this process involves determining information structures, the generation of different types of components and finally deployment tasks and tuning applications. In many applications of this type are coincident components generated from application to application. Current trends in software engineering as MDE, MDA or MDD pretend to automate the generation of applications based on structuring a model to apply transformations to the achievement of the application. This document intends to translate an architectural foundation that facilitates the generation of these applications relying on model-driven architecture but without ignoring the existence and relevance of existing trends mentioned in this summary architectural models.

  10. Molecular Architectural Approach to Novel Electro-Optical Materials

    Energy Technology Data Exchange (ETDEWEB)

    Li, D.; Johal, M.S.; Smilowitz, L.B.; Robinson, J.M.

    1999-06-29

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at Los Alamos National Laboratory (LANL). The goal is to construct polar multilayers with nonlinear optical coefficients larger than classical inorganic crystals such as KDP or quartz. The strategy is to use various chemical interactions such as covalent bonds or hydrogen bonding to build polar structures. We have synthesized novel barbituric acid and melamine derivatives that will spontaneously self-assemble into a supramolecular ribbon according to their complementary H-bond motif. This supramolecular ribbon can then stack into a polar multilayer structure as verified by sum frequency generation (w{sub 1}+w{sub 2}) or second harmonic generation (when w{sub 1}=w{sub 2}). Second harmonic generation yields a value of d{sub 33}=3.2 pm/V for the self-assembled films and sum frequency generation shows a net polar orientation of the methyl groups in the multilayer along the surface normal. X-ray diffraction confirms the layered structure and produces the periodicity of {approximately}41 A, which corresponds well to the width of the supramolecular ribbons ({approximately}40 A).

  11. Architecture Design Approaches and Issues in Cross Layer Systems

    DEFF Research Database (Denmark)

    Cattoni, Andrea Fabio; Sørensen, Troels Bundgaard; Mogensen, Preben

    2012-01-01

    the traditional protocol stack design methodology. However, Cross Layer also carries a risk due to possibly unexpected and undesired effects. In this chapter we want to provide architecture designers with a set of tools and recommendations synthesized from an analysis of the state of art, but enriched...

  12. Lifelong Learning in Architectural Design Studio: The Learning Contract Approach

    Science.gov (United States)

    Hassanpour, B.; Che-Ani, A. I.; Usman, I. M. S.; Johar, S.; Tawil, N. M.

    2015-01-01

    Avant-garde educational systems are striving to find lifelong learning methods. Different fields and majors have tested a variety of proposed models and found varying difficulties and strengths. Architecture is one of the most critical areas of education because of its special characteristics, such as learning by doing and complicated evaluation…

  13. The Integration of Interior Architecture Education with Digital Design Approaches

    Science.gov (United States)

    Yazicioglu, Deniz Ayse

    2011-01-01

    It is inevitable that as a result of progress in technology and the changes in the ways with which design is conceived, interior architecture schools should be updated according to these requirements and that new educational processes should be tried out. It is for this reason that the scope and aim of this study have been determined as being the…

  14. Quantitative Architectural Analysis: A New Approach to Cortical Mapping

    Science.gov (United States)

    Schleicher, Axel; Morosan, Patricia; Amunts, Katrin; Zilles, Karl

    2009-01-01

    Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological…

  15. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata.

    Science.gov (United States)

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2016-06-08

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a "heteromeric" macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into "gene-sized" chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a "gene bank" that facilitates rapid changes in expression of genes required only in specific life history stages. By using "nonmodel" organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Integrating Environmental and Information Systems Management: An Enterprise Architecture Approach

    Science.gov (United States)

    Noran, Ovidiu

    Environmental responsibility is fast becoming an important aspect of strategic management as the reality of climate change settles in and relevant regulations are expected to tighten significantly in the near future. Many businesses react to this challenge by implementing environmental reporting and management systems. However, the environmental initiative is often not properly integrated in the overall business strategy and its information system (IS) and as a result the management does not have timely access to (appropriately aggregated) environmental information. This chapter argues for the benefit of integrating the environmental management (EM) project into the ongoing enterprise architecture (EA) initiative present in all successful companies. This is done by demonstrating how a reference architecture framework and a meta-methodology using EA artefacts can be used to co-design the EM system, the organisation and its IS in order to achieve a much needed synergy.

  17. Molecular biology approaches in bioadhesion research

    Directory of Open Access Journals (Sweden)

    Marcelo Rodrigues

    2014-07-01

    Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

  18. Molecular simulations of hydrocarbon lubricants: Impact of molecular architecture on performance properties

    Science.gov (United States)

    Kioupis, Loukas I.

    2000-07-01

    With the increased power of modern computers, molecular modeling has been used widely and proven to be a valuable tool for elucidating the physical processes important in many industrial and engineering problems. Of particular interest to us is the rheology and physical chemistry of complex fluids, such as hydrocarbon lubricants and polymers. The goal is to provide qualitative and quantitative molecular-level explanations for the behavior of such fluids, and provide guidance in the development of new improved materials. For example, during the production of poly-α-olefin (PAO) synthetic lubricants, the number of the isomer skeletal structures that can be obtained is staggering. Which of the countless PAO isomers produce a lubricant with superior performance properties? How does it behave under different operational conditions of temperature, pressure, and shear rate? A fundamental understanding of the effect that molecular structure has on the oil's rheological and lubricant performance is first needed, in order to answer these questions. To serve this purpose, we have developed efficient molecular dynamics (MD) simulation programs, which utilize multiple time step algorithms and parallel computational techniques. This enables us to conduct simulations of typical PAO isomers and compute the viscosity, as well as several other dynamic and static properties, as a function of temperature, pressure, and shear rate. The key molecular mechanisms that determine important macroscopic properties, such as viscosity index, viscosity-pressure coefficient, traction coefficient, and shear thinning behavior are discussed. Based on this analysis, lubricant and traction fluid structures that have a high likelihood of having desirable properties are proposed. In addition, studies on simple alkane mixtures are presented, in an attempt to understand the more complex polydisperse lubricant fluids, their blends, and their interaction with additives.

  19. Molecular Architecture and Biomedical Leads of Terpenes from Red Sea Marine Invertebrates

    Science.gov (United States)

    Hegazy, Mohamed Elamir F.; Mohamed, Tarik A.; Alhammady, Montaser A.; Shaheen, Alaa M.; Reda, Eman H.; Elshamy, Abdelsamed I.; Aziz, Mina; Paré, Paul W.

    2015-01-01

    Marine invertebrates including sponges, soft coral, tunicates, mollusks and bryozoan have proved to be a prolific source of bioactive natural products. Among marine-derived metabolites, terpenoids have provided a vast array of molecular architectures. These isoprenoid-derived metabolites also exhibit highly specialized biological activities ranging from nerve regeneration to blood-sugar regulation. As a result, intense research activity has been devoted to characterizing invertebrate terpenes from both a chemical and biological standpoint. This review focuses on the chemistry and biology of terpene metabolites isolated from the Red Sea ecosystem, a unique marine biome with one of the highest levels of biodiversity and specifically rich in invertebrate species. PMID:26006713

  20. Molecular Architecture and Biomedical Leads of Terpenes from Red Sea Marine Invertebrates

    Directory of Open Access Journals (Sweden)

    Mohamed Elamir F. Hegazy

    2015-05-01

    Full Text Available Marine invertebrates including sponges, soft coral, tunicates, mollusks and bryozoan have proved to be a prolific source of bioactive natural products. Among marine-derived metabolites, terpenoids have provided a vast array of molecular architectures. These isoprenoid-derived metabolites also exhibit highly specialized biological activities ranging from nerve regeneration to blood-sugar regulation. As a result, intense research activity has been devoted to characterizing invertebrate terpenes from both a chemical and biological standpoint. This review focuses on the chemistry and biology of terpene metabolites isolated from the Red Sea ecosystem, a unique marine biome with one of the highest levels of biodiversity and specifically rich in invertebrate species.

  1. Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular Brush Polymer Architectures

    Science.gov (United States)

    2015-02-09

    Synthesis of Novel Dendrimer and Molecular Brush Polymer Architectures. Research Area:7.4 The views, opinions and/or findings contained in this report...journals: Final Report: Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular

  2. Approaches Regarding Business Logic Modeling in Service Oriented Architecture

    Directory of Open Access Journals (Sweden)

    Alexandra Maria Ioana FLOREA

    2011-01-01

    Full Text Available As part of the Service Oriented Computing (SOC, Service Oriented Architecture (SOA is a technology that has been developing for almost a decade and during this time there have been published many studies, papers and surveys that are referring to the advantages of projects using it. In this article we discuss some ways of using SOA in the business environment, as a result of the need to reengineer the internal business processes with the scope of moving forward towards providing and using standardized services and achieving enterprise interoperability.

  3. Control the Morphologies and the Pore Architectures of Meso porous Silicas through a Dual-Templating Approach

    International Nuclear Information System (INIS)

    Wang, H.; Chen, H.; Xu, Z.; Wang, S.; Li, B.; Li, Y.

    2012-01-01

    Meso porous silica nanospheres were prepared using a chiral cationic low-molecular-weight amphiphile and organic solvents such as toluene, cyclohexane, and tetrachlorocarbon through a dual-templating approach. X-ray diffraction, nitrogen sorption, field emission scanning electron microscopy, and transmission electron microscopy techniques have been used to characterize the meso porous silicas. The volume ratio of toluene to water plays an important role in controlling the morphologies and the pore architectures of the meso porous silicas. It was also found that meso porous silica nano flakes can be prepared by adding tetrahydrofuran to the reaction mixtures.

  4. A Bayesian Approach to Model Selection in Hierarchical Mixtures-of-Experts Architectures.

    Science.gov (United States)

    Tanner, Martin A.; Peng, Fengchun; Jacobs, Robert A.

    1997-03-01

    There does not exist a statistical model that shows good performance on all tasks. Consequently, the model selection problem is unavoidable; investigators must decide which model is best at summarizing the data for each task of interest. This article presents an approach to the model selection problem in hierarchical mixtures-of-experts architectures. These architectures combine aspects of generalized linear models with those of finite mixture models in order to perform tasks via a recursive "divide-and-conquer" strategy. Markov chain Monte Carlo methodology is used to estimate the distribution of the architectures' parameters. One part of our approach to model selection attempts to estimate the worth of each component of an architecture so that relatively unused components can be pruned from the architecture's structure. A second part of this approach uses a Bayesian hypothesis testing procedure in order to differentiate inputs that carry useful information from nuisance inputs. Simulation results suggest that the approach presented here adheres to the dictum of Occam's razor; simple architectures that are adequate for summarizing the data are favored over more complex structures. Copyright 1997 Elsevier Science Ltd. All Rights Reserved.

  5. Integrated Nationwide Electronic Health Records system: Semi-distributed architecture approach.

    Science.gov (United States)

    Fragidis, Leonidas L; Chatzoglou, Prodromos D; Aggelidis, Vassilios P

    2016-11-14

    The integration of heterogeneous electronic health records systems by building an interoperable nationwide electronic health record system provides undisputable benefits in health care, like superior health information quality, medical errors prevention and cost saving. This paper proposes a semi-distributed system architecture approach for an integrated national electronic health record system incorporating the advantages of the two dominant approaches, the centralized architecture and the distributed architecture. The high level design of the main elements for the proposed architecture is provided along with diagrams of execution and operation and data synchronization architecture for the proposed solution. The proposed approach effectively handles issues related to redundancy, consistency, security, privacy, availability, load balancing, maintainability, complexity and interoperability of citizen's health data. The proposed semi-distributed architecture offers a robust interoperability framework without healthcare providers to change their local EHR systems. It is a pragmatic approach taking into account the characteristics of the Greek national healthcare system along with the national public administration data communication network infrastructure, for achieving EHR integration with acceptable implementation cost.

  6. The Enactive Approach to Architectural Experience: A Neurophysiological Perspective on Embodiment, Motivation, and Affordances.

    Science.gov (United States)

    Jelić, Andrea; Tieri, Gaetano; De Matteis, Federico; Babiloni, Fabio; Vecchiato, Giovanni

    2016-01-01

    Over the last few years, the efforts to reveal through neuroscientific lens the relations between the mind, body, and built environment have set a promising direction of using neuroscience for architecture. However, little has been achieved thus far in developing a systematic account that could be employed for interpreting current results and providing a consistent framework for subsequent scientific experimentation. In this context, the enactive perspective is proposed as a guide to studying architectural experience for two key reasons. Firstly, the enactive approach is specifically selected for its capacity to account for the profound connectedness of the organism and the world in an active and dynamic relationship, which is primarily shaped by the features of the body. Thus, particular emphasis is placed on the issues of embodiment and motivational factors as underlying constituents of the body-architecture interactions. Moreover, enactive understanding of the relational coupling between body schema and affordances of architectural spaces singles out the two-way bodily communication between architecture and its inhabitants, which can be also explored in immersive virtual reality settings. Secondly, enactivism has a strong foothold in phenomenological thinking that corresponds to the existing phenomenological discourse in architectural theory and qualitative design approaches. In this way, the enactive approach acknowledges the available common ground between neuroscience and architecture and thus allows a more accurate definition of investigative goals. Accordingly, the outlined model of architectural subject in enactive terms-that is, a model of a human being as embodied, enactive, and situated agent, is proposed as a basis of neuroscientific and phenomenological interpretation of architectural experience.

  7. The enactive approach to architectural experience: a neurophysiological perspective on embodiment, motivation, and affordances

    Directory of Open Access Journals (Sweden)

    Andrea eJelic

    2016-03-01

    Full Text Available Over the last few years, the efforts to reveal through neuroscientific lens the relations between the mind, body, and built environment have set a promising direction of using neuroscience for architecture. However, little has been achieved thus far in developing a systematic account that could be employed for interpreting current results and providing a consistent framework for subsequent scientific experimentation. In this context, the enactive perspective is proposed as a guide to studying architectural experience for two key reasons. Firstly, the enactive approach is specifically selected for its capacity to account for the profound connectedness of the organism and the world in an active and dynamic relationship, which is primarily shaped by the features of the body. Thus, particular emphasis is placed on the issues of embodiment and motivational factors as underlying constituents of the body-architecture interactions. Moreover, enactive understanding of the relational coupling between body schema and affordances of architectural spaces singles out the two-way bodily communication between architecture and its inhabitants, which can be also explored in immersive virtual reality settings. Secondly, enactivism has a strong foothold in phenomenological thinking that corresponds to the existing phenomenological discourse in architectural theory and qualitative design approaches. In this way, the enactive approach acknowledges the available common ground between neuroscience and architecture and thus allows a more accurate definition of investigative goals. Accordingly, the outlined model of architectural subject in enactive terms – that is, a model of a human being as embodied, enactive, and situated agent, is proposed as a basis of neuroscientific and phenomenological interpretation of architectural experience.

  8. How to ensure sustainable interoperability in heterogeneous distributed systems through architectural approach.

    Science.gov (United States)

    Pape-Haugaard, Louise; Frank, Lars

    2011-01-01

    A major obstacle in ensuring ubiquitous information is the utilization of heterogeneous systems in eHealth. The objective in this paper is to illustrate how an architecture for distributed eHealth databases can be designed without lacking the characteristic features of traditional sustainable databases. The approach is firstly to explain traditional architecture in central and homogeneous distributed database computing, followed by a possible approach to use an architectural framework to obtain sustainability across disparate systems i.e. heterogeneous databases, concluded with a discussion. It is seen that through a method of using relaxed ACID properties on a service-oriented architecture it is possible to achieve data consistency which is essential when ensuring sustainable interoperability.

  9. Ring-Opening Polymerization of N-Carboxyanhydrides for Preparation of Polypeptides and Polypeptide-Based Hybrid Materials with Various Molecular Architectures

    KAUST Repository

    Pahovnik, David

    2015-09-01

    Different synthetic approaches utilizing ring-opening polymerization of N-carboxyanhydrides for preparation of polypeptide and polypeptide-based hybrid materials with various molecular architectures are described. An overview of polymerization mechanisms using conventional (various amines) as well as some recently developed initiators (hexamethyldisilazane, N-heterocyclic persistent carbenes, etc.) is presented, and their benefits and drawbacks for preparation of polypeptides with well-defined chain lengths and chain-end functionality are discussed. Recent examples from literature are used to illustrate different possibilities for synthesis of pure polypeptide materials with different molecular architectures bearing various functional groups, which are introduced either by modification of amino acids, before they are transformed into corresponding Ncarboxyanhydrides, or by post-polymerization modifications using protective groups and/or orthogonal functional groups. Different approaches for preparation of polypeptide-based hybrid materials are discussed as well using examples from recent literature. Syntheses of simple block copolymers or copolymers with more complex molecular architectures (graft and star copolymers) as well as modifications of nanoparticles and other surfaces with polypeptides are described.

  10. Contingent self-definition and amorphous regions: a dynamic approach to place brand architecture

    OpenAIRE

    Dinnie, Keith

    2017-01-01

    This article explores the concept of contingent self-definition, whereby place brands employ flexible self-definitional approaches in constructing their place brand architecture. Adopting a view of regions as social constructs, the article builds on and extends previous work on place brand architecture by identifying the underlying factors that drive contingent self-definition decisions. Based on an empirical study of professionals tasked with managing region brands in the Netherlands, eleven...

  11. Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

    Science.gov (United States)

    Chung, Pil Seung; Song, Wonyup; Biegler, Lorenz T.; Jhon, Myung S.

    2017-05-01

    During the operation of hard disk drive (HDD), the perfluoropolyether (PFPE) lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic) and loss (viscous) moduli (G' and G″) by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

  12. Non-equilibrium responses of PFPE lubricants with various atomistic/molecular architecture at elevated temperature

    Directory of Open Access Journals (Sweden)

    Pil Seung Chung

    2017-05-01

    Full Text Available During the operation of hard disk drive (HDD, the perfluoropolyether (PFPE lubricant experiences elastic or viscous shear/elongation deformations, which affect the performance and reliability of the HDD. Therefore, the viscoelastic responses of PFPE could provide a finger print analysis in designing optimal molecular architecture of lubricants to control the tribological phenomena. In this paper, we examine the rheological responses of PFPEs including storage (elastic and loss (viscous moduli (G′ and G″ by monitoring the time-dependent-stress-strain relationship via non-equilibrium molecular dynamics simulations. We analyzed the rheological responses by using Cox-Merz rule, and investigated the molecular structural and thermal effects on the solid-like and liquid-like behaviors of PFPEs. The temperature dependence of the endgroup agglomeration phenomena was examined, where the functional endgroups are decoupled as the temperature increases. By analyzing the relaxation processes, the molecular rheological studies will provide the optimal lubricant selection criteria to enhance the HDD performance and reliability for the heat-assisted magnetic recording applications.

  13. Managing the Evolution of an Enterprise Architecture using a MAS-Product-Line Approach

    Science.gov (United States)

    Pena, Joaquin; Hinchey, Michael G.; Resinas, manuel; Sterritt, Roy; Rash, James L.

    2006-01-01

    We view an evolutionary system ns being n software product line. The core architecture is the unchanging part of the system, and each version of the system may be viewed as a product from the product line. Each "product" may be described as the core architecture with sonre agent-based additions. The result is a multiagent system software product line. We describe an approach to such n Software Product Line-based approach using the MaCMAS Agent-Oriented nzethoclology. The approach scales to enterprise nrchitectures as a multiagent system is an approprinre means of representing a changing enterprise nrchitectclre nnd the inferaction between components in it.

  14. A Cooperative Coevolution Approach to Automate Pattern-based Software Architectural Synthesis

    NARCIS (Netherlands)

    Xu, Y.R.; Liang, P.

    2014-01-01

    To reuse successful experience in software architecture design, architects use architectural patterns as reusable architectural knowledge for architectural synthesis. However, it has been observed that the resulting architecture does not always conform to the initial architectural patterns employed.

  15. Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture: Molecular dynamics study

    International Nuclear Information System (INIS)

    Ilnytskyi, Jaroslav M.; Neher, Dieter; Saphiannikova, Marina

    2011-01-01

    Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.

  16. Molecular concepts of water splitting. Nature's approach

    International Nuclear Information System (INIS)

    Cox, Nicholas; Lubitz, Wolfgang

    2013-01-01

    Based on studies of natural systems, much has also been learned concerning the design principles required for biomimetic catalysis of water splitting and hydrogen evolution. In summary, these include use of abundant and inexpensive metals, the effective protection of the active sites in functional environments, repair/replacement of active components in case of damage, and the optimization of reaction rates. Biomimetic chemistry aims to mimic all these features; many labs are working toward this goal by developing new approaches in the design and synthesis of such systems, encompassing not only the catalytic center, but also smart matrices and assembly via self-organization. More stable catalysts that do not require self-repair may be obtained from fully artificial (inorganic) catalytic systems that are totally different from the biological ones and only apply some basic principles learned from nature. Metals other than Mn/Ca, Fe, and Ni could be used (e.g. Co) in new ligand spheres and other matrices. For light harvesting, charge separation/stabilization, and the effective coupling of the oxidizing/reducing equivalents to the redox catalysts, different methods have been proposed - for example, covalently linked molecular donor-acceptor systems, photo-voltaic devices, semiconductor-based systems, and photoactive metal complexes. The aim of all these approaches is to develop catalytic systems that split water with sunlight into hydrogen and oxygen while displaying high efficiency and long-term stability. Such a system - either biological, biomimetic, or bioinspired - has the potential to be used on a large scale to produce 'solar fuels' (e.g. hydrogen or secondary products thereof). (orig.)

  17. Approaches to USJ Formation Beyond Molecular Implantation

    International Nuclear Information System (INIS)

    Hatem, C.; Renau, A.; Godet, L.; Kontos, A.; Papasouliotis, G.; England, J.; Arevalo, E.

    2008-01-01

    As junction depth requirements approach sub 10 nm and the sensitivity to residual implant damage continues to increase, the capability to produce abrupt, shallow profiles while maintaining low residual damage becomes a difficult challenge. Implantation induced amorphization has been widely applied to reduce channeling tails of implanted dopant profiles for integrated circuit manufacturing. This has been required to meet aggressive junction depth targets. The problem, however, is that pre-amorphization creates high defect densities that remain near the former amorphous-crystalline interface post anneal. These end of range (EOR) defects become of greater concern as the industry begins to move towards millisecond anneal technologies. Millisecond anneal, while capable of close to diffusionless activation and abrupt junctions, has caused concern for its inability to fully repair these EOR defects. There has been a recent focus on removing traditional PAI through molecular implantation with limited success. Towards this end we have investigated alternative techniques to reduce EOR damage while maintaining the junction depth, sheet resistance and abruptness. Here we describe the results of two of these techniques. The subsequent reduction in EOR through the use of each process and the resultant Rs, junction depth and abruptness are detailed.

  18. Sex determination in Medfly: A molecular approach

    International Nuclear Information System (INIS)

    Saccone, G.; Pane, A.; Testa, G.; Santoro, M.; De Martino, G.; Di Paola, F.; Polito, L.C.; Louis, C.

    2000-01-01

    With the aim of developing new strategies of control to limit the damages inflicted on fruit crops by Ceratitis capitata (Wied.) (Medfly), a biotechnological approach is undertaken whereby female viability would be impaired or male viability would be improved following the introduction of specific genes into the genome of C. capitata. Only males will then be mass produced and released in the infested areas after sterilisation (Louis et al. 1987). Such conditional lethal or 'advantageous' genes could be expressed in transgenic flies either female-specifically or male-specifically by using cis regulative sequences obtained from previously isolated endogenous Ceratitis genes (Saccone et al. 1996, 1998). By using molecular strategies based on a subtractive technique, we have recently isolated male-specifically expressed genes in the Medfly. Furthermore, we present the current status of the research on the Ceratitis dsx gene, showing sex-specific alternative splicing as in Drosophila, and on the tra-inaZ strategy to induce in Drosophila flies female-specific conditional lethality

  19. Tuning complement activation and pathway through controlled molecular architecture of dextran chains in nanoparticle corona.

    Science.gov (United States)

    Coty, Jean-Baptiste; Eleamen Oliveira, Elquio; Vauthier, Christine

    2017-11-05

    The understanding of complement activation by nanomaterials is a key to a rational design of safe and efficient nanomedicines. This work proposed a systematic study investigating how molecular design of nanoparticle coronas made of dextran impacts on mechanisms that trigger complement activation. The nanoparticles used for this work consisted of dextran-coated poly(isobutylcyanoacrylate) (PIBCA) nanoparticles have already been thoroughly characterized. Their different capacity to trigger complement activation established on the cleavage of the protein C3 was also already described making these nanoparticles good models to investigate the relation between the molecular feature of their corona and the mechanism by which they triggered complement activation. Results of this new study show that complement activation pathways can be selected by distinct architectures formed by dextran chains composing the nanoparticle corona. Assumptions that explain the relation between complement activation mechanisms triggered by the nanoparticles and the nanoparticle corona molecular feature were proposed. These results are of interest to better understand how the design of dextran-coated nanomaterials will impact interactions with the complement system. It can open perspectives with regard to the selection of a preferential complement activation pathway or prevent the nanoparticles to activate the complement system, based on a rational choice of the corona configuration. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. An efficient implementation of parallel molecular dynamics method on SMP cluster architecture

    International Nuclear Information System (INIS)

    Suzuki, Masaaki; Okuda, Hiroshi; Yagawa, Genki

    2003-01-01

    The authors have applied MPI/OpenMP hybrid parallel programming model to parallelize a molecular dynamics (MD) method on a symmetric multiprocessor (SMP) cluster architecture. In that architecture, it can be expected that the hybrid parallel programming model, which uses the message passing library such as MPI for inter-SMP node communication and the loop directive such as OpenMP for intra-SNP node parallelization, is the most effective one. In this study, the parallel performance of the hybrid style has been compared with that of conventional flat parallel programming style, which uses only MPI, both in cases the fast multipole method (FMM) is employed for computing long-distance interactions and that is not employed. The computer environments used here are Hitachi SR8000/MPP placed at the University of Tokyo. The results of calculation are as follows. Without FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 90% with the hybrid style, 75% with the flat-MPI style for MD simulation with 33,402 atoms. With FMM, the parallel efficiency using 16 SMP nodes (128 PEs) is: 60% with the hybrid style, 48% with the flat-MPI style for MD simulation with 117,649 atoms. (author)

  1. Molecular architectures based on π-conjugated block copolymers for global quantum computation

    International Nuclear Information System (INIS)

    Mujica Martinez, C A; Arce, J C; Reina, J H; Thorwart, M

    2009-01-01

    We propose a molecular setup for the physical implementation of a barrier global quantum computation scheme based on the electron-doped π-conjugated copolymer architecture of nine blocks PPP-PDA-PPP-PA-(CCH-acene)-PA-PPP-PDA-PPP (where each block is an oligomer). The physical carriers of information are electrons coupled through the Coulomb interaction, and the building block of the computing architecture is composed by three adjacent qubit systems in a quasi-linear arrangement, each of them allowing qubit storage, but with the central qubit exhibiting a third accessible state of electronic energy far away from that of the qubits' transition energy. The third state is reached from one of the computational states by means of an on-resonance coherent laser field, and acts as a barrier mechanism for the direct control of qubit entanglement. Initial estimations of the spontaneous emission decay rates associated to the energy level structure allow us to compute a damping rate of order 10 -7 s, which suggest a not so strong coupling to the environment. Our results offer an all-optical, scalable, proposal for global quantum computing based on semiconducting π-conjugated polymers.

  2. Molecular architectures based on pi-conjugated block copolymers for global quantum computation

    Energy Technology Data Exchange (ETDEWEB)

    Mujica Martinez, C A; Arce, J C [Universidad del Valle, Departamento de QuImica, A. A. 25360, Cali (Colombia); Reina, J H [Universidad del Valle, Departamento de Fisica, A. A. 25360, Cali (Colombia); Thorwart, M, E-mail: camujica@univalle.edu.c, E-mail: j.reina-estupinan@physics.ox.ac.u, E-mail: jularce@univalle.edu.c [Institut fuer Theoretische Physik IV, Heinrich-Heine-Universitaet Duesseldorf, 40225 Duesseldorf (Germany)

    2009-05-01

    We propose a molecular setup for the physical implementation of a barrier global quantum computation scheme based on the electron-doped pi-conjugated copolymer architecture of nine blocks PPP-PDA-PPP-PA-(CCH-acene)-PA-PPP-PDA-PPP (where each block is an oligomer). The physical carriers of information are electrons coupled through the Coulomb interaction, and the building block of the computing architecture is composed by three adjacent qubit systems in a quasi-linear arrangement, each of them allowing qubit storage, but with the central qubit exhibiting a third accessible state of electronic energy far away from that of the qubits' transition energy. The third state is reached from one of the computational states by means of an on-resonance coherent laser field, and acts as a barrier mechanism for the direct control of qubit entanglement. Initial estimations of the spontaneous emission decay rates associated to the energy level structure allow us to compute a damping rate of order 10{sup -7} s, which suggest a not so strong coupling to the environment. Our results offer an all-optical, scalable, proposal for global quantum computing based on semiconducting pi-conjugated polymers.

  3. [Ultrastructure and molecular biochemistry on pathogenic fungal cells: the architecture of septal cell walls of dermatophytes].

    Science.gov (United States)

    Kitajima, Y

    2001-01-01

    This review provides abstracts of our research for which the year 2000 prize of The Japanese Society for Medical Mycology was awarded. The study consists of 4 fields: 1)Ultrastructure and biochemistry of the cell walls of dermatophytes. 2) Freeze-fracture electron microscopic study on the membrane systems of pathogenic fungi. 3) Action mechanisms of antifungal agents in terms of membrane structure and functions. 4) Dimorphism and virulence of pathogenic fungi in terms of molecular biology of membrane lipids. Since the detailed contents of these studies were reported in my previous review article (Jpn J Med Mycol 41: 211-217, 2000), I would like to mention these studies only briefly here, together with a detailed review of the septal cell wall architecture of dermatophytes, which I did not cover in my earlier articles.

  4. Super-Resolution Molecular and Functional Imaging of Nanoscale Architectures in Life and Materials Science

    KAUST Repository

    Habuchi, Satoshi

    2014-06-12

    Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.

  5. IT Confidentiality Risk Assessment for an Architecture-Based Approach

    NARCIS (Netherlands)

    Morali, A.; Zambon, Emmanuele; Etalle, Sandro; Overbeek, Paul

    2008-01-01

    Information systems require awareness of risks and a good understanding of vulnerabilities and their exploitations. In this paper, we propose a novel approach for the systematic assessment and analysis of confidentiality risks caused by disclosure of operational and functional information. The

  6. Non-technical approach to the challenges of ecological architecture: Learning from Van der Laan

    Directory of Open Access Journals (Sweden)

    María-Jesús González-Díaz

    2016-06-01

    Full Text Available Up to now, ecology has a strong influence on the development of technical and instrumental aspects of architecture, such as renewable and efficient of resources and energy, CO2 emissions, air quality, water reuse, some social and economical aspects. These concepts define the physical keys and codes of the current ׳sustainable׳ architecture, normally instrumental but rarely and insufficiently theorised. But is not there another way of bringing us to nature? We need a theoretical referent. This is where we place the Van der Laan׳s thoughts: he considers that art completes nature and he builds his theoretical discourse on it, trying to better understand many aspects of architecture. From a conceptual point of view, we find in his works sense of timelessness, universality, special attention on the ׳locus׳ and a strict sense of proportions and use of materials according to nature. Could these concepts complement our current sustainable architecture? How did Laan apply the current codes of ecology in his architecture? His work may help us to get a theoretical interpretation of nature and not only physical. This paper develops this idea through the comparison of thoughts and works of Laan with the current technical approach to ׳sustainable׳ architecture.

  7. Franz Kafka in the Design Studio: A Hermeneutic-Phenomenological Approach to Architectural Design Education

    Science.gov (United States)

    Hisarligil, Beyhan Bolak

    2012-01-01

    This article demonstrates the outcomes of taking a hermeneutic phenomenological approach to architectural design and discusses the potentials for imaginative reasoning in design education. This study tests the use of literature as a verbal form of art and design and the contribution it can make to imaginative design processes--which are all too…

  8. Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure.

    Science.gov (United States)

    Cobb, Nathan J; Sönnichsen, Frank D; McHaourab, Hassane; Surewicz, Witold K

    2007-11-27

    Transmissible spongiform encephalopathies (TSEs) represent a group of fatal neurodegenerative diseases that are associated with conformational conversion of the normally monomeric and alpha-helical prion protein, PrP(C), to the beta-sheet-rich PrP(Sc). This latter conformer is believed to constitute the main component of the infectious TSE agent. In contrast to high-resolution data for the PrP(C) monomer, structures of the pathogenic PrP(Sc) or synthetic PrP(Sc)-like aggregates remain elusive. Here we have used site-directed spin labeling and EPR spectroscopy to probe the molecular architecture of the recombinant PrP amyloid, a misfolded form recently reported to induce transmissible disease in mice overexpressing an N-terminally truncated form of PrP(C). Our data show that, in contrast to earlier, largely theoretical models, the con formational conversion of PrP(C) involves major refolding of the C-terminal alpha-helical region. The core of the amyloid maps to C-terminal residues from approximately 160-220, and these residues form single-molecule layers that stack on top of one another with parallel, in-register alignment of beta-strands. This structural insight has important implications for understanding the molecular basis of prion propagation, as well as hereditary prion diseases, most of which are associated with point mutations in the region found to undergo a refolding to beta-structure.

  9. Molecular architecture of the N-type ATPase rotor ring from Burkholderia pseudomallei.

    Science.gov (United States)

    Schulz, Sarah; Wilkes, Martin; Mills, Deryck J; Kühlbrandt, Werner; Meier, Thomas

    2017-04-01

    The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N 1 N o -type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c-ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c 17 ring is H + specific, demonstrating that the ATPase is proton-coupled. The c 17 ring stoichiometry results in a very high ion-to-ATP ratio of 5.7. We propose that this N-ATPase is a highly efficient proton pump that helps these melioidosis-causing bacteria to survive in the hostile, acidic environment of phagosomes. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  10. A Process Algebraic Approach to Software Architecture Design

    Science.gov (United States)

    Aldini, Alessandro; Bernardo, Marco; Corradini, Flavio

    Process algebra is a formal tool for the specification and the verification of concurrent and distributed systems. It supports compositional modeling through a set of operators able to express concepts like sequential composition, alternative composition, and parallel composition of action-based descriptions. It also supports mathematical reasoning via a two-level semantics, which formalizes the behavior of a description by means of an abstract machine obtained from the application of structural operational rules and then introduces behavioral equivalences able to relate descriptions that are syntactically different. In this chapter, we present the typical behavioral operators and operational semantic rules for a process calculus in which no notion of time, probability, or priority is associated with actions. Then, we discuss the three most studied approaches to the definition of behavioral equivalences - bisimulation, testing, and trace - and we illustrate their congruence properties, sound and complete axiomatizations, modal logic characterizations, and verification algorithms. Finally, we show how these behavioral equivalences and some of their variants are related to each other on the basis of their discriminating power.

  11. Convenience of Statistical Approach in Studies of Architectural Ornament and Other Decorative Elements Specific Application

    Science.gov (United States)

    Priemetz, O.; Samoilov, K.; Mukasheva, M.

    2017-11-01

    An ornament is an actual phenomenon of the architecture modern theory, a common element in the practice of design and construction. It has been an important aspect of shaping for millennia. The description of the methods of its application occupies a large place in the studies on the theory and practice of architecture. However, the problem of the saturation of compositions with ornamentation, the specificity of its themes and forms have not been sufficiently studied yet. This aspect requires accumulation of additional knowledge. The application of quantitative methods for the plastic solutions types and a thematic diversity of facade compositions of buildings constructed in different periods creates another tool for an objective analysis of ornament development. It demonstrates the application of this approach for studying the features of the architectural development in Kazakhstan at the end of the XIX - XXI centuries.

  12. The Critical Approach of ‘Plug’ in Re-Conceptualisation of Architectural Program

    Directory of Open Access Journals (Sweden)

    Bahar Beslioglu

    2014-03-01

    Full Text Available This paper explores the issue of ‘plug’ in designing program within particular experimental studies in architecture. There was what could be called a critical ‘elaboration’ of program in Archigram’s 1964 ‘Plug-In’ City project, while intriguingly the critical approach taken in the 2001 ‘Un-Plug’ project of Francois Roche and Stephanie Lavaux hinted at a ‘re-evaluation’ of ‘plug’ related to program in architecture. The embedded criticism and creative programmatic suggestions in both projects will be discussed from the point of view of using the accumulated urbanscape as a potential for contemplation, a theme that has also been elaborated, both theoretically and experimentally, by the artist/architect Gordon Matta-Clark in his 1978 ‘Balloon Housing’ project. These experimentations - about the ‘plug’ - need to be discussed in order to understand their contributions as traceable sources to program issue in contemporary architecture.

  13. Blended Design Approach of Long Span Structure and Malay Traditional Architecture

    Science.gov (United States)

    Sundari, Titin

    2017-12-01

    The growing population in the world is so fast, which is followed by the increasing need of some new and large activities. Architects face the problem on how to facilitate buildings with various activities such as for large meeting, conference, indoors gymnasium and sports, and many others. The long span structure of building is one of the solutions to solve that problem. Generally, large buildings which implemented this structure will look as a technological, modern and futuristic ones or even neo futuristic performance. But on the other hand, many people still want to enjoy the specific and unique senses of local traditional architecture. So is the Malay people who want an easy pleasant large facilities which can be fulfilled by implementing modern long span building structure technology. In the same time, their unique sense of Malay traditional architecture can still be maintained. To overcome this double problems of design, it needs a blended design approach of long span structure and Malay Traditional Architecture.

  14. Prediction and experimental characterization of the molecular architecture of FRP and ATRP synthesized polyacrylate networks

    OpenAIRE

    Gonçalves, Miguel; Dias, Rolando; Costa, Mário Rui

    2009-01-01

    This work reports experimental and modeling studies concerning the conventional (FRP) and atom transfer radical polymerization (ATRP) of acrylate/diacrylate monomers. In the framework of a recently developed general approach, kinetic models including crosslinking reactions and branching by chain transfer to polymer are discussed for FRP and ATRP polymerization systems. Besides molecular weight distribution (MWD), fairly good predictions of the z-average radius of gyration could be obtained fo...

  15. Chitosan Derivatives: Introducing New Functionalities with a Controlled Molecular Architecture for Innovative Materials

    Directory of Open Access Journals (Sweden)

    Waldo M. Argüelles-Monal

    2018-03-01

    Full Text Available The functionalization of polymeric substances is of great interest for the development of innovative materials for advanced applications. For many decades, the functionalization of chitosan has been a convenient way to improve its properties with the aim of preparing new materials with specialized characteristics. In the present review, we summarize the latest methods for the modification and derivatization of chitin and chitosan under experimental conditions, which allow a control over the macromolecular architecture. This is because an understanding of the interdependence between chemical structure and properties is an important condition for proposing innovative materials. New advances in methods and strategies of functionalization such as the click chemistry approach, grafting onto copolymerization, coupling with cyclodextrins, and reactions in ionic liquids are discussed.

  16. Infill architecture: Design approaches for in-between buildings and 'bond' as integrative element

    Directory of Open Access Journals (Sweden)

    Alfirević Đorđe

    2015-01-01

    Full Text Available The aim of the paper is to draw attention to the view that the two key elements in achieving good quality of architecture infill in immediate, current surroundings, are the selection of optimal creative method of infill architecture and adequate application of 'the bond' as integrative element, The success of achievement and the quality of architectural infill mainly depend on the assessment of various circumstances, but also on the professionalism, creativity, sensibility, and finally innovativeness of the architect, In order for the infill procedure to be carried out adequately, it is necessary to carry out the assessment of quality of the current surroundings that the object will be integrated into, and then to choose the creative approach that will allow the object to establish an optimal dialogue with its surroundings, On a wider scale, both theory and the practice differentiate thee main creative approaches to infill objects: amimetic approach (mimesis, bassociative approach and ccontrasting approach, Which of the stated approaches will be chosen depends primarily on the fact whether the existing physical structure into which the object is being infilled is 'distinct', 'specific' or 'indistinct', but it also depends on the inclination of the designer, 'The bond' is a term which in architecture denotes an element or zone of one object, but in some instances it can refer to the whole object which has been articulated in a specific way, with an aim of reaching the solution for the visual conflict as is often the case in situations when there is a clash between the existing objects and the newly designed or reconstructed object, This paper provides in-depth analysis of different types of bonds, such as 'direction as bond', 'cornice as bond', 'structure as bond', 'texture as bond' and 'material as bond', which indicate complexity and multiple layers of the designing process of object interpolation.

  17. A Principled Approach to the Specification of System Architectures for Space Missions

    Science.gov (United States)

    McKelvin, Mark L. Jr.; Castillo, Robert; Bonanne, Kevin; Bonnici, Michael; Cox, Brian; Gibson, Corrina; Leon, Juan P.; Gomez-Mustafa, Jose; Jimenez, Alejandro; Madni, Azad

    2015-01-01

    Modern space systems are increasing in complexity and scale at an unprecedented pace. Consequently, innovative methods, processes, and tools are needed to cope with the increasing complexity of architecting these systems. A key systems challenge in practice is the ability to scale processes, methods, and tools used to architect complex space systems. Traditionally, the process for specifying space system architectures has largely relied on capturing the system architecture in informal descriptions that are often embedded within loosely coupled design documents and domain expertise. Such informal descriptions often lead to misunderstandings between design teams, ambiguous specifications, difficulty in maintaining consistency as the architecture evolves throughout the system development life cycle, and costly design iterations. Therefore, traditional methods are becoming increasingly inefficient to cope with ever-increasing system complexity. We apply the principles of component-based design and platform-based design to the development of the system architecture for a practical space system to demonstrate feasibility of our approach using SysML. Our results show that we are able to apply a systematic design method to manage system complexity, thus enabling effective data management, semantic coherence and traceability across different levels of abstraction in the design chain. Just as important, our approach enables interoperability among heterogeneous tools in a concurrent engineering model based design environment.

  18. A two-dimensional Zn coordination polymer with a three-dimensional supra-molecular architecture.

    Science.gov (United States)

    Liu, Fuhong; Ding, Yan; Li, Qiuyu; Zhang, Liping

    2017-10-01

    The title compound, poly[bis-{μ 2 -4,4'-bis-[(1,2,4-triazol-1-yl)meth-yl]biphenyl-κ 2 N 4 : N 4' }bis-(nitrato-κ O )zinc(II)], [Zn(NO 3 ) 2 (C 18 H 16 N 6 ) 2 ] n , is a two-dimensional zinc coordination polymer constructed from 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl units. It was synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Zn II cation is located on an inversion centre and is coordinated by two O atoms from two symmetry-related nitrate groups and four N atoms from four symmetry-related 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligands, forming a distorted octa-hedral {ZnN 4 O 2 } coordination geometry. The linear 4,4'-bis-[(1 H -1,2,4-triazol-1-yl)meth-yl]-1,1'-biphenyl ligand links two Zn II cations, generating two-dimensional layers parallel to the crystallographic (132) plane. The parallel layers are connected by C-H⋯O, C-H⋯N, C-H⋯π and π-π stacking inter-actions, resulting in a three-dimensional supra-molecular architecture.

  19. Characterization of the expression, promoter activity and molecular architecture of fibin

    Directory of Open Access Journals (Sweden)

    Hermsdorf Thomas

    2011-05-01

    Full Text Available Abstract Background Fibin was initially discovered as a secreted signal molecule essential for pectoral fin bud initiation in zebrafish. Currently, there is little information about the molecular architecture and biological relevance of fibin in humans and other mammals. Results Fibin is expressed in cerebellum, skeletal muscle and many other embryonic and adult mouse tissues suggesting not only a role during embryonic development but also in adult functions. A 2.5-kbp genomic sequence fragment upstream of the coding sequence is sufficient to drive and regulate fibin expression through stimulation by glucocorticoids, activators of the protein kinase C signalling pathways and manganese ions. Fibin is an evolutionarily conserved protein, carries a cleavable signal peptide (amino acids 1-18 and is glycosylated at Asn30. The two conserved cysteines participate in intermolecular disulfide bond and multimer formation. Although fibin displays all features of a secretory protein, it is mostly retained in the endoplasmic reticulum when heterologously expressed. Conclusion Fibin is functionally relevant during embryogenesis and adult life. Its expression is regulated by a number of cellular signalling pathways and the protein is routed via the secretory pathway. However, proper secretion presumably requires an unknown covalently-linked or associated co-factor.

  20. A Disciplined Architectural Approach to Scaling Data Analysis for Massive, Scientific Data

    Science.gov (United States)

    Crichton, D. J.; Braverman, A. J.; Cinquini, L.; Turmon, M.; Lee, H.; Law, E.

    2014-12-01

    Data collections across remote sensing and ground-based instruments in astronomy, Earth science, and planetary science are outpacing scientists' ability to analyze them. Furthermore, the distribution, structure, and heterogeneity of the measurements themselves pose challenges that limit the scalability of data analysis using traditional approaches. Methods for developing science data processing pipelines, distribution of scientific datasets, and performing analysis will require innovative approaches that integrate cyber-infrastructure, algorithms, and data into more systematic approaches that can more efficiently compute and reduce data, particularly distributed data. This requires the integration of computer science, machine learning, statistics and domain expertise to identify scalable architectures for data analysis. The size of data returned from Earth Science observing satellites and the magnitude of data from climate model output, is predicted to grow into the tens of petabytes challenging current data analysis paradigms. This same kind of growth is present in astronomy and planetary science data. One of the major challenges in data science and related disciplines defining new approaches to scaling systems and analysis in order to increase scientific productivity and yield. Specific needs include: 1) identification of optimized system architectures for analyzing massive, distributed data sets; 2) algorithms for systematic analysis of massive data sets in distributed environments; and 3) the development of software infrastructures that are capable of performing massive, distributed data analysis across a comprehensive data science framework. NASA/JPL has begun an initiative in data science to address these challenges. Our goal is to evaluate how scientific productivity can be improved through optimized architectural topologies that identify how to deploy and manage the access, distribution, computation, and reduction of massive, distributed data, while

  1. Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

    Science.gov (United States)

    Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

    2016-01-20

    The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

  2. Ligand Bridging-Angle-Driven Assembly of Molecular Architectures Based on Quadruply Bonded Mo-Mo Dimers

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai

    2010-12-15

    A systematic exploration of the assembly of Mo₂(O₂C-)₄-based metal–organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo–Mo clusters acting as nodes to give 13 molecular architectures, termed metal–organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo–Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.

  3. Ligand bridging-angle-driven assembly of molecular architectures based on quadruply bonded Mo-Mo dimers.

    Science.gov (United States)

    Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai

    2010-12-15

    A systematic exploration of the assembly of Mo2(O2C-)4-based metal-organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo-Mo clusters acting as nodes to give 13 molecular architectures, termed metal-organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo-Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.

  4. Inelastic neutron scattering investigation of the α-β crossover in glass-formers as a function of molecular architecture

    International Nuclear Information System (INIS)

    Levelut, C.; Faivre, A.; Pelous, J.; Durand, D.

    1999-01-01

    Complete text of publication follows. An experimental investigation of the relaxational processes related to the glass transition in several glass formers with more or less complex molecular architecture is presented. This inelastic neutron scattering study concentrates on the region around 1.1 to 1.5 T g where the two relaxation processes usually identified in most glass formers, the α and the β relaxations, are expected to merge or cross. A recent study comparing the dynamics of Sorbitol and Maltitol (two low molecular and complementary glasses) seems to show that the way on which the α and β processes merge depends on the differences in the chemical architecture of these polyols [1]. In the present work, linear diols, three-arm-star triols and crosslinked polyurethanes, synthesized from the latter are studied. This work is an extension of a previous study of the relaxational processes in cross-linked polyurethanes [2]. For such series of samples of similar chemical composition but with increasing complexity in the architecture, the influence of the molecular complexity on the type of merging between α and β processes is tested. This allows to discuss the α-β cross-over on molecular level. (author)

  5. Combinatorial chemistry approach to development of molecular plastic solar cells

    NARCIS (Netherlands)

    Godovsky, Dmitri; Inganäs, Olle; Brabec, Christoph J.; Sariciftci, N. Serdar; Hummelen, Jan C.; Janssen, Rene A.J.; Prato, M.; Maggini, M.; Segura, Jose; Martin, Nazario

    1999-01-01

    We used a combinatorial chemistry approach to develop the molecular plastic solar cells based on soluble fullerene derivatives or solubilized TCNQ molecules in combination with conjugated polymers. Profiles, formed by the diffusion of low molecular weight component in the spin-cast polymer host were

  6. PDMS Network Structure-Property Relationships: Influence of Molecular Architecture on Mechanical and Wetting Properties

    Science.gov (United States)

    Melillo, Matthew Joseph

    Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from sealants and marine-antifouling coatings to medical devices and absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into and leach out of PDMS networks is of critical importance for the design and use in another application - microfluidic devices. The growing use of PDMS in microfluidic devices raises the concern that some researchers may use this material without fully understanding all of its advantages, drawbacks, and intricacies. The primary goal of this Ph.D. dissertation is to elucidate PDMS network molecular structure to macroscopic property relationships and to demonstrate how molecular architecture can alter dynamic mechanical and wetting characteristics. We prepare PDMS materials by using vinyl/ tetrakis(dimethylsiloxy)silane (TDSS) and silanol/ tetraethylorthosilicate (TEOS) combinations of PDMS end-groups and crosslinkers as two model systems. Under constant curing conditions, we systematically study the effects of polymer molecular weight, loading of crosslinker, and end-group chemical functionality on the extent of gelation and the dynamic mechanical and water wetting properties of end-linked PDMS networks. The extent of the gelation reaction is determined using the Soxhlet extraction to quantify the amount of material that did and did not participate in the crosslinking reactions, termed the gel and sol fractions, respectively. We use the Miller-Macosko model in conjunction with the gel fraction and precise chemical composition (i.e., stoichiometric ratio and molecular weight) to determine the fractions of elastic and pendant material, the molecular weight between chemical crosslinks, and the average effective functionality of the crosslinker molecule. Based on dynamic mechanical testing, we find that the maximum storage moduli are achieved at optimal stoichiometric conditions in the vinyl

  7. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  8. Parametric Approach to Assessing Performance of High-Lift Device Active Flow Control Architectures

    Directory of Open Access Journals (Sweden)

    Yu Cai

    2017-02-01

    Full Text Available Active Flow Control is at present an area of considerable research, with multiple potential aircraft applications. While the majority of research has focused on the performance of the actuators themselves, a system-level perspective is necessary to assess the viability of proposed solutions. This paper demonstrates such an approach, in which major system components are sized based on system flow and redundancy considerations, with the impacts linked directly to the mission performance of the aircraft. Considering the case of a large twin-aisle aircraft, four distinct active flow control architectures that facilitate the simplification of the high-lift mechanism are investigated using the demonstrated approach. The analysis indicates a very strong influence of system total mass flow requirement on architecture performance, both for a typical mission and also over the entire payload-range envelope of the aircraft.

  9. Proceedings International Workshop on Formal Engineering approaches to Software Components and Architectures

    OpenAIRE

    Kofroň, Jan; Tumova, Jana

    2017-01-01

    These are the proceedings of the 14th International Workshop on Formal Engineering approaches to Software Components and Architectures (FESCA). The workshop was held on April 22, 2017 in Uppsala (Sweden) as a satellite event to the European Joint Conference on Theory and Practice of Software (ETAPS'17). The aim of the FESCA workshop is to bring together junior researchers from formal methods, software engineering, and industry interested in the development and application of formal modelling ...

  10. Proceedings 10th International Workshop on Formal Engineering Approaches to Software Components and Architectures

    OpenAIRE

    Buhnova, Barbora; Happe, Lucia; Kofroň, Jan

    2013-01-01

    These are the proceedings of the 10th International Workshop on Formal Engineering approaches to Software Components and Architectures (FESCA). The workshop was held on March 23, 2013 in Rome (Italy) as a satellite event to the European Joint Conference on Theory and Practice of Software (ETAPS'13). The aim of the FESCA workshop is to bring together both young and senior researchers from formal methods, software engineering, and industry interested in the development and application of formal...

  11. An information-theoretic approach to motor action decoding with a reconfigurable parallel architecture.

    Science.gov (United States)

    Craciun, Stefan; Brockmeier, Austin J; George, Alan D; Lam, Herman; Príncipe, José C

    2011-01-01

    Methods for decoding movements from neural spike counts using adaptive filters often rely on minimizing the mean-squared error. However, for non-Gaussian distribution of errors, this approach is not optimal for performance. Therefore, rather than using probabilistic modeling, we propose an alternate non-parametric approach. In order to extract more structure from the input signal (neuronal spike counts) we propose using minimum error entropy (MEE), an information-theoretic approach that minimizes the error entropy as part of an iterative cost function. However, the disadvantage of using MEE as the cost function for adaptive filters is the increase in computational complexity. In this paper we present a comparison between the decoding performance of the analytic Wiener filter and a linear filter trained with MEE, which is then mapped to a parallel architecture in reconfigurable hardware tailored to the computational needs of the MEE filter. We observe considerable speedup from the hardware design. The adaptation of filter weights for the multiple-input, multiple-output linear filters, necessary in motor decoding, is a highly parallelizable algorithm. It can be decomposed into many independent computational blocks with a parallel architecture readily mapped to a field-programmable gate array (FPGA) and scales to large numbers of neurons. By pipelining and parallelizing independent computations in the algorithm, the proposed parallel architecture has sublinear increases in execution time with respect to both window size and filter order.

  12. Thermal force approach to molecular evolution.

    Science.gov (United States)

    Braun, Dieter; Libchaber, Albert

    2004-06-01

    Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

  13. Molecular approach of uranyl/mineral surfaces: experimental approach

    International Nuclear Information System (INIS)

    Drot, R.

    2009-01-01

    The author reports an experimental approach in which different spectroscopic approaches are coupled (laser spectroscopy, X-ray absorption spectroscopy, vibrational spectroscopy) to investigate the mechanisms controlling actinide sorption processes by different substrates, in order to assess radioactive waste storage site safety. Different substrates have been considered: monocrystalline or powdered TiO 2 , montmorillonite, and gibbsite

  14. Beyond Information Architecture: A Systems Integration Approach to Web-site Design

    Directory of Open Access Journals (Sweden)

    Krisellen Maloney

    2017-09-01

    Full Text Available Users' needs and expectations regarding access to information have fundamentally changed, creating a disconnect between how users expect to use a library Web site and how the site was designed. At the same time, library technical infrastructures include legacy systems that were not designedf or the Web environment. The authors propose a framework that combines elements of information architecture with approaches to incremental system design and implementation. The framework allows for the development of a Web site that is responsive to changing user needs, while recognizing the need for libraries to adopt a cost-effective approach to implementation and maintenance.

  15. The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.

    Science.gov (United States)

    Thoden, James B; Holden, Hazel M

    2014-06-01

    Unusual di- and trideoxysugars are often found on the O-antigens of Gram-negative bacteria, on the S-layers of Gram-positive bacteria, and on various natural products. One such sugar is 3-acetamido-3,6-dideoxy-D-glucose. A key step in its biosynthesis, catalyzed by a 3,4-ketoisomerase, is the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. Here we report an X-ray analysis of a 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. For this investigation, the wild-type enzyme, referred to as QdtA, was crystallized in the presence of dTDP and its structure solved to 2.0-Å resolution. The dimeric enzyme adopts a three-dimensional architecture that is characteristic for proteins belonging to the cupin superfamily. In order to trap the dTDP-4-keto-6-deoxyglucose substrate into the active site, a mutant protein, H51N, was subsequently constructed, and the structure of this protein in complex with the dTDP-sugar ligand was solved to 1.9-Å resolution. Taken together, the structures suggest that His 51 serves as a catalytic base, that Tyr 37 likely functions as a catalytic acid, and that His 53 provides a proton shuttle between the C-3' hydroxyl and the C-4' keto group of the hexose. This study reports the first three-dimensional structure of a 3,4-ketoisomerase in complex with its dTDP-sugar substrate and thus sheds new molecular insight into this fascinating class of enzymes. © 2014 The Protein Society.

  16. Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.

    Science.gov (United States)

    Chang, Hang; Han, Ju; Borowsky, Alexander; Loss, Leandro; Gray, Joe W; Spellman, Paul T; Parvin, Bahram

    2013-04-01

    Automated analysis of whole mount tissue sections can provide insights into tumor subtypes and the underlying molecular basis of neoplasm. However, since tumor sections are collected from different laboratories, inherent technical and biological variations impede analysis for very large datasets such as The Cancer Genome Atlas (TCGA). Our objective is to characterize tumor histopathology, through the delineation of the nuclear regions, from hematoxylin and eosin (H&E) stained tissue sections. Such a representation can then be mined for intrinsic subtypes across a large dataset for prediction and molecular association. Furthermore, nuclear segmentation is formulated within a multi-reference graph framework with geodesic constraints, which enables computation of multidimensional representations, on a cell-by-cell basis, for functional enrichment and bioinformatics analysis. Here, we present a novel method, multi-reference graph cut (MRGC), for nuclear segmentation that overcomes technical variations associated with sample preparation by incorporating prior knowledge from manually annotated reference images and local image features. The proposed approach has been validated on manually annotated samples and then applied to a dataset of 377 Glioblastoma Multiforme (GBM) whole slide images from 146 patients. For the GBM cohort, multidimensional representation of the nuclear features and their organization have identified 1) statistically significant subtypes based on several morphometric indexes, 2) whether each subtype can be predictive or not, and 3) that the molecular correlates of predictive subtypes are consistent with the literature. Data and intermediaries for a number of tumor types (GBM, low grade glial, and kidney renal clear carcinoma) are available at: http://tcga.lbl.gov for correlation with TCGA molecular data. The website also provides an interface for panning and zooming of whole mount tissue sections with/without overlaid segmentation results for quality

  17. Cinnamon in Anticancer Armamentarium: A Molecular Approach

    Directory of Open Access Journals (Sweden)

    Anindita Dutta

    2018-01-01

    Full Text Available In recent years, natural bioactive components draw a major attention for their potent anticarcinogenic activity. Cinnamon, one of the traditional spices, most frequently used in almost every household of tropical countries has got enormous efficacy to combat cancer. Cinnamon as a whole and/or its active components exhibited significant antineoplastic activity in different types of cancer. This review has been carried out to elicit the molecular mechanisms of action of cinnamon and its components on oncogenic regulators and related pathways. Web sites of Google Scholar, Medline, and PubMed were searched for articles written in English and published in peer-reviewed journals from 2003 to 2017. The anticarcinogenic potential of cinnamon varies with the type of cancer and also depends on the administered active compound individually or in combination with some chemicals or even extract of cinnamon as a whole. Some of its active components exert chemosensitization of well-known anticancer drugs. These outstanding properties of this spice necessitate its incorporation in both pharmaceuticals and nutraceuticals to explore possibilities of formulation of novel drug from this spice for treatment and prevention strategy of cancer.

  18. A molecular dynamics approach to barrodiffusion

    Science.gov (United States)

    Cooley, James; Marciante, Mathieu; Murillo, Michael

    2016-10-01

    Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

  19. Molecular approach of uranyl/mineral surfaces: theoretical approach

    International Nuclear Information System (INIS)

    Roques, J.

    2009-01-01

    As migration of radio-toxic elements through the geosphere is one of the processes which may affect the safety of a radioactive waste storage site, the author shows that numerical modelling is a support to experimental result exploitation, and allows the development of new interpretation and prediction codes. He shows that molecular modelling can be used to study processes of interaction between an actinide ion (notably a uranyl ion) and a mineral surface (a TiO 2 substrate). He also reports the predictive theoretical study of the interaction between an uranyl ion and a gibbsite substrate

  20. Molecular rheology of branched polymers: decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling.

    Science.gov (United States)

    van Ruymbeke, E; Lee, H; Chang, T; Nikopoulou, A; Hadjichristidis, N; Snijkers, F; Vlassopoulos, D

    2014-07-21

    An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched

  1. Molecular rheology of branched polymers: Decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling

    KAUST Repository

    Van Ruymbeke, Evelyne

    2014-01-01

    An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched

  2. A novel system architecture for the national integration of electronic health records: a semi-centralized approach.

    Science.gov (United States)

    AlJarullah, Asma; El-Masri, Samir

    2013-08-01

    The goal of a national electronic health records integration system is to aggregate electronic health records concerning a particular patient at different healthcare providers' systems to provide a complete medical history of the patient. It holds the promise to address the two most crucial challenges to the healthcare systems: improving healthcare quality and controlling costs. Typical approaches for the national integration of electronic health records are a centralized architecture and a distributed architecture. This paper proposes a new approach for the national integration of electronic health records, the semi-centralized approach, an intermediate solution between the centralized architecture and the distributed architecture that has the benefits of both approaches. The semi-centralized approach is provided with a clearly defined architecture. The main data elements needed by the system are defined and the main system modules that are necessary to achieve an effective and efficient functionality of the system are designed. Best practices and essential requirements are central to the evolution of the proposed architecture. The proposed architecture will provide the basis for designing the simplest and the most effective systems to integrate electronic health records on a nation-wide basis that maintain integrity and consistency across locations, time and systems, and that meet the challenges of interoperability, security, privacy, maintainability, mobility, availability, scalability, and load balancing.

  3. Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

  4. An Architecture, System Engineering, and Acquisition Approach for Space System Software Resiliency

    Science.gov (United States)

    Phillips, Dewanne Marie

    Software intensive space systems can harbor defects and vulnerabilities that may enable external adversaries or malicious insiders to disrupt or disable system functions, risking mission compromise or loss. Mitigating this risk demands a sustained focus on the security and resiliency of the system architecture including software, hardware, and other components. Robust software engineering practices contribute to the foundation of a resilient system so that the system "can take a hit to a critical component and recover in a known, bounded, and generally acceptable period of time". Software resiliency must be a priority and addressed early in the life cycle development to contribute a secure and dependable space system. Those who develop, implement, and operate software intensive space systems must determine the factors and systems engineering practices to address when investing in software resiliency. This dissertation offers methodical approaches for improving space system resiliency through software architecture design, system engineering, increased software security, thereby reducing the risk of latent software defects and vulnerabilities. By providing greater attention to the early life cycle phases of development, we can alter the engineering process to help detect, eliminate, and avoid vulnerabilities before space systems are delivered. To achieve this objective, this dissertation will identify knowledge, techniques, and tools that engineers and managers can utilize to help them recognize how vulnerabilities are produced and discovered so that they can learn to circumvent them in future efforts. We conducted a systematic review of existing architectural practices, standards, security and coding practices, various threats, defects, and vulnerabilities that impact space systems from hundreds of relevant publications and interviews of subject matter experts. We expanded on the system-level body of knowledge for resiliency and identified a new software

  5. Connecting Architecture and Implementation

    Science.gov (United States)

    Buchgeher, Georg; Weinreich, Rainer

    Software architectures are still typically defined and described independently from implementation. To avoid architectural erosion and drift, architectural representation needs to be continuously updated and synchronized with system implementation. Existing approaches for architecture representation like informal architecture documentation, UML diagrams, and Architecture Description Languages (ADLs) provide only limited support for connecting architecture descriptions and implementations. Architecture management tools like Lattix, SonarJ, and Sotoarc and UML-tools tackle this problem by extracting architecture information directly from code. This approach works for low-level architectural abstractions like classes and interfaces in object-oriented systems but fails to support architectural abstractions not found in programming languages. In this paper we present an approach for linking and continuously synchronizing a formalized architecture representation to an implementation. The approach is a synthesis of functionality provided by code-centric architecture management and UML tools and higher-level architecture analysis approaches like ADLs.

  6. A Statistical Approach to Exoplanetary Molecular Spectroscopy Using Spitzer Eclipses

    Science.gov (United States)

    Deming, Drake; Garhart, Emily; Burrows, Adam; Fortney, Jonathan; Knutson, Heather; Todorov, Kamen

    2018-01-01

    Secondary eclipses of exoplanets observed using the Spitzer Space Telescope measure the total emission emergent from exoplanetary atmospheres integrated over broad photometric bands. Spitzer photometry is excellent for measuring day side temperatures, but is less well suited to the detection of molecular absorption or emission features. Even for very hot exoplanets, it can be difficult to attain the accuracy on eclipse depth that is needed to unambiguously interpret the Spitzer results in terms of molecular absorption or emission. However, a statistical approach, wherein we seek deviations from a simple blackbody planet as a function of the planet's equilibrium temperature, shows promise for defining the nature and strength of molecular absorption in ensembles of planets. In this paper, we explore such an approach using secondary eclipses observed for tens of hot exoplanets during Spitzer's Cycles 10, 12, and 13. We focus on the possibility that the hottest planets exhibit molecular features in emission, due to temperature inversions.

  7. Construction of a Hierarchical Architecture of Covalent Organic Frameworks via a Postsynthetic Approach.

    Science.gov (United States)

    Zhang, Gen; Tsujimoto, Masahiko; Packwood, Daniel; Duong, Nghia Tuan; Nishiyama, Yusuke; Kadota, Kentaro; Kitagawa, Susumu; Horike, Satoshi

    2018-02-21

    Covalent organic frameworks (COFs) represent an emerging class of crystalline porous materials that are constructed by the assembly of organic building blocks linked via covalent bonds. Several strategies have been developed for the construction of new COF structures; however, a facile approach to fabricate hierarchical COF architectures with controlled domain structures remains a significant challenge, and has not yet been achieved. In this study, a dynamic covalent chemistry (DCC)-based postsynthetic approach was employed at the solid-liquid interface to construct such structures. Two-dimensional imine-bonded COFs having different aromatic groups were prepared, and a homogeneously mixed-linker structure and a heterogeneously core-shell hollow structure were fabricated by controlling the reactivity of the postsynthetic reactions. Solid-state nuclear magnetic resonance (NMR) spectroscopy and transmission electron microscopy (TEM) confirmed the structures. COFs prepared by a postsynthetic approach exhibit several functional advantages compared with their parent phases. Their Brunauer-Emmett-Teller (BET) surface areas are 2-fold greater than those of their parent phases because of the higher crystallinity. In addition, the hydrophilicity of the material and the stepwise adsorption isotherms of H 2 O vapor in the hierarchical frameworks were precisely controlled, which was feasible because of the distribution of various domains of the two COFs by controlling the postsynthetic reaction. The approach opens new routes for constructing COF architectures with functionalities that are not possible in a single phase.

  8. AN ARCHITECTURAL APPROACH FOR QUALITY IMPROVING OF ANDROID APPLICATIONS DEVELOPMENT WHICH IMPLEMENTED TO COMMUNICATION APPLICATION FOR MECHATRONICS ROBOT LABORATORY ONAFT

    Directory of Open Access Journals (Sweden)

    V. Makarenko

    2017-11-01

    Full Text Available Developing a proper system architecture is a critical factor for the success of the project. After the analysisphase is complete, system design begins. For an effective solution developing it is very important that it will be flexible andscalable. During the system design, its component composition and development tools are determined. The system designphase is an opportunity to maximize the speed and effectiveness of subsequent development.There are quite a lot of architectural approaches for building systems. Despite their small differences, they have much incommon. They all define ways of splitting the application into separate layers. At the same time, in each system, at least, thereis a layer containing the business logic of the application, a layer of data interaction and a layer for displaying data.The "Clean Architecture" approach has been analyzed and adapted to the communication application for mechatronicsrobot laboratory developing. This approach allows to solve all the problems while building the application architecture: itmakes the code modular, tested and easily readable, and also positively affects the quality of development.New architectural components which was introduced by Google in 2017 was considered. The analysis showed that theArchitecture Components fit well into the concept and will interact with the "Clean Architecture" approach. Dagger 2framework was applied for a complete abstraction and simplify testing. Also, it is planned to implement the RxJava library.

  9. Deciphering the genomic architecture of the stickleback brain with a novel multilocus gene-mapping approach.

    Science.gov (United States)

    Li, Zitong; Guo, Baocheng; Yang, Jing; Herczeg, Gábor; Gonda, Abigél; Balázs, Gergely; Shikano, Takahito; Calboli, Federico C F; Merilä, Juha

    2017-03-01

    Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multilocus QTL-mapping approaches based on a de-biased LASSO method. Apart from having more statistical power to detect QTL and reduced rate of false positives than conventional QTL-mapping approaches, the developed methods can handle large marker panels and provide estimates of genomic heritability. Single-locus analyses of an F 2 interpopulation cross with 239 individuals and 15 198, fully informative single nucleotide polymorphisms (SNPs) uncovered 79 QTL associated with variation in stickleback brain size traits. Many of these loci were in strong linkage disequilibrium (LD) with each other, and consequently, a multilocus mapping of individual SNPs, accounting for LD structure in the data, recovered only four significant QTL. However, a multilocus mapping of SNPs grouped by linkage group (LG) identified 14 LGs (1-6 depending on the trait) that influence variation in brain traits. For instance, 17.6% of the variation in relative brain size was explainable by cumulative effects of SNPs distributed over six LGs, whereas 42% of the variation was accounted for by all 21 LGs. Hence, the results suggest that variation in stickleback brain traits is influenced by many small-effect loci. Apart from suggesting moderately heritable (h 2  ≈ 0.15-0.42) multifactorial genetic architecture of brain traits, the results highlight the challenges in identifying the loci contributing to variation in quantitative traits. Nevertheless, the results demonstrate that the novel QTL-mapping approach developed here has distinctive advantages

  10. On the EU approach for DEMO architecture exploration and dealing with uncertainties

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, M., E-mail: matti.coleman@euro-fusion.org [EUROfusion Consortium, Boltzmannstraße 2, 85748 Garching (Germany); CCFE Fusion Association, Culham Science Centre, Abingdon, Oxfordshire OX14 3DB (United Kingdom); Maviglia, F.; Bachmann, C. [EUROfusion Consortium, Boltzmannstraße 2, 85748 Garching (Germany); Anthony, J. [CCFE Fusion Association, Culham Science Centre, Abingdon, Oxfordshire OX14 3DB (United Kingdom); Federici, G. [EUROfusion Consortium, Boltzmannstraße 2, 85748 Garching (Germany); Shannon, M. [EUROfusion Consortium, Boltzmannstraße 2, 85748 Garching (Germany); CCFE Fusion Association, Culham Science Centre, Abingdon, Oxfordshire OX14 3DB (United Kingdom); Wenninger, R. [EUROfusion Consortium, Boltzmannstraße 2, 85748 Garching (Germany); Max-Planck-Institut für Plasmaphysik, 85748 Garching (Germany)

    2016-11-01

    Highlights: • The issue of epistemic uncertainties in the DEMO design basis is described. • An approach to tackle uncertainty by investigating plant architectures is proposed. • The first wall heat load uncertainty is addressed following the proposed approach. - Abstract: One of the difficulties inherent in designing a future fusion reactor is dealing with uncertainty. As the major step between ITER and the commercial exploitation of nuclear fusion energy, DEMO will have to address many challenges – the natures of which are still not fully known. Unlike fission reactors, fusion reactors suffer from the intrinsic complexity of the tokamak (numerous interdependent system parameters) and from the dependence of plasma physics on scale – prohibiting design exploration founded on incremental progression and small-scale experimentation. For DEMO, this means that significant technical uncertainties will exist for some time to come, and a systems engineering design exploration approach must be developed to explore the reactor architecture when faced with these uncertainties. Important uncertainties in the context of fusion reactor design are discussed and a strategy for dealing with these is presented, treating the uncertainty in the first wall loads as an example.

  11. Efficient Machine Learning Approach for Optimizing Scientific Computing Applications on Emerging HPC Architectures

    Energy Technology Data Exchange (ETDEWEB)

    Arumugam, Kamesh [Old Dominion Univ., Norfolk, VA (United States)

    2017-05-01

    the parallel implementation challenges of such irregular applications on different HPC architectures. In particular, we use supervised learning to predict the computation structure and use it to address the control-ow and memory access irregularities in the parallel implementation of such applications on GPUs, Xeon Phis, and heterogeneous architectures composed of multi-core CPUs with GPUs or Xeon Phis. We use numerical simulation of charged particles beam dynamics simulation as a motivating example throughout the dissertation to present our new approach, though they should be equally applicable to a wide range of irregular applications. The machine learning approach presented here use predictive analytics and forecasting techniques to adaptively model and track the irregular memory access pattern at each time step of the simulation to anticipate the future memory access pattern. Access pattern forecasts can then be used to formulate optimization decisions during application execution which improves the performance of the application at a future time step based on the observations from earlier time steps. In heterogeneous architectures, forecasts can also be used to improve the memory performance and resource utilization of all the processing units to deliver a good aggregate performance. We used these optimization techniques and anticipation strategy to design a cache-aware, memory efficient parallel algorithm to address the irregularities in the parallel implementation of charged particles beam dynamics simulation on different HPC architectures. Experimental result using a diverse mix of HPC architectures shows that our approach in using anticipation strategy is effective in maximizing data reuse, ensuring workload balance, minimizing branch and memory divergence, and in improving resource utilization.

  12. Molecular approaches to detect and study the organisms causing ...

    African Journals Online (AJOL)

    This review will summarise the molecular approaches used to detect and analyse the genomes of Babesia bovis, B. bigemina and Anaplasma marginale which cause bovine babesiosis and anaplasmosis. These tick borne diseases are widely distributed in Africa, Asia, Australia, and Central and South America and for ...

  13. Impact of contour on aesthetic judgments and approach-avoidance decisions in architecture

    Science.gov (United States)

    Vartanian, Oshin; Navarrete, Gorka; Chatterjee, Anjan; Fich, Lars Brorson; Leder, Helmut; Modroño, Cristián; Nadal, Marcos; Rostrup, Nicolai; Skov, Martin

    2013-01-01

    On average, we urban dwellers spend about 90% of our time indoors, and share the intuition that the physical features of the places we live and work in influence how we feel and act. However, there is surprisingly little research on how architecture impacts behavior, much less on how it influences brain function. To begin closing this gap, we conducted a functional magnetic resonance imaging study to examine how systematic variation in contour impacts aesthetic judgments and approach-avoidance decisions, outcome measures of interest to both architects and users of spaces alike. As predicted, participants were more likely to judge spaces as beautiful if they were curvilinear than rectilinear. Neuroanatomically, when contemplating beauty, curvilinear contour activated the anterior cingulate cortex exclusively, a region strongly responsive to the reward properties and emotional salience of objects. Complementing this finding, pleasantness—the valence dimension of the affect circumplex—accounted for nearly 60% of the variance in beauty ratings. Furthermore, activation in a distributed brain network known to underlie the aesthetic evaluation of different types of visual stimuli covaried with beauty ratings. In contrast, contour did not affect approach-avoidance decisions, although curvilinear spaces activated the visual cortex. The results suggest that the well-established effect of contour on aesthetic preference can be extended to architecture. Furthermore, the combination of our behavioral and neural evidence underscores the role of emotion in our preference for curvilinear objects in this domain. PMID:23754408

  14. A Study on Technology Architecture and Serving Approaches of Electronic Government System

    Science.gov (United States)

    Liu, Chunnian; Huang, Yiyun; Pan, Qin

    As E-government becomes a very active research area, a lot of solutions to solve citizens' needs are being deployed. This paper provides technology architecture of E-government system and approaches of service in Public Administrations. The proposed electronic system addresses the basic E-government requirements of user friendliness, security, interoperability, transparency and effectiveness in the communication between small and medium sized public organizations and their citizens, businesses and other public organizations. The paper has provided several serving approaches of E-government, which includes SOA, web service, mobile E-government, public library and every has its own characteristics and application scenes. Still, there are a number of E-government issues for further research on organization structure change, including research methodology, data collection analysis, etc.

  15. Implementing the competences-based students-centered learning approach in Architectural Design Education. The case of the T MEDA Pilot Architectural Program at the Hashemite University (Jordan

    Directory of Open Access Journals (Sweden)

    Ahmad A. S. Al Husban

    2016-11-01

    Full Text Available Higher educational systems become increasingly oriented towards the competences-based student-centered learning and outcome approach. Worldwide, these systems are focusing on the students as a whole: focusing on their dimensional, intellectual, professional, psychological, moral, and spiritual. This research was conducted in an attempt to answer the main research question: how can the architectural design courses be designed based on the required competences and how can the teaching, learning activities and assessment methods be structured and aligned in order to allow students to achieve and reach the intended learning outcomes? This research used a case study driven best practice research method to answer the research questions based on the T MEDA pilot architectural program that was implemented at the Hashemite University, Jordan. This research found that it is important for architectural education to adapt the students-centered learning method. Such approach increases the effectiveness of teaching and learning methods, enhances the design studio environment, and focuses on students’ engagement to develop their design process and product. Moreover, this research found that using different assessment methods in architectural design courses help students to develop their learning outcomes; and inform teachers about the effectiveness of their teaching process. Furthermore, the involvement of students in assessment produces effective learning and enhances their design motivation. However, applying competences-based students-centered learning and outcome approach needs more time and staff to apply. Another problem is that some instructors resist changing to the new methods or approaches because they prefer to use their old and traditional systems. The application for this method at the first time needs intensive recourses, more time, and good cooperation between different instructors and course coordinator. However, within the time this method

  16. Effects of Maternal Obesity on Fetal Programming: Molecular Approaches

    Science.gov (United States)

    Neri, Caterina; Edlow, Andrea G.

    2016-01-01

    Maternal obesity has become a worldwide epidemic. Obesity and a high-fat diet have been shown to have deleterious effects on fetal programming, predisposing offspring to adverse cardiometabolic and neurodevelopmental outcomes. Although large epidemiological studies have shown an association between maternal obesity and adverse outcomes for offspring, the underlying mechanisms remain unclear. Molecular approaches have played a key role in elucidating the mechanistic underpinnings of fetal malprogramming in the setting of maternal obesity. These approaches include, among others, characterization of epigenetic modifications, microRNA expression, the gut microbiome, the transcriptome, and evaluation of specific mRNA expression via quantitative reverse transcription polmerase chain reaction (RT-qPCR) in fetuses and offspring of obese females. This work will review the data from animal models and human fluids/cells regarding the effects of maternal obesity on fetal and offspring neurodevelopment and cardiometabolic outcomes, with a particular focus on molecular approaches. PMID:26337113

  17. Molecular imaging: a new approach to nuclear cardiology

    International Nuclear Information System (INIS)

    Dobrucki, L.W.; Sinusas, A.J.

    2005-01-01

    Nuclear cardiology has historically played an important role in detection of cardiovascular disease as well as risk statification. With the growth of molecular biology have come new therapeutic interventions and the requirement for new diagnostic imaging approaches. Noninvasive targeted radiotracer based as well as transporter gene imaging strategies are evolving to meet these new needs, but require the development of an interdisciplinary approach which focuses on molecular processes, as well as the pathogenesis and progression of disease. This progress has been made possible with the availability of transgenic animal models along with many technological advances. Future adaptations of the developing experimental procedures and instrumentations will allow for the smooth translation and application to clinical practice. This review is intended as a brief overview on the subject molecular imaging. Basic concepts and historical perspective of molecular imaging will be reviewed first, followed by description of current technology, and concluding with current applications in cardiology. The emphasis will be on the use of both single photon emission computed tomography (SPECT) and positron emission tomography (PET) radiotracers, although other imaging modalities will be also briefly discussed. The specific approaches presented here will include receptor-based and reporter gene imaging of natural and therapeutical angiogenesis

  18. Novel approach to improve molecular imaging research: Correlation between macroscopic and molecular pathological findings in patients

    Energy Technology Data Exchange (ETDEWEB)

    Boehm, Ingrid, E-mail: i.boehm@uni-bonn.de [Department of Diagnostic Radiology, ZARF Project, Center for Molecular Imaging Research MBMB, Philipps University of Marburg, Baldingerstrasse, 35039 Marburg (Germany)

    2011-09-15

    Purpose: Currently, clinical research approaches are sparse in molecular imaging studies. Moreover, possible links between imaging features and pathological laboratory parameters are unknown, so far. Therefore, the goal was to find a possible relationship between imaging features and peripheral blood cell apoptosis, and thereby to present a novel way to complement molecular imaging research. Materials and methods: The investigation has been done in systemic lupus erythematosus (SLE), a prototype of an autoimmune disease characterized by multiorgan involvement, autoantibody production, and disturbed apoptosis. Retrospectively, radiological findings have been compared to both autoantibody findings and percentage apoptotic blood cells. Results: Two SLE groups could be identified: patients with normal (annexin V binding < 20%), and with increased apoptosis (annexin V binding > 20%) of peripheral blood cells. The frequency of radiological examinations in SLE patients significantly correlated with an increased percentage of apoptotic cells (p < 0.005). In patients with characteristic imaging findings (e.g. lymph node swelling, pleural effusion) an elevated percentage of apoptotic cells was present. In contrast SLE-patients with normal imaging findings or uncharacteristic results of minimal severity had normal percentages of apoptotic blood cells. Conclusion: This correlation between radiographic findings and percentage of apoptotic blood cells provides (1) further insight into pathological mechanisms of SLE, (2) will offer the possibility to introduce apoptotic biomarkers as molecular probes for clinical molecular imaging approaches in future to early diagnose organ complaints in patients with SLE, and (3) is a plea to complement molecular imaging research by this clinical approach.

  19. Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and Its Interaction with Contactin 2 (CNTN2)*

    Science.gov (United States)

    Lu, Zhuoyang; Reddy, M. V. V. V. Sekhar; Liu, Jianfang; Kalichava, Ana; Liu, Jiankang; Zhang, Lei; Chen, Fang; Wang, Yun; Holthauzen, Luis Marcelo F.; White, Mark A.; Seshadrinathan, Suchithra; Zhong, Xiaoying; Ren, Gang; Rudenko, Gabby

    2016-01-01

    Contactin-associated protein-like 2 (CNTNAP2) is a large multidomain neuronal adhesion molecule implicated in a number of neurological disorders, including epilepsy, schizophrenia, autism spectrum disorder, intellectual disability, and language delay. We reveal here by electron microscopy that the architecture of CNTNAP2 is composed of a large, medium, and small lobe that flex with respect to each other. Using epitope labeling and fragments, we assign the F58C, L1, and L2 domains to the large lobe, the FBG and L3 domains to the middle lobe, and the L4 domain to the small lobe of the CNTNAP2 molecular envelope. Our data reveal that CNTNAP2 has a very different architecture compared with neurexin 1α, a fellow member of the neurexin superfamily and a prototype, suggesting that CNTNAP2 uses a different strategy to integrate into the synaptic protein network. We show that the ectodomains of CNTNAP2 and contactin 2 (CNTN2) bind directly and specifically, with low nanomolar affinity. We show further that mutations in CNTNAP2 implicated in autism spectrum disorder are not segregated but are distributed over the whole ectodomain. The molecular shape and dimensions of CNTNAP2 place constraints on how CNTNAP2 integrates in the cleft of axo-glial and neuronal contact sites and how it functions as an organizing and adhesive molecule. PMID:27621318

  20. BUBBLE UP: ALTERNATIVE APPROACHES TO RESEARCH IN THE ACADEMIC ARCHITECTURE STUDIO

    Directory of Open Access Journals (Sweden)

    Gregory Marinic

    2010-07-01

    Full Text Available Increased connectivity among the design disciplines has radically transformed the nature of building today. Architectural education must accordingly adapt to the emerging needs of our changing built environment by providing vital, flexible, and open learning environments. Pedagogies in the academy have typically been rooted in practices that are both reluctant to change and slow to address transformative forces in an honest and open manner. Regrettably, the resilience of such top-down methods continues to bias the lens of learning toward natural performers and the notion of singular genius. Authentic attempts to react to new demands and to introduce change are all too often met with both strong resistance and profound contempt by conservative critics. Mainline architectural academia continues to project a deep ambivalence to new methodologies, alternative approaches to context, broadened conceptual practices, and advanced visualization techniques. Yet such means provide a responsive and resilient structure to re-frame content, expedite delivery, and update pedagogical objectives for the next generation.

  1. Art as behaviour--an ethological approach to visual and verbal art, music and architecture.

    Science.gov (United States)

    Sütterlin, Christa; Schiefenhövel, Wulf; Lehmann, Christian; Forster, Johanna; Apfelauer, Gerhard

    2014-01-01

    In recent years, the fine arts, architecture, music and literature have increasingly been examined from the vantage point of human ethology and evolutionary psychology. In 2011 the authors formed the research group 'Ethology of the Arts' concentrating on the evolution and biology of perception and behaviour. These novel approaches aim at a better understanding of the various facets represented by the arts by taking into focus possible phylogenetic adaptations, which have shaped the artistic capacities of our ancestors. Rather than culture specificity, which is stressed e.g. by cultural anthropology and numerous other disciplines, universal human tendencies to perceive, feel, think and behave are postulated. Artistic expressive behaviour is understood as an integral part of the human condition, whether expressed in ritual, visual, verbal or musical art. The Ethology of the Arts-group's research focuses on visual and verbal art, music and built environment/architecture and is designed to contribute to the incipient interdisciplinarity in the field of evolutionary art research.

  2. A State-Based Modeling Approach for Efficient Performance Evaluation of Embedded System Architectures at Transaction Level

    Directory of Open Access Journals (Sweden)

    Anthony Barreteau

    2012-01-01

    Full Text Available Abstract models are necessary to assist system architects in the evaluation process of hardware/software architectures and to cope with the still increasing complexity of embedded systems. Efficient methods are required to create reliable models of system architectures and to allow early performance evaluation and fast exploration of the design space. In this paper, we present a specific transaction level modeling approach for performance evaluation of hardware/software architectures. This approach relies on a generic execution model that exhibits light modeling effort. Created models are used to evaluate by simulation expected processing and memory resources according to various architectures. The proposed execution model relies on a specific computation method defined to improve the simulation speed of transaction level models. The benefits of the proposed approach are highlighted through two case studies. The first case study is a didactic example illustrating the modeling approach. In this example, a simulation speed-up by a factor of 7,62 is achieved by using the proposed computation method. The second case study concerns the analysis of a communication receiver supporting part of the physical layer of the LTE protocol. In this case study, architecture exploration is led in order to improve the allocation of processing functions.

  3. Adult soft tissue sarcomas: conventional therapies and molecularly targeted approaches.

    Science.gov (United States)

    Mocellin, Simone; Rossi, Carlo R; Brandes, Alba; Nitti, Donato

    2006-02-01

    The therapeutic approach to soft tissue sarcomas (STS) has evolved over the past two decades based on the results from randomized controlled trials, which are guiding physicians in the treatment decision-making process. Despite significant improvements in the control of local disease, a significant number of patients ultimately die of recurrent/metastatic disease following radical surgery due to a lack of effective adjuvant treatments. In addition, the characteristic chemoresistance of STS has compromised the therapeutic value of conventional antineoplastic agents in cases of unresectable advanced/metastatic disease. Therefore, novel therapeutic strategies are urgently needed to improve the prognosis of patients with STS. Recent advances in STS biology are paving the way to the development of molecularly targeted therapeutic strategies, the efficacy of which relies not only on the knowledge of the molecular mechanisms underlying cancer development/progression but also on the personalization of the therapeutic regimen according to the molecular features of individual tumours. In this work, we review the state-of-the-art of conventional treatments for STS and summarize the most promising findings in the development of molecularly targeted therapeutic approaches.

  4. Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

    Science.gov (United States)

    Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V.; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A.; Cichewicz, Robert H.; Alexandrov, Theodore

    2016-01-01

    ABSTRACT Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define

  5. An urban informatics approach to smart city learning in architecture and urban design education

    Directory of Open Access Journals (Sweden)

    Mirko Guaralda

    2013-08-01

    Full Text Available This study aims to redefine spaces of learning to places of learning through the direct engagement of local communities as a way to examine and learn from real world issues in the city. This paper exemplifies Smart City Learning, where the key goal is to promote the generation and exchange of urban design ideas for the future development of South Bank, in Brisbane, Australia, informing the creation of new design policies responding to the needs of local citizens. Specific to this project was the implementation of urban informatics techniques and approaches to promote innovative engagement strategies. Architecture and Urban Design students were encouraged to review and appropriate real-time, ubiquitous technology, social media, and mobile devices that were used by urban residents to augment and mediate the physical and digital layers of urban infrastructures. Our study’s experience found that urban informatics provide an innovative opportunity to enrich students’ place of learning within the city.

  6. Stability of nanofluids: Molecular dynamic approach and experimental study

    International Nuclear Information System (INIS)

    Farzaneh, H.; Behzadmehr, A.; Yaghoubi, M.; Samimi, A.; Sarvari, S.M.H.

    2016-01-01

    Highlights: • Nanofluid stability is investigated and discussed. • A molecular dynamic approach, considering different forces on the nanoparticles, is adopted. • Stability diagrams are presented for different thermo-fluid conditions. • An experimental investigation is carried out to confirm the theoretical approach. - Abstract: Nanofluids as volumetric absorbent in solar energy conversion devices or as working fluid in different heat exchangers have been proposed by various researchers. However, dispersion stability of nanofluids is an important issue that must be well addressed before any industrial applications. Conditions such as severe temperature gradient, high temperature of heat transfer fluid, nanoparticle mean diameters and types of nanoparticles and base fluid are among the most effective parameters on the stability of nanofluid. A molecular dynamic approach, considering kinetic energy of nanoparticles and DLVO potential energy between nanoparticles, is adopted to study the nanofluid stability for different nanofluids at different working conditions. Different forces such as Brownian, thermophoresis, drag and DLVO are considered to introduce the stability diagrams. The latter presents the conditions for which a nanofluid can be stable. In addition an experimental investigation is carried out to find a stable nanofluid and to show the validity of the theoretical approach. There is a good agreement between the experimental and theoretical results that confirms the validity of our theoretical approach.

  7. Toward an Agile Approach to Managing the Effect of Requirements on Software Architecture during Global Software Development

    Directory of Open Access Journals (Sweden)

    Abdulaziz Alsahli

    2016-01-01

    Full Text Available Requirement change management (RCM is a critical activity during software development because poor RCM results in occurrence of defects, thereby resulting in software failure. To achieve RCM, efficient impact analysis is mandatory. A common repository is a good approach to maintain changed requirements, reusing and reducing effort. Thus, a better approach is needed to tailor knowledge for better change management of requirements and architecture during global software development (GSD.The objective of this research is to introduce an innovative approach for handling requirements and architecture changes simultaneously during global software development. The approach makes use of Case-Based Reasoning (CBR and agile practices. Agile practices make our approach iterative, whereas CBR stores requirements and makes them reusable. Twin Peaks is our base model, meaning that requirements and architecture are handled simultaneously. For this research, grounded theory has been applied; similarly, interviews from domain experts were conducted. Interview and literature transcripts formed the basis of data collection in grounded theory. Physical saturation of theory has been achieved through a published case study and developed tool. Expert reviews and statistical analysis have been used for evaluation. The proposed approach resulted in effective change management of requirements and architecture simultaneously during global software development.

  8. New approaches in mathematical biology: Information theory and molecular machines

    International Nuclear Information System (INIS)

    Schneider, T.

    1995-01-01

    My research uses classical information theory to study genetic systems. Information theory was founded by Claude Shannon in the 1940's and has had an enormous impact on communications engineering and computer sciences. Shannon found a way to measure information. This measure can be used to precisely characterize the sequence conservation at nucleic-acid binding sites. The resulting methods, by completely replacing the use of ''consensus sequences'', provide better models for molecular biologists. An excess of conservation led us to do experimental work on bacteriophage T7 promoters and the F plasmid IncD repeats. The wonderful fidelity of telephone communications and compact disk (CD) music can be traced directly to Shannon's channel capacity theorem. When rederived for molecular biology, this theorem explains the surprising precision of many molecular events. Through connections with the Second Law of Thermodyanmics and Maxwell's Demon, this approach also has implications for the development of technology at the molecular level. Discussions of these topics are held on the internet news group bionet.info-theo. (author). (Abstract only)

  9. ADAPTIVE REUSE FOR NEW SOCIAL AND MUNICIPAL FUNCTIONS AS AN ACCEPTABLE APPROACH FOR CONSERVATION OF INDUSTRIAL HERITAGE ARCHITECTURE IN THE CZECH REPUBLIC

    Directory of Open Access Journals (Sweden)

    Oleg Fetisov

    2016-04-01

    Full Text Available The present paper deals with a problem of conservation and adaptive reuse of industrial heritage architecture. The relevance and topicality of the problem of adaptive reuse of industrial heritage architecture for new social and municipal functions as the conservation concept are defined. New insights on the typology of industrial architecture are reviewed (e. g. global changes in all European industry, new concepts and technologies in manufacturing, new features of industrial architecture and their construction and typology, first results of industrialization and changes in the typology of industrial architecture in post-industrial period. General goals and tasks of conservation in context of adaptive reuse of industrial heritage architecture are defined (e. g. historical, architectural and artistic, technical. Adaptive reuse as an acceptable approach for conservation and new use is proposed and reviewed. Moreover, the logical model of adaptive reuse of industrial heritage architecture as an acceptable approach for new use has been developed. Consequently, three general methods for the conservation of industrial heritage architecture by the adaptive reuse approach are developed: historical, architectural and artistic, technical. Relevant functional methods' concepts (social concepts are defined and classified. General beneficial effect of the adaptive reuse approach is given. On the basis of analysis results of experience in adaptive reuse of industrial architecture with new social functions general conclusions are developed.

  10. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Science.gov (United States)

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  11. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Directory of Open Access Journals (Sweden)

    Satish K Guttikonda

    Full Text Available Demand for the commercial use of genetically modified (GM crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  12. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun Ki; Herbst, Roy

    2006-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  13. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun K; Herbst, Roy

    2008-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  14. IMPACT (Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets and Complementary, Innovative and Therapeutic Modalities)

    National Research Council Canada - National Science Library

    Hong, Waun K; Herbst, Roy

    2007-01-01

    .... These projects combine targeted approaches using molecular and imaging techniques to validate activity against a target and monitor response using imaging modalities specific to the receptor using...

  15. Clustering Approaches for Pragmatic Two-Layer IoT Architecture

    Directory of Open Access Journals (Sweden)

    J. Sathish Kumar

    2018-01-01

    Full Text Available Connecting all devices through Internet is now practical due to Internet of Things. IoT assures numerous applications in everyday life of common people, government bodies, business, and society as a whole. Collaboration among the devices in IoT to bring various applications in the real world is a challenging task. In this context, we introduce an application-based two-layer architectural framework for IoT which consists of sensing layer and IoT layer. For any real-time application, sensing devices play an important role. Both these layers are required for accomplishing IoT-based applications. The success of any IoT-based application relies on efficient communication and utilization of the devices and data acquired by the devices at both layers. The grouping of these devices helps to achieve the same, which leads to formation of cluster of devices at various levels. The clustering helps not only in collaboration but also in prolonging overall network lifetime. In this paper, we propose two clustering algorithms based on heuristic and graph, respectively. The proposed clustering approaches are evaluated on IoT platform using standard parameters and compared with different approaches reported in literature.

  16. Exploring a model-driven architecture (MDA) approach to health care information systems development.

    Science.gov (United States)

    Raghupathi, Wullianallur; Umar, Amjad

    2008-05-01

    To explore the potential of the model-driven architecture (MDA) in health care information systems development. An MDA is conceptualized and developed for a health clinic system to track patient information. A prototype of the MDA is implemented using an advanced MDA tool. The UML provides the underlying modeling support in the form of the class diagram. The PIM to PSM transformation rules are applied to generate the prototype application from the model. The result of the research is a complete MDA methodology to developing health care information systems. Additional insights gained include development of transformation rules and documentation of the challenges in the application of MDA to health care. Design guidelines for future MDA applications are described. The model has the potential for generalizability. The overall approach supports limited interoperability and portability. The research demonstrates the applicability of the MDA approach to health care information systems development. When properly implemented, it has the potential to overcome the challenges of platform (vendor) dependency, lack of open standards, interoperability, portability, scalability, and the high cost of implementation.

  17. Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture.

    Science.gov (United States)

    Matvienko, Sergey; Alemasov, Nikolay; Fomin, Eduard

    2015-02-01

    Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.

  18. Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

    Science.gov (United States)

    Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

    2014-01-01

    This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems.

  19. Lightweight enterprise architectures

    CERN Document Server

    Theuerkorn, Fenix

    2004-01-01

    STATE OF ARCHITECTUREArchitectural ChaosRelation of Technology and Architecture The Many Faces of Architecture The Scope of Enterprise Architecture The Need for Enterprise ArchitectureThe History of Architecture The Current Environment Standardization Barriers The Need for Lightweight Architecture in the EnterpriseThe Cost of TechnologyThe Benefits of Enterprise Architecture The Domains of Architecture The Gap between Business and ITWhere Does LEA Fit? LEA's FrameworkFrameworks, Methodologies, and Approaches The Framework of LEATypes of Methodologies Types of ApproachesActual System Environmen

  20. Percolation approach for atomic and molecular cluster formation

    International Nuclear Information System (INIS)

    Knospe, O.; Seifert, G.

    1987-12-01

    We apply a percolation approach for the theoretical analysis of mass spectra of molecular microclusters obtained by adiabatic expansion technique. The evolution of the shape of the experimental size distributions as function of stagnation pressure and stagnation temperature are theoretically reproduced by varying the percolation parameter. Remaining discrepancies between theory and experiment are discussed. In addition, the even-odd alternation as well as the 'magic' shell structure within metallic, secondary ion mass spectra are investigated by introducing statistical weights for the cluster formation probabilities. Shell correction energies of atomic clusters as function of cluster-size are deduced from the experimental data. (orig.)

  1. Toward an Agile Approach to Managing the Effect of Requirements on Software Architecture during Global Software Development

    OpenAIRE

    Alsahli, Abdulaziz; Khan, Hameed; Alyahya, Sultan

    2016-01-01

    Requirement change management (RCM) is a critical activity during software development because poor RCM results in occurrence of defects, thereby resulting in software failure. To achieve RCM, efficient impact analysis is mandatory. A common repository is a good approach to maintain changed requirements, reusing and reducing effort. Thus, a better approach is needed to tailor knowledge for better change management of requirements and architecture during global software development (GSD).The o...

  2. The Molecular Architecture of Cell Adhesion: Dynamic Remodeling Revealed by Videonanoscopy

    Directory of Open Access Journals (Sweden)

    Arnauld eSergé

    2016-05-01

    Full Text Available The plasma membrane delimits the cell, which is the basic unit of living organisms, and is also a privileged site for cell communication with the environment. Cell adhesion can occur through cell-cell and cell-matrix contacts. Adhesion proteins such as integrins and cadherins also constitute receptors for inside-out and outside-in signaling within proteolipidic platforms. Adhesion molecule targeting and stabilization relies on specific features such as preferential segregation by the sub-membrane cytoskeleton meshwork and within membrane proteolipidic microdomains. This review presents an overview of the recent insights brought by the latest developments in microscopy, to unravel the molecular remodeling occurring at cell contacts. The dynamic aspect of cell adhesion was recently highlighted by super-resolution videomicroscopy, also named videonanoscopy. By circumventing the diffraction limit of light, nanoscopy has allowed the monitoring of molecular localization and behavior at the single-molecule level, on fixed and living cells. Accessing molecular-resolution details such as quantitatively monitoring components entering and leaving cell contacts by lateral diffusion and reversible association has revealed an unexpected plasticity. Adhesion structures can be highly specialized, such as focal adhesion in motile cells, as well as immune and neuronal synapses. Spatiotemporal reorganization of adhesion molecules, receptors and adaptors directly relates to structure/function modulation. Assembly of these supramolecular complexes is continuously balanced by dynamic events, remodeling adhesions on various timescales, notably by molecular conformation switches, lateral diffusion within the membrane and endo/exocytosis. Pathological alterations in cell adhesion are involved in cancer evolution, through cancer stem cell interaction with stromal niches, growth, extravasation and metastasis.

  3. An end-to-end security auditing approach for service oriented architectures

    NARCIS (Netherlands)

    Azarmi, M.; Bhargava, B.; Angin, P.; Ranchal, R.; Ahmed, N.; Sinclair, A.; Linderman, M.; Ben Othmane, L.

    2012-01-01

    Service-Oriented Architecture (SOA) is becoming a major paradigm for distributed application development in the recent explosion of Internet services and cloud computing. However, SOA introduces new security challenges not present in the single-hop client-server architectures due to the involvement

  4. Investigating the Role of Cultural Capital and Organisational Habitus in Architectural Education: A Case Study Approach

    Science.gov (United States)

    Payne, Jennifer Chamberlin

    2015-01-01

    Compared to other professions in recent years, architecture has lagged woefully behind in attracting and retaining a diverse population, as defined by class, race and gender. This research investigates the extent to which architecture culturally reproduces itself, specifically examining the socialisation process of students into the subculture of…

  5. Molecular basis of glyphosate resistance: Different approaches through protein engineering

    Science.gov (United States)

    Pollegioni, Loredano; Schonbrunn, Ernst; Siehl, Daniel

    2011-01-01

    Glyphosate (N-phosphonomethyl-glycine) is the most-used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. The extraordinary success of this simple small molecule is mainly due to the high specificity of glyphosate towards the plant enzyme enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway leading to biosynthesis of aromatic amino acids. Starting in 1996, transgenic glyphosate-resistant plants were introduced thus allowing the application of the herbicide to the crop (post-emergence) to remove emerged weeds without crop damage. This review focuses on the evolution of mechanisms of resistance to glyphosate as obtained through natural diversity, the gene shuffling approach to molecular evolution, and a rational, structure-based approach to protein engineering. In addition, we offer rationale for the means by which the modifications made have had their intended effect. PMID:21668647

  6. The influence of molecular architecture and solvent type on the size and structure of poly(benzyl ether) dendrimers by SANS

    NARCIS (Netherlands)

    Evmenenko, G.; Bauer, B.J.; Kleppinger, R.; Forier, B.; Dehaen, W.; Amis, E.J.; Mischenko, N.; Reynaers, H.

    2001-01-01

    The size of poly(benzyl ether) dendrimers with different molecular architectures was measured by small angle neutron scattering (SANS). Both polar and non-polar solvents were used to measure the effect of solvent type. The radius of gyration (Rg) of all of the dendrimers follows a scaling law of Rg

  7. Presenting an Approach for Conducting Knowledge Architecture within Large-Scale Organizations.

    Science.gov (United States)

    Varaee, Touraj; Habibi, Jafar; Mohaghar, Ali

    2015-01-01

    Knowledge architecture (KA) establishes the basic groundwork for the successful implementation of a short-term or long-term knowledge management (KM) program. An example of KA is the design of a prototype before a new vehicle is manufactured. Due to a transformation to large-scale organizations, the traditional architecture of organizations is undergoing fundamental changes. This paper explores the main strengths and weaknesses in the field of KA within large-scale organizations and provides a suitable methodology and supervising framework to overcome specific limitations. This objective was achieved by applying and updating the concepts from the Zachman information architectural framework and the information architectural methodology of enterprise architecture planning (EAP). The proposed solution may be beneficial for architects in knowledge-related areas to successfully accomplish KM within large-scale organizations. The research method is descriptive; its validity is confirmed by performing a case study and polling the opinions of KA experts.

  8. Presenting an Approach for Conducting Knowledge Architecture within Large-Scale Organizations

    Science.gov (United States)

    Varaee, Touraj; Habibi, Jafar; Mohaghar, Ali

    2015-01-01

    Knowledge architecture (KA) establishes the basic groundwork for the successful implementation of a short-term or long-term knowledge management (KM) program. An example of KA is the design of a prototype before a new vehicle is manufactured. Due to a transformation to large-scale organizations, the traditional architecture of organizations is undergoing fundamental changes. This paper explores the main strengths and weaknesses in the field of KA within large-scale organizations and provides a suitable methodology and supervising framework to overcome specific limitations. This objective was achieved by applying and updating the concepts from the Zachman information architectural framework and the information architectural methodology of enterprise architecture planning (EAP). The proposed solution may be beneficial for architects in knowledge-related areas to successfully accomplish KM within large-scale organizations. The research method is descriptive; its validity is confirmed by performing a case study and polling the opinions of KA experts. PMID:25993414

  9. A parallel 3-D discrete wavelet transform architecture using pipelined lifting scheme approach for video coding

    Science.gov (United States)

    Hegde, Ganapathi; Vaya, Pukhraj

    2013-10-01

    This article presents a parallel architecture for 3-D discrete wavelet transform (3-DDWT). The proposed design is based on the 1-D pipelined lifting scheme. The architecture is fully scalable beyond the present coherent Daubechies filter bank (9, 7). This 3-DDWT architecture has advantages such as no group of pictures restriction and reduced memory referencing. It offers low power consumption, low latency and high throughput. The computing technique is based on the concept that lifting scheme minimises the storage requirement. The application specific integrated circuit implementation of the proposed architecture is done by synthesising it using 65 nm Taiwan Semiconductor Manufacturing Company standard cell library. It offers a speed of 486 MHz with a power consumption of 2.56 mW. This architecture is suitable for real-time video compression even with large frame dimensions.

  10. Molecular Therapeutic Approaches for Pediatric Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Sarah K Tasian

    2014-03-01

    Full Text Available Approximately two thirds of children with acute myeloid leukemia (AML are cured with intensive multi-agent chemotherapy. However, primary chemorefractory and relapsed AML remains a significant source of childhood cancer mortality, highlighting the need for new therapies. Further therapy intensification with traditional cytotoxic agents is not feasible given the potential for significant toxicity to normal tissues with conventional chemotherapy and the risk for long-term end-organ dysfunction. Significant emphasis has been placed upon the development of molecularly targeted therapeutic approaches for adults and children with high-risk subtypes of AML with the goal of improving remission induction and minimizing relapse. Several promising agents are currently in clinical testing or late preclinical development for AML, including monoclonal antibodies against leukemia cell surface proteins, kinase inhibitors, proteasome inhibitors, epigenetic agents, and chimeric antigen receptor engineered T cell immunotherapies. Many of these therapies have been specifically tested in children with relapsed/refractory AML via phase 1 and 2 trials with a smaller number of new agents under phase 3 evaluation for children with de novo AML. Although successful identification and implementation of new drugs for children with AML remains a formidable challenge, enthusiasm for novel molecular therapeutic approaches is great given the potential for significant clinical benefit for children who will otherwise fail standard therapy.

  11. Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-core Architectures

    Energy Technology Data Exchange (ETDEWEB)

    Aktulga, Hasan Metin [Michigan State Univ., East Lansing, MI (United States); Coffman, Paul [Argonne National Lab. (ANL), Argonne, IL (United States); Shan, Tzu-Ray [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Knight, Chris [Argonne National Lab. (ANL), Argonne, IL (United States); Jiang, Wei [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-12-01

    Hybrid parallelism allows high performance computing applications to better leverage the increasing on-node parallelism of modern supercomputers. In this paper, we present a hybrid parallel implementation of the widely used LAMMPS/ReaxC package, where the construction of bonded and nonbonded lists and evaluation of complex ReaxFF interactions are implemented efficiently using OpenMP parallelism. Additionally, the performance of the QEq charge equilibration scheme is examined and a dual-solver is implemented. We present the performance of the resulting ReaxC-OMP package on a state-of-the-art multi-core architecture Mira, an IBM BlueGene/Q supercomputer. For system sizes ranging from 32 thousand to 16.6 million particles, speedups in the range of 1.5-4.5x are observed using the new ReaxC-OMP software. Sustained performance improvements have been observed for up to 262,144 cores (1,048,576 processes) of Mira with a weak scaling efficiency of 91.5% in larger simulations containing 16.6 million particles.

  12. Molecular architecture of electroactive and biodegradable copolymers composed of polylactide and carboxyl-capped aniline trimer.

    Science.gov (United States)

    Guo, Baolin; Finne-Wistrand, Anna; Albertsson, Ann-Christine

    2010-04-12

    Two-, four-, and six-armed branched copolymers with electroactive and biodegradable properties were synthesized by coupling reactions between poly(l-lactides) (PLLAs) with different architecture and carboxyl-capped aniline trimer (CCAT). The aniline oligomer CCAT was prepared from amino-capped aniline trimer and succinic anhydride. FT-IR, NMR, and SEC analyses confirmed the structure of the branched copolymers. UV-vis spectra and cyclic voltammetry of CCAT and copolymer solution showed good electroactive properties, similar to those of polyaniline. The water contact angle of the PLLAs was the highest, followed by the undoped copolymer and the doped copolymers. The values of doped four-armed copolymers were 54-63 degrees . Thermal properties of the polymers were studied by DSC and TGA. The copolymers had better thermal stability than the pure PLLAs, and the T(g) between 48-58 degrees C and T(m) between 146-177 degrees C of the copolymers were lower than those of the pure PLLA counterparts. This kind of electroactive and biodegradable copolymer has a great potential for applications in cardiovascular or neuronal tissue engineering.

  13. Approach to design neural cryptography: a generalized architecture and a heuristic rule.

    Science.gov (United States)

    Mu, Nankun; Liao, Xiaofeng; Huang, Tingwen

    2013-06-01

    Neural cryptography, a type of public key exchange protocol, is widely considered as an effective method for sharing a common secret key between two neural networks on public channels. How to design neural cryptography remains a great challenge. In this paper, in order to provide an approach to solve this challenge, a generalized network architecture and a significant heuristic rule are designed. The proposed generic framework is named as tree state classification machine (TSCM), which extends and unifies the existing structures, i.e., tree parity machine (TPM) and tree committee machine (TCM). Furthermore, we carefully study and find that the heuristic rule can improve the security of TSCM-based neural cryptography. Therefore, TSCM and the heuristic rule can guide us to designing a great deal of effective neural cryptography candidates, in which it is possible to achieve the more secure instances. Significantly, in the light of TSCM and the heuristic rule, we further expound that our designed neural cryptography outperforms TPM (the most secure model at present) on security. Finally, a series of numerical simulation experiments are provided to verify validity and applicability of our results.

  14. Evidence and speculation: reimagining approaches to architecture and research within the paediatric hospital.

    Science.gov (United States)

    McLaughlan, Rebecca; Pert, Alan

    2017-11-25

    As the dominant research paradigm within the construction of contemporary healthcare facilities, evidence-based design (EBD) will increasingly impact our expectations of what hospital architecture should be. Research methods within EBD focus on prototyping incremental advances and evaluating what has already been built. Yet medical care is a rapidly evolving system; changes to technology, workforce composition, patient demographics and funding models can create rapid and unpredictable changes to medical practice and modes of care. This dynamism has the potential to curtail or negate the usefulness of current best practice approaches. To imagine new directions for the role of the hospital in society, or innovative ways in which the built environment might support well-being, requires a model that can project beyond existing constraints. Speculative design employs a design-based research methodology to imagine alternative futures and uses the artefacts created through this process to enable broader critical reflection on existing practices. This paper examines the contribution of speculative design within the context of the paediatric hospital as a means of facilitating critical reflection regarding the design of new healthcare facilities. While EBD is largely limited by what has already been built, speculative design offers a complementary research method to meet this limitation. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  15. A Service Oriented Architecture Approach to Achieve Interoperability between Immunization Information Systems in Iran.

    Science.gov (United States)

    Hosseini, Masoud; Ahmadi, Maryam; Dixon, Brian E

    2014-01-01

    Clinical decision support (CDS) systems can support vaccine forecasting and immunization reminders; however, immunization decision-making requires data from fragmented, independent systems. Interoperability and accurate data exchange between immunization information systems (IIS) is an essential factor to utilize Immunization CDS systems. Service oriented architecture (SOA) and Health Level 7 (HL7) are dominant standards for web-based exchange of clinical information. We implemented a system based on SOA and HL7 v3 to support immunization CDS in Iran. We evaluated system performance by exchanging 1500 immunization records for roughly 400 infants between two IISs. System turnaround time is less than a minute for synchronous operation calls and the retrieved immunization history of infants were always identical in different systems. CDS generated reports were accordant to immunization guidelines and the calculations for next visit times were accurate. Interoperability is rare or nonexistent between IIS. Since inter-state data exchange is rare in United States, this approach could be a good prototype to achieve interoperability of immunization information.

  16. A Cut-and-Paste Approach to 3D Graphene-Oxide-Based Architectures.

    Science.gov (United States)

    Luo, Chong; Yeh, Che-Ning; Baltazar, Jesus M Lopez; Tsai, Chao-Lin; Huang, Jiaxing

    2018-04-01

    Properly cut sheets can be converted into complex 3D structures by three basic operations including folding, bending, and pasting to render new functions. Folding and bending are extensively employed in crumpling, origami, and pop-up fabrications for 3D structures. Pasting joins different parts of a material together, and can create new geometries that are fundamentally unattainable by folding and bending. However, it has been much less explored, likely due to limited choice of weldable thin film materials and residue-free glues. Here it is shown that graphene oxide (GO) paper is one such suitable material. Stacked GO sheets can be readily loosened up and even redispersed in water, which upon drying, restack to form solid structures. Therefore, water can be utilized to heal local damage, glue separated pieces, and release internal stress in bent GO papers to fix their shapes. Complex and dynamic 3D GO architectures can thus be fabricated by a cut-and-paste approach, which is also applicable to GO-based hybrid with carbon nanotubes or clay sheets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. A conceptual approach to approximate tree root architecture in infinite slope models

    Science.gov (United States)

    Schmaltz, Elmar; Glade, Thomas

    2016-04-01

    Vegetation-related properties - particularly tree root distribution and coherent hydrologic and mechanical effects on the underlying soil mantle - are commonly not considered in infinite slope models. Indeed, from a geotechnical point of view, these effects appear to be difficult to be reproduced reliably in a physically-based modelling approach. The growth of a tree and the expansion of its root architecture are directly connected with both intrinsic properties such as species and age, and extrinsic factors like topography, availability of nutrients, climate and soil type. These parameters control four main issues of the tree root architecture: 1) Type of rooting; 2) maximum growing distance to the tree stem (radius r); 3) maximum growing depth (height h); and 4) potential deformation of the root system. Geometric solids are able to approximate the distribution of a tree root system. The objective of this paper is to investigate whether it is possible to implement root systems and the connected hydrological and mechanical attributes sufficiently in a 3-dimensional slope stability model. Hereby, a spatio-dynamic vegetation module should cope with the demands of performance, computation time and significance. However, in this presentation, we focus only on the distribution of roots. The assumption is that the horizontal root distribution around a tree stem on a 2-dimensional plane can be described by a circle with the stem located at the centroid and a distinct radius r that is dependent on age and species. We classified three main types of tree root systems and reproduced the species-age-related root distribution with three respective mathematical solids in a synthetic 3-dimensional hillslope ambience. Thus, two solids in an Euclidian space were distinguished to represent the three root systems: i) cylinders with radius r and height h, whilst the dimension of latter defines the shape of a taproot-system or a shallow-root-system respectively; ii) elliptic

  18. EVALUATING AND REFINING THE ‘ENTERPRISE ARCHITECTURE AS STRATEGY’ APPROACH AND ARTEFACTS

    Directory of Open Access Journals (Sweden)

    M. De Vries

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT: Enterprise Architecture (EA is a new discipline that has emerged from the need to create a holistic view of an enterprise, and thereby to discover business/IT integration and alignment opportunities across enterprise structures. Previous EA value propositions that merely focus on IT cost reductions will no longer convince management to invest in EA. Today, EA should enable business strategy in the organisation to create value. This resides in the ability to do enterprise optimisation through process standardisation and integration. In order to do this, a new approach is required to integrate EA into the strategy planning process of the organisation.
    This article explores the use of three key artefacts – operating models, core diagrams, and an operating maturity assessment as defined by Ross, Weill & Robertson [1] – as the basis of this new approach. Action research is applied to a research group to obtain qualitative feedback on the practicality of the artefacts.

    AFRIKAANSE OPSOMMING: Ondernemingsargitektuur (OA is ’n nuwe dissipline wat ontstaan het uit die behoefte om ’n holistiese perspektief van ’n onderneming te skep om sodoende besigheid/IT-integrasie en - belyningsgeleenthede regoor ondernemingstrukture te ontdek. Vorige OA waardeaanbiedings wat hoofsaaklik gefokus het op IT kostebesparings sal bestuur nie meer kan oorreed om in OA te belê nie. Vandag behoort OA bevoegdheid te gee aan ondernemingstrategie om werklik waarde te skep. Hierdie bevoegdheid lê gesetel in ondernemingsoptimering deur middel van prosesstandaardisasie en -integrasie. ’n Nuwe benadering word benodig ten einde OA te integreer met die strategiese beplanningsproses van die organisasie.
    Hierdie artikel ondersoek die gebruik van drie artefakte – operasionele modelle, kerndiagramme, en operasionele volwassenheidsassessering soos gedefinieer deur Ross, Weill & Robertson [1] – as die basis van hierdie nuwe benadering

  19. Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications.

    Science.gov (United States)

    Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman; Ramamurthy, Praveen C

    2017-01-01

    A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1 , exhibited a highest occupied molecular orbital (HOMO) energy level at -5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2 , were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3 .

  20. Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

    Science.gov (United States)

    Needham, Perri J.; Bhuiyan, Ashraf; Walker, Ross C.

    2016-04-01

    We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P-1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.

  1. Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

    Science.gov (United States)

    Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman

    2017-01-01

    A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at −5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2, were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3. PMID:28546844

  2. Biomimicry as an approach for sustainable architecture case of arid regions with hot and dry climate

    Science.gov (United States)

    Bouabdallah, Nabila; M'sellem, Houda; Alkama, Djamel

    2016-07-01

    This paper aims to study the problem of thermal comfort inside buildings located in hot and arid climates. The principal idea behind this research is using concepts based on the potential of nature as an instrument that helps creating appropriate facades with the environment "building skin". The biomimetic architecture imitates nature through the study of form, function, behaviour and ecosystems of biological organisms. This research aims to clarify the possibilities that can be offered by biomimicry architecture to develop architectural bio-inspired building's design that can help to enhance indoor thermal ambiance in buildings located in hot and dry climate which helps to achieve thermal comfort for users.

  3. DOE's Institute for Advanced Architecture and Algorithms: An application-driven approach

    International Nuclear Information System (INIS)

    Murphy, Richard C

    2009-01-01

    This paper describes an application driven methodology for understanding the impact of future architecture decisions on the end of the MPP era. Fundamental transistor device limitations combined with application performance characteristics have created the switch to multicore/multithreaded architectures. Designing large-scale supercomputers to match application demands is particularly challenging since performance characteristics are highly counter-intuitive. In fact, data movement more than FLOPS dominates. This work discusses some basic performance analysis for a set of DOE applications, the limits of CMOS technology, and the impact of both on future architectures.

  4. Experiencing a Problem-Based Learning Approach for Teaching Reconfigurable Architecture Design

    Directory of Open Access Journals (Sweden)

    Erwan Fabiani

    2009-01-01

    Full Text Available This paper presents the “reconfigurable computing” teaching part of a computer science master course (first year on parallel architectures. The practical work sessions of this course rely on active pedagogy using problem-based learning, focused on designing a reconfigurable architecture for the implementation of an application class of image processing algorithms. We show how the successive steps of this project permit the student to experiment with several fundamental concepts of reconfigurable computing at different levels. Specific experiments include exploitation of architectural parallelism, dataflow and communicating component-based design, and configurability-specificity tradeoffs.

  5. Securing cloud services a pragmatic approach to security architecture in the cloud

    CERN Document Server

    Newcombe, Lee

    2012-01-01

    This book provides an overview of security architecture processes and explains how they may be used to derive an appropriate set of security controls to manage the risks associated with working in the Cloud.

  6. The semiotics of landscape design communication: towards a critical visual research approach in landscape architecture.

    NARCIS (Netherlands)

    Raaphorst, K.M.C.; Duchhart, I.; Knaap, van der W.G.M.; Roeleveld, Gerda; Brink, van den A.

    2017-01-01

    In landscape architecture, visual representations are the primary means of communication between stakeholders in design processes. Despite the reliance on visual representations, little critical research has been undertaken by landscape architects on how visual communication forms work or their

  7. Evolution of the Milieu Approach for Software Development for the Polymorphous Computing Architecture Program

    National Research Council Canada - National Science Library

    Dandass, Yoginder

    2004-01-01

    A key goal of the DARPA Polymorphous Computing Architectures (PCA) program is to develop reactive closed-loop systems that are capable of being dynamically reconfigured in order to respond to changing mission scenarios...

  8. Building Quality into Learning Management Systems – An Architecture-Centric Approach

    OpenAIRE

    Avgeriou, P.; Retalis, Simos; Skordalakis, Manolis

    2003-01-01

    The design and development of contemporary Learning Management Systems (LMS), is largely focused on satisfying functional requirements, rather than quality requirements, thus resulting in inefficient systems of poor software and business quality. In order to remedy this problem there is a research trend into specifying and evaluating software architectures for LMS, since quality at-tributes in a system depend profoundly on its architecture. This paper presents a case study of appraising the s...

  9. Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase

    Science.gov (United States)

    Malau, N. D.; Sianturi, M.

    2017-03-01

    Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.

  10. Rapid Molecular Identification of Human Taeniid Cestodes by Pyrosequencing Approach

    Science.gov (United States)

    Thanchomnang, Tongjit; Tantrawatpan, Chairat; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Tourtip, Somjintana; Yamasaki, Hiroshi; Maleewong, Wanchai

    2014-01-01

    Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse. PMID:24945530

  11. Rapid molecular identification of human taeniid cestodes by pyrosequencing approach.

    Directory of Open Access Journals (Sweden)

    Tongjit Thanchomnang

    Full Text Available Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1 gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.

  12. Recent molecular approaches to understanding astrocyte function in vivo

    Directory of Open Access Journals (Sweden)

    David eDavila

    2013-12-01

    Full Text Available Astrocytes are a predominant glial cell type in the nervous systems, and are becoming recognized as important mediators of normal brain function as well as neurodevelopmental, neurological, and neurodegenerative brain diseases. Although numerous potential mechanisms have been proposed to explain the role of astrocytes in the normal and diseased brain, research into the physiological relevance of these mechanisms in vivo is just beginning. In this review, we will summarize recent developments in innovative and powerful molecular approaches, including knockout mouse models, transgenic mouse models, and astrocyte-targeted gene transfer/expression, which have led to advances in understanding astrocyte biology in vivo that were heretofore inaccessible to experimentation. We will examine the recently improved understanding of the roles of astrocytes - with an emphasis on astrocyte signaling - in the context of both the healthy and diseased brain, discuss areas where the role of astrocytes remains debated, and suggest new research directions.

  13. Molecular targets in cancer therapy: the Ron approach

    Directory of Open Access Journals (Sweden)

    Serena Germano

    2011-12-01

    Full Text Available The receptor tyrosine kinase Ron and its ligand, Macrophage Stimulating Protein (MSP, mediate multiple processes involved in the control of cell proliferation, migration and protection from apoptosis. Dysregulated signaling of Ron, due to hyperactivation or loss of negative regulation, is involved in tumor progression and metastasis. Growing evidence indicates that Ron is abnormally expressed and activated in certain types of primary epithelial cancers (i.e. breast, colon, lung, pancreas, bladder and thyroid, where it critically contributes to the maintenance of tumorigenic and invasive phenotype. Furthermore, a positive association between aberrant Ron expression and aggressive biological indicators as well as a worse clinical outcome have been reported in breast, bladder and thyroid carcinomas. Different approaches have proved effective in targeting receptor activation/expression both in vitro and in animal models, leading to reversion of the tumorigenic phenotype. Altogether these results show that Ron is an attractive molecular target for clinical intervention.

  14. Information Integration Architecture Development

    OpenAIRE

    Faulkner, Stéphane; Kolp, Manuel; Nguyen, Duy Thai; Coyette, Adrien; Do, Thanh Tung; 16th International Conference on Software Engineering and Knowledge Engineering

    2004-01-01

    Multi-Agent Systems (MAS) architectures are gaining popularity for building open, distributed, and evolving software required by systems such as information integration applications. Unfortunately, despite considerable work in software architecture during the last decade, few research efforts have aimed at truly defining patterns and languages for designing such multiagent architectures. We propose a modern approach based on organizational structures and architectural description lan...

  15. Molecular genetics and livestock selection. Approaches, opportunities and risks

    International Nuclear Information System (INIS)

    Williams, J.L.

    2005-01-01

    Following domestication, livestock were selected both naturally through adaptation to their environments and by man so that they would fulfil a particular use. As selection methods have become more sophisticated, rapid progress has been made in improving those traits that are easily measured. However, selection has also resulted in decreased diversity. In some cases, improved breeds have replaced local breeds, risking the loss of important survival traits. The advent of molecular genetics provides the opportunity to identify the genes that control particular traits by a gene mapping approach. However, as with selection, the early mapping studies focused on traits that are easy to measure. Where molecular genetics can play a valuable role in livestock production is by providing the means to select effectively for traits that are difficult to measure. Identifying the genes underpinning particular traits requires a population in which these traits are segregating. Fortunately, several experimental populations have been created that have allowed a wide range of traits to be studied. Gene mapping work in these populations has shown that the role of particular genes in controlling variation in a given trait can depend on the genetic background. A second finding is that the most favourable alleles for a trait may in fact. be present in animals that perform poorly for the trait. In the long term, knowledge of -the genes controlling particular traits, and the way they interact with the genetic background, will allow introgression between breeds and the assembly of genotypes that are best suited to particular environments, producing animals with the desired characteristics. If used wisely, this approach will maintain genetic diversity while improving performance over a wide range of desired traits. (author)

  16. Convergent functional architecture of the superior parietal lobule unraveled with multimodal neuroimaging approaches.

    Science.gov (United States)

    Wang, Jiaojian; Yang, Yong; Fan, Lingzhong; Xu, Jinping; Li, Changhai; Liu, Yong; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2015-01-01

    The superior parietal lobule (SPL) plays a pivotal role in many cognitive, perceptive, and motor-related processes. This implies that a mosaic of distinct functional and structural subregions may exist in this area. Recent studies have demonstrated that the ongoing spontaneous fluctuations in the brain at rest are highly structured and, like coactivation patterns, reflect the integration of cortical locations into long-distance networks. This suggests that the internal differentiation of a complex brain region may be revealed by interaction patterns that are reflected in different neuroimaging modalities. On the basis of this perspective, we aimed to identify a convergent functional organization of the SPL using multimodal neuroimaging approaches. The SPL was first parcellated based on its structural connections as well as on its resting-state connectivity and coactivation patterns. Then, post hoc functional characterizations and connectivity analyses were performed for each subregion. The three types of connectivity-based parcellations consistently identified five subregions in the SPL of each hemisphere. The two anterior subregions were found to be primarily involved in action processes and in visually guided visuomotor functions, whereas the three posterior subregions were primarily associated with visual perception, spatial cognition, reasoning, working memory, and attention. This parcellation scheme for the SPL was further supported by revealing distinct connectivity patterns for each subregion in all the used modalities. These results thus indicate a convergent functional architecture of the SPL that can be revealed based on different types of connectivity and is reflected by different functions and interactions. © 2014 Wiley Periodicals, Inc.

  17. Molecular complexity from polyunsaturated substrates: the gold catalysis approach.

    Science.gov (United States)

    Fensterbank, Louis; Malacria, Max

    2014-03-18

    Over the last two decades, electrophilic catalysis relying on platinum(II), gold(I), and gold(III) salts has emerged as a remarkable synthetic methodology. Chemists have discovered a large variety of organic transformations that convert a great assortment of highly functionalized precursors into valuable final products. In many cases, these methodologies offer unique features, allowing access to unprecedented molecular architectures. Due to the mild reaction conditions and high function compatibility, scientists have successfully developed applications in total synthesis of natural products, as well as in asymmetric catalysis. In addition, all these developments have been accompanied by the invention of well-tailored catalysts, so that a palette of different electrophilic agents is now commercially available or readily synthesized at the bench. In some respects, researchers' interests in developing homogeneous gold catalysis can be compared with the Californian gold rush of the 19th century. It has attracted into its fervor thousands of scientists, providing a huge number of versatile and important reports. More notably, it is clear that the contribution to the art of organic synthesis is very valuable, though the quest is not over yet. Because they rely on the intervention of previously unknown types of intermediates, new retrosynthetic disconnections are now possible. In this Account, we discuss our efforts on the use of readily available polyunsaturated precursors, such as enynes, dienynes, allenynes, and allenenes to give access to highly original polycyclic structures in a single operation. These transformations transit via previously undescribed intermediates A, B, D, F, and H that will be encountered later on. All these intermediates have been determined by both ourselves and others by DFT calculations and in some cases have been confirmed on the basis of experimental data. In addition, dual gold activation can be at work in some of these transformations

  18. Solid-state NMR Reveals the Carbon-based Molecular Architecture of Cryptococcus neoformans Fungal Eumelanins in the Cell Wall.

    Science.gov (United States)

    Chatterjee, Subhasish; Prados-Rosales, Rafael; Itin, Boris; Casadevall, Arturo; Stark, Ruth E

    2015-05-29

    Melanin pigments protect against both ionizing radiation and free radicals and have potential soil remediation capabilities. Eumelanins produced by pathogenic Cryptococcus neoformans fungi are virulence factors that render the fungal cells resistant to host defenses and certain antifungal drugs. Because of their insoluble and amorphous characteristics, neither the pigment bonding framework nor the cellular interactions underlying melanization of C. neoformans have yielded to comprehensive molecular-scale investigation. This study used the C. neoformans requirement of exogenous obligatory catecholamine precursors for melanization to produce isotopically enriched pigment "ghosts" and applied 2D (13)C-(13)C correlation solid-state NMR to reveal the carbon-based architecture of intact natural eumelanin assemblies in fungal cells. We demonstrated that the aliphatic moieties of solid C. neoformans melanin ghosts include cell-wall components derived from polysaccharides and/or chitin that are associated proximally with lipid membrane constituents. Prior to development of the mature aromatic fungal pigment, these aliphatic moieties form a chemically resistant framework that could serve as the scaffold for melanin synthesis. The indole-based core aromatic moieties show interconnections that are consistent with proposed melanin structures consisting of stacked planar assemblies, which are associated spatially with the aliphatic scaffold. The pyrrole aromatic carbons of the pigments bind covalently to the aliphatic framework via glycoside or glyceride functional groups. These findings establish that the structure of the pigment assembly changes with time and provide the first biophysical information on the mechanism by which melanin is assembled in the fungal cell wall, offering vital insights that can advance the design of bioinspired conductive nanomaterials and novel therapeutics. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer.

    Science.gov (United States)

    LoPiccolo, Jaclyn; Kim, Seung Joong; Shi, Yi; Wu, Bin; Wu, Haiyan; Chait, Brian T; Singer, Robert H; Sali, Andrej; Brenowitz, Michael; Bresnick, Anne R; Backer, Jonathan M

    2015-12-18

    Phosphoinositide 3-kinases (PI3Ks) are a family of lipid kinases that are activated by growth factor and G-protein-coupled receptors and propagate intracellular signals for growth, survival, proliferation, and metabolism. p85α, a modular protein consisting of five domains, binds and inhibits the enzymatic activity of class IA PI3K catalytic subunits. Here, we describe the structural states of the p85α dimer, based on data from in vivo and in vitro solution characterization. Our in vitro assembly and structural analyses have been enabled by the creation of cysteine-free p85α that is functionally equivalent to native p85α. Analytical ultracentrifugation studies showed that p85α undergoes rapidly reversible monomer-dimer assembly that is highly exothermic in nature. In addition to the documented SH3-PR1 dimerization interaction, we identified a second intermolecular interaction mediated by cSH2 domains at the C-terminal end of the polypeptide. We have demonstrated in vivo concentration-dependent dimerization of p85α using fluorescence fluctuation spectroscopy. Finally, we have defined solution conditions under which the protein is predominantly monomeric or dimeric, providing the basis for small angle x-ray scattering and chemical cross-linking structural analysis of the discrete dimer. These experimental data have been used for the integrative structure determination of the p85α dimer. Our study provides new insight into the structure and assembly of the p85α homodimer and suggests that this protein is a highly dynamic molecule whose conformational flexibility allows it to transiently associate with multiple binding proteins. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Adsorption of human serum albumin: Dependence on molecular architecture of the oppositely charged surface

    Science.gov (United States)

    Sukhishvili, Svetlana A.; Granick, Steve

    1999-05-01

    We contrast the adsorption of human serum albumin (HSA) onto two solid substrates previously primed with the same polyelectrolyte of net opposite charge to form one of two alternative structures: randomly adsorbed polymer and the "brush" configuration. These structures were formed either by the adsorption of quaternized poly-4-vinylpyridine (QPVP) or by end-grafting QPVP chains of the same chemical makeup and the same molecular weight to surfaces onto which QPVP segments did not adsorb. The adsorption of HSA was quantified by using Fourier transform infrared spectroscopy in attenuated total reflection (FTIR-ATR). The two substrates showed striking differences with regard to HSA adsorption. First, the brush substrate induced lesser perturbations in the secondary structure of the adsorbed HSA, reflecting easier conformational adjustment for longer free segments of polyelectrolyte upon binding with the protein. Second, the penetration of HSA into the brush substrate was kinetically retarded relative to the randomly adsorbed polymer, probably due to both pore size restriction and electrostatic sticking between charged groups of HSA and QPVP molecules. Third, release of HSA from the adsorbed layer, as the ionic strength was increased from a low level up to the high level of 1 M NaCl, was largely inhibited for the brush substrate, but occurred easily and rapidly for the substrate with statistically adsorbed QPVP chains. Finally, even after addition of a strong polymeric adsorption competitor (sodium polystyrene sulfonate), HSA remained trapped within a brush substrate though it desorbed slowly from the preadsorbed QPVP layer. This method to produce irreversible trapping of the protein within a brush substrate without major conformational change may find application in biosensor design.

  1. Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

    Directory of Open Access Journals (Sweden)

    Rogier Christophe

    2009-04-01

    Full Text Available Abstract Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the

  2. Molecular genetic approaches to the study of cellular senescence.

    Science.gov (United States)

    Goletz, T J; Smith, J R; Pereira-Smith, O M

    1994-01-01

    Cellular senescence is an inability of cells to synthesize DNA and divide, which results in a terminal loss of proliferation despite the maintenance of basic metabolic processes. Senescence has been proposed as a model for the study of aging at the cellular level, and the basis for this model system and its features have been summarized. Although strong experimental evidence exists to support the hypothesis that cellular senescence is a dominant active process, the mechanisms responsible for this phenomenon remain a mystery. Investigators have taken several approaches to gain a better understanding of senescence. Several groups have documented the differences between young and senescent cells, and others have identified changes that occur during the course of a cell's in vitro life span. Using molecular and biochemical approaches, important changes in gene expression and function of cell-cycle-associated products have been identified. The active production of an inhibitor of DNA synthesis has been demonstrated. This may represent the final step in a cascade of events governing senescence. The study of immortal cells which have escaped senescence has also provided useful information, particularly with regard to the genes governing the senescence program. These studies have identified four complementation groups for indefinite division, which suggests that there are at least four genes or gene pathways in the senescence program. Through the use of microcell-mediated chromosome transfer, chromosomes encoding senescence genes have been identified; efforts to clone these genes are ongoing.(ABSTRACT TRUNCATED AT 250 WORDS)

  3. Fusarium diversity in soil using a specific molecular approach and a cultural approach.

    Science.gov (United States)

    Edel-Hermann, Véronique; Gautheron, Nadine; Mounier, Arnaud; Steinberg, Christian

    2015-04-01

    Fusarium species are ubiquitous in soil. They cause plant and human diseases and can produce mycotoxins. Surveys of Fusarium species diversity in environmental samples usually rely on laborious culture-based methods. In the present study, we have developed a molecular method to analyze Fusarium diversity directly from soil DNA. We designed primers targeting the translation elongation factor 1-alpha (EF-1α) gene and demonstrated their specificity toward Fusarium using a large collection of fungi. We used the specific primers to construct a clone library from three contrasting soils. Sequence analysis confirmed the specificity of the assay, with 750 clones identified as Fusarium and distributed among eight species or species complexes. The Fusarium oxysporum species complex (FOSC) was the most abundant one in the three soils, followed by the Fusarium solani species complex (FSSC). We then compared our molecular approach results with those obtained by isolating Fusarium colonies on two culture media and identifying species by sequencing part of the EF-1α gene. The 750 isolates were distributed into eight species or species complexes, with the same dominant species as with the cloning method. Sequence diversity was much higher in the clone library than in the isolate collection. The molecular approach proved to be a valuable tool to assess Fusarium diversity in environmental samples. Combined with high throughput sequencing, it will allow for in-depth analysis of large numbers of samples. Published by Elsevier B.V.

  4. Architectural Theatricality

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen

    environments and a knowledge gap therefore exists in present hospital designs. Consequently, the purpose of this thesis has been to investigate if any research-based knowledge exist supporting the hypothesis that the interior architectural qualities of eating environments influence patient food intake, health...... and well-being, as well as outline a set of basic design principles ‘predicting’ the future interior architectural qualities of patient eating environments. Methodologically the thesis is based on an explorative study employing an abductive approach and hermeneutic-interpretative strategy utilizing tactics...... and food intake, as well as a series of references exist linking the interior architectural qualities of healthcare environments with the health and wellbeing of patients. On the basis of these findings, the thesis presents the concept of Architectural Theatricality as well as a set of design principles...

  5. A symmetry-controlled and face-driven approach for the assembly of cerium-based molecular polyhedra.

    Science.gov (United States)

    Liu, Yang; Lin, Zhihua; He, Cheng; Zhao, Liang; Duan, Chunying

    2010-12-14

    A well-defined Ce-based molecular tetrahedron and a cube-like architecture were achieved via self-assembly by incorporating NOO tridentate chelators into the rationally designed ligands with C(3) or C(2v) symmetries, respectively.

  6. Research in architecture : reflection on three approaches linking research and design

    NARCIS (Netherlands)

    Colenbrander, B.J.F.; Pereira Roders, A.R.; Veldpaus, L.; Fidanoglu, Esra

    2013-01-01

    Research in Architecture is not new, it is usually known as analysis or pre-design stage. Architects get acquainted with program requirements, project context and/or other inspiring works, including concepts on theory, philosophy or history. Seldom are the architects who design without any

  7. Impact of contour on aesthetic judgments and approach-avoidance decisions in architecture

    DEFF Research Database (Denmark)

    Vartanian, Oshin; Navarrete, Gorka; Chatterjee, Anjan

    2013-01-01

    On average, we urban dwellers spend about 90% of our time indoors, and share the intuition that the physical features of the places we live and work in influence how we feel and act. However, there is surprisingly little research on how architecture impacts behavior, much less on how it influence...

  8. Information security architecture an integrated approach to security in the organization

    CERN Document Server

    Killmeyer, Jan

    2006-01-01

    Information Security Architecture, Second Edition incorporates the knowledge developed during the past decade that has pushed the information security life cycle from infancy to a more mature, understandable, and manageable state. It simplifies security by providing clear and organized methods and by guiding you to the most effective resources available.

  9. Information Architecture for the Web: The IA Matrix Approach to Designing Children's Portals.

    Science.gov (United States)

    Large, Andrew; Beheshti, Jamshid; Cole, Charles

    2002-01-01

    Presents a matrix that can serve as a tool for designing the information architecture of a Web portal in a logical and systematic manner. Highlights include interfaces; metaphors; navigation; interaction; information retrieval; and an example of a children's Web portal to provide access to museum information. (Author/LRW)

  10. The Development of a Coalition Operational Architecture: A British and US Army Approach

    National Research Council Canada - National Science Library

    Galvin, K. E; Madigan, J. C

    2000-01-01

    ... (COA) to support a US Corps operating as a Combined Joint Task Force (CJTF) Headquarters with up to a UK Division as an integral part of its ORBAT would be investigated by staff from both countries' Army Operational Architecture (AOA) teams...

  11. A Survey of Some Approaches to Distributed Data Base & Distributed File System Architecture.

    Science.gov (United States)

    1980-01-01

    BUS POD A DD A 12 12 A = A Cell D = D Cell Figure 7-1: MUFFIN logical architecture - 45 - MUFI January 1980 ".-.Bus Interface V Conventional Processor...and Applied Mathematics (14), * December, 1966. [Kimbleton 791 Kimbleton, Stephen; Wang, Pearl; and Fong, Elizabeth. XNDM: An Experimental Network

  12. An Architectural Approach towards Innovative Renewable Energy Infrastructure in Kapisillit, Greenland

    DEFF Research Database (Denmark)

    Carruth, Susan; Krogh, Peter

    2014-01-01

    workshop with architecture students who were asked to create conceptual strategies, driven by distributed, community-controlled renewable energy, for the future of the village. It culminates in a discussion on how this empirical work contributes towards the construction of a vocabulary of material...

  13. A Project-Based Learning Approach to Programmable Logic Design and Computer Architecture

    Science.gov (United States)

    Kellett, C. M.

    2012-01-01

    This paper describes a course in programmable logic design and computer architecture as it is taught at the University of Newcastle, Australia. The course is designed around a major design project and has two supplemental assessment tasks that are also described. The context of the Computer Engineering degree program within which the course is…

  14. Understanding the Value of Enterprise Architecture for Organizations: A Grounded Theory Approach

    Science.gov (United States)

    Nassiff, Edwin

    2012-01-01

    There is a high rate of information system implementation failures attributed to the lack of alignment between business and information technology strategy. Although enterprise architecture (EA) is a means to correct alignment problems and executives highly rate the importance of EA, it is still not used in most organizations today. Current…

  15. A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.

    Science.gov (United States)

    Ciaccio, Mark F; Finkle, Justin D; Xue, Albert Y; Bagheri, Neda

    2014-07-01

    An organism's ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue-signal-response networks. However, selecting a strategy that answers a specific biological question requires knowledge both of the type of data being collected, and of the strengths and weaknesses of different computational regimes. We broadly explore several computational approaches, and we evaluate their accuracy in predicting a given response. Specifically, we describe how statistical algorithms can be used in the context of integrative and comparative biology to elucidate the genomic, proteomic, and/or cellular networks responsible for robust physiological response. As a case study, we apply this strategy to a dataset of quantitative levels of protein abundance from the mussel, Mytilus galloprovincialis, to uncover the temperature-dependent signaling network. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

  16. Theoretical study of molecular vibrations in electron momentum spectroscopy experiments on furan: An analytical versus a molecular dynamical approach

    International Nuclear Information System (INIS)

    Morini, Filippo; Deleuze, Michael S.; Watanabe, Noboru; Takahashi, Masahiko

    2015-01-01

    The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A 1 symmetry on the 9a 1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing

  17. Molecular concepts of water splitting. Nature's approach

    Energy Technology Data Exchange (ETDEWEB)

    Cox, Nicholas; Lubitz, Wolfgang [Max-Planck-Institut fuer Chemische Energiekonversion, Muelheim an der Ruhr (Germany)

    2013-07-01

    Based on studies of natural systems, much has also been learned concerning the design principles required for biomimetic catalysis of water splitting and hydrogen evolution. In summary, these include use of abundant and inexpensive metals, the effective protection of the active sites in functional environments, repair/replacement of active components in case of damage, and the optimization of reaction rates. Biomimetic chemistry aims to mimic all these features; many labs are working toward this goal by developing new approaches in the design and synthesis of such systems, encompassing not only the catalytic center, but also smart matrices and assembly via self-organization. More stable catalysts that do not require self-repair may be obtained from fully artificial (inorganic) catalytic systems that are totally different from the biological ones and only apply some basic principles learned from nature. Metals other than Mn/Ca, Fe, and Ni could be used (e.g. Co) in new ligand spheres and other matrices. For light harvesting, charge separation/stabilization, and the effective coupling of the oxidizing/reducing equivalents to the redox catalysts, different methods have been proposed - for example, covalently linked molecular donor-acceptor systems, photo-voltaic devices, semiconductor-based systems, and photoactive metal complexes. The aim of all these approaches is to develop catalytic systems that split water with sunlight into hydrogen and oxygen while displaying high efficiency and long-term stability. Such a system - either biological, biomimetic, or bioinspired - has the potential to be used on a large scale to produce 'solar fuels' (e.g. hydrogen or secondary products thereof). (orig.)

  18. Substrate channel in nitrogenase revealed by a molecular dynamics approach.

    Science.gov (United States)

    Smith, Dayle; Danyal, Karamatullah; Raugei, Simone; Seefeldt, Lance C

    2014-04-15

    Mo-dependent nitrogenase catalyzes the biological reduction of N2 to two NH3 molecules at FeMo-cofactor buried deep inside the MoFe protein. Access of substrates, such as N2, to the active site is likely restricted by the surrounding protein, requiring substrate channels that lead from the surface to the active site. Earlier studies on crystallographic structures of the MoFe protein have suggested three putative substrate channels. Here, we have utilized submicrosecond atomistic molecular dynamics simulations to allow the nitrogenase MoFe protein to explore its conformational space in an aqueous solution at physiological ionic strength, revealing a putative substrate channel. The viability of this observed channel was tested by examining the free energy of passage of N2 from the surface through the channel to FeMo-cofactor, resulting in the discovery of a very low energy barrier. These studies point to a viable substrate channel in nitrogenase that appears during thermal motions of the protein in an aqueous environment and that approaches a face of FeMo-cofactor earlier implicated in substrate binding.

  19. Understanding how the complex molecular architecture of mannan-degrading hydrolases contributes to plant cell wall degradation.

    Science.gov (United States)

    Zhang, Xiaoyang; Rogowski, Artur; Zhao, Lei; Hahn, Michael G; Avci, Utku; Knox, J Paul; Gilbert, Harry J

    2014-01-24

    Microbial degradation of plant cell walls is a central component of the carbon cycle and is of increasing importance in environmentally significant industries. Plant cell wall-degrading enzymes have a complex molecular architecture consisting of catalytic modules and, frequently, multiple non-catalytic carbohydrate binding modules (CBMs). It is currently unclear whether the specificities of the CBMs or the topology of the catalytic modules are the primary drivers for the specificity of these enzymes against plant cell walls. Here, we have evaluated the relationship between CBM specificity and their capacity to enhance the activity of GH5 and GH26 mannanases and CE2 esterases against intact plant cell walls. The data show that cellulose and mannan binding CBMs have the greatest impact on the removal of mannan from tobacco and Physcomitrella cell walls, respectively. Although the action of the GH5 mannanase was independent of the context of mannan in tobacco cell walls, a significant proportion of the polysaccharide was inaccessible to the GH26 enzyme. The recalcitrant mannan, however, was fully accessible to the GH26 mannanase appended to a cellulose binding CBM. Although CE2 esterases display similar specificities against acetylated substrates in vitro, only CjCE2C was active against acetylated mannan in Physcomitrella. Appending a mannan binding CBM27 to CjCE2C potentiated its activity against Physcomitrella walls, whereas a xylan binding CBM reduced the capacity of esterases to deacetylate xylan in tobacco walls. This work provides insight into the biological significance for the complex array of hydrolytic enzymes expressed by plant cell wall-degrading microorganisms.

  20. Solid-state NMR Reveals the Carbon-based Molecular Architecture of Cryptococcus neoformans Fungal Eumelanins in the Cell Wall*

    Science.gov (United States)

    Chatterjee, Subhasish; Prados-Rosales, Rafael; Itin, Boris; Casadevall, Arturo; Stark, Ruth E.

    2015-01-01

    Melanin pigments protect against both ionizing radiation and free radicals and have potential soil remediation capabilities. Eumelanins produced by pathogenic Cryptococcus neoformans fungi are virulence factors that render the fungal cells resistant to host defenses and certain antifungal drugs. Because of their insoluble and amorphous characteristics, neither the pigment bonding framework nor the cellular interactions underlying melanization of C. neoformans have yielded to comprehensive molecular-scale investigation. This study used the C. neoformans requirement of exogenous obligatory catecholamine precursors for melanization to produce isotopically enriched pigment “ghosts” and applied 2D 13C-13C correlation solid-state NMR to reveal the carbon-based architecture of intact natural eumelanin assemblies in fungal cells. We demonstrated that the aliphatic moieties of solid C. neoformans melanin ghosts include cell-wall components derived from polysaccharides and/or chitin that are associated proximally with lipid membrane constituents. Prior to development of the mature aromatic fungal pigment, these aliphatic moieties form a chemically resistant framework that could serve as the scaffold for melanin synthesis. The indole-based core aromatic moieties show interconnections that are consistent with proposed melanin structures consisting of stacked planar assemblies, which are associated spatially with the aliphatic scaffold. The pyrrole aromatic carbons of the pigments bind covalently to the aliphatic framework via glycoside or glyceride functional groups. These findings establish that the structure of the pigment assembly changes with time and provide the first biophysical information on the mechanism by which melanin is assembled in the fungal cell wall, offering vital insights that can advance the design of bioinspired conductive nanomaterials and novel therapeutics. PMID:25825492

  1. From Requirements to code: an Architecture-centric Approach for producing Quality Systems

    OpenAIRE

    Bucchiarone, Antonio; Di Ruscio, Davide; Muccini, Henry; Pelliccione, Patrizio

    2009-01-01

    When engineering complex and distributed software and hardware systems (increasingly used in many sectors, such as manufacturing, aerospace, transportation, communication, energy, and health-care), quality has become a big issue, since failures can have economics consequences and can also endanger human life. Model-based specifications of a component-based system permit to explicitly model the structure and behaviour of components and their integration. In particular Software Architectures (S...

  2. The constraints satisfaction problem approach in the design of an architectural functional layout

    Science.gov (United States)

    Zawidzki, Machi; Tateyama, Kazuyoshi; Nishikawa, Ikuko

    2011-09-01

    A design support system with a new strategy for finding the optimal functional configurations of rooms for architectural layouts is presented. A set of configurations satisfying given constraints is generated and ranked according to multiple objectives. The method can be applied to problems in architectural practice, urban or graphic design-wherever allocation of related geometrical elements of known shape is optimized. Although the methodology is shown using simplified examples-a single story residential building with two apartments each having two rooms-the results resemble realistic functional layouts. One example of a practical size problem of a layout of three apartments with a total of 20 rooms is demonstrated, where the generated solution can be used as a base for a realistic architectural blueprint. The discretization of design space is discussed, followed by application of a backtrack search algorithm used for generating a set of potentially 'good' room configurations. Next the solutions are classified by a machine learning method (FFN) as 'proper' or 'improper' according to the internal communication criteria. Examples of interactive ranking of the 'proper' configurations according to multiple criteria and choosing 'the best' ones are presented. The proposed framework is general and universal-the criteria, parameters and weights can be individually defined by a user and the search algorithm can be adjusted to a specific problem.

  3. Organically bound sulphur in coal: A molecular approach

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Leeuw, J.W. de

    1992-01-01

    A critical review of literature concerning the molecular characterization of low and high molecular weight organosulphur constitutents present in coal as well as a detailed analysis of organic sulphur compounds present in flash evaporates and pyrolysates of a suite of coals ranging in sulphur

  4. Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

    Science.gov (United States)

    Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

    2012-01-01

    Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

  5. A simplified approach for the molecular classification of glioblastomas.

    Directory of Open Access Journals (Sweden)

    Marie Le Mercier

    Full Text Available Glioblastoma (GBM is the most common malignant primary brain tumors in adults and exhibit striking aggressiveness. Although GBM constitute a single histological entity, they exhibit considerable variability in biological behavior, resulting in significant differences in terms of prognosis and response to treatment. In an attempt to better understand the biology of GBM, many groups have performed high-scale profiling studies based on gene or protein expression. These studies have revealed the existence of several GBM subtypes. Although there remains to be a clear consensus, two to four major subtypes have been identified. Interestingly, these different subtypes are associated with both differential prognoses and responses to therapy. In the present study, we investigated an alternative immunohistochemistry (IHC-based approach to achieve a molecular classification for GBM. For this purpose, a cohort of 100 surgical GBM samples was retrospectively evaluated by immunohistochemical analysis of EGFR, PDGFRA and p53. The quantitative analysis of these immunostainings allowed us to identify the following two GBM subtypes: the "Classical-like" (CL subtype, characterized by EGFR-positive and p53- and PDGFRA-negative staining and the "Proneural-like" (PNL subtype, characterized by p53- and/or PDGFRA-positive staining. This classification represents an independent prognostic factor in terms of overall survival compared to age, extent of resection and adjuvant treatment, with a significantly longer survival associated with the PNL subtype. Moreover, these two GBM subtypes exhibited different responses to chemotherapy. The addition of temozolomide to conventional radiotherapy significantly improved the survival of patients belonging to the CL subtype, but it did not affect the survival of patients belonging to the PNL subtype. We have thus shown that it is possible to differentiate between different clinically relevant subtypes of GBM by using IHC

  6. A universal approach to electrically connecting nanowire arrays using nanoparticles—application to a novel gas sensor architecture

    Science.gov (United States)

    Parthangal, Prahalad M.; Cavicchi, Richard E.; Zachariah, Michael R.

    2006-08-01

    We report on a novel, in situ approach toward connecting and electrically contacting vertically aligned nanowire arrays using conductive nanoparticles. The utility of the approach is demonstrated by development of a gas sensing device employing this nano-architecture. Well-aligned, single-crystalline zinc oxide nanowires were grown through a direct thermal evaporation process at 550 °C on gold catalyst layers. Electrical contact to the top of the nanowire array was established by creating a contiguous nanoparticle film through electrostatic attachment of conductive gold nanoparticles exclusively onto the tips of nanowires. A gas sensing device was constructed using such an arrangement and the nanowire assembly was found to be sensitive to both reducing (methanol) and oxidizing (nitrous oxides) gases. This assembly approach is amenable to any nanowire array for which a top contact electrode is needed.

  7. A universal approach to electrically connecting nanowire arrays using nanoparticles-application to a novel gas sensor architecture

    International Nuclear Information System (INIS)

    Parthangal, Prahalad M; Cavicchi, Richard E; Zachariah, Michael R

    2006-01-01

    We report on a novel, in situ approach toward connecting and electrically contacting vertically aligned nanowire arrays using conductive nanoparticles. The utility of the approach is demonstrated by development of a gas sensing device employing this nano-architecture. Well-aligned, single-crystalline zinc oxide nanowires were grown through a direct thermal evaporation process at 550 deg. C on gold catalyst layers. Electrical contact to the top of the nanowire array was established by creating a contiguous nanoparticle film through electrostatic attachment of conductive gold nanoparticles exclusively onto the tips of nanowires. A gas sensing device was constructed using such an arrangement and the nanowire assembly was found to be sensitive to both reducing (methanol) and oxidizing (nitrous oxides) gases. This assembly approach is amenable to any nanowire array for which a top contact electrode is needed

  8. Architectural approach to the energy performance of buildings in a hot-dry climate with special reference to Egypt

    Energy Technology Data Exchange (ETDEWEB)

    Hamdy, I F

    1986-01-01

    A thesis is presented on the changing approach to architectural design of buildings in a hot, dry climate in view of the increased recognition of the importance of energy efficiency. The thermal performance of buildings in Egypt is used as an example and the nature of the local climate and human requirements are also studied. Other effects on the thermal performance considered include building form, orientation and surrounding conditions. An evaluative computer model is constructed and its applications allow the prediction on the energy performance of changing design parameters.

  9. Reframing Architecture

    DEFF Research Database (Denmark)

    Riis, Søren

    2013-01-01

    I would like to thank Prof. Stephen Read (2011) and Prof. Andrew Benjamin (2011) for both giving inspiring and elaborate comments on my article “Dwelling in-between walls: the architectural surround”. As I will try to demonstrate below, their two different responses not only supplement my article...... focuses on how the absence of an initial distinction might threaten the endeavour of my paper. In my reply to Read and Benjamin, I will discuss their suggestions and arguments, while at the same time hopefully clarifying the postphenomenological approach to architecture....

  10. Nanorobot architecture for medical target identification

    International Nuclear Information System (INIS)

    Cavalcanti, Adriano; Shirinzadeh, Bijan; Freita, Robert A Jr; Hogg, Tad

    2008-01-01

    This work has an innovative approach for the development of nanorobots with sensors for medicine. The nanorobots operate in a virtual environment comparing random, thermal and chemical control techniques. The nanorobot architecture model has nanobioelectronics as the basis for manufacturing integrated system devices with embedded nanobiosensors and actuators, which facilitates its application for medical target identification and drug delivery. The nanorobot interaction with the described workspace shows how time actuation is improved based on sensor capabilities. Therefore, our work addresses the control and the architecture design for developing practical molecular machines. Advances in nanotechnology are enabling manufacturing nanosensors and actuators through nanobioelectronics and biologically inspired devices. Analysis of integrated system modeling is one important aspect for supporting nanotechnology in the fast development towards one of the most challenging new fields of science: molecular machines. The use of 3D simulation can provide interactive tools for addressing nanorobot choices on sensing, hardware architecture design, manufacturing approaches, and control methodology investigation

  11. Nanorobot architecture for medical target identification

    Energy Technology Data Exchange (ETDEWEB)

    Cavalcanti, Adriano [CAN Center for Automation in Nanobiotech, Melbourne VIC 3168 (Australia); Shirinzadeh, Bijan [Robotics and Mechatronics Research Laboratory, Department of Mechanical Engineering, Monash University, Clayton, Melbourne VIC 3800 (Australia); Freita, Robert A Jr [Institute for Molecular Manufacturing, Pilot Hill, CA 95664 (United States); Hogg, Tad [Hewlett-Packard Laboratories, Palo Alto, CA 94304 (United States)

    2008-01-09

    This work has an innovative approach for the development of nanorobots with sensors for medicine. The nanorobots operate in a virtual environment comparing random, thermal and chemical control techniques. The nanorobot architecture model has nanobioelectronics as the basis for manufacturing integrated system devices with embedded nanobiosensors and actuators, which facilitates its application for medical target identification and drug delivery. The nanorobot interaction with the described workspace shows how time actuation is improved based on sensor capabilities. Therefore, our work addresses the control and the architecture design for developing practical molecular machines. Advances in nanotechnology are enabling manufacturing nanosensors and actuators through nanobioelectronics and biologically inspired devices. Analysis of integrated system modeling is one important aspect for supporting nanotechnology in the fast development towards one of the most challenging new fields of science: molecular machines. The use of 3D simulation can provide interactive tools for addressing nanorobot choices on sensing, hardware architecture design, manufacturing approaches, and control methodology investigation.

  12. PICNIC Architecture.

    Science.gov (United States)

    Saranummi, Niilo

    2005-01-01

    The PICNIC architecture aims at supporting inter-enterprise integration and the facilitation of collaboration between healthcare organisations. The concept of a Regional Health Economy (RHE) is introduced to illustrate the varying nature of inter-enterprise collaboration between healthcare organisations collaborating in providing health services to citizens and patients in a regional setting. The PICNIC architecture comprises a number of PICNIC IT Services, the interfaces between them and presents a way to assemble these into a functioning Regional Health Care Network meeting the needs and concerns of its stakeholders. The PICNIC architecture is presented through a number of views relevant to different stakeholder groups. The stakeholders of the first view are national and regional health authorities and policy makers. The view describes how the architecture enables the implementation of national and regional health policies, strategies and organisational structures. The stakeholders of the second view, the service viewpoint, are the care providers, health professionals, patients and citizens. The view describes how the architecture supports and enables regional care delivery and process management including continuity of care (shared care) and citizen-centred health services. The stakeholders of the third view, the engineering view, are those that design, build and implement the RHCN. The view comprises four sub views: software engineering, IT services engineering, security and data. The proposed architecture is founded into the main stream of how distributed computing environments are evolving. The architecture is realised using the web services approach. A number of well established technology platforms and generic standards exist that can be used to implement the software components. The software components that are specified in PICNIC are implemented in Open Source.

  13. Constructing hierarchical porous nanospheres for versatile microwave response approaches: the effect of architectural design.

    Science.gov (United States)

    Quan, Bin; Liang, Xiaohui; Yi, Heng; Gong, He; Ji, Guangbin; Chen, Jiabin; Xu, Guoyue; Du, Youwei

    2017-10-24

    Owing to their immense potential in functionalized applications, tremendous interest has been devoted to the design and synthesis of nanostructures. The introduction of sufficient amount of microwaves into the absorbers on the premise that the dissipation capacity is strong enough remains a key challenge. Pursuing a general methodology to overcome the incompatibility is of great importance. There is widespread interest in designing the materials with specific architectures. Herein, the common absorber candidates were chosen to feature the hierarchical porous Fe 3 O 4 @C@Fe 3 O 4 nanospheres. Due to the reduced skin effect (induced by low-conductivity Fe 3 O 4 outer layer), multiple interfacial polarizations and scattering (due to the ternary hierarchical structures and nanoporous inner core) as well as the improved magnetic dissipation ability (because of multiple magnetic components), the material design enabled a promising microwave absorption performance. This study not only illustrates the primary mechanisms for the improved microwave absorption performance but also underscores the potential in designing the particular architectures as a strategy for achieving the compatibility characteristics.

  14. An Open Architecture Framework for Electronic Warfare Based Approach to HLA Federate Development

    Directory of Open Access Journals (Sweden)

    HyunSeo Kang

    2018-01-01

    Full Text Available A variety of electronic warfare models are developed in the Electronic Warfare Research Center. An Open Architecture Framework for Electronic Warfare (OAFEw has been developed for reusability of various object models participating in the electronic warfare simulation and for extensibility of the electronic warfare simulator. OAFEw is a kind of component-based software (SW lifecycle management support framework. This OAFEw is defined by six components and ten rules. The purpose of this study is to construct a Distributed Simulation Interface Model, according to the rules of OAFEw, and create Use Case Model of OAFEw Reference Conceptual Model version 1.0. This is embodied in the OAFEw-FOM (Federate Object Model for High-Level Architecture (HLA based distributed simulation. Therefore, we design and implement EW real-time distributed simulation that can work with a model in C++ and MATLAB API (Application Programming Interface. In addition, OAFEw-FOM, electronic component model, and scenario of the electronic warfare domain were designed through simple scenarios for verification, and real-time distributed simulation between C++ and MATLAB was performed through OAFEw-Distributed Simulation Interface.

  15. EASEE: an open architecture approach for modeling battlespace signal and sensor phenomenology

    Science.gov (United States)

    Waldrop, Lauren E.; Wilson, D. Keith; Ekegren, Michael T.; Borden, Christian T.

    2017-04-01

    Open architecture in the context of defense applications encourages collaboration across government agencies and academia. This paper describes a success story in the implementation of an open architecture framework that fosters transparency and modularity in the context of Environmental Awareness for Sensor and Emitter Employment (EASEE), a complex physics-based software package for modeling the effects of terrain and atmospheric conditions on signal propagation and sensor performance. Among the highlighted features in this paper are: (1) a code refactorization to separate sensitive parts of EASEE, thus allowing collaborators the opportunity to view and interact with non-sensitive parts of the EASEE framework with the end goal of supporting collaborative innovation, (2) a data exchange and validation effort to enable the dynamic addition of signatures within EASEE thus supporting a modular notion that components can be easily added or removed to the software without requiring recompilation by developers, and (3) a flexible and extensible XML interface, which aids in decoupling graphical user interfaces from EASEE's calculation engine, and thus encourages adaptability to many different defense applications. In addition to the outlined points above, this paper also addresses EASEE's ability to interface with both proprietary systems such as ArcGIS. A specific use case regarding the implementation of an ArcGIS toolbar that leverages EASEE's XML interface and enables users to set up an EASEE-compliant configuration for probability of detection or optimal sensor placement calculations in various modalities is discussed as well.

  16. Integrating emerging earth science technologies into disaster risk management: an enterprise architecture approach

    Science.gov (United States)

    Evans, J. D.; Hao, W.; Chettri, S. R.

    2014-12-01

    Disaster risk management has grown to rely on earth observations, multi-source data analysis, numerical modeling, and interagency information sharing. The practice and outcomes of disaster risk management will likely undergo further change as several emerging earth science technologies come of age: mobile devices; location-based services; ubiquitous sensors; drones; small satellites; satellite direct readout; Big Data analytics; cloud computing; Web services for predictive modeling, semantic reconciliation, and collaboration; and many others. Integrating these new technologies well requires developing and adapting them to meet current needs; but also rethinking current practice to draw on new capabilities to reach additional objectives. This requires a holistic view of the disaster risk management enterprise and of the analytical or operational capabilities afforded by these technologies. One helpful tool for this assessment, the GEOSS Architecture for the Use of Remote Sensing Products in Disaster Management and Risk Assessment (Evans & Moe, 2013), considers all phases of the disaster risk management lifecycle for a comprehensive set of natural hazard types, and outlines common clusters of activities and their use of information and computation resources. We are using these architectural views, together with insights from current practice, to highlight effective, interrelated roles for emerging earth science technologies in disaster risk management. These roles may be helpful in creating roadmaps for research and development investment at national and international levels.

  17. A Blended Learning Approach to the Teaching of Professional Practice in Architecture

    Directory of Open Access Journals (Sweden)

    Murray Lane

    2015-05-01

    Full Text Available This paper reports on a number of blended learning activities conducted in two subjects of a Master of Architecture degree at a major Australian university. The subjects were related to “professional practice” and as such represent a little researched area of architectural curriculum. The research provides some insight into the student perceptions of learning opportunity and engagement associated with on-line delivery modes. Students from these two subjects were surveyed for their perceptions about the opportunity for learning afforded by the on-line components, and also for their perceived level of engagement. Responses to these perceptions of traditional and on-line modes of delivery are compared and analysed for significant differences. While students were generally positive in response to the learning experiences, analysis of the results shows that students found the traditional modes to assist in their learning significantly more than on-line modes. Students were neutral regarding the opportunity for engagement that on-line modes provided. Analysis of the students’ gender, age and hours of paid work was also conducted to ascertain any relationship with attitudes to the flexibility of on-line delivery; no significant relationship was detected. This study has shown that students were generally resistant to on-line engagement opportunities and their ability to support learning.

  18. Architectural Anthropology

    DEFF Research Database (Denmark)

    Stender, Marie

    Architecture and anthropology have always had a common focus on dwelling, housing, urban life and spatial organisation. Current developments in both disciplines make it even more relevant to explore their boundaries and overlaps. Architects are inspired by anthropological insights and methods......, while recent material and spatial turns in anthropology have also brought an increasing interest in design, architecture and the built environment. Understanding the relationship between the social and the physical is at the heart of both disciplines, and they can obviously benefit from further...... collaboration: How can qualitative anthropological approaches contribute to contemporary architecture? And just as importantly: What can anthropologists learn from architects’ understanding of spatial and material surroundings? Recent theoretical developments in anthropology stress the role of materials...

  19. Architectural Engineers

    DEFF Research Database (Denmark)

    Petersen, Rikke Premer

    engineering is addresses from two perspectives – as an educational response and an occupational constellation. Architecture and engineering are two of the traditional design professions and they frequently meet in the occupational setting, but at educational institutions they remain largely estranged....... The paper builds on a multi-sited study of an architectural engineering program at the Technical University of Denmark and an architectural engineering team within an international engineering consultancy based on Denmark. They are both responding to new tendencies within the building industry where...... the role of engineers and architects increasingly overlap during the design process, but their approaches reflect different perceptions of the consequences. The paper discusses some of the challenges that design education, not only within engineering, is facing today: young designers must be equipped...

  20. A New RTL Design Approach for a DCT/IDCT-Based Image Compression Architecture using the mCBE Algorithm

    Directory of Open Access Journals (Sweden)

    Rachmad Vidya Wicaksana Putra

    2012-09-01

    Full Text Available In the literature, several approaches of designing a DCT/IDCT-based image compression system have been proposed. In this paper, we present a new RTL design approach with as main focus developing a DCT/IDCT-based image compression architecture using a self-created algorithm. This algorithm can efficiently minimize the amount of shifter-adders to substitute multipliers. We call this new algorithm the multiplication from Common Binary Expression (mCBE Algorithm. Besides this algorithm, we propose alternative quantization numbers, which can be implemented simply as shifters in digital hardware. Mostly, these numbers can retain a good compressed-image quality compared to JPEG recommendations. These ideas lead to our design being small in circuit area, multiplierless, and low in complexity. The proposed 8-point 1D-DCT design has only six stages, while the 8-point 1D-IDCT design has only seven stages (one stage being defined as equal to the delay of one shifter or 2-input adder. By using the pipelining method, we can achieve a high-speed architecture with latency as a trade-off consideration. The design has been synthesized and can reach a speed of up to 1.41ns critical path delay (709.22MHz.

  1. Multiple 3d Approaches for the Architectural Study of the Medieval Abbey of Cormery in the Loire Valley

    Science.gov (United States)

    Pouyet, T.

    2017-02-01

    This paper will focus on the technical approaches used for a PhD thesis regarding architecture and spatial organization of benedict abbeys in Touraine in the Middle Ages, in particular the abbey of Cormery in the heart of the Loire Valley. Monastic space is approached in a diachronic way, from the early Middle Ages to the modern times using multi-sources data: architectural study, written sources, ancient maps, various iconographic documents… Many scales are used in the analysis, from the establishment of the abbeys in a territory to the scale of a building like the tower-entrance of the church of Cormery. These methodological axes have been developed in the research unit CITERES for many years and the 3D technology is now used to go further along in that field. The recording in 3D of the buildings of the abbey of Cormery allows us to work at the scale of the monastery and to produce useful data such as sections or orthoimages of the ground and the walls faces which are afterwards drawn and analysed. The study of these documents, crossed with the other historical sources, allowed us to emphasize the presence of walls older than what we thought and to discover construction elements that had not been recognized earlier and which enhance the debate about the construction date St Paul tower and associated the monastic church.

  2. A Multiscale Adaptive Mesh Refinement Approach to Architectured Steel Specification in the Design of a Frameless Stressed Skin Structure

    DEFF Research Database (Denmark)

    Nicholas, Paul; Stasiuk, David; Nørgaard, Esben

    2015-01-01

    This paper describes the development of a modelling approach for the design and fabrication of an incrementally formed, stressed skin metal structure. The term incremental forming refers to a progression of localised plastic deformation to impart 3D form onto a 2D metal sheet, directly from 3D...... design data. A brief introduction presents this fabrication concept, as well as the context of structures whose skin plays a significant structural role. Existing research into ISF privileges either the control of forming parameters to minimise geometric deviation, or the more accurate measurement...... of the impact of the forming process at the scale of the grain. But to enhance structural performance for architectural applications requires that both aspects are considered synthetically. We demonstrate a mesh-based approach that incorporates critical parameters at the scales of structure, element...

  3. Molecular rheology of branched polymers: Decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling

    KAUST Repository

    Van Ruymbeke, Evelyne; Lee, Heecheong; Chang, Taihyun; Nikopoulou, Anastasia; Hadjichristidis, Nikolaos; Snijkers, Frank; Vlassopoulos, Dimitris

    2014-01-01

    the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use

  4. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

    Science.gov (United States)

    Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

    2016-12-01

    Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the K m changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

    Science.gov (United States)

    Newman, Dianne K.; Neubauer, Cajetan; Ricci, Jessica N.; Wu, Chia-Hung; Pearson, Ann

    2016-06-01

    Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

  6. Molecular profiles to biology and pathways: a systems biology approach.

    Science.gov (United States)

    Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

    2016-06-16

    Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

  7. RFID-WSN integrated architecture for energy and delay- aware routing a simulation approach

    CERN Document Server

    Ahmed, Jameel; Tayyab, Muhammad; Nawaz, Menaa

    2015-01-01

    The book identifies the performance challenges concerning Wireless Sensor Networks (WSN) and Radio Frequency Identification (RFID) and analyzes their impact on the performance of routing protocols. It presents a thorough literature survey to identify the issues affecting routing protocol performance, as well as a mathematical model for calculating the end-to-end delays of the routing protocol ACQUIRE; a comparison of two routing protocols (ACQUIRE and DIRECTED DIFFUSION) is also provided for evaluation purposes. On the basis of the results and literature review, recommendations are made for better selection of protocols regarding the nature of the respective application and related challenges. In addition, this book covers a proposed simulator that integrates both RFID and WSN technologies. Therefore, the manuscript is divided in two major parts: an integrated architecture of smart nodes, and a power-optimized protocol for query and information interchange.

  8. A simple three-dimensional macroscopic root water uptake model based on the hydraulic architecture approach

    Directory of Open Access Journals (Sweden)

    V. Couvreur

    2012-08-01

    Full Text Available Many hydrological models including root water uptake (RWU do not consider the dimension of root system hydraulic architecture (HA because explicitly solving water flow in such a complex system is too time consuming. However, they might lack process understanding when basing RWU and plant water stress predictions on functions of variables such as the root length density distribution. On the basis of analytical solutions of water flow in a simple HA, we developed an "implicit" model of the root system HA for simulation of RWU distribution (sink term of Richards' equation and plant water stress in three-dimensional soil water flow models. The new model has three macroscopic parameters defined at the soil element scale, or at the plant scale, rather than for each segment of the root system architecture: the standard sink fraction distribution SSF, the root system equivalent conductance Krs and the compensatory RWU conductance Kcomp. It clearly decouples the process of water stress from compensatory RWU, and its structure is appropriate for hydraulic lift simulation. As compared to a model explicitly solving water flow in a realistic maize root system HA, the implicit model showed to be accurate for predicting RWU distribution and plant collar water potential, with one single set of parameters, in dissimilar water dynamics scenarios. For these scenarios, the computing time of the implicit model was a factor 28 to 214 shorter than that of the explicit one. We also provide a new expression for the effective soil water potential sensed by plants in soils with a heterogeneous water potential distribution, which emerged from the implicit model equations. With the proposed implicit model of the root system HA, new concepts are brought which open avenues towards simple and mechanistic RWU models and water stress functions operational for field scale water dynamics simulation.

  9. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

    Science.gov (United States)

    Dresselhaus, Thomas; Yang, Jack; Kumbhar, Sadhana; Waller, Mark P

    2013-04-09

    Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

  10. An update on conventional and molecular breeding approaches for ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2014-03-05

    Mar 5, 2014 ... review summarizes the updated results of conventional and molecular breeding ... for the development of favorable fibre quality traits in cotton. ... length is the length of fibre with attached seed, and it can be measured with the ...

  11. A graph-clustering approach to search important molecular markers ...

    African Journals Online (AJOL)

    Here, we performed a comprehensive gene level assessment of Parkinson's disease using 16 colorectal cancer samples and nine normal samples. The results show that SLC6A3, SLC18A2, and EN1, etc., are related to Parkinson's disease. Besides, we further mined the underlying molecular mechanism within these ...

  12. molecular biology approach to the search for novel hiv proteases ...

    African Journals Online (AJOL)

    ... which could be tested in the animal models of HIV infection before subjection to clinical trials. Optimistically, the magic HIV therapeutics may be hidden in such insects and may require the application of molecular biology techniques to unravel. KEY WORDS: Antiretroviral drugs, malaria, proteases, restriction enzymes, ...

  13. Architectural prototyping

    DEFF Research Database (Denmark)

    Bardram, Jakob Eyvind; Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2004-01-01

    A major part of software architecture design is learning how specific architectural designs balance the concerns of stakeholders. We explore the notion of "architectural prototypes", correspondingly architectural prototyping, as a means of using executable prototypes to investigate stakeholders...

  14. A three-dimensional vertically aligned functionalized multilayer graphene architecture: an approach for graphene-based thermal interfacial materials.

    Science.gov (United States)

    Liang, Qizhen; Yao, Xuxia; Wang, Wei; Liu, Yan; Wong, Ching Ping

    2011-03-22

    Thermally conductive functionalized multilayer graphene sheets (fMGs) are efficiently aligned in large-scale by a vacuum filtration method at room temperature, as evidenced by SEM images and polarized Raman spectroscopy. A remarkably strong anisotropy in properties of aligned fMGs is observed. High electrical (∼386 S cm(-1)) and thermal conductivity (∼112 W m(-1) K(-1) at 25 °C) and ultralow coefficient of thermal expansion (∼-0.71 ppm K(-1)) in the in-plane direction of A-fMGs are obtained without any reduction process. Aligned fMGs are vertically assembled between contacted silicon/silicon surfaces with pure indium as a metallic medium. Thus-constructed three-dimensional vertically aligned fMG thermal interfacial material (VA-fMG TIM) architecture has significantly higher equivalent thermal conductivity (75.5 W m(-1) K(-1)) and lower contact thermal resistance (5.1 mm2 K W(-1)), compared with their counterpart from A-fMGs that are recumbent between silicon surfaces. This finding provides a throughout approach for a graphene-based TIM assembly as well as knowledge of vertically aligned graphene architectures, which may not only facilitate graphene's application in current demanding thermal management but also promote its widespread applications in electrodes of energy storage devices, conductive polymeric composites, etc.

  15. A Systems Approach to Integrative Biology: An Overview of Statistical Methods to Elucidate Association and Architecture

    OpenAIRE

    Ciaccio, Mark F.; Finkle, Justin D.; Xue, Albert Y.; Bagheri, Neda

    2014-01-01

    An organism’s ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue–signal–...

  16. Extending Failure Modes and Effects Analysis Approach for Reliability Analysis at the Software Architecture Design Level

    NARCIS (Netherlands)

    Sözer, Hasan; Tekinerdogan, B.; Aksit, Mehmet; de Lemos, Rogerio; Gacek, Cristina

    2007-01-01

    Several reliability engineering approaches have been proposed to identify and recover from failures. A well-known and mature approach is the Failure Mode and Effect Analysis (FMEA) method that is usually utilized together with Fault Tree Analysis (FTA) to analyze and diagnose the causes of failures.

  17. Information rich mapping requirement to product architecture through functional system deployment: The multi entity domain approach

    DEFF Research Database (Denmark)

    Hauksdóttir, Dagný; Mortensen, Niels Henrik

    2017-01-01

    may impede the ability to evolve, maintain or reuse systems. In this paper the Multi Entity Domain Approach (MEDA) is presented. The approach combines different design information within the domain views, incorporates both Software and Hardware design and supports iterative requirements definition...

  18. Evolvable Mars Campaign Long Duration Habitation Strategies: Architectural Approaches to Enable Human Exploration Missions

    Science.gov (United States)

    Simon, Matthew A.; Toups, Larry; Howe, A. Scott; Wald, Samuel I.

    2015-01-01

    The Evolvable Mars Campaign (EMC) is the current NASA Mars mission planning effort which seeks to establish sustainable, realistic strategies to enable crewed Mars missions in the mid-2030s timeframe. The primary outcome of the Evolvable Mars Campaign is not to produce "The Plan" for sending humans to Mars, but instead its intent is to inform the Human Exploration and Operations Mission Directorate near-term key decisions and investment priorities to prepare for those types of missions. The FY'15 EMC effort focused upon analysis of integrated mission architectures to identify technically appealing transportation strategies, logistics build-up strategies, and vehicle designs for reaching and exploring Mars moons and Mars surface. As part of the development of this campaign, long duration habitats are required which are capable of supporting crew with limited resupply and crew abort during the Mars transit, Mars moons, and Mars surface segments of EMC missions. In particular, the EMC design team sought to design a single, affordable habitation system whose manufactured units could be outfitted uniquely for each of these missions and reused for multiple crewed missions. This habitat system must provide all of the functionality to safely support 4 crew for long durations while meeting mass and volume constraints for each of the mission segments set by the chosen transportation architecture and propulsion technologies. This paper describes several proposed long-duration habitation strategies to enable the Evolvable Mars Campaign through improvements in mass, cost, and reusability, and presents results of analysis to compare the options and identify promising solutions. The concepts investigated include several monolithic concepts: monolithic clean sheet designs, and concepts which leverage the co-manifested payload capability of NASA's Space Launch System (SLS) to deliver habitable elements within the Universal Payload Adaptor between the SLS upper stage and the Orion

  19. Architecture on Architecture

    DEFF Research Database (Denmark)

    Olesen, Karen

    2016-01-01

    that is not scientific or academic but is more like a latent body of data that we find embedded in existing works of architecture. This information, it is argued, is not limited by the historical context of the work. It can be thought of as a virtual capacity – a reservoir of spatial configurations that can...... correlation between the study of existing architectures and the training of competences to design for present-day realities.......This paper will discuss the challenges faced by architectural education today. It takes as its starting point the double commitment of any school of architecture: on the one hand the task of preserving the particular knowledge that belongs to the discipline of architecture, and on the other hand...

  20. Plant genotoxicity: a molecular cytogenetic approach in plant bioassays.

    Science.gov (United States)

    Maluszynska, Jolanta; Juchimiuk, Jolanta

    2005-06-01

    It is important for the prevention of DNA changes caused by environment to understand the biological consequences of DNA damages and their molecular modes of action that lead to repair or alterations of the genetic material. Numerous genotoxicity assay systems have been developed to identify DNA reactive compounds. The available data show that plant bioassays are important tests in the detection of genotoxic contamination in the environment and the establishment of controlling systems. Plant system can detect a wide range of genetic damage, including gene mutations and chromosome aberrations. Recently introduced molecular cytogenetic methods allow analysis of genotoxicity, both at the chromosomal and DNA level. FISH gives a new possibility of the detection and analysis of chromosomal rearrangements in a great detail. DNA fragmentation can be estimated using the TUNEL test and the single cell gel electrophoresis (Comet assay).

  1. Bioscience methodologies in physical chemistry an engineering and molecular approach

    CERN Document Server

    D'Amore, Alberto

    2013-01-01

    The field of bioscience methodologies in physical chemistry stands at the intersection of the power and generality of classical and quantum physics with the minute molecular complexity of chemistry and biology. This book provides an application of physical principles in explaining and rationalizing chemical and biological phenomena. It does not stick to the classical topics that are conventionally considered as part of physical chemistry; instead it presents principles deciphered from a modern point of view, which is the strength of this book.

  2. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  3. A Complex Approach for Unravelling Musaceae Phylogeny at Molecular Level

    Czech Academy of Sciences Publication Activity Database

    Němcová, Pavla; Hřibová, Eva; Valárik, Miroslav; Doležel, Jaroslav

    2011-01-01

    Roč. 897, SEP 14 (2011), s. 139-142 ISSN 0567-7572. [INTERNATIONAL ISHS-PROMUSA SYMPOSIUM ON GLOBAL PERSPECTIVES ON ASIAN CHALLENGES. Guangzhou, 14.08.2009-16.08.2009] R&D Projects: GA AV ČR IAA600380703 Institutional support: RVO:61389030 Keywords : DArT * low-copy genes * molecular phylogenetics Subject RIV: EF - Botanics http://www.actahort.org/books/897/897_14.htm

  4. Quest: A New Approach to Molecular Staging of Tumors

    Science.gov (United States)

    2004-08-01

    nerve sheath tumors. Cancer Investigation 21:901-918, 2003. "* Book Chapter. Stephens K. Neurofibromatosis. In Molecular Pathology in Clinical Practice...sheath tumors. Cancer Investigation 21:901-918, 2003. (a preprint is provided for your review). 2. Book Chapter. Stephens K. Neurofibromatosis. In...neurofibromatosis. Cancer Res 2002, 62, 1573-1577. 49. Molenaar , W.M., Dijkhuizen, T., van Echten, J., Hoekstra, H.J., van den Berg, E. Cytogenetic support

  5. Toward an integrative molecular approach to wildlife disease.

    Science.gov (United States)

    DeCandia, Alexandra L; Dobson, Andrew P; vonHoldt, Bridgett M

    2018-01-29

    Pathogens pose serious threats to human health, agricultural investment, and biodiversity conservation through the emergence of zoonoses, spillover to domestic livestock, and epizootic outbreaks. As such, wildlife managers are often tasked with mitigating the negative effects of disease. Yet, parasites form a major component of biodiversity that often persist. This is due to logistical challenges of implementing management strategies and to insufficient understanding of host-parasite dynamics. We advocate for an inclusive understanding of molecular diversity in driving parasite infection and variable host disease states in wildlife systems. More specifically, we examine the roles of genetic, epigenetic, and commensal microbial variation in disease pathogenesis. These include mechanisms underlying parasite virulence and host resistance and tolerance, and the development, regulation, and parasite subversion of immune pathways, among other processes. Case studies of devil facial tumor disease in Tasmanian devils (Sarcophilus harrisii) and chytridiomycosis in globally distributed amphibians exemplify the broad range of questions that can be addressed by examining different facets of molecular diversity. For particularly complex systems, integrative molecular analyses present a promising frontier that can provide critical insights necessary to elucidate disease dynamics operating across scales. These insights enable more accurate risk assessment, reconstruction of transmission pathways, discernment of optimal intervention strategies, and development of more effective and ecologically sound treatments that minimize damage to the host population and environment. Such measures are crucial when mitigating threats posed by wildlife disease to humans, domestic animals, and species of conservation concern. © 2018 Society for Conservation Biology.

  6. Metabolistic Architecture

    DEFF Research Database (Denmark)

    2013-01-01

    Textile Spaces presents different approaches to using textile as a spatial definer and artistic medium. The publication collages images and text, art and architecture, science, philosophy and literature, process and product, past, present and future. It forms an insight into soft materials' funct......' functional and poetic potentials, linking the disciplines through fragments that aim to inspire a further look into the artists' and architects' practices, while simultaneously framing these textile visions in a wider context.......Textile Spaces presents different approaches to using textile as a spatial definer and artistic medium. The publication collages images and text, art and architecture, science, philosophy and literature, process and product, past, present and future. It forms an insight into soft materials...

  7. Architectural design led approach to sustainable tourism for the waterfront development of Kunduchi in Tanzania

    Science.gov (United States)

    Leus, M.; Winkels, P.; Hannes, E.

    2018-04-01

    In Kunduchi, located in the Kinondoni district of the Dar es Salaam Region, it is of vital importance for the lives and livelihoods of the indigenous people to preserve the typical ecosystems and ensure the identity and economic resilience of these areas. The problem statement is as follows: In what way can sustainable tourism in Kunduchi serve as an engine for economic and social empowerment? How can Kunduchi be an inspiring example for the development of the coast of Dar Es Salaam in Tanzania that is threatened by large-scale tourist infrastructure? How to design sustainable solutions with respect for the local community and the local traditions? Firstly, a theoretical framework that connects sustainable tourism with the sustainable development of coastal areas is defined. Assumptions made on the basis of the literature review provide parameters that play an important role in the architectural concepts. Secondly, a research by design is presented in order to analyze and evaluate different scenarios to outline the opportunities of sustainable tourism on site of Kunduchi. Sustainable waterfront development is an obvious subtitle since the subtle spatial integration of these projects in the urban and water related context of Dares Salaam is of major importance.

  8. Optimized Architectural Approaches in Hardware and Software Enabling Very High Performance Shared Storage Systems

    CERN Multimedia

    CERN. Geneva

    2004-01-01

    There are issues encountered in high performance storage systems that normally lead to compromises in architecture. Compute clusters tend to have compute phases followed by an I/O phase that must move data from the entire cluster in one operation. That data may then be shared by a large number of clients creating unpredictable read and write patterns. In some cases the aggregate performance of a server cluster must exceed 100 GB/s to minimize the time required for the I/O cycle thus maximizing compute availability. Accessing the same content from multiple points in a shared file system leads to the classical problems of data "hot spots" on the disk drive side and access collisions on the data connectivity side. The traditional method for increasing apparent bandwidth usually includes data replication which is costly in both storage and management. Scaling a model that includes replicated data presents additional management challenges as capacity and bandwidth expand asymmetrically while the system is scaled. ...

  9. Digital museums of the imagined architecture: an integrated approach to the definition of cultural heritage’s knowledge paths

    Directory of Open Access Journals (Sweden)

    Aldo R.D. Accardi

    2016-12-01

    Full Text Available The aim of this work is to highlight a multidisciplinary approach to define new ways of knowledge of architectures and urban contexts that were drawn but never built. In particular, the focus is on a set of 18th century representations, created in the field of scenic illusion. The work was firstly carried out in order to define the structure of a Digital Museum Ontology, a complex semantic resource able to store documents of various typologies. Then, it was elaborated a digital museum project, which starting from existing images will introduce to an interactive way of experiencing the heritage in question. This experimentation has the intent of finding a best practice for the creation of virtual exhibitions. 

  10. A combined reaction class approach with integrated molecular orbital+molecular orbital (IMOMO) methodology: A practical tool for kinetic modeling

    International Nuclear Information System (INIS)

    Truong, Thanh N.; Maity, Dilip K.; Truong, Thanh-Thai T.

    2000-01-01

    We present a new practical computational methodology for predicting thermal rate constants of reactions involving large molecules or a large number of elementary reactions in the same class. This methodology combines the integrated molecular orbital+molecular orbital (IMOMO) approach with our recently proposed reaction class models for tunneling. With the new methodology, we show that it is possible to significantly reduce the computational cost by several orders of magnitude while compromising the accuracy in the predicted rate constants by less than 40% over a wide range of temperatures. Another important result is that the computational cost increases only slightly as the system size increases. (c) 2000 American Institute of Physics

  11. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  12. Molecular hydrodynamic approach to dynamical correlations in quantum liquids

    International Nuclear Information System (INIS)

    Rabani, Eran; Reichman, David R.

    2002-01-01

    A quantum molecular hydrodynamic formalism is developed for the study of dynamics in quantum liquids. The method combines exact static input, generated by path-integral Monte Carlo, and an approximate form of the quantum memory function for the solution of the exact quantum generalized Langevin equation under consideration. This methodology is applied to the study of the spectrum of density fluctuations in liquid para-H 2 . Using a physically motivated approximation for the memory function, semiquantitative agreement is obtained for S(k,ω) in comparison to the recent experiments of Bermejo et al. [Phys. Rev. Lett. 84, 5359 (2000)]. Improvement of the methodology and future applications are discussed

  13. MULTI: a shared memory approach to cooperative molecular modeling.

    Science.gov (United States)

    Darden, T; Johnson, P; Smith, H

    1991-03-01

    A general purpose molecular modeling system, MULTI, based on the UNIX shared memory and semaphore facilities for interprocess communication is described. In addition to the normal querying or monitoring of geometric data, MULTI also provides processes for manipulating conformations, and for displaying peptide or nucleic acid ribbons, Connolly surfaces, close nonbonded contacts, crystal-symmetry related images, least-squares superpositions, and so forth. This paper outlines the basic techniques used in MULTI to ensure cooperation among these specialized processes, and then describes how they can work together to provide a flexible modeling environment.

  14. Functional architecture of visual emotion recognition ability: A latent variable approach.

    Science.gov (United States)

    Lewis, Gary J; Lefevre, Carmen E; Young, Andrew W

    2016-05-01

    Emotion recognition has been a focus of considerable attention for several decades. However, despite this interest, the underlying structure of individual differences in emotion recognition ability has been largely overlooked and thus is poorly understood. For example, limited knowledge exists concerning whether recognition ability for one emotion (e.g., disgust) generalizes to other emotions (e.g., anger, fear). Furthermore, it is unclear whether emotion recognition ability generalizes across modalities, such that those who are good at recognizing emotions from the face, for example, are also good at identifying emotions from nonfacial cues (such as cues conveyed via the body). The primary goal of the current set of studies was to address these questions through establishing the structure of individual differences in visual emotion recognition ability. In three independent samples (Study 1: n = 640; Study 2: n = 389; Study 3: n = 303), we observed that the ability to recognize visually presented emotions is based on different sources of variation: a supramodal emotion-general factor, supramodal emotion-specific factors, and face- and within-modality emotion-specific factors. In addition, we found evidence that general intelligence and alexithymia were associated with supramodal emotion recognition ability. Autism-like traits, empathic concern, and alexithymia were independently associated with face-specific emotion recognition ability. These results (a) provide a platform for further individual differences research on emotion recognition ability, (b) indicate that differentiating levels within the architecture of emotion recognition ability is of high importance, and (c) show that the capacity to understand expressions of emotion in others is linked to broader affective and cognitive processes. (c) 2016 APA, all rights reserved).

  15. Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm.

    Science.gov (United States)

    Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

    2015-05-01

    The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

  16. First approach to molecular epidemiology of bovine tuberculosis in Colombia

    Directory of Open Access Journals (Sweden)

    Jimena Jojoa-Jojoa

    2015-12-01

    Full Text Available Objective. To investigate the presence of Mycobacterium bovis and other Mycobacterium species in samples of cattle and buffalo in Colombia, to start the molecular characterization of M. bovis in the country. Material and methods. 492 samples were collected from herds identified with the presence of infected animals through the PPD, by the Group of Bovine Tuberculosis ICA Colombian Agricultural Institute in eight departments of Colombia. Lymph nodes of head, thorax and abdomen, gross lesions of tissues with tuberculosis, nasal swabs, milk, blood and fresh cheeses were included. Samples were subjected to detection of Mycobacterium bovis and other mycobacteria by conventional microbiological analysis and PCR-6110 and spoligotyping molecular assays. Results. In the samples analyzed especially in lymph nodes, Mycobacterium bovis was demonstrated with genotypes reported and not previously reported in the world, as well as M. tuberculosis in Antioquia, Cundinamarca, Boyacá and Magdalena departments. Conclusions. In Colombia there are at least 7 genotypes of M. bovis that are infected and sick cattle and buffalo from four different departments becoming serious threat to public health.

  17. Microprobing the Molecular Spatial Distribution and Structural Architecture of Feed-type Sorghum Seed Tissue (Sorghum Bicolor L.) using the Synchrotron Radiation Infrared Microspectroscopy Technique

    International Nuclear Information System (INIS)

    Yu, P.

    2011-01-01

    Sorghum seed (Sorghum bicolor L.) has unique degradation and fermentation behaviours compared with other cereal grains such as wheat, barley and corn. This may be related to its cell and cell-wall architecture. The advanced synchrotron radiation infrared microspectroscopy (SR-IMS) technique enables the study of cell or living cell biochemistry within cellular dimensions. The objective of this study was to use the SR-IMS imaging technique to microprobe molecular spatial distribution and cell architecture of the sorghum seed tissue comprehensively. High-density mapping was carried out using SR-IMS on beamline U2B at the National Synchrotron Light Source (Brookhaven National Laboratory, NY, USA). Molecular images were systematically recorded from the outside to the inside of the seed tissue under various chemical functional groups and their ratios [peaks at ∼1725 (carbonyl C=O ester), 1650 (amide I), 1657 (protein secondary structure α-helix), 1628 (protein secondary structure β-sheet), 1550 (amide II), 1515 (aromatic compounds of lignin), 1428, 1371, 1245 (cellulosic compounds in plant seed tissue), 1025 (non-structural CHO, starch granules), 1246 (cellulosic material), 1160 (CHO), 1150 (CHO), 1080 (CHO), 930 (CHO), 860 (CHO), 3350 (OH and NH stretching), 2960 (CH 3 anti-symmetric), 2929 (CH 2 anti-symmetric), 2877 (CH 3 symmetric) and 2848 cm -1 (CH 2 asymmetric)]. The relative protein secondary structure α-helix to β-sheet ratio image, protein amide I to starch granule ratio image, and anti-symmetric CH 3 to CH 2 ratio image were also investigated within the intact sorghum seed tissue. The results showed unique cell architecture, and the molecular spatial distribution and intensity in the sorghum seed tissue (which were analyzed through microprobe molecular imaging) were generated using SR-IMS. This imaging technique and methodology has high potential and could be used for scientists to develop specific cereal grain varieties with targeted food and feed

  18. A Domain-Driven Approach to Digital Curation and Preservation of 3D Architectural Data

    DEFF Research Database (Denmark)

    Lindlar, Michelle; Tamke, Martin

    2014-01-01

    and geometric enrichment, consistent naming schemas and ontologies, as well as pre-ingest tasks in OAIS compliant digital preservation workflows. In a first step, the project identified stakeholders for methods and processes. Since the project strives for a holistic digital preservation approach, different...

  19. A FINITE-ELEMENTS APPROACH TO THE STUDY OF FUNCTIONAL ARCHITECTURE IN SKELETAL-MUSCLE

    NARCIS (Netherlands)

    OTTEN, E; HULLIGER, M

    1994-01-01

    A mathematical model that simulates the mechanical processes inside a skeletal muscle under various conditions of muscle recruitment was formulated. The model is based on the finite-elements approach and simulates both contractile and passive elastic elements. Apart from the classic strategy of

  20. An approach to spin-resolved molecular gas microscopy

    Science.gov (United States)

    Covey, Jacob P.; De Marco, Luigi; Acevedo, Óscar L.; Rey, Ana Maria; Ye, Jun

    2018-04-01

    Ultracold polar molecules are an ideal platform for studying many-body physics with long-range dipolar interactions. Experiments in this field have progressed enormously, and several groups are pursuing advanced apparatus for manipulation of molecules with electric fields as well as single-atom-resolved in situ detection. Such detection has become ubiquitous for atoms in optical lattices and tweezer arrays, but has yet to be demonstrated for ultracold polar molecules. Here we present a proposal for the implementation of site-resolved microscopy for polar molecules, and specifically discuss a technique for spin-resolved molecular detection. We use numerical simulation of spin dynamics of lattice-confined polar molecules to show how such a scheme would be of utility in a spin-diffusion experiment.

  1. Complement Involvement in Periodontitis: Molecular Mechanisms and Rational Therapeutic Approaches.

    Science.gov (United States)

    Hajishengallis, George; Maekawa, Tomoki; Abe, Toshiharu; Hajishengallis, Evlambia; Lambris, John D

    2015-01-01

    The complement system is a network of interacting fluid-phase and cell surface-associated molecules that trigger, amplify, and regulate immune and inflammatory signaling pathways. Dysregulation of this finely balanced network can destabilize host-microbe homeostasis and cause inflammatory tissue damage. Evidence from clinical and animal model-based studies suggests that complement is implicated in the pathogenesis of periodontitis, a polymicrobial community-induced chronic inflammatory disease that destroys the tooth-supporting tissues. This review discusses molecular mechanisms of complement involvement in the dysbiotic transformation of the periodontal microbiome and the resulting destructive inflammation, culminating in loss of periodontal bone support. These mechanistic studies have additionally identified potential therapeutic targets. In this regard, interventional studies in preclinical models have provided proof-of-concept for using complement inhibitors for the treatment of human periodontitis.

  2. Dust and gas distribution in molecular clouds: an observational approach

    International Nuclear Information System (INIS)

    Campeggio, Loretta; Elia, Davide; Maiolo, Berlinda M T; Strafella, Francesco; Cecchi-Pestellini, Cesare

    2005-01-01

    The interstellar medium (ISM), gas and dust, appears to be arranged in clouds, whose dimensions, masses and densities span a large range of scales: from giant molecular clouds to small isolated globules. The structure of these objects show a high degree of complexity appearing, in the range of the observed scales, as a non-homogeneous ('clumpy') distribution of matter. The arrangement of the ISM is clearly relevant for the study of the fragmentation of the clouds and then of the star formation processes. To quantify observationally the ISM structure, many methods have been developed and our study is focused on some of them, exploiting multiwavelength observations of IS objects. The investigations presented here have been carried out by considering both the dust absorption (in optical and near IR wavelengths) and the gas emission (in the submm-radio spectral range). We present the maps obtained from the reduction of raw data and a first tentative analysis by means of methods as the structure function, the autocorrelation, and the Δ-variance. These are appropriate tools to highlight the complex structure of the ISM with reference to the paradigm given by the supersonic turbulence. Three observational cases are briefly discussed. In order to analyse the structure of objects characterized by different sizes, we applied the above-mentioned algorithms to the extinction map of the dark globule CB 107 and to the CO(J = 1-0) integrated intensity map of Vela Molecular Ridge, D Cloud. Finally we compare the results obtained with synthetic fractal maps known as 'fractional Brownian motion' fBm images

  3. Geometrical approach to central molecular chirality: a chirality selection rule

    OpenAIRE

    Capozziello, S.; Lattanzi, A.

    2004-01-01

    Chirality is of primary importance in many areas of chemistry and has been extensively investigated since its discovery. We introduce here the description of central chirality for tetrahedral molecules using a geometrical approach based on complex numbers. According to this representation, for a molecule having n chiral centres, it is possible to define an index of chirality. Consequently a chirality selection rule has been derived which allows the characterization of a molecule as achiral, e...

  4. Molecular approaches to the modification of insect pest populations

    International Nuclear Information System (INIS)

    Crampton, J.M.; Stowell, S.; Parkes, R.; Karras, M.; Sinden, R.E.

    2000-01-01

    After considerable research effort over the last decade or more, the ability to routinely introduce specific genes and other DNA constructs (such as linked promoter:gene cassettes) into a range of pest insect genomes at high efficiency using transgenic approaches is fast becoming a reality. The critical issue that now needs to be addressed is how best to incorporate these techniques into SIT in order to improve its effectiveness or efficiency. Manipulation of insect pest genomes using transgenic approaches may be used in two ways. It may be used as an analytical tool, or to introduce or modify either endogenous or heterologous genes and their expression in the pest insect of choice. In this way, new strains may be generated with a set of desired characteristics beneficial to SIT. In order to realise the full potential of the technology, a number of issues and research areas is being explored and progress to date is reviewed below. Specific examples are drawn from work on mosquito systems in order to illustrate the approaches available to identify genes and promoters of interest and the potential applications to SIT

  5. Polymer Molecular Architecture As a Tool for Controlling the Rheological Properties of Aqueous Polyacrylamide Solutions for Enhanced Oil Recovery

    NARCIS (Netherlands)

    Wever, Diego A. Z.; Polgar, Lorenzo M.; Stuart, Marc C. A.; Picchioni, Francesco; Broekhuis, Antonius A.

    2013-01-01

    The controlled synthesis of high molecular weight branched polyacrylamide (PAM) has been accomplished by using atomic transfer radical polymerization (ATRP) of acrylamide (AM) in water at room temperature. Halogen-functionalized aliphatic polyketones acted as macroinitiators in the polymerization.

  6. A Risk-Constrained Multi-Stage Decision Making Approach to the Architectural Analysis of Mars Missions

    Science.gov (United States)

    Kuwata, Yoshiaki; Pavone, Marco; Balaram, J. (Bob)

    2012-01-01

    This paper presents a novel risk-constrained multi-stage decision making approach to the architectural analysis of planetary rover missions. In particular, focusing on a 2018 Mars rover concept, which was considered as part of a potential Mars Sample Return campaign, we model the entry, descent, and landing (EDL) phase and the rover traverse phase as four sequential decision-making stages. The problem is to find a sequence of divert and driving maneuvers so that the rover drive is minimized and the probability of a mission failure (e.g., due to a failed landing) is below a user specified bound. By solving this problem for several different values of the model parameters (e.g., divert authority), this approach enables rigorous, accurate and systematic trade-offs for the EDL system vs. the mobility system, and, more in general, cross-domain trade-offs for the different phases of a space mission. The overall optimization problem can be seen as a chance-constrained dynamic programming problem, with the additional complexity that 1) in some stages the disturbances do not have any probabilistic characterization, and 2) the state space is extremely large (i.e, hundreds of millions of states for trade-offs with high-resolution Martian maps). To this purpose, we solve the problem by performing an unconventional combination of average and minimax cost analysis and by leveraging high efficient computation tools from the image processing community. Preliminary trade-off results are presented.

  7. Cleaning graphene: A first quantum/classical molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Delfour, L.; Magaud, L., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr [Institut Néel, CNRS/Université Grenoble Alpes, 25 Avenue des Martyrs, 38054 Grenoble (France); Davydova, A.; Despiau-Pujo, E., E-mail: emilie.despiau-pujo@cea.fr, E-mail: laurence.magaud@grenoble.cnrs.fr; Cunge, G. [LTM, CNRS/Université Grenoble Alpes/CEA, 17 Avenue des Martyrs, 38054 Grenoble (France); Graves, D. B. [Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, California 94720 (United States)

    2016-03-28

    Graphene outstanding properties created a huge interest in the condensed matter community and unprecedented fundings at the international scale in the hope of application developments. Recently, there have been several reports of incomplete removal of the polymer resists used to transfer as-grown graphene from one substrate to another, resulting in altered graphene transport properties. Finding a large-scale solution to clean graphene from adsorbed residues is highly desirable and one promising possibility would be to use hydrogen plasmas. In this spirit, we couple here quantum and classical molecular dynamics simulations to explore the kinetic energy ranges required by atomic hydrogen to selectively etch a simple residue—a CH{sub 3} group—without irreversibly damaging the graphene. For incident energies in the 2–15 eV range, the CH{sub 3} radical can be etched by forming a volatile CH{sub 4} compound which leaves the surface, either in the CH{sub 4} form or breaking into CH{sub 3} + H fragments, without further defect formation. At this energy, adsorption of H atoms on graphene is possible and further annealing will be required to recover pristine graphene.

  8. A Motion Planning Approach to Studying Molecular Motions

    KAUST Repository

    Amato, Nancy M.

    2010-01-01

    While structurally very different, protein and RNA molecules share an important attribute. The motions they undergo are strongly related to the function they perform. For example, many diseases such as Mad Cow disease or Alzheimer\\'s disease are associated with protein misfolding and aggregation. Similarly, RNA folding velocity may regulate the plasmid copy number, and RNA folding kinetics can regulate gene expression at the translational level. Knowledge of the stability, folding, kinetics and detailed mechanics of the folding process may help provide insight into how proteins and RNAs fold. In this paper, we present an overview of our work with a computational method we have adapted from robotic motion planning to study molecular motions. We have validated against experimental data and have demonstrated that our method can capture biological results such as stochastic folding pathways, population kinetics of various conformations, and relative folding rates. Thus, our method provides both a detailed view (e.g., individual pathways) and a global view (e.g., population kinetics, relative folding rates, and reaction coordinates) of energy landscapes of both proteins and RNAs. We have validated these techniques by showing that we observe the same relative folding rates as shown in experiments for structurally similar protein molecules that exhibit different folding behaviors. Our analysis has also been able to predict the same relative gene expression rate for wild-type MS2 phage RNA and three of its mutants.

  9. Fracture of Polymers and Interfaces: A Universal Molecular Approach

    Science.gov (United States)

    Wool, Richard

    2003-03-01

    Fracture of polymers, linear or crosslinked, can be viewed as a breaking of molecular connectivity via disentanglement or bond rupture. When treated as a vector percolation phenomenon, we find that it captures the essential physics of fracture and makes broad accurate predictions for strength S, and fracture energy G, of polymers and their interfaces. In the bulk, we find that G ˜ [p-pc], and S ˜ [p-pc]^1/2, where p is the local normalized entanglement density and pc is the percolation threshold. For interfaces, p = nL/w, where n is the areal density of chains of length L ˜M (mol wt) in an interface of width w. For incompatible interfaces of width w, G ˜ [w-wc]; when reinforced with n compatibilizers, G ˜ (n - nc]. For welding, p ˜ L, the welding time tw ˜ L. For adhesion with sticker group X on the polymer and receptor groups Y on the solid, the strength first increases with X, Y and X-Y strength and then decreases after a predictable maximum. For thermosets, the modulus E ˜ [p-pc]^3 and the strength S ˜ [p-pc]^2. Numerous experimental examples are given to support the above universal relations for fracture.

  10. Infrared exploration of the architectural heritage: from passive infrared thermography to hybrid infrared thermography (HIRT approach

    Directory of Open Access Journals (Sweden)

    Sfarra, S.

    2016-09-01

    Full Text Available Up to now, infrared thermographic approaches have been considered either passive or active. In the latter case, the heat flux is historically attributed to a non-natural heat source. The use of the sun has recently been incorporated into the active approach thanks to multi-temporal inspections. In this paper, an innovative hybrid thermographic (HIRT approach is illustrated. It combines both the time component and the solar source to obtain quantitative information such as the defect depth. Thermograms were obtained by inspecting the facade of the Santa Maria Collemaggio church (L’Aquila, Italy, whereas quantitative results related to the sub-superficial discontinuities were obtained thanks to the use of advanced techniques. Experimental results linked to passive approach (i.e., the mosaicking procedure of the thermograms performed by selecting a set of historic churches are also included in order to explain, when and where, the hybrid procedure should be used.Hasta la fecha, los enfoques sobre la termografía infrarroja han sido considerados, o pasivos, o activos. En este último caso, el flujo de calor se obtiene a través de una fuente de calor no natural. El uso de energía solar ha sido recientemente incorporado al enfoque activo gracias a los estudios multitemporales. En este trabajo, se ilustra un enfoque innovador de la termografía híbrida (HIRT. Se combina tanto el componente de tiempo y la fuente de energía solar para recuperar la información cuantitativa así como la profundidad del defecto. Las imágenes térmicas se obtuvieron mediante el análisis de la fachada de la Iglesia de Santa María Collemaggio (L’Aquila, Italia, mientras que los resultados cuantitativos inherentes a las discontinuidades sub-superficiales se obtuvieron gracias al uso de otras técnicas avanzadas. Los resultados experimentales vinculados al enfoque pasivo (es decir, el proceso de mosaico de las imágenes térmicas derivan de un conjunto de Iglesias

  11. Logical-Rule Models of Classification Response Times: A Synthesis of Mental-Architecture, Random-Walk, and Decision-Bound Approaches

    Science.gov (United States)

    Fific, Mario; Little, Daniel R.; Nosofsky, Robert M.

    2010-01-01

    We formalize and provide tests of a set of logical-rule models for predicting perceptual classification response times (RTs) and choice probabilities. The models are developed by synthesizing mental-architecture, random-walk, and decision-bound approaches. According to the models, people make independent decisions about the locations of stimuli…

  12. Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

    Science.gov (United States)

    Bryce, Richard A; Hillier, Ian H

    2014-01-01

    The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

  13. How organisation of architecture documentation affects architectural knowledge retrieval

    NARCIS (Netherlands)

    de Graaf, K.A.; Liang, P.; Tang, A.; Vliet, J.C.

    A common approach to software architecture documentation in industry projects is the use of file-based documents. This approach offers a single-dimensional arrangement of the architectural knowledge. Knowledge retrieval from file-based architecture documentation is efficient if the organisation of

  14. Software architecture evolution

    DEFF Research Database (Denmark)

    Barais, Olivier; Le Meur, Anne-Francoise; Duchien, Laurence

    2008-01-01

    Software architectures must frequently evolve to cope with changing requirements, and this evolution often implies integrating new concerns. Unfortunately, when the new concerns are crosscutting, existing architecture description languages provide little or no support for this kind of evolution....... The software architect must modify multiple elements of the architecture manually, which risks introducing inconsistencies. This chapter provides an overview, comparison and detailed treatment of the various state-of-the-art approaches to describing and evolving software architectures. Furthermore, we discuss...... one particular framework named Tran SAT, which addresses the above problems of software architecture evolution. Tran SAT provides a new element in the software architecture descriptions language, called an architectural aspect, for describing new concerns and their integration into an existing...

  15. An Approach Using Parallel Architecture to Storage DICOM Images in Distributed File System

    International Nuclear Information System (INIS)

    Soares, Tiago S; Prado, Thiago C; Dantas, M A R; De Macedo, Douglas D J; Bauer, Michael A

    2012-01-01

    Telemedicine is a very important area in medical field that is expanding daily motivated by many researchers interested in improving medical applications. In Brazil was started in 2005, in the State of Santa Catarina has a developed server called the CyclopsDCMServer, which the purpose to embrace the HDF for the manipulation of medical images (DICOM) using a distributed file system. Since then, many researches were initiated in order to seek better performance. Our approach for this server represents an additional parallel implementation in I/O operations since HDF version 5 has an essential feature for our work which supports parallel I/O, based upon the MPI paradigm. Early experiments using four parallel nodes, provide good performance when compare to the serial HDF implemented in the CyclopsDCMServer.

  16. DP 71 AND BETA DYSTROGLYCAN INTERACTION: A MOLECULAR MODELING APPROACH TO UNDERSTAND DUCHENNE MUSCULAR DYSTROPHY

    Directory of Open Access Journals (Sweden)

    Simanti Bhattacharya,

    2013-12-01

    Full Text Available Dp 71 is the most prevalent and widely expressed non muscle isoform of dystrophin (Dp and its mutations are associated with Duchenne muscular dystrophy, a severe form of muscular disorder. Dp 71 deviates from the canonical Dp by means of its truncated N terminal which also has abolished certain amino acids that comprise WW domain in the canonical form. This WW domain is very crucial for Dp’s interaction with partner proteins to establish a bridge between extra cellular matrices and cellular cytoskeleton. In our current study we have employed molecular modeling technique to understand the structural architecture of the N terminal region of Dp 71 and its deviation from the canonical form. We have further extended our studies to analyze the interaction probabilities between Dp 71 and β-DG applying molecular docking. Our studies for the first time have revealed that in spite of the underlying differences in terms of amino acids and structural organization, Dp 71 can interact with β-DG with its N terminal region which shares the similar molecular surface with the canonical form of Dp. These findings have opened up a platform to investigate the molecular interactions, spatio temporal orientations of the amino acids of Dp 71 and β-DG to understand the onset of DMD in much more greater detail

  17. Reversible and Selective Encapsulation of Dextromethorphan and β-Estradiol Using an Asymmetric Molecular Capsule Assembled via the Weak-Link Approach.

    Science.gov (United States)

    Mendez-Arroyo, Jose; d'Aquino, Andrea I; Chinen, Alyssa B; Manraj, Yashin D; Mirkin, Chad A

    2017-02-01

    An allosterically regulated, asymmetric receptor featuring a binding cavity large enough to accommodate three-dimensional pharmaceutical guest molecules as opposed to planar, rigid aromatics, was synthesized via the Weak-Link Approach. This architecture is capable of switching between an expanded, flexible "open" configuration and a collapsed, rigid "closed" one. The structure of the molecular receptor can be completely modulated in situ through the use of simple ionic effectors, which reversibly control the coordination state of the Pt(II) metal hinges to open and close the molecular receptor. The substantial change in binding cavity size and electrostatic charge between the two configurations is used to explore the capture and release of two guest molecules, dextromethorphan and β-estradiol, which are widely found as pollutants in groundwater.

  18. A New RTL Design Approach for a DCT/IDCT-Based Image Compression Architecture using the mCBE Algorithm

    Directory of Open Access Journals (Sweden)

    Rachmad Vidya Wicaksana Putra

    2013-09-01

    Full Text Available In  the  literature, several approaches  of  designing  a  DCT/IDCT-based image compression system have been proposed.  In this paper,  we present a new RTL design approach with as main  focus developing a  DCT/IDCT-based image compression  architecture  using  a  self-created  algorithm.  This  algorithm  can efficiently  minimize  the  amount  of  shifter -adders  to  substitute  multiplier s.  We call  this  new  algorithm  the  multiplication  from  Common  Binary  Expression (mCBE  Algorithm. Besides this algorithm, we propose alternative quantization numbers,  which  can  be  implemented  simply  as  shifters  in  digital  hardware. Mostly, these numbers can retain a good compressed-image quality  compared to JPEG  recommendations.  These  ideas  lead  to  our  design  being  small  in  circuit area,  multiplierless,  and  low  in  complexity.  The  proposed  8-point  1D-DCT design  has  only  six  stages,  while  the  8-point  1D-IDCT  design  has  only  seven stages  (one  stage  being  defined as  equal  to  the  delay  of  one  shifter  or  2-input adder. By using the pipelining method, we can achieve a high-speed architecture with latency as    a  trade-off consideration. The  design has been synthesized and can reach a speed of up to 1.41ns critical path delay (709.22MHz. 

  19. Biotechnological and molecular approaches for vanillin production: a review.

    Science.gov (United States)

    Kaur, Baljinder; Chakraborty, Debkumar

    2013-02-01

    Vanillin is one of the most widely used flavoring agents in the world. As the annual world market demand of vanillin could not be met by natural extraction, chemical synthesis, or tissue culture technology, thus biotechnological approaches may be replacement routes to make production of bio-vanillin economically viable. This review's main focus is to highlight significant aspects of biotechnology with emphasis on the production of vanillin from eugenol, isoeugenol, lignin, ferulic acid, sugars, phenolic stilbenes, vanillic acid, aromatic amino acids, and waste residues by applying fungi, bacteria, and plant cells. Production of biovanillin using GRAS lactic acid bacteria and metabolically engineered microorganisms, genetic organization of vanillin biosynthesis operons/gene cassettes and finally the stability of biovanillin generated through various biotechnological procedures are also critically reviewed in the later sections of the review.

  20. A simple approach to CO cooling in molecular clouds

    Science.gov (United States)

    Whitworth, A. P.; Jaffa, S. E.

    2018-03-01

    Carbon monoxide plays an important role in interstellar molecular clouds, both as a coolant, and as a diagnostic molecule. However, a proper evaluation of the cooling rate due to CO requires a determination of the populations of many levels, the spontaneous and stimulated radiative de-excitation rates between these levels, and the transfer of the emitted multi-line radiation; additionally, this must be done for three isotopologues. It would be useful to have a simple analytic formulation that avoided these complications and the associated computational overhead; this could then be used in situations where CO plays an important role as a coolant, but the details of this role are not the main concern. We derive such a formulation here, by first considering the two asymptotic forms that obtain in the limits of (a) low volume-density and optical depth, and (b) high volume-density and optical depth. These forms are then combined in such a way as to fit the detailed numerical results from Goldsmith & Langer (1978, ApJ, 222, 881; hereafter GL78). The GL78 results cover low temperatures, and a range of physical conditions where the interplay of thermal and sub-thermal excitation, optical-depth effects, and the contributions from rare isotopologues, are all important. The fit is obtained using the Metropolis-Hastings method, and reproduces the results of GL78 well. It is a purely local and analytic function of state — specifically a function of the density, ρ, isothermal sound speed, a, CO abundance, XCO, and velocity divergence, ∇ṡυ. As an illustration of its use, we consider the cooling layer following a slow steady non-magnetic planar J-shock. We show that, in this idealised configuration, if the post-shock cooling is dominated by CO and its isotopologues, the thickness of the post-shock cooling layer is very small and approximately independent of the pre-shock velocity, υo, or pre-shock isothermal sound speed, ao.

  1. Description of ionization in the molecular approach to atomic collisions. II

    International Nuclear Information System (INIS)

    Errea, L.F.; Mendez, L.; Riera, A.; Sevila, I.; Harel, C.; Jouin, H.; Pons, B.

    2002-01-01

    We complement a previous article [Harel et al., Phys. Rev. A 55, 287 (1997)] that studied the characteristics of the description of ionization by the molecular approach to atomic collisions, by comparing the wave functions with accurate counterparts. We show how the failure of the basis to describe the phase of the ionizing wave function results in a trapping of the corresponding population in some molecular channels. The time evolution of the molecular wave function then departs from the exact one and the ionization and capture mechanisms appear as interlocked. We thus elucidate the question of the 'natural' boundary of the molecular approach and draw further consequences as to the choice of pseudostates and the use of translation factors

  2. Art and architecture as experience: an alternative approach to bridging art history and the neurosciences.

    Science.gov (United States)

    Zschocke, Nina

    2012-08-01

    In 1972, Michael Baxandal characterizes the processes responsible for the cultural relativism of art experience as highly complex and unknown in their physiological detail. While art history still shows considerable interest in the brain sciences forty years later, most cross-disciplinary studies today are referring to the neurosciences in an attempt to seek scientific legitimization of variations of a generalized and largely deterministic model of perception, reducing interaction between a work of art and its observers to a set of biological automatisms. I will challenge such an approach and take up art theory's interest in the historico-cultural and situational dimensions of art experience. Looking at two examples of large-scale installation and sculptural post-war American art, I will explore instable perceptions of depth and changing experiences of space that indicate complex interactions between perceptual and higher cognitive processes. The argument will draw on recent theories describing neuronal processes underlying multistable phenomena, eye movement, visual attention and decision-making. As I will show a large number of neuroscientific studies provide theoretical models that help us analyse not the anthropological constants but the influence of cultural, individual and situational variables on aesthetic experience.

  3. Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma.

    Science.gov (United States)

    Peng, Xiao-Nu; Wang, Jing; Zhang, Wei

    2017-08-01

    Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.

  4. Molecular Approaches to Understanding C & N Dynamics in MArine Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Arturo Massol; James Tiedje; Jizhong Zhou; Allan Devol

    2007-05-16

    Continental margin sediments constitute only about 10% of the total sediment surface area in the world’s oceans, nevertheless they are the dominant sites of nitrogen (N) cycling. Recent studies suggest that the oceanic nitrogen budget is unbalanced, primarily due to a higher nitrogen removal rate in contrast to the fixation rate, and it has been suggested that denitrification activity contributes significantly to this imbalance. Although denitrification in marine environments has been studied intensively at the process level, little is known about the species abundance, composition, distribution, and functional differences of the denitrifying population. Understanding the diversity of microbial populations in marine environments, their responses to various environmental factors such as NO3-, and how this impact the rate of denitrification is critical to predict global N dynamics. Environmental Microbiology has the prompt to study the influence of each microbial population on a biogeochemical process within a given ecosystem. Culture-dependent and –independent techniques using nucleic acid probes can access the identity and activity of cultured and uncultured microorganisms. Nucleic acid probes can target distintict genes which set phylogenetic relationships, such as rDNA 16S, DNA gyrase (gyrB) and RNA polymerase sigma 70 factor (rpoD). In the other hand, the genetic capabilities and their expression could be tracked using probes that target several functional genes, such as nirS, nirK, nosZ, and nifH, which are genes involved in denitrification. Selective detection of cells actively expressing functional genes within a community using In Situ Reverse Transcription-PCR (ISRT-PCR) could become a powerful culture-independent technique in microbial ecology. Here we describe an approach to study the expression of nirS genes in denitrifying bacteria. Pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans, as well as co-cultures with non

  5. Molecular Phytopathology: Current Approaches and Main Directions in Diagnostics of Woody Plant Diseases

    Directory of Open Access Journals (Sweden)

    O. Yu. Baranov

    2014-08-01

    Full Text Available In the article the authors describe the prospects for diagnosis of woody plants diseases based on the use of modern methods of molecular plant pathology. The metagenomic approach based on the analysis of complex pathogens, including non-pathogenic microflora is described. The use the multicopy universal loci characterized by a number of advantages in determining taxonomic affiliation of infectious agents during phytopathological molecular analysis is proposed.

  6. Dating Antarctic ice sheet collapse: Proposing a molecular genetic approach

    Science.gov (United States)

    Strugnell, Jan M.; Pedro, Joel B.; Wilson, Nerida G.

    2018-01-01

    Sea levels at the end of this century are projected to be 0.26-0.98 m higher than today. The upper end of this range, and even higher estimates, cannot be ruled out because of major uncertainties in the dynamic response of polar ice sheets to a warming climate. Here, we propose an ecological genetics approach that can provide insight into the past stability and configuration of the West Antarctic Ice Sheet (WAIS). We propose independent testing of the hypothesis that a trans-Antarctic seaway occurred at the last interglacial. Examination of the genomic signatures of bottom-dwelling marine species using the latest methods can provide an independent window into the integrity of the WAIS more than 100,000 years ago. Periods of connectivity facilitated by trans-Antarctic seaways could be revealed by dating coalescent events recorded in DNA. These methods allow alternative scenarios to be tested against a fit to genomic data. Ideal candidate taxa for this work would need to possess a circumpolar distribution, a benthic habitat, and some level of genetic structure indicated by phylogeographical investigation. The purpose of this perspective piece is to set out an ecological genetics method to help resolve when the West Antarctic Ice Shelf last collapsed.

  7. Architectural slicing

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak; Hansen, Klaus Marius

    2013-01-01

    Architectural prototyping is a widely used practice, con- cerned with taking architectural decisions through experiments with light- weight implementations. However, many architectural decisions are only taken when systems are already (partially) implemented. This is prob- lematic in the context...... of architectural prototyping since experiments with full systems are complex and expensive and thus architectural learn- ing is hindered. In this paper, we propose a novel technique for harvest- ing architectural prototypes from existing systems, \\architectural slic- ing", based on dynamic program slicing. Given...... a system and a slicing criterion, architectural slicing produces an architectural prototype that contain the elements in the architecture that are dependent on the ele- ments in the slicing criterion. Furthermore, we present an initial design and implementation of an architectural slicer for Java....

  8. A Real Time AI Approach to Discrimination Boost Phase Optical Sensor Systems in SDI Architectures

    Science.gov (United States)

    Sloggett, David R.

    1990-04-01

    are resolved by sensor systems feature data can be extracted on individual objects that can be used by the defence system to attempt to discriminate between warheads, decoys and other penetration aids. This paper reviews work that has arisen from joint US SDIO and UK MOD research programmes into the feasibility of Theatre Missile Defence (TMD) systems that would be suitable for deploy ment and operation in a European theatre. The paper focuses on the problems of threat classification and discrimination in TtD systems and highlights the role of optical sensors. The paper discusses the integration of data derived from optical and radar sensors 6 and expands upon work previously reported into the use of an Artificial Intelligence (AI) approach to object classification and discrimination.

  9. Molecular and Morpho-Agronomical Characterization of Root Architecture at Seedling and Reproductive Stages for Drought Tolerance in Wheat.

    Directory of Open Access Journals (Sweden)

    Ram Sewak Singh Tomar

    Full Text Available Water availability is a major limiting factor for wheat (Triticum aestivum L. production in rain-fed agricultural systems worldwide. Root architecture is important for water and nutrition acquisition for all crops, including wheat. A set of 158 diverse wheat genotypes of Australian (72 and Indian (86 origin were studied for morpho-agronomical traits in field under irrigated and drought stress conditions during 2010-11 and 2011-12.Out of these 31 Indian wheat genotypes comprising 28 hexaploid (Triticum aestivum L. and 3 tetraploid (T. durum were characterized for root traits at reproductive stage in polyvinyl chloride (PVC pipes. Roots of drought tolerant genotypes grew upto137cm (C306 as compared to sensitive one of 63cm with a mean value of 94.8cm. Root architecture traits of four drought tolerant (C306, HW2004, HD2888 and NI5439 and drought sensitive (HD2877, HD2012, HD2851 and MACS2496 genotypes were also observed at 6 and 9 days old seedling stage. The genotypes did not show any significant variation for root traits except for longer coleoptiles and shoot and higher absorptive surface area in drought tolerant genotypes. The visible evaluation of root images using WinRhizo Tron root scanner of drought tolerant genotype HW2004 indicated compact root system with longer depth while drought sensitive genotype HD2877 exhibited higher horizontal root spread and less depth at reproductive stage. Thirty SSR markers were used to study genetic variation which ranged from 0.12 to 0.77 with an average value of 0.57. The genotypes were categorized into three subgroups as highly tolerant, sensitive, moderately sensitive and tolerant as intermediate group based on UPGMA cluster, STRUCTURE and principal coordinate analyses. The genotypic clustering was positively correlated to grouping based on root and morpho-agronomical traits. The genetic variability identified in current study demonstrated these traits can be used to improve drought tolerance and

  10. Molecular and Morpho-Agronomical Characterization of Root Architecture at Seedling and Reproductive Stages for Drought Tolerance in Wheat

    Science.gov (United States)

    Vinod; Naik, Bhojaraja K.; Chand, Suresh; Deshmukh, Rupesh; Mallick, Niharika; Singh, Sanjay; Singh, Nagendra Kumar; Tomar, S. M. S.

    2016-01-01

    Water availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root architecture is important for water and nutrition acquisition for all crops, including wheat. A set of 158 diverse wheat genotypes of Australian (72) and Indian (86) origin were studied for morpho-agronomical traits in field under irrigated and drought stress conditions during 2010–11 and 2011-12.Out of these 31 Indian wheat genotypes comprising 28 hexaploid (Triticum aestivum L.) and 3 tetraploid (T. durum) were characterized for root traits at reproductive stage in polyvinyl chloride (PVC) pipes. Roots of drought tolerant genotypes grew upto137cm (C306) as compared to sensitive one of 63cm with a mean value of 94.8cm. Root architecture traits of four drought tolerant (C306, HW2004, HD2888 and NI5439) and drought sensitive (HD2877, HD2012, HD2851 and MACS2496) genotypes were also observed at 6 and 9 days old seedling stage. The genotypes did not show any significant variation for root traits except for longer coleoptiles and shoot and higher absorptive surface area in drought tolerant genotypes. The visible evaluation of root images using WinRhizo Tron root scanner of drought tolerant genotype HW2004 indicated compact root system with longer depth while drought sensitive genotype HD2877 exhibited higher horizontal root spread and less depth at reproductive stage. Thirty SSR markers were used to study genetic variation which ranged from 0.12 to 0.77 with an average value of 0.57. The genotypes were categorized into three subgroups as highly tolerant, sensitive, moderately sensitive and tolerant as intermediate group based on UPGMA cluster, STRUCTURE and principal coordinate analyses. The genotypic clustering was positively correlated to grouping based on root and morpho-agronomical traits. The genetic variability identified in current study demonstrated these traits can be used to improve drought tolerance and association

  11. Architectural Theatricality

    DEFF Research Database (Denmark)

    Tvedebrink, Tenna Doktor Olsen; Fisker, Anna Marie; Kirkegaard, Poul Henning

    2013-01-01

    In the attempt to improve patient treatment and recovery, researchers focus on applying concepts of hospitality to hospitals. Often these concepts are dominated by hotel-metaphors focusing on host–guest relationships or concierge services. Motivated by a project trying to improve patient treatment...... is known for his writings on theatricality, understood as a holistic design approach emphasizing the contextual, cultural, ritual and social meanings rooted in architecture. Relative hereto, the International Food Design Society recently argued, in a similar holistic manner, that the methodology used...... to provide an aesthetic eating experience includes knowledge on both food and design. Based on a hermeneutic reading of Semper’s theory, our thesis is that this holistic design approach is important when debating concepts of hospitality in hospitals. We use this approach to argue for how ‘food design...

  12. Novel in situ multiharmonic EQCM-D approach to characterize complex carbon pore architectures for capacitive deionization of brackish water

    International Nuclear Information System (INIS)

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Aurbach, Doron; Daikhin, Leonid; Presser, Volker

    2016-01-01

    Multiharmonic analysis by electrochemical quartz-crystal microbalance with dissipation monitoring (EQCM-D) is introduced as an excellent tool for quantitative studying electrosorption of ions from aqueous solution in mesoporous (BP-880) or mixed micro-mesoporous (BP-2000) carbon electrodes. Finding the optimal conditions for gravimetric analysis of the ionic content in the charged carbon electrodes, we propose a novel approach to modeling the charge-dependent gravimetric characteristics by incorporation of Gouy-Chapman-Stern electric double layer model for ions electrosorption into meso- and micro-mesoporous carbon electrodes. All three parameters of the gravimetric equation evaluated by fitting it to the experimental mass changes curves were validated using supplementary nitrogen gas sorption analysis and complementing atomic force microscopy. Important overlap between gravimetric EQCM-D analysis of the ionic content of porous carbon electrodes and the classical capacitive deionization models has been established. The necessity and usefulness of non-gravimetric EQCM-D characterizations of complex carbon architectures, providing insight into their unique viscoelastic behavior and porous structure changes, have been discussed in detail. (paper)

  13. A new approach for generating bispecific antibodies based on a common light chain format and the stable architecture of human immunoglobulin G1.

    Science.gov (United States)

    De Nardis, Camilla; Hendriks, Linda J A; Poirier, Emilie; Arvinte, Tudor; Gros, Piet; Bakker, Alexander B H; de Kruif, John

    2017-09-01

    Bispecific antibodies combine two different antigen-binding sites in a single molecule, enabling more specific targeting, novel mechanisms of action, and higher clinical efficacies. Although they have the potential to outperform conventional monoclonal antibodies, many bispecific antibodies have issues regarding production, stability, and pharmacokinetic properties. Here, we describe a new approach for generating bispecific antibodies using a common light chain format and exploiting the stable architecture of human immunoglobulin G 1 We used iterative experimental validation and computational modeling to identify multiple Fc variant pairs that drive efficient heterodimerization of the antibody heavy chains. Accelerated stability studies enabled selection of one Fc variant pair dubbed "DEKK" consisting of substitutions L351D and L368E in one heavy chain combined with L351K and T366K in the other. Solving the crystal structure of the DEKK Fc region at a resolution of 2.3 Å enabled detailed analysis of the interactions inducing CH3 interface heterodimerization. Local shifts in the IgG backbone accommodate the introduction of lysine side chains that form stabilizing salt-bridge interactions with substituted and native residues in the opposite chain. Overall, the CH3 domain adapted to these shifts at the interface, yielding a stable Fc conformation very similar to that in wild-type IgG. Using the DEKK format, we generated the bispecific antibody MCLA-128, targeting human EGF receptors 2 and 3. MCLA-128 could be readily produced and purified at industrial scale with a standard mammalian cell culture platform and a routine purification protocol. Long-term accelerated stability assays confirmed that MCLA-128 is highly stable and has excellent biophysical characteristics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Engineering nanomaterials with a combined electrochemical and molecular biomimetic approach

    Science.gov (United States)

    Dai, Haixia

    Biocomposite materials, such as bones, teeth, and shells, are created using mild aqueous solution-based processes near room temperature. Proteins add flexibility to these processes by facilitating the nucleation, growth, and ordering of specific inorganic materials into hierarchical structures. We aim to develop a biomimetic strategy for engineering technologically relevant inorganic materials with controlled compositions and structures, as Nature does, using proteins to orchestrate material formation and assembly. This approach involves three basic steps: (i) preparation of inorganic substrates compatible with combinatorial polypeptide screening; (ii) identification of inorganic-binding polypeptides and their engineering into inorganic-binding proteins; and (iii) protein-mediated inorganic nucleation and organization. Cuprous oxide (Cu2O), a p-type semiconductor, has been used to demonstrate all three steps. Zinc oxide (ZnO), an n-type semiconductor, has been used to show the generality of selected steps. Step (i), preparation of high quality inorganic substrates to select inorganic-binding polypeptides, was accomplished using electrochemical microfabrication to grow and pattern Cu2O and ZnO. Raman spectroscopy and x-ray photoelectron spectroscopy were used to verify phase purity and compositional stability of these surfaces during polypeptide screening. Step (ii), accomplished in collaboration with personnel in Prof Baneyx' lab at the University of Washington, involved incubating the inorganic substrates with the FliTrx(TM) random peptide library to identify cysteine-constrained dodecapeptides that bind the targeted inorganic. Insertion of a Cu2O-binding dodecapeptide into the DNA-binding protein TraI endowed the engineered TraI with strong affinity for Cu2O (Kd ≈ 10 -8 M). Finally, step (iii) involved nonequilibrium synthesis and organization of Cu2O nanoparticles, taking advantage of the inorganic and DNA recognition properties of the engineered TraI. The

  15. Evaluation of the molecular level visualisation approach for teaching and learning chemistry in Thailand

    Science.gov (United States)

    Phenglengdi, Butsari

    This research evaluates the use of a molecular level visualisation approach in Thai secondary schools. The goal is to obtain insights about the usefulness of this approach, and to examine possible improvements in how the approach might be applied in the future. The methodology used for this research used both qualitative and quantitative approaches. Data were collected in the form of pre- and post-intervention multiple choice questions, open-ended-questions, drawing exercises, one-to-one interviews and video recordings of class activity. The research was conducted in two phases, involving a total of 261 students from the 11th Grade in Thailand. The use of VisChem animations in three studies was evaluated in Phase I. Study 1 was a pilot study exploring the benefits of incorporating VisChem animations to portray the molecular level. Study 2 compared test results between students exposed to these animations of molecular level events, and those not. Finally, in Study 3, test results were gathered from different types of schools (a rural school, a city school, and a university school). The results showed that students (and teachers) had misconceptions at the molecular level, and VisChem animations could help students understand chemistry concepts at the molecular level across all three types of schools. While the animation treatment group had a better score on the topic of states of water, the non-animation treatment group had a better score on the topic of dissolving sodium chloride in water than the animation group. The molecular level visualisation approach as a learning design was evaluated in Phase II. This approach involved a combination of VisChem animations, pictures, and diagrams together with the seven-step VisChem learning design. The study involved three classes of students, each with a different treatment, described as Class A - Traditional approach; Class B - VisChem animations with traditional approach; and Class C - Molecular level visualisation approach

  16. Annual dynamics of daylight variability and contrast a simulation-based approach to quantifying visual effects in architecture

    CERN Document Server

    Rockcastle, Siobhan

    2013-01-01

    Daylight is a dynamic source of illumination in architectural space, creating diverse and ephemeral configurations of light and shadow within the built environment. Perceptual qualities of daylight, such as contrast and temporal variability, are essential to our understanding of both material and visual effects in architecture. Although spatial contrast and light variability are fundamental to the visual experience of architecture, architects still rely primarily on intuition to evaluate their designs because there are few metrics that address these factors. Through an analysis of contemporary

  17. A Sustainable, Reliable Mission-Systems Architecture that Supports a System of Systems Approach to Space Exploration

    Science.gov (United States)

    Watson, Steve; Orr, Jim; O'Neil, Graham

    2004-01-01

    A mission-systems architecture based on a highly modular "systems of systems" infrastructure utilizing open-standards hardware and software interfaces as the enabling technology is absolutely essential for an affordable and sustainable space exploration program. This architecture requires (a) robust communication between heterogeneous systems, (b) high reliability, (c) minimal mission-to-mission reconfiguration, (d) affordable development, system integration, and verification of systems, and (e) minimum sustaining engineering. This paper proposes such an architecture. Lessons learned from the space shuttle program are applied to help define and refine the model.

  18. Information Architecture: Looking Ahead.

    Science.gov (United States)

    Rosenfeld, Louis

    2002-01-01

    Considers the future of the field of information architecture. Highlights include a comparison with the growth of the field of professional management; the design of information systems since the Web; more demanding users; the need for an interdisciplinary approach; and how to define information architecture. (LRW)

  19. Gradient Architecture as Means of Phase Diagram Manipulation in Copolymers: Accessing Both LCOT and UCOT in High Molecular Weight Styrene/n-Butyl Acrylate Systems

    Science.gov (United States)

    Mok, Michelle; Burghardt, Wesley; Ellison, Christopher; Torkelson, John

    2009-03-01

    Traditionally, phase transitions of block copolymers could only be tuned through molecular weight and relative block length. Here, we introduce comonomer sequence design through gradient compositions as a means of further manipulating phase diagram boundaries. In such gradient copolymers, the reduced repulsion between chain segments allows access to phase transitions even at high molecular weights (MW). Rheological and x-ray scattering studies were performed to study the impact of comonomer sequence on phase behavior in styrene/n-butyl acrylate (S/nBA) systems. In S/nBA block copolymers, only upper critical ordering behavior was observed. In contrast, by using a gradient architecture of higher MW we observed both upper and lower ordering transitions similar to those seen in very weakly segregating S/n-butyl methacrylate block copolymers, where such dual ordering transitions were first detected by Russell et al. This is the first study to access a miscibility gap in gradient copolymers. Access to such behavior is very rare in blends and block copolymers, limited to low MW and/or very weakly segregating systems.

  20. The role of molecular architecture and layer composition on the properties and performance of CuPc-C6 photovoltaic devices

    International Nuclear Information System (INIS)

    Schultes, S.M.; Sullivan, P.; Heutz, S.; Sanderson, B.M.; Jones, T.S.

    2005-01-01

    We have studied the effects of molecular architecture, co-deposition and annealing on the properties and performance of photovoltaic cells based on copper phthalocyanine (CuPc)-fullerene (C 6 ) heterojunctions. Significant improvements in performance are achieved when mixed CuPc:C 6 layers are incorporated into the device structure due to the creation of an intermolecularly mixed donor (D)-acceptor (A) blend that favours efficient exciton dissociation. We utilise the control afforded by organic molecular beam deposition to show that the mixed-layer composition plays an important role in determining device performance and correlate device efficiency to the morphological and spectroscopic properties of the organic layers. A maximum power conversion efficiency of η p = 1.17% is achieved for devices containing a mixed layer of ratio 75:25 CuPc:C 6 surrounded by thin continuous layers of pure organic material at the electrode interfaces. A structure containing a compositional gradient where the CuPc:C 6 composition is varied from purely D to purely A via three mixed layers of increasing A composition leads to a further improvements in efficiency (η p = 1.36%). Finally, we use thermal annealing to show how structural defects and morphological templating of organic thin films reduces the interfacial area for exciton separation and yields poor device performance

  1. Towards a Media Architecture

    DEFF Research Database (Denmark)

    Ebsen, Tobias

    2010-01-01

    This text explores the concept of media architecture as a phenomenon of visual culture that describes the use of screen-technology in new spatial configurations in practices of architecture and art. I shall argue that this phenomenon is not necessarily a revolutionary new approach, but rather...... a result of conceptual changes in both modes visual representation and in expressions of architecture. These are changes the may be described as an evolution of ideas and consequent experiments that can be traced back to changes in the history of art and the various styles and ideologies of architecture....

  2. Controlling Microstructure-Transport Interplay in Highly Phase-Separated Perfluorosulfonated Aromatic Multiblock Ionomers via Molecular Architecture Design.

    Science.gov (United States)

    Nguyen, Huu-Dat; Assumma, Luca; Judeinstein, Patrick; Mercier, Regis; Porcar, Lionel; Jestin, Jacques; Iojoiu, Cristina; Lyonnard, Sandrine

    2017-01-18

    Proton-conducting multiblock polysulfones bearing perfluorosulfonic acid side chains were designed to encode nanoscale phase-separation, well-defined hydrophilic/hydrophobic interfaces, and optimized transport properties. Herein, we show that the superacid side chains yield highly ordered morphologies that can be tailored by best compromising ion-exchange capacity and block lengths. The obtained microstructures were extensively characterized by small-angle neutron scattering (SANS) over an extended range of hydration. Peculiar swelling behaviors were evidenced at two different scales and attributed to the dilution of locally flat polymer particles. We evidence the direct correlation between the quality of interfaces, the topology and connectivity of ionic nanodomains, the block superstructure long-range organization, and the transport properties. In particular, we found that the proton conductivity linearly depends on the microscopic expansion of both ionic and block domains. These findings indicate that neat nanoscale phase-separation and block-induced long-range connectivity can be optimized by designing aromatic ionomers with controlled architectures to improve the performances of polymer electrolyte membranes.

  3. Enterprise architecture management

    DEFF Research Database (Denmark)

    Rahimi, Fatemeh; Gøtze, John; Møller, Charles

    2017-01-01

    Despite the growing interest in enterprise architecture management, researchers and practitioners lack a shared understanding of its applications in organizations. Building on findings from a literature review and eight case studies, we develop a taxonomy that categorizes applications of enterprise...... architecture management based on three classes of enterprise architecture scope. Organizations may adopt enterprise architecture management to help form, plan, and implement IT strategies; help plan and implement business strategies; or to further complement the business strategy-formation process....... The findings challenge the traditional IT-centric view of enterprise architecture management application and suggest enterprise architecture management as an approach that could support the consistent design and evolution of an organization as a whole....

  4. Enterprise architecture management

    DEFF Research Database (Denmark)

    Rahimi, Fatemeh; Gøtze, John; Møller, Charles

    2017-01-01

    architecture management based on three classes of enterprise architecture scope. Organizations may adopt enterprise architecture management to help form, plan, and implement IT strategies; help plan and implement business strategies; or to further complement the business strategy-formation process......Despite the growing interest in enterprise architecture management, researchers and practitioners lack a shared understanding of its applications in organizations. Building on findings from a literature review and eight case studies, we develop a taxonomy that categorizes applications of enterprise....... The findings challenge the traditional IT-centric view of enterprise architecture management application and suggest enterprise architecture management as an approach that could support the consistent design and evolution of an organization as a whole....

  5. Proteomic-Biostatistic Integrated Approach for Finding the Underlying Molecular Determinants of Hypertension in Human Plasma.

    Science.gov (United States)

    Gajjala, Prathibha R; Jankowski, Vera; Heinze, Georg; Bilo, Grzegorz; Zanchetti, Alberto; Noels, Heidi; Liehn, Elisa; Perco, Paul; Schulz, Anna; Delles, Christian; Kork, Felix; Biessen, Erik; Narkiewicz, Krzysztof; Kawecka-Jaszcz, Kalina; Floege, Juergen; Soranna, Davide; Zidek, Walter; Jankowski, Joachim

    2017-08-01

    Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis. Using biostatistical methods, plasma peptides specific for hypertension were identified, and a model was developed using least absolute shrinkage and selection operator logistic regression. The underlying peptides were identified and sequenced off-line using matrix-assisted laser desorption ionization orbitrap mass spectrometry. By comparison of the molecular composition of the plasma samples, 27 molecular determinants were identified differently expressed in cases from controls. Seventy percent of the molecular determinants selected were found to occur less likely in hypertensive patients. In cross-validation, the overall R 2 was 0.434, and the area under the curve was 0.891 with 95% confidence interval 0.8482 to 0.9349, P hypertensive patients were found to be -2.007±0.3568 and 3.383±0.2643, respectively, P hypertensives and normotensives. The identified molecular determinants may be the starting point for further studies to clarify the molecular causes of hypertension. © 2017 American Heart Association, Inc.

  6. Preparation and antifouling properties of 2-(meth-acryloyloxy)ethyl cholinephosphate based polymers modified surface with different molecular architectures by ATRP.

    Science.gov (United States)

    Jiang, Yuchen; Su, Yuling; Zhao, Lili; Meng, Fancui; Wang, Quanxin; Ding, Chunmei; Luo, Jianbin; Li, Jianshu

    2017-08-01

    Choline phosphate (CP) containing polymers modified surfaces have been shown good resist to the adhesion of proteins while prompt the attaching of mammalian cells due to the dipole pairing between the CP groups of the polymer and the phosphorylcholine (PC) groups on the cell membrane. However, the antifouling activities of CP modified surface against microbes have not been investigated at present. In addition, CP containing polymers modified surface with different molecular architectures has not been prepared and studied. To this end, glass slides surface modified with two different 2-(meth-acryloyloxy)ethyl cholinephosphate (MCP) containing polymer (PMCP) structures, i.e. brush-like (Glass-PMCP) and bottle brush-like (Glass-PHEMA-g-PMCP) architectures, were prepared in this work by surface-initiated atom transfer radical polymerization (SI-ATRP). The surface physichemical and antifouling properties of the prepared surfaces were characterized and studied. The Glass-PMCP shows improved antifouling properties against proteins and bacteria as compared to pristine glass slides (Glass-OH) and glass slides grafted with poly(2-hydroxyethyl methacrylate) (Glass-PHEMA). Notably, a synergetic fouling resistant properties of PHEMA and PMCP is presented for Glass-PHEMA-g-PMCP, which shows superior antifouling activities over Glass-PHEMA and Glass-PMCP. Furthermore, glass slides containing PMCP, i.e. Glass-PMCP and Glas-PHEMA-g-PMCP, decrease platelet adhesion and prevent their activation significantly. Therefore, the combination of antifouling PHEMA and PMCP into one system holds potential for prevention of bacterial fouling and biomaterial-centered infections. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Layered Fault Management Architecture

    National Research Council Canada - National Science Library

    Sztipanovits, Janos

    2004-01-01

    ... UAVs or Organic Air Vehicles. The approach of this effort was to analyze fault management requirements of formation flight for fleets of UAVs, and develop a layered fault management architecture which demonstrates significant...

  8. A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks

    Directory of Open Access Journals (Sweden)

    Xuezhong Zhou

    2018-05-01

    Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine

  9. Precision medicine and molecular imaging: new targeted approaches toward cancer therapeutic and diagnosis

    Science.gov (United States)

    Ghasemi, Mojtaba; Nabipour, Iraj; Omrani, Abdolmajid; Alipour, Zeinab; Assadi, Majid

    2016-01-01

    This paper presents a review of the importance and role of precision medicine and molecular imaging technologies in cancer diagnosis with therapeutics and diagnostics purposes. Precision medicine is progressively becoming a hot topic in all disciplines related to biomedical investigation and has the capacity to become the paradigm for clinical practice. The future of medicine lies in early diagnosis and individually appropriate treatments, a concept that has been named precision medicine, i.e. delivering the right treatment to the right patient at the right time. Molecular imaging is quickly being recognized as a tool with the potential to ameliorate every aspect of cancer treatment. On the other hand, emerging high-throughput technologies such as omics techniques and systems approaches have generated a paradigm shift for biological systems in advanced life science research. In this review, we describe the precision medicine, difference between precision medicine and personalized medicine, precision medicine initiative, systems biology/medicine approaches (such as genomics, radiogenomics, transcriptomics, proteomics, and metabolomics), P4 medicine, relationship between systems biology/medicine approaches and precision medicine, and molecular imaging modalities and their utility in cancer treatment and diagnosis. Accordingly, the precision medicine and molecular imaging will enable us to accelerate and improve cancer management in future medicine. PMID:28078184

  10. Precision medicine and molecular imaging: new targeted approaches toward cancer therapeutic and diagnosis.

    Science.gov (United States)

    Ghasemi, Mojtaba; Nabipour, Iraj; Omrani, Abdolmajid; Alipour, Zeinab; Assadi, Majid

    2016-01-01

    This paper presents a review of the importance and role of precision medicine and molecular imaging technologies in cancer diagnosis with therapeutics and diagnostics purposes. Precision medicine is progressively becoming a hot topic in all disciplines related to biomedical investigation and has the capacity to become the paradigm for clinical practice. The future of medicine lies in early diagnosis and individually appropriate treatments, a concept that has been named precision medicine, i.e. delivering the right treatment to the right patient at the right time. Molecular imaging is quickly being recognized as a tool with the potential to ameliorate every aspect of cancer treatment. On the other hand, emerging high-throughput technologies such as omics techniques and systems approaches have generated a paradigm shift for biological systems in advanced life science research. In this review, we describe the precision medicine, difference between precision medicine and personalized medicine, precision medicine initiative, systems biology/medicine approaches (such as genomics, radiogenomics, transcriptomics, proteomics, and metabolomics), P4 medicine, relationship between systems biology/medicine approaches and precision medicine, and molecular imaging modalities and their utility in cancer treatment and diagnosis. Accordingly, the precision medicine and molecular imaging will enable us to accelerate and improve cancer management in future medicine.

  11. A novel approach to locomotion learning: Actor-Critic architecture using central pattern generators and dynamic motor primitives.

    Science.gov (United States)

    Li, Cai; Lowe, Robert; Ziemke, Tom

    2014-01-01

    In this article, we propose an architecture of a bio-inspired controller that addresses the problem of learning different locomotion gaits for different robot morphologies. The modeling objective is split into two: baseline motion modeling and dynamics adaptation. Baseline motion modeling aims to achieve fundamental functions of a certain type of locomotion and dynamics adaptation provides a "reshaping" function for adapting the baseline motion to desired motion. Based on this assumption, a three-layer architecture is developed using central pattern generators (CPGs, a bio-inspired locomotor center for the baseline motion) and dynamic motor primitives (DMPs, a model with universal "reshaping" functions). In this article, we use this architecture with the actor-critic algorithms for finding a good "reshaping" function. In order to demonstrate the learning power of the actor-critic based architecture, we tested it on two experiments: (1) learning to crawl on a humanoid and, (2) learning to gallop on a puppy robot. Two types of actor-critic algorithms (policy search and policy gradient) are compared in order to evaluate the advantages and disadvantages of different actor-critic based learning algorithms for different morphologies. Finally, based on the analysis of the experimental results, a generic view/architecture for locomotion learning is discussed in the conclusion.

  12. A Novel Approach to Locomotion Learning: Actor-Critic Architecture using Central Pattern Generators and Dynamic Motor Primitives

    Directory of Open Access Journals (Sweden)

    Cai eLi

    2014-10-01

    Full Text Available In this article, we propose an architecture of a bio-inspired controller that addresses the problem of learning different locomotion gaits for different robot morphologies. The modelling objective is split into two: baseline motion modelling and dynamics adaptation. Baseline motion modelling aims to achieve fundamental functions of a certain type of locomotion and dynamics adaptation provides a ``reshaping function for adapting the baseline motion to desired motion. Based on this assumption, a three-layer architecture is developed using central pattern generators (CPGs, a bio-inspired locomotor center for the the baseline motion and dynamic motor primitives (DMPs, a model with universal ``reshaping functions. In this article, we use this architecture with the actor-critic algorithms for finding a good ``reshaping function. In order to demonstrate the learning power of the actor-critic based architecture, we tested it on two experiments: 1 learning to crawl on a humanoid and, 2 learning to gallop on a puppy robot. Two types of actor-critic algorithms (policy search and policy gradient are compared in order to evaluate the advantages and disadvantages of different actor-critic based learning algorithms for different morphologies. Finally, based on the analysis of the experimental results, a generic view/architecture for locomotion learning is discussed in the conclusion.

  13. Robotic architectures

    CSIR Research Space (South Africa)

    Mtshali, M

    2010-01-01

    Full Text Available In the development of mobile robotic systems, a robotic architecture plays a crucial role in interconnecting all the sub-systems and controlling the system. The design of robotic architectures for mobile autonomous robots is a challenging...

  14. Harnessing the Risk-Related Data Supply Chain: An Information Architecture Approach to Enriching Human System Research and Operations Knowledge

    Science.gov (United States)

    Buquo, Lynn E.; Johnson-Throop, Kathy A.

    2011-01-01

    An Information Architecture facilitates the understanding and, hence, harnessing of the human system risk-related data supply chain which enhances the ability to securely collect, integrate, and share data assets that improve human system research and operations. By mapping the risk-related data flow from raw data to useable information and knowledge (think of it as a data supply chain), the Human Research Program (HRP) and Space Life Science Directorate (SLSD) are building an information architecture plan to leverage their existing, and often shared, IT infrastructure.

  15. Architecture & Environment

    Science.gov (United States)

    Erickson, Mary; Delahunt, Michael

    2010-01-01

    Most art teachers would agree that architecture is an important form of visual art, but they do not always include it in their curriculums. In this article, the authors share core ideas from "Architecture and Environment," a teaching resource that they developed out of a long-term interest in teaching architecture and their fascination with the…

  16. An Architecture for Performance Optimization in a Collaborative Knowledge-Based Approach for  Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Juan Ramon Velasco

    2011-09-01

    Full Text Available Over the past few years, Intelligent Spaces (ISs have received the attention of many Wireless Sensor Network researchers. Recently, several studies have been devoted to identify their common capacities and to set up ISs over these networks. However, little attention has been paid to integrating Fuzzy Rule-Based Systems into collaborative Wireless Sensor Networks for the purpose of implementing ISs. This work presents a distributed architecture proposal for collaborative Fuzzy Rule-Based Systems embedded in Wireless Sensor Networks, which has been designed to optimize the implementation of ISs. This architecture includes the following: (a an optimized design for the inference engine; (b a visual interface; (c a module to reduce the redundancy and complexity of the knowledge bases; (d a module to evaluate the accuracy of the new knowledge base; (e a module to adapt the format of the rules to the structure used by the inference engine; and (f a communications protocol. As a real-world application of this architecture and the proposed methodologies, we show an application to the problem of modeling two plagues of the olive tree: prays (olive moth, Prays oleae Bern. and repilo (caused by the fungus Spilocaea oleagina. The results show that the architecture presented in this paper significantly decreases the consumption of resources (memory, CPU and battery without a substantial decrease in the accuracy of the inferred values.

  17. A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

    Directory of Open Access Journals (Sweden)

    Satoshi Uchida

    2018-02-01

    Full Text Available Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”. In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

  18. A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

    Science.gov (United States)

    Uchida, Satoshi; Yamamoto, Hitoshi; Okada, Isamu; Sasaki, Tatsuya

    2018-02-01

    Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”). In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

  19. An approach towards understanding the structure of complex molecular systems: the case of lower aliphatic alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Vrhovsek, Aleksander; Gereben, Orsolya; Pothoczki, Szilvia; Pusztai, Laszlo [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, H-1525 Budapest, PO Box 49 (Hungary); Tomsic, Matija; Jamnik, Andrej [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, SI-1001 Ljubljana (Slovenia); Kohara, Shinji, E-mail: aleksander.vrhovsek@gmail.co [Research and Utilization Division, Japan Synchrotron Radiation Research Institute (JASRI, SPring-8), 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-10-13

    An extensive study of liquid aliphatic alcohols methanol, ethanol, and propanol, applying reverse Monte Carlo modelling as a method of interpretation of diffraction data, is presented. The emphasis is on the evaluation of several computational strategies in view of their suitability to obtain high quality molecular models via the reverse Monte Carlo procedure. A consistent set of distances of closest approach and fixed neighbour constraints applicable to all three investigated systems was developed. An all-atom description is compared with a united-atom approach. The potentialities of employment of neutron diffraction data of completely deuterated and isotopically substituted samples, x-ray diffraction data, and results of either molecular dynamics or Monte Carlo calculations were investigated. Results show that parallel application of x-ray and neutron diffraction data, the latter being from completely deuterated samples, within an all-atom reverse Monte Carlo procedure is the most successful strategy towards attaining reliable, detailed, and well-structured molecular models, especially if the models are subsequently refined with the results of molecular dynamics simulations.

  20. Predicting and Modeling RNA Architecture

    Science.gov (United States)

    Westhof, Eric; Masquida, Benoît; Jossinet, Fabrice

    2011-01-01

    SUMMARY A general approach for modeling the architecture of large and structured RNA molecules is described. The method exploits the modularity and the hierarchical folding of RNA architecture that is viewed as the assembly of preformed double-stranded helices defined by Watson-Crick base pairs and RNA modules maintained by non-Watson-Crick base pairs. Despite the extensive molecular neutrality observed in RNA structures, specificity in RNA folding is achieved through global constraints like lengths of helices, coaxiality of helical stacks, and structures adopted at the junctions of helices. The Assemble integrated suite of computer tools allows for sequence and structure analysis as well as interactive modeling by homology or ab initio assembly with possibilities for fitting within electronic density maps. The local key role of non-Watson-Crick pairs guides RNA architecture formation and offers metrics for assessing the accuracy of three-dimensional models in a more useful way than usual root mean square deviation (RMSD) values. PMID:20504963

  1. New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals

    Directory of Open Access Journals (Sweden)

    RENATA V. VELHO

    2015-08-01

    Full Text Available With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

  2. New approaches to the treatment of orphan genetic disorders: Mitigating molecular pathologies using chemicals.

    Science.gov (United States)

    Velho, Renata V; Sperb-Ludwig, Fernanda; Schwartz, Ida V D

    2015-08-01

    With the advance and popularization of molecular techniques, the identification of genetic mutations that cause diseases has increased dramatically. Thus, the number of laboratories available to investigate a given disorder and the number of subsequent diagnosis have increased over time. Although it is necessary to identify mutations and provide diagnosis, it is also critical to develop specific therapeutic approaches based on this information. This review aims to highlight recent advances in mutation-targeted therapies with chemicals that mitigate mutational pathology at the molecular level, for disorders that, for the most part, have no effective treatment. Currently, there are several strategies being used to correct different types of mutations, including the following: the identification and characterization of translational readthrough compounds; antisense oligonucleotide-mediated splicing redirection; mismatch repair; and exon skipping. These therapies and other approaches are reviewed in this paper.

  3. Translating clinical research of Molecular Biology into a personalized, multidisciplinary approach of colorectal cancer patients.

    Science.gov (United States)

    Strambu, V; Garofil, D; Pop, F; Radu, P; Bratucu, M; Popa, F

    2014-03-15

    Although multimodal treatment has brought important benefit, there is still great heterogeneity regarding the indication and response to chemotherapy in Stage II and III, and individual variations related to both overall survival and toxicity of new therapies in metastatic disease or tumor relapse. Recent research in molecular biology led to the development of a large scale of genetic biomarkers, but their clinical use is not concordant with the high expectations. The Aim of this review is to identify and discuss the molecular markers with proven clinical applicability as prognostic and/or predictive factors in CRC and also to establish a feasible algorithm of molecular testing, as routine practice, in the personalized, multidisciplinary approach of colorectal cancer patients in our country. Despite the revolution that occurred in the field of molecular marker research, only Serum CEA, Immunohistochemical analysis of mismatch repair proteins and PCR testing for KRAS and BRAF mutations have confirmed their clinical utility in the management of colorectal cancer. Their implementation in the current practice should partially resolve some of the controversies related to this heterogenic pathology, in matters of prognosis in different TNM stages, stage II patient risk stratification, diagnosis of hereditary CRC and likelihood of benefit from anti EGFR therapy in metastatic disease. The proposed algorithms of molecular testing are very useful but still imperfect and require further validation and constant optimization.

  4. Can architecture be barbaric?

    Science.gov (United States)

    Hürol, Yonca

    2009-06-01

    The title of this article is adapted from Theodor W. Adorno's famous dictum: 'To write poetry after Auschwitz is barbaric.' After the catastrophic earthquake in Kocaeli, Turkey on the 17th of August 1999, in which more than 40,000 people died or were lost, Necdet Teymur, who was then the dean of the Faculty of Architecture of the Middle East Technical University, referred to Adorno in one of his 'earthquake poems' and asked: 'Is architecture possible after 17th of August?' The main objective of this article is to interpret Teymur's question in respect of its connection to Adorno's philosophy with a view to make a contribution to the politics and ethics of architecture in Turkey. Teymur's question helps in providing a new interpretation of a critical approach to architecture and architectural technology through Adorno's philosophy. The paper also presents a discussion of Adorno's dictum, which serves for a better understanding of its universality/particularity.

  5. An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer.

    Science.gov (United States)

    Omer, Ankur; Singh, Poonam

    2017-05-01

    A serious challenge in cancer treatment is to reposition the activity of various already known drug candidates against cancer. There is a need to rewrite and systematically analyze the detailed mechanistic aspect of cellular networks to gain insight into the novel role played by various molecules. Most Human Immunodeficiency Virus infection-associated cancers are caused by oncogenic viruses like Human Papilloma Viruses and Epstein-Bar Virus. As the onset of AIDS-associated cancers marks the severity of AIDS, there might be possible interconnections between the targets and mechanism of both the diseases. We have explored the possibility of certain antiviral compounds to act against major AIDS-associated cancers: Kaposi's Sarcoma, Non-Hodgkin Lymphoma, and Cervical Cancer with the help of systems pharmacology approach that includes screening for targets and molecules through the construction of a series of drug-target and drug-target-diseases network. Two molecules (Calanolide A and Chaetochromin B) and the target "HRAS" were finally screened with the help of molecular docking and molecular dynamics simulation. The results provide novel antiviral molecules against HRAS target to treat AIDS defining cancers and an insight for understanding the pharmacological, therapeutic aspects of similar unexplored molecules against various cancers.

  6. Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

    Energy Technology Data Exchange (ETDEWEB)

    Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016 (India)

    2016-03-21

    The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 3{sub 10}- and α-helix of acetyl(alanine){sub n}NH{sub 2} (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm{sup −1} is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine){sub 20} and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.

  7. Synthesis-Based Software Architecture Design

    NARCIS (Netherlands)

    Tekinerdogan, B.; Aksit, Mehmet; Aksit, Mehmet

    2001-01-01

    During the last decade several architecture design approaches have been introduced. These approaches however have to cope with several obstacles and software architecture design remains a difficult problem. To cope with these obstacles this chapter introduces a novel architecture design approach.

  8. Towards Adaptive Evolutionary Architecture

    DEFF Research Database (Denmark)

    Bak, Sebastian HOlt; Rask, Nina; Risi, Sebastian

    2016-01-01

    This paper presents first results from an interdisciplinary project, in which the fields of architecture, philosophy and artificial life are combined to explore possible futures of architecture. Through an interactive evolutionary installation, called EvoCurtain, we investigate aspects of how...... to the development of designs tailored to the individual preferences of inhabitants, changing the roles of architects and designers entirely. Architecture-as-it-could-be is a philosophical approach conducted through artistic methods to anticipate the technological futures of human-centered development within...

  9. Macroscopic and molecular approaches of enrofloxacin retention in soils in presence of Cu(II).

    Science.gov (United States)

    Graouer-Bacart, Mareen; Sayen, Stéphanie; Guillon, Emmanuel

    2013-10-15

    The co-adsorption of copper and the fluoroquinolone antibiotic enrofloxacin (ENR) at the water-soil interface was studied by means of batch adsorption experiments, and extended X-ray absorption fine structure (EXAFS) spectroscopy. The system was investigated over a pH range between 6 and 10, at different contact times, ionic strengths, and ENR concentrations. Adsorption coefficient - Kd - was determined at relevant environmental concentrations and the value obtained in water at a ionic strength imposed by the soil and at soil natural pH was equal to 0.66Lg(-1). ENR adsorption onto the soil showed strong pH dependence illustrating the influence of the electrostatic interactions in the sorption processes. The simultaneous co-adsorption of ENR and Cu(II) on the soil was also investigated. The presence of Cu(II) strongly influenced the retention of the antibiotic, leading to an increase up to 35% of adsorbed ENR amount. The combined quantitative and spectroscopic results showed that Cu(II) and ENR directly interacted at the water-soil interface to form ternary surface complexes. Cu K-edge EXAFS data indicated a molecular structure where the carboxylate and carbonyl groups of ENR coordinate to Cu(II) to form a 6-membered chelate ring and where Cu(II) bridges between ENR and the soil surface sites. Cu(II) bonds bidentately to the surface in an inner-sphere mode. Thus, the spectroscopic data allowed us to propose the formation of ternary surface complexes with the molecular architecture soil-Cu(II)-ENR. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Architectural Analysis of Dynamically Reconfigurable Systems

    Science.gov (United States)

    Lindvall, Mikael; Godfrey, Sally; Ackermann, Chris; Ray, Arnab; Yonkwa, Lyly

    2010-01-01

    oTpics include: the problem (increased flexibility of architectural styles decrease analyzability, behavior emerges and varies depending on the configuration, does the resulting system run according to the intended design, and architectural decisions can impede or facilitate testing); top down approach to architecture analysis, detection of defects and deviations, and architecture and its testability; currently targeted projects GMSEC and CFS; analyzing software architectures; analyzing runtime events; actual architecture recognition; GMPUB in Dynamic SAVE; sample output from new approach; taking message timing delays into account; CFS examples of architecture and testability; some recommendations for improved testablity; and CFS examples of abstract interfaces and testability; CFS example of opening some internal details.

  11. Benchmarking the stochastic time-dependent variational approach for excitation dynamics in molecular aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Chorošajev, Vladimir [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius (Lithuania); Gelzinis, Andrius; Valkunas, Leonas [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius (Lithuania); Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Sauletekio 3, 10222 Vilnius (Lithuania); Abramavicius, Darius, E-mail: darius.abramavicius@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius (Lithuania)

    2016-12-20

    Highlights: • The Davydov ansatze can be used for finite temperature simulations with an extension. • The accuracy is high if the system is strongly coupled to the environmental phonons. • The approach can simulate time-resolved fluorescence spectra. - Abstract: Time dependent variational approach is a convenient method to characterize the excitation dynamics in molecular aggregates for different strengths of system-bath interaction a, which does not require any additional perturbative schemes. Until recently, however, this method was only applicable in zero temperature case. It has become possible to extend this method for finite temperatures with the introduction of stochastic time dependent variational approach. Here we present a comparison between this approach and the exact hierarchical equations of motion approach for describing excitation dynamics in a broad range of temperatures. We calculate electronic population evolution, absorption and auxiliary time resolved fluorescence spectra in different regimes and find that the stochastic approach shows excellent agreement with the exact approach when the system-bath coupling is sufficiently large and temperatures are high. The differences between the two methods are larger, when temperatures are lower or the system-bath coupling is small.

  12. Molecular approaches to improvement of Jatropha curcas Linn. as a sustainable energy crop.

    Science.gov (United States)

    Sudhakar Johnson, T; Eswaran, Nalini; Sujatha, M

    2011-09-01

    With the increase in crude oil prices, climate change concerns and limited reserves of fossil fuel, attention has been diverted to alternate renewable energy sources such as biofuel and biomass. Among the potential biofuel crops, Jatropha curcas L, a non-domesticated shrub, has been gaining importance as the most promising oilseed, as it does not compete with the edible oil supplies. Economic relevance of J. curcas for biodiesel production has promoted world-wide prospecting of its germplasm for crop improvement and breeding. However, lack of adequate genetic variation and non-availability of improved varieties limited its prospects of being a successful energy crop. In this review, we present the progress made in molecular breeding approaches with particular reference to tissue culture and genetic transformation, genetic diversity assessment using molecular markers, large-scale transcriptome and proteome studies, identification of candidate genes for trait improvement, whole genome sequencing and the current interest by various public and private sector companies in commercial-scale cultivation, which highlights the revival of Jatropha as a sustainable energy crop. The information generated from molecular markers, transcriptome profiling and whole genome sequencing could accelerate the genetic upgradation of J. curcas through molecular breeding.

  13. Usher syndrome (sensorineural deafness and retinitis pigmentosa): pathogenesis, molecular diagnosis and therapeutic approaches.

    Science.gov (United States)

    Bonnet, Crystel; El-Amraoui, Aziz

    2012-02-01

    Usher syndrome (USH) is the most prevalent cause of hereditary deafness-blindness in humans. In this review, we pinpoint new insights regarding the molecular mechanisms defective in this syndrome, its molecular diagnosis and prospective therapies. Animal models wherein USH proteins were targeted at different maturation stages of the auditory hair cells have been engineered, shedding new light on the development and functioning of the hair bundle, the sound receptive structure. Improved protocols and guidelines for early molecular diagnosis of USH (USH genotyping microarrays, otochips and complete Sanger sequencing of the 366 coding exons of identified USH genes) have been developed. Approaches to alleviate or cure hearing and visual impairments have been initiated, leading to various degrees of functional rescuing. Whereas the mechanisms underlying hearing impairment in USH patients are being unraveled, showing in particular that USH1 proteins are involved in the shaping of the hair bundle and the functioning of the mechanoelectrical transduction machinery, the mechanisms underlying the retinal defects are still unclear. Efforts to improve clinical diagnosis have been successful. Yet, despite some encouraging results, further development of therapeutic approaches is necessary to ultimately treat this dual sensory defect.

  14. Companion diagnostics and molecular imaging-enhanced approaches for oncology clinical trials.

    Science.gov (United States)

    Van Heertum, Ronald L; Scarimbolo, Robert; Ford, Robert; Berdougo, Eli; O'Neal, Michael

    2015-01-01

    In the era of personalized medicine, diagnostic approaches are helping pharmaceutical and biotechnology sponsors streamline the clinical trial process. Molecular assays and diagnostic imaging are routinely being used to stratify patients for treatment, monitor disease, and provide reliable early clinical phase assessments. The importance of diagnostic approaches in drug development is highlighted by the rapidly expanding global cancer diagnostics market and the emergent attention of regulatory agencies worldwide, who are beginning to offer more structured platforms and guidance for this area. In this paper, we highlight the key benefits of using companion diagnostics and diagnostic imaging with a focus on oncology clinical trials. Nuclear imaging using widely available radiopharmaceuticals in conjunction with molecular imaging of oncology targets has opened the door to more accurate disease assessment and the modernization of standard criteria for the evaluation, staging, and treatment responses of cancer patients. Furthermore, the introduction and validation of quantitative molecular imaging continues to drive and optimize the field of oncology diagnostics. Given their pivotal role in disease assessment and treatment, the validation and commercialization of diagnostic tools will continue to advance oncology clinical trials, support new oncology drugs, and promote better patient outcomes.

  15. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    Science.gov (United States)

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. Structural comparison of tRNA m1A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions

    Directory of Open Access Journals (Sweden)

    Guelorget Amandine

    2011-12-01

    Full Text Available Abstract Background tRNA m1A58 methyltransferases (TrmI catalyze the transfer of a methyl group from S-adenosyl-L-methionine to nitrogen 1 of adenine 58 in the T-loop of tRNAs from all three domains of life. The m1A58 modification has been shown to be essential for cell growth in yeast and for adaptation to high temperatures in thermophilic organisms. These enzymes were shown to be active as tetramers. The crystal structures of five TrmIs from hyperthermophilic archaea and thermophilic or mesophilic bacteria have previously been determined, the optimal growth temperature of these organisms ranging from 37°C to 100°C. All TrmIs are assembled as tetramers formed by dimers of tightly assembled dimers. Results In this study, we present a comparative structural analysis of these TrmIs, which highlights factors that allow them to function over a large range of temperature. The monomers of the five enzymes are structurally highly similar, but the inter-monomer contacts differ strongly. Our analysis shows that bacterial enzymes from thermophilic organisms display additional intermolecular ionic interactions across the dimer interfaces, whereas hyperthermophilic enzymes present additional hydrophobic contacts. Moreover, as an alternative to two bidentate ionic interactions that stabilize the tetrameric interface in all other TrmI proteins, the tetramer of the archaeal P. abyssi enzyme is strengthened by four intersubunit disulfide bridges. Conclusions The availability of crystal structures of TrmIs from mesophilic, thermophilic or hyperthermophilic organisms allows a detailed analysis of the architecture of this protein family. Our structural comparisons provide insight into the different molecular strategies used to achieve the tetrameric organization in order to maintain the enzyme activity under extreme conditions.

  17. XML-based approaches for the integration of heterogeneous bio-molecular data.

    Science.gov (United States)

    Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

    2009-10-15

    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

  18. A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

    Science.gov (United States)

    Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

    2014-03-11

    We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

  19. Integrated Sedimentological Approach to Assess Reservoir Quality and Architecture of Khuff Carbonates: Outcrop Analog, Central Saudi Arabia

    Science.gov (United States)

    Osman, Mutsim; Abdullatif, Osman

    2017-04-01

    The Permian to Triassic Khuff carbonate reservoirs (and equivalents) in the Middle East are estimated to contain about 38.4% of the world's natural gas reserves. Excellent exposed outcrops in central Saudi Arabia provide good outcrop equivalents to subsurface Khuff reservoirs. This study conduct high resolution outcrop scale investigations on an analog reservoir for upper Khartam of Khuff Formation. The main objective is to reconstruct litho- and chemo- stratigraphic outcrop analog model that may serve to characterize reservoir high resolution (interwell) heterogeneity, continuity and architecture. Given the fact of the limitation of subsurface data and toolsin capturing interwell reservoir heterogeneity, which in turn increases the value of this study.The methods applied integrate sedimentological, stratigraphic petrographic, petrophysical data and chemical analyses for major, trace and rare earth elements. In addition, laser scanning survey (LIDAR) was also utilized in this study. The results of the stratigraphic investigations revealed that the lithofacies range from mudstone, wackestone, packestone and grainstone. These lithofacies represent environments ranging from supratidal, intertidal, subtidal and shoal complex. Several meter-scale and less high resolution sequences and composite sequences within 4th and 5th order cycles were also recognized in the outcrop analog. The lithofacies and architectural analysis revealed several vertically and laterally stacked sequences at the outcrop as revealed from the stratigraphic sections and the lidar scan. Chemostratigraphy is effective in identifying lithofacies and sequences within the outcrop analog. Moreover, different chemical signatures were also recognized and allowed establishing and correlating high resolution lithofacies, reservoir zones, layers and surfaces bounding reservoirs and non-reservoir zones at scale of meters or less. The results of this high resolution outcrop analog study might help to understand

  20. Integrating survey and molecular approaches to better understand wildlife disease ecology.

    Directory of Open Access Journals (Sweden)

    Brendan D Cowled

    Full Text Available Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design versus transmission (molecular case series study design and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37-45%. The median Salmonella DICE coefficient (or Salmonella genetic similarity was 52% (interquartile range [IQR]: 42-62%. Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is

  1. A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

    Science.gov (United States)

    Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

    2016-07-01

    A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

  2. Integrating Survey and Molecular Approaches to Better Understand Wildlife Disease Ecology

    Science.gov (United States)

    Cowled, Brendan D.; Ward, Michael P.; Laffan, Shawn W.; Galea, Francesca; Garner, M. Graeme; MacDonald, Anna J.; Marsh, Ian; Muellner, Petra; Negus, Katherine; Quasim, Sumaiya; Woolnough, Andrew P.; Sarre, Stephen D.

    2012-01-01

    Infectious wildlife diseases have enormous global impacts, leading to human pandemics, global biodiversity declines and socio-economic hardship. Understanding how infection persists and is transmitted in wildlife is critical for managing diseases, but our understanding is limited. Our study aim was to better understand how infectious disease persists in wildlife populations by integrating genetics, ecology and epidemiology approaches. Specifically, we aimed to determine whether environmental or host factors were stronger drivers of Salmonella persistence or transmission within a remote and isolated wild pig (Sus scrofa) population. We determined the Salmonella infection status of wild pigs. Salmonella isolates were genotyped and a range of data was collected on putative risk factors for Salmonella transmission. We a priori identified several plausible biological hypotheses for Salmonella prevalence (cross sectional study design) versus transmission (molecular case series study design) and fit the data to these models. There were 543 wild pig Salmonella observations, sampled at 93 unique locations. Salmonella prevalence was 41% (95% confidence interval [CI]: 37–45%). The median Salmonella DICE coefficient (or Salmonella genetic similarity) was 52% (interquartile range [IQR]: 42–62%). Using the traditional cross sectional prevalence study design, the only supported model was based on the hypothesis that abundance of available ecological resources determines Salmonella prevalence in wild pigs. In the molecular study design, spatial proximity and herd membership as well as some individual risk factors (sex, condition score and relative density) determined transmission between pigs. Traditional cross sectional surveys and molecular epidemiological approaches are complementary and together can enhance understanding of disease ecology: abundance of ecological resources critical for wildlife influences Salmonella prevalence, whereas Salmonella transmission is driven by

  3. Architectural Contestation

    NARCIS (Netherlands)

    Merle, J.

    2012-01-01

    This dissertation addresses the reductive reading of Georges Bataille's work done within the field of architectural criticism and theory which tends to set aside the fundamental ‘broken’ totality of Bataille's oeuvre and also to narrowly interpret it as a mere critique of architectural form,

  4. Architecture Sustainability

    NARCIS (Netherlands)

    Avgeriou, Paris; Stal, Michael; Hilliard, Rich

    2013-01-01

    Software architecture is the foundation of software system development, encompassing a system's architects' and stakeholders' strategic decisions. A special issue of IEEE Software is intended to raise awareness of architecture sustainability issues and increase interest and work in the area. The

  5. Memory architecture

    NARCIS (Netherlands)

    2012-01-01

    A memory architecture is presented. The memory architecture comprises a first memory and a second memory. The first memory has at least a bank with a first width addressable by a single address. The second memory has a plurality of banks of a second width, said banks being addressable by components

  6. An Electronic Structure Approach to Charge Transfer and Transport in Molecular Building Blocks for Organic Optoelectronics

    Science.gov (United States)

    Hendrickson, Heidi Phillips

    A fundamental understanding of charge separation in organic materials is necessary for the rational design of optoelectronic devices suited for renewable energy applications and requires a combination of theoretical, computational, and experimental methods. Density functional theory (DFT) and time-dependent (TD)DFT are cost effective ab-initio approaches for calculating fundamental properties of large molecular systems, however conventional DFT methods have been known to fail in accurately characterizing frontier orbital gaps and charge transfer states in molecular systems. In this dissertation, these shortcomings are addressed by implementing an optimally-tuned range-separated hybrid (OT-RSH) functional approach within DFT and TDDFT. The first part of this thesis presents the way in which RSH-DFT addresses the shortcomings in conventional DFT. Environmentally-corrected RSH-DFT frontier orbital energies are shown to correspond to thin film measurements for a set of organic semiconducting molecules. Likewise, the improved RSH-TDDFT description of charge transfer excitations is benchmarked using a model ethene dimer and silsesquioxane molecules. In the second part of this thesis, RSH-DFT is applied to chromophore-functionalized silsesquioxanes, which are currently investigated as candidates for building blocks in optoelectronic applications. RSH-DFT provides insight into the nature of absorptive and emissive states in silsesquioxanes. While absorption primarily involves transitions localized on one chromophore, charge transfer between chromophores and between chromophore and silsesquioxane cage have been identified. The RSH-DFT approach, including a protocol accounting for complex environmental effects on charge transfer energies, was tested and validated against experimental measurements. The third part of this thesis addresses quantum transport through nano-scale junctions. The ability to quantify a molecular junction via spectroscopic methods is crucial to their

  7. Parallel computations of molecular dynamics trajectories using the stochastic path approach

    Science.gov (United States)

    Zaloj, Veaceslav; Elber, Ron

    2000-06-01

    A novel protocol to parallelize molecular dynamics trajectories is discussed and tested on a cluster of PCs running the NT operating system. The new technique does not propagate the solution in small time steps, but uses instead a global optimization of a functional of the whole trajectory. The new approach is especially attractive for parallel and distributed computing and its advantages (and disadvantages) are presented. Two numerical examples are discussed: (a) A conformational transition in a solvated dipeptide, and (b) The R→T conformational transition in solvated hemoglobin.

  8. Architectural Narratives

    DEFF Research Database (Denmark)

    Kiib, Hans

    2010-01-01

    a functional framework for these concepts, but tries increasingly to endow the main idea of the cultural project with a spatially aesthetic expression - a shift towards “experience architecture.” A great number of these projects typically recycle and reinterpret narratives related to historical buildings......In this essay, I focus on the combination of programs and the architecture of cultural projects that have emerged within the last few years. These projects are characterized as “hybrid cultural projects,” because they intend to combine experience with entertainment, play, and learning. This essay...... and architectural heritage; another group tries to embed new performative technologies in expressive architectural representation. Finally, this essay provides a theoretical framework for the analysis of the political rationales of these projects and for the architectural representation bridges the gap between...

  9. A sedimentological approach to refining reservoir architecture in a mature hydrocarbon province: the Brent Province, UK North Sea

    Energy Technology Data Exchange (ETDEWEB)

    Hampson, G.J.; Sixsmith, P.J.; Johnson, H.D. [Imperial College, London (United Kingdom). Dept. of Earth Science and Engineering

    2004-04-01

    Improved reservoir characterisation in the mature Brent Province of the North Sea, aimed at maximising both in-field and near-field hydrocarbon potential, requires a clearer understanding of sub-seismic stratigraphy and facies distributions. In this context, we present a regional, high-resolution sequence stratigraphic framework for the Brent Group, UK North Sea based on extensive sedimentological re-interpretation of core and wireline-log data, combined with palynostratigraphy and published literature. This framework is used to place individual reservoirs in an appropriate regional context, thus resulting in the identification of subtle sedimentological and tectono-stratigraphic features of reservoir architecture that have been previously overlooked. We emphasise the following insights gained from our regional, high-resolution sequence stratigraphic synthesis: (1) improved definition of temporal and spatial trends in deposition both within and between individual reservoirs, (2) development of regionally consistent, predictive sedimentological models for two enigmatic reservoir intervals (the Broom and Tarbert Formations), and (3) recognition of subtle local tectono-stratigraphic controls on reservoir architecture, and their links to the regional, Middle Jurassic structural evolution of the northern North Sea. We discuss the potential applications of these insights to the identification of additional exploration potential and to improved ultimate recovery. (author)

  10. Geomorphology and till architecture of terrestrial palaeo-ice streams of the southwest Laurentide Ice Sheet: A borehole stratigraphic approach

    Science.gov (United States)

    Norris, Sophie L.; Evans, David J. A.; Cofaigh, Colm Ó.

    2018-04-01

    A multidimensional study, utilising geomorphological mapping and the analysis of regional borehole stratigraphy, is employed to elucidate the regional till architecture of terrestrial palaeo-ice streams relating to the Late Wisconsinan southwest Laurentide Ice Sheet. Detailed mapping over a 57,400 km2 area of southwestern Saskatchewan confirms previous reconstructions of a former southerly flowing ice stream, demarcated by a 800 km long corridor of megaflutes and mega-scale glacial lineations (Ice Stream 1) and cross cut by three, formerly southeast flowing ice streams (Ice Streams 2A, B and C). Analysis of the lithologic and geophysical characteristics of 197 borehole samples within these corridors reveals 17 stratigraphic units comprising multiple tills and associated stratified sediments overlying preglacial deposits, the till thicknesses varying with both topography and distance down corridor. Reconciling this regional till architecture with the surficial geomorphology reveals that surficial units are spatially consistent with a dynamic switch in flow direction, recorded by the cross cutting corridors of Ice Streams 1, 2A, B and C. The general thickening of tills towards lobate ice stream margins is consistent with subglacial deformation theory and variations in this pattern on a more localised scale are attributed to influences of subglacial topography including thickening at buried valley margins, thinning over uplands and thickening in overridden ice-marginal landforms.

  11. Porous sheet-like and sphere-like nano-architectures of SnO2 nanoparticles via a solvent-thermal approach and their gas-sensing performances

    International Nuclear Information System (INIS)

    Jie Liu; Tang, Xin-Cun; Xiao, Yuan-Hua; Hai Jia,; Gong, Mei-Li; Huang, Fu-Qin

    2013-01-01

    Highlights: • Porous sheet-like and sphere-like nano-architectures of SnO 2 nanoparticles have been prepared. • A solvent-thermal approach without surfactant or polymer templates simply by changing the volume ratio of DMF to water. • The formation mechanism of nano-architectures is proposed in this article. • Porous sphere-like SnO 2 nano-architectures exhibit good sensitivity to the reduce vapors tested. • Sheet-like materials show better selectivity to ethanol. -- Abstract: Porous sheet-like and sphere-like nano-architectures of SnO 2 nanoparticles have been prepared via a solvent-thermal approach in the absence of any surfactant or polymer templates by simply changing the volume ratio of DMF to water. The nano-materials have been characterized by FESEM, XRD, IR, TEM and BET. A mechanism for the formation of nano-architectures is also proposed based on the assembly behaviors of DMF in water. The gas sensors constructed with porous sphere-like SnO 2 nano-architectures exhibit much higher sensitivity to the reduce vapors tested, compared to those from porous sheet-like SnO 2 materials, while the sheet-like materials show better selectivity to ethanol. The nano-architectures fabricated with the facile method are promising candidates for building chemical sensors with tunable performances

  12. A New Approach for Flexible Molecular Docking Based on Swarm Intelligence

    Directory of Open Access Journals (Sweden)

    Yi Fu

    2015-01-01

    Full Text Available Molecular docking methods play an important role in the field of computer-aided drug design. In the work, on the basis of the molecular docking program AutoDock, we present QLDock as a tool for flexible molecular docking. For the energy evaluation, the algorithm uses the binding free energy function that is provided by the AutoDock 4.2 tool. The new search algorithm combines the features of a quantum-behaved particle swarm optimization (QPSO algorithm and local search method of Solis and Wets for solving the highly flexible protein-ligand docking problem. We compute the interaction of 23 protein-ligand complexes and compare the results with those of the QDock and AutoDock programs. The experimental results show that our approach leads to substantially lower docking energy and higher docking precision in comparison to Lamarckian genetic algorithm and QPSO algorithm alone. QPSO-ls algorithm was able to identify the correct binding mode of 74% of the complexes. In comparison, the accuracy of QPSO and LGA is 52% and 61%, respectively. This difference in performance rises with increasing complexity of the ligand. Thus, the novel algorithm QPSO-ls may be used to dock ligand with many rotatable bonds with high accuracy.

  13. A neural network approach to the study of internal energy flow in molecular systems

    International Nuclear Information System (INIS)

    Sumpter, B.G.; Getino, C.; Noid, D.W.

    1992-01-01

    Neural networks are used to develop a new technique for efficient analysis of data obtained from molecular-dynamics calculations and is applied to the study of mode energy flow in molecular systems. The methodology is based on teaching an appropriate neural network the relationship between phase-space points along a classical trajectory and mode energies for stretch, bend, and torsion vibrations. Results are discussed for reactive and nonreactive classical trajectories of hydrogen peroxide (H 2 O 2 ) on a semiempirical potential-energy surface. The neural-network approach is shown to produce reasonably accurate values for the mode energies, with average errors between 1% and 12%, and is applicable to any region within the 24-dimensional phase space of H 2 O 2 . In addition, the generic knowledge learned by the neural network allows calculations to be made for other molecular systems. Results are discussed for a series of tetratomic molecules: H 2 X 2 , X=C, N, O, Si, S, or Se, and preliminary results are given for energy flow predictions in macromolecules

  14. Evolutionary history of genus Macrobrachium inferred from mitochondrial markers: a molecular clock approach.

    Science.gov (United States)

    Jose, Deepak; Harikrishnan, Mahadevan

    2018-04-17

    Caridea, an infraorder of shrimps coming under Pleocyemata was first reported from the oceans before 417 million years followed by their radiation recorded during the Permian period. Hitherto, about 3877 extant caridean species were accounted within which one quarter constitute freshwater species. Freshwater prawns of genus Macrobrachium (Infraorder Caridea; Family Palaemonidae), with more than 240 species are inhabitants of diverse aquatic habitats like coastal lagoons, lakes, tropical streams, ponds and rivers. Previous studies on Macrobrachium relied on the highly variable morphological characters which were insufficient for accurate diagnosis of natural species groups. Present study focuses on the utility of molecular markers (viz. COI and 16S rRNA) for resolving the evolutionary history of genus Macrobrachium using a combination of phylogeny and timescale components. It is for the first time a molecular clock approach had been carried out towards genus Macrobrachium in a broad aspect with the incorporation of congeners inhabiting diverse geographical realms including endemic species M. striatum from South West coast of India. Molecular results obtained revealed the phylogenetic relationships between congeners of genus Macrobrachium at intra/inter-continental level along with the corresponding evolutionary time estimates.

  15. Identification of bioflavonoid as fusion inhibitor of dengue virus using molecular docking approach

    Directory of Open Access Journals (Sweden)

    Asif Mir

    Full Text Available Dengue virus with four distinct serotypes belongs to Flavivirus, poses a significant threat to human health and becomes an emerging global problem. Membrane fusion is a central molecular event during viral entry into host cell. To prevent viral infection it is necessary to interrupt the virus replication at an early stage of attachment. Dengue Virus (DENV envelope protein experiences conformational changes and it causes the virus to fuse with host cell. Hinge region movement of domain I and II in envelope protein facilitates the fusion process. Small molecules that bind in this pocket may have the ability to interrupt the conformational changes that trigger fusion process. We chose different flavonoids (baicalein, fisetin, hesperetin, naringenin/ naringin, quercetin and rutin that possess anti dengue activity. Molecular docking analysis was done to examine the inhibitory effect of flavonoids against envelope protein of DENV-2. Results manifest quercetin (flavonoid found in Carica papaya, apple and even in lemon as the only flavone that can interrupt the fusion process of virus by inhibiting the hinge region movement and by blocking the conformational rearrangement in envelope protein. These novel findings using computational approach are worthwhile and will be a bridge to check the efficacy of compounds using appropriate animal model under In vivo studies. This information can be used by new techniques and provides a way to control dengue virus infection. Keywords: Dengue virus, Inhibitor identification, Molecular docking, Interaction analysis

  16. An analytic approach to 2D electronic PE spectra of molecular systems

    International Nuclear Information System (INIS)

    Szoecs, V.

    2011-01-01

    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: → RWA approach to electronic photon echo. → A straightforward calculation of 2D electronic spectrograms in finite molecular systems. → Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the δ-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  17. Multilevel Molecular Modeling Approach for a Rational Design of Ionic Current Sensors for Nanofluidics.

    Science.gov (United States)

    Kirch, Alexsandro; de Almeida, James M; Miranda, Caetano R

    2018-05-10

    The complexity displayed by nanofluidic-based systems involves electronic and dynamic aspects occurring across different size and time scales. To properly model such kind of system, we introduced a top-down multilevel approach, combining molecular dynamics simulations (MD) with first-principles electronic transport calculations. The potential of this technique was demonstrated by investigating how the water and ionic flow through a (6,6) carbon nanotube (CNT) influences its electronic transport properties. We showed that the confinement on the CNT favors the partially hydrated Na, Cl, and Li ions to exchange charge with the nanotube. This leads to a change in the electronic transmittance, allowing for the distinguishing of cations from anions. Such an ionic trace may handle an indirect measurement of the ionic current that is recorded as a sensing output. With this case study, we are able to show the potential of this top-down multilevel approach, to be applied on the design of novel nanofluidic devices.

  18. Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach

    Energy Technology Data Exchange (ETDEWEB)

    Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu

    2016-07-15

    Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.

  19. Iterative Calibration: A Novel Approach for Calibrating the Molecular Clock Using Complex Geological Events.

    Science.gov (United States)

    Loeza-Quintana, Tzitziki; Adamowicz, Sarah J

    2018-02-01

    During the past 50 years, the molecular clock has become one of the main tools for providing a time scale for the history of life. In the era of robust molecular evolutionary analysis, clock calibration is still one of the most basic steps needing attention. When fossil records are limited, well-dated geological events are the main resource for calibration. However, biogeographic calibrations have often been used in a simplistic manner, for example assuming simultaneous vicariant divergence of multiple sister lineages. Here, we propose a novel iterative calibration approach to define the most appropriate calibration date by seeking congruence between the dates assigned to multiple allopatric divergences and the geological history. Exploring patterns of molecular divergence in 16 trans-Bering sister clades of echinoderms, we demonstrate that the iterative calibration is predominantly advantageous when using complex geological or climatological events-such as the opening/reclosure of the Bering Strait-providing a powerful tool for clock dating that can be applied to other biogeographic calibration systems and further taxa. Using Bayesian analysis, we observed that evolutionary rate variability in the COI-5P gene is generally distributed in a clock-like fashion for Northern echinoderms. The results reveal a large range of genetic divergences, consistent with multiple pulses of trans-Bering migrations. A resulting rate of 2.8% pairwise Kimura-2-parameter sequence divergence per million years is suggested for the COI-5P gene in Northern echinoderms. Given that molecular rates may vary across latitudes and taxa, this study provides a new context for dating the evolutionary history of Arctic marine life.

  20. Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

    Science.gov (United States)

    Yip, Hin-Lap

    Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

  1. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

    KAUST Repository

    Jiang, Hanlun

    2016-12-06

    MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

  2. Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

    Science.gov (United States)

    Falk, Bryan; Reed, Robert N.

    2015-01-01

    Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

  3. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.

    Science.gov (United States)

    Jiang, Hanlun; Zhu, Lizhe; Héliou, Amélie; Gao, Xin; Bernauer, Julie; Huang, Xuhui

    2017-01-01

    MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

  4. Role of molecular testing in the multidisciplinary diagnostic approach of ichthyosis.

    Science.gov (United States)

    Diociaiuti, Andrea; El Hachem, May; Pisaneschi, Elisa; Giancristoforo, Simona; Genovese, Silvia; Sirleto, Pietro; Boldrini, Renata; Angioni, Adriano

    2016-01-13

    The term ichthyosis describes a generalized disorder of cornification characterized by scaling and/or hyperkeratosis of different skin regions. Mutations in a broad group of genes related to keratinocyte differentiation and epidermal barrier function have been demonstrated to play a causative role in disease development. Ichthyosis may be classified in syndromic or non-syndromic forms based on the occurrence or absence of extracutaneous signs. In this setting, the diagnosis of ichthyosis is an integrated multistep process requiring a multidisciplinary approach in order to formulate the appropriate diagnostic hypothesis and to address the genetic testing. Due to the complex features of the different ichthyoses and the high number of genes involved we have investigated a group of 64 patients, affected by syndromic and non-syndromic diseases, using Next Generation Sequencing as a new tool for the molecular diagnosis. Using this innovative molecular approach we were able to find pathogenic mutations in 53 out of 64 patients resulting in 82.8 % total detection rate. An interesting result from the analysis of the data is the high rate of novel sequence variations found compared to known mutations and the relevant rate of homozygous mutations. The possibility to analyze a large number of genes associated with various diseases allows to study cases with phenotypes not well-determined, giving the opportunity to make new genotype-phenotype correlation. In some cases there were discrepancies between clinical features and histology or electron microscopy and only molecular analysis allowed to definitively resolve the diagnostic dilemma. The genetic diagnosis of ichthyosis leads to a more accurate and effective genetic counseling, allowing correct evaluation of the risk of recurrence, particularly in families with consanguineous background.

  5. An integral IT-approach using EAI architectures; Der integrale IT-Ansatz mittels EAI-Architekturen

    Energy Technology Data Exchange (ETDEWEB)

    Zengaffinen, A.

    2003-07-01

    This article examines the question if there is any information technology (IT) on the market that meets the needs of an energy utility for an integral and comprehensive tool to control its operations. The possibilities offered by so-called 'Enterprise Application Integration' (EAI) are examined and the intelligent linking-up of various sources of data is discussed. The current and future situations in typical utilities are looked at, where the unbundling of activities threatens to make business processes that are already complex even more so. Various models for the integration of existing IT applications such those using 'peer-to-peer' architectures, data warehousing and 'middleware' applications as well as their advantages and disadvantages are discussed. An example is given of integration using a 'middleware' solution in the maintenance area. A well-tried project implementation process is described.

  6. “Pushing the Envelope” a modeling-based approach to the development of organic, responsive architectural form

    Directory of Open Access Journals (Sweden)

    David Yearley

    2012-11-01

    Full Text Available This paper tests design procedures for the development of complex, organic architectural forms. It illustrates a postgraduate student design process, implementing a development sequence based on the intelligent manipulation of architectural envelopes using a variety of existing modeling tools and emerging digital techniques. These stages of development respond to imposed spatial and environmental constraints. The tests began with full-scale modeling of small segments. The major constraints at this stage were spatial requirements and the physical characteristics of materials. The forms derived from the bending properties of prestressed green timber and the dimensions of shingle cladding. This was followed by digital 3D modeling using common commercial applications. At this stage initial models were derived from a traditional space requirement brief. The envelopes for these activities were then manipulated to respond to the spatial limitations imposed by surrounding buildings. This digital modeling process metaphorically “pushed the limits” as vertices of the envelope model were stretched and shifted to achieve a perceived “fit” between the two sets of spatial dimensions. The spatially manipulated geometry was then imported into Ecotect, an environmental analysis package. As an example, the envelope’s morphology and cladding material options on the acoustic qualities of the surrounding space were tested. The improved geometry was then imported into a Virtual Reality room, in which the spatial experience was simulated in presentations to the design team and potential occupants. This room utilized six projectors to create an immersive experience to users wearing stereoscopic goggles, and moving in a space surrounded by three large screens, creating a CAVE-like presentation space. Finally there was an attempt to complete the circle by returning from the simulated world to the physical worlds, by creating full-scale models from the digital

  7. Architectural technology

    DEFF Research Database (Denmark)

    2005-01-01

    The booklet offers an overall introduction to the Institute of Architectural Technology and its projects and activities, and an invitation to the reader to contact the institute or the individual researcher for further information. The research, which takes place at the Institute of Architectural...... Technology at the Roayl Danish Academy of Fine Arts, School of Architecture, reflects a spread between strategic, goal-oriented pilot projects, commissioned by a ministry, a fund or a private company, and on the other hand projects which originate from strong personal interests and enthusiasm of individual...

  8. Systemic Architecture

    DEFF Research Database (Denmark)

    Poletto, Marco; Pasquero, Claudia

    -up or tactical design, behavioural space and the boundary of the natural and the artificial realms within the city and architecture. A new kind of "real-time world-city" is illustrated in the form of an operational design manual for the assemblage of proto-architectures, the incubation of proto-gardens...... and the coding of proto-interfaces. These prototypes of machinic architecture materialize as synthetic hybrids embedded with biological life (proto-gardens), computational power, behavioural responsiveness (cyber-gardens), spatial articulation (coMachines and fibrous structures), remote sensing (FUNclouds...

  9. Humanizing Architecture

    DEFF Research Database (Denmark)

    Toft, Tanya Søndergaard

    2015-01-01

    The article proposes the urban digital gallery as an opportunity to explore the relationship between ‘human’ and ‘technology,’ through the programming of media architecture. It takes a curatorial perspective when proposing an ontological shift from considering media facades as visual spectacles...... agency and a sense of being by way of dematerializing architecture. This is achieved by way of programming the symbolic to provide new emotional realizations and situations of enlightenment in the public audience. This reflects a greater potential to humanize the digital in media architecture....

  10. Organic molecular paleohypsometry: A new approach to reconstructing the paleoelevation history of an orogen

    Science.gov (United States)

    Hren, M. T.; Ouimet, W. B.

    2017-12-01

    Paleoelevation data is critical to understanding the links and feedbacks between rock-uplift and erosion yet few approaches have proved successful in quantifying changes in paleoelevation rapidly eroding, tropical landscapes. In addition, quantitative methods of reconstructing paleoelevation from marine sedimentary archives are lacking. Here we present a new approach to quantifying changes in paleoelevation that is based on the geochemical signature of organic matter exported via the main river networks of an orogen. This new approach builds on fundamentals of stable isotope paleoaltimetry and is akin to the theory behind cosmogenic isotope records of catchment-integrated erosion. Specifically, we utilize predictable patterns of precipitation and organic molecular biomarker stable isotopes to relate the hypsometry of organic matter in a catchment to the geochemical signal in exported organic carbon. We present data from two sites (the cold temperate White Mountains of New Hampshire, USA and the tropical, rapidly eroding landscape of Taiwan) to demonstrate this relationship between exported carbon geochemistry and catchment hypsometry and the validity of this approach.

  11. A Network Biology Approach to Discover the Molecular Biomarker Associated with Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Liwei Zhuang

    2014-01-01

    Full Text Available In recent years, high throughput technologies such as microarray platform have provided a new avenue for hepatocellular carcinoma (HCC investigation. Traditionally, gene sets enrichment analysis of survival related genes is commonly used to reveal the underlying functional mechanisms. However, this approach usually produces too many candidate genes and cannot discover detailed signaling transduction cascades, which greatly limits their clinical application such as biomarker development. In this study, we have proposed a network biology approach to discover novel biomarkers from multidimensional omics data. This approach effectively combines clinical survival data with topological characteristics of human protein interaction networks and patients expression profiling data. It can produce novel network based biomarkers together with biological understanding of molecular mechanism. We have analyzed eighty HCC expression profiling arrays and identified that extracellular matrix and programmed cell death are the main themes related to HCC progression. Compared with traditional enrichment analysis, this approach can provide concrete and testable hypothesis on functional mechanism. Furthermore, the identified subnetworks can potentially be used as suitable targets for therapeutic intervention in HCC.

  12. Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach

    OpenAIRE

    Ahmed, Bilal; Ali Ashfaq, Usman; Mirza, Muhammad Usman

    2017-01-01

    Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding ...

  13. Enterprise Architecture Analysis with XML

    OpenAIRE

    Boer, Frank; Bonsangue, Marcello; Jacob, Joost; Stam, A.; Torre, Leon

    2005-01-01

    htmlabstractThis paper shows how XML can be used for static and dynamic analysis of architectures. Our analysis is based on the distinction between symbolic and semantic models of architectures. The core of a symbolic model consists of its signature that specifies symbolically its structural elements and their relationships. A semantic model is defined as a formal interpretation of the symbolic model. This provides a formal approach to the design of architectural description languages and a g...

  14. Documenting the ICT Architecture of TSI

    NARCIS (Netherlands)

    Wieringa, Roelf J.; Blanken, Henk; Fokkinga, M.M.

    2001-01-01

    We use the business and software architecture of Travel Service International (TSI) as a case study to validate our approach to ICT architecture. The techniques discussed are explained at length in a textbook by Wieringa.

  15. Molecular fingerprinting of principal neurons in the rodent hippocampus: A neuroinformatics approach.

    Science.gov (United States)

    Hamilton, D J; White, C M; Rees, C L; Wheeler, D W; Ascoli, G A

    2017-09-10

    Neurons are often classified by their morphological and molecular properties. The online knowledge base Hippocampome.org primarily defines neuron types from the rodent hippocampal formation based on their main neurotransmitter (glutamate or GABA) and the spatial distributions of their axons and dendrites. For each neuron type, this open-access resource reports any and all published information regarding the presence or absence of known molecular markers, including calcium-binding proteins, neuropeptides, receptors, channels, transcription factors, and other molecules of biomedical relevance. The resulting chemical profile is relatively sparse: even for the best studied neuron types, the expression or lack thereof of fewer than 70 molecules has been firmly established to date. The mouse genome-wide in situ hybridization mapping of the Allen Brain Atlas provides a wealth of data that, when appropriately analyzed, can substantially augment the molecular marker knowledge in Hippocampome.org. Here we focus on the principal cell layers of dentate gyrus (DG), CA3, CA2, and CA1, which together contain approximately 90% of hippocampal neurons. These four anatomical parcels are densely packed with somata of mostly excitatory projection neurons. Thus, gene expression data for those layers can be justifiably linked to the respective principal neuron types: granule cells in DG and pyramidal cells in CA3, CA2, and CA1. In order to enable consistent interpretation across genes and regions, we screened the whole-genome dataset against known molecular markers of those neuron types. The resulting threshold values allow over 6000 very-high confidence (>99.5%) expressed/not-expressed assignments, expanding the biochemical information content of Hippocampome.org more than five-fold. Many of these newly identified molecular markers are potential pharmacological targets for major neurological and psychiatric conditions. Furthermore, our approach yields reasonable expression

  16. Agent Architectures for Compliance

    Science.gov (United States)

    Burgemeestre, Brigitte; Hulstijn, Joris; Tan, Yao-Hua

    A Normative Multi-Agent System consists of autonomous agents who must comply with social norms. Different kinds of norms make different assumptions about the cognitive architecture of the agents. For example, a principle-based norm assumes that agents can reflect upon the consequences of their actions; a rule-based formulation only assumes that agents can avoid violations. In this paper we present several cognitive agent architectures for self-monitoring and compliance. We show how different assumptions about the cognitive architecture lead to different information needs when assessing compliance. The approach is validated with a case study of horizontal monitoring, an approach to corporate tax auditing recently introduced by the Dutch Customs and Tax Authority.

  17. Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

    Science.gov (United States)

    Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

    2018-01-01

    We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

  18. Capability and Development Risk Management in System-of-Systems Architectures: A Portfolio Approach to Decision-Making

    Science.gov (United States)

    2012-04-30

    tool that provides a means of balancing capability development against cost and interdependent risks through the use of modern portfolio theory ...Focardi, 2007; Tutuncu & Cornuejols, 2007) that are extensions of modern portfolio and control theory . The reformulation allows for possible changes...Acquisition: Wave Model context • An Investment Portfolio Approach – Mean Variance Approach – Mean - Variance : A Robust Version • Concept

  19. Molecular approaches to solar energy conversion: the energetic cost of charge separation from molecular-excited states.

    Science.gov (United States)

    Durrant, James R

    2013-08-13

    This review starts with a brief overview of the technological potential of molecular-based solar cell technologies. It then goes on to focus on the core scientific challenge associated with using molecular light-absorbing materials for solar energy conversion, namely the separation of short-lived, molecular-excited states into sufficiently long-lived, energetic, separated charges capable of generating an external photocurrent. Comparisons are made between different molecular-based solar cell technologies, with particular focus on the function of dye-sensitized photoelectrochemical solar cells as well as parallels with the function of photosynthetic reaction centres. The core theme of this review is that generating charge carriers with sufficient lifetime and a high quantum yield from molecular-excited states comes at a significant energetic cost-such that the energy stored in these charge-separated states is typically substantially less than the energy of the initially generated excited state. The role of this energetic loss in limiting the efficiency of solar energy conversion by such devices is emphasized, and strategies to minimize this energy loss are compared and contrasted.

  20. Modern classification of neoplasms: reconciling differences between morphologic and molecular approaches

    International Nuclear Information System (INIS)

    Berman, Jules

    2005-01-01

    For over 150 years, pathologists have relied on histomorphology to classify and diagnose neoplasms. Their success has been stunning, permitting the accurate diagnosis of thousands of different types of neoplasms using only a microscope and a trained eye. In the past two decades, cancer genomics has challenged the supremacy of histomorphology by identifying genetic alterations shared by morphologically diverse tumors and by finding genetic features that distinguish subgroups of morphologically homogeneous tumors. The Developmental Lineage Classification and Taxonomy of Neoplasms groups neoplasms by their embryologic origin. The putative value of this classification is based on the expectation that tumors of a common developmental lineage will share common metabolic pathways and common responses to drugs that target these pathways. The purpose of this manuscript is to show that grouping tumors according to their developmental lineage can reconcile certain fundamental discrepancies resulting from morphologic and molecular approaches to neoplasm classification. In this study, six issues in tumor classification are described that exemplify the growing rift between morphologic and molecular approaches to tumor classification: 1) the morphologic separation between epithelial and non-epithelial tumors; 2) the grouping of tumors based on shared cellular functions; 3) the distinction between germ cell tumors and pluripotent tumors of non-germ cell origin; 4) the distinction between tumors that have lost their differentiation and tumors that arise from uncommitted stem cells; 5) the molecular properties shared by morphologically disparate tumors that have a common developmental lineage, and 6) the problem of re-classifying morphologically identical but clinically distinct subsets of tumors. The discussion of these issues in the context of describing different methods of tumor classification is intended to underscore the clinical value of a robust tumor classification. A

  1. ADAPTIVE REUSE FOR NEW SOCIAL AND MUNICIPAL FUNCTIONS AS AN ACCEPTABLE APPROACH FOR CONSERVATION OF INDUSTRIAL HERITAGE ARCHITECTURE IN THE CZECH REPUBLIC

    OpenAIRE

    Oleg Fetisov

    2016-01-01

    The present paper deals with a problem of conservation and adaptive reuse of industrial heritage architecture. The relevance and topicality of the problem of adaptive reuse of industrial heritage architecture for new social and municipal functions as the conservation concept are defined. New insights on the typology of industrial architecture are reviewed (e. g. global changes in all European industry, new concepts and technologies in manufacturing, new features of industrial architecture and...

  2. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    Science.gov (United States)

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Developmental psychopathology in an era of molecular genetics and neuroimaging: A developmental neurogenetics approach.

    Science.gov (United States)

    Hyde, Luke W

    2015-05-01

    The emerging field of neurogenetics seeks to model the complex pathways from gene to brain to behavior. This field has focused on imaging genetics techniques that examine how variability in common genetic polymorphisms predict differences in brain structure and function. These studies are informed by other complimentary techniques (e.g., animal models and multimodal imaging) and have recently begun to incorporate the environment through examination of Imaging Gene × Environment interactions. Though neurogenetics has the potential to inform our understanding of the development of psychopathology, there has been little integration between principles of neurogenetics and developmental psychopathology. The paper describes a neurogenetics and Imaging Gene × Environment approach and how these approaches have been usefully applied to the study of psychopathology. Six tenets of developmental psychopathology (the structure of phenotypes, the importance of exploring mechanisms, the conditional nature of risk, the complexity of multilevel pathways, the role of development, and the importance of who is studied) are identified, and how these principles can further neurogenetics applications to understanding the development of psychopathology is discussed. A major issue of this piece is how neurogenetics and current imaging and molecular genetics approaches can be incorporated into developmental psychopathology perspectives with a goal of providing models for better understanding pathways from among genes, environments, the brain, and behavior.

  4. Molecular docking of Glycine max and Medicago truncatula ureases with urea; bioinformatics approaches.

    Science.gov (United States)

    Filiz, Ertugrul; Vatansever, Recep; Ozyigit, Ibrahim Ilker

    2016-03-01

    Urease (EC 3.5.1.5) is a nickel-dependent metalloenzyme catalyzing the hydrolysis of urea into ammonia and carbon dioxide. It is present in many bacteria, fungi, yeasts and plants. Most species, with few exceptions, use nickel metalloenzyme urease to hydrolyze urea, which is one of the commonly used nitrogen fertilizer in plant growth thus its enzymatic hydrolysis possesses vital importance in agricultural practices. Considering the essentiality and importance of urea and urease activity in most plants, this study aimed to comparatively investigate the ureases of two important legume species such as Glycine max (soybean) and Medicago truncatula (barrel medic) from Fabaceae family. With additional plant species, primary and secondary structures of 37 plant ureases were comparatively analyzed using various bioinformatics tools. A structure based phylogeny was constructed using predicted 3D models of G. max and M. truncatula, whose crystallographic structures are not available, along with three additional solved urease structures from Canavalia ensiformis (PDB: 4GY7), Bacillus pasteurii (PDB: 4UBP) and Klebsiella aerogenes (PDB: 1FWJ). In addition, urease structures of these species were docked with urea to analyze the binding affinities, interacting amino acids and atom distances in urease-urea complexes. Furthermore, mutable amino acids which could potentially affect the protein active site, stability and flexibility as well as overall protein stability were analyzed in urease structures of G. max and M. truncatula. Plant ureases demonstrated similar physico-chemical properties with 833-878 amino acid residues and 89.39-90.91 kDa molecular weight with mainly acidic (5.15-6.10 pI) nature. Four protein domain structures such as urease gamma, urease beta, urease alpha and amidohydro 1 characterized the plant ureases. Secondary structure of plant ureases also demonstrated conserved protein architecture, with predominantly α-helix and random coil structures. In

  5. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

    Energy Technology Data Exchange (ETDEWEB)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2016-03-21

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

  6. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

    Science.gov (United States)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  7. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

    International Nuclear Information System (INIS)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-01-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S N 2 reaction (Cl − + CH 3 Cl → ClCH 3 + Cl − ) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF

  8. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

    Science.gov (United States)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-07

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  9. Architectural freedom and industrialized architecture

    DEFF Research Database (Denmark)

    Vestergaard, Inge

    2012-01-01

    to explain that architecture can be thought as a complex and diverse design through customization, telling exactly the revitalized storey about the change to a contemporary sustainable and better performing expression in direct relation to the given context. Through the last couple of years we have...... proportions, to organize the process on site choosing either one room wall components or several rooms wall components – either horizontally or vertically. Combined with the seamless joint the playing with these possibilities the new industrialized architecture can deliver variations in choice of solutions...... for retrofit design. If we add the question of the installations e.g. ventilation to this systematic thinking of building technique we get a diverse and functional architecture, thereby creating a new and clearer story telling about new and smart system based thinking behind architectural expression....

  10. Architectural freedom and industrialized architecture

    DEFF Research Database (Denmark)

    Vestergaard, Inge

    2012-01-01

    to explain that architecture can be thought as a complex and diverse design through customization, telling exactly the revitalized storey about the change to a contemporary sustainable and better performing expression in direct relation to the given context. Through the last couple of years we have...... expression in the specific housing area. It is the aim of this article to expand the different design strategies which architects can use – to give the individual project attitudes and designs with architectural quality. Through the customized component production it is possible to choose different...... for retrofit design. If we add the question of the installations e.g. ventilation to this systematic thinking of building technique we get a diverse and functional architecture, thereby creating a new and clearer story telling about new and smart system based thinking behind architectural expression....

  11. Architectural freedom and industrialised architecture

    DEFF Research Database (Denmark)

    Vestergaard, Inge

    2012-01-01

    Architectural freedom and industrialized architecture. Inge Vestergaard, Associate Professor, Cand. Arch. Aarhus School of Architecture, Denmark Noerreport 20, 8000 Aarhus C Telephone +45 89 36 0000 E-mai l inge.vestergaard@aarch.dk Based on the repetitive architecture from the "building boom" 1960...... customization, telling exactly the revitalized storey about the change to a contemporary sustainable and better performed expression in direct relation to the given context. Through the last couple of years we have in Denmark been focusing a more sustainable and low energy building technique, which also include...... to the building physic problems a new industrialized period has started based on light weight elements basically made of wooden structures, faced with different suitable materials meant for individual expression for the specific housing area. It is the purpose of this article to widen up the different design...

  12. Intracellular antibody capture: A molecular biology approach to inhibitors of protein-protein interactions.

    Science.gov (United States)

    Zhang, Jing; Rabbitts, Terence H

    2014-11-01

    Many proteins of interest in basic biology, translational research studies and for clinical targeting in diseases reside inside the cell and function by interacting with other macromolecules. Protein complexes control basic processes such as development and cell division but also abnormal cell growth when mutations occur such as found in cancer. Interfering with protein-protein interactions is an important aspiration in both basic and disease biology but small molecule inhibitors have been difficult and expensive to isolate. Recently, we have adapted molecular biology techniques to develop a simple set of protocols for isolation of high affinity antibody fragments (in the form of single VH domains) that function within the reducing environment of higher organism cells and can bind to their target molecules. The method called Intracellular Antibody Capture (IAC) has been used to develop inhibitory anti-RAS and anti-LMO2 single domains that have been used for target validation of these antigens in pre-clinical cancer models and illustrate the efficacy of the IAC approach to generation of drug surrogates. Future use of inhibitory VH antibody fragments as drugs in their own right (we term these macrodrugs to distinguish them from small molecule drugs) requires their delivery to target cells in vivo but they can also be templates for small molecule drug development that emulate the binding sites of the antibody fragments. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Mass Spectrometry-based Approaches to Understand the Molecular Basis of Memory

    Directory of Open Access Journals (Sweden)

    Arthur Henriques Pontes

    2016-10-01

    Full Text Available The central nervous system is responsible for an array of cognitive functions such as memory, learning, language and attention. These processes tend to take place in distinct brain regions; yet, they need to be integrated to give rise to adaptive or meaningful behavior. Since cognitive processes result from underlying cellular and molecular changes, genomics and transcriptomics assays have been applied to human and animal models to understand such events. Nevertheless, genes and RNAs are not the end products of most biological functions. In order to gain further insights toward the understanding of brain processes, the field of proteomics has been of increasing importance in the past years. Advancements in liquid chromatography-tandem mass spectrometry (LC-MS/MS have enable the identification and quantification of thousand of proteins with high accuracy and sensitivity, fostering a revolution in the neurosciences. Herein, we review the molecular bases of explicit memory in the hippocampus. We outline the principles of mass spectrometry (MS-based proteomics, highlighting the use of this analytical tool to study memory formation. In addition, we discuss MS-based targeted approaches as the future of protein analysis.

  14. Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems

    Science.gov (United States)

    Stella, L.; Lorenz, C. D.; Kantorovich, L.

    2014-04-01

    The generalized Langevin equation (GLE) has been recently suggested to simulate the time evolution of classical solid and molecular systems when considering general nonequilibrium processes. In this approach, a part of the whole system (an open system), which interacts and exchanges energy with its dissipative environment, is studied. Because the GLE is derived by projecting out exactly the harmonic environment, the coupling to it is realistic, while the equations of motion are non-Markovian. Although the GLE formalism has already found promising applications, e.g., in nanotribology and as a powerful thermostat for equilibration in classical molecular dynamics simulations, efficient algorithms to solve the GLE for realistic memory kernels are highly nontrivial, especially if the memory kernels decay nonexponentially. This is due to the fact that one has to generate a colored noise and take account of the memory effects in a consistent manner. In this paper, we present a simple, yet efficient, algorithm for solving the GLE for practical memory kernels and we demonstrate its capability for the exactly solvable case of a harmonic oscillator coupled to a Debye bath.

  15. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-01-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

  16. Molecular nanomagnets and magnetic nanoparticles: the EMR contribution to a common approach.

    Science.gov (United States)

    Fittipaldi, M; Sorace, L; Barra, A-L; Sangregorio, C; Sessoli, R; Gatteschi, D

    2009-08-21

    The current status and future developments of the use of electron magnetic resonance (EMR) for the investigation of magnetic nano-systems is here reviewed. The aim is to stimulate efforts to provide a unified view of the properties of magnetic nanoparticles (MNP) comprising a few hundred magnetic centres, and molecular nanomagnets which contain up to ca. one hundred magnetic centres (MNM). The size of the systems is becoming the same but the approaches to the interpretation of their properties are still different, being bottom up for the latter and top down for the former. We make the point here of the need for a common viewpoint, highlighting the status of the two fields and giving some hints for the future developments. EMR has been a powerful tool for the investigation of magnetic nano-objects and it can provide a tool of fundamental importance for the development of a unified view.

  17. Stepwise Construction of Heterobimetallic Cages by an Extended Molecular Library Approach.

    Science.gov (United States)

    Hardy, Matthias; Struch, Niklas; Topić, Filip; Schnakenburg, Gregor; Rissanen, Kari; Lützen, Arne

    2018-04-02

    Two novel heterobimetallic complexes, a trigonal-bipyramidal and a cubic one, have been synthesized and characterized using the same C 3 -symmetric metalloligand, prepared by a simple subcomponent self-assembly strategy. Adopting the molecular library approach, we chose a mononuclear, preorganized iron(II) complex as the metalloligand capable of self-assembly into a trigonal-bipyramidal or a cubic aggregate upon coordination to cis-protected C 2 -symmetric palladium(II) or unprotected tetravalent palladium(II) ions, respectively. The trigonal-bipyramidal complex was characterized by NMR and UV-vis spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and single-crystal X-ray diffraction. The cubic structure was characterized by NMR and UV-vis spectroscopy and ESI-MS.

  18. Delimiting invasive Myriophyllum aquaticum in Kashmir Himalaya using a molecular phylogenetic approach.

    Science.gov (United States)

    Shah, M A; Ali, M A; Al-Hemaid, F M; Reshi, Z A

    2014-09-12

    Myriophyllum aquaticum (Vell.) Verdc. (family Haloragaceae) is one of the most invasive and destructive South American aquatic plant species and is present in a wide range of geographic regions, including the Kashmir Himalaya. Confusion regarding the taxonomic delimitation of M. aquaticum in the Himalayan region impedes effective and targeted management. Hence, our goal was improve the identification of M. aquaticum for exclusive delimitation from other related species in the study region using a molecular phylogenetic approach. A maximum parsimony tree recovered from phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA was used to authenticate the identification of M. aquaticum. The results of this study can be used for targeted management of this tropical invader into the temperate Kashmir Himalaya.

  19. Synthesis of Norbornene Derived Helical Copolymer by Simple Molecular Marriage Approach to Produce Smart Nanocarrier.

    Science.gov (United States)

    Mane, Shivshankar R; Sathyan, Ashlin; Shunmugam, Raja

    2017-03-22

    A novel library of norbornene derived helical copolymer has been synthesized through the coupling of two homopolymers via Molecular Marriage Approach. The helicity is governed by the non-covalent interactions like hydrogen bonding, π-π stacking and the influence of hydrophobic and hydrophilic motifs. The detailed characterization of the copolymer (Copoly 1) has been provided and the super structures are confirmed through dynamic light scattering (DLS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The observed size of the aggregates was about 200 nm. The density functional theory (DFT) is favorably supported for the formation of proposed structure of Copoly 1. Circular dichroism (CD) measurement has confirmed the one handed helical structure of the copolymer. Reservoir capability of this pH responsive polymer (Copoly 1) to encapsulate anti-cancer drug doxorubicin (DOX) warrants its potential applications in the field of bio-medical sciences.

  20. Screening of photosynthetic pigments for herbicidal activity with a new computational molecular approach.

    Science.gov (United States)

    Krishnaraj, R Navanietha; Chandran, Saravanan; Pal, Parimal; Berchmans, Sheela

    2013-12-01

    There is an immense interest among the researchers to identify new herbicides which are effective against the herbs without affecting the environment. In this work, photosynthetic pigments are used as the ligands to predict their herbicidal activity. The enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is a good target for the herbicides. Homology modeling of the target enzyme is done using Modeler 9.11 and the model is validated. Docking studies were performed with AutoDock Vina algorithm to predict the binding of the natural pigments such as β-carotene, chlorophyll a, chlorophyll b, phycoerythrin and phycocyanin to the target. β-carotene, phycoerythrin and phycocyanin have higher binding energies indicating the herbicidal activity of the pigments. This work reports a procedure to screen herbicides with computational molecular approach. These pigments will serve as potential bioherbicides in the future.

  1. A review of gastrointestinal microbiology with special emphasis on molecular microbial ecology approaches

    International Nuclear Information System (INIS)

    Mackie, R.I.; Cann, I.K.O.

    2005-01-01

    All animals, including humans, are adapted to life in a microbial world. Large populations of micro-organisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological and protective functions of the host animal. Bacteria have traditionally been classified mainly on the basis of phenotypic properties. Despite the vast amount of knowledge generated for ruminal and other intestinal ecosystems using traditional techniques, the basic requisites for ecological studies, namely, enumeration and identification of all community members, have limitations. The two major problems faced by microbial ecologists are bias introduced by culture-based enumeration and characterization techniques, and the lack of a phylogenetically-based classification scheme. Modem molecular ecology techniques based on sequence comparisons of nucleic acids (DNA or RNA) can be used to provide molecular characterization while at the same time providing a classification scheme that predicts natural evolutionary relationships. These molecular methods provide results that are independent of growth conditions and media used. Also, using these techniques, bacteria can be classified and identified before they can be grown in pure culture. These nucleic acid-based techniques will enable gut microbiologists to answer the most difficult question in microbial ecology: namely, describing the exact role or function a specific bacterium plays in its natural environment and its quantitative contribution to the whole. However, rather than replacing the classical culture-based system, the new molecular-based techniques can be used in combination with the classical approach to improve cultivation, speciation and evaluation of diversity. The study of microbial

  2. Architectural freedom and industrialised architecture

    DEFF Research Database (Denmark)

    Vestergaard, Inge

    2012-01-01

    to the building physic problems a new industrialized period has started based on light weight elements basically made of wooden structures, faced with different suitable materials meant for individual expression for the specific housing area. It is the purpose of this article to widen up the different design...... to this systematic thinking of the building technique we get a diverse and functional architecture. Creating a new and clearer story telling about new and smart system based thinking behind the architectural expression....

  3. Use of Modular Approach to Obtain Molecular Glasses for Photonics: Triphenyl Moieties

    OpenAIRE

    Traskovskis, K; Kokars, V; Tokmakovs, A; Mihailovs, I; Rutkis, M

    2012-01-01

    Small molecular weight amorphous phase forming materials is a new emerging class of electro optical materials. While general principles linking molecular structure and material thermal and amorphous phase stability characteristics remain unresolved, molecular glasses have several considerable advantages such as relatively simple synthesis and purification, increased chromophore density and well defined structure. A wide spread strategy for obtaining molecular compounds capable of forming stab...

  4. Examination of taxonomic uncertainties surrounding Brucella abortus bv. 7 by phenotypic and molecular approaches.

    Science.gov (United States)

    Garin-Bastuji, Bruno; Mick, Virginie; Le Carrou, Gilles; Allix, Sebastien; Perrett, Lorraine L; Dawson, Claire E; Groussaud, Pauline; Stubberfield, Emma J; Koylass, Mark; Whatmore, Adrian M

    2014-03-01

    Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5. To formally clarify the situation, all isolates previously identified as B. abortus bv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to the B. abortus species. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into the Brucella classification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity of Brucella taxonomy. This study suggests that worldwide collections could include strains misidentified as B. abortus bv. 7, and it highlights the need to verify their real taxonomic position.

  5. Thumbs down: a molecular-morphogenetic approach to avian digit homology.

    Science.gov (United States)

    Capek, Daniel; Metscher, Brian D; Müller, Gerd B

    2014-01-01

    Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain. © 2013 Wiley Periodicals, Inc.

  6. Interface, a dispersed architecture

    NARCIS (Netherlands)

    Vissers, C.A.

    1976-01-01

    Past and current specification techniques use timing diagrams and written text to describe the phenomenology of an interface. This paper treats an interface as the architecture of a number of processes, which are dispersed over the related system parts and the message path. This approach yields a

  7. Architecture of Intermodal Complex

    NARCIS (Netherlands)

    Lee, S.; Herneoja, Aulikki; Österlund, Toni; Markkanen, Piia

    This paper focuses on the conception and design of architecture as the work of producing media about buildings and other environmental artifacts. I approach
    the questions regarding simplicity and complexity through "interdependence" and "intermodality." I believe the two concepts offer more

  8. Radiology systems architecture.

    Science.gov (United States)

    Deibel, S R; Greenes, R A

    1996-05-01

    This article focuses on the software requirements for enterprise integration in radiology. The needs of a future radiology systems architecture are examined, both at a concrete functional level and at an abstract system-properties level. A component-based approach to software development is described and is validated in the context of each of the abstract system requirements for future radiology computing environments.

  9. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches

    OpenAIRE

    Rodrigues, Paula; Venâncio, Armando; Lima, Nelson

    2011-01-01

    Section Flavi is one of the most significant Sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by MALDI-TOF ICMS, and to evaluate the discriminatory power of the various approaches in species identification. Methods and ...

  10. Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

    Science.gov (United States)

    Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

    2017-09-01

    Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Harnessing the Risk-Related Data Supply Chain: An Information Architecture Approach to Enriching Human System Research and Operations Knowledge

    Science.gov (United States)

    Buquo, Lynn; Johnson-Throop, Kathy

    2010-01-01

    NASA's Human Research Program (HRP) and Space Life Sciences Directorate (SLSD), not unlike many NASA organizations today, struggle with the inherent inefficiencies caused by dependencies on heterogeneous data systems and silos of data and information spread across decentralized discipline domains. The capture of operational and research-based data/information (both in-flight and ground-based) in disparate IT systems impedes the extent to which that data/information can be efficiently and securely shared, analyzed, and enriched into knowledge that directly and more rapidly supports HRP's research-focused human system risk mitigation efforts and SLSD s operationally oriented risk management efforts. As a result, an integrated effort is underway to more fully understand and document how specific sets of risk-related data/information are generated and used and in what IT systems that data/information currently resides. By mapping the risk-related data flow from raw data to useable information and knowledge (think of it as the data supply chain), HRP and SLSD are building an information architecture plan to leverage their existing, shared IT infrastructure. In addition, it is important to create a centralized structured tool to represent risks including attributes such as likelihood, consequence, contributing factors, and the evidence supporting the information in all these fields. Representing the risks in this way enables reasoning about the risks, e.g. revisiting a risk assessment when a mitigation strategy is unavailable, updating a risk assessment when new information becomes available, etc. Such a system also provides a concise way to communicate the risks both within the organization as well as with collaborators. Understanding and, hence, harnessing the human system risk-related data supply chain enhances both organizations' abilities to securely collect, integrate, and share data assets that improve human system research and operations.

  12. Architectural geometry

    KAUST Repository

    Pottmann, Helmut; Eigensatz, Michael; Vaxman, Amir; Wallner, Johannes

    2014-01-01

    Around 2005 it became apparent in the geometry processing community that freeform architecture contains many problems of a geometric nature to be solved, and many opportunities for optimization which however require geometric understanding. This area of research, which has been called architectural geometry, meanwhile contains a great wealth of individual contributions which are relevant in various fields. For mathematicians, the relation to discrete differential geometry is significant, in particular the integrable system viewpoint. Besides, new application contexts have become available for quite some old-established concepts. Regarding graphics and geometry processing, architectural geometry yields interesting new questions but also new objects, e.g. replacing meshes by other combinatorial arrangements. Numerical optimization plays a major role but in itself would be powerless without geometric understanding. Summing up, architectural geometry has become a rewarding field of study. We here survey the main directions which have been pursued, we show real projects where geometric considerations have played a role, and we outline open problems which we think are significant for the future development of both theory and practice of architectural geometry.

  13. Architectural geometry

    KAUST Repository

    Pottmann, Helmut

    2014-11-26

    Around 2005 it became apparent in the geometry processing community that freeform architecture contains many problems of a geometric nature to be solved, and many opportunities for optimization which however require geometric understanding. This area of research, which has been called architectural geometry, meanwhile contains a great wealth of individual contributions which are relevant in various fields. For mathematicians, the relation to discrete differential geometry is significant, in particular the integrable system viewpoint. Besides, new application contexts have become available for quite some old-established concepts. Regarding graphics and geometry processing, architectural geometry yields interesting new questions but also new objects, e.g. replacing meshes by other combinatorial arrangements. Numerical optimization plays a major role but in itself would be powerless without geometric understanding. Summing up, architectural geometry has become a rewarding field of study. We here survey the main directions which have been pursued, we show real projects where geometric considerations have played a role, and we outline open problems which we think are significant for the future development of both theory and practice of architectural geometry.

  14. PRO_LIGAND: an approach to de novo molecular design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores.

    Science.gov (United States)

    Waszkowycz, B; Clark, D E; Frenkel, D; Li, J; Murray, C W; Robson, B; Westhead, D R

    1994-11-11

    A computational approach for molecular design, PRO_LIGAND, has been developed within the PROMETHEUS molecular design and simulation system in order to provide a unified framework for the de novo generation of diverse molecules which are either similar or complementary to a specified target. In this instance, the target is a pharmacophore derived from a series of active structures either by a novel interpretation of molecular field analysis data or by a pharmacophore-mapping procedure based on clique detection. After a brief introduction to PRO_LIGAND, a detailed description is given of the two pharmacophore generation procedures and their abilities are demonstrated by the elucidation of pharmacophores for steroid binding and ACE inhibition, respectively. As a further indication of its efficacy in aiding the rational drug design process, PRO_LIGAND is then employed to build novel organic molecules to satisfy the physicochemical constraints implied by the pharmacophores.

  15. Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

    Science.gov (United States)

    Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

    2018-02-01

    Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

  16. Relational Architecture

    DEFF Research Database (Denmark)

    Reeh, Henrik

    2018-01-01

    in a scholarly institution (element #3), as well as the certified PhD scholar (element #4) and the architectural profession, notably its labour market (element #5). This first layer outlines the contemporary context which allows architectural research to take place in a dynamic relationship to doctoral education...... a human and institutional development going on since around 1990 when the present PhD institution was first implemented in Denmark. To be sure, the model is centred around the PhD dissertation (element #1). But it involves four more components: the PhD candidate (element #2), his or her supervisor...... and interrelated fields in which history, place, and sound come to emphasize architecture’s relational qualities rather than the apparent three-dimensional solidity of constructed space. A third layer of relational architecture is at stake in the professional experiences after the defence of the authors...

  17. Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach.

    Science.gov (United States)

    Ahmed, Bilal; Ali Ashfaq, Usman; Usman Mirza, Muhammad

    2018-05-01

    Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding affinity. Finally, 10 molecules (Kushenol K, Rosmarinic acid, Reserpic acid, Munjistin, Leachianone G, Cephamycin C, Arctigenin, 3-O-acetylpadmatin, Geniposide and Obtusin) were selected that showed strong bonding with the pancreatic lipase. MD simulations were performed on top five compounds using AMBER16. The simulated complexes revealed stability and ligands remained inside the binding pocket. This study concluded that these finalised molecules can be used as drug candidate to control obesity.

  18. In Silico Design of Human IMPDH Inhibitors Using Pharmacophore Mapping and Molecular Docking Approaches

    Directory of Open Access Journals (Sweden)

    Rui-Juan Li

    2015-01-01

    Full Text Available Inosine 5′-monophosphate dehydrogenase (IMPDH is one of the crucial enzymes in the de novo biosynthesis of guanosine nucleotides. It has served as an attractive target in immunosuppressive, anticancer, antiviral, and antiparasitic therapeutic strategies. In this study, pharmacophore mapping and molecular docking approaches were employed to discover novel Homo sapiens IMPDH (hIMPDH inhibitors. The Güner-Henry (GH scoring method was used to evaluate the quality of generated pharmacophore hypotheses. One of the generated pharmacophore hypotheses was found to possess a GH score of 0.67. Ten potential compounds were selected from the ZINC database using a pharmacophore mapping approach and docked into the IMPDH active site. We find two hits (i.e., ZINC02090792 and ZINC00048033 that match well the optimal pharmacophore features used in this investigation, and it is found that they form interactions with key residues of IMPDH. We propose that these two hits are lead compounds for the development of novel hIMPDH inhibitors.

  19. Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach

    International Nuclear Information System (INIS)

    Yakubovich, Alexander V.; Solov'yov, Andrey V.; Surdutovich, Eugene

    2011-01-01

    We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion-beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo-mechanical effects caused by the propagation of ions through the biological environment and in particular on the possibility of the creation of the shock waves in the vicinity of the ion tracks. We demonstrate that at the initial stages after ion's passage the shock wave is so strong that it can contribute to the DNA damage due to large pressure gradients developed at the distances of a few nanometers from the ionic tracks. This novel mechanism of the DNA damage provides an important contribution to the cumulative biodamage caused by low-energy secondary electrons, holes and free radicals.

  20. Imaging and Molecular Markers for Patients with Lung Cancer: Approaches with Molecular Targets, Complementary/Innovative Treatment, and Therapeutic Modalities

    Science.gov (United States)

    2011-02-01

    Therapeutic and Imaging Agents to Lung Cancer (PI and co-PI: Renata Pasqualini , Ph.D., Wadih Arap, M.D., Ph.D.) The studies outlined in this proposal...with Drs. Pasqualini , Arap, and Wistuba. The IHC staining of lung cancer TMAs (390 cases) has been completed. We are working with investigators to...Project 3, R. Pasqualini ). This project was completed and a manuscript is in preparation by Dr. Pasqualini’s lab. b) Molecular abnormalities

  1. New Energy Architecture. Myanmar

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-06-15

    A global transition towards a new energy architecture is under way, driven by countries' need to respond to the changing dynamics of economic growth, environmental sustainability and energy security. The World Economic Forum, in collaboration with Accenture, has created the New Energy Architecture Initiative to address and accelerate this transition. The Initiative supports the development of national strategies and policy frameworks as countries seek to achieve the combined goals of energy security and access, sustainability, and economic growth and development. The World Economic Forum has formed a partnership with the Ministry of Energy of Myanmar to help apply the Initiative's approach to this developing and resource-rich nation. The Asian Development Bank and the World Economic Forum's Project Adviser, Accenture, have collaborated with the Forum on this consultation process, and have been supported by relevant government, industry and civil society stakeholders. The consultation process aims to understand the nation's current energy architecture challenges and provide an overview of a path to a New Energy Architecture through a series of insights. These insights could form the basis for a long-term multistakeholder roadmap to build Myanmar's energy sector in a way that is secure and sustainable, and promotes economic growth as the country makes its democratic transition. While not all recommendations can be implemented in the near term, they do provide options for creating a prioritized roadmap for Myanmar's energy transition. This report is the culmination of a nine-month multistakeholder process investigating Myanmar's energy architecture. Over the course of many visits to the country, the team has conducted numerous interviews, multistakeholder workshops, and learning and data-gathering exercises to ensure a comprehensive range of information and views. The team has also engaged with a variety of stakeholders to better inform their findings, which have come

  2. New Energy Architecture. Myanmar

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-06-15

    A global transition towards a new energy architecture is under way, driven by countries' need to respond to the changing dynamics of economic growth, environmental sustainability and energy security. The World Economic Forum, in collaboration with Accenture, has created the New Energy Architecture Initiative to address and accelerate this transition. The Initiative supports the development of national strategies and policy frameworks as countries seek to achieve the combined goals of energy security and access, sustainability, and economic growth and development. The World Economic Forum has formed a partnership with the Ministry of Energy of Myanmar to help apply the Initiative's approach to this developing and resource-rich nation. The Asian Development Bank and the World Economic Forum's Project Adviser, Accenture, have collaborated with the Forum on this consultation process, and have been supported by relevant government, industry and civil society stakeholders. The consultation process aims to understand the nation's current energy architecture challenges and provide an overview of a path to a New Energy Architecture through a series of insights. These insights could form the basis for a long-term multistakeholder roadmap to build Myanmar's energy sector in a way that is secure and sustainable, and promotes economic growth as the country makes its democratic transition. While not all recommendations can be implemented in the near term, they do provide options for creating a prioritized roadmap for Myanmar's energy transition. This report is the culmination of a nine-month multistakeholder process investigating Myanmar's energy architecture. Over the course of many visits to the country, the team has conducted numerous interviews, multistakeholder workshops, and learning and data-gathering exercises to ensure a comprehensive range of information and views. The team has also engaged with a variety of stakeholders to better

  3. Neural Architectures for Control

    Science.gov (United States)

    Peterson, James K.

    1991-01-01

    The cerebellar model articulated controller (CMAC) neural architectures are shown to be viable for the purposes of real-time learning and control. Software tools for the exploration of CMAC performance are developed for three hardware platforms, the MacIntosh, the IBM PC, and the SUN workstation. All algorithm development was done using the C programming language. These software tools were then used to implement an adaptive critic neuro-control design that learns in real-time how to back up a trailer truck. The truck backer-upper experiment is a standard performance measure in the neural network literature, but previously the training of the controllers was done off-line. With the CMAC neural architectures, it was possible to train the neuro-controllers on-line in real-time on a MS-DOS PC 386. CMAC neural architectures are also used in conjunction with a hierarchical planning approach to find collision-free paths over 2-D analog valued obstacle fields. The method constructs a coarse resolution version of the original problem and then finds the corresponding coarse optimal path using multipass dynamic programming. CMAC artificial neural architectures are used to estimate the analog transition costs that dynamic programming requires. The CMAC architectures are trained in real-time for each obstacle field presented. The coarse optimal path is then used as a baseline for the construction of a fine scale optimal path through the original obstacle array. These results are a very good indication of the potential power of the neural architectures in control design. In order to reach as wide an audience as possible, we have run a seminar on neuro-control that has met once per week since 20 May 1991. This seminar has thoroughly discussed the CMAC architecture, relevant portions of classical control, back propagation through time, and adaptive critic designs.

  4. Evolution of the Ethane Architecture

    National Research Council Canada - National Science Library

    Casado, Martin; Shenker, Scott

    2009-01-01

    The Ethane architecture, developed at Stanford University, demonstrated that a novel approach to building secure networks could support superior low-level security and flexible policy-based control over individual flows...

  5. AUTOMATIC ARCHITECTURAL STYLE RECOGNITION

    Directory of Open Access Journals (Sweden)

    M. Mathias

    2012-09-01

    Full Text Available Procedural modeling has proven to be a very valuable tool in the field of architecture. In the last few years, research has soared to automatically create procedural models from images. However, current algorithms for this process of inverse procedural modeling rely on the assumption that the building style is known. So far, the determination of the building style has remained a manual task. In this paper, we propose an algorithm which automates this process through classification of architectural styles from facade images. Our classifier first identifies the images containing buildings, then separates individual facades within an image and determines the building style. This information could then be used to initialize the building reconstruction process. We have trained our classifier to distinguish between several distinct architectural styles, namely Flemish Renaissance, Haussmannian and Neoclassical. Finally, we demonstrate our approach on various street-side images.

  6. A Federated Enterprise Architecture and MBSE Modeling Framework for Integrating Design Automation into a Global PLM Approach

    OpenAIRE

    Vosgien , Thomas; Rigger , Eugen; Schwarz , Martin; Shea , Kristina

    2017-01-01

    Part 1: PLM Maturity, Implementation and Adoption; International audience; PLM and Design Automation (DA) are two interdependent and necessary approaches to increase the performance and efficiency of product development processes. Often, DA systems’ usability suffers due to a lack of integration in industrial business environments stemming from the independent consideration of PLM and DA. This article proposes a methodological and modeling framework for developing and deploying DA solutions w...

  7. Toward an understanding of the molecular mechanisms of barnacle larval settlement: A comparative transcriptomic approach

    KAUST Repository

    Chen, Zhang-Fan

    2011-07-29

    Background: The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. Methodology and Principal Findings: Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. Conclusions: Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species. © 2011 Chen et al.

  8. Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

    Directory of Open Access Journals (Sweden)

    Andrea A. F. Mourão

    Full Text Available ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó individuals were collected in Paraná and Tietê rivers (SP, Brazil. For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

  9. Insights using a molecular approach into the life cycle of a tapeworm infecting great white sharks.

    Science.gov (United States)

    Randhawa, Haseeb S

    2011-04-01

    The great white shark Carcharodon carcharias Linnaeus, 1758 is a versatile and fierce predator (and responsible for many shark attacks on humans). This apex predator feeds on a wide range of organisms including teleosts, other elasmobranchs, cephalopods, pinnipeds, and cetaceans. Although much is known about its diet, no trophic links have been empirically identified as being involved in the transmission of its tapeworm parasites. Recently, the use of molecular tools combined with phylogenetics has proven useful to identify larval and immature stages of marine tapeworms; utilization of the technique has been increasing rapidly. However, the usefulness of this approach remains limited by the availability of molecular data. Here, I employed gene sequence data from the D2 region of the large subunit of ribosomal DNA to link adults of the tapeworm Clistobothrium carcharodoni Dailey and Vogelbein, 1990 (Cestoda: Tetraphyllidea) to larvae for which sequence data for this gene are available. The sequences from the adult tapeworms were genetically identical (0% sequence divergence) to those available on GenBank for "SP" 'small' Scolex pleuronectis recovered from the striped dolphin (Stenella coeruleoalba) and Risso's dolphin (Grampus griseus). This study is the first to provide empirical evidence linking the trophic interaction between great white sharks and cetaceans as a definitive route for the successful transmission of a tetraphyllidean tapeworm. Using the intensity of infection data from this shark and from cetaceans as proxies for the extent of predation, I estimate that this individual shark would have consumed between 9 to 83 G. griseus , fresh, dead, or both, in its lifetime.

  10. Translation of New Molecular Imaging Approaches to the Clinical Setting: Bridging the Gap to Implementation.

    Science.gov (United States)

    van Es, Suzanne C; Venema, Clasina M; Glaudemans, Andor W J M; Lub-de Hooge, Marjolijn N; Elias, Sjoerd G; Boellaard, Ronald; Hospers, Geke A P; Schröder, Carolina P; de Vries, Elisabeth G E

    2016-02-01

    Molecular imaging with PET is a rapidly emerging technique. In breast cancer patients, more than 45 different PET tracers have been or are presently being tested. With a good rationale, after development of the tracer and proven feasibility, it is of interest to evaluate whether there is a potential meaningful role for the tracer in the clinical setting-such as in staging, in the (early) prediction of a treatment response, or in supporting drug choices. So far, only (18)F-FDG PET has been incorporated into breast cancer guidelines. For proof of the clinical relevance of tracers, especially for analysis in a multicenter setting, standardization of the technology and access to the novel PET tracer are required. However, resources for PET implementation research are limited. Therefore, next to randomized studies, novel approaches are required for proving the clinical value of PET tracers with the smallest possible number of patients. The aim of this review is to describe the process of the development of PET tracers and the level of evidence needed for the use of these tracers in breast cancer. Several breast cancer trials have been performed with the PET tracers (18)F-FDG, 3'-deoxy-3'-(18)F-fluorothymidine ((18)F-FLT), and (18)F-fluoroestradiol ((18)F-FES). We studied them to learn lessons for the implementation of novel tracers. After defining the gap between a good rationale for a tracer and implementation in the clinical setting, we propose solutions to fill the gap to try to bring more PET tracers to daily clinical practice. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  11. Explicit hydration of ammonium ion by correlated methods employing molecular tailoring approach

    Science.gov (United States)

    Singh, Gurmeet; Verma, Rahul; Wagle, Swapnil; Gadre, Shridhar R.

    2017-11-01

    Explicit hydration studies of ions require accurate estimation of interaction energies. This work explores the explicit hydration of the ammonium ion (NH4+) employing Møller-Plesset second order (MP2) perturbation theory, an accurate yet relatively less expensive correlated method. Several initial geometries of NH4+(H2O)n (n = 4 to 13) clusters are subjected to MP2 level geometry optimisation with correlation consistent aug-cc-pVDZ (aVDZ) basis set. For large clusters (viz. n > 8), molecular tailoring approach (MTA) is used for single point energy evaluation at MP2/aVTZ level for the estimation of MP2 level binding energies (BEs) at complete basis set (CBS) limit. The minimal nature of the clusters upto n ≤ 8 is confirmed by performing vibrational frequency calculations at MP2/aVDZ level of theory, whereas for larger clusters (9 ≤ n ≤ 13) such calculations are effected via grafted MTA (GMTA) method. The zero point energy (ZPE) corrections are done for all the isomers lying within 1 kcal/mol of the lowest energy one. The resulting frequencies in N-H region (2900-3500 cm-1) and in O-H stretching region (3300-3900 cm-1) are in found to be in excellent agreement with the available experimental findings for 4 ≤ n ≤ 13. Furthermore, GMTA is also applied for calculating the BEs of these clusters at coupled cluster singles and doubles with perturbative triples (CCSD(T)) level of theory with aVDZ basis set. This work thus represents an art of the possible on contemporary multi-core computers for studying explicit molecular hydration at correlated level theories.

  12. Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach.

    Directory of Open Access Journals (Sweden)

    Yuno Lee

    Full Text Available Repeat proteins have recently attracted much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural and biophysical features. In particular, repeat proteins show high stability against temperature and chaotic agents. Despite many studies, structural features for the stability of repeat proteins remain poorly understood. Here we present an interesting result from in silico analyses pursuing the factors which affect the stability of repeat proteins. Previously developed repebody structure based on variable lymphocytes receptors (VLRs which consists of leucine-rich repeat (LRR modules was used as initial structure for the present study. We constructed extra six repebody structures with varying numbers of repeat modules and those structures were used for molecular dynamics simulations. For the structures, the intramolecular interactions including backbone H-bonds, van der Waals energy, and hydrophobicity were investigated and then the radius of gyration, solvent-accessible surface area, ratio of secondary structure, and hydration free energy were also calculated to find out the relationship between the number of LRR modules and stability of the protein. Our results show that the intramolecular interactions lead to more compact structure and smaller surface area of the repebodies, which are critical for the stability of repeat proteins. The other features were also well compatible with the experimental results. Based on our observations, the repebody-5 was proposed as the best structure from the all repebodies in structure optimization process. The present study successfully demonstrated that our computer-based molecular modeling approach can significantly contribute to the experiment-based protein engineering challenge.

  13. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

    Directory of Open Access Journals (Sweden)

    Maurer Till

    2005-04-01

    Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

  14. Representation of architectural artifacts: definition of an approach combining the complexity of the 3d digital instance with the intelligibility of the theoretical model.

    Directory of Open Access Journals (Sweden)

    David Lo Buglio

    2012-12-01

    Full Text Available EnWith the arrival of digital technologies in the field of architectural documentation, many tools and methods for data acquisition have been considerably developed. However, these developments are primarily used for recording colorimetric and dimensional properties of the objects processed. The actors, of the disciplines concerned by 3D digitization of architectural heritage, are facing with a large number of data, leaving the survey far from its cognitive dimension. In this context, it seems necessary to provide innovative solutions in order to increase the informational value of the representations produced by strengthen relations between "multiplicity" of data and "intelligibility" of the theoretical model. With the purpose of answering to the lack of methodology we perceived, this article therefore offers an approach to the creation of representation systems that articulate the digital instance with the geometric/semantic model.ItGrazie all’introduzione delle tecnologie digitali nel campo della documentazione architettonica, molti strumenti e metodi di acquisizione hanno avuto un notevole sviluppo. Tuttavia, questi sviluppi si sono principalmente concentrati sulla registrazione e sulla restituzione delle proprietà geometriche e colorimetriche degli oggetti di studio. Le discipline interessate alla digitalizzazione 3D del patrimonio architettonico hanno pertanto la possibilità di produrre delle grandi quantità di dati attraverso un’evoluzione delle pratiche di documentazione che potrebbero progressivamente far scomparire la dimensione cognitiva del rilievo. In questo contesto, appare necessario fornire soluzioni innovative per aumentare il valore informativo delle rappresentazioni digitali tramite l’identificazione delle relazioni potenziali che è possibile costruire fra le nozioni di "molteplicità" ed "intelligibilità". Per rispondere a questo deficit metodologico, questo articolo presenta le basi di un approccio per la

  15. Endogenous Molecular-Cellular Network Cancer Theory: A Systems Biology Approach.

    Science.gov (United States)

    Wang, Gaowei; Yuan, Ruoshi; Zhu, Xiaomei; Ao, Ping

    2018-01-01

    In light of ever apparent limitation of the current dominant cancer mutation theory, a quantitative hypothesis for cancer genesis and progression, endogenous molecular-cellular network hypothesis has been proposed from the systems biology perspective, now for more than 10 years. It was intended to include both the genetic and epigenetic causes to understand cancer. Its development enters the stage of meaningful interaction with experimental and clinical data and the limitation of the traditional cancer mutation theory becomes more evident. Under this endogenous network hypothesis, we established a core working network of hepatocellular carcinoma (HCC) according to the hypothesis and quantified the working network by a nonlinear dynamical system. We showed that the two stable states of the working network reproduce the main known features of normal liver and HCC at both the modular and molecular levels. Using endogenous network hypothesis and validated working network, we explored genetic mutation pattern in cancer and potential strategies to cure or relieve HCC from a totally new perspective. Patterns of genetic mutations have been traditionally analyzed by posteriori statistical association approaches in light of traditional cancer mutation theory. One may wonder the possibility of a priori determination of any mutation regularity. Here, we found that based on the endogenous network theory the features of genetic mutations in cancers may be predicted without any prior knowledge of mutation propensities. Normal hepatocyte and cancerous hepatocyte stable states, specified by distinct patterns of expressions or activities of proteins in the network, provide means to directly identify a set of most probable genetic mutations and their effects in HCC. As the key proteins and main interactions in the network are conserved through cell types in an organism, similar mutational features may also be found in other cancers. This analysis yielded straightforward and testable

  16. Textile Architecture

    DEFF Research Database (Denmark)

    Heimdal, Elisabeth Jacobsen

    2010-01-01

    Textiles can be used as building skins, adding new aesthetic and functional qualities to architecture. Just like we as humans can put on a coat, buildings can also get dressed. Depending on our mood, or on the weather, we can change coat, and so can the building. But the idea of using textiles...

  17. Pushouts in software architecture design

    OpenAIRE

    Riché, T. L.; Gonçalves, Rui; Marker, B.; Batory, D.

    2012-01-01

    A classical approach to program derivation is to progressively extend a simple specification and then incrementally refine it to an implementation. We claim this approach is hard or impractical when reverse engineering legacy software architectures. We present a case study that shows optimizations and pushouts--in addition to refinements and extensions--are essential for practical stepwise development of complex software architectures. NSF CCF 0724979 NSF CNS 0509338 NSF CCF 0917167 ...

  18. Using a data-centric event-driven architecture approach in the integration of real-time systems at DTP2

    Energy Technology Data Exchange (ETDEWEB)

    Tuominen, Janne, E-mail: janne.m.tuominen@tut.fi; Viinikainen, Mikko; Alho, Pekka; Mattila, Jouni

    2014-10-15

    Integration of heterogeneous and distributed systems is a challenging task, because they might be running on different platforms and written with different implementation languages by multiple organizations. Data-centricity and event-driven architecture (EDA) are concepts that help to implement versatile and well-scaling distributed systems. This paper focuses on the implementation of inter-subsystem communication in a prototype distributed remote handling control system developed at Divertor Test Platform 2 (DTP2). The control system consists of a variety of heterogeneous subsystems, including a client–server web application and hard real-time controllers. A standardized middleware solution (Data Distribution Services (DDS)) that supports a data-centric EDA approach is used to integrate the system. One of the greatest challenges in integrating a system with a data-centric EDA approach is in defining the global data space model. The selected middleware is currently only used for non-deterministic communication. For future application, we evaluated the performance of point-to-point communication with and without the presence of additional network load to ensure applicability to real-time systems. We found that, under certain limitations, the middleware can be used for soft real-time communication. Hard real-time use will require more validation with a more suitable environment.

  19. Using a data-centric event-driven architecture approach in the integration of real-time systems at DTP2

    International Nuclear Information System (INIS)

    Tuominen, Janne; Viinikainen, Mikko; Alho, Pekka; Mattila, Jouni

    2014-01-01

    Integration of heterogeneous and distributed systems is a challenging task, because they might be running on different platforms and written with different implementation languages by multiple organizations. Data-centricity and event-driven architecture (EDA) are concepts that help to implement versatile and well-scaling distributed systems. This paper focuses on the implementation of inter-subsystem communication in a prototype distributed remote handling control system developed at Divertor Test Platform 2 (DTP2). The control system consists of a variety of heterogeneous subsystems, including a client–server web application and hard real-time controllers. A standardized middleware solution (Data Distribution Services (DDS)) that supports a data-centric EDA approach is used to integrate the system. One of the greatest challenges in integrating a system with a data-centric EDA approach is in defining the global data space model. The selected middleware is currently only used for non-deterministic communication. For future application, we evaluated the performance of point-to-point communication with and without the presence of additional network load to ensure applicability to real-time systems. We found that, under certain limitations, the middleware can be used for soft real-time communication. Hard real-time use will require more validation with a more suitable environment

  20. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

    Science.gov (United States)

    Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

    2008-04-01

    We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

  1. Relative Stabilities and Reactivities of Isolated Versus Conjugated Alkenes: Reconciliation Via a Molecular Orbital Approach

    Science.gov (United States)

    Sotiriou-Leventis, Chariklia; Hanna, Samir B.; Leventis, Nicholas

    1996-04-01

    The well-accepted practice of generating a pair of molecular orbitals, one of lower energy and another of higher energy than the original pair of overlapping atomic orbitals, and the concept of a particle in a one-dimensional box are implemented in a simplified, nonmathematical method that explains the relative stabilities and reactivities of alkenes with conjugated versus isolated double bonds. In this method, Huckel-type MO's of higher polyenes are constructed by energy rules of linear combination of atomic orbitals. One additional rule is obeyed: bonding molecular orbitals overlap only with bonding molecular orbitals, and antibonding molecular orbitals overlap only with antibonding molecular orbitals.

  2. From green architecture to architectural green

    DEFF Research Database (Denmark)

    Earon, Ofri

    2011-01-01

    that describes the architectural exclusivity of this particular architecture genre. The adjective green expresses architectural qualities differentiating green architecture from none-green architecture. Currently, adding trees and vegetation to the building’s facade is the main architectural characteristics...... they have overshadowed the architectural potential of green architecture. The paper questions how a green space should perform, look like and function. Two examples are chosen to demonstrate thorough integrations between green and space. The examples are public buildings categorized as pavilions. One......The paper investigates the topic of green architecture from an architectural point of view and not an energy point of view. The purpose of the paper is to establish a debate about the architectural language and spatial characteristics of green architecture. In this light, green becomes an adjective...

  3. Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review.

    Science.gov (United States)

    Tripathi, Niraj; Khare, Dhirendra

    2016-10-01

    Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.

  4. Advances in conservation endocrinology: the application of molecular approaches to the conservation of endangered species.

    Science.gov (United States)

    Tubbs, Christopher; McDonough, Caitlin E; Felton, Rachel; Milnes, Matthew R

    2014-07-01

    Among the numerous societal benefits of comparative endocrinology is the application of our collective knowledge of hormone signaling towards the conservation of threatened and endangered species - conservation endocrinology. For several decades endocrinologists have used longitudinal hormone profiles to monitor reproductive status in a multitude of species. Knowledge of reproductive status among individuals has been used to assist in the management of captive and free-ranging populations. More recently, researchers have begun utilizing molecular and cell-based techniques to gain a more complete understanding of hormone signaling in wildlife species, and to identify potential causes of disrupted hormone signaling. In this review we examine various in vitro approaches we have used to compare estrogen receptor binding and activation by endogenous hormones and phytoestrogens in two species of rhinoceros; southern white and greater one-horned. We have found many of these techniques valuable and practical in species where access to research subjects and/or tissues is limited due to their conservation status. From cell-free, competitive binding assays to full-length receptor activation assays; each technique has strengths and weaknesses related to cost, sensitivity, complexity of the protocols, and relevance to in vivo signaling. We then present a novel approach, in which receptor activation assays are performed in primary cell lines derived from the species of interest, to minimize the artifacts of traditional heterologous expression systems. Finally, we speculate on the promise of next generation sequencing and transcriptome profiling as tools for characterizing hormone signaling in threatened and endangered species. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Approaches to overall architecture of transport systems for spent fuel and high level waste: examples from Europe and Canada

    International Nuclear Information System (INIS)

    Roland, V.; Neider, T.

    2006-01-01

    As over the years, the nuclear industry worldwide was developing and building a clean, efficient and safe energy supply, it also built along the essential link for any global industry, transportation. The early approach at IAEA of creating international recommendations that then would be integrated into national laws came as a blessing to the structuration of transport This enabled a clear, recognized safety regime that has a proven world track record of outstanding safety. It also gave us a common language, and one may say that within the nuclear community, there is indeed a nuclear transport community. Because of steady and large flows of material for the nuclear cycles, countries where reprocessing of spent fuel takes place had to implement early on large transport structures and organizations. In most countries where reprocessing is not yet the main path for spent fuel management, like in the USA and in Canada, large scale transport for the back-end is still at the inception stage. Today the industry must demonstrate that waste is properly managed and that the peaceful use of nuclear energy delivers indeed the best economic and environmental value. Transport has to answer a part of this challenge if the industry is to grow further. The paper will illustrate how the current continental Europe systems of transport progressively evolved so as to make daily deliveries of spent nuclear fuel to the COGEMA La Hague reprocessing plant a strong, dependable and effective system. It also shows that this experience is in the background of a major study ordered by Ontario Power Generation from COGEMA Logistics, as a contribution to the work of the trust now examining approaches to long-term management of spent fuel in Canada. (author)

  6. The architectural design of networks of protein domain architectures.

    Science.gov (United States)

    Hsu, Chia-Hsin; Chen, Chien-Kuo; Hwang, Ming-Jing

    2013-08-23

    Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.

  7. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2011-01-01

    Full Text Available Abstract Background Lung cancer is the leading cause of cancer deaths worldwide. Many studies have investigated the carcinogenic process and identified the biomarkers for signature classification. However, based on the research dedicated to this field, there is no highly sensitive network-based method for carcinogenesis characterization and diagnosis from the systems perspective. Methods In this study, a systems biology approach integrating microarray gene expression profiles and protein-protein interaction information was proposed to develop a network-based biomarker for molecular investigation into the network mechanism of lung carcinogenesis and diagnosis of lung cancer. The network-based biomarker consists of two protein association networks constructed for cancer samples and non-cancer samples. Results Based on the network-based biomarker, a total of 40 significant proteins in lung carcinogenesis were identified with carcinogenesis relevance values (CRVs. In addition, the network-based biomarker, acting as the screening test, proved to be effective in diagnosing smokers with signs of lung cancer. Conclusions A network-based biomarker using constructed protein association networks is a useful tool to highlight the pathways and mechanisms of the lung carcinogenic process and, more importantly, provides potential therapeutic targets to combat cancer.

  8. Visceral Leishmaniasis: Advancements in vaccine development via classical and molecular approaches

    Directory of Open Access Journals (Sweden)

    Sumit eJoshi

    2014-08-01

    Full Text Available Visceral Leishmaniasis (VL or kala-azar, a vector-borne protozoan disease, shows endemicity in larger areas of the tropical, subtropical and the Mediterranean countries. WHO report suggested that nearly 500,000 new cases of VL occur annually, including 100,000 cases from India itself. Treatment with available anti-leishmanial drugs are not cost effective, with varied efficacies and higher relapse rate, which poses a major challenge to current kala-azar control program in Indian subcontinent. Therefore, a vaccine against VL is imperative and knowing the fact that recovered individuals developed lifelong immunity against re-infection, it is feasible. Vaccine development program, though time taking, has recently gained momentum with the emergence of omic era i.e. from genomics to immunomics. Classical as well as molecular methodologies has been overtaken with alternative strategies wherein proteomics based knowledge combined with computational techniques (immunoinformatics speed up the identification and detailed characterization of new antigens for potential vaccine candidates. This may eventually help in the designing of polyvalent synthetic and recombinant chimeric vaccines as an effective intervention measures to control the disease in endemic areas. This review focuses on such newer approaches being utilized for vaccine development against VL.

  9. Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

    Science.gov (United States)

    Mather, Alison E; Vaughan, Timothy G; French, Nigel P

    2015-11-01

    Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Mitochondrial Molecular Pathophysiology of Nonalcoholic Fatty Liver Disease: A Proteomics Approach

    Directory of Open Access Journals (Sweden)

    Natalia Nuño-Lámbarri

    2016-03-01

    Full Text Available Nonalcoholic fatty liver disease (NAFLD is a chronic liver condition that can progress to nonalcoholic steatohepatitis, cirrhosis and cancer. It is considered an emerging health problem due to malnourishment or a high-fat diet (HFD intake, which is observed worldwide. It is well known that the hepatocytes’ apoptosis phenomenon is one of the most important features of NAFLD. Thus, this review focuses on revealing, through a proteomics approach, the complex network of protein interactions that promote fibrosis, liver cell stress, and apoptosis. According to different types of in vitro and murine models, it has been found that oxidative/nitrative protein stress leads to mitochondrial dysfunction, which plays a major role in stimulating NAFLD damage. Human studies have revealed the importance of novel biomarkers, such as retinol-binding protein 4, lumican, transgelin 2 and hemoglobin, which have a significant role in the disease. The post-genome era has brought proteomics technology, which allows the determination of molecular pathogenesis in NAFLD. This has led to the search for biomarkers which improve early diagnosis and optimal treatment and which may effectively prevent fatal consequences such as cirrhosis or cancer.

  11. Molecular genetic approach to human meningioma: loss of genes on chromosome 22

    International Nuclear Information System (INIS)

    Seizinger, B.R.; De La Monte, S.; Atkins, L.; Gusella, J.F.; Martuza, R.L.

    1987-01-01

    A molecular genetic approach employing polymorphic DNA markers has been used to investigate the role of chromosomal aberrations in meningioma, one of the most common tumors of the human nervous system. Comparison of the alleles detected by DNA markers in tumor DNA versus DNA from normal tissue revealed chromosomal alterations present in primary surgical specimens. In agreement with cytogenetic studies of cultured meningiomas, the most frequent alteration detected was loss of heterozygosity on chromosome 22. Forty of 51 patients were constitutionally heterozygous for at least one chromosome 22 DNA marker. Seventeen of the 40 constitutionally heterozygotic patients (43%) displayed hemizygosity for the corresponding marker in their meningioma tumor tissues. Loss of heterozygosity was also detected at a significantly lower frequency for markers on several other autosomes. In view of the striking association between acoustic neuroma and meningioma in bilateral acoustic neurofibromatosis and the discovery that acoustic neuromas display specific loss of genes on chromosome 22, the authors propose that a common mechanism involving chromosome 22 is operative in the development of both tumor types. Fine-structure mapping to reveal partial deletions in meningiomas may provide the means to clone and characterize a gene (or genes) of importance for tumorigenesis in this and possibly other clinically associated tumors of the human nervous system

  12. Continuum multiple-scattering approach to electron-molecule scattering and molecular photoionization

    International Nuclear Information System (INIS)

    Dehmer, J.L.; Dill, D.

    1979-01-01

    The multiple-scattering approach to the electronic continuum of molecules is described. The continuum multiple-scattering model (CMSM) was developed as a survey tool and, as such was required to satisfy two requirements. First, it had to have a very broad scope, which means (i) molecules of arbitrary geometry and complexity containing any atom in the periodic system, (ii) continuum electron energies from 0-1000 eV, and (iii) capability to treat a large range of processes involving both photoionization and electron scattering. Second, the structure of the theory was required to lend itself to transparent, physical interpretation of major spectral features such as shape resonances. A comprehensive theoretical framework for the continuum multiple scattering method is presented, as well as its applications to electron-molecule scattering and molecular photoionization. Highlights of recent applications in these two areas are reviewed. The major impact of the resulting studies over the last few years has been to establish the importance of shape resonances in electron collisions and photoionization of practically all (non-hydride) molecules

  13. Molecular features of grass allergens and development of biotechnological approaches for allergy prevention.

    Science.gov (United States)

    Devis, Deborah L; Davies, Janet M; Zhang, Dabing

    2017-09-01

    Allergic diseases are characterized by elevated allergen-specific IgE and excessive inflammatory cell responses. Among the reported plant allergens, grass pollen and grain allergens, derived from agriculturally important members of the Poaceae family such as rice, wheat and barley, are the most dominant and difficult to prevent. Although many allergen homologs have been predicted from species such as wheat and timothy grass, fundamental aspects such as the evolution and function of plant pollen allergens remain largely unclear. With the development of genetic engineering and genomics, more primary sequences, functions and structures of plant allergens have been uncovered, and molecular component-based allergen-specific immunotherapies are being developed. In this review, we aim to provide an update on (i) the distribution and importance of pollen and grain allergens of the Poaceae family, (ii) the origin and evolution, and functional aspects of plant pollen allergens, (iii) developments of allergen-specific immunotherapy for pollen allergy using biotechnology and (iv) development of less allergenic plants using gene engineering techniques. We also discuss future trends in revealing fundamental aspects of grass pollen allergens and possible biotechnological approaches to reduce the amount of pollen allergens in grasses. Copyright © 2017. Published by Elsevier Inc.

  14. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

    Science.gov (United States)

    Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

    2013-09-10

    Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

  15. Molecular biological approaches to the study of vectors in relation to malaria control

    Directory of Open Access Journals (Sweden)

    J. M. Crampton

    1992-01-01

    Full Text Available To a large extent, control of malaria vectors relies on the elimination of breeding sites and the application of chemical agents. There are increasing problems associated with the use of synthetic insecticides for vector control, including the evolution of resistance, the high cost of developing and registering new insecticides and an awareness of pollution from insecticide residues. These factors have stimulated interest in the application of molecular biology to the study of mosquito vectors of malaria; focussing primarily on two aspects. First, the improvement of existing control measures through the development of simplified DNA probe systems suitable for identification of vectors of malaria. The development of synthetic, non-radioactive DNA probes suitable for identification of species in the Anopheles gambiae complex is described with the aim of defining a simplified methodology wich is suitable for entomologist in the field. The second aspect to be considered is the development of completely novel strategies through the development of completely novel strategies through the genetic manipulation of insect vectors of malaria in order to alter their ability to transmit the disease. The major requirements for producing transgenic mosquitoes are outlined together with the progress wich has been made to date and discussed in relation to the prospects which this type of approach has for the future control of malaria.

  16. Solitary thyroid metastasis from colon cancer: fine-needle aspiration cytology and molecular biology approach.

    Science.gov (United States)

    Onorati, M; Uboldi, P; Bianchi, C L; Nicola, M; Corradini, G M; Veronese, S; Fascì, A I; Di Nuovo, F

    2015-01-01

    Thyroid gland is one of the most vascularized organs of the body, nevertheless clinical and surgical series report an incidence of secondary malignancies in this gland of only 3%. Colorectal carcinoma metastatic to the thyroid gland is not as uncommon as previously believed, infact the number of cases seems to be increased in recent years due to the more frequent use of fine-needle aspiration cytology (FNAC) guided by ultrasonography. Although kidney, breast and lung metastases to the thyroid are frequent, metastasis from colon cancer is clinically rare with 52 cases reported in the literature in the last 5 decades and three cases described as solitary thyroid metastasis from the colon cancer without any other visceral metastases. To the best of our knowledge, we report the fourth case of solitary, asymptomatic thyroid metastasis from colon cancer without involvement of other organs. We discuss the importance of FNAC to detect metastatazing process as a compulsory step of the diagnostic and therapeutic management algorithm, combined with a molecular biology approach. A review of the last 5 decades literature, to update the number of cases described to date, is also included.

  17. Development of a model for the rational design of molecular imprinted polymer: Computational approach for combined molecular dynamics/quantum mechanics calculations

    International Nuclear Information System (INIS)

    Dong Cunku; Li Xin; Guo Zechong; Qi Jingyao

    2009-01-01

    A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and 1 H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.

  18. Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    NARCIS (Netherlands)

    Ribeiro de Jesus, P.R.

    2015-01-01

    Biochemical, physiological and molecular responses of Ricinus communis seeds and seedlings to different temperatures: a multi-omics approach

    by Paulo Roberto Ribeiro de Jesus

    The main objective of this thesis was to provide a detailed

  19. Approaches for cytogenetic and molecular analyses of small flow-sorted cell populations from childhood leukemia bone marrow samples

    DEFF Research Database (Denmark)

    Obro, Nina Friesgaard; Madsen, Hans O.; Ryder, Lars Peter

    2011-01-01

    defined cell populations with subsequent analyses of leukemia-associated cytogenetic and molecular marker. The approaches described here optimize the use of the same tube of unfixed, antibody-stained BM cells for flow-sorting of small cell populations and subsequent exploratory FISH and PCR-based analyses....

  20. Topochemical approach to efficiently produce main-chain poly(bile acid)s with high molecular weights.

    Science.gov (United States)

    Li, Weina; Li, Xuesong; Zhu, Wei; Li, Changxu; Xu, Dan; Ju, Yong; Li, Guangtao

    2011-07-21

    Based on a topochemical approach, a strategy for efficiently producing main-chain poly(bile acid)s in the solid state was developed. This strategy allows for facile and scalable synthesis of main-chain poly(bile acid)s not only with high molecular weights, but also with quantitative conversions and yields.