Sample records for fold representation technical

  1. Handling the Difficulties of Technical School Students in the Construction and Interpretation of Graphic Representations

    ERIC Educational Resources Information Center

    Marinos, Andreas

    2010-01-01

    In this work, an attempt is made to evaluate the errors that have to do with the interpretation and construction of graphic representations. Although the students are studying in the second year of technical high school (secondary education), i.e. in schools with an emphasis in technical subjects (post junior secondary), it is observed that they…

  2. Predicting RNA folding thermodynamics with a reduced chain representation model

    PubMed Central

    CAO, SONG; CHEN, SHI-JIE

    2005-01-01

    Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule. PMID:16251382

  3. 37 CFR 11.101 - Competence.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... competent representation to a client. Competent representation requires the legal, scientific, and technical knowledge, skill, thoroughness and preparation reasonably necessary for the representation. ... COMMERCE REPRESENTATION OF OTHERS BEFORE THE UNITED STATES PATENT AND TRADEMARK OFFICE USPTO Rules of...

  4. 37 CFR 11.101 - Competence.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... competent representation to a client. Competent representation requires the legal, scientific, and technical knowledge, skill, thoroughness and preparation reasonably necessary for the representation. ... COMMERCE REPRESENTATION OF OTHERS BEFORE THE UNITED STATES PATENT AND TRADEMARK OFFICE USPTO Rules of...

  5. Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods.

    PubMed

    Qu, Kaiyang; Han, Ke; Wu, Song; Wang, Guohua; Wei, Leyi

    2017-09-22

    DNA-binding proteins play vital roles in cellular processes, such as DNA packaging, replication, transcription, regulation, and other DNA-associated activities. The current main prediction method is based on machine learning, and its accuracy mainly depends on the features extraction method. Therefore, using an efficient feature representation method is important to enhance the classification accuracy. However, existing feature representation methods cannot efficiently distinguish DNA-binding proteins from non-DNA-binding proteins. In this paper, a multi-feature representation method, which combines three feature representation methods, namely, K-Skip-N-Grams, Information theory, and Sequential and structural features (SSF), is used to represent the protein sequences and improve feature representation ability. In addition, the classifier is a support vector machine. The mixed-feature representation method is evaluated using 10-fold cross-validation and a test set. Feature vectors, which are obtained from a combination of three feature extractions, show the best performance in 10-fold cross-validation both under non-dimensional reduction and dimensional reduction by max-relevance-max-distance. Moreover, the reduced mixed feature method performs better than the non-reduced mixed feature technique. The feature vectors, which are a combination of SSF and K-Skip-N-Grams, show the best performance in the test set. Among these methods, mixed features exhibit superiority over the single features.

  6. Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

    PubMed Central

    Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele

    2009-01-01

    Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins. PMID:19593364

  7. Analysis of the free-energy surface of proteins from reversible folding simulations.

    PubMed

    Allen, Lucy R; Krivov, Sergei V; Paci, Emanuele

    2009-07-01

    Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

  8. The Representation of Sentences in Memory. Technical Report No. 144.

    ERIC Educational Resources Information Center

    Goetz, Ernest T.; And Others

    Associative theory characterizes the memory's representation of a sentence as a collection of independently linked concepts. In contrast, Gestalt theory says that the representation underlying each proposition expressed in a sentence is an integral unit. A review of research indicates that previous results either have been equivocal or have…

  9. A two-level generative model for cloth representation and shape from shading.

    PubMed

    Han, Feng; Zhu, Song-Chun

    2007-07-01

    In this paper, we present a two-level generative model for representing the images and surface depth maps of drapery and clothes. The upper level consists of a number of folds which will generate the high contrast (ridge) areas with a dictionary of shading primitives (for 2D images) and fold primitives (for 3D depth maps). These primitives are represented in parametric forms and are learned in a supervised learning phase using 3D surfaces of clothes acquired through photometric stereo. The lower level consists of the remaining flat areas which fill between the folds with a smoothness prior (Markov random field). We show that the classical ill-posed problem-shape from shading (SFS) can be much improved by this two-level model for its reduced dimensionality and incorporation of middle-level visual knowledge, i.e., the dictionary of primitives. Given an input image, we first infer the folds and compute a sketch graph using a sketch pursuit algorithm as in the primal sketch [10], [11]. The 3D folds are estimated by parameter fitting using the fold dictionary and they form the "skeleton" of the drapery/cloth surfaces. Then, the lower level is computed by conventional SFS method using the fold areas as boundary conditions. The two levels interact at the final stage by optimizing a joint Bayesian posterior probability on the depth map. We show a number of experiments which demonstrate more robust results in comparison with state-of-the-art work. In a broader scope, our representation can be viewed as a two-level inhomogeneous MRF model which is applicable to general shape-from-X problems. Our study is an attempt to revisit Marr's idea [23] of computing the 2(1/2)D sketch from primal sketch. In a companion paper [2], we study shape from stereo based on a similar two-level generative sketch representation.

  10. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mozrzymas, Marek; Horodecki, Michał; Studziński, Michał

    We consider the structure of algebra of operators, acting in n-fold tensor product space, which are partially transposed on the last term. Using purely algebraical methods we show that this algebra is semi-simple and then, considering its regular representation, we derive basic properties of the algebra. In particular, we describe all irreducible representations of the algebra of partially transposed operators and derive expressions for matrix elements of the representations. It appears that there are two kinds of irreducible representations of the algebra. The first one is strictly connected with the representations of the group S(n − 1) induced by irreduciblemore » representations of the group S(n − 2). The second kind is structurally connected with irreducible representations of the group S(n − 1)« less

  11. Anaphora and Logical Form: On Formal Meaning Representations for Natural Language. Technical Report No. 36.

    ERIC Educational Resources Information Center

    Nash-Webber, Bonnie; Reiter, Raymond

    This paper describes a computational approach to certain problems of anaphora in natural language and argues in favor of formal meaning representation languages (MRLs) for natural language. After presenting arguments in favor of formal meaning representation languages, appropriate MRLs are discussed. Minimal requirements include provisions for…

  12. [The representation of the mental patient in motion pictures].

    PubMed

    Veyrat, J G

    1994-11-01

    By the examples of 80 movies from different countries, the study describes the representation of mental patients, in the films. They are shown as victims of family and society. And the psychiatric hospital is never shown as therapeutic, but only used for keeping away, and bringing back the stray sheep to the social fold.

  13. Identifying knowledge activism in worker health and safety representation: A cluster analysis.

    PubMed

    Hall, Alan; Oudyk, John; King, Andrew; Naqvi, Syed; Lewchuk, Wayne

    2016-01-01

    Although worker representation in OHS has been widely recognized as contributing to health and safety improvements at work, few studies have examined the role that worker representatives play in this process. Using a large quantitative sample, this paper seeks to confirm findings from an earlier exploratory qualitative study that worker representatives can be differentiated by the knowledge intensive tactics and strategies that they use to achieve changes in their workplace. Just under 900 worker health and safety representatives in Ontario completed surveys which asked them to report on the amount of time they devoted to different types of representation activities (i.e., technical activities such as inspections and report writing vs. political activities such as mobilizing workers to build support), the kinds of conditions or hazards they tried to address through their representation (e.g., housekeeping vs. modifications in ventilation systems), and their reported success in making positive improvements. A cluster analysis was used to determine whether the worker representatives could be distinguished in terms of the relative time devoted to different activities and the clusters were then compared with reference to types of intervention efforts and outcomes. The cluster analysis identified three distinct groupings of representatives with significant differences in reported types of interventions and in their level of reported impact. Two of the clusters were consistent with the findings in the exploratory study, identified as knowledge activism for greater emphasis on knowledge based political activity and technical-legal representation for greater emphasis on formalized technical oriented procedures and legal regulations. Knowledge activists were more likely to take on challenging interventions and they reported more impact across the full range of interventions. This paper provides further support for the concepts of knowledge activism and technical-legal representation when differentiating the strategic orientations and impact of worker health and safety representatives, with important implications for education, political support and recruitment. © 2015 Wiley Periodicals, Inc.

  14. The changing demographic, legal, and technological contexts of political representation.

    PubMed

    Forest, Benjamin

    2005-10-25

    Three developments have created challenges for political representation in the U.S. and particularly for the use of territorially based representation (election by district). First, the demographic complexity of the U.S. population has grown both in absolute terms and in terms of residential patterns. Second, legal developments since the 1960s have recognized an increasing number of groups as eligible for voting rights protection. Third, the growing technical capacities of computer technology, particularly Geographic Information Systems, have allowed political parties and other organizations to create election districts with increasingly precise political and demographic characteristics. Scholars have made considerable progress in measuring and evaluating the racial and partisan biases of districting plans, and some states have tried to use Geographic Information Systems technology to produce more representative districts. However, case studies of Texas and Arizona illustrate that such analytic and technical advances have not overcome the basic contradictions that underlie the American system of territorial political representation.

  15. The Intercultural Component in Textbooks for Teaching a Service Technical Writing Course

    ERIC Educational Resources Information Center

    Matveeva, Natalia

    2007-01-01

    This research article investigates new developments in the representation of the intercultural component in textbooks for a service technical writing course. Through textual analysis, using quantitative and qualitative techniques, I report discourse analysis of 15 technical writing textbooks published during 1993-2006. The theoretical and…

  16. Discrimination of Dynamic Tactile Contact by Temporally Precise Event Sensing in Spiking Neuromorphic Networks

    PubMed Central

    Lee, Wang Wei; Kukreja, Sunil L.; Thakor, Nitish V.

    2017-01-01

    This paper presents a neuromorphic tactile encoding methodology that utilizes a temporally precise event-based representation of sensory signals. We introduce a novel concept where touch signals are characterized as patterns of millisecond precise binary events to denote pressure changes. This approach is amenable to a sparse signal representation and enables the extraction of relevant features from thousands of sensing elements with sub-millisecond temporal precision. We also proposed measures adopted from computational neuroscience to study the information content within the spiking representations of artificial tactile signals. Implemented on a state-of-the-art 4096 element tactile sensor array with 5.2 kHz sampling frequency, we demonstrate the classification of transient impact events while utilizing 20 times less communication bandwidth compared to frame based representations. Spiking sensor responses to a large library of contact conditions were also synthesized using finite element simulations, illustrating an 8-fold improvement in information content and a 4-fold reduction in classification latency when millisecond-precise temporal structures are available. Our research represents a significant advance, demonstrating that a neuromorphic spatiotemporal representation of touch is well suited to rapid identification of critical contact events, making it suitable for dynamic tactile sensing in robotic and prosthetic applications. PMID:28197065

  17. Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

    PubMed

    Emperador, Agustí; Orozco, Modesto

    2017-03-14

    We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

  18. The Atom in a Molecule: Implications for Molecular Structure and Properties

    DTIC Science & Technology

    2016-05-23

    unlimited. PA Clearance #16075.” Atomic- Product Representations of Molecules Employ “van der Waals” products of atomic states to represent molecules...representation the electrons “stay home” with each nucleus. Atomic fragment operators are well-defined over product representations. Expectation values of...release; distribution unlimited. PA Clearance #16075.” Hamiltonian Matrix in the Atomic- Product Basis Technical Questions Addressed: J. Chem. Phys

  19. Drawing Lines with Light in Holographic Space

    NASA Astrophysics Data System (ADS)

    Chang, Yin-Ren; Richardson, Martin

    2013-02-01

    This paper explores the dynamic and expressive possibilities of holographic art through a comparison of art history and technical media such as photography, film and holographic technologies. Examples of modern art and creative expression of time and motions are examined using the early 20th century art movement, Cubism, where subjects are portrayed to be seen simultaneously from different angles. Folding space is represented as subject matter as it can depict space from multiple points of time. The paper also investigates the way holographic art has explored time and space. The lenticular lens-based media reveal a more subjective poetic art in the form of the lyrical images and messages as spectators pass through time, or walk along with the piece of work through an interactive process. It is argued that photographic practice is another example of artistic representation in the form of aesthetic medium of time movement and as such shares a common ground with other dynamic expression that require time based interaction.

  20. Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.

    PubMed

    Pulawski, Wojciech; Jamroz, Michal; Kolinski, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-11-28

    The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.

  1. The Role of High-Dimensional Diffusive Search, Stabilization, and Frustration in Protein Folding

    PubMed Central

    Rimratchada, Supreecha; McLeish, Tom C.B.; Radford, Sheena E.; Paci, Emanuele

    2014-01-01

    Proteins are polymeric molecules with many degrees of conformational freedom whose internal energetic interactions are typically screened to small distances. Therefore, in the high-dimensional conformation space of a protein, the energy landscape is locally relatively flat, in contrast to low-dimensional representations, where, because of the induced entropic contribution to the full free energy, it appears funnel-like. Proteins explore the conformation space by searching these flat subspaces to find a narrow energetic alley that we call a hypergutter and then explore the next, lower-dimensional, subspace. Such a framework provides an effective representation of the energy landscape and folding kinetics that does justice to the essential characteristic of high-dimensionality of the search-space. It also illuminates the important role of nonnative interactions in defining folding pathways. This principle is here illustrated using a coarse-grained model of a family of three-helix bundle proteins whose conformations, once secondary structure has formed, can be defined by six rotational degrees of freedom. Two folding mechanisms are possible, one of which involves an intermediate. The stabilization of intermediate subspaces (or states in low-dimensional projection) in protein folding can either speed up or slow down the folding rate depending on the amount of native and nonnative contacts made in those subspaces. The folding rate increases due to reduced-dimension pathways arising from the mere presence of intermediate states, but decreases if the contacts in the intermediate are very stable and introduce sizeable topological or energetic frustration that needs to be overcome. Remarkably, the hypergutter framework, although depending on just a few physically meaningful parameters, can reproduce all the types of experimentally observed curvature in chevron plots for realizations of this fold. PMID:24739172

  2. A novel representation of the conformational structure of transfer RNAs. Correlation of the folding patterns of the polynucleotide chain with the base sequence and the nucleotide backbone torsions.

    PubMed Central

    Srinivasan, A R; Yathindra, N

    1977-01-01

    A novel description of the conformational characteristics of all the individual nucleotides and the phosphodiesters in tRNAs is presented in the form of a circular plot. This representation furnishes information of the base sequence with the folding patterns of the polynucleotide chain as one traverses along the circumference and with the individual nucleotide and phosphodiester linkage torsions along the radii. The circular plot obtained for yeast tRNAPhe strikingly distinguishes the helical and the loop regions. The variation of the different nucleotide torsions along the entire chain length and their effect on the secondary helical and tertiary loop regions become readily apparent. PMID:339206

  3. Visualising elastic anisotropy: theoretical background and computational implementation

    NASA Astrophysics Data System (ADS)

    Nordmann, J.; Aßmus, M.; Altenbach, H.

    2018-02-01

    In this article, we present the technical realisation for visualisations of characteristic parameters of the fourth-order elasticity tensor, which is classified by three-dimensional symmetry groups. Hereby, expressions for spatial representations of uc(Young)'s modulus and bulk modulus as well as plane representations of shear modulus and uc(Poisson)'s ratio are derived and transferred into a comprehensible form to computer algebra systems. Additionally, we present approaches for spatial representations of both latter parameters. These three- and two-dimensional representations are implemented into the software MATrix LABoratory. Exemplary representations of characteristic materials complete the present treatise.

  4. How a submarine returns to periscope depth: analysing complex socio-technical systems using Cognitive Work Analysis.

    PubMed

    Stanton, Neville A; Bessell, Kevin

    2014-01-01

    This paper presents the application of Cognitive Work Analysis to the description of the functions, situations, activities, decisions, strategies, and competencies of a Trafalgar class submarine when performing the function of returning to periscope depth. All five phases of Cognitive Work Analysis are presented, namely: Work Domain Analysis, Control Task Analysis, Strategies Analysis, Social Organisation and Cooperation Analysis, and Worker Competencies Analysis. Complex socio-technical systems are difficult to analyse but Cognitive Work Analysis offers an integrated way of analysing complex systems with the core of functional means-ends analysis underlying all of the other representations. The joined-up analysis offers a coherent framework for understanding how socio-technical systems work. Data were collected through observation and interviews at different sites across the UK. The resultant representations present a statement of how the work domain and current activities are configured in this complex socio-technical system. This is intended to provide a baseline, from which all future conceptions of the domain may be compared. The strength of the analysis is in the multiple representations from which the constraints acting on the work may be analysed. Future research needs to challenge the assumptions behind these constraints in order to develop new ways of working. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  5. The changing demographic, legal, and technological contexts of political representation

    PubMed Central

    Forest, Benjamin

    2005-01-01

    Three developments have created challenges for political representation in the U.S. and particularly for the use of territorially based representation (election by district). First, the demographic complexity of the U.S. population has grown both in absolute terms and in terms of residential patterns. Second, legal developments since the 1960s have recognized an increasing number of groups as eligible for voting rights protection. Third, the growing technical capacities of computer technology, particularly Geographic Information Systems, have allowed political parties and other organizations to create election districts with increasingly precise political and demographic characteristics. Scholars have made considerable progress in measuring and evaluating the racial and partisan biases of districting plans, and some states have tried to use Geographic Information Systems technology to produce more representative districts. However, case studies of Texas and Arizona illustrate that such analytic and technical advances have not overcome the basic contradictions that underlie the American system of territorial political representation. PMID:16230615

  6. Charles Morris's Semiotic Model and Analytical Studies of Visual and Verbal Representations in Technical Communication

    ERIC Educational Resources Information Center

    Fan, Jiang-Ping

    2006-01-01

    In this article, the author demonstrates that the semiotic model proposed by Charles Morris enables us to optimize our understanding of technical communication practices and provides a good point of inquiry. To illustrate this point, the author exemplifies the semiotic approaches by scholars in technical communication and elaborates Morris's model…

  7. Kinematics, structural mechanics, and design of origami structures with smooth folds

    NASA Astrophysics Data System (ADS)

    Peraza Hernandez, Edwin Alexander

    Origami provides novel approaches to the fabrication, assembly, and functionality of engineering structures in various fields such as aerospace, robotics, etc. With the increase in complexity of the geometry and materials for origami structures that provide engineering utility, computational models and design methods for such structures have become essential. Currently available models and design methods for origami structures are generally limited to the idealization of the folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures having non-negligible thickness or maximum curvature at the folds restricted by material limitations. Thus, for general structures, creased folds of merely zeroth-order geometric continuity are not appropriate representations of structural response and a new approach is needed. The first contribution of this dissertation is a model for the kinematics of origami structures having realistic folds of non-zero surface area and exhibiting higher-order geometric continuity, here termed smooth folds. The geometry of the smooth folds and the constraints on their associated kinematic variables are presented. A numerical implementation of the model allowing for kinematic simulation of structures having arbitrary fold patterns is also described. Examples illustrating the capability of the model to capture realistic structural folding response are provided. Subsequently, a method for solving the origami design problem of determining the geometry of a single planar sheet and its pattern of smooth folds that morphs into a given three-dimensional goal shape, discretized as a polygonal mesh, is presented. The design parameterization of the planar sheet and the constraints that allow for a valid pattern of smooth folds and approximation of the goal shape in a known folded configuration are presented. Various testing examples considering goal shapes of diverse geometries are provided. Afterwards, a model for the structural mechanics of origami continuum bodies with smooth folds is presented. Such a model entails the integration of the presented kinematic model and existing plate theories in order to obtain a structural representation for folds having non-zero thickness and comprised of arbitrary materials. The model is validated against finite element analysis. The last contribution addresses the design and analysis of active material-based self-folding structures that morph via simultaneous folding towards a given three-dimensional goal shape starting from a planar configuration. Implementation examples including shape memory alloy (SMA)-based self-folding structures are provided.

  8. Extreme Folding

    NASA Astrophysics Data System (ADS)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  9. The Warrant for Constructivist Practice within Educational Technology.

    ERIC Educational Resources Information Center

    Bopry, Jeanette

    1999-01-01

    Discusses educational technology as a form of technical rationality and considers the conflict between practitioners' epistemological position as constructivists and technical rationality. Topics include cybernetics; autonomous systems theory; enactive constructivism; representation versus effective action; mind and memory; enaction in artificial…

  10. Using the Computer Game "FoldIt" to Entice Students to Explore External Representations of Protein Structure in a Biochemistry Course for Nonmajors

    ERIC Educational Resources Information Center

    Farley, Peter C.

    2013-01-01

    This article describes a novel approach to teaching novice Biochemistry students visual literacy skills and understanding of some aspects of protein structure using the internet resource FoldIt and a worksheet based on selected Introductory Puzzles from this computer game. In responding to a questionnaire, students indicated that they (94%)…

  11. Knowledge Representation in a Physics Tutor. COINS Technical Report 86-37.

    ERIC Educational Resources Information Center

    Murray, Tom; Woolf, Beverly

    This paper is based on the idea that designing a knowledge representation for an intelligent physics computer tutoring system depends, in part, on the target behavior anticipated from the student. In addition, the document distinguishes between qualitative and quantitative competence in physics. These competencies are illustrated through questions…

  12. Robustness of atomistic Gō models in predicting native-like folding intermediates

    NASA Astrophysics Data System (ADS)

    Estácio, S. G.; Fernandes, C. S.; Krobath, H.; Faísca, P. F. N.; Shakhnovich, E. I.

    2012-08-01

    Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.

  13. 3D Model Generation From the Engineering Drawing

    NASA Astrophysics Data System (ADS)

    Vaský, Jozef; Eliáš, Michal; Bezák, Pavol; Červeňanská, Zuzana; Izakovič, Ladislav

    2010-01-01

    The contribution deals with the transformation of engineering drawings in a paper form into a 3D computer representation. A 3D computer model can be further processed in CAD/CAM system, it can be modified, archived, and a technical drawing can be then generated from it as well. The transformation process from paper form to the data one is a complex and difficult one, particularly owing to the different types of drawings, forms of displayed objects and encountered errors and deviations from technical standards. The algorithm for 3D model generating from an orthogonal vector input representing a simplified technical drawing of the rotational part is described in this contribution. The algorithm was experimentally implemented as ObjectARX application in the AutoCAD system and the test sample as the representation of the rotational part was used for verificaton.

  14. Visual Hemispheric Specialization: A Computational Theory. Technical Report #7.

    ERIC Educational Resources Information Center

    Kosslyn, Stephen M.

    Visual recognition, navigation, tracking, and imagery are posited to involve some of the same types of representations and processes. The first part of this paper develops a theory of some of the shared types of representations and processing modules. The theory is developed in light of neurophysiological and neuroanatomical data from non-human…

  15. A Qualitative Study of African American Women in Engineering Technology Programs in Community Colleges

    ERIC Educational Resources Information Center

    Blakley, Jacquelyn

    2016-01-01

    This study examined the experiences of African American women in engineering technology programs in community colleges. There is a lack of representation of African American women in engineering technology programs throughout higher education, especially in community/technical colleges. There is also lack of representation of African American…

  16. "It's More Flexible": Persistence of Women Engineers in the Academy

    ERIC Educational Resources Information Center

    Mlambo, Yeukai Angela; Mabokela, Reitumetse Obakeng

    2017-01-01

    The under-representation of women in engineering is an issue of concern for policy-makers. While much of the existing literature has focussed on understanding reasons for women's under-representation in engineering and related technical fields, there is a paucity of research that examines why women who are already in engineering persist. This…

  17. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    NASA Astrophysics Data System (ADS)

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  18. An analysis of science content and representations in introductory college physics textbooks and multimodal learning resources

    NASA Astrophysics Data System (ADS)

    Donnelly, Suzanne M.

    This study features a comparative descriptive analysis of the physics content and representations surrounding the first law of thermodynamics as presented in four widely used introductory college physics textbooks representing each of four physics textbook categories (calculus-based, algebra/trigonometry-based, conceptual, and technical/applied). Introducing and employing a newly developed theoretical framework, multimodal generative learning theory (MGLT), an analysis of the multimodal characteristics of textbook and multimedia representations of physics principles was conducted. The modal affordances of textbook representations were identified, characterized, and compared across the four physics textbook categories in the context of their support of problem-solving. Keywords: college science, science textbooks, multimodal learning theory, thermodynamics, representations

  19. 77 FR 66194 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-02

    ... Effectiveness of a Proposed Rule Change To Make Technical Change to SPY Position Limit Pilot Program and Representation Regarding Timing of Submission of Pilot Report October 26, 2012. Pursuant to Section 19(b)(1) of... technical amendment to Interpretation and Policy [[Page 66195

  20. Outsiders Looking In: Tutor Expertise in Engineering Writing

    ERIC Educational Resources Information Center

    Bengesai, Annah

    2015-01-01

    Drawing on an academic literacies approach, this article explores the representations of technical communication by non-content expert tutors teaching the Technical Communication for Engineering course at a South African university. The course is offered to all first year engineering students as a developmental academic literacy course. It is…

  1. DOE scientific and technical information management

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beasly, M.

    The objective of this paper was a discussion of the mission objectives and program activities of the DOE Office of Scientific and Technical Information. Topics of discussion were: (1) program direction and structure; (2) representation in gov`t and international organizations; (3) management of information; and (4) consultation and assistance.

  2. Technical structure of the global nanoscience and nanotechnology literature

    NASA Astrophysics Data System (ADS)

    Kostoff, Ronald N.; Koytcheff, Raymond G.; Lau, Clifford G. Y.

    2007-10-01

    Text mining was used to extract technical intelligence from the open source global nanotechnology and nanoscience research literature. An extensive nanotechnology/nanoscience-focused query was applied to the Science Citation Index/Social Science Citation Index (SCI/SSCI) databases. The nanotechnology/nanoscience research literature technical structure (taxonomy) was obtained using computational linguistics/document clustering and factor analysis. The infrastructure (prolific authors, key journals/institutions/countries, most cited authors/journals/documents) for each of the clusters generated by the document clustering algorithm was obtained using bibliometrics. Another novel addition was the use of phrase auto-correlation maps to show technical thrust areas based on phrase co-occurrence in Abstracts, and the use of phrase-phrase cross-correlation maps to show technical thrust areas based on phrase relations due to the sharing of common co-occurring phrases. The ˜400 most cited nanotechnology papers since 1991 were grouped, and their characteristics generated. Whereas the main analysis provided technical thrusts of all nanotechnology papers retrieved, analysis of the most cited papers allowed their characteristics to be displayed. Finally, most cited papers from selected time periods were extracted, along with all publications from those time periods, and the institutions and countries were compared based on their representation in the most cited documents list relative to their representation in the most publications list.

  3. What Makes a Word Difficult? Insights into the Mental Representation of Technical Terms

    ERIC Educational Resources Information Center

    Jucks, Regina; Paus, Elisabeth

    2012-01-01

    Learning from texts requires reflection on how far one has mastered the material. Learners use such metacognitive processes to decide whether to engage in deeper learning activities or not. This article examines how the lexical surface of specialist concepts influences their mental representation. Lexical encodings that are the concise wordings of…

  4. Automation of Technical Service Functions in Academic, Public, and Special Libraries in Tennessee: Report of a Survey.

    ERIC Educational Resources Information Center

    Denton, Ann; Mahood, Ramona M.

    Members of the Tennessee Library Association's Technical Services Roundtable examined the extent to which the developing technology of automation is being utilized by the state's libraries. The survey encompassed technical service activities and had a two-fold thrust: to determine how automation is being employed, and to compile an inventory of…

  5. PITTSBURGH TECHNICAL HEALTH TRAINING INSTITUTE DEMONSTRATION PROJECT. FINAL REPORT, VOLUME II.

    ERIC Educational Resources Information Center

    KISHKUNAS, LOUIS J.

    APPENDIXES TO THE "FINAL REPORT," VOLUME I (VT 005 511), ARE INCLUDED--(1) A SCHEMATIC REPRESENTATION OF CURRICULUM DEVELOPMENT, (2) TECHNICAL BEHAVIOR CHECKLISTS, (3) PERFORMANCE INVENTORY FORMS USED IN ON-THE-JOB OBSERVATIONS, (4) REPORT FORM FOR TYPICAL JOB BEHAVIOR OF EMPLOYEE, (5) COOPERATING AREA HEALTH INSTITUTIONS, (6) TABLES OF Z SCORES…

  6. Technical variations in low-input RNA-seq methodologies.

    PubMed

    Bhargava, Vipul; Head, Steven R; Ordoukhanian, Phillip; Mercola, Mark; Subramaniam, Shankar

    2014-01-14

    Recent advances in RNA-seq methodologies from limiting amounts of mRNA have facilitated the characterization of rare cell-types in various biological systems. So far, however, technical variations in these methods have not been adequately characterized, vis-à-vis sensitivity, starting with reduced levels of mRNA. Here, we generated sequencing libraries from limiting amounts of mRNA using three amplification-based methods, viz. Smart-seq, DP-seq and CEL-seq, and demonstrated significant technical variations in these libraries. Reduction in mRNA levels led to inefficient amplification of the majority of low to moderately expressed transcripts. Furthermore, noise in primer hybridization and/or enzyme incorporation was magnified during the amplification step resulting in significant distortions in fold changes of the transcripts. Consequently, the majority of the differentially expressed transcripts identified were either high-expressed and/or exhibited high fold changes. High technical variations ultimately masked subtle biological differences mandating the development of improved amplification-based strategies for quantitative transcriptomics from limiting amounts of mRNA.

  7. Toward a Theory of Representation Design

    DTIC Science & Technology

    1989-05-01

    understanding. This report describes research done at the Artificial Inteligence Laboratory of the Massachusetts Institute of Technology. Support for this...AD-A210 885 Technical Report 1128 Toward a Theory of Representation Design Jeffrey Van Baale MIT Artificial Intelligence Laboratory DTIC ELECTE A... Artificial Intelligence Laboratory 545 Technology Square Cambridge, MA 02139 11. CONTROLLING OFFICE NAME AND ADDRESS 11. REPORT DATE Advanced Research

  8. Representations of Technology in the "Technical Stories" for Children of Otto Witt, Early 20th Century Swedish Technology Educator

    ERIC Educational Resources Information Center

    Axell, Cecilia; Hallström, Jonas

    2013-01-01

    Children's fiction in school libraries have played and still play a role in mediating representations of technology and attitudes towards technology to schoolchildren. In early 20th century Sweden, elementary education, including textbooks and literature that were used in teaching, accounted for the main mediation of technological knowledge to…

  9. Structure-based barcoding of proteins.

    PubMed

    Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

    2014-01-01

    A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

  10. The Impact of the Assimilation of Hyperspectral Infrared Retrieved Profiles on Advanced Weather and Research Model Simulations of a Non-Convective Wind Event

    NASA Technical Reports Server (NTRS)

    Brendt. Emily; Zavodsky, Bradley; Jedlovec, Gary; Elmer, Nicholas

    2014-01-01

    Tropopause folds are identified by warm, dry, high-potential vorticity, ozone-rich air and are one explanation for damaging non-convective wind events. Could improved model representation of stratospheric air and associated tropopause folding improve non-convective wind forecasts and high wind warnings? The goal of this study is to assess the impact of assimilating Hyperspectral Infrared (IR) profiles on forecasting stratospheric air, tropopause folds, and associated non-convective winds: (1) AIRS: Atmospheric Infrared Sounder (2) IASI: Infrared Atmospheric Sounding Interferometer (3) CrIMSS: Cross-track Infrared and Microwave Sounding Suite

  11. A semi-analytical description of protein folding that incorporates detailed geometrical information

    PubMed Central

    Suzuki, Yoko; Noel, Jeffrey K.; Onuchic, José N.

    2011-01-01

    Much has been done to study the interplay between geometric and energetic effects on the protein folding energy landscape. Numerical techniques such as molecular dynamics simulations are able to maintain a precise geometrical representation of the protein. Analytical approaches, however, often focus on the energetic aspects of folding, including geometrical information only in an average way. Here, we investigate a semi-analytical expression of folding that explicitly includes geometrical effects. We consider a Hamiltonian corresponding to a Gaussian filament with structure-based interactions. The model captures local features of protein folding often averaged over by mean-field theories, for example, loop contact formation and excluded volume. We explore the thermodynamics and folding mechanisms of beta-hairpin and alpha-helical structures as functions of temperature and Q, the fraction of native contacts formed. Excluded volume is shown to be an important component of a protein Hamiltonian, since it both dominates the cooperativity of the folding transition and alters folding mechanisms. Understanding geometrical effects in analytical formulae will help illuminate the consequences of the approximations required for the study of larger proteins. PMID:21721664

  12. Use of a single bipolar electrode in the posterior arytenoid muscles for bilateral monitoring of the recurrent laryngeal nerves in thyroid surgery.

    PubMed

    Haerle, Stephan; Sidler, D; Linder, Th; Mueller, W

    2008-12-01

    The aims were to assess the technical feasibility of using a single electrode in the posterior arytenoid muscles (PAM) for intraoperative monitoring of the recurrent laryngeal nerve (RLN) in thyroid surgery, to validate the new method against the insertion of electrodes placed in the vocal cord muscle, and to report the results of the clinical application of the new concept. A total of 52 patients were enrolled. The handling and safety of RLN monitoring was tested by simultaneous registration of the EMG response from vocal fold electrodes and PAM electrodes. Acoustically and electromyographically we found nearly the same values for the arytenoid muscles as for the vocal folds, although the signals taken from the vocal folds were slightly stronger. PAM recording using a single bipolar electrode is technically feasible and as reliable compared to the standard vocal cord monitoring.

  13. Dark and bright solitons for the two-dimensional complex modified Korteweg-de Vries and Maxwell-Bloch system with time-dependent coefficient

    NASA Astrophysics Data System (ADS)

    Shaikhova, G.; Ozat, N.; Yesmakhanova, K.; Bekova, G.

    2018-02-01

    In this work, we present Lax pair for two-dimensional complex modified Korteweg-de Vries and Maxwell-Bloch (cmKdV-MB) system with the time-dependent coefficient. Dark and bright soliton solutions for the cmKdV-MB system with variable coefficient are received by Darboux transformation. Moreover, the determinant representation of the one-fold and two-fold Darboux transformation for the cmKdV-MB system with time-dependent coefficient is presented.

  14. Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation

    NASA Astrophysics Data System (ADS)

    Qin, Sanbo; Mittal, Jeetain; Zhou, Huan-Xiang

    2013-08-01

    We have developed a ‘postprocessing’ method for modeling biochemical processes such as protein folding under crowded conditions (Qin and Zhou 2009 Biophys. J. 97 12-19). In contrast to the direct simulation approach, in which the protein undergoing folding is simulated along with crowders, the postprocessing method requires only the folding simulation without crowders. The influence of the crowders is then obtained by taking conformations from the crowder-free simulation and calculating the free energies of transferring to the crowders. This postprocessing yields the folding free energy surface of the protein under crowding. Here the postprocessing results for the folding of three small proteins under ‘repulsive’ crowding are validated by those obtained previously by the direct simulation approach (Mittal and Best 2010 Biophys. J. 98 315-20). This validation confirms the accuracy of the postprocessing approach and highlights its distinct advantages in modeling biochemical processes under cell-like crowded conditions, such as enabling an atomistic representation of the test proteins.

  15. Managerial Cost Accounting for a Technical Information Center.

    ERIC Educational Resources Information Center

    Helmkamp, John G.

    A two-fold solution to the cost information deficiency problem is proposed. A formal managerial cost accounting system is designed expressly for the two information services of retrospective search and selective dissemination. The system was employed during a trial period to test its effectiveness in a technical information center. Once…

  16. New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow.

    PubMed

    Kalgin, Igor V; Caflisch, Amedeo; Chekmarev, Sergei F; Karplus, Martin

    2013-05-23

    A new analysis of the 20 μs equilibrium folding/unfolding molecular dynamics simulations of the three-stranded antiparallel β-sheet miniprotein (beta3s) in implicit solvent is presented. The conformation space is reduced in dimensionality by introduction of linear combinations of hydrogen bond distances as the collective variables making use of a specially adapted principal component analysis (PCA); i.e., to make structured conformations more pronounced, only the formed bonds are included in determining the principal components. It is shown that a three-dimensional (3D) subspace gives a meaningful representation of the folding behavior. The first component, to which eight native hydrogen bonds make the major contribution (four in each beta hairpin), is found to play the role of the reaction coordinate for the overall folding process, while the second and third components distinguish the structured conformations. The representative points of the trajectory in the 3D space are grouped into conformational clusters that correspond to locally stable conformations of beta3s identified in earlier work. A simplified kinetic network based on the three components is constructed, and it is complemented by a hydrodynamic analysis. The latter, making use of "passive tracers" in 3D space, indicates that the folding flow is much more complex than suggested by the kinetic network. A 2D representation of streamlines shows there are vortices which correspond to repeated local rearrangement, not only around minima of the free energy surface but also in flat regions between minima. The vortices revealed by the hydrodynamic analysis are apparently not evident in folding pathways generated by transition-path sampling. Making use of the fact that the values of the collective hydrogen bond variables are linearly related to the Cartesian coordinate space, the RMSD between clusters is determined. Interestingly, the transition rates show an approximate exponential correlation with distance in the hydrogen bond subspace. Comparison with the many published studies shows good agreement with the present analysis for the parts that can be compared, supporting the robust character of our understanding of this "hydrogen atom" of protein folding.

  17. Generic framework for mining cellular automata models on protein-folding simulations.

    PubMed

    Diaz, N; Tischer, I

    2016-05-13

    Cellular automata model identification is an important way of building simplified simulation models. In this study, we describe a generic architectural framework to ease the development process of new metaheuristic-based algorithms for cellular automata model identification in protein-folding trajectories. Our framework was developed by a methodology based on design patterns that allow an improved experience for new algorithms development. The usefulness of the proposed framework is demonstrated by the implementation of four algorithms, able to obtain extremely precise cellular automata models of the protein-folding process with a protein contact map representation. Dynamic rules obtained by the proposed approach are discussed, and future use for the new tool is outlined.

  18. Technical Education as a Tool for Ensuring Sustainable Development: A Case of India

    ERIC Educational Resources Information Center

    Sharma, Gagan Deep; Uppal, Raminder Singh; Mahendru, Mandeep

    2016-01-01

    This paper notes that education needs to essentially lead to sustainable development serving two-fold purpose--eradicating the problems of unemployment and poverty; and ensuring equitable distribution of wealth while ensuring the right understanding leading to a peaceful, prosperous and developed world. In its current state, technical education…

  19. LETTER TO THE EDITOR: Landau levels on the hyperbolic plane

    NASA Astrophysics Data System (ADS)

    Fakhri, H.; Shariati, M.

    2004-11-01

    The quantum states of a spinless charged particle on a hyperbolic plane in the presence of a uniform magnetic field with a generalized quantization condition are proved to be the bases of the irreducible Hilbert representation spaces of the Lie algebra u(1, 1). The dynamical symmetry group U(1, 1) with the explicit form of the Lie algebra generators is extracted. It is also shown that the energy has an infinite-fold degeneracy in each of the representation spaces which are allocated to the different values of the magnetic field strength. Based on the simultaneous shift of two parameters, it is also noted that the quantum states realize the representations of Lie algebra u(2) by shifting the magnetic field strength.

  20. Israeli Special Libraries

    ERIC Educational Resources Information Center

    Foster, Barbara

    1974-01-01

    Israel is sprinkled with a noteworthy representation of special libraries which run the gamut from modest kibbutz efforts to highly technical scientific and humanities libraries. A few examples are discussed here. (Author/CH)

  1. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition

    PubMed Central

    Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Stafford, William Noble; Leslie, Christina

    2007-01-01

    Background Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, called string kernels, for use with support vector machine (SVM) classifiers. However, while some of these approaches exhibit state-of-the-art performance at the binary protein classification problem, i.e. discriminating between a particular protein class and all other classes, few of these studies have addressed the real problem of multi-class superfamily or fold recognition. Moreover, there are only limited software tools and systems for SVM-based protein classification available to the bioinformatics community. Results We present a new multi-class SVM-based protein fold and superfamily recognition system and web server called SVM-Fold, which can be found at . Our system uses an efficient implementation of a state-of-the-art string kernel for sequence profiles, called the profile kernel, where the underlying feature representation is a histogram of inexact matching k-mer frequencies. We also employ a novel machine learning approach to solve the difficult multi-class problem of classifying a sequence of amino acids into one of many known protein structural classes. Binary one-vs-the-rest SVM classifiers that are trained to recognize individual structural classes yield prediction scores that are not comparable, so that standard "one-vs-all" classification fails to perform well. Moreover, SVMs for classes at different levels of the protein structural hierarchy may make useful predictions, but one-vs-all does not try to combine these multiple predictions. To deal with these problems, our method learns relative weights between one-vs-the-rest classifiers and encodes information about the protein structural hierarchy for multi-class prediction. In large-scale benchmark results based on the SCOP database, our code weighting approach significantly improves on the standard one-vs-all method for both the superfamily and fold prediction in the remote homology setting and on the fold recognition problem. Moreover, our code weight learning algorithm strongly outperforms nearest-neighbor methods based on PSI-BLAST in terms of prediction accuracy on every structure classification problem we consider. Conclusion By combining state-of-the-art SVM kernel methods with a novel multi-class algorithm, the SVM-Fold system delivers efficient and accurate protein fold and superfamily recognition. PMID:17570145

  2. Managing ISR sharing policies at the network edge using Controlled English

    NASA Astrophysics Data System (ADS)

    Parizas, Christos; Pizzocaro, Diego; Preece, Alun; Zerfos, Petros

    2013-05-01

    In domains such as emergency response and military operations the sharing of Intelligence, Surveillance and Reconnaissance (ISR) assets among different coalition partners is regulated through policies. Traditionally, poli­ cies are created at the center of a coalitions network by high-level decision makers and expressed in low-level policy languages (e.g. Common Information Model SPL) by technical personnel, which makes them difficult to be understood by non-technical users at the edge of the network. Moreover, policies must often be modified by negotiation among coalition partners, typically in rapid response to the changing operational situation. Com­ monly, the users who must cope first with situational changes are those on the edge, so it would be very effective if they were able to create and negotiate policies themselves. We investigate the use of Controlled English (CE) as a means to define a policy representation that is both human-friendly and machine processable. We show how a CE model can capture a variety of policy types, including those based on a traditional asset ownership model, and those defining team-based asset sharing across a coalition. The use of CE is intended to benefit coalition networks by bridging the gap between technical and non-technical users in terms of policy creation and negoti­ ation, while at the same time being directly processable by a policy-checking system without transformation to any other technical representation.

  3. Analysis-Driven Design of Representations For Sensing-Action Systems

    DTIC Science & Technology

    2017-10-01

    from the Defense Technical Information Center (DTIC) (http://www.dtic.mil). AFRL-RY-WP-TR-2017-0196 HAS BEEN REVIEWED AND IS APPROVED FOR...Layered Sensing Exploitation Division This report is published in the interest of scientific and technical information exchange, and its...collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources

  4. Polarized 3-folds in a codimension 10 weighted homogeneous F4 variety

    NASA Astrophysics Data System (ADS)

    Qureshi, Muhammad Imran

    2017-10-01

    We describe the construction of a codimension 10 weighted homogeneous variety wΣF4(μ , u) corresponding to the exceptional Lie group F4 by explicit computation of its graded ring structure. We give a formula for the Hilbert series of the generic weighted wΣF4(μ , u) in terms of representation theoretic data of F4. We also construct some families of polarized 3-folds in codimension 10 whose general member is a weighted complete intersection of some wΣF4(μ , u) .

  5. Mechanically and optically reliable folding structure with a hyperelastic material for seamless foldable displays

    NASA Astrophysics Data System (ADS)

    Kwon, Hyuk-Jun; Shim, HongShik; Kim, Sunkook; Choi, Woong; Chun, Youngtea; Kee, InSeo; Lee, SangYoon

    2011-04-01

    We report a mechanically and optically robust folding structure to realize a foldable active matrix organic-light-emitting-diode (AMOLED) display without a visible crease at the junction. A nonlinear stress analysis, based on a finite element method, provided an optimized design. The folding-unfolding test on the structure exhibited negligible deterioration of the relative brightness at the junction of the individual panels up to 105 cycles at a folding radius of 1 mm, indicating highly reliable mechanical and optical tolerances. These results demonstrate the feasibility of seamless foldable AMOLED displays, with potentially important technical implications on fabricating large size flexible displays.

  6. Pertinent Factors that Affect the Representation of Women and Minorities in Scientific, Engineering, and Technical Careers

    DTIC Science & Technology

    1990-07-01

    Upon the Supply of Minority and Women Scientists, Engineers , and Technologists (SETs) for Defense Industries and Installations." The purpose of the...the causes of the underrepresentation of minorities and women in scientific, engineering , and technolog- ical (SET) careers, and to establish a...DT ?copy- ARI Research Note 90-80 AD-A231 827 Pertinent Factors that Affect the Representation of Women and Minorities in Scientific, Engineering

  7. Technical Report for Contract N00039-82-C-0235, 15 November 1981-30 September 1983

    DTIC Science & Technology

    1983-09-30

    Management of Data, Ann Arbor, Rich., June 1982. -. 2 ’’.’ , . .. ’,, .* ,° • ,"%,.° % °%" ° %- " "%" . . ." " -.. . . ,.%. Interactive Mathematical ...developed and implemented a hierachical representation for mathematical expres- sioms that includes display position, expression dimensions, font...etc) in internal forms are accepted and converted to box frames which can be displayed. 2. Strophe’s representation of mathematical expressions is

  8. Technical Desiderata for the Integration of Genomic Data into Electronic Health Records

    PubMed Central

    Masys, Daniel R.; Jarvik, Gail P.; Abernethy, Neil F.; Anderson, Nicholas R.; Papanicolaou, George J.; Paltoo, Dina N.; Hoffman, Mark A.; Kohane, Isaac S.; Levy, Howard P.

    2012-01-01

    The era of “Personalized Medicine,” guided by individual molecular variation in DNA, RNA, expressed proteins and other forms of high volume molecular data brings new requirements and challenges to the design and implementation of Electronic Health Records (EHRs). In this article we describe the characteristics of biomolecular data that differentiate it from other classes of data commonly found in EHRs, enumerate a set of technical desiderata for its management in healthcare settings, and offer a candidate technical approach to its compact and efficient representation in operational systems. PMID:22223081

  9. An Evaluation of Selected NASA Scientific and Technical Information Products: Results of a Pilot Study.

    ERIC Educational Resources Information Center

    Pinelli, Thomas E.; Glassman, Myron

    A pilot study was conducted to evaluate selected NASA (National Aeronautics and Space Administration) scientific and technical information (STI) products. The study, which utilized survey research in the form of a self-administered mail questionnaire, had a two-fold purpose--to gather baseline data on the use and perceived usefulness of selected…

  10. 7 CFR 3401.13 - Composition of peer review groups.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... following factors: (a) The level of formal scientific or technical education by the individual; (b) The... balanced membership, e.g., minority and female representation and an equitable age distribution. ...

  11. 7 CFR 3401.13 - Composition of peer review groups.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... following factors: (a) The level of formal scientific or technical education by the individual; (b) The... balanced membership, e.g., minority and female representation and an equitable age distribution. ...

  12. 7 CFR 3401.13 - Composition of peer review groups.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... following factors: (a) The level of formal scientific or technical education by the individual; (b) The... balanced membership, e.g., minority and female representation and an equitable age distribution. ...

  13. 7 CFR 3401.13 - Composition of peer review groups.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... following factors: (a) The level of formal scientific or technical education by the individual; (b) The... balanced membership, e.g., minority and female representation and an equitable age distribution. ...

  14. CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

    PubMed

    Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

    2013-07-01

    The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold.

  15. CABS-fold: server for the de novo and consensus-based prediction of protein structure

    PubMed Central

    Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

    2013-01-01

    The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold. PMID:23748950

  16. Digital controller for a Baum folding machine. [providing automatic counting and machine shutoff

    NASA Technical Reports Server (NTRS)

    Bryant, W. H. (Inventor)

    1974-01-01

    A digital controller for controlling the operation of a folding machine enables automatic folding of a desired number of sheets responsive to entry of that number into a selector. The controller includes three decade counter stages for corresponding rows of units, tens and hundreds push buttons. Each stage including a decimal-to-BCD encoder, a buffer register, and a digital or binary counter. The BCD representation of the selected count for each digit is loaded into the respective decade down counters. Pulses generated by a sensor and associated circuitry are used to decrease the count in the decade counters. When the content of the decade counter reaches either 0 or 1, a solenoid control valve is actuated which interrupts operation of the machine. A repeat switch, when actuated, prevents clearing of the buffer registers so that multiple groups of the same number of sheets can be folded without reentering the number into the selector.

  17. 7 CFR 3400.11 - Composition of peer review groups.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... following factors: (1) The level of formal scientific or technical education by the individual; (2) The... balanced membership, e.g., minority and female representation and an equitable age distribution. (b...

  18. 7 CFR 3400.11 - Composition of peer review groups.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... following factors: (1) The level of formal scientific or technical education by the individual; (2) The... balanced membership, e.g., minority and female representation and an equitable age distribution. (b...

  19. 7 CFR 3400.11 - Composition of peer review groups.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... following factors: (1) The level of formal scientific or technical education by the individual; (2) The... balanced membership, e.g., minority and female representation and an equitable age distribution. (b...

  20. 7 CFR 3400.11 - Composition of peer review groups.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... following factors: (1) The level of formal scientific or technical education by the individual; (2) The... balanced membership, e.g., minority and female representation and an equitable age distribution. (b...

  1. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.

    PubMed

    Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

    2018-02-28

    We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.

  2. New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow

    PubMed Central

    Kalgin, Igor V.; Caflisch, Amedeo; Chekmarev, Sergei F.; Karplus, Martin

    2013-01-01

    A new analysis of the 20 μs equilibrium folding/unfolding molecular dynamics simulations of the three-stranded antiparallel β-sheet miniprotein (beta3s) in implicit solvent is presented. The conformation space is reduced in dimensionality by introduction of linear combinations of hydrogen bond distances as the collective variables making use of a specially adapted Principal Component Analysis (PCA); i.e., to make structured conformations more pronounced, only the formed bonds are included in determining the principal components. It is shown that a three-dimensional (3D) subspace gives a meaningful representation of the folding behavior. The first component, to which eight native hydrogen bonds make the major contribution (four in each beta hairpin), is found to play the role of the reaction coordinate for the overall folding process, while the second and third components distinguish the structured conformations. The representative points of the trajectory in the 3D space are grouped into conformational clusters that correspond to locally stable conformations of beta3s identified in earlier work. A simplified kinetic network based on the three components is constructed and it is complemented by a hydrodynamic analysis. The latter, making use of “passive tracers” in 3D space, indicates that the folding flow is much more complex than suggested by the kinetic network. A 2D representation of streamlines shows there are vortices which correspond to repeated local rearrangement, not only around minima of the free energy surface, but also in flat regions between minima. The vortices revealed by the hydrodynamic analysis are apparently not evident in folding pathways generated by transition-path sampling. Making use of the fact that the values of the collective hydrogen bond variables are linearly related to the Cartesian coordinate space, the RMSD between clusters is determined. Interestingly, the transition rates show an approximate exponential correlation with distance in the hydrogen bond subspace. Comparison with the many published studies shows good agreement with the present analysis for the parts that can be compared, supporting the robust character of our understanding of this “hydrogen atom” of protein folding. PMID:23621790

  3. Modeling cotton (Gossypium spp) leaves and canopy using computer aided geometric design (CAGD)

    USDA-ARS?s Scientific Manuscript database

    The goal of this research is to develop a geometrically accurate model of cotton crop canopies for exploring changes in canopy microenvironment and physiological function with leaf structure. We develop an accurate representation of the leaves, including changes in three-dimensional folding and orie...

  4. Terrestrial biosphere models underestimate photosynthetic capacity and CO2 assimilation in the Arctic.

    PubMed

    Rogers, Alistair; Serbin, Shawn P; Ely, Kim S; Sloan, Victoria L; Wullschleger, Stan D

    2017-12-01

    Terrestrial biosphere models (TBMs) are highly sensitive to model representation of photosynthesis, in particular the parameters maximum carboxylation rate and maximum electron transport rate at 25°C (V c,max.25 and J max.25 , respectively). Many TBMs do not include representation of Arctic plants, and those that do rely on understanding and parameterization from temperate species. We measured photosynthetic CO 2 response curves and leaf nitrogen (N) content in species representing the dominant vascular plant functional types found on the coastal tundra near Barrow, Alaska. The activation energies associated with the temperature response functions of V c,max and J max were 17% lower than commonly used values. When scaled to 25°C, V c,max.25 and J max.25 were two- to five-fold higher than the values used to parameterize current TBMs. This high photosynthetic capacity was attributable to a high leaf N content and the high fraction of N invested in Rubisco. Leaf-level modeling demonstrated that current parameterization of TBMs resulted in a two-fold underestimation of the capacity for leaf-level CO 2 assimilation in Arctic vegetation. This study highlights the poor representation of Arctic photosynthesis in TBMs, and provides the critical data necessary to improve our ability to project the response of the Arctic to global environmental change. No claim to original US Government works. New Phytologist © 2017 New Phytologist Trust.

  5. Terrestrial biosphere models underestimate photosynthetic capacity and CO 2 assimilation in the Arctic

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rogers, Alistair; Serbin, Shawn P.; Ely, Kim S.

    Terrestrial biosphere models (TBMs) are highly sensitive to model representation of photosynthesis, in particular the parameters maximum carboxylation rate and maximum electron transport rate at 25°C (V c,max.25 and J max.25, respectively). Many TBMs do not include representation of Arctic plants, and those that do rely on understanding and parameterization from temperate species. We then measured photosynthetic CO 2 response curves and leaf nitrogen (N) content in species representing the dominant vascular plant functional types found on the coastal tundra near Barrow, Alaska. The activation energies associated with the temperature response functions of Vc,max and Jmax were 17% lower thanmore » commonly used values. When scaled to 25°C, Vc,max.25 and J max.25 were two- to five-fold higher than the values used to parameterize current TBMs. This high photosynthetic capacity was attributable to a high leaf N content and the high fraction of N invested in Rubisco. Leaf-level modeling demonstrated that current parameterization of TBMs resulted in a two-fold underestimation of the capacity for leaf-level CO 2 assimilation in Arctic vegetation. Our study highlights the poor representation of Arctic photosynthesis in TBMs, and provides the critical data necessary to improve our ability to project the response of the Arctic to global environmental change.« less

  6. Terrestrial biosphere models underestimate photosynthetic capacity and CO 2 assimilation in the Arctic

    DOE PAGES

    Rogers, Alistair; Serbin, Shawn P.; Ely, Kim S.; ...

    2017-09-06

    Terrestrial biosphere models (TBMs) are highly sensitive to model representation of photosynthesis, in particular the parameters maximum carboxylation rate and maximum electron transport rate at 25°C (V c,max.25 and J max.25, respectively). Many TBMs do not include representation of Arctic plants, and those that do rely on understanding and parameterization from temperate species. We then measured photosynthetic CO 2 response curves and leaf nitrogen (N) content in species representing the dominant vascular plant functional types found on the coastal tundra near Barrow, Alaska. The activation energies associated with the temperature response functions of Vc,max and Jmax were 17% lower thanmore » commonly used values. When scaled to 25°C, Vc,max.25 and J max.25 were two- to five-fold higher than the values used to parameterize current TBMs. This high photosynthetic capacity was attributable to a high leaf N content and the high fraction of N invested in Rubisco. Leaf-level modeling demonstrated that current parameterization of TBMs resulted in a two-fold underestimation of the capacity for leaf-level CO 2 assimilation in Arctic vegetation. Our study highlights the poor representation of Arctic photosynthesis in TBMs, and provides the critical data necessary to improve our ability to project the response of the Arctic to global environmental change.« less

  7. Three-dimensional visual feature representation in the primary visual cortex

    PubMed Central

    Tanaka, Shigeru; Moon, Chan-Hong; Fukuda, Mitsuhiro; Kim, Seong-Gi

    2011-01-01

    In the cat primary visual cortex, it is accepted that neurons optimally responding to similar stimulus orientations are clustered in a column extending from the superficial to deep layers. The cerebral cortex is, however, folded inside a skull, which makes gyri and fundi. The primary visual area of cats, area 17, is located on the fold of the cortex called the lateral gyrus. These facts raise the question of how to reconcile the tangential arrangement of the orientation columns with the curvature of the gyrus. In the present study, we show a possible configuration of feature representation in the visual cortex using a three-dimensional (3D) self-organization model. We took into account preferred orientation, preferred direction, ocular dominance and retinotopy, assuming isotropic interaction. We performed computer simulation only in the middle layer at the beginning and expanded the range of simulation gradually to other layers, which was found to be a unique method in the present model for obtaining orientation columns spanning all the layers in the flat cortex. Vertical columns of preferred orientations were found in the flat parts of the model cortex. On the other hand, in the curved parts, preferred orientations were represented in wedge-like columns rather than straight columns, and preferred directions were frequently reversed in the deeper layers. Singularities associated with orientation representation appeared as warped lines in the 3D model cortex. Direction reversal appeared on the sheets that were delimited by orientation-singularity lines. These structures emerged from the balance between periodic arrangements of preferred orientations and vertical alignment of same orientations. Our theoretical predictions about orientation representation were confirmed by multi-slice, high-resolution functional MRI in the cat visual cortex. We obtained a close agreement between theoretical predictions and experimental observations. The present study throws a doubt about the conventional columnar view of orientation representation, although more experimental data are needed. PMID:21724370

  8. Three-dimensional visual feature representation in the primary visual cortex.

    PubMed

    Tanaka, Shigeru; Moon, Chan-Hong; Fukuda, Mitsuhiro; Kim, Seong-Gi

    2011-12-01

    In the cat primary visual cortex, it is accepted that neurons optimally responding to similar stimulus orientations are clustered in a column extending from the superficial to deep layers. The cerebral cortex is, however, folded inside a skull, which makes gyri and fundi. The primary visual area of cats, area 17, is located on the fold of the cortex called the lateral gyrus. These facts raise the question of how to reconcile the tangential arrangement of the orientation columns with the curvature of the gyrus. In the present study, we show a possible configuration of feature representation in the visual cortex using a three-dimensional (3D) self-organization model. We took into account preferred orientation, preferred direction, ocular dominance and retinotopy, assuming isotropic interaction. We performed computer simulation only in the middle layer at the beginning and expanded the range of simulation gradually to other layers, which was found to be a unique method in the present model for obtaining orientation columns spanning all the layers in the flat cortex. Vertical columns of preferred orientations were found in the flat parts of the model cortex. On the other hand, in the curved parts, preferred orientations were represented in wedge-like columns rather than straight columns, and preferred directions were frequently reversed in the deeper layers. Singularities associated with orientation representation appeared as warped lines in the 3D model cortex. Direction reversal appeared on the sheets that were delimited by orientation-singularity lines. These structures emerged from the balance between periodic arrangements of preferred orientations and vertical alignment of the same orientations. Our theoretical predictions about orientation representation were confirmed by multi-slice, high-resolution functional MRI in the cat visual cortex. We obtained a close agreement between theoretical predictions and experimental observations. The present study throws a doubt about the conventional columnar view of orientation representation, although more experimental data are needed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Human Behaviour Representation in Constructive Modelling (Representation du comportement humain dans des modelisations creatives)

    DTIC Science & Technology

    2009-09-01

    involved in R&T activities. RTO reports both to the Military Committee of NATO and to the Conference of National Armament Directors. It comprises a...4 11.5.3 Project Description 11-5 Chapter 12 – Technical Evaluation Report 12-1 12.1 Executive Summary 12-1 12.2 Introduction 12-2 12.3...modelling human factors has been slow over the past decade, other forums have been reporting a number of theoretical and applied papers on human behaviour

  10. Human Behaviour Representation in Constructive Modelling (Representation du comportement humain dans des modelisations creatives)

    DTIC Science & Technology

    2009-09-01

    ordination with other NATO bodies involved in R&T activities. RTO reports both to the Military Committee of NATO and to the Conference of National...Aims 11-4 11.5.2 Background 11-4 11.5.3 Project Description 11-5 Chapter 12 – Technical Evaluation Report 12-1 12.1 Executive Summary 12-1...track. Although progress in modelling human factors has been slow over the past decade, other forums have been reporting a number of theoretical and

  11. Mass spectrometry for water vapor measurements in the UT/LS

    NASA Astrophysics Data System (ADS)

    Kaufmann, S.; Voigt, C.; Schäuble, D.; Schäfler, A.; Schlager, H.; Thornberry, T. D.; Fahey, D. W.

    2012-12-01

    Water vapor in the lower stratosphere plays a crucial role for the atmospheric radiation budget (Solomon et al., 2011). However, large uncertainties remain in measuring atmospheric water vapor mixing ratios below 10 ppmv typical for the lower stratosphere. To this end, we have developed the Atmospheric Ionization Mass Spectrometer (AIMS) for the accurate and fast detection of water vapor in the UT/LS from aircraft. In the AIMS instrument atmospheric air is directly ionized in a discharge ion source and the resulting water vapor clusters H3O+(H2O)n (n = 0..3) are detected with a linear quadrupole mass spectrometer as a direct measure of the atmospheric water vapor mixing ratio. AIMS is calibrated in-flight with a H2O calibration source using the catalytic reaction of H2 and O2 on a heated platinum surface to form gaseous H2O. This calibration setup combined with the water vapor mass spectrometry offers a powerful technical development in atmospheric hygrometry, enriching existing H2O measurement techniques by a new independent method. Here, we present AIMS water vapor measurements performed during the CONCERT2011 campaign (Contrail and Cirrus Experiment) with the DLR research aircraft Falcon. In September 2011 a deep stratospheric intrusion was probed over northern Europe with a dynamical tropopause lowered down to 6 km. We found sharp humidity gradients between tropospheric and stratospheric air at the edge of the tropopause fold, which we crossed 4 times at altitudes between 6 and 11 km. In the center of the tropopause fold, we measured water vapor mixing ratios down to 4 ppmv. The observed water vapor distribution is compared to water vapor analysis fields of the ECMWF's Integrated Forecast System (IFS) to evaluate the representation water vapor in this specific meteorological situation.

  12. Probabilistic analysis for identifying the driving force of protein folding

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yoshihiko; Yamamori, Yu; Matubayasi, Nobuyuki

    2018-03-01

    Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

  13. 48 CFR 242.7401 - Procedures.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Procedures. 242.7401 Section 242.7401 Federal Acquisition Regulations System DEFENSE ACQUISITION REGULATIONS SYSTEM, DEPARTMENT OF DEFENSE CONTRACT MANAGEMENT CONTRACT ADMINISTRATION AND AUDIT SERVICES Technical Representation at...

  14. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Koenig, Robert; Institute for Quantum Information, California Institute of Technology, Pasadena, California 91125; Mitchison, Graeme

    In its most basic form, the finite quantum de Finetti theorem states that the reduced k-partite density operator of an n-partite symmetric state can be approximated by a convex combination of k-fold product states. Variations of this result include Renner's 'exponential' approximation by 'almost-product' states, a theorem which deals with certain triples of representations of the unitary group, and the result of D'Cruz et al. [e-print quant-ph/0606139;Phys. Rev. Lett. 98, 160406 (2007)] for infinite-dimensional systems. We show how these theorems follow from a single, general de Finetti theorem for representations of symmetry groups, each instance corresponding to a particular choicemore » of symmetry group and representation of that group. This gives some insight into the nature of the set of approximating states and leads to some new results, including an exponential theorem for infinite-dimensional systems.« less

  15. Wigner functions for noncommutative quantum mechanics: A group representation based construction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chowdhury, S. Hasibul Hassan, E-mail: shhchowdhury@gmail.com; Department of Mathematics and Statistics, Concordia University, Montréal, Québec H3G 1M8; Ali, S. Twareque, E-mail: twareque.ali@concordia.ca

    This paper is devoted to the construction and analysis of the Wigner functions for noncommutative quantum mechanics, their marginal distributions, and star-products, following a technique developed earlier, viz, using the unitary irreducible representations of the group G{sub NC}, which is the three fold central extension of the Abelian group of ℝ{sup 4}. These representations have been exhaustively studied in earlier papers. The group G{sub NC} is identified with the kinematical symmetry group of noncommutative quantum mechanics of a system with two degrees of freedom. The Wigner functions studied here reflect different levels of non-commutativity—both the operators of position and thosemore » of momentum not commuting, the position operators not commuting and finally, the case of standard quantum mechanics, obeying the canonical commutation relations only.« less

  16. Two methods of Haustral fold detection from computed tomographic virtual colonoscopy images

    NASA Astrophysics Data System (ADS)

    Chowdhury, Ananda S.; Tan, Sovira; Yao, Jianhua; Linguraru, Marius G.; Summers, Ronald M.

    2009-02-01

    Virtual colonoscopy (VC) has gained popularity as a new colon diagnostic method over the last decade. VC is a new, less invasive alternative to the usually practiced optical colonoscopy for colorectal polyp and cancer screening, the second major cause of cancer related deaths in industrial nations. Haustral (colonic) folds serve as important landmarks for virtual endoscopic navigation in the existing computer-aided-diagnosis (CAD) system. In this paper, we propose and compare two different methods of haustral fold detection from volumetric computed tomographic virtual colonoscopy images. The colon lumen is segmented from the input using modified region growing and fuzzy connectedness. The first method for fold detection uses a level set that evolves on a mesh representation of the colon surface. The colon surface is obtained from the segmented colon lumen using the Marching Cubes algorithm. The second method for fold detection, based on a combination of heat diffusion and fuzzy c-means algorithm, is employed on the segmented colon volume. Folds obtained on the colon volume using this method are then transferred to the corresponding colon surface. After experimentation with different datasets, results are found to be promising. The results also demonstrate that the first method has a tendency of slight under-segmentation while the second method tends to slightly over-segment the folds.

  17. Visualization in Research and Science Teachers' Professional Development

    ERIC Educational Resources Information Center

    Chang Rundgren, Shu-Nu; Yao, Bao-Jun

    2014-01-01

    Based on the importance and widely use of visualization in science, this article has a three-fold aim related to the terms of visualization, representation and model that in recent years have been introduced to the field of science education without clear differentiation. Firstly, the three terms are discussed with examples to provide a common…

  18. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

    PubMed Central

    2017-01-01

    Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

  19. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    PubMed

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at multiple levels, from atomistic to coarse-grained representations. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.

  20. A simplified formalism of the algebra of partially transposed permutation operators with applications

    NASA Astrophysics Data System (ADS)

    Mozrzymas, Marek; Studziński, Michał; Horodecki, Michał

    2018-03-01

    Herein we continue the study of the representation theory of the algebra of permutation operators acting on the n -fold tensor product space, partially transposed on the last subsystem. We develop the concept of partially reduced irreducible representations, which allows us to significantly simplify previously proved theorems and, most importantly, derive new results for irreducible representations of the mentioned algebra. In our analysis we are able to reduce the complexity of the central expressions by getting rid of sums over all permutations from the symmetric group, obtaining equations which are much more handy in practical applications. We also find relatively simple matrix representations for the generators of the underlying algebra. The obtained simplifications and developments are applied to derive the characteristics of a deterministic port-based teleportation scheme written purely in terms of irreducible representations of the studied algebra. We solve an eigenproblem for the generators of the algebra, which is the first step towards a hybrid port-based teleportation scheme and gives us new proofs of the asymptotic behaviour of teleportation fidelity. We also show a connection between the density operator characterising port-based teleportation and a particular matrix composed of an irreducible representation of the symmetric group, which encodes properties of the investigated algebra.

  1. Proceedings of the Workshop on Directional Acoustic Sensors Held in Newport, Rhode Island on 17-18 April 2001

    DTIC Science & Technology

    2001-04-18

    representation of the acoustic field, the first three terms of which represent the scalar, vector, and tensor (or dyadic ) components of the field, referred to by...encouragement and financial support. We also thank Ms. Kathy Stark of America House Communications , Newport, RI, for the planning and administration of this...Connectivity between warfighter and technical community • Technical competency for integrity of total warfighting system • Full access to our

  2. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

    PubMed Central

    Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

    2018-01-01

    Abstract We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$\\mathcal {E}$\\end{document}SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base–phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation. PMID:29272539

  3. Structural Bridges through Fold Space.

    PubMed

    Edwards, Hannah; Deane, Charlotte M

    2015-09-01

    Several protein structure classification schemes exist that partition the protein universe into structural units called folds. Yet these schemes do not discuss how these units sit relative to each other in a global structure space. In this paper we construct networks that describe such global relationships between folds in the form of structural bridges. We generate these networks using four different structural alignment methods across multiple score thresholds. The networks constructed using the different methods remain a similar distance apart regardless of the probability threshold defining a structural bridge. This suggests that at least some structural bridges are method specific and that any attempt to build a picture of structural space should not be reliant on a single structural superposition method. Despite these differences all representations agree on an organisation of fold space into five principal community structures: all-α, all-β sandwiches, all-β barrels, α/β and α + β. We project estimated fold ages onto the networks and find that not only are the pairings of unconnected folds associated with higher age differences than bridged folds, but this difference increases with the number of networks displaying an edge. We also examine different centrality measures for folds within the networks and how these relate to fold age. While these measures interpret the central core of fold space in varied ways they all identify the disposition of ancestral folds to fall within this core and that of the more recently evolved structures to provide the peripheral landscape. These findings suggest that evolutionary information is encoded along these structural bridges. Finally, we identify four highly central pivotal folds representing dominant topological features which act as key attractors within our landscapes.

  4. Electroactive Polymeric Materials for Supercapacitors

    DTIC Science & Technology

    2017-06-16

    composites either using transition metal oxides or different 3D carbon structures to maximize the pseudocapacitance. TECHNICAL APPROACH Our... printing /coating. Figure 9. Schematic representation of CNT forest well plate and a photograph of CNT well sample alongside a penny placed for size

  5. 7 CFR 3415.11 - Composition of peer review groups.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., EDUCATION, AND EXTENSION SERVICE, DEPARTMENT OF AGRICULTURE BIOTECHNOLOGY RISK ASSESSMENT RESEARCH GRANTS... level of formal scientific or technical education by the individual and the extent to which an... minority and female representation and an equitable age distribution. (b) [Reserved] ...

  6. Education, ethics, and solidarity in international cooperation.

    PubMed

    Castro, Janete Lima de; Vilar, Rosana Lucia Alves de; Germano, Raimunda Medeiros

    2015-01-01

    The article analyzes an experience in technical cooperation between Brazil and Andean countries in the form of the International Course in the Management of Human Resource Policies in Health. This exploratory documental study encompassed a number of Latin American countries whose institutions of higher education had partnerships with the Federal University of Rio Grande do Norte, mediated by the Pan American Health Organization Representation in Brazil. The course experience shows that fundamental values like ethics and solidarity are determinant to the success of technical cooperation processes.

  7. Grid-cell representations in mental simulation

    PubMed Central

    Bellmund, Jacob LS; Deuker, Lorena; Navarro Schröder, Tobias; Doeller, Christian F

    2016-01-01

    Anticipating the future is a key motif of the brain, possibly supported by mental simulation of upcoming events. Rodent single-cell recordings suggest the ability of spatially tuned cells to represent subsequent locations. Grid-like representations have been observed in the human entorhinal cortex during virtual and imagined navigation. However, hitherto it remains unknown if grid-like representations contribute to mental simulation in the absence of imagined movement. Participants imagined directions between building locations in a large-scale virtual-reality city while undergoing fMRI without re-exposure to the environment. Using multi-voxel pattern analysis, we provide evidence for representations of absolute imagined direction at a resolution of 30° in the parahippocampal gyrus, consistent with the head-direction system. Furthermore, we capitalize on the six-fold rotational symmetry of grid-cell firing to demonstrate a 60° periodic pattern-similarity structure in the entorhinal cortex. Our findings imply a role of the entorhinal grid-system in mental simulation and future thinking beyond spatial navigation. DOI: http://dx.doi.org/10.7554/eLife.17089.001 PMID:27572056

  8. RNAiFold: a web server for RNA inverse folding and molecular design.

    PubMed

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  9. The role of atomic level steric effects and attractive forces in protein folding.

    PubMed

    Lammert, Heiko; Wolynes, Peter G; Onuchic, José N

    2012-02-01

    Protein folding into tertiary structures is controlled by an interplay of attractive contact interactions and steric effects. We investigate the balance between these contributions using structure-based models using an all-atom representation of the structure combined with a coarse-grained contact potential. Tertiary contact interactions between atoms are collected into a single broad attractive well between the C(β) atoms between each residue pair in a native contact. Through the width of these contact potentials we control their tolerance for deviations from the ideal structure and the spatial range of attractive interactions. In the compact native state dominant packing constraints limit the effects of a coarse-grained contact potential. During folding, however, the broad attractive potentials allow an early collapse that starts before the native local structure is completely adopted. As a consequence the folding transition is broadened and the free energy barrier is decreased. Eventually two-state folding behavior is lost completely for systems with very broad attractive potentials. The stabilization of native-like residue interactions in non-perfect geometries early in the folding process frequently leads to structural traps. Global mirror images are a notable example. These traps are penalized by the details of the repulsive interactions only after further collapse. Successful folding to the native state requires simultaneous guidance from both attractive and repulsive interactions. Copyright © 2011 Wiley Periodicals, Inc.

  10. Mathematical Notation in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Pasterczyk, Catherine E.

    1990-01-01

    Discusses ways in which using mathematical symbols to search online bibliographic databases in scientific and technical areas can improve search results. The representations used for Greek letters, relations, binary operators, arrows, and miscellaneous special symbols in the MathSci, Inspec, Compendex, and Chemical Abstracts databases are…

  11. Thinkable Models.

    ERIC Educational Resources Information Center

    Lawler, Robert W.

    1996-01-01

    Argues that the organization of cognitive structures for technical domains can be visualized as a network of connected thinkable models. Describes a taxonomy of models that has been developed and discusses the issue of how representations relate to human modes of perception and action. Contains 25 references. (DDR)

  12. Signal-to-noise enhancement techniques for quantum cascade absorption spectrometers employing optimal filtering and other approaches

    NASA Astrophysics Data System (ADS)

    Disselkamp, R. S.; Kelly, J. F.; Sams, R. L.; Anderson, G. A.

    Optical feedback to the laser source in tunable diode laser spectroscopy (TDLS) is known to create intensity modulation noise due to elatoning and optical feedback (i.e. multiplicative technical noise) that usually limits spectral signal-to-noise (S/N). The large technical noise often limits absorption spectroscopy to noise floors 100-fold greater than the Poisson shot noise limit due to fluctuations in the laser intensity. The high output powers generated from quantum cascade (QC) lasers, along with their high gain, makes these injection laser systems especially susceptible to technical noise. In this article we discuss a method of using optimal filtering to reduce technical noise. We have observed S/N enhancements ranging from 20% to a factor of 50. The degree to which optimal filtering enhances S/N depends on the similarity between the Fourier components of the technical noise and those of the signal, with lower S/N enhancements observed for more similar Fourier decompositions of the signal and technical noise. We also examine the linearity of optimal filtered spectra in both time and intensity. This was accomplished by creating a synthetic spectrum for the species being studied (CH4, N2O, CO2 and H2O in ambient air) utilizing line positions and linewidths with an assumed Voigt profile from a commercial database (HITRAN). Agreement better than 0.036% in wavenumber and 1.64% in intensity (up to a 260-fold intensity ratio employed) was observed. Our results suggest that rapid ex post facto digital optimal filtering can be used to enhance S/N for routine trace gas detection.

  13. Improved Design of Tunnel Supports : Volume 1 : Simplified Analysis for Ground-Structure Interaction in Tunneling

    DOT National Transportation Integrated Search

    1980-06-01

    The purpose of this report is to provide the tunneling profession with improved practical tools in the technical or design area, which provide more accurate representations of the ground-structure interaction in tunneling. The design methods range fr...

  14. Innovation Analysis | Energy Analysis | NREL

    Science.gov Websites

    . New empirical methods for estimating technical and commercial impact (based on patent citations and Commercial Breakthroughs, NREL employed regression models and multivariate simulations to compare social in the marketplace and found that: Web presence may provide a better representation of the commercial

  15. Ferrotoroidial propertiesof Non-Crystallographic Pointgroups

    NASA Astrophysics Data System (ADS)

    Sireesha, G.; Devi, S. Uma; Yamini Sankar, CH.

    2017-08-01

    Primary ferroic crystals are the crystals with domain states that are distinguished by properties like spontaneous magnetization, strain, or polarisation. Secondary ferroic crystals are the crystals with domain states that are distinguished by piezoelectric tensor and they are named as Ferromagnetotoroidic (eV2), Ferromagnetoelastic (aeV [V2]) crystals respectively. Here “e” denotes zero rank tensor that changes under spatial inversion, “a” denotes zero rank tensor that changes under time inversion, and “V” denotes a polar vector. Recent observations (Van Aken et al., 2007) identified the fourth type of primary ferroic crystals, a ferrotoroidic crystal with domains distinguished by a toroidial moment. The number of independent constants of quasi crystals is theoretically derived by Wenge Yang et al., (1995). He also formulated the number of independent components of any physical property tensor of quasi crystals using group representation theory. This paper accounts the effect of symmetry on some ferrotoroidial properties of quasi Crystals with 5-fold, 8-fold, 10-fold and 12-fold symmetries using group theoretical methods. Also the number of independent constants is calculated and tabulated that helps in describing the ferrotoroidial properties.

  16. Two parametric voice source models and their asymptotic analysis

    NASA Astrophysics Data System (ADS)

    Leonov, A. S.; Sorokin, V. N.

    2014-05-01

    The paper studies the asymptotic behavior of the function for the area of the glottis near moments of its opening and closing for two mathematical voice source models. It is shown that in the first model, the asymptotics of the area function obeys a power law with an exponent of no less that 1. Detailed analysis makes it possible to refine these limits depending on the relative sizes of the intervals of a closed and open glottis. This work also studies another parametric model of the area of the glottis, which is based on a simplified physical-geometrical representation of vocal-fold vibration processes. This is a special variant of the well-known two-mass model and contains five parameters: the period of the main tone, equivalent masses on the lower and upper edge of vocal folds, the coefficient of elastic resistance of the lower vocal fold, and the delay time between openings of the upper and lower folds. It is established that the asymptotics of the obtained function for the area of the glottis obey a power law with an exponent of 1 both for opening and closing.

  17. N-fold Darboux Transformation for Integrable Couplings of AKNS Equations

    NASA Astrophysics Data System (ADS)

    Yu, Jing; Chen, Shou-Ting; Han, Jing-Wei; Ma, Wen-Xiu

    2018-04-01

    For the integrable couplings of Ablowitz-Kaup-Newell-Segur (ICAKNS) equations, N-fold Darboux transformation (DT) TN, which is a 4 × 4 matrix, is constructed in this paper. Each element of this matrix is expressed by a ratio of the (4N + 1)-order determinant and 4N-order determinant of eigenfunctions. By making use of these formulae, the determinant expressions of N-transformed new solutions p [N], q [N], r [N] and s [N] are generated by this N-fold DT. Furthermore, when the reduced conditions q = ‑p* and s = ‑r* are chosen, we obtain determinant representations of N-fold DT and N-transformed solutions for the integrable couplings of nonlinear Schrödinger (ICNLS) equations. Starting from the zero seed solutions, one-soliton solutions are explicitly given as an example. Supported by the National Natural Science Foundation of China under Grant Nos. 61771174, 11371326, 11371361, 11301454, and 11271168, Natural Science Fund for Colleges and Universities of Jiangsu Province of China under Grant No. 17KJB110020, and General Research Project of Department of Education of Zhejiang Province (Y201636538)

  18. Facilitating Understanding of Movements in Dynamic Visualizations: An Embodied Perspective

    ERIC Educational Resources Information Center

    de Koning, Bjorn B.; Tabbers, Huib K.

    2011-01-01

    Learners studying mechanical or technical processes via dynamic visualizations often fail to build an accurate mental representation of the system's movements. Based on embodied theories of cognition assuming that action, perception, and cognition are closely intertwined, this paper proposes that the learning effectiveness of dynamic…

  19. 75 FR 5225 - Professional Conduct for Practitioners: Rules, Procedures, Representation, and Appearances

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-02

    ... Justice (DOJ); clarify who is authorized to represent applicants and petitioners in cases before DHS... regulations; make technical and procedural changes; and conform terminology. This rule enhances the integrity... existing regulations; and eliminates references to procedural matters that are solely within the authority...

  20. Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

    PubMed Central

    An, Na; Fleming, Aaron M.; Middleton, Eric G.; Burrows, Cynthia J.

    2014-01-01

    Human telomeric DNA consists of tandem repeats of the sequence 5′-TTAGGG-3′ that can fold into various G-quadruplexes, including the hybrid, basket, and propeller folds. In this report, we demonstrate use of the α-hemolysin ion channel to analyze these subtle topological changes at a nanometer scale by providing structure-dependent electrical signatures through DNA–protein interactions. Whereas the dimensions of hybrid and basket folds allowed them to enter the protein vestibule, the propeller fold exceeds the size of the latch region, producing only brief collisions. After attaching a 25-mer poly-2′-deoxyadenosine extension to these structures, unraveling kinetics also were evaluated. Both the locations where the unfolding processes occur and the molecular shapes of the G-quadruplexes play important roles in determining their unfolding profiles. These results provide insights into the application of α-hemolysin as a molecular sieve to differentiate nanostructures as well as the potential technical hurdles DNA secondary structures may present to nanopore technology. PMID:25225404

  1. Impact of the Assimilation of Hyperspectral Infrared Profiles on Advanced Weather and Research Model Simulations of a Non-Convective Wind Event

    NASA Technical Reports Server (NTRS)

    Berndt, Emily B.; Zavodsky, Bradley T; Jedlovec, Gary J.; Elmer, Nicholas J.

    2013-01-01

    Non-convective wind events commonly occur with passing extratropical cyclones and have significant societal and economic impacts. Since non-convective winds often occur in the absence of specific phenomena such as a thunderstorm, tornado, or hurricane, the public are less likely to heed high wind warnings and continue daily activities. Thus non-convective wind events result in as many fatalities as straight line thunderstorm winds. One physical explanation for non-convective winds includes tropopause folds. Improved model representation of stratospheric air and associated non-convective wind events could improve non-convective wind forecasts and associated warnings. In recent years, satellite data assimilation has improved skill in forecasting extratropical cyclones; however errors still remain in forecasting the position and strength of extratropical cyclones as well as the tropopause folding process. The goal of this study is to determine the impact of assimilating satellite temperature and moisture retrieved profiles from hyperspectral infrared (IR) sounders (i.e. Atmospheric Infrared Sounder (AIRS), Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI)) on the model representation of the tropopause fold and an associated high wind event that impacted the Northeast United States on 09 February 2013. Model simulations using the Advanced Research Weather Research and Forecasting Model (ARW) were conducted on a 12-km grid with cycled data assimilation mimicking the operational North American Model (NAM). The results from the satellite assimilation run are compared to a control experiment (without hyperspectral IR retrievals), North American Regional Reanalysis (NARR) reanalysis, and Rapid Refresh analyses.

  2. Technical efficiency in milk production in underdeveloped production environment of India*.

    PubMed

    Bardhan, Dwaipayan; Sharma, Murari Lal

    2013-12-01

    The study was undertaken in Kumaon division of Uttarakhand state of India with the objective of estimating technical efficiency in milk production across different herd-size category households and factors influencing it. Total of 60 farm households having representation from different herd-size categories drawn from six randomly selected villages of plain and hilly regions of the division constituted the ultimate sampling units of the study. Stochastic frontier production function analysis was used to estimate the technical efficiency in milk production. Multivariate regression equations were fitted taking technical efficiency index as the regressand to identify the factors significantly influencing technical efficiency in milk production. The study revealed that variation in output across farms in the study area was due to difference in their technical efficiency levels. However, it was interesting to note that smallholder producers were more technically efficient in milk production than their larger counterparts, especially in the plains. Apart from herd size, intensity of market participation had significant and positive impact on technical efficiency in the plains. This provides definite indication that increasing the level of commercialization of dairy farms would have beneficial impact on their production efficiency.

  3. A Review of the Evolution of Naval Data Automation and the Optical Media Mass Storage Alternatives Related to Naval Aviation Technical Documentation.

    DTIC Science & Technology

    1987-09-01

    workstation (ADMS) and associated literature and laser printouts * Athol Fodon and Jim Tillinghast-- Palantir Corporation--for their analysis...TILL.CcI’:i1iCO technical ocumentaton. An \\obiective of :his research -,as toaave .:o:m . This author specillcaiY ’commi-issioned’ the Palantir Corporation...formats, letter size, illustrations, pictures, fold-out pages and relative familiarity with fleet users. The Palantir Corporation analyzed and compared

  4. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

    PubMed Central

    Zhou, Rui; Maisuradze, Gia G.; Suñol, David; Todorovski, Toni; Macias, Maria J.; Xiao, Yi; Scheraga, Harold A.; Czaplewski, Cezary; Liwo, Adam

    2014-01-01

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding. PMID:25489078

  5. Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Gō-like Modeling

    PubMed Central

    Kaya, Hüseyin; Liu, Zhirong; Chan, Hue Sun

    2005-01-01

    It has been demonstrated that a “near-Levinthal” cooperative mechanism, whereby the common Gō interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a Cα protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in Gō-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of ∼17–30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum Gō-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. PMID:15863486

  6. Effects of desolvation barriers and sidechains on local-nonlocal coupling and chevron behaviors in coarse-grained models of protein folding.

    PubMed

    Chen, Tao; Chan, Hue Sun

    2014-04-14

    Local-nonlocal coupling is an organizational principle in protein folding. It envisions a cooperative energetic interplay between local conformational preferences and favorable nonlocal contacts. Previous theoretical studies by our group showed that two classes of native-centric coarse-grained models can capture the experimentally observed high degrees of protein folding cooperativity and diversity in folding rates. These models either embody an explicit local-nonlocal coupling mechanism or incorporate desolvation barriers in the models' pairwise interactions. Here a conceptual connection is made between these two paradigmatic coarse-grained interaction schemes by showing that desolvation barriers enhance local-nonlocal coupling. Furthermore, we find that a class of coarse-grained protein models with a single-site representation of sidechains also increases local-nonlocal coupling relative to mainchain models without sidechains. Enhanced local-nonlocal coupling generally leads to higher folding cooperativity and chevron plots with more linear folding arms. For the sidechain models studied, the chevron plot simulated with entirely native-centric intrachain interactions behaves very similarly to the corresponding chevron plots simulated with interactions that are partly modulated by sequence- and denaturant-dependent transfer free energies. In these essentially native-centric models, the mild chevron rollovers in the simulated folding arm are caused by occasionally populated intermediates as well as the movement of the unfolded and putative folding transition states. The strength and limitation of the models are analyzed by comparison with experiment. New formulations of sidechain models that may provide a physical account for nonnative interactions are also explored.

  7. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

    PubMed

    Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

    2014-12-23

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

  8. An efficient approach to CI: General matrix element formulas for spin-coupled particle-hole excitations

    NASA Astrophysics Data System (ADS)

    Tavan, Paul; Schulten, Klaus

    1980-03-01

    A new, efficient algorithm for the evaluation of the matrix elements of the CI Hamiltonian in the basis of spin-coupled ν-fold excitations (over orthonormal orbitals) is developed for even electron systems. For this purpose we construct an orthonormal, spin-adapted CI basis in the framework of second quantization. As a prerequisite, spin and space parts of the fermion operators have to be separated; this makes it possible to introduce the representation theory of the permutation group. The ν-fold excitation operators are Serber spin-coupled products of particle-hole excitations. This construction is also designed for CI calculations from multireference (open-shell) states. The 2N-electron Hamiltonian is expanded in terms of spin-coupled particle-hole operators which map any ν-fold excitation on ν-, and ν±1-, and ν±2-fold excitations. For the calculation of the CI matrix this leaves one with only the evaluation of overlap matrix elements between spin-coupled excitations. This leads to a set of ten general matrix element formulas which contain Serber representation matrices of the permutation group Sν×Sν as parameters. Because of the Serber structure of the CI basis these group-theoretical parameters are kept to a minimum such that they can be stored readily in the central memory of a computer for ν?4 and even for higher excitations. As the computational effort required to obtain the CI matrix elements from the general formulas is very small, the algorithm presented appears to constitute for even electron systems a promising alternative to existing CI methods for multiply excited configurations, e.g., the unitary group approach. Our method makes possible the adaptation of spatial symmetries and the selection of any subset of configurations. The algorithm has been implemented in a computer program and tested extensively for ν?4 and singlet ground and excited states.

  9. Representations in Simulated Workplaces

    ERIC Educational Resources Information Center

    van Schaik, Martijn; Terwel, Jan; van Oers, Bert

    2014-01-01

    In vocational education students are to be prepared to participate in communities of practice. Hence they need technical skills as well as content knowledge e.g. science and mathematics. Research has shown that the instructional strategy of guided co-construction may lead to deeper understandings within a practice. The research questions in this…

  10. 7 CFR 801.12 - Design requirements incorporated by reference.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... reference: General Code (1.10.) G-S.5.5. Money Values, Mathematical Agreement G-T.1. Acceptance Tolerances G.... Tolerance Values T.3. For Test Weight Per Bushel Indications or Recorded Representations UR.3.2. Other... Standards and Technology's (NIST) Handbook 44, “Specifications, Tolerances, and Other Technical Requirements...

  11. Semiclassical propagation: Hilbert space vs. Wigner representation

    NASA Astrophysics Data System (ADS)

    Gottwald, Fabian; Ivanov, Sergei D.

    2018-03-01

    A unified viewpoint on the van Vleck and Herman-Kluk propagators in Hilbert space and their recently developed counterparts in Wigner representation is presented. Based on this viewpoint, the Wigner Herman-Kluk propagator is conceptually the most general one. Nonetheless, the respective semiclassical expressions for expectation values in terms of the density matrix and the Wigner function are mathematically proven here to coincide. The only remaining difference is a mere technical flexibility of the Wigner version in choosing the Gaussians' width for the underlying coherent states beyond minimal uncertainty. This flexibility is investigated numerically on prototypical potentials and it turns out to provide neither qualitative nor quantitative improvements. Given the aforementioned generality, utilizing the Wigner representation for semiclassical propagation thus leads to the same performance as employing the respective most-developed (Hilbert-space) methods for the density matrix.

  12. Technosocial Modeling of IED Threat Scenarios and Attacks

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Whitney, Paul D.; Brothers, Alan J.; Coles, Garill A.

    2009-03-23

    This paper describes an approach for integrating sociological and technical models to develop more complete threat assessment. Current approaches to analyzing and addressing threats tend to focus on the technical factors. This paper addresses development of predictive models that encompass behavioral as well as these technical factors. Using improvised explosive device (IED) attacks as motivation, this model supports identification of intervention activities 'left of boom' as well as prioritizing attack modalities. We show how Bayes nets integrate social factors associated with IED attacks into general threat model containing technical and organizational steps from planning through obtaining the IED to initiationmore » of the attack. The social models are computationally-based representations of relevant social science literature that describes human decision making and physical factors. When combined with technical models, the resulting model provides improved knowledge integration into threat assessment for monitoring. This paper discusses the construction of IED threat scenarios, integration of diverse factors into an analytical framework for threat assessment, indicator identification for future threats, and future research directions.« less

  13. Molecular Dynamics based on a Generalized Born solvation model: application to protein folding

    NASA Astrophysics Data System (ADS)

    Onufriev, Alexey

    2004-03-01

    An accurate description of the aqueous environment is essential for realistic biomolecular simulations, but may become very expensive computationally. We have developed a version of the Generalized Born model suitable for describing large conformational changes in macromolecules. The model represents the solvent implicitly as continuum with the dielectric properties of water, and include charge screening effects of salt. The computational cost associated with the use of this model in Molecular Dynamics simulations is generally considerably smaller than the cost of representing water explicitly. Also, compared to traditional Molecular Dynamics simulations based on explicit water representation, conformational changes occur much faster in implicit solvation environment due to the absence of viscosity. The combined speed-up allow one to probe conformational changes that occur on much longer effective time-scales. We apply the model to folding of a 46-residue three helix bundle protein (residues 10-55 of protein A, PDB ID 1BDD). Starting from an unfolded structure at 450 K, the protein folds to the lowest energy state in 6 ns of simulation time, which takes about a day on a 16 processor SGI machine. The predicted structure differs from the native one by 2.4 A (backbone RMSD). Analysis of the structures seen on the folding pathway reveals details of the folding process unavailable form experiment.

  14. Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

    PubMed Central

    Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, Bingbing; Zhang, John Z. H.; Mei, Ye

    2015-01-01

    A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. PMID:26039188

  15. Discrete-state phasor neural networks

    NASA Astrophysics Data System (ADS)

    Noest, André J.

    1988-08-01

    An associative memory network with local variables assuming one of q equidistant positions on the unit circle (q-state phasors) is introduced, and its recall behavior is solved exactly for any q when the interactions are sparse and asymmetric. Such models can describe natural or artifical networks of (neuro-)biological, chemical, or electronic limit-cycle oscillators with q-fold instead of circular symmetry, or similar optical computing devices using a phase-encoded data representation.

  16. Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications

    PubMed Central

    Chng, Choon-Peng; Yang, Lee-Wei

    2008-01-01

    Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed. PMID:19812774

  17. Impact of incomplete correspondence between document titles and texts on users' representations: a cognitive and linguistic analysis based on 25 technical documents.

    PubMed

    Eyrolle, Hélène; Virbel, Jacques; Lemarié, Julie

    2008-03-01

    Based on previous research in the field of cognitive psychology, highlighting the facilitatory effects of titles on several text-related activities, this paper looks at the extent to which titles reflect text content. An exploratory study of real-life technical documents investigated the content of their Subject lines, which linguistic analyses had led us to regard as titles. The study showed that most of the titles supplied by the writers failed to represent the documents' contents and that most users failed to detect this lack of validity.

  18. A Multiresolution Experiment to Enable Impacts of High Fidelity Environments on Unmanned Ground Vehicle Representation

    DTIC Science & Technology

    2009-06-01

    Center Geotechnical and Structures Laboratory (ERDC-GSL). Their contributions include the technical integration work of ANVEL , OneSAF, and MATREX...6  3.1  ANVEL Overview...15  4.4.3.  OneSAF Tasks ................................................................................. 16  4.4.4.  OneSAF/ ANVEL Scenario Execution

  19. Representing Practice: Practice Models, Patterns, Bundles

    ERIC Educational Resources Information Center

    Falconer, Isobel; Finlay, Janet; Fincher, Sally

    2011-01-01

    This article critiques learning design as a representation for sharing and developing practice, based on synthesis of three projects. Starting with the findings of the Mod4L Models of Practice project, it argues that the technical origins of learning design, and the consequent focus on structure and sequence, limit its usefulness for sharing…

  20. Construction and Evaluation of Animated Teachable Agents

    ERIC Educational Resources Information Center

    Bodenheimer, Bobby; Williams, Betsy; Kramer, Mattie Ruth; Viswanath, Karun; Balachandran, Ramya; Belynne, Kadira; Biswas, Gautam

    2009-01-01

    This article describes the design decisions, technical approach, and evaluation of the animation and interface components for an agent-based system that allows learners to learn by teaching. Students learn by teaching an animated agent using a visual representation. The agent can answer questions about what she has been taught and take quizzes.…

  1. New Communications Technology and Distance Education: Implications for Commonwealth Countries of the South. Papers on Information Technology No. 239.

    ERIC Educational Resources Information Center

    Bates, A. W.

    This review of the technical possibilities of audio, television, computing, and combination media addresses the main factors influencing decisions about each technology's suitability for distance teaching, including access, costs, symbolic representation, student control, teacher control, existing structures, learning skills to be developed, and…

  2. Balancing the Building Team: Gender Issues in the Building Professions. Report 284.

    ERIC Educational Resources Information Center

    Court, Gill; Moralee, Janet

    The following activities were conducted to identify strategies for improving the representation of women in professional, managerial, and technical occupations in the United Kingdom's building industry: literature review; mail questionnaire to which 468 (63.8%) of the 733 women contacted responded; group discussions with 32 women employed in the…

  3. TORPEDO: Networked Access to Full-Text and Page-Image Representations of Physics Journals and Technical Reports.

    ERIC Educational Resources Information Center

    Atkinson, Roderick D.; Stackpole, Laurie E.

    1995-01-01

    The Naval Research Laboratory (NRL) Library and the American Physical Society (APS) are experimenting with electronically disseminating journals and reports in a project called TORPEDO (The Optical Retrieval Project: Electronic Documents Online). Scanned journals and reports are converted to ASCII, then attached to bibliographic information, and…

  4. Pretechnical Post Secondary Remedial Programs Training Institute. Final Report.

    ERIC Educational Resources Information Center

    Tompkins, Jack E.

    To promote and accelerate the creation of remedial training programs in technical institutes and community colleges, 46 participants from a wide geographic representation and from varied positions were selected to attend a 5-day training institute. Presentations by consultants and group discussions were utilized to meet the objects of developing a…

  5. Police Reform, Task Force Rhetoric, and Traces of Dissent: Rethinking Consensus-as-Outcome in Collaborative Writing Situations

    ERIC Educational Resources Information Center

    Knievel, Michael

    2008-01-01

    Pedagogical and scholarly representations of collaborative writing and knowledge construction in technical communication have traditionally recognized consensus as the logical outcome of collaborative work, even as scholars and teachers have acknowledged the value of conflict and "dissensus" in the process of collaborative knowledge…

  6. Tyche 3.0 Simulation Engine Project Review

    DTIC Science & Technology

    2014-10-09

    la Reine (en droit du Canada), telle que représentée par le ministre de la Défense nationale, 2014 DRDC-RDDC-2014-C220 Page 2 RECORD OF...During the technical evaluation, it was found that the representation of internal data as class objects and collections had performance drawbacks and

  7. Sequential Processes in Image Generation: An Objective Measure. Technical Report #6.

    ERIC Educational Resources Information Center

    Kosslyn, Stephen M.; And Others

    This paper investigates the processes by which visual mental images--the precept-like short-term memory representations--are created from information stored in long-term memory. It also presents a new method for studying image generation. Three experiments were conducted using college students as subjects. In the first experiment, a Podgorny and…

  8. Writing in the Field of Education: The "Inquiry" on Portuguese Schools (1875)

    ERIC Educational Resources Information Center

    Magalhães, Justino

    2016-01-01

    Writing is basically representation. Ways of writing have evolved and become adapted to circumstances and needs at material, symbolic, formal, technical, social and cultural levels. Moreover, there are forms of writing within educational writing. In the history of educational writing, it is possible to identify and distinguish educational writing,…

  9. Representing System Behaviors and Expert Behaviors for Intelligent Tutoring. Technical Report No. 108.

    ERIC Educational Resources Information Center

    Towne, Douglas M.; And Others

    Simulation-based software tools that can infer system behaviors from a deep model of the system have the potential for automatically building the semantic representations required to support intelligent tutoring in fault diagnosis. The Intelligent Maintenance Training System (IMTS) is such a resource, designed for use in training troubleshooting…

  10. 7 CFR 632.23 - Access to land unit and records.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... land unit and records. Any authorized NRCS employee or agent is to have the right of access to land under application or contract and the right to examine any program records to ascertain the accuracy of any representations made in the application or contract. This includes the right to furnish technical...

  11. Reference Manual for Machine-Readable Bibliographic Descriptions.

    ERIC Educational Resources Information Center

    Martin, M. D., Comp.

    UNESCO, in cooperation with several other organizations, has produced a manual, the scope and purpose of which has been to define, for most types of scientific and technical literature, a set of data elements which will constitute an adequate bibliographic citation, and to define the representation of these data elements as they should appear in a…

  12. Nanotechnology Standardization Activities – Support of U.S. Representation on ISO/TC 229 Nanotechnologies

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Benko, Heather

    In carrying out its responsibilities on behalf of the United States, ANSI provides comprehensive, administrative support and expertise on international protocols and procedures to: (1) the U.S. Technical Advisory Group (TAG) to the International Organization for Standardization’s (ISO) Technical Committee (TC) 229 Nanotechnologies, and (2) the corresponding U.S. TAG Working Groups tasked with formulating U.S. positions on topics relevant to nanotechnology standardization. Additionally, secretariat and procedural support is provided for the ISO/TC 229 WG 3 on health, safety and environment, for which the United States was assigned leadership by the participating national body members of ISO/TC 229. As the officialmore » entity that serves as the U.S. representative to ISO, ANSI provides not only expert coordination of U.S. positions and representation at ISO but also strategic direction, advice and procedural expertise to facilitate navigation of international issues to promote U.S. positions for incorporation into the ISO/TC 229 program of work necessary to support U.S. objectives.« less

  13. [Vascular lesions of vocal folds--part 1: horizontal vascular lesions].

    PubMed

    Voigt-Zimmermann, S; Arens, C

    2014-12-01

    In recent decades, the endoscopic methods and technologies for laryngeal examination have improved so much that not only epithelial changes, but also vascular changes are recognizable at earlier stages. When comparing newer and older literature, the associated increasingly differentiated descriptions of such visible vascular changes of the vocal folds lead to terminological blurring and shifts of meaning. This complicates the technical-scientific discourse. The aim of the present work is a theoretical and conceptual clarification of early vascular changes of vocal folds. Horizontal changes of benigne vascular diseases, e. g. vessel ectasia, meander, increasing number and branching of vessels, change of direction may develop in to manifest vascular lesions, like varicosis, polyps and in case of ruptures to haemorrhages of vocal folds. These beginning and reversible vascular changes, when early detected and discussed basing on etiological knowledge, may lead to more differentiated prognostic statements and adequate therapeutic decisions, e. g. phonosurgery, functional voice therapy, voice hygiene and voice rest. Vertical vascular changes, like vessel loops, occur primarily in laryngeal papilloma, pre-cancerous and cancerous changes of the vocal folds. Already in small cancerous lesions of the vocal folds the vascular architecture is completely destroyed. © Georg Thieme Verlag KG Stuttgart · New York.

  14. Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins.

    PubMed

    Delic, Marizela; Göngrich, Rebecca; Mattanovich, Diethard; Gasser, Brigitte

    2014-07-20

    Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.

  15. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    PubMed

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  16. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

    PubMed Central

    Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-01-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  17. Technical paper contest for women 1992. Space challenges: Earth and beyond

    NASA Technical Reports Server (NTRS)

    Orans, Robin (Editor)

    1993-01-01

    Two of the major concerns of the NASA Ames Research Center (NASA ARC) Advisory Committee for Women (ACW) are that recruitment of women scientists, engineers, and technicians needs to increase and that barriers to advancement need to be removed for improved representation of women in middle and upper management and scientific positions. One strategy that addressed this concern was the ACW sponsorship of a Technical Paper Contest for Women at Ames Research Center. Other sponsors of the Contest were the Ames Equal Opportunity Council and the Ames Contractor Council. The Technical Paper Contest for Women greatly increased the visibility of both the civil service women and the women who work for contractors at Ames. The women had the opportunity to hone their written and oral presentation skills. Networking among Ames women increased.

  18. Statistical mechanics of simple models of protein folding and design.

    PubMed Central

    Pande, V S; Grosberg, A Y; Tanaka, T

    1997-01-01

    It is now believed that the primary equilibrium aspects of simple models of protein folding are understood theoretically. However, current theories often resort to rather heavy mathematics to overcome some technical difficulties inherent in the problem or start from a phenomenological model. To this end, we take a new approach in this pedagogical review of the statistical mechanics of protein folding. The benefit of our approach is a drastic mathematical simplification of the theory, without resort to any new approximations or phenomenological prescriptions. Indeed, the results we obtain agree precisely with previous calculations. Because of this simplification, we are able to present here a thorough and self contained treatment of the problem. Topics discussed include the statistical mechanics of the random energy model (REM), tests of the validity of REM as a model for heteropolymer freezing, freezing transition of random sequences, phase diagram of designed ("minimally frustrated") sequences, and the degree to which errors in the interactions employed in simulations of either folding and design can still lead to correct folding behavior. Images FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 6 PMID:9414231

  19. The Use of Red Green Blue Air Mass Imagery to Investigate the Role of Stratospheric Air in a Non-convective Wind Event

    NASA Technical Reports Server (NTRS)

    Berndt, E. B.; Zavodsky, B. T.; Jedlovec, G. J.; Molthan, A. L.

    2013-01-01

    Non-convective wind events commonly occur with passing extratropical cyclones and have significant societal and economic impacts. Since non-convective winds often occur in the absence of specific phenomena such as a thunderstorm, tornado, or hurricane, the public are less likely to heed high wind warnings and continue daily activities. Thus non-convective wind events result in as many fatalities as straight line thunderstorm winds. One physical explanation for non-convective winds includes tropopause folds. Improved model representation of stratospheric air and associated non-convective wind events could improve non-convective wind forecasts and associated warnings. In recent years, satellite data assimilation has improved skill in forecasting extratropical cyclones; however errors still remain in forecasting the position and strength of extratropical cyclones as well as the tropopause folding process. The goal of this study is to determine the impact of assimilating satellite temperature and moisture retrieved profiles from hyperspectral infrared (IR) sounders (i.e. Atmospheric Infrared Sounder (AIRS), Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI)) on the model representation of the tropopause fold and an associated high wind event that impacted the Northeast United States on 09 February 2013. Model simulations using the Advanced Research Weather Research and Forecasting Model (ARW) were conducted on a 12-km grid with cycled data assimilation mimicking the operational North American Model (NAM). The results from the satellite assimilation run are compared to a control experiment (without hyperspectral IR retrievals), Modern Era-Retrospective Analysis for Research and Applications (MERRA) reanalysis, and Rapid Refresh analyses.

  20. Genetic algorithms for protein threading.

    PubMed

    Yadgari, J; Amir, A; Unger, R

    1998-01-01

    Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible. As a result, in the last few years researchers have started to address the "inverse folding problem": Identifying and aligning a sequence to the fold with which it is most compatible, a process known as "threading". In two meetings in which protein folding predictions were objectively evaluated, it became clear that threading as a concept promises a real breakthrough, but that much improvement is still needed in the technique itself. Threading is a NP-hard problem, and thus no general polynomial solution can be expected. Still a practical approach with demonstrated ability to find optimal solutions in many cases, and acceptable solutions in other cases, is needed. We applied the technique of Genetic Algorithms in order to significantly improve the ability of threading algorithms to find the optimal alignment of a sequence to a structure, i.e. the alignment with the minimum free energy. A major progress reported here is the design of a representation of the threading alignment as a string of fixed length. With this representation validation of alignments and genetic operators are effectively implemented. Appropriate data structure and parameters have been selected. It is shown that Genetic Algorithm threading is effective and is able to find the optimal alignment in a few test cases. Furthermore, the described algorithm is shown to perform well even without pre-definition of core elements. Existing threading methods are dependent on such constraints to make their calculations feasible. But the concept of core elements is inherently arbitrary and should be avoided if possible. While a rigorous proof is hard to submit yet an, we present indications that indeed Genetic Algorithm threading is capable of finding consistently good solutions of full alignments in search spaces of size up to 10(70).

  1. The Impact of the Assimilation of Hyperspectral Infrared Retrieved Profiles on Advanced Weather and Research Model Simulations of a Non-Convective Wind Event

    NASA Technical Reports Server (NTRS)

    Berndt, Emily; Zavodsky, Bradley; Jedlovec, Gary; Elmer, Nicholas

    2013-01-01

    Non-convective wind events commonly occur with passing extratropical cyclones and have significant societal and economic impacts. Since non-convective winds often occur in the absence of specific phenomena such as a thunderstorm, tornado, or hurricane, the public are less likely to heed high wind warnings and continue daily activities. Thus non-convective wind events result in as many fatalities as straight line thunderstorm winds. One physical explanation for non-convective winds includes tropopause folds. Improved model representation of stratospheric air and associated non-convective wind events could improve non-convective wind forecasts and associated warnings. In recent years, satellite data assimilation has improved skill in forecasting extratropical cyclones; however errors still remain in forecasting the position and strength of extratropical cyclones as well as the tropopause folding process. The goal of this study is to determine the impact of assimilating satellite temperature and moisture retrieved profiles from hyperspectral infrared (IR) sounders (i.e. Atmospheric Infrared Sounder (AIRS), Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI)) on the model representation of the tropopause fold and an associated high wind event that impacted the Northeast United States on 09 February 2013. Model simulations using the Advanced Research Weather Research and Forecasting Model (ARW) were conducted on a 12-km grid with cycled data assimilation mimicking the operational North American Model (NAM). The results from the satellite assimilation run are compared to a control experiment (without hyperspectral IR retrievals), Modern Era-Retrospective Analysis for Research and Applications (MERRA) reanalysis, and Rapid Refresh analyses.

  2. Impact of the Assimilation of Hyperspectral Infrared Retrieved Profiles on Advanced Weather and Research Model Simulations of a Non-Convective Wind Event

    NASA Technical Reports Server (NTRS)

    Berndt, E. B.; Zavodsky, B. T.; Folmer, M. J.; Jedlovec, G. J.

    2014-01-01

    Non-convective wind events commonly occur with passing extratropical cyclones and have significant societal and economic impacts. Since non-convective winds often occur in the absence of specific phenomena such as a thunderstorm, tornado, or hurricane, the public are less likely to heed high wind warnings and continue daily activities. Thus non-convective wind events result in as many fatalities as straight line thunderstorm winds. One physical explanation for non-convective winds includes tropopause folds. Improved model representation of stratospheric air and associated non-convective wind events could improve non-convective wind forecasts and associated warnings. In recent years, satellite data assimilation has improved skill in forecasting extratropical cyclones; however errors still remain in forecasting the position and strength of extratropical cyclones as well as the tropopause folding process. The goal of this study is to determine the impact of assimilating satellite temperature and moisture retrieved profiles from hyperspectral infrared (IR) sounders (i.e. Atmospheric Infrared Sounder (AIRS), Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI)) on the model representation of the tropopause fold and an associated high wind event that impacted the Northeast United States on 09 February 2013. Model simulations using the Advanced Research Weather Research and Forecasting Model (ARW) were conducted on a 12-km grid with cycled data assimilation mimicking the operational North American Model (NAM). The results from the satellite assimilation run are compared to a control experiment (without hyperspectral IR retrievals), 32-km North American Regional Reanalysis (NARR) interpolated to a 12-km grid, and 13-km Rapid Refresh analyses.

  3. Impact of the Assimilation of Hyperspectral Infrared Retrieved Profiles on Advanced Weather and Research Model Simulations of a Non-Convective Wind Event

    NASA Technical Reports Server (NTRS)

    Berndt, E. B.; Zavodsky, B. T.; Jedlovec, G. J.

    2014-01-01

    Non-convective wind events commonly occur with passing extratropical cyclones and have significant societal and economic impacts. Since non-convective winds often occur in the absence of specific phenomena such as a thunderstorm, tornado, or hurricane, the public are less likely to heed high wind warnings and continue daily activities. Thus non-convective wind events result in as many fatalities as straight line thunderstorm winds. One physical explanation for non-convective winds includes tropopause folds. Improved model representation of stratospheric air and associated non-convective wind events could improve non-convective wind forecasts and associated warnings. In recent years, satellite data assimilation has improved skill in forecasting extratropical cyclones; however errors still remain in forecasting the position and strength of extratropical cyclones as well as the tropopause folding process. The goal of this study is to determine the impact of assimilating satellite temperature and moisture retrieved profiles from hyperspectral infrared (IR) sounders (i.e. Atmospheric Infrared Sounder (AIRS), Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI)) on the model representation of the tropopause fold and an associated high wind event that impacted the Northeast United States on 09 February 2013. Model simulations using the Advanced Research Weather Research and Forecasting Model (ARW) were conducted on a 12-km grid with cycled data assimilation mimicking the operational North American Model (NAM). The results from the satellite assimilation run are compared to a control experiment (without hyperspectral IR retrievals), Modern Era-Retrospective Analysis for Research and Applications (MERRA) reanalysis, and Rapid Refresh analyses.

  4. Clinical Investigation Program: Annual Progress Report

    DTIC Science & Technology

    1992-09-30

    Academy of Surgical Research, Chicago, Illinois; Yucatan Miniature Swine as a Model System for the Studyt of Vocal Fold Vibratory Function; 6th Annual...34(14)e". (15) Study Objective: Compare two enteral formulas in respect to nutritional aspects. (16) Technical Approach: Protocol will take place in

  5. Discretized torsional dynamics and the folding of an RNA chain.

    PubMed

    Fernández, A; Salthú, R; Cendra, H

    1999-08-01

    The aim of this work is to implement a discrete coarse codification of local torsional states of the RNA chain backbone in order to explore the long-time limit dynamics and ultimately obtain a coarse solution to the RNA folding problem. A discrete representation of the soft-mode dynamics is turned into an algorithm for a rough structure prediction. The algorithm itself is inherently parallel, as it evaluates concurrent folding possibilities by pattern recognition, but it may be implemented in a personal computer as a chain of perturbation-translation-renormalization cycles performed on a binary matrix of local topological constraints. This requires suitable representational tools and a periodic quenching of the dynamics for system renormalization. A binary coding of local topological constraints associated with each structural motif is introduced, with each local topological constraint corresponding to a local torsional state. This treatment enables us to adopt a computation time step far larger than hydrodynamic drag time scales. Accordingly, the solvent is no longer treated as a hydrodynamic drag medium. Instead we incorporate its capacity for forming local conformation-dependent dielectric domains. Each translation of the matrix of local topological constraints (LTM's) depends on the conformation-dependent local dielectric created by a confined solvent. Folding pathways are resolved as transitions between patterns of locally encoded structural signals which change within the 1 ns-100 ms time scale range. These coarse folding pathways are generated by a search at regular intervals for structural patterns in the LTM. Each pattern is recorded as a base-pairing pattern (BPP) matrix, a consensus-evaluation operation subject to a renormalization feedback loop. Since several mutually conflicting consensus evaluations might occur at a given time, the need arises for a probabilistic approach appropriate for an ensemble of RNA molecules. Thus, a statistical dynamics of consensus formation is determined by the time evolution of the base pairing probability matrix. These dynamics are generated for a functional RNA molecule, a representative of the so-called group I ribozymes, in order to test the model. The resulting ensemble of conformations is sharply peaked and the most probable structure features the predominance of all phylogenetically conserved intrachain helices tantamount to ribozyme function. Furthermore, the magnesium-aided cooperativity that leads to the shaping of the catalytic core is elucidated. Once the predictive folding algorithm has been implemented, the validity of the so-called "adiabatic approximation" is tested. This approximation requires that conformational microstates be lumped up into BPP's which are treated as quasiequilibrium states, while folding pathways are coarsely represented as sequences of BPP transitions. To test the validity of this adiabatic ansatz, a computation of the coarse Shannon information entropy sigma associated to the specific partition of conformation space into BPP's is performed taking into account the LTM evolution and contrasted with the adiabatic computation. The results reveal a subordination of torsional microstate dynamics to BPP transitions within time scales relevant to folding. This adiabatic entrainment in the long-time limit is thus identified as responsible for the expediency of the folding process.

  6. Distant failure prediction for early stage NSCLC by analyzing PET with sparse representation

    NASA Astrophysics Data System (ADS)

    Hao, Hongxia; Zhou, Zhiguo; Wang, Jing

    2017-03-01

    Positron emission tomography (PET) imaging has been widely explored for treatment outcome prediction. Radiomicsdriven methods provide a new insight to quantitatively explore underlying information from PET images. However, it is still a challenging problem to automatically extract clinically meaningful features for prognosis. In this work, we develop a PET-guided distant failure predictive model for early stage non-small cell lung cancer (NSCLC) patients after stereotactic ablative radiotherapy (SABR) by using sparse representation. The proposed method does not need precalculated features and can learn intrinsically distinctive features contributing to classification of patients with distant failure. The proposed framework includes two main parts: 1) intra-tumor heterogeneity description; and 2) dictionary pair learning based sparse representation. Tumor heterogeneity is initially captured through anisotropic kernel and represented as a set of concatenated vectors, which forms the sample gallery. Then, given a test tumor image, its identity (i.e., distant failure or not) is classified by applying the dictionary pair learning based sparse representation. We evaluate the proposed approach on 48 NSCLC patients treated by SABR at our institute. Experimental results show that the proposed approach can achieve an area under the characteristic curve (AUC) of 0.70 with a sensitivity of 69.87% and a specificity of 69.51% using a five-fold cross validation.

  7. Sparse Representation of Smooth Linear Operators

    DTIC Science & Technology

    1990-08-01

    8217,ns, m = 0,2 ,...,I where Sm is defined by Eq. (2.3). We further define Rk, 2 to be the orthogonal n k,2complement of S, 2 in S,+ 1, smk EDR ,2 Sk,2 1...1987. [9] L. Greengard and J. Strain . The fast Gauss transform. Technical report, Department of Computer Science, Yale University, 1989. [10] A

  8. Differences in Writers' Initial Task Representations. Technical Report No. 35.

    ERIC Educational Resources Information Center

    Carey, Linda; And Others

    An exploratory study investigated how writers represent their task to themselves before beginning to write. Using data from verbal protocols, the initial plans of 12 writers (5 experts and 7 student writers) who were working on an expository writing task were examined. The protocols were coded for types of planning. Independent measures of the…

  9. Review of Winograd and Flores'"Understanding Computers and Cognition": A Favorable Interpretation. ONR Technical Report #21.

    ERIC Educational Resources Information Center

    Clancey, William J.

    Artificial Intelligence researchers and cognitive scientists commonly believe that thinking involves manipulating representations. Thinking involves search, inference, and making choices. This is how we model reasoning and what goes on in the brain is similar. Winograd and Flores present a radically different view, claiming that our knowledge is…

  10. Neighborhoods of Words in the Mental Lexicon. Research on Speech Perception. Technical Report No. 6.

    ERIC Educational Resources Information Center

    Luce, Paul A.

    A study employed computational and experimental methods to address a number of issues related to the representation and structural organization of spoken words in the mental lexicon. Using a computerized lexicon consisting of phonetic transcriptions of 20,000 words, "similarity neighborhoods" for each of the transcriptions were computed.…

  11. Occupational BAB Norms. Technical Report.

    ERIC Educational Resources Information Center

    Sung, Yong H.; Dong, Hei-Ki

    The Ball Aptitude Battery (BAB) is a multiple ability test battery of specific work skills. It is designed for use in career counseling and personnel selection. The 14 BAB tests yield 16 ability scores: Clerical, Idea Fluency, Tonal Memory, Pitch Descrimination, Inductive Reasoning, Word Association, Writing Speed, Paper Folding, Vocabulary,…

  12. Space station automation of common module power management and distribution, volume 2

    NASA Technical Reports Server (NTRS)

    Ashworth, B.; Riedesel, J.; Myers, C.; Jakstas, L.; Smith, D.

    1990-01-01

    The new Space Station Module Power Management and Distribution System (SSM/PMAD) testbed automation system is described. The subjects discussed include testbed 120 volt dc star bus configuration and operation, SSM/PMAD automation system architecture, fault recovery and management expert system (FRAMES) rules english representation, the SSM/PMAD user interface, and the SSM/PMAD future direction. Several appendices are presented and include the following: SSM/PMAD interface user manual version 1.0, SSM/PMAD lowest level processor (LLP) reference, SSM/PMAD technical reference version 1.0, SSM/PMAD LLP visual control logic representation's (VCLR's), SSM/PMAD LLP/FRAMES interface control document (ICD) , and SSM/PMAD LLP switchgear interface controller (SIC) ICD.

  13. In the public interest: assessing expert and stakeholder influence in public deliberation about biobanks.

    PubMed

    MacLean, Samantha; Burgess, Michael M

    2010-07-01

    Providing technical and experiential information without overwhelming participants' perspectives presents a major challenge to public involvement in policy decisions. This article reports the design and analysis of a case study on incorporating expert and stakeholder knowledge without including them as deliberators, while supporting deliberative participants' ability to introduce and critically assess different perspectives. Analysis of audio-recorded deliberations illustrates how expert and stakeholder knowledge was cited, criticized and incorporated into deliberations. In conclusion, separating experts and stakeholders from deliberations may be an important prima facie principle when the goal is to enhance citizen representation on technical issues and related policy.

  14. Techniques for capturing expert knowledge - An expert systems/hypertext approach

    NASA Technical Reports Server (NTRS)

    Lafferty, Larry; Taylor, Greg; Schumann, Robin; Evans, Randy; Koller, Albert M., Jr.

    1990-01-01

    The knowledge-acquisition strategy developed for the Explosive Hazards Classification (EHC) Expert System is described in which expert systems and hypertext are combined, and broad applications are proposed. The EHC expert system is based on rapid prototyping in which primary knowledge acquisition from experts is not emphasized; the explosive hazards technical bulletin, technical guidance, and minimal interviewing are used to develop the knowledge-based system. Hypertext is used to capture the technical information with respect to four issues including procedural, materials, test, and classification issues. The hypertext display allows the integration of multiple knowlege representations such as clarifications or opinions, and thereby allows the performance of a broad range of tasks on a single machine. Among other recommendations, it is suggested that the integration of hypertext and expert systems makes the resulting synergistic system highly efficient.

  15. Role of National Immunization Technical Advisory Group on improvement of immunization programmes in the Islamic Republic of Iran.

    PubMed

    Zahraei, Seyed Mohsen; Marandi, Alireza; Sadrizadeh, Bijan; Gouya, Mehdi Mohammad; Rezaei, Parviz; Vazirian, Parviz; Yaghini, Fatheme

    2010-04-19

    The National Immunization Technical Advisory Group (NITAG) was established in Iran in 1982 and has made many important technical recommendations (e.g., regarding polio eradication, introduction of new vaccines, organizing special studies) that have contributed to a dramatic decline in vaccine preventable disease burden. The NITAG consists of experts from the Ministry of Health and Medical Education (MOHME), vaccine manufacturers, and medical universities with national Expanded Program of Immunization (EPI) staff serving as the secretariat. It is not completely independent from MOHME or EPI. It meets on a quarterly basis, and publishes national guidelines and immunization schedules that are updated regularly. Although primarily an advisory body, representation from MOHME members, including the EPI manager, ensures almost universal implementation of NITAG recommendations. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Mice with a "monoclonal nose": perturbations in an olfactory map impair odor discrimination.

    PubMed

    Fleischmann, Alexander; Shykind, Benjamin M; Sosulski, Dara L; Franks, Kevin M; Glinka, Meredith E; Mei, Dan Feng; Sun, Yonghua; Kirkland, Jennifer; Mendelsohn, Monica; Albers, Mark W; Axel, Richard

    2008-12-26

    We have altered the neural representation of odors in the brain by generating a mouse with a "monoclonal nose" in which greater than 95% of the sensory neurons express a single odorant receptor, M71. As a consequence, the frequency of sensory neurons expressing endogenous receptor genes is reduced 20-fold. We observe that these mice can smell, but odor discrimination and performance in associative olfactory learning tasks are impaired. However, these mice cannot detect the M71 ligand acetophenone despite the observation that virtually all sensory neurons and glomeruli are activated by this odor. The M71 transgenic mice readily detect other odors in the presence of acetophenone. These observations have implications for how receptor activation in the periphery is represented in the brain and how these representations encode odors.

  17. 10-MWe solar-thermal central-receiver pilot plant: collector subsystem foundation construction. Revision No. 1

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1979-12-18

    Bid documents are provided for the construction of the collector subsystem foundation of the Barstow Solar Pilot Plant, including invitation to bid, bid form, representations and certifications, construction contract, and labor standards provisions of the Davis-Bacon Act. Instructions to bidders, general provisions and general conditions are included. Technical specifications are provided for the construction. (LEW)

  18. A Multimedia Knowledge Representation for an "Intelligent" Computerized Tutor. Technical Report No. 142.

    ERIC Educational Resources Information Center

    Baggett, Patricia; Ehrenfeucht, Andrzej

    The intended end product of the research project described is an "intelligent" multimedia tutoring system for procedural tasks, in particular, the repair of physical objects. This paper presents the data structure that will be used, i.e., a graph with five types of nodes (mental, abstract, motoric or action, visual, and verbal) and two types of…

  19. A Discussion of "Nadia": A Case Study of Extraordinary Drawing Ability in an Autistic Child. Technical Report No. 9.

    ERIC Educational Resources Information Center

    Pariser, David A.

    The case study of Nadia, an autistic child, documents the phenomenally accurate drawings she made. Nadia's precocious drawing capacity raises questions about the drawing hypothesis adhered to by F. Goodenough and D. B. Harris and Gestalt theories of perception and representation. The argument is made that Nadia drew realistically because she…

  20. An Integrated Textbook, Video, and Software Environment for Novice and Expert Prolog Programmers. Technical Report No. 23.

    ERIC Educational Resources Information Center

    Eisenstadt, Marc; Brayshaw, Mike

    This paper describes a Prolog execution model which serves as the uniform basis of textbook material, video-based teaching material, and an advanced graphical user interface for Prolog programmers. The model, based upon an augmented AND/OR tree representation of Prolog programs, uses an enriched "status box" in place of the traditional…

  1. Representation of dental care and oral health in children's drawings.

    PubMed

    Torriani, D D; Goettems, M L; Cademartori, M G; Fernandez, R R; Bussoletti, D M

    2014-06-01

    Paediatric dentistry requires knowledge of preventive measures, restorative skills and an understanding of child development. This exploratory, descriptive and qualitative study has analysed children's drawings regarding their perception of dental treatment and oral health. Children aged from six to ten years attending a dental school for treatment were randomly invited to create a drawing about 'dental treatment' and 'oral health'. Verbal expressions made by the children whilst drawing were also recorded and attached to the drawings. These representations were analysed and categorised using Vygotsky postulations for context reading. During the drawing analysis different themes emerged. Five categories regarding perceptions of dental treatment were identified: personal relationship; power relation; trauma; childhood resistance; and contextualisation of dental care in the child's life. Three categories relating to oral health were determined: dichotomy of health/sickness; ludic representation of health; and sickness seen as a process. Drawing can be used to understand children's emotions and expectations about dental treatment. Besides possessing technical skills and scientific knowledge, dentists have an obligation to pay attention to children's feelings.

  2. Analysis of technical alternative technologies for the development of context-driven composable environmental representations for JSB

    NASA Astrophysics Data System (ADS)

    Hummel, John R.; Bergenthal, Jeff J.; Seng, William F.; Moulton, Joseph R., Jr.; Prager, S. D.

    2004-08-01

    The Joint Synthetic Battlespace for the Air Force (JSB-AF) is being developed to provide realistic representations of friendly and threat capabilities and the natural environmental conditions to support a variety of Department of Defense missions including training, mission rehearsal, decision support, acquisition, deployment, employment, operations, and the development of Courses of Action. This paper addresses three critical JSB issues associated with providing environ-mental representations to Modeling and Simulation (M&S) applications. First, how should the requirements for envi-ronmental functionality in a JSB-AF application be collected, analyzed, and used to define an Authoritative Environ-mental Representation (AER)? Second, how can JSB-AF AERs be generated? Third, once an AER has been generated, how should it be "served up" to the JSB-AF components? Our analyses of these issues will be presented from a general M&S perspective, with examples given from a JSB-AF centered view. In the context of this effort, the term "representa-tions" is meant to incorporate both basic environmental "data" (e.g., temperature, pressure, slope, elevation, etc.) and "effects", properties that can be derived from these data using physics-based models or empirical relationship from the fundamental data (e.g., extinction coefficients, radiance, soil moisture strength, etc.) We present a state-of-the-art review of the existing processes and technologies that address these questions.

  3. Summary of the 1st International Workshop on Networked Reality in Telecommunication

    NASA Astrophysics Data System (ADS)

    Davis, T.

    1994-05-01

    s of workshop papers are presented. Networked reality refers to the array of technologies and services involved in collecting a representation of reality at one location and using it to reconstruct an artificial representation of that reality at a remote location. The term encompasses transmission of the required information between the sites, and also includes the psychological, cultural, and legal implications of introducing derived communication systems. Networked reality is clearly derived from the emerging virtual reality technology base but is intended to go beyond the latter to include its integration with the required telecommunication technologies. A noteworthy feature of the Networked Reality '94 technical program is the extent of emphasis on social (particularly medical) impacts of the technology.

  4. Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

    PubMed Central

    Woodside, Michael T.; Block, Steven M.

    2015-01-01

    Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

  5. Discrete variable representation in electronic structure theory: quadrature grids for least-squares tensor hypercontraction.

    PubMed

    Parrish, Robert M; Hohenstein, Edward G; Martínez, Todd J; Sherrill, C David

    2013-05-21

    We investigate the application of molecular quadratures obtained from either standard Becke-type grids or discrete variable representation (DVR) techniques to the recently developed least-squares tensor hypercontraction (LS-THC) representation of the electron repulsion integral (ERI) tensor. LS-THC uses least-squares fitting to renormalize a two-sided pseudospectral decomposition of the ERI, over a physical-space quadrature grid. While this procedure is technically applicable with any choice of grid, the best efficiency is obtained when the quadrature is tuned to accurately reproduce the overlap metric for quadratic products of the primary orbital basis. Properly selected Becke DFT grids can roughly attain this property. Additionally, we provide algorithms for adopting the DVR techniques of the dynamics community to produce two different classes of grids which approximately attain this property. The simplest algorithm is radial discrete variable representation (R-DVR), which diagonalizes the finite auxiliary-basis representation of the radial coordinate for each atom, and then combines Lebedev-Laikov spherical quadratures and Becke atomic partitioning to produce the full molecular quadrature grid. The other algorithm is full discrete variable representation (F-DVR), which uses approximate simultaneous diagonalization of the finite auxiliary-basis representation of the full position operator to produce non-direct-product quadrature grids. The qualitative features of all three grid classes are discussed, and then the relative efficiencies of these grids are compared in the context of LS-THC-DF-MP2. Coarse Becke grids are found to give essentially the same accuracy and efficiency as R-DVR grids; however, the latter are built from explicit knowledge of the basis set and may guide future development of atom-centered grids. F-DVR is found to provide reasonable accuracy with markedly fewer points than either Becke or R-DVR schemes.

  6. Advanced Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Technical Exchange Meeting

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Curtis

    2013-09-01

    During FY13, the INL developed an advanced SMR PRA framework which has been described in the report Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Detailed Technical Framework Specification, INL/EXT-13-28974 (April 2013). In this framework, the various areas are considered: Probabilistic models to provide information specific to advanced SMRs Representation of specific SMR design issues such as having co-located modules and passive safety features Use of modern open-source and readily available analysis methods Internal and external events resulting in impacts to safety All-hazards considerations Methods to support the identification of design vulnerabilities Mechanistic and probabilistic data needs to support modelingmore » and tools In order to describe this framework more fully and obtain feedback on the proposed approaches, the INL hosted a technical exchange meeting during August 2013. This report describes the outcomes of that meeting.« less

  7. Quaternionic representation of the genetic code.

    PubMed

    Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

    2016-03-01

    A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Perceptual Learning Selectively Refines Orientation Representations in Early Visual Cortex

    PubMed Central

    Jehee, Janneke F.M.; Ling, Sam; Swisher, Jascha D.; van Bergen, Ruben S.; Tong, Frank

    2013-01-01

    Although practice has long been known to improve perceptual performance, the neural basis of this improvement in humans remains unclear. Using fMRI in conjunction with a novel signal detection-based analysis, we show that extensive practice selectively enhances the neural representation of trained orientations in the human visual cortex. Twelve observers practiced discriminating small changes in the orientation of a laterally presented grating over 20 or more daily one-hour training sessions. Training on average led to a two-fold improvement in discrimination sensitivity, specific to the trained orientation and the trained location, with minimal improvement found for untrained orthogonal orientations or for orientations presented in the untrained hemifield. We measured the strength of orientation-selective responses in individual voxels in early visual areas (V1–V4) using signal detection measures, both pre- and post-training. Although the overall amplitude of the BOLD response was no greater after training, practice nonetheless specifically enhanced the neural representation of the trained orientation at the trained location. This training-specific enhancement of orientation-selective responses was observed in the primary visual cortex (V1) as well as higher extrastriate visual areas V2–V4, and moreover, reliably predicted individual differences in the behavioral effects of perceptual learning. These results demonstrate that extensive training can lead to targeted functional reorganization of the human visual cortex, refining the cortical representation of behaviorally relevant information. PMID:23175828

  9. A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

    PubMed Central

    2015-01-01

    Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

  10. A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories.

    PubMed

    Ramanathan, Ravishankar; Muñoz, Victor

    2015-06-25

    Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics.

  11. Nonreplication of an Association of Apolipoprotein E2 With Sinistrality

    PubMed Central

    Piper, Brian J.; Yasen, Alia L.; Taylor, Amy E.; Ruiz, Jonatan R.; Gaynor, J. William; Dayger, Catherine A.; Gonzalez-Gross, Marcela; Kwon, Oh D.; Nilsson, Lars-Göran; Day, Ian N. M.; Raber, Jacob; Miller, Jeremy K.

    2013-01-01

    A recent report found that left-handed adolescents were over three-fold more likely to have an Apolipoprotein (APOE) ε2 allele. This study was unable to replicate this association in young-adults (N=166). A meta-analysis of nine other datasets (N = 360 to 7,559, Power > 0.999) including that of National Alzheimer’s Coordinating Center also failed to find an over-representation of ε2 among left-handers indicating that this earlier outcome was most likely a statistical artifact. PMID:22721421

  12. Product Definition Data Interface (PDDI) Product Specification

    DTIC Science & Technology

    1991-07-01

    syntax of the language gives a precise specification of the data without interpretation of it. M - Constituent Read Block. CSECT - Control Section, the...to conform to the PDDI Access Software’s internal data representation so that it may be further processed. JCL - Job Control Language - IBM language...software development and life cycle * phases. OUALITY CONTROL - The planned and systematic application of all actions (management/technical) necessary to

  13. The Nature of Conceptual Understanding in Biomedicine: The Deep Structure of Complex Ideas and the Development of Misconceptions. Technical Report No. 440.

    ERIC Educational Resources Information Center

    Feltovich, Paul J.; And Others

    This report presents a general framework for studying the acquisition and cognitive representation of biomedical concepts and analyzing the nature and development of misconceptions. The central approach of the report is a selective and highly concentrated analysis of the true nature of clusters of complex concepts and the manner in which they are…

  14. Algorithms in Learning, Teaching, and Instructional Design. Studies in Systematic Instruction and Training Technical Report 51201.

    ERIC Educational Resources Information Center

    Gerlach, Vernon S.; And Others

    An algorithm is defined here as an unambiguous procedure which will always produce the correct result when applied to any problem of a given class of problems. This paper gives an extended discussion of the definition of an algorithm. It also explores in detail the elements of an algorithm, the representation of algorithms in standard prose, flow…

  15. Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins.

    PubMed

    Campagne, F; Weinstein, H

    1999-01-01

    An algorithmic method for drawing residue-based schematic diagrams of proteins on a 2D page is presented and illustrated. The method allows the creation of rendering engines dedicated to a given family of sequences, or fold. The initial implementation provides an engine that can produce a 2D diagram representing secondary structure for any transmembrane protein sequence. We present the details of the strategy for automating the drawing of these diagrams. The most important part of this strategy is the development of an algorithm for laying out residues of a loop that connects to arbitrary points of a 2D plane. As implemented, this algorithm is suitable for real-time modification of the loop layout. This work is of interest for the representation and analysis of data from (1) protein databases, (2) mutagenesis results, or (3) various kinds of protein context-dependent annotations or data.

  16. Proposals for a Dynamic Library. Technical Report.

    ERIC Educational Resources Information Center

    Salton, Gerard

    The current library environment is first examined, and an attempt is made to explain why the standard approaches to the library problem have been less productive than had been anticipated. A new design is then introduced for modern library operations based on a two-fold strategy: on the input side, the widest possible utilization should be made of…

  17. High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion

    USDA-ARS?s Scientific Manuscript database

    Fluorescence in situ hybridization (FISH) has not been readily exploited for physical mapping of molecular markers in plants due to the technical challenge to visualize small single-copy probes. Signal amplification using tyramide (tyr) FISH can increase sensitivity up to 100 fold. We used tyr-FISH ...

  18. Bacterial Artificial Chromosome Libraries for Mouse Sequencing and Functional Analysis

    PubMed Central

    Osoegawa, Kazutoyo; Tateno, Minako; Woon, Peng Yeong; Frengen, Eirik; Mammoser, Aaron G.; Catanese, Joseph J.; Hayashizaki, Yoshihide; de Jong, Pieter J.

    2000-01-01

    Bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) libraries providing a combined 33-fold representation of the murine genome have been constructed using two different restriction enzymes for genomic digestion. A large-insert PAC library was prepared from the 129S6/SvEvTac strain in a bacterial/mammalian shuttle vector to facilitate functional gene studies. For genome mapping and sequencing, we prepared BAC libraries from the 129S6/SvEvTac and the C57BL/6J strains. The average insert sizes for the three libraries range between 130 kb and 200 kb. Based on the numbers of clones and the observed average insert sizes, we estimate each library to have slightly in excess of 10-fold genome representation. The average number of clones found after hybridization screening with 28 probes was in the range of 9–14 clones per marker. To explore the fidelity of the genomic representation in the three libraries, we analyzed three contigs, each established after screening with a single unique marker. New markers were established from the end sequences and screened against all the contig members to determine if any of the BACs and PACs are chimeric or rearranged. Only one chimeric clone and six potential deletions have been observed after extensive analysis of 113 PAC and BAC clones. Seventy-one of the 113 clones were conclusively nonchimeric because both end markers or sequences were mapped to the other confirmed contig members. We could not exclude chimerism for the remaining 41 clones because one or both of the insert termini did not contain unique sequence to design markers. The low rate of chimerism, ∼1%, and the low level of detected rearrangements support the anticipated usefulness of the BAC libraries for genome research. [The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AQ797173–AQ797398.] PMID:10645956

  19. Representation of natural numbers in quantum mechanics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Benioff, Paul

    2001-03-01

    This paper represents one approach to making explicit some of the assumptions and conditions implied in the widespread representation of numbers by composite quantum systems. Any nonempty set and associated operations is a set of natural numbers or a model of arithmetic if the set and operations satisfy the axioms of number theory or arithmetic. This paper is limited to k-ary representations of length L and to the axioms for arithmetic modulo k{sup L}. A model of the axioms is described based on an abstract L-fold tensor product Hilbert space H{sup arith}. Unitary maps of this space onto a physicalmore » parameter based product space H{sup phy} are then described. Each of these maps makes states in H{sup phy}, and the induced operators, a model of the axioms. Consequences of the existence of many of these maps are discussed along with the dependence of Grover's and Shor's algorithms on these maps. The importance of the main physical requirement, that the basic arithmetic operations are efficiently implementable, is discussed. This condition states that there exist physically realizable Hamiltonians that can implement the basic arithmetic operations and that the space-time and thermodynamic resources required are polynomial in L.« less

  20. Extracting Information from Electronic Medical Records to Identify the Obesity Status of a Patient Based on Comorbidities and Bodyweight Measures.

    PubMed

    Figueroa, Rosa L; Flores, Christopher A

    2016-08-01

    Obesity is a chronic disease with an increasing impact on the world's population. In this work, we present a method of identifying obesity automatically using text mining techniques and information related to body weight measures and obesity comorbidities. We used a dataset of 3015 de-identified medical records that contain labels for two classification problems. The first classification problem distinguishes between obesity, overweight, normal weight, and underweight. The second classification problem differentiates between obesity types: super obesity, morbid obesity, severe obesity and moderate obesity. We used a Bag of Words approach to represent the records together with unigram and bigram representations of the features. We implemented two approaches: a hierarchical method and a nonhierarchical one. We used Support Vector Machine and Naïve Bayes together with ten-fold cross validation to evaluate and compare performances. Our results indicate that the hierarchical approach does not work as well as the nonhierarchical one. In general, our results show that Support Vector Machine obtains better performances than Naïve Bayes for both classification problems. We also observed that bigram representation improves performance compared with unigram representation.

  1. High fold computer disk storage DATABASE for fast extended analysis of γ-rays events

    NASA Astrophysics Data System (ADS)

    Stézowski, O.; Finck, Ch.; Prévost, D.

    1999-03-01

    Recently spectacular technical developments have been achieved to increase the resolving power of large γ-ray spectrometers. With these new eyes, physicists are able to study the intricate nature of atomic nuclei. Concurrently more and more complex multidimensional analyses are needed to investigate very weak phenomena. In this article, we first present a software (DATABASE) allowing high fold coincidences γ-rays events to be stored on hard disk. Then, a non-conventional method of analysis, anti-gating procedure, is described. Two physical examples are given to explain how it can be used and Monte Carlo simulations have been performed to test the validity of this method.

  2. Dynamics and elastic interactions of the discrete multi-dark soliton solutions for the Kaup-Newell lattice equation

    NASA Astrophysics Data System (ADS)

    Liu, Nan; Wen, Xiao-Yong

    2018-03-01

    Under consideration in this paper is the Kaup-Newell (KN) lattice equation which is an integrable discretization of the KN equation. Infinitely, many conservation laws and discrete N-fold Darboux transformation (DT) for this system are constructed and established based on its Lax representation. Via the resulting N-fold DT, the discrete multi-dark soliton solutions in terms of determinants are derived from non-vanishing background. Propagation and elastic interaction structures of such solitons are shown graphically. Overtaking interaction phenomena between/among the two, three and four solitons are discussed. Numerical simulations are used to explore their dynamical behaviors of such multi-dark solitons. Numerical results show that their evolutions are stable against a small noise. Results in this paper might be helpful for understanding the propagation of nonlinear Alfvén waves in plasmas.

  3. Representation of the quantum Fourier transform on multilevel basic elements by a sequence of selective rotation operators

    NASA Astrophysics Data System (ADS)

    Ermilov, A. S.; Zobov, V. E.

    2007-12-01

    To experimentally realize quantum computations on d-level basic elements (qudits) at d > 2, it is necessary to develop schemes for the technical realization of elementary logical operators. We have found sequences of selective rotation operators that represent the operators of the quantum Fourier transform (Walsh-Hadamard matrices) for d = 3-10. For the prime numbers 3, 5, and 7, the well-known method of linear algebra is applied, whereas, for the factorable numbers 6, 9, and 10, the representation of virtual spins is used (which we previously applied for d = 4, 8). Selective rotations can be realized, for example, by means of pulses of an RF magnetic field for systems of quadrupole nuclei or laser pulses for atoms and ions in traps.

  4. Computer integrated documentation

    NASA Technical Reports Server (NTRS)

    Boy, Guy

    1991-01-01

    The main technical issues of the Computer Integrated Documentation (CID) project are presented. The problem of automation of documents management and maintenance is analyzed both from an artificial intelligence viewpoint and from a human factors viewpoint. Possible technologies for CID are reviewed: conventional approaches to indexing and information retrieval; hypertext; and knowledge based systems. A particular effort was made to provide an appropriate representation for contextual knowledge. This representation is used to generate context on hypertext links. Thus, indexing in CID is context sensitive. The implementation of the current version of CID is described. It includes a hypertext data base, a knowledge based management and maintenance system, and a user interface. A series is also presented of theoretical considerations as navigation in hyperspace, acquisition of indexing knowledge, generation and maintenance of a large documentation, and relation to other work.

  5. GLYDE-II: The GLYcan data exchange format

    PubMed Central

    Ranzinger, Rene; Kochut, Krys J.; Miller, John A.; Eavenson, Matthew; Lütteke, Thomas; York, William S.

    2017-01-01

    Summary The GLYcan Data Exchange (GLYDE) standard has been developed for the representation of the chemical structures of monosaccharides, glycans and glycoconjugates using a connection table formalism formatted in XML. This format allows structures, including those that do not exist in any database, to be unambiguously represented and shared by diverse computational tools. GLYDE implements a partonomy model based on human language along with rules that provide consistent structural representations, including a robust namespace for specifying monosaccharides. This approach facilitates the reuse of data processing software at the level of granularity that is most appropriate for extraction of the desired information. GLYDE-II has already been used as a key element of several glycoinformatics tools. The philosophical and technical underpinnings of GLYDE-II and recent implementation of its enhanced features are described. PMID:28955652

  6. a Study on Mental Representations for Realistic Visualization the Particular Case of Ski Trail Mapping

    NASA Astrophysics Data System (ADS)

    Balzarini, R.; Dalmasso, A.; Murat, M.

    2015-08-01

    This article presents preliminary results from a research project in progress that brings together geographers, cognitive scientists, historians and computer scientists. The project investigates the evolution of a particular territorial model: ski trails maps. Ski resorts, tourist and sporting innovations for mountain economies since the 1930s, have needed cartographic representations corresponding to new practices of the space.Painter artists have been involved in producing ski maps with painting techniques and panoramic views, which are by far the most common type of map, because they allow the resorts to look impressive to potential visitors. These techniques have evolved throughout the mutations of the ski resorts. Paper ski maps no longer meet the needs of a large part of the customers; the question now arises of their adaptation to digital media. In a computerized process perspective, the early stage of the project aims to identify the artist-representations, based on conceptual and technical rules, which are handled by users-skiers to perform a task (location, wayfinding, decision-making) and can be transferred to a computer system. This article presents the experimental phase that analyzes artist and user mental representations that are at stake during the making and the reading of a paper ski map. It particularly focuses on how the invention of the artist influences map reading.

  7. Masculinity, vulnerability and prevention of STD/HIV/AIDS among male adolescents: social representations in a land reform settlement.

    PubMed

    Arraes, Camila de Oliveira; Palos, Marinésia Aparecida Prado; Barbosa, Maria Alves; Teles, Sheila Araujo; Souza, Márcia Maria de; Matos, Marcos André de

    2013-01-01

    to analyze the relationship of masculinity, vulnerability and prevention of STD / HIV / AIDS among adolescent males of a land reform settlement in central Brazil. a qualitative study using as precepts the strands of social representations with teenagers between 12 to 24 years. three categories emerged - Perception of vulnerability; Gender and vulnerability; and, Prevention and vulnerability to STD / HIV / AIDS. Adolescents felt invulnerable to sexually transmitted diseases anchored in the social representations in favor of the male hegemony. An ignorance about forms of prevention for STD / HIV / AIDS was demonstrated in their statements. It is believed that institutional projects such as the School Health Program and the Men's Health Care Program constitute essential tools to minimize factors of vulnerability in this population, since the school is recognized as a social facility that promotes socialization of experiences and contributes to the construction of the identity of the adolescent. the social representations of masculinity collaborate for the vulnerable behavior of the adolescents for the acquisition of sexually transmitted diseases. One hopes that this study can contribute to the production of knowledge and technical-scientific improvement of the professionals, especially the nurse, in order to discuss issues related to male sexuality of adolescents in the situation of the land reform settlement.

  8. Strategic Mobility 21: ICODES Extension Technical Plan

    DTIC Science & Technology

    2006-09-30

    re-planning tasks in a dynamically changing decision- making environment (Figure 2). The internal ontology is divided into logical domains that can...another web browser window opens. This window is divided into two sections. One section displays a graphical representation of the conveyance and its...referenced objects with attributes that can be reasoned about by the TRANSWAY agents. Context is provided by an internal ontology that is divided into

  9. Joint Sparse Representation for Robust Multimodal Biometrics Recognition

    DTIC Science & Technology

    2012-01-01

    described in III. Experimental evaluations on a comprehensive multimodal dataset and a face database have been described in section V. Finally, in...WVU Multimodal Dataset The WVU multimodal dataset is a comprehensive collection of different biometric modalities such as fingerprint, iris, palmprint ...Martnez and R. Benavente, “The AR face database ,” CVC Technical Report, June 1998. [29] U. Park and A. Jain, “Face matching and retrieval using soft

  10. Close Air Support versus Close Combat Attack

    DTIC Science & Technology

    2012-12-06

    levels, little Army representation in the Joint Operations Center (JOC), a lack of proper equipment and training and fluid situations made centrally...Symbols are the most fluid of the parts, able to be shaped and changed as time proceeds and are therefore placed on the outside of the onion peel...rituals as “collective activities that are technically superfluous to reach desired ends but that, within a culture, are considered socially essential

  11. Formal Transformations from Graphically-Based Object-Oriented Representations to Theory-Based Specifications

    DTIC Science & Technology

    1996-06-01

    for Software Synthesis." KBSE 󈨡. IEEE, 1993. 51. Kang, Kyo C., et al. Feature-Oriented Domain Analysis ( FODA ) Feasibility Study. Technical Report...and usefulness in domain analysis and modeling. Rumbaugh uses three distinct views to describe a domain: (1) the object model describes structural...Gibbons describe a methodology where Structured Analysis is used to build a hierarchical system structure chart. This structure chart is then translated

  12. JPRS Report, Supplement, East Europe, Recent Legislation.

    DTIC Science & Technology

    1991-08-02

    value of the designated land corre- damage shall be determined based on the cadastral net sponds with the average Gold Crown value of the coop- income...Republic of Croatia appoints chiefs Cultural- informational centers of the Republic of of consular representations based on the recommenda- Croatia abroad...Europe Recent Legislation 19980202 134/ rI QUALI•TST•O•ED a REPRODUCED BY U.S. DEPARTMENT OF COMMERCE NATIONAL TECHNICAL INFORMATION SERVICE SPRINGFIELD

  13. An Examination of the Interaction between Modelling and Its Relationship with Construction Kits: Lessons from the Past and for the Future

    ERIC Educational Resources Information Center

    Parkinson, Eric F.

    2004-01-01

    Construction kits have played a significant part in nurturing the growth and development of the minds and manipulation-based skills of children (and adults) in formal and non-formal education settings. These kits have origins rooted in the representation of the built world and now have a diversity of form and function, including technical versions…

  14. Knowledge-Based Software Development Tools

    DTIC Science & Technology

    1993-09-01

    GREEN, C., AND WESTFOLD, S. Knowledge-based programming self-applied. In Machine Intelligence 10, J. E. Hayes, D. Mitchie, and Y. Pao, Eds., Wiley...Technical Report KES.U.84.2, Kestrel Institute, April 1984. [181 KORF, R. E. Toward a model of representation changes. Artificial Intelligence 14, 1...Artificial Intelligence 27, 1 (February 1985), 43-96. Replinted in Readings in Artificial Intelligence and Software Engineering, C. Rich •ad R. Waters

  15. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hsu, P. J.; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1)more » ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics.« less

  16. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms

    NASA Astrophysics Data System (ADS)

    Hsu, P. J.; Cheong, S. A.; Lai, S. K.

    2014-05-01

    Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics.

  17. Biophysical and structural considerations for protein sequence evolution

    PubMed Central

    2011-01-01

    Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

  18. Getting the picture: A mixed-methods inquiry into how visual representations are interpreted by students, incorporated within textbooks, and integrated into middle-school science classrooms

    NASA Astrophysics Data System (ADS)

    Lee, Victor Raymond

    Modern-day middle school science textbooks are heavily populated with colorful images, technical diagrams, and other forms of visual representations. These representations are commonly perceived by educators to be useful aids to support student learning of unfamiliar scientific ideas. However, as the number of representations in science textbooks has seemingly increased in recent decades, concerns have been voiced that many current of these representations are actually undermining instructional goals; they may be introducing substantial conceptual and interpretive difficulties for students. To date, very little empirical work has been done to examine how the representations used in instructional materials have changed, and what influences these changes exert on student understanding. Furthermore, there has also been limited attention given to the extent to which current representational-use routines in science classrooms may mitigate or limit interpretive difficulties. This dissertation seeks to do three things: First, it examines the nature of the relationship between published representations and students' reasoning about the natural world. Second, it considers the ways in which representations are used in textbooks and how that has changed over a span of five decades. Third, this dissertation provides an in-depth look into how middle school science classrooms naturally use these visual representations and what kinds of support are being provided. With respect to the three goals of this dissertation, three pools of data were collected and analyzed for this study. First, interview data was collected in which 32 middle school students interpreted and reasoned with a set of more and less problematic published textbook representations. Quantitative analyses of the interview data suggest that, counter to what has been anticipated in the literature, there were no significant differences in the conceptualizations of students in the different groups. An accompanying qualitative analysis probes further into why this was the case. In addition to the interview data, a corpus of graphic representations from 34 science textbooks (published between 1943-2005) was catalogued and examined for compositional trends and changes. This historical textbook analysis of images and illustrations reveals that, consistent with expectations, there has indeed been an overall increase in the number of representations in a given instructional unit. Yet, despite the increase, there is very little shift in the instructional functions that those representations serve. Where the most dramatic changes appear are with the individual representations themselves and how they are used to relate scientific ideas to middle school students. Finally, a set of video-recorded classroom observations with three different teachers was collected in order to study representational-use routines. A numerical analysis of classroom episodes suggests that it is fairly common for the majority of representations that are used to appear fleetingly and not be discussed again. When representations are reused or reintroduced, a qualitative analysis reveals that they are often accompanied by interpretive support from the teacher, which may steer students away from misinterpretations.

  19. Word maturity indices with latent semantic analysis: why, when, and where is Procrustes rotation applied?

    PubMed

    Jorge-Botana, Guillermo; Olmos, Ricardo; Luzón, José M

    2018-01-01

    The aim of this paper is to describe and explain one useful computational methodology to model the semantic development of word representation: Word maturity. In particular, the methodology is based on the longitudinal word monitoring created by Kirylev and Landauer using latent semantic analysis for the representation of lexical units. The paper is divided into two parts. First, the steps required to model the development of the meaning of words are explained in detail. We describe the technical and theoretical aspects of each step. Second, we provide a simple example of application of this methodology with some simple tools that can be used by applied researchers. This paper can serve as a user-friendly guide for researchers interested in modeling changes in the semantic representations of words. Some current aspects of the technique and future directions are also discussed. WIREs Cogn Sci 2018, 9:e1457. doi: 10.1002/wcs.1457 This article is categorized under: Computer Science > Natural Language Processing Linguistics > Language Acquisition Psychology > Development and Aging. © 2017 Wiley Periodicals, Inc.

  20. Network embedding-based representation learning for single cell RNA-seq data.

    PubMed

    Li, Xiangyu; Chen, Weizheng; Chen, Yang; Zhang, Xuegong; Gu, Jin; Zhang, Michael Q

    2017-11-02

    Single cell RNA-seq (scRNA-seq) techniques can reveal valuable insights of cell-to-cell heterogeneities. Projection of high-dimensional data into a low-dimensional subspace is a powerful strategy in general for mining such big data. However, scRNA-seq suffers from higher noise and lower coverage than traditional bulk RNA-seq, hence bringing in new computational difficulties. One major challenge is how to deal with the frequent drop-out events. The events, usually caused by the stochastic burst effect in gene transcription and the technical failure of RNA transcript capture, often render traditional dimension reduction methods work inefficiently. To overcome this problem, we have developed a novel Single Cell Representation Learning (SCRL) method based on network embedding. This method can efficiently implement data-driven non-linear projection and incorporate prior biological knowledge (such as pathway information) to learn more meaningful low-dimensional representations for both cells and genes. Benchmark results show that SCRL outperforms other dimensional reduction methods on several recent scRNA-seq datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Universal Racah matrices and adjoint knot polynomials: Arborescent knots

    NASA Astrophysics Data System (ADS)

    Mironov, A.; Morozov, A.

    2016-04-01

    By now it is well established that the quantum dimensions of descendants of the adjoint representation can be described in a universal form, independent of a particular family of simple Lie algebras. The Rosso-Jones formula then implies a universal description of the adjoint knot polynomials for torus knots, which in particular unifies the HOMFLY (SUN) and Kauffman (SON) polynomials. For E8 the adjoint representation is also fundamental. We suggest to extend the universality from the dimensions to the Racah matrices and this immediately produces a unified description of the adjoint knot polynomials for all arborescent (double-fat) knots, including twist, 2-bridge and pretzel. Technically we develop together the universality and the "eigenvalue conjecture", which expresses the Racah and mixing matrices through the eigenvalues of the quantum R-matrix, and for dealing with the adjoint polynomials one has to extend it to the previously unknown 6 × 6 case. The adjoint polynomials do not distinguish between mutants and therefore are not very efficient in knot theory, however, universal polynomials in higher representations can probably be better in this respect.

  2. The origins of thalamic inputs to grasp zones in frontal cortex of macaque monkeys

    PubMed Central

    Stepniewska, Iwona; Kaas, Jon H.

    2015-01-01

    The hand representation in primary motor cortex (M1) is instrumental to manual dexterity in primates. In Old World monkeys, rostral and caudal aspects of the hand representation are located in the precentral gyrus and the anterior bank of the central sulcus, respectively. We previously reported the organization of the cortico-cortical connections of the grasp zone in rostral M1. Here we describe the organization of thalamocortical connections that were labeled from the same tracer injections. Thalamocortical connections of a grasp zone in ventral premotor cortex (PMv) and the M1 orofacial representation are included for direct comparison. The M1 grasp zone was primarily connected with ventral lateral divisions of motor thalamus. The largest proportion of inputs originated in the posterior division (VLp) followed by the medial and the anterior divisions. Thalamic inputs to the M1 grasp zone originated in more lateral aspects of VLp as compared to the origins of thalamic inputs to the M1 orofacial representation. Inputs to M1 from thalamic divisions connected with cerebellum constituted three fold the density of inputs from divisions connected with basal ganglia, whereas the ratio of inputs was more balanced for the grasp zone in PMv. Privileged access of the cerebellothalamic pathway to the grasp zone in rostral M1 is consistent with the connection patterns previously reported for the precentral gyrus. Thus, cerebellar nuclei are likely more involved than basal ganglia nuclei with the contributions of rostral M1 to manual dexterity. PMID:26254903

  3. The origins of thalamic inputs to grasp zones in frontal cortex of macaque monkeys.

    PubMed

    Gharbawie, Omar A; Stepniewska, Iwona; Kaas, Jon H

    2016-07-01

    The hand representation in primary motor cortex (M1) is instrumental to manual dexterity in primates. In Old World monkeys, rostral and caudal aspects of the hand representation are located in the precentral gyrus and the anterior bank of the central sulcus, respectively. We previously reported the organization of the cortico-cortical connections of the grasp zone in rostral M1. Here we describe the organization of thalamocortical connections that were labeled from the same tracer injections. Thalamocortical connections of a grasp zone in ventral premotor cortex (PMv) and the M1 orofacial representation are included for direct comparison. The M1 grasp zone was primarily connected with ventral lateral divisions of motor thalamus. The largest proportion of inputs originated in the posterior division (VLp) followed by the medial and the anterior divisions. Thalamic inputs to the M1 grasp zone originated in more lateral aspects of VLp as compared to the origins of thalamic inputs to the M1 orofacial representation. Inputs to M1 from thalamic divisions connected with cerebellum constituted three fold the density of inputs from divisions connected with basal ganglia, whereas the ratio of inputs was more balanced for the grasp zone in PMv. Privileged access of the cerebellothalamic pathway to the grasp zone in rostral M1 is consistent with the connection patterns previously reported for the precentral gyrus. Thus, cerebellar nuclei are likely more involved than basal ganglia nuclei with the contributions of rostral M1 to manual dexterity.

  4. Bilateral Vocal Fold Medialization: A Treatment for Abductor Spasmodic Dysphonia.

    PubMed

    Dewan, Karuna; Berke, Gerald S

    2017-11-10

    Abductor spasmodic dysphonia, a difficult-to-treat laryngologic condition, is characterized by spasms causing the vocal folds to remain abducted despite efforts to adduct them during phonation. Traditional treatment for abductor spasmodic dysphonia-botulinum toxin injection into the posterior cricoarytenoid muscle-can be both technically challenging and uncomfortable. Due to the difficulty of needle placement, it is often unsuccessful. The purpose of this investigation is to present a previously undescribed treatment for abductor spasmodic dysphonia-bilateral vocal fold medialization. A retrospective case review of all cases of abductor spasmodic dysphonia treated in a tertiary care laryngology practice with bilateral vocal fold medialization over a 10-year period was performed. The Voice Handicap Index and the Voice-Related Quality of Life surveys were utilized to assess patient satisfaction with voice outcome. Six patients with abductor spasmodic dysphonia treated with bilateral vocal fold medialization were identified. Disease severity ranged from mild to severe. All six patients reported statistically significant improvement in nearly all Voice Handicap Index and Voice-Related Quality of Life parameters. They reported fewer voice breaks and greater ease of communication. Results were noted immediately and symptoms continue to be well controlled for many years following medialization. Bilateral vocal fold medialization is a safe and effective treatment for abductor spasmodic dysphonia. It is performed under local anesthesia and provides phonation improvement in the short and long term. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  5. Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). Hanford Environmental Dose Reconstruction Project

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ramsdell, J.V. Jr.; Simonen, C.A.; Burk, K.W.

    1994-02-01

    The purpose of the Hanford Environmental Dose Reconstruction (HEDR) Project is to estimate radiation doses that individuals may have received from operations at the Hanford Site since 1944. This report deals specifically with the atmospheric transport model, Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). RATCHET is a major rework of the MESOILT2 model used in the first phase of the HEDR Project; only the bookkeeping framework escaped major changes. Changes to the code include (1) significant changes in the representation of atmospheric processes and (2) incorporation of Monte Carlo methods for representing uncertainty in input data, model parameters,more » and coefficients. To a large extent, the revisions to the model are based on recommendations of a peer working group that met in March 1991. Technical bases for other portions of the atmospheric transport model are addressed in two other documents. This report has three major sections: a description of the model, a user`s guide, and a programmer`s guide. These sections discuss RATCHET from three different perspectives. The first provides a technical description of the code with emphasis on details such as the representation of the model domain, the data required by the model, and the equations used to make the model calculations. The technical description is followed by a user`s guide to the model with emphasis on running the code. The user`s guide contains information about the model input and output. The third section is a programmer`s guide to the code. It discusses the hardware and software required to run the code. The programmer`s guide also discusses program structure and each of the program elements.« less

  6. Technical evaluation of a CAD system for orthopaedic shoe-upper design.

    PubMed

    Lord, M; Foulston, J; Smith, P J

    1991-01-01

    Computer aided design is now employed routinely in the volume shoe trade. New styles are developed on a three-dimensional image of the last followed by automated pattern generation and engineering. It is suggested that such systems could be useful in the orthopaedic footwear industry although the different requirements for these bespoke products need careful consideration. A clinical trial has been conducted on the Shoemaster (Clarks Shoes) upper design system both to assess its technical capabilities and to consider its role in improvement of service and cosmetic appearance. This particular system works throughout on a three-dimensional representation of the shoe last, which offers particular advantages for integration with shape capture and reproduction. The report concentrates on the technical evaluation to assess (a) its ability to work with unusual last shapes dictated by medical requirements and (b) its potential for integration into a complete computer system for design of both shoe lasts and shoe uppers. The trial indicates that this particular system is promising in both respects.

  7. Loading Rate Effects on the One-Dimensional Compressibility of Four Partially Saturated Soils

    DTIC Science & Technology

    1986-12-01

    representations are referred to as constitutive models. Numerous constitutive models incorporating loading rate effects have been developed ( Baladi and Rohani...and probably more indicative of the true values of applied pressure and average strain produced during the test. A technique developed by Baladi and...Sand," Technical Report No. AFWL-TR-66-146, Air Force Weapons Laboratory, Kirtland Air Force Base, New Mexico, June, 1967. 4. Baladi , George Y., and

  8. Report of the Working Group on Large-Scale Computing in Aeronautics.

    DTIC Science & Technology

    1984-06-01

    incompressible approximations that are presently made in the lifting line or lifting surface representations of rotor blades. Finally, viscous effects in the forms... Effects of Rotor Model Degradation in the Accuracy of Rotocraft Real-Time Simulation, NASA TN D-8378;1977. 20. Gullen, R. K., Cattell, C. S., and Overton...assistance to member nations for the purpose of increasing their scientific and technical potential; - Recommending effective ways for the member nations

  9. Safety in Numbers

    DTIC Science & Technology

    2010-11-27

    analysis and verification. While at Wisconsin, Dr. Gopan was awarded the CISCO fellowship for two consecutive years. Mr. John Phillips has many years...using short (56-bit) keys for encryption (e.g., with DES or RC5) [45]. Today, it is used to understand protein folding [10]. IBM‘s World Community...Bicocca. Dipartimento di Informatica, Sistemistica e Comunicazione. Laboratorio di Test e Analisi del Software, Milano. Technical Report LTA:2004:05

  10. Modification of the Technical Properties of Lactobacillus johnsonii NCC 533 by Supplementing the Growth Medium with Unsaturated Fatty Acids ▿

    PubMed Central

    Muller, J. A.; Ross, R. P.; Sybesma, W. F. H.; Fitzgerald, G. F.; Stanton, C.

    2011-01-01

    The aim of this study was to investigate the influence of supplementing growth medium with unsaturated fatty acids on the technical properties of the probiotic strain Lactobacillus johnsonii NCC 533, such as heat and acid tolerance, and inhibition of Salmonella enterica serovar Typhimurium infection. Our results showed that the membrane composition and morphology of L. johnsonii NCC 533 were significantly changed by supplementing a minimal Lactobacillus medium with oleic, linoleic, and linolenic acids. The ratio of saturated to unsaturated plus cyclic fatty acids in the bacterial membrane decreased by almost 2-fold when minimal medium was supplemented with unsaturated fatty acids (10 μg/ml). The subsequent acid and heat tolerance of L. johnsonii decreased by 6- and 20-fold when the strain was grown in the presence of linoleic and linolenic acids, respectively, compared with growth in oleic acid (all at 10 μg/ml). Following acid exposure, significantly higher (P < 0.05) oleic acid content was detected in the membrane when growth medium was supplemented with linoleic or linolenic acid, indicating that saturation of the membrane fatty acids occurred during acid stress. Cell integrity was determined in real time during stressed conditions using a fluorescent viability kit in combination with flow cytometric analysis. Following heat shock (at 62.5°C for 5 min), L. johnsonii was unable to form colonies; however, 60% of the bacteria showed no cell integrity loss, which could indicate that the elevated heat inactivated vital processes within the cell, rendering it incapable of replication. Furthermore, L. johnsonii grown in fatty acid-enriched minimal medium had different adhesion properties and caused a 2-fold decrease in S. enterica serovar Typhimurium UK1-lux invasion of HT-29 epithelial cells compared with bacteria grown in minimal medium alone. This could be related to changes in the hydrophobicity and fluidity of the membrane. Our study shows that technical properties underlying probiotic survivability can be affected by nutrient composition of the growth medium. PMID:21821758

  11. Modification of the technical properties of Lactobacillus johnsonii NCC 533 by supplementing the growth medium with unsaturated fatty acids.

    PubMed

    Muller, J A; Ross, R P; Sybesma, W F H; Fitzgerald, G F; Stanton, C

    2011-10-01

    The aim of this study was to investigate the influence of supplementing growth medium with unsaturated fatty acids on the technical properties of the probiotic strain Lactobacillus johnsonii NCC 533, such as heat and acid tolerance, and inhibition of Salmonella enterica serovar Typhimurium infection. Our results showed that the membrane composition and morphology of L. johnsonii NCC 533 were significantly changed by supplementing a minimal Lactobacillus medium with oleic, linoleic, and linolenic acids. The ratio of saturated to unsaturated plus cyclic fatty acids in the bacterial membrane decreased by almost 2-fold when minimal medium was supplemented with unsaturated fatty acids (10 μg/ml). The subsequent acid and heat tolerance of L. johnsonii decreased by 6- and 20-fold when the strain was grown in the presence of linoleic and linolenic acids, respectively, compared with growth in oleic acid (all at 10 μg/ml). Following acid exposure, significantly higher (P < 0.05) oleic acid content was detected in the membrane when growth medium was supplemented with linoleic or linolenic acid, indicating that saturation of the membrane fatty acids occurred during acid stress. Cell integrity was determined in real time during stressed conditions using a fluorescent viability kit in combination with flow cytometric analysis. Following heat shock (at 62.5°C for 5 min), L. johnsonii was unable to form colonies; however, 60% of the bacteria showed no cell integrity loss, which could indicate that the elevated heat inactivated vital processes within the cell, rendering it incapable of replication. Furthermore, L. johnsonii grown in fatty acid-enriched minimal medium had different adhesion properties and caused a 2-fold decrease in S. enterica serovar Typhimurium UK1-lux invasion of HT-29 epithelial cells compared with bacteria grown in minimal medium alone. This could be related to changes in the hydrophobicity and fluidity of the membrane. Our study shows that technical properties underlying probiotic survivability can be affected by nutrient composition of the growth medium.

  12. Comparison of L-system applications towards plant modelling, music rendering and score generation using visual language programming

    NASA Astrophysics Data System (ADS)

    Lim, Chen Kim; Tan, Kian Lam; Yusran, Hazwanni; Suppramaniam, Vicknesh

    2017-10-01

    Visual language or visual representation has been used in the past few years in order to express the knowledge in graphic. One of the important graphical elements is fractal and L-Systems is a mathematic-based grammatical model for modelling cell development and plant topology. From the plant model, L-Systems can be interpreted as music sound and score. In this paper, LSound which is a Visual Language Programming (VLP) framework has been developed to model plant to music sound and generate music score and vice versa. The objectives of this research has three folds: (i) To expand the grammar dictionary of L-Systems music based on visual programming, (ii) To design and produce a user-friendly and icon based visual language framework typically for L-Systems musical score generation which helps the basic learners in musical field and (iii) To generate music score from plant models and vice versa using L-Systems method. This research undergoes a four phases methodology where the plant is first modelled, then the music is interpreted, followed by the output of music sound through MIDI and finally score is generated. LSound is technically compared to other existing applications in the aspects of the capability of modelling the plant, rendering the music and generating the sound. It has been found that LSound is a flexible framework in which the plant can be easily altered through arrow-based programming and the music score can be altered through the music symbols and notes. This work encourages non-experts to understand L-Systems and music hand-in-hand.

  13. From experimental imaging techniques to virtual embryology.

    PubMed

    Weninger, Wolfgang J; Tassy, Olivier; Darras, Sébastien; Geyer, Stefan H; Thieffry, Denis

    2004-01-01

    Modern embryology increasingly relies on descriptive and functional three dimensional (3D) and four dimensional (4D) analysis of physically, optically, or virtually sectioned specimens. To cope with the technical requirements, new methods for high detailed in vivo imaging, as well as the generation of high resolution digital volume data sets for the accurate visualisation of transgene activity and gene product presence, in the context of embryo morphology, were recently developed and are under construction. These methods profoundly change the scientific applicability, appearance and style of modern embryo representations. In this paper, we present an overview of the emerging techniques to create, visualise and administrate embryo representations (databases, digital data sets, 3-4D embryo reconstructions, models, etc.), and discuss the implications of these new methods on the work of modern embryologists, including, research, teaching, the selection of specific model organisms, and potential collaborators.

  14. Hierarchy, causation and explanation: ubiquity, locality and pluralism

    PubMed Central

    Love, Alan C.

    2012-01-01

    The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified ‘levels’ of organization and suggests that attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily ‘local’ and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended—many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry. PMID:23386966

  15. Feasibility analysis of wastewater and solid waste systems for application in Indonesia.

    PubMed

    Kerstens, S M; Leusbrock, I; Zeeman, G

    2015-10-15

    Indonesia is one of many developing countries with a backlog in achieving targets for the implementation of wastewater and solid waste collection, treatment and recovery systems. Therefore a technical and financial feasibility analysis of these systems was performed using Indonesia as an example. COD, BOD, nitrogen, phosphorus and pathogen removal efficiencies, energy requirements, sludge production, land use and resource recovery potential (phosphorus, energy, duckweed, compost, water) for on-site, community based and off-site wastewater systems were determined. Solid waste systems (conventional, centralized and decentralized resource recovery) were analyzed according to land requirement, compost and energy production and recovery of plastic and paper. In the financial analysis, investments, operational costs & benefits and Total Lifecycle Costs (TLC) of all investigated options were compared. Technical performance and TLC were used to guide system selection for implementation in different residential settings. An analysis was undertaken to determine the effect of price variations of recoverable resources and land prices on TLC. A 10-fold increase in land prices for land intensive wastewater systems resulted in a 5 times higher TLC, whereas a 4-fold increase in the recovered resource selling price resulted in maximum 1.3 times higher TLC. For solid waste, these impacts were reversed - land price and resource selling price variations resulted in a maximum difference in TLC of 1.8 and 4 respectively. Technical and financial performance analysis can support decision makers in system selection and anticipate the impact of price variations on long-term operation. The technical analysis was based on published results of international research and the approach can be applied for other tropical, developing countries. All costs were converted to per capita unit costs and can be updated to assess other countries' estimated costs and benefits. Consequently, the approach can be used to guide wastewater and solid waste system planning in developing countries. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. A Non-technical User-Oriented Display Notation for XACML Conditions

    NASA Astrophysics Data System (ADS)

    Stepien, Bernard; Felty, Amy; Matwin, Stan

    Ideally, access control to resources in complex IT systems ought to be handled by business decision makers who own a given resource (e.g., the pay and benefits section of an organization should decide and manage the access rules to the payroll system). To make this happen, the security and database communities need to develop vendor-independent access management tools, useable by decision makers, rather than technical personnel detached from a given business function. We have developed and implemented such tool, based on XACML. The XACML is an important emerging tool for managing complex access control applications. As a formal notation, based on an XML schema representing the grammar of a given application, XACML is precise and non-ambiguous. But this very property puts it out of reach of non-technical users. We propose a new notation for displaying and editing XACML rules that is independent of XML, and we develop an editor for it. Our notation combines a tree representation of logical expressions with an accessible natural language layer. Our early experience indicates that such rules can be grasped by non-technical users wishing to develop and control rules for accessing their own resources.

  17. Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex.

    PubMed

    Zhao, Yong; Kan, Zhong-yuan; Zeng, Zhi-xiong; Hao, Yu-hua; Chen, Hua; Tan, Zheng

    2004-10-20

    Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.

  18. Approximate matching of structured motifs in DNA sequences.

    PubMed

    El-Mabrouk, Nadia; Raffinot, Mathieu; Duchesne, Jean-Eudes; Lajoie, Mathieu; Luc, Nicolas

    2005-04-01

    Several methods have been developed for identifying more or less complex RNA structures in a genome. All these methods are based on the search for conserved primary and secondary sub-structures. In this paper, we present a simple formal representation of a helix, which is a combination of sequence and folding constraints, as a constrained regular expression. This representation allows us to develop a well-founded algorithm that searches for all approximate matches of a helix in a genome. The algorithm is based on an alignment graph constructed from several copies of a pushdown automaton, arranged one on top of another. This is a first attempt to take advantage of the possibilities of pushdown automata in the context of approximate matching. The worst time complexity is O(krpn), where k is the error threshold, n the size of the genome, p the size of the secondary expression, and r its number of union symbols. We then extend the algorithm to search for pseudo-knots and secondary structures containing an arbitrary number of helices.

  19. An evaluation of selected NASA scientific and technical information products: Results of a pilot study

    NASA Technical Reports Server (NTRS)

    Pinelli, Thomas E.; Glassman, Myron

    1989-01-01

    A pilot study was conducted to evaluate selected NASA scientific and technical information (STI) products. The study, which utilized survey research in the form of a self-administered mail questionnaire, had a two-fold purpose -- to gather baseline data regarding the use and perceived usefulness of selected NASA STI products and to develop/validate questions that could be used in a future study concerned with the role of the U.S. government technical report in aeronautics. The sample frame consisted of 25,000 members of the American Institute of Aeronautics and Astronautics in the U.S. with academic, government or industrial affiliation. Simple random sampling was used to select 2000 individuals to participate in the study. Three hundred fifty-three usable questionnaires (17 percent response rate) were received by the established cutoff date. The findings indicate that: (1) NASA STI is used and is generally perceived as being important; (2) the use rate for NASA-authored conference/meeting papers, journal articles, and technical reports is fairly uniform; (3) a considerable number of respondents are unfamiliar with STAR (Scientific and Technical Aerospace Reports), IAA (International Aerospace Abstracts), SCAN (Selected Current Aerospace Notices), and the RECON on-line retrieval system; (4) a considerable number of respondents who are familiar with these media do not use them; and (5) the perceived quality of NASA-authored journal articles and technical reports is very good.

  20. The NATO thesaurus project

    NASA Technical Reports Server (NTRS)

    Krueger, Jonathan

    1990-01-01

    This document describes functionality to be developed to support the NATO technical thesaurus. Described are the specificity of the thesaurus structure and function; the distinction between the thesaurus information and its representation in a given online, machine readable, or printed form; the enhancement of the thesaurus with the assignment of COSATI codes (fields and groups) to posting terms, the integration of DTIC DRIT and NASA thesauri related terminology, translation of posting terms into French; and the provision of a basis for system design.

  1. Improved Foundry Castings Utilizing CAD/CAM (Computer Aided Design/ Computer Aided Manufacture). Volume 1. Overview

    DTIC Science & Technology

    1988-06-30

    casting. 68 Figure 1-9: Line printer representation of roll solidification. 69 Figure I1-1: Test casting model. 76 Figure 11-2: Division of test casting...writing new casting analysis and design routines. The new routines would take advantage of advanced criteria for predicting casting soundness and cast...properties and technical advances in computer hardware and software. 11 2. CONCLUSIONS UPCAST, a comprehensive software package, has been developed for

  2. United States Air Force Graduate Student Summer Support Program (1987). Program Technical Report. Volume 2

    DTIC Science & Technology

    1987-12-01

    Metabolism (VMAX) Using Quantitative Structure- Activity Relationships (QSAR) 17 Directed Motion Doppler Shift Effects on Mitric Oxide (0,0) Gamma Band...chemiluminescence values were observed at characteristic times after adding glucose to the disks. We also produced virus-sized nanoparticles (Glucose...These nanoparticles were able to penetrate a .2 um filter,and they retained their enzymatic activity for weeks. They produced 20-fold greater

  3. A phase transition in energy-filtered RNA secondary structures.

    PubMed

    Han, Hillary S W; Reidys, Christian M

    2012-10-01

    In this article we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model that is only dependent on the diagram representation and is not sequence-specific, we prove the following dichotomy result. Mfe structures derived via the Turner energy parameters contain only finitely many complex irreducible substructures, and just minor parameter changes produce a class of mfe structures that contain a large number of small irreducibles. We localize the exact point at which the distribution of irreducibles experiences this phase transition from a discrete limit to a central limit distribution and, subsequently, put our result into the context of quantifying the effect of sparsification of the folding of these respective mfe structures. We show that the sparsification of realistic mfe structures leads to a constant time and space reduction, and that the sparsification of the folding of structures with modified parameters leads to a linear time and space reduction. We, furthermore, identify the limit distribution at the phase transition as a Rayleigh distribution.

  4. Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

    PubMed Central

    Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

    2013-01-01

    Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

  5. The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

    PubMed

    Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

    2015-10-26

    The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

  6. All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

    PubMed Central

    2017-01-01

    Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

  7. The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

    PubMed Central

    Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

    2015-01-01

    The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. PMID:26498066

  8. Alternative modes of client binding enable functional plasticity of Hsp70

    NASA Astrophysics Data System (ADS)

    Mashaghi, Alireza; Bezrukavnikov, Sergey; Minde, David P.; Wentink, Anne S.; Kityk, Roman; Zachmann-Brand, Beate; Mayer, Matthias P.; Kramer, Günter; Bukau, Bernd; Tans, Sander J.

    2016-11-01

    The Hsp70 system is a central hub of chaperone activity in all domains of life. Hsp70 performs a plethora of tasks, including folding assistance, protection against aggregation, protein trafficking, and enzyme activity regulation, and interacts with non-folded chains, as well as near-native, misfolded, and aggregated proteins. Hsp70 is thought to achieve its many physiological roles by binding peptide segments that extend from these different protein conformers within a groove that can be covered by an ATP-driven helical lid. However, it has been difficult to test directly how Hsp70 interacts with protein substrates in different stages of folding and how it affects their structure. Moreover, recent indications of diverse lid conformations in Hsp70-substrate complexes raise the possibility of additional interaction mechanisms. Addressing these issues is technically challenging, given the conformational dynamics of both chaperone and client, the transient nature of their interaction, and the involvement of co-chaperones and the ATP hydrolysis cycle. Here, using optical tweezers, we show that the bacterial Hsp70 homologue (DnaK) binds and stabilizes not only extended peptide segments, but also partially folded and near-native protein structures. The Hsp70 lid and groove act synergistically when stabilizing folded structures: stabilization is abolished when the lid is truncated and less efficient when the groove is mutated. The diversity of binding modes has important consequences: Hsp70 can both stabilize and destabilize folded structures, in a nucleotide-regulated manner; like Hsp90 and GroEL, Hsp70 can affect the late stages of protein folding; and Hsp70 can suppress aggregation by protecting partially folded structures as well as unfolded protein chains. Overall, these findings in the DnaK system indicate an extension of the Hsp70 canonical model that potentially affects a wide range of physiological roles of the Hsp70 system.

  9. Radiation Dose Assessments of Solar Particle Events with Spectral Representation at High Energies for the Improvement of Radiation Protection

    NASA Technical Reports Server (NTRS)

    Kim, Myung-Hee; Atwell, William; Tylka, Allan J.; Dietrich, William F.; Cucinotta, Francis A.

    2010-01-01

    For radiation dose assessments of major solar particle events (SPEs), spectral functional forms of SPEs have been made by fitting available satellite measurements up to approx.100 MeV. However, very high-energy protons (above 500 MeV) have been observed with neutron monitors (NMs) in ground level enhancements (GLEs), which generally present the most severe radiation hazards to astronauts. Due to technical difficulties in converting NM data into absolutely normalized fluence measurements, those functional forms were made with little or no use of NM data. A new analysis of NM data has found that a double power law in rigidity (the so-called Band function) generally provides a satisfactory representation of the combined satellite and NM data from approx.10 MeV to approx.10 GeV in major SPEs (Tylka & Dietrich 2009). We use the Band function fits to re-assess human exposures from large SPEs. Using different spectral representations of large SPEs, variations of exposure levels were compared. The results can be applied to the development of approaches of improved radiation protection for astronauts, as well as the optimization of mission planning and shielding for future space missions.

  10. `It's more flexible': persistence of women engineers in the academy

    NASA Astrophysics Data System (ADS)

    Mlambo, Yeukai Angela; Mabokela, Reitumetse Obakeng

    2017-05-01

    The under-representation of women in engineering is an issue of concern for policy-makers. While much of the existing literature has focussed on understanding reasons for women's under-representation in engineering and related technical fields, there is a paucity of research that examines why women who are already in engineering persist. This study aims to answer the question, why do women engineers in academe persist in a discipline that is generally perceived to be inhospitable to women. Three main challenges, namely gender discrimination, lack of institutional and disciplinary support, and the rigid nature of the workplace, emerged as key impediments to women engineers in the private sector. In contrast, women engineers in the academy identified the flexibility offered by academic environments, the presence of personal support networks, and a passion for teaching and students as critical factors that influenced their decision to remain in academia.

  11. Cancer Tissue Engineering: A Novel 3D Polystyrene Scaffold for In Vitro Isolation and Amplification of Lymphoma Cancer Cells from Heterogeneous Cell Mixtures

    PubMed Central

    Caicedo-Carvajal, Carlos E.; Liu, Qing; Remache, Yvonne; Goy, Andre; Suh, K. Stephen

    2011-01-01

    Isolation and amplification of primary lymphoma cells in vitro setting is technically and biologically challenging task. To optimize culture environment and mimic in vivo conditions, lymphoma cell lines were used as a test case and were grown in 3-dimension (3D) using a novel 3D tissue culture polystyrene scaffold with neonatal stromal cells to represent a lymphoma microenvironment. In this model, the cell proliferation was enhanced more than 200-fold or 20,000% neoplastic surplus in 7 days when less than 1% lymphoma cells were cocultured with 100-fold excess of neonatal stroma cells, representing 3.2-fold higher proliferative rate than 2D coculture model. The lymphoma cells grew and aggregated to form clusters during 3D coculture and did not maintained the parental phenotype to grow in single-cell suspension. The cluster size was over 5-fold bigger in the 3D coculture by day 4 than 2D coculture system and contained less than 0.00001% of neonatal fibroblast trace. This preliminary data indicate that novel 3D scaffold geometry and coculturing environment can be customized to amplify primary cancer cells from blood or tissues related to hematological cancer and subsequently used for personalized drug screening procedures. PMID:22073378

  12. Clinical experience with Gray's minithyrotomy procedure.

    PubMed

    Paniello, Randal C; Sulica, Lucian; Khosla, Siddarth M; Smith, Marshall E

    2008-06-01

    Endoscopic approaches for submucosal vocal fold surgery may limit the surgeon's ability to release scars or to precisely implant filler material such as fat. In 1999, Gray et al described the "minithyrotomy" approach to this region. Technical aspects of this important new technique, clinical indications, and early results are reviewed. We performed a retrospective review and compiled the data of the office records, clinical notes, and videostroboscopic examinations of all of the four authors' patients who underwent this procedure. Twenty-one patients underwent 22 minithyrotomy procedures for vocal fold scarring (6), lateralizing scar following polytetrafluoroethylene removal or trauma (5), scar with radiation fibrosis (2), sulcus vocalis (2), or presbylarynx or bowing (6) - bilaterally in 14 operations and unilaterally in 8. There were 13 male patients and 8 female patients, with a mean age of 58.3 years (range, 22 to 87 years). The mean follow-up was 9.1 months (range, 1 to 46 months). After submucosal vocal fold exploration, autologous fat was implanted in 20 of the 21 patients. Postoperative videostroboscopy demonstrated improved mucosal pliability in 19 cases and improved glottal closure in 20 cases. Most patients noted voice improvement. Complications were minimal. Gray's minithyrotomy is a highly effective approach for treating vocal fold scar processes, bowing, sulcus vocalis, and, potentially, other conditions.

  13. Protein folding on the ribosome studied using NMR spectroscopy

    PubMed Central

    Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

    2013-01-01

    NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

  14. Mechanical restoration of large-scale folded multilayers using the finite element method: Application to the Zagros Simply Folded Belt, N-Iraq

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Reif, Daniel; Grasemann, Bernhard

    2010-05-01

    There are a large number of numerical finite element studies concerned with modeling the evolution of folded geological layers through time. This body of research includes many aspects of folding and many different approaches, such as two- and three-dimensional studies, single-layer folding, detachment folding, development of chevron folds, Newtonian, power-law viscous and more complex rheologies, influence of anisotropy, pure-shear, simple-shear and other boundary conditions and so forth. In recent years, studies of multilayer folding emerged, thanks to more advanced mesh generator software and increased computational power. Common to all of these studies is the fact that they consider a forward directed time evolution, as in nature. Very few studies use the finite element method for reverse-time simulations. In such studies, folded geological layers are taken as initial conditions for the numerical simulation. The folding process is reversed by changing the signs of the boundary conditions that supposedly drove the folding process. In such studies, the geometry of the geological layers before the folding process is searched and the amount of shortening necessary for the final folded geometry can be calculated. In contrast to a kinematic or geometric fold restoration procedure, the described approach takes the mechanical behavior of the geological layers into account, such as rheology and the relative strength of the individual layers. This approach is therefore called mechanical restoration of folds. In this study, the concept of mechanical restoration is applied to a two-dimensional 50km long NE-SW-cross-section through the Zagros Simply Folded Belt in Iraqi Kurdistan, NE from the city of Erbil. The Simply Folded Belt is dominated by gentle to open folding and faults are either absent or record only minor offset. Therefore, this region is ideal for testing the concept of mechanical restoration. The profile used is constructed from structural field measurements and digital elevation models using the dip-domain method for balancing the cross-section. The lithology consists of Cretaceous to Cenozoic sediments. Massive carbonate rock units act as the competent layers compared to the incompetent behavior of siltstone, claystone and marl layers. We show the first results of the mechanical restoration of the Zagros cross-section and we discuss advantages and disadvantages, as well as some technical aspects of the applied method. First results indicate that a shortening of at least 50% was necessary to create the present-day folded cross-section. This value is higher than estimates of the amount of shortening solely based on kinematic or geometric restoration. One particular problem that is discussed is the presence of (unnaturally) sharp edges in a balanced cross-section produced using the dip-domain method, which need to be eliminated for mechanical restoration calculations to get reasonable results.

  15. Integrated Information Support System (IISS). Volume 8. User Interface Subsystem. Part 39. Electronic Documentation System (EDS) User’s Manual

    DTIC Science & Technology

    1990-09-30

    conveying any rights or permission to manufacture, use, or market any patented invention that may in any way be related thereto. This technical report...Definition - Select .... 7-9 7-6 Character Class Definition - Other Options 7-10 7-7 Pattern/Action/State Defintion -Select 7-11 7-8 Pattern/Action/State...representation. Compound Document: A document which may contain mixed content i.e. text, graphics, etc. Conforming SGML Application: An SGML application that

  16. Research in advanced formal theorem-proving techniques

    NASA Technical Reports Server (NTRS)

    Rulifson, J. F.

    1971-01-01

    The present status is summarized of a continuing research program aimed at the design and implementation of a language for expressing problem-solving procedures in several areas of artificial intelligence, including program synthesis, robot planning, and theorem proving. Notations, concepts, and procedures common to the representation and solution of many of these problems were abstracted and incorporated as features into the language. The areas of research covered are described, and abstracts of six papers that contain extensive description and technical detail of the work are presented.

  17. Technical note: false catastrophic age-at-death profiles in commingled bone deposits.

    PubMed

    Sołtysiak, Arkadiusz

    2013-12-01

    Age-at-death profiles obtained using the minimum number of individuals (MNI) for mass deposits of commingled human remains may be biased by over-representation of subadult individuals. A computer simulation designed in the R environment has shown that this effect may lead to misinterpretation of such samples even in cases where the completeness rate is relatively high. The simulation demonstrates that the use of the Most Likely Number of Individuals (MLNI) substantially reduces this bias. Copyright © 2013 Wiley Periodicals, Inc.

  18. Fifth Conference on Artificial Intelligence for Space Applications

    NASA Technical Reports Server (NTRS)

    Odell, Steve L. (Compiler)

    1990-01-01

    The Fifth Conference on Artificial Intelligence for Space Applications brings together diverse technical and scientific work in order to help those who employ AI methods in space applications to identify common goals and to address issues of general interest in the AI community. Topics include the following: automation for Space Station; intelligent control, testing, and fault diagnosis; robotics and vision; planning and scheduling; simulation, modeling, and tutoring; development tools and automatic programming; knowledge representation and acquisition; and knowledge base/data base integration.

  19. Future Combat System Spinout 1 Technical Field Test - Establishing and Implementing Models and Simulations System of Systems Verification, Validation and Accreditation Practices, Methodologies and Procedures

    DTIC Science & Technology

    2009-11-24

    assisted by the Brigade Combat Team (BCT) Modernization effort, the use of Models and Simulations ( M &S) becomes more crucial in supporting major...in 2008 via a slice of the Current Force (CF) BCT structure. To ensure realistic operational context, a M &S System-of- Systems (SoS) level...messages, and constructive representation of platforms, vehicles, and terrain. The M &S federation also provided test control, data collection, and live

  20. USGS Scientific Visualization Laboratory

    USGS Publications Warehouse

    ,

    1995-01-01

    The U.S. Geological Survey's (USGS) Scientific Visualization Laboratory at the National Center in Reston, Va., provides a central facility where USGS employees can use state-of-the-art equipment for projects ranging from presentation graphics preparation to complex visual representations of scientific data. Equipment including color printers, black-and-white and color scanners, film recorders, video equipment, and DOS, Apple Macintosh, and UNIX platforms with software are available for both technical and nontechnical users. The laboratory staff provides assistance and demonstrations in the use of the hardware and software products.

  1. Self-teaching neural network learns difficult reactor control problem

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jouse, W.C.

    1989-01-01

    A self-teaching neural network used as an adaptive controller quickly learns to control an unstable reactor configuration. The network models the behavior of a human operator. It is trained by allowing it to operate the reactivity control impulsively. It is punished whenever either the power or fuel temperature stray outside technical limits. Using a simple paradigm, the network constructs an internal representation of the punishment and of the reactor system. The reactor is constrained to small power orbits.

  2. A 20-Channel Receive-Only Mouse Array Coil for a 3T Clinical MRI System

    PubMed Central

    Keil, Boris; Wiggins, Graham C.; Triantafyllou, Christina; Wald, Lawrence L.; Meise, Florian M.; Schreiber, Laura M.; Klose, Klaus J.; Heverhagen, Johannes T.

    2010-01-01

    A 20-channel phased-array coil for Magnetic Resonance Imaging (MRI) of mice has been designed, constructed and validated with bench measurements and high resolution accelerated imaging. The technical challenges of designing a small, high density array have been overcome using individual small-diameter coil elements arranged on a cylinder in a hexagonal overlapping design with adjacent low impedance preamplifiers to further decouple the array elements. Signal-to-noise ratio (SNR) and noise amplification in accelerated imaging were simulated and quantitatively evaluated in phantoms and in vivo mouse images. Comparison between the 20-channel mouse array and a length-matched quadrature driven small animal birdcage coil showed an SNR increase at the periphery and in the center of the phantom of 3-fold and 1.3-fold, respectively. Comparison to a shorter but SNR-optimized birdcage coil (aspect ratio 1:1 and only half mouse coverage) showed an SNR gain of 2-fold at the edge of the phantom and similar SNR in the center. G-factor measurements indicate that the coil is well suited to acquire highly accelerated images. PMID:21433066

  3. Purification, crystallization and preliminary crystallographic analysis of the SH2 domain of IL-2-inducible T-cell kinase.

    PubMed

    Joseph, Raji E; Ginder, Nathaniel D; Hoy, Julie A; Nix, Jay C; Honzatko, Richard B; Andreotti, Amy H

    2011-02-01

    Proline is a unique amino acid owing to the relatively small energy difference between the cis and trans conformations of its peptide bond. The X-Pro imide bond readily undergoes cis-trans isomerization in the context of short peptides as well as some proteins. However, the direct detection of cis-trans proline isomerization in folded proteins is technically challenging. NMR spectroscopy is well suited to the direct detection of proline isomerization in folded proteins. It is less clear how well X-ray crystallography can reveal this conformational exchange event in folded proteins. Conformational heterogeneity owing to cis-trans proline isomerization in the Src homology 2 (SH2) domain of the IL-2-inducible T-cell kinase (ITK) has been extensively characterized by NMR. Using the ITK SH2 domain as a test system, an attempt was made to determine whether proline isomerization could be detected in a crystal structure of the ITK SH2 domain. As a first step towards this goal, the purification, crystallization and preliminary characterization of the ITK SH2 domain are described.

  4. Technical Bases to Aid in the Decision of Conducting Full Power Ground Nuclear Tests for Space Fission Reactors

    NASA Astrophysics Data System (ADS)

    Hixson, Laurie L.; Houts, Michael G.; Clement, Steven D.

    2004-02-01

    The extent to which, if any, full power ground nuclear testing of space reactors should be performed has been a point of discussion within the industry for decades. Do the benefits outweigh the risks? Are there equivalent alternatives? Can a test facility be constructed (or modified) in a reasonable amount of time? Is the test article an accurate representation of the flight system? Are the costs too restrictive? The obvious benefits of full power ground nuclear testing; obtaining systems integrated reliability data on a full-scale, complete end-to-end system; come at some programmatic risk. Safety related information is not obtained from a full-power ground nuclear test. This paper will discuss and assess these and other technical considerations essential in the decision to conduct full power ground nuclear-or alternative-tests.

  5. Synthetic, multi-layer, self-oscillating vocal fold model fabrication.

    PubMed

    Murray, Preston R; Thomson, Scott L

    2011-12-02

    Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry, clinical instrument development, laryngeal aerodynamics, vocal fold contact pressure, and subglottal acoustics (a more comprehensive list can be found in Kniesburges et al.) Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration). In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.

  6. MR enterography in nonresponsive adult celiac disease: Correlation with endoscopic, pathologic, serologic, and genetic features.

    PubMed

    Radmard, Amir Reza; Hashemi Taheri, Amir Pejman; Salehian Nik, Elham; Kooraki, Soheil; Kolahdoozan, Shadi; Mirminachi, Babak; Sotoudeh, Masoud; Ekhlasi, Golnaz; Malekzadeh, Reza; Shahbazkhani, Bijan

    2017-10-01

    To assess small bowel abnormalities on magnetic resonance enterography (MRE) in adult patients with nonresponsive celiac disease (CD) and investigate their associations with endoscopic, histopathologic, serologic, and genetic features. This prospective study was carried out between September 2012 and August 2013. After approval by the Ethics Committee of our institution, informed consent was acquired from all participants. Forty consecutive patients with nonresponsive CD, aged 17-76 years, underwent MRE using a 1.5T unit. Sequences included T 2 -HASTE, True-FISP, pre- and postcontrast VIBE to assess the quantitative (number of ileal and jejunal folds) and qualitative (fold pattern abnormalities, mural thickening, increased enhancement, bowel dilatation, or intussusception) measures. Endoscopic manifestations were categorized as normal/mild vs. severe. Histopathological results were divided into mild and severe. Genotyping of HLA-DQ2 and DQ8 was performed. Serum levels of tissue-transglutaminase, endomysial, and gliadin antibodies were also determined. Logistic regression analysis and receiver operating characteristic (ROC) curve were used. Twenty-nine (72.5%) cases showed abnormal MRE. Reversed jejunoileal fold pattern had significant association with severe endoscopic (odds ratio [OR] = 8.38, 95% confidence interval [CI] 1.73-40.5) and pathologic features (OR = 7.36, 95% CI 1.33-40.54). An increased number of ileal folds/inch was significantly associated with severe MARSH score and positive HLA-DQ8. (P < 0.001 and P = 0.026, respectively). Ileal fold number had the highest areas under the curve for prediction of severe endoscopic (AUC: 0.75, P = 0.009) and pathologic (AUC: 0.84, P < 0.001) findings and positive anti-transglutaminase antibody (AUC: 0.85, P = 0.027). Fold pattern reversal on MRE is highly associated with endoscopic and pathologic features of refractory celiac disease (RCD). Increased ileal folds showed higher correlation with endoscopic-pathologic features, HLA-DQ8, and anti-transglutaminase level. MRE might be more sensitive for detection of increased ileal folds in CD rather than reduction of duodenal and jejunal folds due to better distension of ileal loops. 2 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2017;46:1096-1106. © 2017 International Society for Magnetic Resonance in Medicine.

  7. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    NASA Astrophysics Data System (ADS)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  8. Is Beauty in the Eyes of the Beholder? Aesthetic Quality versus Technical Skill in Movement Evaluation of Tai Chi.

    PubMed

    Zamparo, Paola; Zorzi, Elena; Marcantoni, Sara; Cesari, Paola

    2015-01-01

    The aim of this study was to compare experts to naïve practitioners in rating the beauty and the technical quality of a Tai Chi sequence observed in video-clips (of high and middle level performances). Our hypothesis are: i) movement evaluation will correlate with the level of skill expressed in the kinematics of the observed action but ii) only experts will be able to unravel the technical component from the aesthetic component of the observed action. The judgments delivered indicate that both expert and non-expert observers are able to discern a good from a mediocre performance; however, as expected, only experts discriminate the technical from the aesthetic component of the action evaluated and do this independently of the level of skill shown by the model (high or middle level performances). Furthermore, the judgments delivered were strongly related to the kinematic variables measured in the observed model, indicating that observers rely on specific movement kinematics (e.g. movement amplitude, jerk and duration) for action evaluation. These results provide evidence of the complementary functional role of visual and motor action representation in movement evaluation and underline the role of expertise in judging the aesthetic quality of movements.

  9. Is Beauty in the Eyes of the Beholder? Aesthetic Quality versus Technical Skill in Movement Evaluation of Tai Chi

    PubMed Central

    2015-01-01

    The aim of this study was to compare experts to naïve practitioners in rating the beauty and the technical quality of a Tai Chi sequence observed in video-clips (of high and middle level performances). Our hypothesis are: i) movement evaluation will correlate with the level of skill expressed in the kinematics of the observed action but ii) only experts will be able to unravel the technical component from the aesthetic component of the observed action. The judgments delivered indicate that both expert and non-expert observers are able to discern a good from a mediocre performance; however, as expected, only experts discriminate the technical from the aesthetic component of the action evaluated and do this independently of the level of skill shown by the model (high or middle level performances). Furthermore, the judgments delivered were strongly related to the kinematic variables measured in the observed model, indicating that observers rely on specific movement kinematics (e.g. movement amplitude, jerk and duration) for action evaluation. These results provide evidence of the complementary functional role of visual and motor action representation in movement evaluation and underline the role of expertise in judging the aesthetic quality of movements. PMID:26047473

  10. cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

    PubMed

    Martin-Herranz, Daniel E; Ribeiro, António J M; Krueger, Felix; Thornton, Janet M; Reik, Wolf; Stubbs, Thomas M

    2017-11-16

    DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome. Herein, we present customised Reduced Representation Bisulfite Sequencing (cuRRBS), a novel and easy-to-use computational method that solves this problem. By computing the optimal enzymatic digestions and size selection steps required, cuRRBS generalises the traditional MspI-based Reduced Representation Bisulfite Sequencing (RRBS) protocol to all restriction enzyme combinations. In addition, cuRRBS estimates the fold-reduction in sequencing costs and provides a robustness value for the personalised RRBS protocol, allowing users to tailor the protocol to their experimental needs. Moreover, we show in silico that cuRRBS-defined restriction enzymes consistently out-perform MspI digestion in many biological systems, considering both CpG and CHG contexts. Finally, we have validated the accuracy of cuRRBS predictions for single and double enzyme digestions using two independent experimental datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. How Fast Do Objects Fall in Visual Memory? Uncovering the Temporal and Spatial Features of Representational Gravity

    PubMed Central

    De Sá Teixeira, Nuno

    2016-01-01

    Visual memory for the spatial location where a moving target vanishes has been found to be systematically displaced downward in the direction of gravity. Moreover, it was recently reported that the magnitude of the downward error increases steadily with increasing retention intervals imposed after object’s offset and before observers are allowed to perform the spatial localization task, in a pattern where the remembered vanishing location drifts downward as if following a falling trajectory. This outcome was taken to reflect the dynamics of a representational model of earth’s gravity. The present study aims to establish the spatial and temporal features of this downward drift by taking into account the dynamics of the motor response. The obtained results show that the memory for the last location of the target drifts downward with time, thus replicating previous results. Moreover, the time taken for completion of the behavioural localization movements seems to add to the imposed retention intervals in determining the temporal frame during which the visual memory is updated. Overall, it is reported that the representation of spatial location drifts downward by about 3 pixels for each two-fold increase of time until response. The outcomes are discussed in relation to a predictive internal model of gravity which outputs an on-line spatial update of remembered objects’ location. PMID:26910260

  12. How Fast Do Objects Fall in Visual Memory? Uncovering the Temporal and Spatial Features of Representational Gravity.

    PubMed

    De Sá Teixeira, Nuno

    2016-01-01

    Visual memory for the spatial location where a moving target vanishes has been found to be systematically displaced downward in the direction of gravity. Moreover, it was recently reported that the magnitude of the downward error increases steadily with increasing retention intervals imposed after object's offset and before observers are allowed to perform the spatial localization task, in a pattern where the remembered vanishing location drifts downward as if following a falling trajectory. This outcome was taken to reflect the dynamics of a representational model of earth's gravity. The present study aims to establish the spatial and temporal features of this downward drift by taking into account the dynamics of the motor response. The obtained results show that the memory for the last location of the target drifts downward with time, thus replicating previous results. Moreover, the time taken for completion of the behavioural localization movements seems to add to the imposed retention intervals in determining the temporal frame during which the visual memory is updated. Overall, it is reported that the representation of spatial location drifts downward by about 3 pixels for each two-fold increase of time until response. The outcomes are discussed in relation to a predictive internal model of gravity which outputs an on-line spatial update of remembered objects' location.

  13. [Manual rotation of occiput posterior presentation].

    PubMed

    Le Ray, C; Goffinet, F

    2011-10-01

    Delivery in occiput posterior position is associated with a higher risk of cesarean section, operative vaginal delivery and severe perineal tears. We report the technic of manual rotation described by Tarnier and Chantreuil and used daily in our maternity center. Only five studies were published on this topic; all of them demonstrate that manual rotation decreases the risk of cesarean section. Moreover, it could decrease the risk of prolonged second stage, chorioamnionitis and third and fourth degree tears in comparison with expectant management. However, manual rotation is associated with a two-fold higher risk of cervical and vaginal lacerations. Manual rotation performed with an adequate technic is an efficient and safe manœuvre to avoid complications associated with occiput posterior vaginal delivery. Copyright © 2011. Published by Elsevier SAS.

  14. Library Resources for Bac End Sequencing. Final Technical Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pieter J. de Jong

    2000-10-01

    Studies directed towards the specific aims outlined for this research award are summarized. The RPCI II Human Bac Library has been expanded by the addition of 6.9-fold genomic coverage. This segment has been generated from a MBOI partial digest of the same anonymous donor DNA used for the rest of the library. A new cloning vector, pTARBAC1, has been constructed and used in the construction of RPCI-II segment 5. This new cloning vector provides a new strategy in identifying targeted genomic regions and will greatly facilitate a large-scale analysis for positional cloning. A new maleCS7BC/6J mouse BAC library has beenmore » constructed. RPCI-23 contain 576 plates (approx 210,000 clones) and represents approximately 11-fold coverage of the mouse genome.« less

  15. Identification of Alzheimer's disease and mild cognitive impairment using multimodal sparse hierarchical extreme learning machine.

    PubMed

    Kim, Jongin; Lee, Boreom

    2018-05-07

    Different modalities such as structural MRI, FDG-PET, and CSF have complementary information, which is likely to be very useful for diagnosis of AD and MCI. Therefore, it is possible to develop a more effective and accurate AD/MCI automatic diagnosis method by integrating complementary information of different modalities. In this paper, we propose multi-modal sparse hierarchical extreme leaning machine (MSH-ELM). We used volume and mean intensity extracted from 93 regions of interest (ROIs) as features of MRI and FDG-PET, respectively, and used p-tau, t-tau, and Aβ42 as CSF features. In detail, high-level representation was individually extracted from each of MRI, FDG-PET, and CSF using a stacked sparse extreme learning machine auto-encoder (sELM-AE). Then, another stacked sELM-AE was devised to acquire a joint hierarchical feature representation by fusing the high-level representations obtained from each modality. Finally, we classified joint hierarchical feature representation using a kernel-based extreme learning machine (KELM). The results of MSH-ELM were compared with those of conventional ELM, single kernel support vector machine (SK-SVM), multiple kernel support vector machine (MK-SVM) and stacked auto-encoder (SAE). Performance was evaluated through 10-fold cross-validation. In the classification of AD vs. HC and MCI vs. HC problem, the proposed MSH-ELM method showed mean balanced accuracies of 96.10% and 86.46%, respectively, which is much better than those of competing methods. In summary, the proposed algorithm exhibits consistently better performance than SK-SVM, ELM, MK-SVM and SAE in the two binary classification problems (AD vs. HC and MCI vs. HC). © 2018 Wiley Periodicals, Inc.

  16. Feynman formulae and phase space Feynman path integrals for tau-quantization of some Lévy-Khintchine type Hamilton functions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Butko, Yana A., E-mail: yanabutko@yandex.ru, E-mail: kinderknecht@math.uni-sb.de; Grothaus, Martin, E-mail: grothaus@mathematik.uni-kl.de; Smolyanov, Oleg G., E-mail: Smolyanov@yandex.ru

    2016-02-15

    Evolution semigroups generated by pseudo-differential operators are considered. These operators are obtained by different (parameterized by a number τ) procedures of quantization from a certain class of functions (or symbols) defined on the phase space. This class contains Hamilton functions of particles with variable mass in magnetic and potential fields and more general symbols given by the Lévy-Khintchine formula. The considered semigroups are represented as limits of n-fold iterated integrals when n tends to infinity. Such representations are called Feynman formulae. Some of these representations are constructed with the help of another pseudo-differential operator, obtained by the same procedure ofmore » quantization; such representations are called Hamiltonian Feynman formulae. Some representations are based on integral operators with elementary kernels; these are called Lagrangian Feynman formulae. Langrangian Feynman formulae provide approximations of evolution semigroups, suitable for direct computations and numerical modeling of the corresponding dynamics. Hamiltonian Feynman formulae allow to represent the considered semigroups by means of Feynman path integrals. In the article, a family of phase space Feynman pseudomeasures corresponding to different procedures of quantization is introduced. The considered evolution semigroups are represented as phase space Feynman path integrals with respect to these Feynman pseudomeasures, i.e., different quantizations correspond to Feynman path integrals with the same integrand but with respect to different pseudomeasures. This answers Berezin’s problem of distinguishing a procedure of quantization on the language of Feynman path integrals. Moreover, the obtained Lagrangian Feynman formulae allow also to calculate these phase space Feynman path integrals and to connect them with some functional integrals with respect to probability measures.« less

  17. A deep learning pipeline for Indian dance style classification

    NASA Astrophysics Data System (ADS)

    Dewan, Swati; Agarwal, Shubham; Singh, Navjyoti

    2018-04-01

    In this paper, we address the problem of dance style classification to classify Indian dance or any dance in general. We propose a 3-step deep learning pipeline. First, we extract 14 essential joint locations of the dancer from each video frame, this helps us to derive any body region location within the frame, we use this in the second step which forms the main part of our pipeline. Here, we divide the dancer into regions of important motion in each video frame. We then extract patches centered at these regions. Main discriminative motion is captured in these patches. We stack the features from all such patches of a frame into a single vector and form our hierarchical dance pose descriptor. Finally, in the third step, we build a high level representation of the dance video using the hierarchical descriptors and train it using a Recurrent Neural Network (RNN) for classification. Our novelty also lies in the way we use multiple representations for a single video. This helps us to: (1) Overcome the RNN limitation of learning small sequences over big sequences such as dance; (2) Extract more data from the available dataset for effective deep learning by training multiple representations. Our contributions in this paper are three-folds: (1) We provide a deep learning pipeline for classification of any form of dance; (2) We prove that a segmented representation of a dance video works well with sequence learning techniques for recognition purposes; (3) We extend and refine the ICD dataset and provide a new dataset for evaluation of dance. Our model performs comparable or better in some cases than the state-of-the-art on action recognition benchmarks.

  18. Inscriptional Representations of the Moon by Nonscientists

    NASA Astrophysics Data System (ADS)

    Grundstrom, Erika; Taylor, R. S.

    2009-05-01

    During this International Year of Astronomy, there is a great deal of focus on the observations Galileo made to provide evidence for the heliocentric model of the Solar System. The Moon was a regular focus of Galileo's investigations and of his detailed inscriptions (i.e., technical drawings). These inscriptions, which identified the presence of mountains, valleys, and craters, provided strong evidence against the prevailing view that the Moon was "perfect” in the classical sense. We have embarked upon a project of the general public's perception of the Moon. Visitors to Vanderbilt University's Dyer Observatory were asked to make an accurate "technical drawing” of the Moon, such as "one that a scientist might make.” Many families were in attendance, which permitted a wide assortment of ages in the individuals who agreed to participate, ranging from age 4 through 55. During this first phase of the project we identified several interesting patterns. First, for the phase of the Moon, 90% were drawn as full, 3% as crescent, and 7% as gibbous. Second, for the surface features of the moon, 83% included craters and 13% included mountains. The second phase of the study, currently underway, will examine changes in the inscriptional representations of the Moon by observatory visitors after they are given the opportunity to view the Moon in detail through one of the observatory's telescopes. This work is supported in part by grants from the Vanderbilt University Learning Sciences Institute (LSI) and the Institute of Educational Sciences (IES).

  19. Bringing 3D Printing to Geophysical Science Education

    NASA Astrophysics Data System (ADS)

    Boghosian, A.; Turrin, M.; Porter, D. F.

    2014-12-01

    3D printing technology has been embraced by many technical fields, and is rapidly making its way into peoples' homes and schools. While there is a growing educational and hobbyist community engaged in the STEM focused technical and intellectual challenges associated with 3D printing, there is unrealized potential for the earth science community to use 3D printing to communicate scientific research to the public. Moreover, 3D printing offers scientists the opportunity to connect students and the public with novel visualizations of real data. As opposed to introducing terrestrial measurements through the use of colormaps and gradients, scientists can represent 3D concepts with 3D models, offering a more intuitive education tool. Furthermore, the tactile aspect of models make geophysical concepts accessible to a wide range of learning styles like kinesthetic or tactile, and learners including both visually impaired and color-blind students.We present a workflow whereby scientists, students, and the general public will be able to 3D print their own versions of geophysical datasets, even adding time through layering to include a 4th dimension, for a "4D" print. This will enable scientists with unique and expert insights into the data to easily create the tools they need to communicate their research. It will allow educators to quickly produce teaching aids for their students. Most importantly, it will enable the students themselves to translate the 2D representation of geophysical data into a 3D representation of that same data, reinforcing spatial reasoning.

  20. Most Common Publication Types in Radiology Journals:: What is the Level of Evidence?

    PubMed

    Rosenkrantz, Andrew B; Pinnamaneni, Niveditha; Babb, James S; Doshi, Ankur M

    2016-05-01

    This study aimed to assess the most common publication types in radiology journals, as well as temporal trends and association with citation frequency. PubMed was searched to extract all published articles having the following "Publication Type" indices: "validation studies," "meta-analysis," "clinical trial," "comparative study," "evaluation study," "guideline," "multicenter study," "randomized study," "review," "editorial," "case report," and "technical report." The percentage of articles within each category published within clinical radiology journals was computed. Normalized percentages for each category were also computed on an annual basis. Citation counts within a 2-year window following publication were obtained using Web of Science. Overall trends were assessed. Publication types with the highest fraction in radiology journals were technical reports, evaluation studies, and case reports (4.8% to 5.8%). Publication types with the lowest fraction in radiology journals were randomized trials, multicenter studies, and meta-analyses (0.8% to 1.5%). Case reports showed a significant decrease since 1999, with accelerating decline since 2007 (P = 0.002). Publication types with highest citation counts were meta-analyses, guidelines, and multicenter studies (8.1 ± 10.7 to 12.9 ± 5.1). Publication types with lowest citation counts were case reports, editorials, and technical reports (1.4 ± 2.4 to 2.9 ± 4.3). The representation in radiology journals and citation frequency of the publication types showed weak inverse correlation (r = -0.372). Radiology journals have historically had relatively greater representation of less frequently cited publication types. Various strategies, including methodological training, multidisciplinary collaboration, national support networks, as well as encouragement of higher level of evidence by funding agencies and radiology journals themselves, are warranted to improve the impact of radiological research. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  1. [Lengthening temporalis myoplasty: Technical refinements].

    PubMed

    Guerreschi, P; Labbé, D

    2015-10-01

    First described by Labbé in 1997, the lengthening temporalis myoplasty (LTM) ensures the transfer of the entire temporal muscle from the coronoid process to the upper half of the lip without interposition of aponeurotic tissue. Thanks to brain plasticity, the temporal muscle is able to change its function because it is entirely mobilized towards another effector: the labial commissure. After 6 months of speech rehabilitation, the muscle loses its chewing function and it acquires its new smiling function. We describe as far as possible all the technical points to guide surgeons who would like to perform this powerful surgical procedure. We show the coronoid process approaches both through an upper temporal fossa approach and a lower nasolabial fold approach. Rehabilitation starts 3 weeks after the surgery following a standardized protocol to move from a mandibular smile to a voluntary smile, and then a spontaneous smile in 3 steps. The LTM is the main part of a one-stage global treatment of the paralyzed face. It constitutes a dynamic palliative treatment usually started at the sequelae stage, 18 months after the outcome of a peripheral facial paralysis. This one-stage procedure is a reproducible and relevant surgical technique in the difficult treatment of peripheral facial paralysis. An active muscle is transferred to reanimate the labial commissure and to recreate a mobile nasolabial fold. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  2. Combining Physicochemical and Evolutionary Information for Protein Contact Prediction

    PubMed Central

    Schneider, Michael; Brock, Oliver

    2014-01-01

    We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information—evolutionary and physicochemical—we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/. PMID:25338092

  3. EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

    PubMed Central

    Amidi, Afshine; Megalooikonomou, Vasileios; Paragios, Nikos

    2018-01-01

    During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The two-layer architecture was investigated on a large dataset of 63,558 enzymes from the PDB and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet. PMID:29740518

  4. EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation.

    PubMed

    Amidi, Afshine; Amidi, Shervine; Vlachakis, Dimitrios; Megalooikonomou, Vasileios; Paragios, Nikos; Zacharaki, Evangelia I

    2018-01-01

    During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The two-layer architecture was investigated on a large dataset of 63,558 enzymes from the PDB and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.

  5. PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

    PubMed

    Pasi, Marco; Lavery, Richard; Ceres, Nicoletta

    2013-01-08

    We present a coarse-grain protein model PaLaCe (Pasi-Lavery-Ceres) that has been developed principally to allow fast computational studies of protein mechanics and to clarify the links between mechanics and function. PaLaCe uses a two-tier protein representation with one to three pseudoatoms representing each amino acid for the main nonbonded interactions, combined with atomic-scale peptide groups and some side chain atoms to allow the explicit representation of backbone hydrogen bonds and to simplify the treatment of bonded interactions. The PaLaCe force field is composed of physics-based terms, parametrized using Boltzmann inversion of conformational probability distributions derived from a protein structure data set, and iteratively refined to reproduce the experimental distributions. PaLaCe has been implemented in the MMTK simulation package and can be used for energy minimization, normal mode calculations, and molecular or stochastic dynamics. We present simulations with PaLaCe that test its ability to maintain stable structures for folded proteins, reproduce their dynamic fluctuations, and correctly model large-scale, force-induced conformational changes.

  6. In silico toxicity prediction by support vector machine and SMILES representation-based string kernel.

    PubMed

    Cao, D-S; Zhao, J-C; Yang, Y-N; Zhao, C-X; Yan, J; Liu, S; Hu, Q-N; Xu, Q-S; Liang, Y-Z

    2012-01-01

    There is a great need to assess the harmful effects or toxicities of chemicals to which man is exposed. In the present paper, the simplified molecular input line entry specification (SMILES) representation-based string kernel, together with the state-of-the-art support vector machine (SVM) algorithm, were used to classify the toxicity of chemicals from the US Environmental Protection Agency Distributed Structure-Searchable Toxicity (DSSTox) database network. In this method, the molecular structure can be directly encoded by a series of SMILES substrings that represent the presence of some chemical elements and different kinds of chemical bonds (double, triple and stereochemistry) in the molecules. Thus, SMILES string kernel can accurately and directly measure the similarities of molecules by a series of local information hidden in the molecules. Two model validation approaches, five-fold cross-validation and independent validation set, were used for assessing the predictive capability of our developed models. The results obtained indicate that SVM based on the SMILES string kernel can be regarded as a very promising and alternative modelling approach for potential toxicity prediction of chemicals.

  7. Two-dimensional shape classification using generalized Fourier representation and neural networks

    NASA Astrophysics Data System (ADS)

    Chodorowski, Artur; Gustavsson, Tomas; Mattsson, Ulf

    2000-04-01

    A shape-based classification method is developed based upon the Generalized Fourier Representation (GFR). GFR can be regarded as an extension of traditional polar Fourier descriptors, suitable for description of closed objects, both convex and concave, with or without holes. Explicit relations of GFR coefficients to regular moments, moment invariants and affine moment invariants are given in the paper. The dual linear relation between GFR coefficients and regular moments was used to compare shape features derive from GFR descriptors and Hu's moment invariants. the GFR was then applied to a clinical problem within oral medicine and used to represent the contours of the lesions in the oral cavity. The lesions studied were leukoplakia and different forms of lichenoid reactions. Shape features were extracted from GFR coefficients in order to classify potentially cancerous oral lesions. Alternative classifiers were investigated based on a multilayer perceptron with different architectures and extensions. The overall classification accuracy for recognition of potentially cancerous oral lesions when using neural network classifier was 85%, while the classification between leukoplakia and reticular lichenoid reactions gave 96% (5-fold cross-validated) recognition rate.

  8. Anterior petroclinoid fold fenestration: an adjunct to clipping of postero-laterally projecting posterior communicating aneurysms.

    PubMed

    Nossek, Erez; Setton, Avi; Dehdashti, Amir R; Chalif, David J

    2014-10-01

    Proximally located posterior communicating artery (PCoA) aneurysms, projecting postero-laterally in proximity to the tentorium, may pose a technical challenge for microsurgical clipping due to obscuration of the proximal aneurysmal neck by the anterior petroclinoid fold. We describe an efficacious technique utilizing fenestration of the anterior petroclinoid fold to facilitate visualization and clipping of PCoA aneurysms abutting this aspect of the tentorium. Of 86 cases of PCoA aneurysms treated between 2003 and 2013, the technique was used in nine (10.5 %) patients to allow for adequate clipping. A 3 mm fenestration in the anterior petroclinoid ligament is created adjacent and lateral to the anterior clinoid process. This fenestration is then widened into a small wedge corridor by bipolar coagulation. In all cases, the proximal aneurysm neck was visualized after the wedge fenestration. Additionally, an adequate corridor for placement of the proximal clip blade was uniformly established. All cases were adequately clipped, with complete occlusion of the aneurysm neck and fundus with preservation of the PCoA. There were two intraoperative ruptures not related to creation of the wedge fenestration. One patient experienced post-operative partial third nerve palsy, which resolved during follow-up. We describe a technique of fenestration of the anterior petroclinoid fold to establish a critical and safe corridor for both visualization and clipping of PCoA aneurysms.

  9. Assessment of Fine Needle Aspiration Feasibility and Specimen Adequacy for Molecular Diagnostics of Benign Vocal Fold Lesions

    PubMed Central

    Li, Nicole Y. K.; Dailey, Seth; Thibeault, Susan L.

    2014-01-01

    Objectives/Hypothesis The use of molecular testing is becoming more significant for the diagnosis and classification of disease. The application of fine-needle aspiration (FNA) biopsy as the means of sampling lesions in union with molecular testing could be a powerful combination in laryngology. The objectives of this study were to investigate 1) if FNA was feasible to sample benign vocal fold lesions; 2) if FNA samples provided sufficient RNA quality for molecular analysis; and 3) if gene expression of FNA samples matched paired surgical excised specimens. Study Design Prospective cross-sectional. Methods Fifteen vocal fold specimens were obtained from adult patients undergoing routine surgical removal for benign vocal fold lesions using FNA and surgical excision. Comparisons were made between FNA and excision biopsies for RNA quality. Correlative analysis was completed for RNA expression of nine genes, including decorin (DCN), connective tissue growth factor (CTGF), vascular endothelial growth factor (VEGF), collagen type VI alpha 3 (COL6A3), superoxide dismutase 1 (SOD1), glutathione S-transferase (GST2), collagen type I alpha 2 (COL1A2), ATP binding cassette (ABC), and procollagen I alpha 1 (COL1A1). Results FNA and excision samples demonstrated similar RNA quality (P > 0.05). Per gene expression, four out of nine genes were moderately correlated between the paired samples (P < 0.05). Conclusions FNA of the vocal fold lamina propria is technically feasible to perform. Further improvement in the FNA technology is desirable to optimize RNA quality for reliable gene expression analysis. PMID:23404571

  10. Fractal Parameter Space of Lorenz-like Attractors: A Hierarchical Approach

    NASA Astrophysics Data System (ADS)

    Xing, Tingli; Wojcik, Jeremy; Zaks, Michael A.; Shilnikov, Andrey

    2014-12-01

    Using bi-parametric sweeping based on symbolic representation we reveal self-similar fractal structures induced by hetero- and homoclinic bifurcations of saddle singularities in the parameter space of two systems with deterministic chaos. We start with the system displaying a few homoclinic bifurcations of higher codimension: resonant saddle, orbitflip and inclination switch that all can give rise to the onset of the Lorenz-type attractor. It discloses a universal unfolding pattern in the case of systems of autonomous ordinary differential equations possessing two-fold symmetry or "Z2-systems" with the characteristic separatrix butterfly. The second system is the classic Lorenz model of 1963, originated in fluid mechanics.

  11. Adaptive regulation of sparseness by feedforward inhibition

    PubMed Central

    Assisi, Collins; Stopfer, Mark; Laurent, Gilles; Bazhenov, Maxim

    2014-01-01

    In the mushroom body of insects, odors are represented by very few spikes in a small number of neurons, a highly efficient strategy known as sparse coding. Physiological studies of these neurons have shown that sparseness is maintained across thousand-fold changes in odor concentration. Using a realistic computational model, we propose that sparseness in the olfactory system is regulated by adaptive feedforward inhibition. When odor concentration changes, feedforward inhibition modulates the duration of the temporal window over which the mushroom body neurons may integrate excitatory presynaptic input. This simple adaptive mechanism could maintain the sparseness of sensory representations across wide ranges of stimulus conditions. PMID:17660812

  12. Proceedings of the 7th US/German Workshop on Salt Repository Research, Design, and Operation.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hansen, Francis D.; Steininger, Walter; Bollingerfehr, Willhelm

    The 7th US/German Workshop on Salt Repository Research, Design, and Operation was held in Washington, DC on September 7-9, 2016. Over fifty participants representing governmental agencies, internationally recognized salt research groups, universities, and private companies helped advance the technical basis for salt disposal of radioactive waste. Representatives from several United States federal agencies were able to attend, including the Department of Energy´s Office of Environmental Management and Office of Nuclear Energy, the Environmental Protection Agency, the Nuclear Regulatory Commission, and the Nuclear Waste Technical Review Board. A similar representation from the German ministries showcased the covenant established in a Memorandummore » of Understanding executed between the United States and Germany in 2011. The US/German workshops´ results and activities also contribute significantly to the Nuclear Energy Agency Salt Club repository research agenda.« less

  13. Computer technologies and institutional memory

    NASA Technical Reports Server (NTRS)

    Bell, Christopher; Lachman, Roy

    1989-01-01

    NASA programs for manned space flight are in their 27th year. Scientists and engineers who worked continuously on the development of aerospace technology during that period are approaching retirement. The resulting loss to the organization will be considerable. Although this problem is general to the NASA community, the problem was explored in terms of the institutional memory and technical expertise of a single individual in the Man-Systems division. The main domain of the expert was spacecraft lighting, which became the subject area for analysis in these studies. The report starts with an analysis of the cumulative expertise and institutional memory of technical employees of organizations such as NASA. A set of solutions to this problem are examined and found inadequate. Two solutions were investigated at length: hypertext and expert systems. Illustrative examples were provided of hypertext and expert system representation of spacecraft lighting. These computer technologies can be used to ameliorate the problem of the loss of invaluable personnel.

  14. Genome size diversity in orchids: consequences and evolution

    PubMed Central

    Leitch, I. J.; Kahandawala, I.; Suda, J.; Hanson, L.; Ingrouille, M. J.; Chase, M. W.; Fay, M. F.

    2009-01-01

    Background The amount of DNA comprising the genome of an organism (its genome size) varies a remarkable 40 000-fold across eukaryotes, yet most groups are characterized by much narrower ranges (e.g. 14-fold in gymnosperms, 3- to 4-fold in mammals). Angiosperms stand out as one of the most variable groups with genome sizes varying nearly 2000-fold. Nevertheless within angiosperms the majority of families are characterized by genomes which are small and vary little. Species with large genomes are mostly restricted to a few monocots families including Orchidaceae. Scope A survey of the literature revealed that genome size data for Orchidaceae are comparatively rare representing just 327 species. Nevertheless they reveal that Orchidaceae are currently the most variable angiosperm family with genome sizes ranging 168-fold (1C = 0·33–55·4 pg). Analysing the data provided insights into the distribution, evolution and possible consequences to the plant of this genome size diversity. Conclusions Superimposing the data onto the increasingly robust phylogenetic tree of Orchidaceae revealed how different subfamilies were characterized by distinct genome size profiles. Epidendroideae possessed the greatest range of genome sizes, although the majority of species had small genomes. In contrast, the largest genomes were found in subfamilies Cypripedioideae and Vanilloideae. Genome size evolution within this subfamily was analysed as this is the only one with reasonable representation of data. This approach highlighted striking differences in genome size and karyotype evolution between the closely related Cypripedium, Paphiopedilum and Phragmipedium. As to the consequences of genome size diversity, various studies revealed that this has both practical (e.g. application of genetic fingerprinting techniques) and biological consequences (e.g. affecting where and when an orchid may grow) and emphasizes the importance of obtaining further genome size data given the considerable phylogenetic gaps which have been highlighted by the current study. PMID:19168860

  15. Engine Structural Analysis Software

    NASA Technical Reports Server (NTRS)

    McKnight, R. L.; Maffeo, R. J.; Schrantz, S.; Hartle, M. S.; Bechtel, G. S.; Lewis, K.; Ridgway, M.; Chamis, Christos C. (Technical Monitor)

    2001-01-01

    The report describes the technical effort to develop: (1) geometry recipes for nozzles, inlets, disks, frames, shafts, and ducts in finite element form, (2) component design tools for nozzles, inlets, disks, frames, shafts, and ducts which utilize the recipes and (3) an integrated design tool which combines the simulations of the nozzles, inlets, disks, frames, shafts, and ducts with the previously developed combustor, turbine blade, and turbine vane models for a total engine representation. These developments will be accomplished in cooperation and in conjunction with comparable efforts of NASA Glenn Research Center.

  16. Performance Management and Optimization of Semiconductor Design Projects

    NASA Astrophysics Data System (ADS)

    Hinrichs, Neele; Olbrich, Markus; Barke, Erich

    2010-06-01

    The semiconductor industry is characterized by fast technological changes and small time-to-market windows. Improving productivity is the key factor to stand up to the competitors and thus successfully persist in the market. In this paper a Performance Management System for analyzing, optimizing and evaluating chip design projects is presented. A task graph representation is used to optimize the design process regarding time, cost and workload of resources. Key Performance Indicators are defined in the main areas cost, profit, resources, process and technical output to appraise the project.

  17. Analysis models for the estimation of oceanic fields

    NASA Technical Reports Server (NTRS)

    Carter, E. F.; Robinson, A. R.

    1987-01-01

    A general model for statistically optimal estimates is presented for dealing with scalar, vector and multivariate datasets. The method deals with anisotropic fields and treats space and time dependence equivalently. Problems addressed include the analysis, or the production of synoptic time series of regularly gridded fields from irregular and gappy datasets, and the estimate of fields by compositing observations from several different instruments and sampling schemes. Technical issues are discussed, including the convergence of statistical estimates, the choice of representation of the correlations, the influential domain of an observation, and the efficiency of numerical computations.

  18. Development of optimized techniques and requirements for computer enhancement of structural weld radiographs. Volume 1: Technical report

    NASA Technical Reports Server (NTRS)

    Adams, J. R.; Hawley, S. W.; Peterson, G. R.; Salinger, S. S.; Workman, R. A.

    1971-01-01

    A hardware and software specification covering requirements for the computer enhancement of structural weld radiographs was considered. Three scanning systems were used to digitize more than 15 weld radiographs. The performance of these systems was evaluated by determining modulation transfer functions and noise characteristics. Enhancement techniques were developed and applied to the digitized radiographs. The scanning parameters of spot size and spacing and film density were studied to optimize the information content of the digital representation of the image.

  19. A Computationally Efficient Hypothesis Testing Method for Epistasis Analysis using Multifactor Dimensionality Reduction

    PubMed Central

    Pattin, Kristine A.; White, Bill C.; Barney, Nate; Gui, Jiang; Nelson, Heather H.; Kelsey, Karl R.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

    2008-01-01

    Multifactor dimensionality reduction (MDR) was developed as a nonparametric and model-free data mining method for detecting, characterizing, and interpreting epistasis in the absence of significant main effects in genetic and epidemiologic studies of complex traits such as disease susceptibility. The goal of MDR is to change the representation of the data using a constructive induction algorithm to make nonadditive interactions easier to detect using any classification method such as naïve Bayes or logistic regression. Traditionally, MDR constructed variables have been evaluated with a naïve Bayes classifier that is combined with 10-fold cross validation to obtain an estimate of predictive accuracy or generalizability of epistasis models. Traditionally, we have used permutation testing to statistically evaluate the significance of models obtained through MDR. The advantage of permutation testing is that it controls for false-positives due to multiple testing. The disadvantage is that permutation testing is computationally expensive. This is in an important issue that arises in the context of detecting epistasis on a genome-wide scale. The goal of the present study was to develop and evaluate several alternatives to large-scale permutation testing for assessing the statistical significance of MDR models. Using data simulated from 70 different epistasis models, we compared the power and type I error rate of MDR using a 1000-fold permutation test with hypothesis testing using an extreme value distribution (EVD). We find that this new hypothesis testing method provides a reasonable alternative to the computationally expensive 1000-fold permutation test and is 50 times faster. We then demonstrate this new method by applying it to a genetic epidemiology study of bladder cancer susceptibility that was previously analyzed using MDR and assessed using a 1000-fold permutation test. PMID:18671250

  20. A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis.

    PubMed

    Liu, Bin; Wang, Xiaolong; Lin, Lei; Dong, Qiwen; Wang, Xuan

    2008-12-01

    Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate methods for solving these problems. A key step to improve the performance of the SVM-based methods is to find a suitable representation of protein sequences. In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequency profiles are calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into Top-n-grams. The protein sequences are transformed into fixed-dimension feature vectors by the occurrence times of each Top-n-gram. The training vectors are evaluated by SVM to train classifiers which are then used to classify the test protein sequences. We demonstrate that the prediction performance of remote homology detection and fold recognition can be improved by combining Top-n-grams and latent semantic analysis (LSA), which is an efficient feature extraction technique from natural language processing. When tested on superfamily and fold benchmarks, the method combining Top-n-grams and LSA gives significantly better results compared to related methods. The method based on Top-n-grams significantly outperforms the methods based on many other building blocks including N-grams, patterns, motifs and binary profiles. Therefore, Top-n-gram is a good building block of the protein sequences and can be widely used in many tasks of the computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the prediction of protein binding sites.

  1. Wrinkling instabilities in soft bilayered systems

    PubMed Central

    Budday, Silvia; Andres, Sebastian; Walter, Bastian

    2017-01-01

    Wrinkling phenomena control the surface morphology of many technical and biological systems. While primary wrinkling has been extensively studied, experimentally, analytically and computationally, higher-order instabilities remain insufficiently understood, especially in systems with stiffness contrasts well below 100. Here, we use the model system of an elastomeric bilayer to experimentally characterize primary and secondary wrinkling at moderate stiffness contrasts. We systematically vary the film thickness and substrate prestretch to explore which parameters modulate the emergence of secondary instabilities, including period-doubling, period-tripling and wrinkle-to-fold transitions. Our experiments suggest that period-doubling is the favourable secondary instability mode and that period-tripling can emerge under disturbed boundary conditions. High substrate prestretch can suppress period-doubling and primary wrinkles immediately transform into folds. We combine analytical models with computational simulations to predict the onset of primary wrinkling, the post-buckling behaviour, secondary bifurcations and the wrinkle-to-fold transition. Understanding the mechanisms of pattern selection and identifying the critical control parameters of wrinkling will allow us to fabricate smart surfaces with tunable properties and to control undesired surface patterns like in the asthmatic airway. This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications.’ PMID:28373385

  2. On a Continuum Limit for Loop Quantum Cosmology

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Corichi, Alejandro; Center for Fundamental Theory, Institute for Gravitation and the Cosmos, Pennsylvania State University, University Park PA 16802; Vukasinac, Tatjana

    2008-03-06

    The use of non-regular representations of the Heisenberg-Weyl commutation relations has proved to be useful for studying conceptual and technical issues in quantum gravity. Of particular relevance is the study of Loop Quantum Cosmology (LQC), symmetry reduced theory that is related to Loop Quantum Gravity, and that is based on a non-regular, polymeric representation. Recently, a soluble model was used by Ashtekar, Corichi and Singh to study the relation between Loop Quantum Cosmology and the standard Wheeler-DeWitt theory and, in particular, the passage to the limit in which the auxiliary parameter (interpreted as ''quantum geometry discreetness'') is sent to zeromore » in hope to get rid of this 'regulator' that dictates the LQC dynamics at each 'scale'. In this note we outline the first steps toward reformulating this question within the program developed by the authors for studying the continuum limit of polymeric theories, which was successfully applied to simple systems such as a Simple Harmonic Oscillator.« less

  3. Human Sensibility Ergonomics Approach to Vehicle Simulator Based on Dynamics

    NASA Astrophysics Data System (ADS)

    Son, Kwon; Choi, Kyung-Hyun; Yoon, Ji-Sup

    Simulators have been used to evaluate drivers' reactions to various transportation products. Most research, however, has concentrated on their technical performance. This paper considers driver's motion perception on a vehicle simulator through the analysis of human sensibility ergonomics. A sensibility ergonomic method is proposed in order to improve the reliability of vehicle simulators. A simulator in a passenger vehicle consists of three main modules such as vehicle dynamics, virtual environment, and motion representation modules. To evaluate drivers' feedback, human perceptions are categorized into a set verbal expressions collected and investigated to find the most appropriate ones for translation and angular accelerations of the simulator. The cut-off frequency of the washout filter in the representation module is selected as one sensibility factor. Sensibility experiments were carried out to find a correlation between the expressions and the cut-off frequency of the filter. This study suggests a methodology to obtain an ergonomic database that can be applied to the sensibility evaluation of dynamic simulators.

  4. Coordinating complex decision support activities across distributed applications

    NASA Technical Reports Server (NTRS)

    Adler, Richard M.

    1994-01-01

    Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

  5. Graphical representations of 1991 steam-electric power plant operation and air emissions data. Final report, July 1993-September 1994

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rothschild, S.S.; Chen, J.

    1994-11-01

    The report provides graphical representations of data derived from the U.S. Department of Energy's (DOE's) Energy Information Administration's (EIA's) Form EIA-767 (Steam Electric Plant Operation and Design Report). The U.S. EPA has contributed funding to DOE for this effort. The report summarizes information from the EIA-767 database that is otherwise not readily available to the community of electric utility data users or other members of the general public. To facilitate interpretation by non-technical readers, the report emphasizes graphical displays of data, consisting of 98 charts and 3 tables. The graphics present national data, national coal data, regional data, specified statemore » data, and specified operating utility company data. Data tables show sulfur dioxide (SO2) and nitrogen oxide (NOx) emissions by state, and the highest emitting electric utility companies. Charts show SO2 and NOx emissions by fuel type, fuel type and sulfur content, and fuel type and boiler capacity.« less

  6. Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements.

    PubMed

    Devonshire, Alison S; Elaswarapu, Ramnath; Foy, Carole A

    2010-11-24

    Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mRNA expression makes the evaluation and standardization of transcriptomic data problematic due to differences in protocols, data processing and analysis methods. Thus, universal RNA standards, such as those developed by the External RNA Controls Consortium (ERCC), are proposed to aid validation of research findings from diverse platforms such as microarrays and RT-qPCR, and play a role in quality control (QC) processes as transcriptomic profiling becomes more commonplace in the clinical setting. Panels of ERCC RNA standards were constructed in order to test the utility of these reference materials (RMs) for performance characterization of two selected gene expression platforms, and for discrimination of biomarker profiles between groups. The linear range, limits of detection and reproducibility of microarray and RT-qPCR measurements were evaluated using panels of RNA standards. Transcripts of low abundance (≤ 10 copies/ng total RNA) showed more than double the technical variability compared to higher copy number transcripts on both platforms. Microarray profiling of two simulated 'normal' and 'disease' panels, each consisting of eight different RNA standards, yielded robust discrimination between the panels and between standards with varying fold change ratios, showing no systematic effects due to different labelling and hybridization runs. Also, comparison of microarray and RT-qPCR data for fold changes showed agreement for the two platforms. ERCC RNA standards provide a generic means of evaluating different aspects of platform performance, and can provide information on the technical variation associated with quantification of biomarkers expressed at different levels of physiological abundance. Distinct panels of standards serve as an ideal quality control tool kit for determining the accuracy of fold change cut-off threshold and the impact of experimentally-derived noise on the discrimination of normal and disease profiles.

  7. Classical simulation of quantum many-body systems

    NASA Astrophysics Data System (ADS)

    Huang, Yichen

    Classical simulation of quantum many-body systems is in general a challenging problem for the simple reason that the dimension of the Hilbert space grows exponentially with the system size. In particular, merely encoding a generic quantum many-body state requires an exponential number of bits. However, condensed matter physicists are mostly interested in local Hamiltonians and especially their ground states, which are highly non-generic. Thus, we might hope that at least some physical systems allow efficient classical simulation. Starting with one-dimensional (1D) quantum systems (i.e., the simplest nontrivial case), the first basic question is: Which classes of states have efficient classical representations? It turns out that this question is quantitatively related to the amount of entanglement in the state, for states with "little entanglement'' are well approximated by matrix product states (a data structure that can be manipulated efficiently on a classical computer). At a technical level, the mathematical notion for "little entanglement'' is area law, which has been proved for unique ground states in 1D gapped systems. We establish an area law for constant-fold degenerate ground states in 1D gapped systems and thus explain the effectiveness of matrix-product-state methods in (e.g.) symmetry breaking phases. This result might not be intuitively trivial as degenerate ground states in gapped systems can be long-range correlated. Suppose an efficient classical representation exists. How can one find it efficiently? The density matrix renormalization group is the leading numerical method for computing ground states in 1D quantum systems. However, it is a heuristic algorithm and the possibility that it may fail in some cases cannot be completely ruled out. Recently, a provably efficient variant of the density matrix renormalization group has been developed for frustration-free 1D gapped systems. We generalize this algorithm to all (i.e., possibly frustrated) 1D gapped systems. Note that the ground-state energy of 1D gapless Hamiltonians is computationally intractable even in the presence of translational invariance. It is tempting to extend methods and tools in 1D to two and higher dimensions (2+D), e.g., matrix product states are generalized to tensor network states. Since an area law for entanglement (if formulated properly) implies efficient matrix product state representations in 1D, an interesting question is whether a similar implication holds in 2+D. Roughly speaking, we show that an area law for entanglement (in any reasonable formulation) does not always imply efficient tensor network representations of the ground states of 2+D local Hamiltonians even in the presence of translational invariance. It should be emphasized that this result does not contradict with the common sense that in practice quantum states with more entanglement usually require more space to be stored classically; rather, it demonstrates that the relationship between entanglement and efficient classical representations is still far from being well understood. Excited eigenstates participate in the dynamics of quantum systems and are particularly relevant to the phenomenon of many-body localization (absence of transport at finite temperature in strongly correlated systems). We study the entanglement of excited eigenstates in random spin chains and expect that its singularities coincide with dynamical quantum phase transitions. This expectation is confirmed in the disordered quantum Ising chain using both analytical and numerical methods. Finally, we study the problem of generating ground states (possibly with topological order) in 1D gapped systems using quantum circuits. This is an interesting problem both in theory and in practice. It not only characterizes the essential difference between the entanglement patterns that give rise to trivial and nontrivial topological order, but also quantifies the difficulty of preparing quantum states with a quantum computer (in experiments).

  8. Locality, reflection, and wave-particle duality

    NASA Astrophysics Data System (ADS)

    Mugur-Schächter, Mioara

    1987-08-01

    Bell's theorem is believed to establish that the quantum mechanical predictions do not generally admit a causal representation compatible with Einsten's principle of separability, thereby proving incompatibility between quantum mechanics and relativity. This interpretation is contested via two convergent approaches which lead to a sharp distinction between quantum nonseparability and violation of Einstein's theory of relativity. In a first approach we explicate from the quantum mechanical formalism a concept of “reflected dependence.” Founded on this concept, we produce a causal representation of the quantum mechanical probability measure involved in Bell's proof, which is clearly separable in Einstein's sense, i.e., it does not involve supraluminal velocities, and nevertheless is “nonlocal” in Bell's sense. So Bell locality and Einstein separability are distinct qualifications, and Bell nonlocality (or Bell nonseparability) and Einstein separability are not incompatible. It is then proved explicitly that with respect to the mentioned representation Bell's derivation does not hold. So Bell's derivation does not establish that any Einstein-separable representation is incompatible with quantum mechanics. This first—negative—conclusion is a syntactic fact. The characteristics of the representation and of the reasoning involved in the mentioned counterexample to the usual interpretation of Bell's theorem suggest that the representation used—notwithstanding its ability to bring forth the specified syntactic fact—is not factually true. Factual truth and syntactic properties also have to be radically distinguished in their turn. So, in a second approach, starting from de Broglie's initial relativistic model of a microsystem, a deeper, factually acceptable representation is constructed. The analyses leading to this second representation show that quantum mechanics does indeed involve basically a certain sort of nonseparability, called here de Broglie-Bohr quantum nonseparability. But the de Broglie-Bohr quantum nonseparability is shown to stem directly from the relativistic character of the considerations which led Louis de Broglie to the fundamental relation p = h/λ, thereby being essentially consistent with relativity. As to Einstein separability, it appears to be a still insufficiently specified concept of which a future, improved specification, will probably be explicitly harmonizable with the de Broglie-Bohr quantum nonseparability. The ensemble of the conclusions obtained here brings forth a new concept of causality, a concept of folded, zigzag, reflexive causality, with respect to which the type of causality conceived of up to now appears as a particular case of outstretched, one-way causality. The reflexive causality is found compatible with the results of Aspect's experiment, and it suggests new experiments. Considered globally, the conclusions obtained in the present work might convert the conceptual situation created by Bell's proof into a process of unification of quantum mechanics and relativity.

  9. Technical aspects of pediatric epilepsy surgery: Report of a multicenter, multinational web-based survey by the ILAE Task Force on Pediatric Epilepsy Surgery.

    PubMed

    Cukiert, Arthur; Rydenhag, Bertil; Harkness, William; Cross, J Helen; Gaillard, William D

    2016-02-01

    Surgical techniques may vary extensively between centers. We report on a web-based survey aimed at evaluating the current technical approaches in different centers around the world performing epilepsy surgery in children. The intention of the survey was to establish technical standards. A request was made to 88 centers to complete a web-based survey comprising 51 questions. There were 14 questions related to general issues, 13 questions investigating the different technical aspects for children undergoing epilepsy surgery, and 24 questions investigating surgical strategies in pediatric epilepsy surgery. Fifty-two centers covering a wide geographic representation completed the questionnaire. The median number of resective procedures per center per year was 47. Some important technical practices appeared (>80% of the responses) such as the use of prophylactic antibiotics (98%), the use of high-speed drills for bone opening (88%), nonresorbable material for bone flap closure (85%), head fixation (90%), use of the surgical microscope (100%), and of free bone flaps. Other questions, such as the use of drains, electrocorticography (ECoG) and preoperative withdrawal of valproate, led to mixed, inconclusive results. Complications were noted in 3.8% of the patients submitted to cortical resection, 9.9% hemispheric surgery, 5% callosotomy, 1.8% depth electrode implantation, 5.9% subdural grids implantation, 11.9% hypothalamic hamartoma resection, 0.9% vagus nerve stimulation (VNS), and 0.5% deep brain stimulation. There were no major differences across regions or countries in any of the subitems above. The present data offer the first overview of the technical aspects of pediatric epilepsy surgery worldwide. Surprisingly, there seem to be more similarities than differences. That aside many of the evaluated issues should be examined by adequately designed multicenter randomized controlled trials (RCTs). Further knowledge on these technical issues might lead to increased standardization and lower costs in the future, as well as definitive practice guidelines. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

  10. Low-field MRI can be more sensitive than high-field MRI

    NASA Astrophysics Data System (ADS)

    Coffey, Aaron M.; Truong, Milton L.; Chekmenev, Eduard Y.

    2013-12-01

    MRI signal-to-noise ratio (SNR) is the key factor for image quality. Conventionally, SNR is proportional to nuclear spin polarization, which scales linearly with magnetic field strength. Yet ever-stronger magnets present numerous technical and financial limitations. Low-field MRI can mitigate these constraints with equivalent SNR from non-equilibrium ‘hyperpolarization' schemes, which increase polarization by orders of magnitude independently of the magnetic field. Here, theory and experimental validation demonstrate that combination of field independent polarization (e.g. hyperpolarization) with frequency optimized MRI detection coils (i.e. multi-turn coils using the maximum allowed conductor length) results in low-field MRI sensitivity approaching and even rivaling that of high-field MRI. Four read-out frequencies were tested using samples with identical numbers of 1H and 13C spins. Experimental SNRs at 0.0475 T were ∼40% of those obtained at 4.7 T. Conservatively, theoretical SNRs at 0.0475 T 1.13-fold higher than those at 4.7 T were possible despite an ∼100-fold lower detection frequency, indicating feasibility of high-sensitivity MRI without technically challenging, expensive high-field magnets. The data at 4.7 T and 0.0475 T was obtained from different spectrometers with different RF probes. The SNR comparison between the two field strengths accounted for many differences in parameters such as system noise figures and variations in the probe detection coils including Q factors and coil diameters.

  11. Concepts of formal concept analysis

    NASA Astrophysics Data System (ADS)

    Žáček, Martin; Homola, Dan; Miarka, Rostislav

    2017-07-01

    The aim of this article is apply of Formal Concept Analysis on concept of world. Formal concept analysis (FCA) as a methodology of data analysis, information management and knowledge representation has potential to be applied to a verity of linguistic problems. FCA is mathematical theory for concepts and concept hierarchies that reflects an understanding of concept. Formal concept analysis explicitly formalizes extension and intension of a concept, their mutual relationships. A distinguishing feature of FCA is an inherent integration of three components of conceptual processing of data and knowledge, namely, the discovery and reasoning with concepts in data, discovery and reasoning with dependencies in data, and visualization of data, concepts, and dependencies with folding/unfolding capabilities.

  12. [Feature extraction for breast cancer data based on geometric algebra theory and feature selection using differential evolution].

    PubMed

    Li, Jing; Hong, Wenxue

    2014-12-01

    The feature extraction and feature selection are the important issues in pattern recognition. Based on the geometric algebra representation of vector, a new feature extraction method using blade coefficient of geometric algebra was proposed in this study. At the same time, an improved differential evolution (DE) feature selection method was proposed to solve the elevated high dimension issue. The simple linear discriminant analysis was used as the classifier. The result of the 10-fold cross-validation (10 CV) classification of public breast cancer biomedical dataset was more than 96% and proved superior to that of the original features and traditional feature extraction method.

  13. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    NASA Astrophysics Data System (ADS)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  14. X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, S.; Park, S.; Makowski, L.

    Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each aminomore » acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.« less

  15. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface.

    PubMed

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  16. Design by Analogy: Achieving More Patentable Ideas from One Creative Design

    NASA Astrophysics Data System (ADS)

    Jia, Li-Zhen; Wu, Chun-Long; Zhu, Xue-Hong; Tan, Run-Hua

    2018-12-01

    A patent is a kind of technical document to protect intellectual property for individuals or enterprises. Patentable idea generation is a crucial step for patent application and analogy is confirmed to be an effective technique to inspire creative ideas. Analogy-based design usually starts from representation of an analogy source and is followed by the retrieval of appropriate analogs, mapping of design knowledge and adaptation of target solution. To diffuse one core idea into other new contexts and achieve more patentable ideas, this paper mainly centered on the first two stages of analogy-based design and proposed a patentable ideation framework. The analogical information of the source system, including source design problems and solution, was mined comprehensively through International Patent Classification analysis and represented in the form of function, behavior and structure. Three heuristics were suggested for searching the set of candidate target systems with a similar design problem, where the source design could be transferred. To systematize the process of source representation, analogs retrieval, idea transfer, and solution generation, an ideation model was put forward. Finally, the bladeless fan was selected as a source design to illustrate the application of this work. The design output shows that the representation and heuristics are beneficial, and this systematic ideation method can help the engineer or designer enhance creativity and discover more patentable opportunities.

  17. Structural classification of proteins using texture descriptors extracted from the cellular automata image.

    PubMed

    Kavianpour, Hamidreza; Vasighi, Mahdi

    2017-02-01

    Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational methods and intelligence systems can have an important role in performing structural classification of proteins. Most of protein sequences are saved in databanks as characters and strings and a numerical representation is essential for applying machine learning methods. In this work, a binary representation of protein sequences is introduced based on reduced amino acids alphabets according to surrounding hydrophobicity index. Many important features which are hidden in these long binary sequences can be clearly displayed through their cellular automata images. The extracted features from these images are used to build a classification model by support vector machine. Comparing to previous studies on the several benchmark datasets, the promising classification rates obtained by tenfold cross-validation imply that the current approach can help in revealing some inherent features deeply hidden in protein sequences and improve the quality of predicting protein structural class.

  18. Fourth Conference on Artificial Intelligence for Space Applications

    NASA Technical Reports Server (NTRS)

    Odell, Stephen L. (Compiler); Denton, Judith S. (Compiler); Vereen, Mary (Compiler)

    1988-01-01

    Proceedings of a conference held in Huntsville, Alabama, on November 15-16, 1988. The Fourth Conference on Artificial Intelligence for Space Applications brings together diverse technical and scientific work in order to help those who employ AI methods in space applications to identify common goals and to address issues of general interest in the AI community. Topics include the following: space applications of expert systems in fault diagnostics, in telemetry monitoring and data collection, in design and systems integration; and in planning and scheduling; knowledge representation, capture, verification, and management; robotics and vision; adaptive learning; and automatic programming.

  19. From emblems to diagrams: Kepler's new pictorial language of scientific representation.

    PubMed

    Chen-Morris, Raz

    2009-01-01

    Kepler's treatise on optics of 1604 furnished, along with technical solutions to problems in medieval perspective, a mathematically-based visual language for the observation of nature. This language, based on Kepler's theory of retinal pictures, ascribed a new role to geometrical diagrams. This paper examines Kepler's pictorial language against the backdrop of alchemical emblems that flourished in and around the court of Rudolf II in Prague. It highlights the cultural context in which Kepler's optics was immersed, and the way in which Kepler attempted to demarcate his new science from other modes of the investigation of nature.

  20. Retrospective indexing (RI) - A computer-aided indexing technique

    NASA Technical Reports Server (NTRS)

    Buchan, Ronald L.

    1990-01-01

    An account is given of a method for data base-updating designated 'computer-aided indexing' (CAI) which has been very efficiently implemented at NASA's Scientific and Technical Information Facility by means of retrospective indexing. Novel terms added to the NASA Thesaurus will therefore proceed directly into both the NASA-RECON aerospace information system and its portion of the ESA-Information Retrieval Service, giving users full access to material thus indexed. If a given term appears in the title of a record, it is given special weight. An illustrative graphic representation of the CAI search strategy is presented.

  1. International Land Model Benchmarking (ILAMB) Workshop Report, Technical Report DOE/SC-0186

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hoffman, Forrest M.; Koven, Charles D.; Kappel-Aleks, Gretchen

    2016-11-01

    As Earth system models become increasingly complex, there is a growing need for comprehensive and multi-faceted evaluation of model projections. To advance understanding of biogeochemical processes and their interactions with hydrology and climate under conditions of increasing atmospheric carbon dioxide, new analysis methods are required that use observations to constrain model predictions, inform model development, and identify needed measurements and field experiments. Better representations of biogeochemistry–climate feedbacks and ecosystem processes in these models are essential for reducing uncertainties associated with projections of climate change during the remainder of the 21st century.

  2. Innovations in clinical trials informatics.

    PubMed

    Summers, Ron; Vyas, Hiten; Dudhal, Nilesh; Doherty, Neil F; Coombs, Crispin R; Hepworth, Mark

    2008-01-01

    This paper will investigate innovations in information management for use in clinical trials. The application typifies a complex, adaptive, distributed and information-rich environment for which continuous innovation is necessary. Organisational innovation is highlighted as well as the technical innovations in workflow processes and their representation as an integrated set of web services. Benefits realization uncovers further innovations in the business strand of the work undertaken. Following the description of the development of this information management system, the semantic web is postulated as a possible solution to tame the complexity related to information management issues found within clinical trials support systems.

  3. On I/O Virtualization Management

    NASA Astrophysics Data System (ADS)

    Danciu, Vitalian A.; Metzker, Martin G.

    The quick adoption of virtualization technology in general and the advent of the Cloud business model entail new requirements on the structure and the configuration of back-end I/O systems. Several approaches to virtualization of I/O links are being introduced, which aim at implementing a more flexible I/O channel configuration without compromising performance. While previously the management of I/O devices could be limited to basic technical requirments (e.g. the establishment and termination of fixed-point links), the additional flexibility carries in its wake additional management requirements on the representation and control of I/O sub-systems.

  4. [Work in medicine: some issues concerning professional autonomy].

    PubMed

    Schraiber, L B

    1995-01-01

    The author analyzes several issues pertaining to medical practice as related to the technical autonomy characterizing professional activity in this field. She points to the coexistente of a scientific side and an empirical/pragmatic side of medicine, the latter known as the medical art. The article also discusses the complexity of medical command of technological rationality which presides over the practical use of scientific knowledge. The author defines work in medicine as a "tensive structure" and examines its consequences for self-representation by physicians, their daily work, and themselves as agents of professional labor and subjects of action.

  5. The Effect of Recovery Duration on Technical Proficiency during Small Sided Games of Football.

    PubMed

    McLean, Scott; Kerhervé, Hugo; Naughton, Mitchell; Lovell, Geoff P; Gorman, Adam D; Solomon, Colin

    2016-07-08

    The aim of this study was to determine the effect of increasing the duration of the recovery periods separating serial bouts of small sided games (SSG) of football on technical skills (TS). Twelve semi-professional footballers (mean ± SD; age 21 ± 3 years; VO 2peak 64 ± 7 mL∙min∙kg -1 ; playing experience 15 ± 3 years) completed two SSG sessions, consisting of 3 vs. 3 players and 6 bouts of 2 min, separated by either 30 s recovery (REC-30) or 120 s recovery (REC-120). Sixteen TS, including passing, possession, and defensive related variables, and exercise intensity (heart rate, rating of perceived exertion, time motion descriptors) during the bouts were measured. Repeated measures ANOVA were used to determine differences between-conditions, for TS. The number of successful tackles was significantly higher, and the average time each team maintained possession was significantly lower in REC-120 compared to REC-30. There were no significant differences for all other TS variables, or exercise intensity measures between REC-30 and REC-120. Overall, a four-fold increase in the duration of recovery separating SSG bouts did not alter the technical skill execution of players. The experience and skill level of the players, combined with an apparent regulation of effort through pacing, may have assisted in the maintenance of technical skill execution.

  6. Three-Dimensional Computational Fluid Dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Haworth, D.C.; O'Rourke, P.J.; Ranganathan, R.

    1998-09-01

    Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.

  7. Metric 3-Leibniz algebras and M2-branes

    NASA Astrophysics Data System (ADS)

    Méndez-Escobar, Elena

    2010-08-01

    This thesis is concerned with superconformal Chern-Simons theories with matter in 3 dimensions. The interest in these theories is two-fold. On the one hand, it is a new family of theories in which to test the AdS/CFT correspondence and on the other, they are important to study one of the main objects of M-theory (M2-branes). All these theories have something in common: they can be written in terms of 3-Leibniz algebras. Here we study the structure theory of such algebras, paying special attention to a subclass of them that gives rise to maximal supersymmetry and that was the first to appear in this context: 3-Lie algebras. In chapter 2, we review the structure theory of metric Lie algebras and their unitary representations. In chapter 3, we study metric 3-Leibniz algebras and show, by specialising a construction originally due to Faulkner, that they are in one to one correspondence with pairs of real metric Lie algebras and unitary representations of them. We also show a third characterisation for six extreme cases of 3-Leibniz algebras as graded Lie (super)algebras. In chapter 4, we study metric 3-Lie algebras in detail. We prove a structural result and also classify those with a maximally isotropic centre, which is the requirement that ensures unitarity of the corresponding conformal field theory. Finally, in chapter 5, we study the universal structure of superpotentials in this class of superconformal Chern-Simons theories with matter in three dimensions. We provide a uniform formulation for all these theories and establish the connection between the amount of supersymmetry preserved and the gauge Lie algebra and the appropriate unitary representation to be used to write down the Lagrangian. The conditions for supersymmetry enhancement are then expressed equivalently in the language of representation theory of Lie algebras or the language of 3-Leibniz algebras.

  8. Autonomy, evidence and intuition: nurses and decision-making.

    PubMed

    Traynor, Michael; Boland, Maggie; Buus, Niels

    2010-07-01

    This paper is a report of a study conducted to examine how nurses represent professional clinical decision-making processes, and to determine what light Jamous and Peloille's 'Indeterminacy/Technicality ratio' concept can shed on these representations. Classic definitions of professional work feature autonomy of decision-making and control over the field of work. Sociologists Jamous and Peloille have described professional work as being high in 'indeterminacy' (the use of tacit judgements) relative to technicality (activity able to be codified). The rise of the evidence-based practice movement has been seen as increasing the realm of technical decision-making in healthcare, and it is relevant to analyse nurses' professional discourse and study how they respond to this increase. Three focus groups with qualified nurses attending post-qualifying courses at a London university were held in 2008. Participants were asked to talk about influences on their decision-making. The discussions were tape-recorded, transcribed and subjected to discourse analysis. Participants described their decision-making as influenced by both indeterminate and technical features. They acknowledged useful influences from both domains, but pointed to their personal 'experience' as the final arbiter of decision-making. Their accounts of decision-making created a sense of professional autonomy while at the same time protecting it against external critique. Pre- and post-registration nurse education could encourage robust discussion of the definition and roles of 'irrational' aspects of decision-making and how these might be understood as components of credible professional practice.

  9. Review of USGS Open-file Report 95-525 ("Cartographic and digital standard for geologic map information") and plans for development of Federal draft standards for geologic map information

    USGS Publications Warehouse

    Soller, David R.

    1996-01-01

    This report summarizes a technical review of USGS Open-File Report 95-525, 'Cartographic and Digital Standard for Geologic Map Information' and OFR 95-526 (diskettes containing digital representations of the standard symbols). If you are considering the purchase or use of those documents, you should read this report first. For some purposes, OFR 95-525 (the printed document) will prove to be an excellent resource. However, technical review identified significant problems with the two documents that will be addressed by various Federal and State committees composed of geologists and cartographers, as noted below. Therefore, the 2-year review period noted in OFR 95-525 is no longer applicable. Until those problems are resolved and formal standards are issued, you may consult the following World-Wide Web (WWW) site which contains information about development of geologic map standards: URL: http://ncgmp.usgs.gov/ngmdbproject/home.html

  10. The future viability of algae-derived biodiesel under economic and technical uncertainties.

    PubMed

    Brownbridge, George; Azadi, Pooya; Smallbone, Andrew; Bhave, Amit; Taylor, Benjamin; Kraft, Markus

    2014-01-01

    This study presents a techno-economic assessment of algae-derived biodiesel under economic and technical uncertainties associated with the development of algal biorefineries. A global sensitivity analysis was performed using a High Dimensional Model Representation (HDMR) method. It was found that, considering reasonable ranges over which each parameter can vary, the sensitivity of the biodiesel production cost to the key input parameters decreases in the following order: algae oil content>algae annual productivity per unit area>plant production capacity>carbon price increase rate. It was also found that the Return on Investment (ROI) is highly sensitive to the algae oil content, and to a lesser extent to the algae annual productivity, crude oil price and price increase rate, plant production capacity, and carbon price increase rate. For a large scale plant (100,000 tonnes of biodiesel per year) the production cost of biodiesel is likely to be £0.8-1.6 per kg. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Technical note: The Linked Paleo Data framework - a common tongue for paleoclimatology

    NASA Astrophysics Data System (ADS)

    McKay, Nicholas P.; Emile-Geay, Julien

    2016-04-01

    Paleoclimatology is a highly collaborative scientific endeavor, increasingly reliant on online databases for data sharing. Yet there is currently no universal way to describe, store and share paleoclimate data: in other words, no standard. Data standards are often regarded by scientists as mere technicalities, though they underlie much scientific and technological innovation, as well as facilitating collaborations between research groups. In this article, we propose a preliminary data standard for paleoclimate data, general enough to accommodate all the archive and measurement types encountered in a large international collaboration (PAGES 2k). We also introduce a vehicle for such structured data (Linked Paleo Data, or LiPD), leveraging recent advances in knowledge representation (Linked Open Data).The LiPD framework enables quick querying and extraction, and we expect that it will facilitate the writing of open-source community codes to access, analyze, model and visualize paleoclimate observations. We welcome community feedback on this standard, and encourage paleoclimatologists to experiment with the format for their own purposes.

  12. Associative Algebraic Approach to Logarithmic CFT in the Bulk: The Continuum Limit of the {gl(1|1)} Periodic Spin Chain, Howe Duality and the Interchiral Algebra

    NASA Astrophysics Data System (ADS)

    Gainutdinov, A. M.; Read, N.; Saleur, H.

    2016-01-01

    We develop in this paper the principles of an associative algebraic approach to bulk logarithmic conformal field theories (LCFTs). We concentrate on the closed {gl(1|1)} spin-chain and its continuum limit—the {c=-2} symplectic fermions theory—and rely on two technical companion papers, Gainutdinov et al. (Nucl Phys B 871:245-288, 2013) and Gainutdinov et al. (Nucl Phys B 871:289-329, 2013). Our main result is that the algebra of local Hamiltonians, the Jones-Temperley-Lieb algebra JTL N , goes over in the continuum limit to a bigger algebra than {V}, the product of the left and right Virasoro algebras. This algebra, {S}—which we call interchiral, mixes the left and right moving sectors, and is generated, in the symplectic fermions case, by the additional field {S(z,bar{z})≡ S_{αβ} ψ^α(z)bar{ψ}^β(bar{z})}, with a symmetric form {S_{αβ}} and conformal weights (1,1). We discuss in detail how the space of states of the LCFT (technically, a Krein space) decomposes onto representations of this algebra, and how this decomposition is related with properties of the finite spin-chain. We show that there is a complete correspondence between algebraic properties of finite periodic spin chains and the continuum limit. An important technical aspect of our analysis involves the fundamental new observation that the action of JTL N in the {gl(1|1)} spin chain is in fact isomorphic to an enveloping algebra of a certain Lie algebra, itself a non semi-simple version of {sp_{N-2}}. The semi-simple part of JTL N is represented by {U sp_{N-2}}, providing a beautiful example of a classical Howe duality, for which we have a non semi-simple version in the full JTL N image represented in the spin-chain. On the continuum side, simple modules over {S} are identified with "fundamental" representations of {sp_∞}.

  13. SU(5) grand unified theory, its polytopes and 5-fold symmetric aperiodic tiling

    NASA Astrophysics Data System (ADS)

    Koca, Mehmet; Koca, Nazife Ozdes; Al-Siyabi, Abeer

    We associate the lepton-quark families with the vertices of the 4D polytopes 5-cell (0001)A4 and the rectified 5-cell (0100)A4 derived from the SU(5) Coxeter-Dynkin diagram. The off-diagonal gauge bosons are associated with the root polytope (1001)A4 whose facets are tetrahedra and the triangular prisms. The edge-vertex relations are interpreted as the SU(5) charge conservation. The Dynkin diagram symmetry of the SU(5) diagram can be interpreted as a kind of particle-antiparticle symmetry. The Voronoi cell of the root lattice consists of the union of the polytopes (1000)A4 + (0100)A4 + (0010)A4 + (0001)A4 whose facets are 20 rhombohedra. We construct the Delone (Delaunay) cells of the root lattice as the alternating 5-cell and the rectified 5-cell, a kind of dual to the Voronoi cell. The vertices of the Delone cells closest to the origin consist of the root vectors representing the gauge bosons. The faces of the rhombohedra project onto the Coxeter plane as thick and thin rhombs leading to Penrose-like tiling of the plane which can be used for the description of the 5-fold symmetric quasicrystallography. The model can be extended to SO(10) and even to SO(11) by noting the Coxeter-Dynkin diagram embedding A4 ⊂ D5 ⊂ B5. Another embedding can be made through the relation A4 ⊂ D5 ⊂ E6 for more popular GUT‧s. Appendix A includes the quaternionic representations of the Coxeter-Weyl groups W(A4) ⊂ W(H4) which can be obtained directly from W(E8) by projection. This leads to relations of the SU(5) polytopes with the quasicrystallography in 4D and E8 polytopes. Appendix B discusses the branching of the polytopes in terms of the irreducible representations of the Coxeter-Weyl group W(A4) ≈ S5.

  14. Reviews and syntheses: Hidden forests, the role of vegetated coastal habitats in the ocean carbon budget

    NASA Astrophysics Data System (ADS)

    Duarte, Carlos M.

    2017-01-01

    Vegetated coastal habitats, including seagrass and macroalgal beds, mangrove forests and salt marshes, form highly productive ecosystems, but their contribution to the global carbon budget remains overlooked, and these forests remain hidden in representations of the global carbon budget. Despite being confined to a narrow belt around the shoreline of the world's oceans, where they cover less than 7 million km2, vegetated coastal habitats support about 1 to 10 % of the global marine net primary production and generate a large organic carbon surplus of about 40 % of their net primary production (NPP), which is either buried in sediments within these habitats or exported away. Large, 10-fold uncertainties in the area covered by vegetated coastal habitats, along with variability about carbon flux estimates, result in a 10-fold bracket around the estimates of their contribution to organic carbon sequestration in sediments and the deep sea from 73 to 866 Tg C yr-1, representing between 3 % and 1/3 of oceanic CO2 uptake. Up to 1/2 of this carbon sequestration occurs in sink reservoirs (sediments or the deep sea) beyond these habitats. The organic carbon exported that does not reach depositional sites subsidizes the metabolism of heterotrophic organisms. In addition to a significant contribution to organic carbon production and sequestration, vegetated coastal habitats contribute as much to carbonate accumulation as coral reefs do. While globally relevant, the magnitude of global carbon fluxes supported by salt-marsh, mangrove, seagrass and macroalgal habitats is declining due to rapid habitat loss, contributing to loss of CO2 sequestration, storage capacity and carbon subsidies. Incorporating the carbon fluxes' vegetated coastal habitats' support into depictions of the carbon budget of the global ocean and its perturbations will improve current representations of the carbon budget of the global ocean.

  15. Computational Vision in Uv-Mapping of Textured Meshes Coming from Photogrammetric Recovery: Unwrapping Frescoed Vaults

    NASA Astrophysics Data System (ADS)

    Robleda, P. G.; Caroti, G.; Martínez-Espejo Zaragoza, I.; Piemonte, A.

    2016-06-01

    Sometimes it is difficult to represent "on paper" the existing reality of architectonic elements, depending on the complexity of his geometry, but not only in cases with complex geometries: non-relief surfaces, can need a "special planar format" for its graphical representation. Nowadays, there are a lot of methods to obtain tridimensional recovery of our Cultural Heritage with different ranges of the relationship accuracy / costs, even getting high accuracy using "low-cost" recovery methods as digital photogrammetry, which allow us easily to obtain a graphical representation "on paper": ortho-images of different points of view. This can be useful for many purposes but, for others, an orthographic projection is not really very interesting. In non-site restoration tasks of frescoed vaults, a "planar format" representation in needed to see in true magnitude the paintings represented on the intrados vault, because of the general methodology used: gluing the fresco on a fabric, removing the fresco-fabric from the support, moving to laboratory, removing the fresco from the fabric, restoring the fresco, gluing back the restored fresco on another fabric, laying the restored fresco on the original location and removing the fabric. Because of this, many times, an unfolded model is needed, in a similar way a cylinder or cone can be unfolded, but in this case with a texture included: UV unwrapping. Unfold and fold-back processes, can be especially interesting in restoration field of frescoed vaults and domes at: chromatic recovery of paintings, reconstruction of partially missed geometries, transference of paintings on surfaces, etc.

  16. A Structural Analysis of the Lewiston Basin, Clarkston, WA

    NASA Astrophysics Data System (ADS)

    Alloway, M.; Watkinson, A.; Reidel, S. P.

    2010-12-01

    The Lewiston Structure is located in southeastern Washington / west-central Idaho and is a generally E-W trending asymmetric, non-cylindrical anticline in the Columbia River Basalt Group (CRBG) that transfers displacement into the Limekiln fault system to the southeast. A serial cross-section analysis and 3-D construction of this structure shows how the fold varies along its trend and sheds light on the deformational history of the Lewiston Basin. Construction of the fold’s 3-D form shows that the fold’s wavelength increases and amplitude decreases eastward along its trend. Balanced cross-sections show approximately 5% shortening across the structure which is consistent with the Yakima Fold Belt (YFB). Although the structure is similar to the YFB, it does not form part of a belt and its local nature has been suggested to mark the cratonic boundary of the Cretaceous. Discovery of an angular unconformity in the Grande Ronde Basalt - reverse polarity unit 1 (GRB-R1) proves that the NE trending section of the fold was deforming during emplacement of R1 and allows separation of the fold into two structural domains. Analysis of the two domains using the Gauss method for heterogeneous fault-slip data indicate NW-SE shortening during R1 time and N-S shortening for post CRBG emplacement. Furthermore, slip data for strain-inversion and specification of spatial-distribution patterns help identify the existence of a transpressional tectonic environment. The nature of faulting associated with the Lewiston Structure is a topic of some debate, namely the presence of a reverse fault on the southern limb of the fold conspicuously hidden by the Snake River. The reverse fault under debate outcrops to the east of the field area and is GRB-R2 (reverse polarity unit 2) thrust over Pliocene gravels. Better control on unit thicknesses and map contacts rule out the possibility of a reverse fault exposed on the surface of the southern limb of the fold in the field area. This major fault dies out or becomes blind before reaching the ID-WA border and the conspicuous change in attitude from the north side of the river to the south is accommodated by an abrupt fold hinge beneath the river. Three-dimensional representation of how the structure varies along its trend, not to scale. A-A' crosses the location where the Snake River changes direction from E-W to S-N. G-G' was modified from Garwood and Bush (2005) and is outside of the field area.

  17. Designing water demand management schemes using a socio-technical modelling approach.

    PubMed

    Baki, Sotiria; Rozos, Evangelos; Makropoulos, Christos

    2018-05-01

    Although it is now widely acknowledged that urban water systems (UWSs) are complex socio-technical systems and that a shift towards a socio-technical approach is critical in achieving sustainable urban water management, still, more often than not, UWSs are designed using a segmented modelling approach. As such, either the analysis focuses on the description of the purely technical sub-system, without explicitly taking into account the system's dynamic socio-economic processes, or a more interdisciplinary approach is followed, but delivered through relatively coarse models, which often fail to provide a thorough representation of the urban water cycle and hence cannot deliver accurate estimations of the hydrosystem's responses. In this work we propose an integrated modelling approach for the study of the complete socio-technical UWS that also takes into account socio-economic and climatic variability. We have developed an integrated model, which is used to investigate the diffusion of household water conservation technologies and its effects on the UWS, under different socio-economic and climatic scenarios. The integrated model is formed by coupling a System Dynamics model that simulates the water technology adoption process, and the Urban Water Optioneering Tool (UWOT) for the detailed simulation of the urban water cycle. The model and approach are tested and demonstrated in an urban redevelopment area in Athens, Greece under different socio-economic scenarios and policy interventions. It is suggested that the proposed approach can establish quantifiable links between socio-economic change and UWS responses and therefore assist decision makers in designing more effective and resilient long-term strategies for water conservation. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

    PubMed

    Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Discrete Haar transform and protein structure.

    PubMed

    Morosetti, S

    1997-12-01

    The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree. The reconstructed structures were compared with the experimental ones, and analyzed by visual inspection and statistical analysis. When half of the Haar coefficients were used, all the reconstructed structures were not yet collapsed to a tertiary folding, but they showed yet realized most of the secondary motifs. These results indicate a substantial separation of structural information in the space of Haar transform, with the secondary structural information mainly present in the Haar coefficients of lower degrees, and the tertiary one present in the higher degree coefficients. Because of this separation, the representation of the folded structures in the space of Haar transform seems a promising candidate to encompass the problem of premature convergence in genetic algorithms.

  20. Structure and tectonic evolution of the NE segment of the Polish-Ukrainian Carpathians during the Late Cenozoic: subsurface cross-sections and palinspastic models

    NASA Astrophysics Data System (ADS)

    Kuśmierek, Jan; Baran, Urszula

    2016-08-01

    The discrepant arrangement of the Carpathian nappes and syntectonic deposits of the Carpathian Foredeep reveals the oroclinal migration of the subduction direction of the platform margin during the Late Cenozoic. Formation of the nappes was induced by their detachment from disintegrated segments of the European Platform; the segments were shortened as a result of their vertical rotation in zones of compressional sutures. It finds expression in local occurrence of the backward vergence of folding against the generally forward vergence toward the Carpathian Foredeep. The precompressional configuration of sedimentation areas of particular nappes was reconstructed with application of the palinspastic method, on the basis of the hitherto undervalued model which emphasizes the influence of the subduction and differentiated morphology of the platform basement on the tectonic evolution of the fold and thrust belt. Superposition of the palaeogeographic representations and the present geometry of the orogen allows understanding of the impact of the magnitudes of tectonic displacements on the differentiation of the geological structure in the NE segment of the Carpathians. The differentiation has inspired different views of Polish and Ukrainian geologists on structural classification and evolution of the frontal thrusts.

  1. Learning from technical documents: the role of intermodal referring expressions.

    PubMed

    Dupont, Vincent; Bestgen, Yves

    2006-01-01

    We investigated the impact of two types of intermodal referring expressions on efficiency of instructions for use. User manuals for software or technical devices such as a video recording system frequently combine verbal instructions and illustrations. Much research has shown that the presence of an illustration has a beneficial effect on learning. The present study focuses on a factor that modulates this beneficial effect. The combination of text and an illustration can be effective only if the user integrates the information coming from these two media. This integration depends largely on the intermodal referential expressions, the function of which is to mark explicitly the relations between the text and the illustration. In an experiment (N = 104), we compared the effectiveness of two intermodal referring expressions often used in procedural texts: indexes (numbers introduced in the illustrations and in the instructions to establish cross-references) and icons (visual representations of the components of the device, which are inserted in the verbal instructions). The icons condition led to the most efficient use of the device. This experiment shows that learning from multimedia documents depends on the possibility of effectively connecting the verbal instructions to the illustration. Taking into account the ergonomic properties of the cross-media referring expressions should allow text designers to improve the effectiveness of technical documents.

  2. Assessment of undiscovered petroleum resources of the Arctic Alaska Petroleum Province

    USGS Publications Warehouse

    Houseknecht, David W.; Bird, Kenneth J.; Garrity, Christopher P.

    2012-01-01

    The Arctic Alaska Petroleum Province encompasses all lands and adjacent continental shelf areas north of the Brooks Range-Herald arch tectonic belts and south of the northern (outboard) margin of the Alaska rift shoulder. Even though only a small part is thoroughly explored, it is one of the most prolific petroleum provinces in North America, with total known resources (cumulative production plus proved reserves) of about 28 billion barrels of oil equivalent. For assessment purposes, the province is divided into a platform assessment unit, comprising the Alaska rift shoulder and its relatively undeformed flanks, and a fold-and-thrust belt assessment unit, comprising the deformed area north of the Brooks Range and Herald arch tectonic belts. Mean estimates of undiscovered, technically recoverable resources include nearly 28 billion barrels of oil and 122 trillion cubic feet of nonassociated gas in the platform assessment unit and 2 billion barrels of oil and 59 trillion cubic feet of nonassociated gas in the fold-and-thrust belt assessment unit.

  3. Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

    PubMed

    Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

    2014-07-01

    Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  4. A Self-Synthesis Approach to Perceptual Learning for Multisensory Fusion in Robotics

    PubMed Central

    Axenie, Cristian; Richter, Christoph; Conradt, Jörg

    2016-01-01

    Biological and technical systems operate in a rich multimodal environment. Due to the diversity of incoming sensory streams a system perceives and the variety of motor capabilities a system exhibits there is no single representation and no singular unambiguous interpretation of such a complex scene. In this work we propose a novel sensory processing architecture, inspired by the distributed macro-architecture of the mammalian cortex. The underlying computation is performed by a network of computational maps, each representing a different sensory quantity. All the different sensory streams enter the system through multiple parallel channels. The system autonomously associates and combines them into a coherent representation, given incoming observations. These processes are adaptive and involve learning. The proposed framework introduces mechanisms for self-creation and learning of the functional relations between the computational maps, encoding sensorimotor streams, directly from the data. Its intrinsic scalability, parallelisation, and automatic adaptation to unforeseen sensory perturbations make our approach a promising candidate for robust multisensory fusion in robotic systems. We demonstrate this by applying our model to a 3D motion estimation on a quadrotor. PMID:27775621

  5. Digital devices: big challenge in color management

    NASA Astrophysics Data System (ADS)

    Vauderwange, Oliver; Curticapean, Dan; Dreβler, Paul; Wozniak, Peter

    2014-09-01

    The paper will present how the students learn to find technical solutions in color management by using adequate digital devices and recognize the specific upcoming tasks in this area. Several issues, problems and their solutions will be discussed. The scientific background offer specific didactical solutions in this area of optics. Color management is the major item of this paper. Color management is a crucial responsibility for media engineers and designers. Print, screen and mobile applications must independently display the same colors. Predictability and consistency in the color representation are the aims of a color management system. This is only possible in a standardized and audited production workflow. Nowadays digital media have a fast-paced development process. An increasing number of different digital devices with different display sizes and display technologies are a great challenge for every color management system. The authors will present their experience in the field of color management. The design and development of a suitable learning environment with the required infrastructure is in the focus. The combination of theoretical and practical lectures creates a deeper understanding in the area of the digital color representation.

  6. LeRC-HT: NASA Lewis Research Center General Multiblock Navier-Stokes Heat Transfer Code Developed

    NASA Technical Reports Server (NTRS)

    Heidmann, James D.; Gaugler, Raymond E.

    1999-01-01

    For the last several years, LeRC-HT, a three-dimensional computational fluid dynamics (CFD) computer code for analyzing gas turbine flow and convective heat transfer, has been evolving at the NASA Lewis Research Center. The code is unique in its ability to give a highly detailed representation of the flow field very close to solid surfaces. This is necessary for an accurate representation of fluid heat transfer and viscous shear stresses. The code has been used extensively for both internal cooling passage flows and hot gas path flows--including detailed film cooling calculations, complex tip-clearance gap flows, and heat transfer. In its current form, this code has a multiblock grid capability and has been validated for a number of turbine configurations. The code has been developed and used primarily as a research tool (at least 35 technical papers have been published relative to the code and its application), but it should be useful for detailed design analysis. We now plan to make this code available to selected users for further evaluation.

  7. [Cooperation and conflict in childbirth care: representations and practices of nurses and obstetricians].

    PubMed

    Angulo-Tuesta, Antonia; Giffin, Karen; Gama, Andréa de Sousa; d'Orsi, Eleonora; Barbosa, Gisele Peixoto

    2003-01-01

    In Brazil, where birthing generally occurs in hospitals and under the care of obstetricians, the incorporation of nurses is a strategy that has been used recently in an attempt to improve obstetric care. This study, conducted in two maternity hospitals in Rio de Janeiro, focuses on representations of obstetricians and nurses regarding teamwork and analyzes how the dimensions of power, cooperation/conflict, and technical autonomy are permeated by dualistic conceptions which influence the quality of health care for women during childbirth. On the one hand, the results show a consensus regarding the advantages of professional cooperation in the improvement of health care, assuming the existence of a clear definition of professional roles. At the same time, conflicts regarding therapeutic conduct during the birth process reflect the professionals' perceptions of autonomy and the influence of professional hierarchies, in which obstetric care is seen to depend on the "objective observation" of the women giving birth. The degree of conflict is differentiated according to the institutional context and related to dualistic conceptions such as objective/subjective, rational/emotional, and male/female.

  8. Factors shaping the evolution of electronic documentation systems

    NASA Technical Reports Server (NTRS)

    Dede, Christopher J.; Sullivan, Tim R.; Scace, Jacque R.

    1990-01-01

    The main goal is to prepare the space station technical and managerial structure for likely changes in the creation, capture, transfer, and utilization of knowledge. By anticipating advances, the design of Space Station Project (SSP) information systems can be tailored to facilitate a progression of increasingly sophisticated strategies as the space station evolves. Future generations of advanced information systems will use increases in power to deliver environmentally meaningful, contextually targeted, interconnected data (knowledge). The concept of a Knowledge Base Management System is emerging when the problem is focused on how information systems can perform such a conversion of raw data. Such a system would include traditional management functions for large space databases. Added artificial intelligence features might encompass co-existing knowledge representation schemes; effective control structures for deductive, plausible, and inductive reasoning; means for knowledge acquisition, refinement, and validation; explanation facilities; and dynamic human intervention. The major areas covered include: alternative knowledge representation approaches; advanced user interface capabilities; computer-supported cooperative work; the evolution of information system hardware; standardization, compatibility, and connectivity; and organizational impacts of information intensive environments.

  9. Vector analogues of the Maggi-Rubinowicz theory of edge diffraction

    NASA Astrophysics Data System (ADS)

    Meneghini, R.; Shu, P.; Bay, J.

    1980-10-01

    The Maggi-Rubinowicz technique for scalar and electromagnetic fields is interpreted as a transformation of an integral over an open surface to a line integral around its rim. Maggi-Rubinowicz analogues are found for several vector physical optics representations. For diffraction from a circular aperture, a numerical comparison between these formulations shows the two methods are in agreement. To circumvent certain convergence difficulties in the Maggi-Rubinowicz integrals that occur as the observer approaches the shadow boundary, a variable mesh integration is used. For the examples considered, where the ratio of the aperture diameter to wavelength is about ten, the Maggi-Rubinowicz formulation yields an 8 to 10 fold decrease in computation time relative to the physical optics formulation.

  10. Vector analogues of the Maggi-Rubinowicz theory of edge diffraction

    NASA Technical Reports Server (NTRS)

    Meneghini, R.; Shu, P.; Bay, J.

    1980-01-01

    The Maggi-Rubinowicz technique for scalar and electromagnetic fields is interpreted as a transformation of an integral over an open surface to a line integral around its rim. Maggi-Rubinowicz analogues are found for several vector physical optics representations. For diffraction from a circular aperture, a numerical comparison between these formulations shows the two methods are in agreement. To circumvent certain convergence difficulties in the Maggi-Rubinowicz integrals that occur as the observer approaches the shadow boundary, a variable mesh integration is used. For the examples considered, where the ratio of the aperture diameter to wavelength is about ten, the Maggi-Rubinowicz formulation yields an 8 to 10 fold decrease in computation time relative to the physical optics formulation.

  11. Reactive Scheduling in Multipurpose Batch Plants

    NASA Astrophysics Data System (ADS)

    Narayani, A.; Shaik, Munawar A.

    2010-10-01

    Scheduling is an important operation in process industries for improving resource utilization resulting in direct economic benefits. It has a two-fold objective of fulfilling customer orders within the specified time as well as maximizing the plant profit. Unexpected disturbances such as machine breakdown, arrival of rush orders and cancellation of orders affect the schedule of the plant. Reactive scheduling is generation of a new schedule which has minimum deviation from the original schedule in spite of the occurrence of unexpected events in the plant operation. Recently, Shaik & Floudas (2009) proposed a novel unified model for short-term scheduling of multipurpose batch plants using unit-specific event-based continuous time representation. In this paper, we extend the model of Shaik & Floudas (2009) to handle reactive scheduling.

  12. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

    PubMed

    Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

    2010-04-30

    Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity.

  13. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.

    PubMed

    Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

    2011-04-29

    Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. © 2011 Raveh et al.

  14. Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

    PubMed Central

    Raveh, Barak; London, Nir; Zimmerman, Lior; Schueler-Furman, Ora

    2011-01-01

    Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions. PMID:21572516

  15. Comparison of 3D representations depicting micro folds: overlapping imagery vs. time-of-flight laser scanner

    NASA Astrophysics Data System (ADS)

    Vaiopoulos, Aristidis D.; Georgopoulos, Andreas; Lozios, Stylianos G.

    2012-10-01

    A relatively new field of interest, which continuously gains grounds nowadays, is digital 3D modeling. However, the methodologies, the accuracy and the time and effort required to produce a high quality 3D model have been changing drastically the last few years. Whereas in the early days of digital 3D modeling, 3D models were only accessible to computer experts in animation, working many hours in expensive sophisticated software, today 3D modeling has become reasonably fast and convenient. On top of that, with online 3D modeling software, such as 123D Catch, nearly everyone can produce 3D models with minimum effort and at no cost. The only requirement is panoramic overlapping images, of the (still) objects the user wishes to model. This approach however, has limitations in the accuracy of the model. An objective of the study is to examine these limitations by assessing the accuracy of this 3D modeling methodology, with a Terrestrial Laser Scanner (TLS). Therefore, the scope of this study is to present and compare 3D models, produced with two different methods: 1) Traditional TLS method with the instrument ScanStation 2 by Leica and 2) Panoramic overlapping images obtained with DSLR camera and processed with 123D Catch free software. The main objective of the study is to evaluate advantages and disadvantages of the two 3D model producing methodologies. The area represented with the 3D models, features multi-scale folding in a cipollino marble formation. The most interesting part and most challenging to capture accurately, is an outcrop which includes vertically orientated micro folds. These micro folds have dimensions of a few centimeters while a relatively strong relief is evident between them (perhaps due to different material composition). The area of interest is located in Mt. Hymittos, Greece.

  16. Channel representation in physically based models coupling groundwater and surface water: pitfalls and how to avoid them.

    PubMed

    Käser, Daniel; Graf, Tobias; Cochand, Fabien; McLaren, Rob; Therrien, René; Brunner, Philip

    2014-01-01

    Recent models that couple three-dimensional subsurface flow with two-dimensional overland flow are valuable tools for quantifying complex groundwater/stream interactions and for evaluating their influence on watershed processes. For the modeler who is used to defining streams as a boundary condition, the representation of channels in integrated models raises a number of conceptual and technical issues. These models are far more sensitive to channel topography than conventional groundwater models. On all spatial scales, both the topography of a channel and its connection with the floodplain are important. For example, the geometry of river banks influences bank storage and overbank flooding; the slope of the river is a primary control on the behavior of a catchment; and at the finer scale bedform characteristics affect hyporheic exchange. Accurate data on streambed topography, however, are seldom available, and the spatial resolution of digital elevation models is typically too coarse in river environments, resulting in unrealistic or undulating streambeds. Modelers therefore perform some kind of manual yet often cumbersome correction to the available topography. In this context, the paper identifies some common pitfalls, and provides guidance to overcome these. Both aspects of topographic representation and mesh discretization are addressed. Additionally, two tutorials are provided to illustrate: (1) the interpolation of channel cross-sectional data and (2) the refinement of a mesh along a stream in areas of high topographic variability. © 2014, National Ground Water Association.

  17. Petri nets as a modeling tool for discrete concurrent tasks of the human operator. [describing sequential and parallel demands on human operators

    NASA Technical Reports Server (NTRS)

    Schumacher, W.; Geiser, G.

    1978-01-01

    The basic concepts of Petri nets are reviewed as well as their application as the fundamental model of technical systems with concurrent discrete events such as hardware systems and software models of computers. The use of Petri nets is proposed for modeling the human operator dealing with concurrent discrete tasks. Their properties useful in modeling the human operator are discussed and practical examples are given. By means of and experimental investigation of binary concurrent tasks which are presented in a serial manner, the representation of human behavior by Petri nets is demonstrated.

  18. Risk Interfaces to Support Integrated Systems Analysis and Development

    NASA Technical Reports Server (NTRS)

    Mindock, Jennifer; Lumpkins, Sarah; Shelhamer, Mark; Anton, Wilma; Havenhill, Maria

    2016-01-01

    Objectives for systems analysis capability: Develop integrated understanding of how a complex human physiological-socio-technical mission system behaves in spaceflight. Why? Support development of integrated solutions that prevent unwanted outcomes (Implementable approaches to minimize mission resources(mass, power, crew time, etc.)); Support development of tools for autonomy (need for exploration) (Assess and maintain resilience -individuals, teams, integrated system). Output of this exercise: -Representation of interfaces based on Human System Risk Board (HSRB) Risk Summary information and simple status based on Human Research Roadmap; Consolidated HSRB information applied to support communication; Point-of-Departure for HRP Element planning; Ability to track and communicate status of collaborations. 4

  19. Hubble Space Telescope Design Engineering Knowledgebase (HSTDEK)

    NASA Technical Reports Server (NTRS)

    Johannes, James D.; Everetts, Clark

    1989-01-01

    The research covered here pays specific attention to the development of tools to assist knowledge engineers in acquiring knowledge and to assist other technical, engineering, and management personnel in automatically performing knowledge capture as part of their everyday work without adding any extra work to what they already do. Requirements for data products, the knowledge base, and methods for mapping knowledge in the documents onto the knowledge representations are discussed, as are some of the difficulties of capturing in the knowledge base the structure of the design process itself, along with a model of the system designed. The capture of knowledge describing the interactions of different components is also discussed briefly.

  20. An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values.

    PubMed

    Alberti, Claudio; Daniels, Noah; Hernaez, Mikel; Voges, Jan; Goldfeder, Rachel L; Hernandez-Lopez, Ana A; Mattavelli, Marco; Berger, Bonnie

    2016-01-01

    This paper provides the specification and an initial validation of an evaluation framework for the comparison of lossy compressors of genome sequencing quality values. The goal is to define reference data, test sets, tools and metrics that shall be used to evaluate the impact of lossy compression of quality values on human genome variant calling. The functionality of the framework is validated referring to two state-of-the-art genomic compressors. This work has been spurred by the current activity within the ISO/IEC SC29/WG11 technical committee (a.k.a. MPEG), which is investigating the possibility of starting a standardization activity for genomic information representation.

  1. THE DIALOGICAL SELF IN PSYCHOANALYSIS.

    PubMed

    Muller, Felipe

    2016-10-01

    This paper describes the shift that appears to be taking place in contemporary psychoanalysis, as reflected among intersubjective approaches, from a monological conception of the self to a dialogical one. The monological self emphasizes the separation between mind, body, and external world, focusing on the representational and descriptive/referential function of language. In contrast, the dialogical self emphasizes practices, the permeable nature of relationships between subjects, and the constitutive function of language. This paper attempts to explain the growing emphasis on the dialogical self, understood from a theoretical, metatheoretical, and technical point of view, using contemporary intersubjective approaches to illustrate this shift. © 2016 The Psychoanalytic Quarterly, Inc.

  2. Research and applications: Artificial intelligence

    NASA Technical Reports Server (NTRS)

    Raphael, B.; Fikes, R. E.; Chaitin, L. J.; Hart, P. E.; Duda, R. O.; Nilsson, N. J.

    1971-01-01

    A program of research in the field of artificial intelligence is presented. The research areas discussed include automatic theorem proving, representations of real-world environments, problem-solving methods, the design of a programming system for problem-solving research, techniques for general scene analysis based upon television data, and the problems of assembling an integrated robot system. Major accomplishments include the development of a new problem-solving system that uses both formal logical inference and informal heuristic methods, the development of a method of automatic learning by generalization, and the design of the overall structure of a new complete robot system. Eight appendices to the report contain extensive technical details of the work described.

  3. Design of automatic rotor blades folding system using NiTi shape memory alloy actuator

    NASA Astrophysics Data System (ADS)

    Ali, M. I. F.; Abdullah, E. J.

    2016-10-01

    This present paper will study the requirements for development of a new Automatic Rotor Blades Folding (ARBF) system that could possibly solve the availability, compatibility and complexity issue of upgrading a manual to a fully automatic rotor blades folding system of a helicopter. As a subject matter, the Royal Malaysian Navy Super Lynx Mk 100 was chosen as the baseline model. The aim of the study was to propose a design of SMART ARBF's Shape Memory Alloy (SMA) actuator and proof of operating concept using a developed scale down prototype model. The performance target for the full folding sequence is less than ten minutes. Further analysis on design requirements was carried out, which consisted of three main phases. Phase 1 was studying the SMA behavior on the Nickel Titanium (NiTi) SMA wire and spring (extension type). Technical values like activation requirement, contraction length, and stroke- power and stroke-temperature relationship were gathered. Phase 2 was the development of the prototype where the proposed design of stepped-retractable SMA actuator was introduced. A complete model of the SMART ARBF system that consisted of a base, a main rotor hub, four main rotor blades, four SMA actuators and also electrical wiring connections was fabricated and assembled. Phase 3 was test and analysis whereby a PINENG-PN968s-10000mAh Power Bank's 5 volts, which was reduced to 2.5 volts using LM2596 Step-Down Converter, powered and activated the NiTi spring inside each actuator. The bias spring (compression type), which functions to protract and push the blades to spread position, will compress together with the retraction of actuators and pull the blades to the folding position. Once the power was removed and SMA spring deactivated, the bias spring stiffness will extend the SMA spring and casing and push the blades back to spread position. The timing for the whole revolution was recorded. Based on the experimental analysis, the recorded timing for folding sequence is 2.5 minutes in average and therefore met the required criteria.

  4. Accelerated triacylglycerol production and altered fatty acid composition in oleaginous microalga Neochloris oleoabundans by overexpression of diacylglycerol acyltransferase 2.

    PubMed

    Klaitong, Paeka; Fa-Aroonsawat, Sirirat; Chungjatupornchai, Wipa

    2017-04-12

    Microalgae are promising sources of lipid triacylglycerol (TAG) for biodiesel production. However, to date, microalgal biodiesel is technically feasible, but not yet economically viable. Increasing TAG content and productivity are important to achieve economic viability of microalgal biodiesel. To increase TAG content, oleaginous microalga Neochloris oleoabundans was genetically engineered with an endogenous key enzyme diacylglycerol acyltransferase 2 (NeoDGAT2) responsible for TAG biosynthesis. The integration of NeoDGAT2 expression cassettes in N. oleoabundans transformant was confirmed by PCR. The neutral lipid accumulation in the transformant detected by Nile red staining was accelerated and 1.9-fold higher than in wild type; the lipid bodies in the transformant visualized under fluorescence microscope were also larger. The NeoDGAT2 transcript was two-fold higher in the transformant than wild type. Remarkably higher lipid accumulation was found in the transformant than wild type: total lipid content increased 1.6-to 2.3-fold up to 74.5 ± 4.0% dry cell weight (DCW) and total lipid productivity increased 1.6- to 3.2-fold up to 14.6 ± 2.0 mg/L/day; while TAG content increased 1.8- to 3.2-fold up to 46.1 ± 1.6% DCW and TAG productivity increased 1.6- to 4.3-fold up to 8.9 ± 1.3 mg/L/day. A significantly altered fatty acid composition was detected in the transformant compared to wild type; the levels of saturated fatty acid C16:0 increased double to 49%, whereas C18:0 was reduced triple to 6%. Long-term stability was observed in the transformant continuously maintained in solid medium over 100 generations in a period of about 4 years. Our results demonstrate the increased TAG content and productivity in N. oleoabundans by NeoDGAT2 overexpression that may offer the first step towards making microalgae an economically feasible source for biodiesel production. The strategy for genetically improved microalga presented in this study can be applied to other microalgal species possessing desired characteristics for industrial biofuel production.

  5. Design of a large dual polarized Ku band reflectarray for space borne radar altimeter

    NASA Technical Reports Server (NTRS)

    Hodges, Richard E.; Zawadzki, Mark

    2004-01-01

    We describe the design of a large dual-beam, dual polarized reflectarray designed for a space-based radar altimeter. This application requires a 2.16 X 0.35 m aperture that can be folded for launch stowage. Low mass and >50% efficiency are also required. A reflectarray antenna offers the best approach but also presents unique technical challenges since a reflectarry has never been used in a space based radar application. In what follows, we describe the design, analysis and measurements of a breadboard test array built to demonstrate the reflectarray concept.

  6. Going single but not solo with podocytes: potentials, limitations, and pitfalls of single-cell analysis.

    PubMed

    Schiffer, Mario

    2017-11-01

    Single-cell RNA-sequence (RNA-seq) is a widely used tool to study biological questions in single cells. The discussed study identified 92 genes being predominantly expressed in podocytes based on a 5-fold higher expression compared with endothelial and mesangial cells. In addition to technical pitfalls, the question that is discussed in this commentary is whether results of a single-cell RNAseq study are able to deliver expression data that truly characterize a podocyte. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

  7. Sequestration of vacuum energy and the end of the universe.

    PubMed

    Kaloper, Nemanja; Padilla, Antonio

    2015-03-13

    Recently, we proposed a mechanism for sequestering the standard model vacuum energy that predicts that the Universe will collapse. Here we present a simple mechanism for bringing about this collapse, employing a scalar field whose potential is linear and becomes negative, providing the negative energy density required to end the expansion. The slope of the potential is chosen to allow for the expansion to last until the current Hubble time, about 10^{10} years, to accommodate our Universe. Crucially, this choice is technically natural due to a shift symmetry. Moreover, vacuum energy sequestering selects radiatively stable initial conditions for the collapse, which guarantee that immediately before the turnaround the Universe is dominated by the linear potential which drives an epoch of accelerated expansion for at least an e fold. Thus, a single, technically natural choice for the slope ensures that the collapse is imminent and is preceded by the current stage of cosmic acceleration, giving a new answer to the "why now?"

  8. A Perpendicular Biased 2nd Harmonic Cavity for the Fermilab Booster

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tan, C. Y.; Dey, J.; Madrak, R. L.

    2015-07-13

    A perpendicular biased 2nd harmonic cavity is currently being designed for the Fermilab Booster. Its purpose cavity is to flatten the bucket at injection and thus change the longitudinal beam distribution so that space charge effects are decreased. It can also with transition crossing. The reason for the choice of perpendicular biasing over parallel biasing is that the Q of the cavity is much higher and thus allows the accelerating voltage to be a factor of two higher than a similar parallel biased cavity. This cavity will also provide a higher accelerating voltage per meter than the present folded transmissionmore » line cavity. However, this type of cavity presents technical challenges that need to be addressed. The two major issues are cooling of the garnet material from the effects of the RF and the cavity itself from eddy current heating because of the 15 Hz bias field ramp. This paper will address the technical challenge of preventing the garnet from overheating.« less

  9. Imaging windows for long-term intravital imaging: General overview and technical insights.

    PubMed

    Alieva, Maria; Ritsma, Laila; Giedt, Randy J; Weissleder, Ralph; van Rheenen, Jacco

    2014-01-01

    Intravital microscopy is increasingly used to visualize and quantitate dynamic biological processes at the (sub)cellular level in live animals. By visualizing tissues through imaging windows, individual cells (e.g., cancer, host, or stem cells) can be tracked and studied over a time-span of days to months. Several imaging windows have been developed to access tissues including the brain, superficial fascia, mammary glands, liver, kidney, pancreas, and small intestine among others. Here, we review the development of imaging windows and compare the most commonly used long-term imaging windows for cancer biology: the cranial imaging window, the dorsal skin fold chamber, the mammary imaging window, and the abdominal imaging window. Moreover, we provide technical details, considerations, and trouble-shooting tips on the surgical procedures and microscopy setups for each imaging window and explain different strategies to assure imaging of the same area over multiple imaging sessions. This review aims to be a useful resource for establishing the long-term intravital imaging procedure.

  10. 4D Infant Cortical Surface Atlas Construction using Spherical Patch-based Sparse Representation.

    PubMed

    Wu, Zhengwang; Li, Gang; Meng, Yu; Wang, Li; Lin, Weili; Shen, Dinggang

    2017-09-01

    The 4D infant cortical surface atlas with densely sampled time points is highly needed for neuroimaging analysis of early brain development. In this paper, we build the 4D infant cortical surface atlas firstly covering 6 postnatal years with 11 time points (i.e., 1, 3, 6, 9, 12, 18, 24, 36, 48, 60, and 72 months), based on 339 longitudinal MRI scans from 50 healthy infants. To build the 4D cortical surface atlas, first , we adopt a two-stage groupwise surface registration strategy to ensure both longitudinal consistency and unbiasedness. Second , instead of simply averaging over the co-registered surfaces, a spherical patch-based sparse representation is developed to overcome possible surface registration errors across different subjects. The central idea is that, for each local spherical patch in the atlas space, we build a dictionary, which includes the samples of current local patches and their spatially-neighboring patches of all co-registered surfaces, and then the current local patch in the atlas is sparsely represented using the built dictionary. Compared to the atlas built with the conventional methods, the 4D infant cortical surface atlas constructed by our method preserves more details of cortical folding patterns, thus leading to boosted accuracy in registration of new infant cortical surfaces.

  11. Numerical cognition is resilient to dramatic changes in early sensory experience.

    PubMed

    Kanjlia, Shipra; Feigenson, Lisa; Bedny, Marina

    2018-06-20

    Humans and non-human animals can approximate large visual quantities without counting. The approximate number representations underlying this ability are noisy, with the amount of noise proportional to the quantity being represented. Numerate humans also have access to a separate system for representing exact quantities using number symbols and words; it is this second, exact system that supports most of formal mathematics. Although numerical approximation abilities and symbolic number abilities are distinct in representational format and in their phylogenetic and ontogenetic histories, they appear to be linked throughout development--individuals who can more precisely discriminate quantities without counting are better at math. The origins of this relationship are debated. On the one hand, symbolic number abilities may be directly linked to, perhaps even rooted in, numerical approximation abilities. On the other hand, the relationship between the two systems may simply reflect their independent relationships with visual abilities. To test this possibility, we asked whether approximate number and symbolic math abilities are linked in congenitally blind individuals who have never experienced visual sets or used visual strategies to learn math. Congenitally blind and blind-folded sighted participants completed an auditory numerical approximation task, as well as a symbolic arithmetic task and non-math control tasks. We found that the precision of approximate number representations was identical across congenitally blind and sighted groups, suggesting that the development of the Approximate Number System (ANS) does not depend on visual experience. Crucially, the relationship between numerical approximation and symbolic math abilities is preserved in congenitally blind individuals. These data support the idea that the Approximate Number System and symbolic number abilities are intrinsically linked, rather than indirectly linked through visual abilities. Copyright © 2018. Published by Elsevier B.V.

  12. Antibody Epitope Analysis to Investigate Folded Structure, Allosteric Conformation, and Evolutionary Lineage of Proteins.

    PubMed

    Wong, Sienna; Jin, J-P

    2017-01-01

    Study of folded structure of proteins provides insights into their biological functions, conformational dynamics and molecular evolution. Current methods of elucidating folded structure of proteins are laborious, low-throughput, and constrained by various limitations. Arising from these methods is the need for a sensitive, quantitative, rapid and high-throughput method not only analysing the folded structure of proteins, but also to monitor dynamic changes under physiological or experimental conditions. In this focused review, we outline the foundation and limitations of current protein structure-determination methods prior to discussing the advantages of an emerging antibody epitope analysis for applications in structural, conformational and evolutionary studies of proteins. We discuss the application of this method using representative examples in monitoring allosteric conformation of regulatory proteins and the determination of the evolutionary lineage of related proteins and protein isoforms. The versatility of the method described herein is validated by the ability to modulate a variety of assay parameters to meet the needs of the user in order to monitor protein conformation. Furthermore, the assay has been used to clarify the lineage of troponin isoforms beyond what has been depicted by sequence homology alone, demonstrating the nonlinear evolutionary relationship between primary structure and tertiary structure of proteins. The antibody epitope analysis method is a highly adaptable technique of protein conformation elucidation, which can be easily applied without the need for specialized equipment or technical expertise. When applied in a systematic and strategic manner, this method has the potential to reveal novel and biomedically meaningful information for structure-function relationship and evolutionary lineage of proteins. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  13. Colours in black and white: the depiction of lightness and brightness in achromatic engravings before the invention of photography.

    PubMed

    Zavagno, Daniele; Massironi, Manfredo

    2006-01-01

    What is it like to see the world in black and white? In the pioneer days of cinema, when movies displayed grey worlds, was it true that no 'colours' were actually seen? Did every object seen in those projections appear grey in the same way? The answer is obviously no--people in those glorious days were seeing a world full of light, shadows, and objects in which colours were expressed in terms of lightness. But the marvels of grey worlds have not always been so richly displayed. Before the invention of photography, the depiction of scenes in black-and-white had to face some technical and perceptual challenges. We have studied the technical and perceptual constraints that XV-XVIII century engravers had to face in order to translate actual colours into shades of grey. An indeterminacy principle is considered, according to which artists had to prefer the representation of some object or scene features over others (for example brightness over lightness). The reasons for this lay between the kind of grey scale technically available and the kind of information used in the construction of 3-D scenes. With the invention of photography, photomechanical reproductions, and new printing solutions, artists had at their disposal a continuous grey scale that greatly reduces the constraints of the indeterminacy principle.

  14. Final technical report DOE award DE-SC0007206 Improving CESM Efficiency to Study Variable C:N:P Stoichiometry in the Oceans

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Primeau, Francois William

    2016-02-11

    This report lists the accomplishments of the project, which includes: (1) analysis of inorganic nutrient concentration data as well as suspended particulate organic matter data in the ocean to demonstrate that the carbon to nitrogen to phosphorus ratios (C:N:P) of biological uptake and export vary on large spatial scales, (2) the development of a new computationally efficient method for simulating biogeochemical tracers in earth system models, (3) the application of the method to help calibrate an improved representation of dissolved organic matter in the ocean that includes variable C:N:P stoichiometry. This research is important because biological uptake of carbon andmore » nutrients in the upper ocean and export by sinking particles and downward mixing of dissolved organic matter helps maintain a vertical gradient in the carbon dioxide concentration in the ocean. This gradient is key to understanding the partitioning of CO2 between the ocean and the atmosphere. The final report lists seven peer reviewed scientific publications, one Ph.D. thesis, one technical report and two papers in preparation.« less

  15. A Hidden Portrait by Edgar Degas

    NASA Astrophysics Data System (ADS)

    Thurrowgood, David; Paterson, David; de Jonge, Martin D.; Kirkham, Robin; Thurrowgood, Saul; Howard, Daryl L.

    2016-08-01

    The preservation and understanding of cultural heritage depends increasingly on in-depth chemical studies. Rapid technological advances are forging connections between scientists and arts communities, enabling revolutionary new techniques for non-invasive technical study of culturally significant, highly prized artworks. We have applied a non-invasive, rapid, high definition X-ray fluorescence (XRF) elemental mapping technique to a French Impressionist painting using a synchrotron radiation source, and show how this technology can advance scholarly art interpretation and preservation. We have obtained detailed technical understanding of a painting which could not be resolved by conventional techniques. Here we show 31.6 megapixel scanning XRF derived elemental maps and report a novel image processing methodology utilising these maps to produce a false colour representation of a “hidden” portrait by Edgar Degas. This work provides a cohesive methodology for both imaging and understanding the chemical composition of artworks, and enables scholarly understandings of cultural heritage, many of which have eluded conventional technologies. We anticipate that the outcome from this work will encourage the reassessment of some of the world’s great art treasures.

  16. Agricultural illustrations of 19th century Korea: 'Imwon gyeongjeji' (Treatises on Management of Forest and Garden) by Seo Yugu.

    PubMed

    Chung, Hyung-Min

    2011-01-01

    The generative relationship between text and image has long been established. Its structure evolved historically as a result of varying understandings of the functions of art and technology. Agriculture illustration, which emerged in China during the Song dynasty, is a prime example of this creative dialogue in which aspects of both disciplines were combined. Political, technological, and aesthetic concerns informed the reformulations of this new genre. This paper will address agricultural illustrations on nineteenth-century Korea, when notable changes occurred in the visualization of agricultural texts. It will explore changes in the understanding of the roles of agriculture, technology, and labor through an analysis of shifts in modes of illustration and the texts selected. The relationship between technology and visual representations during late Joseon Korea will be contextualized through an exploration of the evolution of technical drawing in East Asia. This paper will suggest that the recognition of imagery's ability to convey textual and technical information provided an important alternative paradigm for the presentation and use of knowledge.

  17. [Decision-making process and administrative practice: managing the State Health Secretariat in Bahia, Brazil].

    PubMed

    Coelho, Thereza Christina Bahia; Paim, Jairnilson Silva

    2005-01-01

    This case study is based on research performed by the Bahia State Health Secretariat (SESAB), aimed at analyzing management practices during the implementation of a State government administrative reform. The institutional agenda shows evidence of limited participation by civil society and technical and operational staff in problem selection and prioritization, resulting from a work process pressured by high-level executive government staff. Decisions regarding "output" (projects, services, and activities) were made under the responsibility of subordinate operational levels and did not appear as issues in the institutional routine. Concerns related to "input" (financial and human resources) consumed most of the high-level efforts, with internal and external negotiations and compromises to assure access to them. Meanwhile the possible "outcome", namely public health status, represents the "occult subject" of the institutional discourse. Information emerges in institutional disputes as a technical "power resource" in its medical, epidemiological, health, and administrative dimensions. The issue of government "representation" and allied interests is based on ideological dispositions and authoritarian practices, thus contradicting the need for management transparency and modernization.

  18. A Hidden Portrait by Edgar Degas

    PubMed Central

    Thurrowgood, David; Paterson, David; de Jonge, Martin D.; Kirkham, Robin; Thurrowgood, Saul; Howard, Daryl L.

    2016-01-01

    The preservation and understanding of cultural heritage depends increasingly on in-depth chemical studies. Rapid technological advances are forging connections between scientists and arts communities, enabling revolutionary new techniques for non-invasive technical study of culturally significant, highly prized artworks. We have applied a non-invasive, rapid, high definition X-ray fluorescence (XRF) elemental mapping technique to a French Impressionist painting using a synchrotron radiation source, and show how this technology can advance scholarly art interpretation and preservation. We have obtained detailed technical understanding of a painting which could not be resolved by conventional techniques. Here we show 31.6 megapixel scanning XRF derived elemental maps and report a novel image processing methodology utilising these maps to produce a false colour representation of a “hidden” portrait by Edgar Degas. This work provides a cohesive methodology for both imaging and understanding the chemical composition of artworks, and enables scholarly understandings of cultural heritage, many of which have eluded conventional technologies. We anticipate that the outcome from this work will encourage the reassessment of some of the world’s great art treasures. PMID:27490856

  19. Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus

    PubMed Central

    Labudde, Dirk

    2015-01-01

    The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations. PMID:26180540

  20. Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus.

    PubMed

    Grunert, Steffen; Labudde, Dirk

    2015-01-01

    The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations.

  1. Technology development for cobalt F-T catalysts. Quarterly technical progress report number 10, January 1--March 31, 1995

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Singleton, A.H.

    1995-06-28

    The goal of this project is the development of a commercially-viable, cobalt-based Fischer-Tropsch (F-T) catalyst for use in a slurry bubble column reactor. The major objectives of this work are (1) to develop a cobalt-based F-T catalyst with low (< 5%) methane selectivity, (2) to develop a cobalt-based F-T catalyst with water-gas shift activity, and (3) to combine both these improvements into one catalyst. The project consists of five major tasks: catalyst development; catalyst testing; catalyst reproducibility tests; catalyst aging tests; and preliminary design and cost estimate for a demonstrate scale catalyst production facility. Technical accomplishments during this reporting periodmore » include the following. It appears that the higher activity obtained for the catalysts prepared using an organic solution and reduced directly without prior calcination was the result of higher dispersions obtained under such pretreatment. A Ru-promoted Co catalyst on alumina with 30% Co loading exhibited a 4-fold increase in dispersion and a 2-fold increase in activity in the fixed-bed reactor from that obtained with the non-promoted catalyst. Several reactor runs have again focused on pushing conversion to higher levels. The maximum conversion obtained has been 49.7% with 26g catalyst. Further investigations of the effect of reaction temperature on the performance of Co catalysts during F-T synthesis were started using a low activity catalyst and one of the most active catalysts. The three 1 kg catalyst batches prepared by Calsicat for the reproducibility and aging studies were tested in both the fixed-bed and slurry bubble column reactors under the standard reaction conditions. The effects of adding various promoters to some cobalt catalysts have also been addressed. Results are presented and discussed.« less

  2. A unified representation of findings in clinical radiology using the UMLS and DICOM.

    PubMed

    Bertaud, Valérie; Lasbleiz, Jérémy; Mougin, Fleur; Burgun, Anita; Duvauferrier, Régis

    2008-09-01

    Collecting and analyzing findings constitute the basis of medical activity. Computer assisted medical activity raises the problem of modelling findings. We propose a unified representation of findings integrating the representations of findings in the GAMUTS in Radiology [M.M. Reeder, B. Felson, GAMUTS in radiology Comprehensive lists of roentgen differential diagnosis, fourth ed., 2003], the Unified Medical Language System (UMLS), and the Digital Imaging and Communication in Medicine Structured Report (DICOM-SR). Starting from a corpus of findings in bone and joint radiology [M.M. Reeder, B. Felson, GAMUTS in Radiology comprehensive lists of roentgen differential diagnosis, fourth ed., 2003] (3481 words), an automated mapping to the UMLS was performed with the Metamap Program. The resulting UMLS terms and Semantic Types were analyzed in order to find a generic template in accordance with DICOM-SR structure. UMLS Concepts were missing for 45% of the GAMUTS findings. Three kinds of regularities were observed in the way the Semantic Types were combined: "pathological findings", "physiological findings" and "anatomical findings". A generic and original DICOM-SR template modelling finding was proposed. It was evaluated for representing GAMUTS jaws findings. 21% missing terms had to be picked up from Radlex (5%) or created (16%). This article shows that it is possible to represent findings using the UMLS and the DICOM SR formalism with a semi-automated method. The Metamap program helped to find a model to represent the semantic structure of free texts with standardized terms (UMLS Concepts). Nevertheless, the coverage of the UMLS is not comprehensive. This study shows that the UMLS should include more technical concepts and more concepts regarding findings, signs and symptoms to be suitable for radiology representation. The semi-automated translation of the whole GAMUTS using the UMLS concepts and the DICOM SR relations could help to create or supplement the DCMR Templates and Context Groups pertaining to the description of imaging findings.

  3. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library.

    PubMed

    Sánchez, Cecilia Castaño; Smith, Timothy P L; Wiedmann, Ralph T; Vallejo, Roger L; Salem, Mohamed; Yao, Jianbo; Rexroad, Caird E

    2009-11-25

    To enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expressed Sequence Tags (ESTs) have been used for single nucleotide polymorphism (SNP) discovery in salmonids. In those strategies, the salmonid semi-tetraploid genomes often led to assemblies of paralogous sequences and therefore resulted in a high rate of false positive SNP identification. Sequencing genomic DNA using primers identified from ESTs proved to be an effective but time consuming methodology of SNP identification in rainbow trout, therefore not suitable for high throughput SNP discovery. In this study, we employed a high-throughput strategy that used pyrosequencing technology to generate data from a reduced representation library constructed with genomic DNA pooled from 96 unrelated rainbow trout that represent the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock population. The reduced representation library consisted of 440 bp fragments resulting from complete digestion with the restriction enzyme HaeIII; sequencing produced 2,000,000 reads providing an average 6 fold coverage of the estimated 150,000 unique genomic restriction fragments (300,000 fragment ends). Three independent data analyses identified 22,022 to 47,128 putative SNPs on 13,140 to 24,627 independent contigs. A set of 384 putative SNPs, randomly selected from the sets produced by the three analyses were genotyped on individual fish to determine the validation rate of putative SNPs among analyses, distinguish apparent SNPs that actually represent paralogous loci in the tetraploid genome, examine Mendelian segregation, and place the validated SNPs on the rainbow trout linkage map. Approximately 48% (183) of the putative SNPs were validated; 167 markers were successfully incorporated into the rainbow trout linkage map. In addition, 2% of the sequences from the validated markers were associated with rainbow trout transcripts. The use of reduced representation libraries and pyrosequencing technology proved to be an effective strategy for the discovery of a high number of putative SNPs in rainbow trout; however, modifications to the technique to decrease the false discovery rate resulting from the evolutionary recent genome duplication would be desirable.

  4. Learning Mediated by an Educational Hypermedia

    NASA Astrophysics Data System (ADS)

    Fagundes, Adriano Luiz; da Silva, Tatiana; Barroso, Marta Feijó

    2015-12-01

    The phases of the Moon is a learning subject composed of smaller units here elaborated by adopting the theory of cognitive load, including aspects related to visualization in science education and taking into account learning difficulties documented in the research literature on science/astronomy teaching as theoretical guiding. The complete research process involved 77 students attending an undergraduate physics course and included data collection instruments to investigate technical aspects of the material, quality of contents and learning. This work focused on learning mediated by a hypermedia digital resource. The instruments used at this stage were pre-testing and learning evaluation allowing a qualitative and quantitative assessment. The questions pointed to the knowledge of the Moon as a body without its own light, to representations of schematic diagrams with sequences of lunar phases and the possibility of observing the Sun and the Moon according to the time of the day, an explanation and a representation of the dynamics of synchronous rotation motion of the Moon. The result provided an overall average increase of 33% in learning. We point out the features of the material that may have contributed to a highest quality as a learning tool.

  5. Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

    PubMed Central

    Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

    2012-01-01

    Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

  6. A general representation scheme for crystalline solids based on Voronoi-tessellation real feature values and atomic property data

    PubMed Central

    Jalem, Randy; Nakayama, Masanobu; Noda, Yusuke; Le, Tam; Takeuchi, Ichiro; Tateyama, Yoshitaka; Yamazaki, Hisatsugu

    2018-01-01

    Abstract Increasing attention has been paid to materials informatics approaches that promise efficient and fast discovery and optimization of functional inorganic materials. Technical breakthrough is urgently requested to advance this field and efforts have been made in the development of materials descriptors to encode or represent characteristics of crystalline solids, such as chemical composition, crystal structure, electronic structure, etc. We propose a general representation scheme for crystalline solids that lifts restrictions on atom ordering, cell periodicity, and system cell size based on structural descriptors of directly binned Voronoi-tessellation real feature values and atomic/chemical descriptors based on the electronegativity of elements in the crystal. Comparison was made vs. radial distribution function (RDF) feature vector, in terms of predictive accuracy on density functional theory (DFT) material properties: cohesive energy (CE), density (d), electronic band gap (BG), and decomposition energy (Ed). It was confirmed that the proposed feature vector from Voronoi real value binning generally outperforms the RDF-based one for the prediction of aforementioned properties. Together with electronegativity-based features, Voronoi-tessellation features from a given crystal structure that are derived from second-nearest neighbor information contribute significantly towards prediction. PMID:29707064

  7. A general representation scheme for crystalline solids based on Voronoi-tessellation real feature values and atomic property data.

    PubMed

    Jalem, Randy; Nakayama, Masanobu; Noda, Yusuke; Le, Tam; Takeuchi, Ichiro; Tateyama, Yoshitaka; Yamazaki, Hisatsugu

    2018-01-01

    Increasing attention has been paid to materials informatics approaches that promise efficient and fast discovery and optimization of functional inorganic materials. Technical breakthrough is urgently requested to advance this field and efforts have been made in the development of materials descriptors to encode or represent characteristics of crystalline solids, such as chemical composition, crystal structure, electronic structure, etc. We propose a general representation scheme for crystalline solids that lifts restrictions on atom ordering, cell periodicity, and system cell size based on structural descriptors of directly binned Voronoi-tessellation real feature values and atomic/chemical descriptors based on the electronegativity of elements in the crystal. Comparison was made vs. radial distribution function (RDF) feature vector, in terms of predictive accuracy on density functional theory (DFT) material properties: cohesive energy (CE), density ( d ), electronic band gap (BG), and decomposition energy (Ed). It was confirmed that the proposed feature vector from Voronoi real value binning generally outperforms the RDF-based one for the prediction of aforementioned properties. Together with electronegativity-based features, Voronoi-tessellation features from a given crystal structure that are derived from second-nearest neighbor information contribute significantly towards prediction.

  8. An extensible simulation environment and movement metrics for testing walking behavior in agent-based models

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Paul M. Torrens; Atsushi Nara; Xun Li

    2012-01-01

    Human movement is a significant ingredient of many social, environmental, and technical systems, yet the importance of movement is often discounted in considering systems complexity. Movement is commonly abstracted in agent-based modeling (which is perhaps the methodological vehicle for modeling complex systems), despite the influence of movement upon information exchange and adaptation in a system. In particular, agent-based models of urban pedestrians often treat movement in proxy form at the expense of faithfully treating movement behavior with realistic agency. There exists little consensus about which method is appropriate for representing movement in agent-based schemes. In this paper, we examine popularly-usedmore » methods to drive movement in agent-based models, first by introducing a methodology that can flexibly handle many representations of movement at many different scales and second, introducing a suite of tools to benchmark agent movement between models and against real-world trajectory data. We find that most popular movement schemes do a relatively poor job of representing movement, but that some schemes may well be 'good enough' for some applications. We also discuss potential avenues for improving the representation of movement in agent-based frameworks.« less

  9. Development of a Highly Automated and Multiplexed Targeted Proteome Pipeline and Assay for 112 Rat Brain Synaptic Proteins

    PubMed Central

    Colangelo, Christopher M.; Ivosev, Gordana; Chung, Lisa; Abbott, Thomas; Shifman, Mark; Sakaue, Fumika; Cox, David; Kitchen, Rob R.; Burton, Lyle; Tate, Stephen A; Gulcicek, Erol; Bonner, Ron; Rinehart, Jesse; Nairn, Angus C.; Williams, Kenneth R.

    2015-01-01

    We present a comprehensive workflow for large scale (>1000 transitions/run) label-free LC-MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling (xMRM) that improves Signal/Noise by >2-fold, and automatic peak modeling. Improvements to data analysis include a novel Q/C metric, Normalized Group Area Ratio (NGAR), MLR normalization, weighted regression analysis, and data dissemination through the Yale Protein Expression Database. As a proof of principle we developed a robust 90 minute LC-MRM assay for Mouse/Rat Post-Synaptic Density (PSD) fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (1.0) and protein fold change (0.94) between the label-free and SIS analyses. Overall, our first method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay. PMID:25476245

  10. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone.

    PubMed

    Ganesh, Sangita; Bristow, Laura A; Larsen, Morten; Sarode, Neha; Thamdrup, Bo; Stewart, Frank J

    2015-12-01

    The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4nMNd(-1)) fell to zero and N2 production by denitrification (0.5-1.7nMNd(-1)) and anammox (0.3-1.9nMNd(-1)) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.

  11. Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

    PubMed Central

    Ganesh, Sangita; Bristow, Laura A; Larsen, Morten; Sarode, Neha; Thamdrup, Bo; Stewart, Frank J

    2015-01-01

    The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2–1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5–9.4nMNd−1) fell to zero and N2 production by denitrification (0.5–1.7nMNd−1) and anammox (0.3–1.9nMNd−1) declined by 53–85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs. PMID:25848875

  12. Probing the free energy landscape of the FBP28WW domain using multiple techniques.

    PubMed

    Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

    2009-05-01

    The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.

  13. Active engagement in a web-based tutorial to prevent obesity grounded in Fuzzy-Trace Theory predicts higher knowledge and gist comprehension.

    PubMed

    Brust-Renck, Priscila G; Reyna, Valerie F; Wilhelms, Evan A; Wolfe, Christopher R; Widmer, Colin L; Cedillos-Whynott, Elizabeth M; Morant, A Kate

    2017-08-01

    We used Sharable Knowledge Objects (SKOs) to create an Intelligent Tutoring System (ITS) grounded in Fuzzy-Trace Theory to teach women about obesity prevention: GistFit, getting the gist of healthy eating and exercise. The theory predicts that reliance on gist mental representations (as opposed to verbatim) is more effective in reducing health risks and improving decision making. Technical information was translated into decision-relevant gist representations and gist principles (i.e., healthy values). The SKO was hypothesized to facilitate extracting these gist representations and principles by engaging women in dialogue, "understanding" their responses, and replying appropriately to prompt additional engagement. Participants were randomly assigned to either the obesity prevention tutorial (GistFit) or a control tutorial containing different content using the same technology. Participants were administered assessments of knowledge about nutrition and exercise, gist comprehension, gist principles, behavioral intentions and self-reported behavior. An analysis of engagement in tutorial dialogues and responses to multiple-choice questions to check understanding throughout the tutorial revealed significant correlations between these conversations and scores on subsequent knowledge tests and gist comprehension. Knowledge and comprehension measures correlated with healthier behavior and greater intentions to perform healthy behavior. Differences between GistFit and control tutorials were greater for participants who engaged more fully. Thus, results are consistent with the hypothesis that active engagement with a new gist-based ITS, rather than a passive memorization of verbatim details, was associated with an array of known psychosocial mediators of preventive health decisions, such as knowledge acquisition, and gist comprehension.

  14. Challenges in building intelligent systems for space mission operations

    NASA Technical Reports Server (NTRS)

    Hartman, Wayne

    1991-01-01

    The purpose here is to provide a top-level look at the stewardship functions performed in space operations, and to identify the major issues and challenges that must be addressed to build intelligent systems that can realistically support operations functions. The focus is on decision support activities involving monitoring, state assessment, goal generation, plan generation, and plan execution. The bottom line is that problem solving in the space operations domain is a very complex process. A variety of knowledge constructs, representations, and reasoning processes are necessary to support effective human problem solving. Emulating these kinds of capabilities in intelligent systems offers major technical challenges that the artificial intelligence community is only beginning to address.

  15. NASA climate data catalog

    NASA Technical Reports Server (NTRS)

    Reph, M. G.

    1984-01-01

    This document provides a summary of information available in the NASA Climate Data Catalog. The catalog provides scientific users with technical information about selected climate parameter data sets and the associated sensor measurements from which they are derived. It is an integral part of the Pilot Climate Data System (PCDS), an interactive, scientific management system for locating, obtaining, manipulating, and displaying climate research data. The catalog is maintained in a machine readable representation which can easily be accessed via the PCDS. The purposes, format and content of the catalog are discussed. Summarized information is provided about each of the data sets currently described in the catalog. Sample detailed descriptions are included for individual data sets or families of related data sets.

  16. Thinking and meddling with boundaries: Critical reflections on Matthew Weinstein's narrative of street medics, red-zones and glop

    NASA Astrophysics Data System (ADS)

    Alsop, Steve

    2015-03-01

    In pursuit of more mindful notions of hybridity, this review essay provides a series of reflections on Mathew Weinstein's representations of Street Medics and `sciences for the red zones of neoliberalism'. My analysis draws on three popular ways of thinking with boundaries to offer a critical reading of the boundary-work that the essay performs with respect to three dialectics: (1) technical and political; (2) disciplinarily and multidisciplinarities; and (3) structures and agencies. I conclude with reflections on my boundary labour as a researcher, writer and pedagogue and how such cultural work might learn to live better with difference, ambiguities, hybrids and cross-hybrid learning.

  17. High level functions for the intuitive use of an assistive robot.

    PubMed

    Lebec, Olivier; Ben Ghezala, Mohamed Walid; Leynart, Violaine; Laffont, Isabelle; Fattal, Charles; Devilliers, Laurence; Chastagnol, Clement; Martin, Jean-Claude; Mezouar, Youcef; Korrapatti, Hermanth; Dupourqué, Vincent; Leroux, Christophe

    2013-06-01

    This document presents the research project ARMEN (Assistive Robotics to Maintain Elderly People in a Natural environment), aimed at the development of a user friendly robot with advanced functions for assistance to elderly or disabled persons at home. Focus is given to the robot SAM (Smart Autonomous Majordomo) and its new features of navigation, manipulation, object recognition, and knowledge representation developed for the intuitive supervision of the robot. The results of the technical evaluations show the value and potential of these functions for practical applications. The paper also documents the details of the clinical evaluations carried out with elderly and disabled persons in a therapeutic setting to validate the project.

  18. Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS).

    PubMed

    Braun, Joerg E; Serebrov, Victor

    2017-01-01

    Recent development of single-molecule techniques to study pre-mRNA splicing has provided insights into the dynamic nature of the spliceosome. Colocalization single-molecule spectroscopy (CoSMoS) allows following spliceosome assembly in real time at single-molecule resolution in the full complexity of cellular extracts. A detailed protocol of CoSMoS has been published previously (Anderson and Hoskins, Methods Mol Biol 1126:217-241, 2014). Here, we provide an update on the technical advances since the first CoSMoS studies including slide surface treatment, data processing, and representation. We describe various labeling strategies to generate RNA reporters with multiple dyes (or other moieties) at specific locations.

  19. Is High Fidelity Simulation the Most Effective Method for the Development of Non-Technical Skills in Nursing? A Review of the Current Evidence

    PubMed Central

    Lewis, Robin; Strachan, Alasdair; Smith, Michelle McKenzie

    2012-01-01

    Aim: To review the literature on the use of simulation in the development of non-technical skills in nursing Background: The potential risks to patients associated with learning 'at the bedside' are becoming increasingly unacceptable, and the search for innovative education and training methods that do not expose the patient to preventable errors continues. All the evidence shows that a significant proportion of adverse events in health care is caused by problems relating to the application of the 'non-technical' skills of communication, teamwork, leadership and decision-making. Results: Simulation is positively associated with significantly improved interpersonal communication skills at patient handover, and it has also been clearly shown to improve team behaviours in a wide variety of clinical contexts and clinical personnel, associated with improved team performance in the management of crisis situations. It also enables the effective development of transferable, transformational leadership skills, and has also been demonstrated to improve students' critical thinking and clinical reasoning in complex care situations, and to aid in the development of students' self-efficacy and confidence in their own clinical abilities. Conclusion: High fidelity simulation is able to provide participants with a learning environment in which to develop non-technical skills, that is safe and controlled so that the participants are able to make mistakes, correct those mistakes in real time and learn from them, without fear of compromising patient safety. Participants in simulation are also able to rehearse the clinical management of rare, complex or crisis situations in a valid representation of clinical practice, before practising on patients. PMID:22893783

  20. Minimal surgical access to treat gynecomastia with the use of a power-assisted arthroscopic-endoscopic cartilage shaver.

    PubMed

    Prado, Arturo C; Castillo, Paulo F

    2005-03-01

    Gynecomastia is the most common benign condition of the male breast. The authors present a new method of treatment for gynecomastia that combines traditional liposuction in conjunction with a shaver technique to effectively remove the fibrofatty and the glandular tissues of the male breast and avoid areolar incisions. Twenty-five patients were treated in this fashion, and each patient demonstrated a smooth, masculine breast contour with well-concealed scars in the inframammary folds, eliminating the stigma of breast surgery. The procedure is technically straightforward and provides consistent results. It is offered as an additional option for the treatment of gynecomastia.

  1. Aerobic nonaseptic growth of Verticillium on coffee waste waters and cane blackstrap molasses at a pilot plant scale

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Espinosa, R.; Maldonado, O.; Menchu, J.F.

    1977-01-01

    An evaluation is made of the pilot plant studies on the biosynthesis of Verticillium sp. both on coffee waste waters and blackstrap molasses. The purpose of the study was two-fold: the first to produce a filamentous fungi as a source of protein and the second to alleviate the serious water pollution resulting from the processing of coffee berries. The molasses was studied as an alternative medium to enable year-round operation of the plant since coffee is a seasonal crop. The results indicated that the growth of Verticillium is technically feasible in a batch operation. (JSR)

  2. Time-resolved circular dichroism: Application to the study of conformal changes in biomolecules

    NASA Astrophysics Data System (ADS)

    Hache, F.

    2010-06-01

    Circular dichroism (CD) is known to be a very sensitive probe of the conformation of molecules and biomolecules. It is therefore tempting to implement CD in a pump-probe experiment in order to measure ultrarapid conformational changes which occur in photochemical processes. We present two technical developments of such time-resolved CD experiments. The first one relies on the modulation of the probe polarization from left to right circular whereas the second one measures the pump-induced ellipticity of the probe with a Babinet-Soleil compensator. Some applications are described and extension of these techniques towards the study of elementary protein folding processes is discussed.

  3. The graphical brain: Belief propagation and active inference

    PubMed Central

    Friston, Karl J.; Parr, Thomas; de Vries, Bert

    2018-01-01

    This paper considers functional integration in the brain from a computational perspective. We ask what sort of neuronal message passing is mandated by active inference—and what implications this has for context-sensitive connectivity at microscopic and macroscopic levels. In particular, we formulate neuronal processing as belief propagation under deep generative models. Crucially, these models can entertain both discrete and continuous states, leading to distinct schemes for belief updating that play out on the same (neuronal) architecture. Technically, we use Forney (normal) factor graphs to elucidate the requisite message passing in terms of its form and scheduling. To accommodate mixed generative models (of discrete and continuous states), one also has to consider link nodes or factors that enable discrete and continuous representations to talk to each other. When mapping the implicit computational architecture onto neuronal connectivity, several interesting features emerge. For example, Bayesian model averaging and comparison, which link discrete and continuous states, may be implemented in thalamocortical loops. These and other considerations speak to a computational connectome that is inherently state dependent and self-organizing in ways that yield to a principled (variational) account. We conclude with simulations of reading that illustrate the implicit neuronal message passing, with a special focus on how discrete (semantic) representations inform, and are informed by, continuous (visual) sampling of the sensorium. Author Summary This paper considers functional integration in the brain from a computational perspective. We ask what sort of neuronal message passing is mandated by active inference—and what implications this has for context-sensitive connectivity at microscopic and macroscopic levels. In particular, we formulate neuronal processing as belief propagation under deep generative models that can entertain both discrete and continuous states. This leads to distinct schemes for belief updating that play out on the same (neuronal) architecture. Technically, we use Forney (normal) factor graphs to characterize the requisite message passing, and link this formal characterization to canonical microcircuits and extrinsic connectivity in the brain. PMID:29417960

  4. Integrated VR platform for 3D and image-based models: a step toward interactive image-based virtual environments

    NASA Astrophysics Data System (ADS)

    Yoon, Jayoung; Kim, Gerard J.

    2003-04-01

    Traditionally, three dimension models have been used for building virtual worlds, and a data structure called the "scene graph" is often employed to organize these 3D objects in the virtual space. On the other hand, image-based rendering has recently been suggested as a probable alternative VR platform for its photo-realism, however, due to limited interactivity, it has only been used for simple navigation systems. To combine the merits of these two approaches to object/scene representations, this paper proposes for a scene graph structure in which both 3D models and various image-based scenes/objects can be defined, traversed, and rendered together. In fact, as suggested by Shade et al., these different representations can be used as different LOD's for a given object. For instance, an object might be rendered using a 3D model at close range, a billboard at an intermediate range, and as part of an environment map at far range. The ultimate objective of this mixed platform is to breath more interactivity into the image based rendered VE's by employing 3D models as well. There are several technical challenges in devising such a platform: designing scene graph nodes for various types of image based techniques, establishing criteria for LOD/representation selection, handling their transitions, implementing appropriate interaction schemes, and correctly rendering the overall scene. Currently, we have extended the scene graph structure of the Sense8's WorldToolKit, to accommodate new node types for environment maps billboards, moving textures and sprites, "Tour-into-the-Picture" structure, and view interpolated objects. As for choosing the right LOD level, the usual viewing distance and image space criteria are used, however, the switching between the image and 3D model occurs at a distance from the user where the user starts to perceive the object's internal depth. Also, during interaction, regardless of the viewing distance, a 3D representation would be used, it if exists. Before rendering, objects are conservatively culled from the view frustum using the representation with the largest volume. Finally, we carried out experiments to verify the theoretical derivation of the switching rule and obtained positive results.

  5. Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.

    PubMed

    Poblete, Simón; Bottaro, Sandro; Bussi, Giovanni

    2018-03-29

    Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand they can also help to identify the essential degrees of freedom and interactions for the description of a number of structures. With the aim to provide an all-atom representation in an explicit solvent to the predictions of our SPlit and conQueR (SPQR) coarse-grained model of RNA, we recently introduced a backmapping procedure which enforces the predicted structure into an atomistic one by means of steered molecular dynamics. These simulations minimize the ERMSD, a particular metric which deals exclusively with the relative arrangement of nucleobases, between the atomistic representation and the target structure. In this paper, we explore the effects of this approach on the resulting interaction networks and backbone conformations by applying it on a set of fragments using as a target their native structure. We find that the geometry of the target structures can be reliably recovered, with limitations in the regions with unpaired bases such as bulges. In addition, we observe that the folding pathway can also change depending on the parameters used in the definition of the ERMSD and the use of other metrics such as the RMSD. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. A persistent lack of international representation on editorial boards in environmental biology.

    PubMed

    Espin, Johanna; Palmas, Sebastian; Carrasco-Rueda, Farah; Riemer, Kristina; Allen, Pablo E; Berkebile, Nathan; Hecht, Kirsten A; Kastner-Wilcox, Kay; Núñez-Regueiro, Mauricio M; Prince, Candice; Rios, Constanza; Ross, Erica; Sangha, Bhagatveer; Tyler, Tia; Ungvari-Martin, Judit; Villegas, Mariana; Cataldo, Tara T; Bruna, Emilio M

    2017-12-01

    The scholars comprising journal editorial boards play a critical role in defining the trajectory of knowledge in their field. Nevertheless, studies of editorial board composition remain rare, especially those focusing on journals publishing research in the increasingly globalized fields of science, technology, engineering, and math (STEM). Using metrics for quantifying the diversity of ecological communities, we quantified international representation on the 1985-2014 editorial boards of 24 environmental biology journals. Over the course of 3 decades, there were 3,827 unique scientists based in 70 countries who served as editors. The size of the editorial community increased over time-the number of editors serving in 2014 was 4-fold greater than in 1985-as did the number of countries in which editors were based. Nevertheless, editors based outside the "Global North" (the group of economically developed countries with high per capita gross domestic product [GDP] that collectively concentrate most global wealth) were extremely rare. Furthermore, 67.18% of all editors were based in either the United States or the United Kingdom. Consequently, geographic diversity-already low in 1985-remained unchanged through 2014. We argue that this limited geographic diversity can detrimentally affect the creativity of scholarship published in journals, the progress and direction of research, the composition of the STEM workforce, and the development of science in Latin America, Africa, the Middle East, and much of Asia (i.e., the "Global South").

  7. Genome U-Plot: a whole genome visualization.

    PubMed

    Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

    2018-05-15

    The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

  8. Nuclear DNA C‐values in 30 Species Double the Familial Representation in Pteridophytes

    PubMed Central

    OBERMAYER, RENATE; LEITCH, ILIA J.; HANSON, LYNDA; BENNETT, MICHAEL D.

    2002-01-01

    Nuclear DNA C‐values and genome size are important biodiversity characters with fundamental biological significance. Yet C‐value data for pteridophytes, a diverse group of vascular plants with approx. 9000 extant species, remain scarce. A recent survey by Bennett and Leitch (2001, Annals of Botany 87: 335–345) found that C‐values were reported for only 48 pteridophyte species. To improve phylogenetic representation in this group and to check previously reported estimates, C‐values for 30 taxa in 17 families were measured using flow cytometry for all but one species. This technique proved generally applicable, but the ease with which C‐value data were generated varied greatly between materials. Comparing the new data with those previously published revealed several large discrepancies. After discounting doubtful data, C‐values for 62 pteridophyte species remained acceptable for analysis. The present work has increased the number of such species’ C‐values by 93 %, and more than doubled the number of families represented (from 10 to 21). Analysis shows that pteridophyte C‐values vary approx. 450‐fold, from 0·16 pg in Selaginella kraussiana to 72·7 pg in Psilotum nudum var. gasa. Superimposing C‐value data onto a robust phylogeny of pteridophytes suggests some possible trends in C‐value evolution and highlights areas for future work. PMID:12197518

  9. Intrapartum fetal heart rate classification from trajectory in Sparse SVM feature space.

    PubMed

    Spilka, J; Frecon, J; Leonarduzzi, R; Pustelnik, N; Abry, P; Doret, M

    2015-01-01

    Intrapartum fetal heart rate (FHR) constitutes a prominent source of information for the assessment of fetal reactions to stress events during delivery. Yet, early detection of fetal acidosis remains a challenging signal processing task. The originality of the present contribution are three-fold: multiscale representations and wavelet leader based multifractal analysis are used to quantify FHR variability ; Supervised classification is achieved by means of Sparse-SVM that aim jointly to achieve optimal detection performance and to select relevant features in a multivariate setting ; Trajectories in the feature space accounting for the evolution along time of features while labor progresses are involved in the construction of indices quantifying fetal health. The classification performance permitted by this combination of tools are quantified on a intrapartum FHR large database (≃ 1250 subjects) collected at a French academic public hospital.

  10. 4Pi-confocal microscopy of live cells

    NASA Astrophysics Data System (ADS)

    Bahlmann, Karsten; Jakobs, Stefan; Hell, Stefan W.

    2002-06-01

    By coherently adding the spherical wavefronts of two opposing lenses, two-photon excitation 4Pi-confocal fluorescence microscopy has achieved three-dimensional imaging with an axial resolution 3-7 times better than confocal microscopy. So far this improvement was possible only in glycerol-mounted, fixed cells. Here we report 4Pi-confocal microscopy of watery objects and its application to the imaging of live cells. Water immersion 4Pi-confocal microscopy of membrane stained live Escherichia coli bacteria attains a 4.3 fold better axial resolution as compared to the best water immersion confocal microscope. The resolution enhancement results into a vastly improved three-dimensional representation of the bacteria. The first images of live biological samples with an all-directional resolution in the 190-280 nm range are presented here, thus establishing a new resolution benchmark in live cell microscopy.

  11. Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.

    PubMed

    Greenman, C D; Cooke, S L; Marshall, J; Stratton, M R; Campbell, P J

    2016-01-01

    Breakage-fusion-bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. Here we study the evolution space of breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are [Formula: see text] qualitatively distinct evolutions involving [Formula: see text] breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the process to show these evolutions are not equally likely, and also describe how amplicons become localized. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples.

  12. Reproducibility and quantitation of amplicon sequencing-based detection

    PubMed Central

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-01-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities. PMID:21346791

  13. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    PubMed

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Brookian structural plays in the National Petroleum Reserve, Alaska

    USGS Publications Warehouse

    Potter, Christopher J.; Moore, Thomas E.

    2003-01-01

    As part of the U.S. Geological Survey assessment of undiscovered oil and gas resources in the National Petroleum Reserve-Alaska (NPRA), two structural plays were assessed in thrust-faulted and folded Upper Cretaceous rocks of the Brookian megasequence. These are the Brookian Topset Structural Play and the Torok Structural Play, located in the Brooks Range foothills and the southern part of the coastal plain, within the Tertiary-age frontal part of the Jurassic to Tertiary Brooks Range orogenic belt. A new regional structural interpretation, developed through regional seismic analyses, reconnaissance field investigations, and new thermal constraints, guided the geologic evaluation and risking of these plays. Volumetric parameters were derived from seismic reflection data, well data and oil and gas field analogs. The fundamental elements of the Brookian Topset Structural Play, exemplified by the undeveloped Umiat oil field, include: (1) reservoirs in Nanushuk Group and uppermost Torok Formation shallow-marine to nonmarine sandstones draped over anticlines caused by structural thickening in underlying Torok mudstones; (2) seals provided by overlying shale drapes in the Nanushuk, and locally by thrust faults; (3) Torok, gamma-ray-zone (GRZ) or pebble shale source rocks; (4) remigration of hydrocarbons from early formed (Late Cretaceous) stratigraphic traps disrupted by 60 Ma thrusting, into newly formed structural traps. The 60 Ma thrusting was probably accompanied by new generation and migration of natural gas resulting from late structural thickening and tectonic loading. Subsurface data from the Umiat field and other seismic reflection data within the play area indicate that the structural traps are commonly compartmentalized by thrust faults. The fundamental elements of the Torok Structural Play, exemplified by the undeveloped East Kurupa gas accumulation just south of NPRA, include: (1) reservoirs in lower Torok Formation basin-floor sandstones, and perhaps in small sandstone bodies intercalated with middle to upper Torok mudstones; (2) structural traps provided by folded sandstone bodies above thrust faults within a pervasively deformed passive-roof duplex beneath the foothills and a less-strongly deformed domain to the north; (3) seals provided by Torok mudstone, both stratigraphically above the sandstone bodies and smeared along bounding thrust faults; (4) Torok, GRZ, pebble shale, or Kingak Shale source rocks; (5) a migration and charging scenario similar to that of the Brookian Topset Structural Play. According to our estimates, the Brookian Topset Structural Play contains 137 million barrels of technically recoverable oil and 10.6 trillion cubic feet (TCF) of technically recoverable, non-associated natural gas, with both values representing the mean estimate (expected value). The Torok Structural Play contains about 35 million barrels of technically recoverable oil and 17.9 TCF of technically recoverable, nonassociated natural gas.

  15. [Traffic accidents: a qualitative approach from Campinas, São Paulo, Brazil].

    PubMed

    Queiroz, Marcos S; Oliveira, Patrícia C P

    2002-01-01

    This article takes an interdisciplinary qualitative approach to the problem of traffic accidents in Campinas, São Paulo, Brazil. The authors begin by analyzing the "municipalization" (i.e., decentralization to the municipal level) of transport and traffic management in Campinas based on social representations by members of the local government's technical staff. Data demonstrate a significant drop in traffic accident mortality in Campinas in the last ten years. The findings illustrate how new transport and traffic policies had several positive effects. Special attention is given to the objectives, strategies, and obstacles dealt with by local government in the "municipalization" of traffic. The paper concludes by emphasizing the need for specific public policies to revitalize urban mass transportation, including special traffic safety educational programs.

  16. Asymptotic behaviour of two-point functions in multi-species models

    NASA Astrophysics Data System (ADS)

    Kozlowski, Karol K.; Ragoucy, Eric

    2016-05-01

    We extract the long-distance asymptotic behaviour of two-point correlation functions in massless quantum integrable models containing multi-species excitations. For such a purpose, we extend to these models the method of a large-distance regime re-summation of the form factor expansion of correlation functions. The key feature of our analysis is a technical hypothesis on the large-volume behaviour of the form factors of local operators in such models. We check the validity of this hypothesis on the example of the SU (3)-invariant XXX magnet by means of the determinant representations for the form factors of local operators in this model. Our approach confirms the structure of the critical exponents obtained previously for numerous models solvable by the nested Bethe Ansatz.

  17. Simulation of sodium pumps for nuclear power plants. Technical report 1 Oct 80-1 May 81

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Boadu, H.O.

    1981-05-01

    A single-phase pump model for analysis of transients in sodium cooled fast breeder nuclear power plants has been presented, where homologous characteristic curves are used to predict the behavior of the pump during operating transients. The pump model has been incorporated into BRENDA and FFTF; two system cases to simulate Clinch River Breeder Reactor Plant (CRBRP) and the Fast Flux Test Facility (FFTF) respectively. Two simulation test results for BRENDA which is one loop representation of a three loop plant have been presented. They are: (1) Primary pump coastdown to natural circulation coupled with scram failure, and (2) 10 percentmore » deviation of primary speed with plant controllers incorporated.« less

  18. Book Review: Book review

    NASA Astrophysics Data System (ADS)

    Wüthrich, Christian

    Symmetry considerations stand at the core of classical and quantum physics. No modern-and few older-physical theories forgo the immense services that these considerations offer. It is therefore only natural that philosophers of physics have increasingly started to study the motivations for, as well as the technical implementations and the interpretative implications of, symmetries in fundamental physics. Apart from the extraordinary foundational interest of symmetries, they provide a vehicle to study more general philosophical issues such as the relation between the physical world and its representations and between physics and mathematics. Moreover, traditional problems in metaphysics and philosophy of science such as the nature and status of laws of nature, scientific realism, and determinism naturally arise in, and enjoy substantial fertilisation from, the context of symmetries in physics.

  19. Technical skills measurement based on a cyber-physical system for endovascular surgery simulation.

    PubMed

    Tercero, Carlos; Kodama, Hirokatsu; Shi, Chaoyang; Ooe, Katsutoshi; Ikeda, Seiichi; Fukuda, Toshio; Arai, Fumihito; Negoro, Makoto; Kwon, Guiryong; Najdovski, Zoran

    2013-09-01

    Quantification of medical skills is a challenge, particularly simulator-based training. In the case of endovascular intervention, it is desirable that a simulator accurately recreates the morphology and mechanical characteristics of the vasculature while enabling scoring. For this purpose, we propose a cyber-physical system composed of optical sensors for a catheter's body motion encoding, a magnetic tracker for motion capture of an operator's hands, and opto-mechatronic sensors for measuring the interaction of the catheter tip with the vasculature model wall. Two pilot studies were conducted for measuring technical skills, one for distinguishing novices from experts and the other for measuring unnecessary motion. The proficiency levels were measurable between expert and novice and also between individual novice users. The results enabled scoring of the user's proficiency level, using sensitivity, reaction time, time to complete a task and respect for tissue integrity as evaluation criteria. Additionally, unnecessary motion was also measurable. The development of cyber-physical simulators for other domains of medicine depend on the study of photoelastic materials for human tissue modelling, and enables quantitative evaluation of skills using surgical instruments and a realistic representation of human tissue. Copyright © 2012 John Wiley & Sons, Ltd.

  20. User testing and stakeholder feedback contributed to the development of understandable and useful Summary of Findings tables for Cochrane reviews.

    PubMed

    Rosenbaum, Sarah E; Glenton, Claire; Nylund, Hilde Kari; Oxman, Andrew D

    2010-06-01

    To develop a Summary of Findings (SoF) table for use in Cochrane reviews that is understandable and useful for health professionals, acceptable to Cochrane Collaboration stakeholders, and feasible to implement. We gathered stakeholder feedback on the format and content of an SoF table from an advisory group of more than 50 participants and their constituencies through e-mail consultations. We conducted user tests using a think-aloud protocol method, collecting feedback from 21 health professionals and researchers in Norway and the UK. We analyzed the feedback, defined problem areas, and generated new solutions in brainstorming workshops. Stakeholders were concerned about precision in the data representation and about production feasibility. User testing revealed unexpected comprehension problems, mainly confusion about what the different numbers referred to (class reference). Resolving the tension between achieving table precision and table simplicity became the main focus of the working group. User testing led to a table more useful and understandable for clinical audiences. We arrived at an SoF table that was acceptable to the stakeholders and in principle feasible to implement technically. Some challenges remain, including presenting continuous outcomes and technical/editorial implementation.

  1. Utilizing neuronavigation for virtual electrode representation and safe resection following SEEG; a technical report.

    PubMed

    Brandmeir, Nicholas; Sather, Michael

    2018-02-20

    One of the most effective treatments for epilepsy is resection, but it remains underutilized. Efforts must be made to increase the ease, safety, and efficacy of epilepsy resection to improve utilization. Studies have shown an improved risk profile of stereoelectroencephalography (SEEG) over subdural grids (SDG) for invasive monitoring. One limitation to increased adoption of SEEG at epilepsy centers is the theoretical difficulty of planning a delayed resection once electrodes are removed. Our objective was to develop and present a technique using readily available neuronavigation technology to guide a cortical, non-lesional epilepsy resection with co-registration of imaging during invasive monitoring to imaging in an explanted patient, allowing for virtual visualization of electrodes. An example case taking advantage of the technique described above as an adjunct for an anatomically guided resection is presented with technical details and images. Intraoperative neuronavigation was successfully used to virtually represent previously removed SEEG electrodes and accuracy could be easily verified by examining scars on the scalp, bone, dura and pia. The simple technique presented can be a useful adjunct to resection following SEEG. This may help increase the adoption of SEEG, even when resection is planned.

  2. Depictive and metric body size estimation in anorexia nervosa and bulimia nervosa: A systematic review and meta-analysis.

    PubMed

    Mölbert, Simone Claire; Klein, Lukas; Thaler, Anne; Mohler, Betty J; Brozzo, Chiara; Martus, Peter; Karnath, Hans-Otto; Zipfel, Stephan; Giel, Katrin Elisabeth

    2017-11-01

    A distorted representation of one's own body is a diagnostic criterion and core psychopathology of both anorexia nervosa (AN) and bulimia nervosa (BN). Despite recent technical advances in research, it is still unknown whether this body image disturbance is characterized by body dissatisfaction and a low ideal weight and/or includes a distorted perception or processing of body size. In this article, we provide an update and meta-analysis of 42 articles summarizing measures and results for body size estimation (BSE) from 926 individuals with AN, 536 individuals with BN and 1920 controls. We replicate findings that individuals with AN and BN overestimate their body size as compared to controls (ES=0.63). Our meta-regression shows that metric methods (BSE by direct or indirect spatial measures) yield larger effect sizes than depictive methods (BSE by evaluating distorted pictures), and that effect sizes are larger for patients with BN than for patients with AN. To interpret these results, we suggest a revised theoretical framework for BSE that accounts for differences between depictive and metric BSE methods regarding the underlying body representations (conceptual vs. perceptual, implicit vs. explicit). We also discuss clinical implications and argue for the importance of multimethod approaches to investigate body image disturbance. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Spatial Information in Support of 3D Flood Damage Assessment of Buildings at Micro Level: A Review

    NASA Astrophysics Data System (ADS)

    Amirebrahimi, S.; Rajabifard, A.; Sabri, S.; Mendis, P.

    2016-10-01

    Floods, as the most common and costliest natural disaster around the globe, have adverse impacts on buildings which are considered as major contributors to the overall economic damage. With emphasis on risk management methods for reducing the risks to structures and people, estimating damage from potential flood events becomes an important task for identifying and implementing the optimal flood risk-reduction solutions. While traditional Flood Damage Assessment (FDA) methods focus on simple representation of buildings for large-scale damage assessment purposes, recent emphasis on buildings' flood resilience resulted in development of a sophisticated method that allows for a detailed and effective damage evaluation at the scale of building and its components. In pursuit of finding the suitable spatial information model to satisfy the needs of implementing such frameworks, this article explores the technical developments for an effective representation of buildings, floods and other required information within the built environment. The search begins with the Geospatial domain and investigates the state-of-the-art and relevant developments from data point of view in this area. It is further extended to other relevant disciplines in the Architecture, Engineering and Construction domain (AEC/FM) and finally, even some overlapping areas between these domains are considered and explored.

  4. Detailed clinical models: representing knowledge, data and semantics in healthcare information technology.

    PubMed

    Goossen, William T F

    2014-07-01

    This paper will present an overview of the developmental effort in harmonizing clinical knowledge modeling using the Detailed Clinical Models (DCMs), and will explain how it can contribute to the preservation of Electronic Health Records (EHR) data. Clinical knowledge modeling is vital for the management and preservation of EHR and data. Such modeling provides common data elements and terminology binding with the intention of capturing and managing clinical information over time and location independent from technology. Any EHR data exchange without an agreed clinical knowledge modeling will potentially result in loss of information. Many attempts exist from the past to model clinical knowledge for the benefits of semantic interoperability using standardized data representation and common terminologies. The objective of each project is similar with respect to consistent representation of clinical data, using standardized terminologies, and an overall logical approach. However, the conceptual, logical, and the technical expressions are quite different in one clinical knowledge modeling approach versus another. There currently are synergies under the Clinical Information Modeling Initiative (CIMI) in order to create a harmonized reference model for clinical knowledge models. The goal for the CIMI is to create a reference model and formalisms based on for instance the DCM (ISO/TS 13972), among other work. A global repository of DCMs may potentially be established in the future.

  5. The Effect of Subsurface Parameterizations on Modeled Flows in the Catchment Land Surface Model, Fortuna 2.5

    NASA Astrophysics Data System (ADS)

    Roningen, J. M.; Eylander, J. B.

    2014-12-01

    Groundwater use and management is subject to economic, legal, technical, and informational constraints and incentives at a variety of spatial and temporal scales. Planned and de facto management practices influenced by tax structures, legal frameworks, and agricultural and trade policies that vary at the country scale may have medium- and long-term effects on the ability of a region to support current and projected agricultural and industrial development. USACE is working to explore and develop global-scale, physically-based frameworks to serve as a baseline for hydrologic policy comparisons and consequence assessment, and such frameworks must include a reasonable representation of groundwater systems. To this end, we demonstrate the effects of different subsurface parameterizations, scaling, and meteorological forcings on surface and subsurface components of the Catchment Land Surface Model Fortuna v2.5 (Koster et al. 2000). We use the Land Information System 7 (Kumar et al. 2006) to process model runs using meteorological components of the Air Force Weather Agency's AGRMET forcing data from 2006 through 2011. Seasonal patterns and trends are examined in areas of the Upper Nile basin, northern China, and the Mississippi Valley. We also discuss the relevance of the model's representation of the catchment deficit with respect to local hydrogeologic structures.

  6. Structural prediction and analysis of VIH-related peptides from selected crustacean species.

    PubMed

    Nagaraju, Ganji Purna Chandra; Kumari, Nunna Siva; Prasad, Ganji Lakshmi Vara; Rajitha, Balney; Meenu, Madan; Rao, Manam Sreenivasa; Naik, Bannoth Reddya

    2009-08-17

    The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous extra technical aspects. As a result, no structural information is available for VIH peptide sequences registered in the Genbank. In this situation, it is not surprising that predictive methods have achieved great interest. Here, in this study the molt-inhibiting hormone (MIH) of the kuruma prawn (Marsupenaeus japonicus) is used, to predict the structure of four VIHrelated peptides in the crustacean species. The high similarity of the 3D-structures and the calculated physiochemical characteristics of these peptides suggest a common fold for the entire family.

  7. Turning limited experimental information into 3D models of RNA.

    PubMed

    Flores, Samuel Coulbourn; Altman, Russ B

    2010-09-01

    Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

  8. Acoustic Wave Guiding by Reconfigurable Tessellated Arrays

    NASA Astrophysics Data System (ADS)

    Zou, Chengzhe; Lynd, Danielle T.; Harne, Ryan L.

    2018-01-01

    The reconfiguration of origami tessellations is a prime vehicle to harness for adapting system properties governed by a structural form. While the knowledge of mechanical property changes associated with origami tessellation folding has been extensively built up, the opportunities to integrate other physics into a framework of tessellated, adaptive structures remain to be fully exploited. Acoustics appears to be a prime domain to marry with origami science. Specifically, deep technical analogies are revealed between wave-guiding properties achieved via digital methods that virtually reposition array elements and the actual repositioning of facets by folding origami-inspired tessellations. Here we capitalize on this analogy to investigate acoustic arrays established upon facet layouts of origami-inspired tessellations. We show that a concept of reconfigurable tessellated arrays may guide waves more effectively than traditional digitally phased arrays using fewer transducer elements. Moreover, we show that the refinement of tessellated arrays trends to the ideal case of classical wave radiators or receivers grounded in principles of geometrical acoustics. By linear wave physics shared among myriad scientific disciplines and across orders of magnitude in length scale, these discoveries may cultivate numerous opportunities for wave-guiding adaptive structures inspired by low-dimensional origami tessellations.

  9. Coarse-grained, foldable, physical model of the polypeptide chain.

    PubMed

    Chakraborty, Promita; Zuckermann, Ronald N

    2013-08-13

    Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.

  10. Improving power to detect changes in blood miRNA expression by accounting for sources of variability in experimental designs.

    PubMed

    Daniels, Sarah I; Sillé, Fenna C M; Goldbaum, Audrey; Yee, Brenda; Key, Ellen F; Zhang, Luoping; Smith, Martyn T; Thomas, Reuben

    2014-12-01

    Blood miRNAs are a new promising area of disease research, but variability in miRNA measurements may limit detection of true-positive findings. Here, we measured sources of miRNA variability and determine whether repeated measures can improve power to detect fold-change differences between comparison groups. Blood from healthy volunteers (N = 12) was collected at three time points. The miRNAs were extracted by a method predetermined to give the highest miRNA yield. Nine different miRNAs were quantified using different qPCR assays and analyzed using mixed models to identify sources of variability. A larger number of miRNAs from a publicly available blood miRNA microarray dataset with repeated measures were used for a bootstrapping procedure to investigate effects of repeated measures on power to detect fold changes in miRNA expression for a theoretical case-control study. Technical variability in qPCR replicates was identified as a significant source of variability (P < 0.05) for all nine miRNAs tested. Variability was larger in the TaqMan qPCR assays (SD = 0.15-0.61) versus the qScript qPCR assays (SD = 0.08-0.14). Inter- and intraindividual and extraction variability also contributed significantly for two miRNAs. The bootstrapping procedure demonstrated that repeated measures (20%-50% of N) increased detection of a 2-fold change for approximately 10% to 45% more miRNAs. Statistical power to detect small fold changes in blood miRNAs can be improved by accounting for sources of variability using repeated measures and choosing appropriate methods to minimize variability in miRNA quantification. This study demonstrates the importance of including repeated measures in experimental designs for blood miRNA research. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology." ©2014 American Association for Cancer Research.

  11. Optimal contact definition for reconstruction of contact maps.

    PubMed

    Duarte, Jose M; Sathyapriya, Rajagopal; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

    2010-05-27

    Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11A around the Cbeta atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2A RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.

  12. Optimal contact definition for reconstruction of Contact Maps

    PubMed Central

    2010-01-01

    Background Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Conclusions Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap. PMID:20507547

  13. Master equations and the theory of stochastic path integrals

    NASA Astrophysics Data System (ADS)

    Weber, Markus F.; Frey, Erwin

    2017-04-01

    This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations. We focus on numerical and analytical methods going beyond the low-noise limit and provide a unified framework for the study of master equations. After deriving the forward and backward master equations from the Chapman-Kolmogorov equation, we show how the two master equations can be cast into either of four linear partial differential equations (PDEs). Three of these PDEs are discussed in detail. The first PDE governs the time evolution of a generalized probability generating function whose basis depends on the stochastic process under consideration. Spectral methods, WKB approximations, and a variational approach have been proposed for the analysis of the PDE. The second PDE is novel and is obeyed by a distribution that is marginalized over an initial state. It proves useful for the computation of mean extinction times. The third PDE describes the time evolution of a ‘generating functional’, which generalizes the so-called Poisson representation. Subsequently, the solutions of the PDEs are expressed in terms of two path integrals: a ‘forward’ and a ‘backward’ path integral. Combined with inverse transformations, one obtains two distinct path integral representations of the conditional probability distribution solving the master equations. We exemplify both path integrals in analysing elementary chemical reactions. Moreover, we show how a well-known path integral representation of averaged observables can be recovered from them. Upon expanding the forward and the backward path integrals around stationary paths, we then discuss and extend a recent method for the computation of rare event probabilities. Besides, we also derive path integral representations for processes with continuous state spaces whose forward and backward master equations admit Kramers-Moyal expansions. A truncation of the backward expansion at the level of a diffusion approximation recovers a classic path integral representation of the (backward) Fokker-Planck equation. One can rewrite this path integral in terms of an Onsager-Machlup function and, for purely diffusive Brownian motion, it simplifies to the path integral of Wiener. To make this review accessible to a broad community, we have used the language of probability theory rather than quantum (field) theory and do not assume any knowledge of the latter. The probabilistic structures underpinning various technical concepts, such as coherent states, the Doi-shift, and normal-ordered observables, are thereby made explicit.

  14. Master equations and the theory of stochastic path integrals.

    PubMed

    Weber, Markus F; Frey, Erwin

    2017-04-01

    This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations. We focus on numerical and analytical methods going beyond the low-noise limit and provide a unified framework for the study of master equations. After deriving the forward and backward master equations from the Chapman-Kolmogorov equation, we show how the two master equations can be cast into either of four linear partial differential equations (PDEs). Three of these PDEs are discussed in detail. The first PDE governs the time evolution of a generalized probability generating function whose basis depends on the stochastic process under consideration. Spectral methods, WKB approximations, and a variational approach have been proposed for the analysis of the PDE. The second PDE is novel and is obeyed by a distribution that is marginalized over an initial state. It proves useful for the computation of mean extinction times. The third PDE describes the time evolution of a 'generating functional', which generalizes the so-called Poisson representation. Subsequently, the solutions of the PDEs are expressed in terms of two path integrals: a 'forward' and a 'backward' path integral. Combined with inverse transformations, one obtains two distinct path integral representations of the conditional probability distribution solving the master equations. We exemplify both path integrals in analysing elementary chemical reactions. Moreover, we show how a well-known path integral representation of averaged observables can be recovered from them. Upon expanding the forward and the backward path integrals around stationary paths, we then discuss and extend a recent method for the computation of rare event probabilities. Besides, we also derive path integral representations for processes with continuous state spaces whose forward and backward master equations admit Kramers-Moyal expansions. A truncation of the backward expansion at the level of a diffusion approximation recovers a classic path integral representation of the (backward) Fokker-Planck equation. One can rewrite this path integral in terms of an Onsager-Machlup function and, for purely diffusive Brownian motion, it simplifies to the path integral of Wiener. To make this review accessible to a broad community, we have used the language of probability theory rather than quantum (field) theory and do not assume any knowledge of the latter. The probabilistic structures underpinning various technical concepts, such as coherent states, the Doi-shift, and normal-ordered observables, are thereby made explicit.

  15. Social representations of older adults regarding quality of life.

    PubMed

    Ferreira, Marielle Cristina Gonçalves; Tura, Luiz Fernando Rangel; Silva, Rafael Celestino da; Ferreira, Márcia de Assunção

    2017-01-01

    to identify the social representations of older adults regarding quality of life, and to analyze the care practices adopted to promote it. qualitative, exploratory, descriptive research, applying the Theory of Social Representations. Thirty older people from a Health Academy of Rio de Janeiro participated in the study. The software Alceste was used, and lexical analysis of data was performed. social representations of quality of life are based on the social determinants of health; they evidence knowledge and practices of care by valuing physical activities. The practices promoting quality of life comprise healthy eating habits, daily physical exercise, social participation, interaction and socialization, accomplishment of leisure activities and daily tasks with independence and autonomy, and support and family contact. the elderly have a global understanding of the concept of quality of life, coordinate knowledge built in daily life and knowledge coming from the technical-professional field, which evidences the multidimensionality of the concept. identificar as representações sociais de idosos sobre qualidade de vida e analisar as práticas de cuidado por eles adotadas para promovê-la. pesquisa qualitativa, exploratória, descritiva, com aplicação da Teoria das Representações Sociais. Participaram 30 idosos de uma Academia Carioca de Saúde. Utilizou-se o software Alceste e realizou-se análise lexical dos dados. As representações sociais de qualidade de vida sustentam-se nos determinantes sociais de saúde, evidenciam saberes e práticas de cuidado, com valorização de atividades físicas. As práticas promotoras de qualidade de vida congregam hábitos alimentares saudáveis, exercícios físicos diários, participação social, convívio e interação, realização de atividades de lazer e tarefas cotidianas com independência e autonomia, apoio e contato familiar. Os idosos têm uma compreensão global do conceito de qualidade de vida, articulam saberes construídos no cotidiano e advindos do campo técnico-profissional, o que evidencia a multidimensionalidade do conceito.

  16. Comparison of concentric needle versus hooked-wire electrodes in the canine larynx.

    PubMed

    Jaffe, D M; Solomon, N P; Robinson, R A; Hoffman, H T; Luschei, E S

    1998-05-01

    The use of a specific electrode type in laryngeal electromyography has not been standardized. Laryngeal electromyography is usually performed with hooked-wire electrodes or concentric needle electrodes. Hooked-wire electrodes have the advantage of allowing laryngeal movement with ease and comfort, whereas the concentric needle electrodes have benefits from a technical aspect and may be advanced, withdrawn, or redirected during attempts to appropriately place the electrode. This study examines whether hooked-wire electrodes permit more stable recordings than standard concentric needle electrodes at rest and after large-scale movements of the larynx and surrounding structures. A histologic comparison of tissue injury resulting from placement and removal of the two electrode types is also made by evaluation of the vocal folds. Electrodes were percutaneously placed into the thyroarytenoid muscles of 10 adult canines. Amplitude of electromyographic activity was measured and compared during vagal stimulation before and after large-scale laryngeal movements. Signal consistency over time was examined. Animals were killed and vocal fold injury was graded and compared histologically. Waveform morphology did not consistently differ between electrode types. The variability of electromyographic amplitude was greater for the hooked-wire electrode (p < 0.05), whereas the mean amplitude measures before and after large-scale laryngeal movements did not differ (p > 0.05). Inflammatory responses and hematoma formation were also similar. Waveform morphology of electromyographic signals registered from both electrode types show similar complex action potentials. There is no difference between the hooked-wire electrode and the concentric needle electrode in terms of electrode stability or vocal fold injury in the thyroarytenoid muscle after large-scale laryngeal movements.

  17. [Surgical assessment of complications after thyroid gland operations].

    PubMed

    Dralle, H

    2015-01-01

    The extent, magnitude and technical equipment used for thyroid surgery has changed considerably in Germany during the last decade. The number of thyroidectomies due to benign goiter have decreased while the extent of thyroidectomy, nowadays preferentially total thyroidectomy, has increased. Due to an increased awareness of surgical complications the number of malpractice claims is increasing. In contrast to surgical databases the frequency of complications in malpractice claims reflects the individual impact of complications on the quality of life. In contrast to surgical databases unilateral and bilateral vocal fold palsy are therefore at the forefront of malpractice claims. As guidelines are often not applicable for the individual surgical expert review, the question arises which are the relevant criteria for the professional expert witness assessing the severity of the individual complication. While in surgical databases major complications after thyroidectomy, such as vocal fold palsy, hypoparathyroidism, hemorrhage and infections are equally frequent (1-3 %), in malpractice claims vocal fold palsy is significantly more frequent (50 %) compared to hypoparathyroidism (15 %), hemorrhage and infections (about 5 % each). To avoid bilateral nerve palsy intraoperative nerve monitoring has become of utmost importance for surgical strategy and malpractice suits alike. For surgical expert review documentation of individual risk-oriented indications, the surgical approach and postoperative management are highly important. Guidelines only define the treatment corridors of good clinical practice. Surgical expert reviews in malpractice suits concerning quality of care and causality between surgical management, complications and sequelae of complications are therefore highly dependent on the grounds and documentation of risk-oriented indications for thyroidectomy, intraoperative and postoperative surgical management.

  18. QIN DAWG Validation of Gradient Nonlinearity Bias Correction Workflow for Quantitative Diffusion-Weighted Imaging in Multicenter Trials.

    PubMed

    Malyarenko, Dariya I; Wilmes, Lisa J; Arlinghaus, Lori R; Jacobs, Michael A; Huang, Wei; Helmer, Karl G; Taouli, Bachir; Yankeelov, Thomas E; Newitt, David; Chenevert, Thomas L

    2016-12-01

    Previous research has shown that system-dependent gradient nonlinearity (GNL) introduces a significant spatial bias (nonuniformity) in apparent diffusion coefficient (ADC) maps. Here, the feasibility of centralized retrospective system-specific correction of GNL bias for quantitative diffusion-weighted imaging (DWI) in multisite clinical trials is demonstrated across diverse scanners independent of the scanned object. Using corrector maps generated from system characterization by ice-water phantom measurement completed in the previous project phase, GNL bias correction was performed for test ADC measurements from an independent DWI phantom (room temperature agar) at two offset locations in the bore. The precomputed three-dimensional GNL correctors were retrospectively applied to test DWI scans by the central analysis site. The correction was blinded to reference DWI of the agar phantom at magnet isocenter where the GNL bias is negligible. The performance was evaluated from changes in ADC region of interest histogram statistics before and after correction with respect to the unbiased reference ADC values provided by sites. Both absolute error and nonuniformity of the ADC map induced by GNL (median, 12%; range, -35% to +10%) were substantially reduced by correction (7-fold in median and 3-fold in range). The residual ADC nonuniformity errors were attributed to measurement noise and other non-GNL sources. Correction of systematic GNL bias resulted in a 2-fold decrease in technical variability across scanners (down to site temperature range). The described validation of GNL bias correction marks progress toward implementation of this technology in multicenter trials that utilize quantitative DWI.

  19. QIN DAWG Validation of Gradient Nonlinearity Bias Correction Workflow for Quantitative Diffusion-Weighted Imaging in Multicenter Trials

    PubMed Central

    Malyarenko, Dariya I.; Wilmes, Lisa J.; Arlinghaus, Lori R.; Jacobs, Michael A.; Huang, Wei; Helmer, Karl G.; Taouli, Bachir; Yankeelov, Thomas E.; Newitt, David; Chenevert, Thomas L.

    2017-01-01

    Previous research has shown that system-dependent gradient nonlinearity (GNL) introduces a significant spatial bias (nonuniformity) in apparent diffusion coefficient (ADC) maps. Here, the feasibility of centralized retrospective system-specific correction of GNL bias for quantitative diffusion-weighted imaging (DWI) in multisite clinical trials is demonstrated across diverse scanners independent of the scanned object. Using corrector maps generated from system characterization by ice-water phantom measurement completed in the previous project phase, GNL bias correction was performed for test ADC measurements from an independent DWI phantom (room temperature agar) at two offset locations in the bore. The precomputed three-dimensional GNL correctors were retrospectively applied to test DWI scans by the central analysis site. The correction was blinded to reference DWI of the agar phantom at magnet isocenter where the GNL bias is negligible. The performance was evaluated from changes in ADC region of interest histogram statistics before and after correction with respect to the unbiased reference ADC values provided by sites. Both absolute error and nonuniformity of the ADC map induced by GNL (median, 12%; range, −35% to +10%) were substantially reduced by correction (7-fold in median and 3-fold in range). The residual ADC nonuniformity errors were attributed to measurement noise and other non-GNL sources. Correction of systematic GNL bias resulted in a 2-fold decrease in technical variability across scanners (down to site temperature range). The described validation of GNL bias correction marks progress toward implementation of this technology in multicenter trials that utilize quantitative DWI. PMID:28105469

  20. [The effect of smoking and forced use of the voice to development of the vocal polyps].

    PubMed

    Gnjatic, M; Stankovic, P; Djukić, V

    2009-01-01

    Dysphonia is often caused by polyps which are benign changes of pseudotumors. With their presence they are hampering with glotis oclusion. Laryngomicroscopy of general and endotracheal anaesthesia has been preformed on all of the patients. Microsurgical technique has been used to remove the polyps. Bioptic material was analyzed in pathophysiological laboratory of clinic of pathology in Banjaluka. All of the results were presented through tables and graphic representations. Frequency of polyps through age and sex groups, along with the examination of ethyological factors in emergence of polyps of vocal cords. Results are in accordance with the results of other authors who were involved in similar problematics. Through analysis of our data we percieve that the abuse of voice is part of ethiological factors that lead not only to emergence of vocal fold lesions but aswell as other benign changes.

  1. The simulation approach to lipid-protein interactions.

    PubMed

    Paramo, Teresa; Garzón, Diana; Holdbrook, Daniel A; Khalid, Syma; Bond, Peter J

    2013-01-01

    The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.

  2. Deep Gaze Velocity Analysis During Mammographic Reading for Biometric Identification of Radiologists

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yoon, Hong-Jun; Alamudun, Folami T.; Hudson, Kathy

    Several studies have confirmed that the gaze velocity of the human eye can be utilized as a behavioral biometric or personalized biomarker. In this study, we leverage the local feature representation capacity of convolutional neural networks (CNNs) for eye gaze velocity analysis as the basis for biometric identification of radiologists performing breast cancer screening. Using gaze data collected from 10 radiologists reading 100 mammograms of various diagnoses, we compared the performance of a CNN-based classification algorithm with two deep learning classifiers, deep neural network and deep belief network, and a previously presented hidden Markov model classifier. The study showed thatmore » the CNN classifier is superior compared to alternative classification methods based on macro F1-scores derived from 10-fold cross-validation experiments. Our results further support the efficacy of eye gaze velocity as a biometric identifier of medical imaging experts.« less

  3. Low abundance of microsatellite repeats in the genome of the Brown-headed Cowbird (Molothrus ater)

    USGS Publications Warehouse

    Longmire, Jonathan L.; Hahn, D.C.; Roach, J.L.

    1999-01-01

    A cosmid library made from brown-headed cowbird (Molothrus ater) DNA was examined for representation of 17 distinct microsatellite motifs including all possible mono-, di-, and trinucleotide microsatellites, and the tetranucleotide repeat (GATA)n. The overall density of microsatellites within cowbird DNA was found to be one repeat per 89 kb and the frequency of the most abundant motif, (AGC)n, was once every 382 kb. The abundance of microsatellites within the cowbird genome is estimated to be reduced approximately 15-fold compared to humans. The reduced frequency of microsatellites seen in this study is consistent with previous observations indicating reduced numbers of microsatellites and other interspersed repeats in avian DNA. In addition to providing new information concerning the abundance of microsatellites within an avian genome, these results provide useful insights for selecting cloning strategies that might be used in the development of locus-specific microsatellite markers for avian studies.

  4. A Method for WD40 Repeat Detection and Secondary Structure Prediction

    PubMed Central

    Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

    2013-01-01

    WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

  5. A non-planar two-loop three-point function beyond multiple polylogarithms

    NASA Astrophysics Data System (ADS)

    von Manteuffel, Andreas; Tancredi, Lorenzo

    2017-06-01

    We consider the analytic calculation of a two-loop non-planar three-point function which contributes to the two-loop amplitudes for t\\overline{t} production and γγ production in gluon fusion through a massive top-quark loop. All subtopology integrals can be written in terms of multiple polylogarithms over an irrational alphabet and we employ a new method for the integration of the differential equations which does not rely on the rationalization of the latter. The top topology integrals, instead, in spite of the absence of a massive three-particle cut, cannot be evaluated in terms of multiple polylogarithms and require the introduction of integrals over complete elliptic integrals and polylogarithms. We provide one-fold integral representations for the solutions and continue them analytically to all relevant regions of the phase space in terms of real functions, extracting all imaginary parts explicitly. The numerical evaluation of our expressions becomes straightforward in this way.

  6. The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

    PubMed

    Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

    2013-11-13

    The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

  7. Deep Gaze Velocity Analysis During Mammographic Reading for Biometric Identification of Radiologists

    DOE PAGES

    Yoon, Hong-Jun; Alamudun, Folami T.; Hudson, Kathy; ...

    2018-01-24

    Several studies have confirmed that the gaze velocity of the human eye can be utilized as a behavioral biometric or personalized biomarker. In this study, we leverage the local feature representation capacity of convolutional neural networks (CNNs) for eye gaze velocity analysis as the basis for biometric identification of radiologists performing breast cancer screening. Using gaze data collected from 10 radiologists reading 100 mammograms of various diagnoses, we compared the performance of a CNN-based classification algorithm with two deep learning classifiers, deep neural network and deep belief network, and a previously presented hidden Markov model classifier. The study showed thatmore » the CNN classifier is superior compared to alternative classification methods based on macro F1-scores derived from 10-fold cross-validation experiments. Our results further support the efficacy of eye gaze velocity as a biometric identifier of medical imaging experts.« less

  8. Slates from Uruguay: a traditional natural stone

    NASA Astrophysics Data System (ADS)

    Morales Demarco, M.; Oyhantçabal, P.; Stein, K.-J.; Siegesmund, S.

    2012-04-01

    Slates were traditionally used as roofing material or for cladding worldwide and also in Uruguay. In regions where this resource was easily mined, the widespread application of slates in constructions resulted in the development of characteristic cultural landscapes. The application of slates in a wider sense is nowadays open for all uses of dimensional stone, compared to the restricted use as roofing or cladding material in the past. This has been achieved by the discovery and mining of new deposits within the last 25 years worldwide. Furthermore, the optimization of mining techniques that allows the excavation of larger blocks and the technical development for further handling of the blocks has contributed to an open spectrum of applications. The slate deposits from Uruguay are associated with the Neoproterozoic thrust and fold belt of the Dom Feliciano Belt. The slates are linked to calc-silicate strata in a greenschist facies volcano-sedimentary sequence and the deposits are located in the limb of a regional fold, where bedding and cleavage are parallel. The main lithotype is a layered and fine-grained calcareous phyllite with a quite diverse palette of colors: light green, grey, dark grey, reddish and black. The mined slate is split into slabs 0.5 - 2cm thick. The technical properties were investigated in a very systematic way with respect to the new European standards, showing values comparable to those registered for internationally known slates. In the past, the average production in Uruguay was around 4000 tons/year and a historical maximum of 13,000 tons was reached in 1993. The oscillations in the regional demand were the cause of several flourishing and decay cycles in the activity, but our investigation shows a considerable volume of indicated resources and therefore a very good potential. Exploration for colors and qualities and quantification of reserves is a prerequisite for the development of the sector.

  9. Point-of-use water disinfection using ultraviolet and visible light-emitting diodes.

    PubMed

    Lui, Gough Yumu; Roser, David; Corkish, Richard; Ashbolt, Nicholas J; Stuetz, Richard

    2016-05-15

    Improvements in point-of-use (POU) drinking water disinfection technologies for remote and regional communities are urgently needed. Conceptually, UV-C light-emitting diodes (LEDs) overcome many drawbacks of low-pressure mercury tube based UV devices, and UV-A or visible light LEDs also show potential. To realistically evaluate the promise of LED disinfection, our study assessed the performance of a model 1.3 L reactor, similar in size to solar disinfection bottles. In all, 12 different commercial or semi-commercial LED arrays (270-740 nm) were compared for their ability to inactivate Escherichia coli K12 ATCC W3110 and Enterococcus faecalis ATCC 19433 over 6h. Five log10 and greater reductions were consistently achieved using the 270, 365, 385 and 405 nm arrays. The output of the 310 nm array was insufficient for useful disinfection while 430 and 455 nm performance was marginal (≈ 4.2 and 2.3-log10s E. coli and E. faecalis over the 6h). No significant disinfection was observed with the 525, 590, 623, 660 and 740 nm arrays. Delays in log-phase inactivation of E. coli were observed, particularly with UV-A wavelengths. The radiation doses required for >3-log10 reduction of E. coli and E. faecalis differed by 10 fold at 270 nm but only 1.5-2.5 fold at 365-455 nm. Action spectra, consistent with the literature, were observed with both indicators. The design process revealed cost and technical constraints pertaining to LED electrical efficiency, availability and lifetime. We concluded that POU LED disinfection using existing LED technology is already technically possible. UV-C LEDs offer speed and energy demand advantages, while UV-A/violet units are safer. Both approaches still require further costing and engineering development. Our study provides data needed for such work. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. A scalable multi-process model of root nitrogen uptake

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Walker, Anthony P.

    This article is a Commentary on McMurtrie & Näsholm et al., 218: 119–130. Roots are represented in Terrestrial Ecosystem Models (TEMs) in much less detail than their equivalent above-ground resource acquisition organs – leaves. Often roots in TEMs are simply resource sinks, and below-ground resource acquisition is commonly simulated without any relationship to root dynamics at all, though there are exceptions (e.g. Zaehle & Friend, 2010). The representation of roots as carbon (C) and nitrogen (N) sinks without complementary source functions can lead to strange sensitivities in a model. For example, reducing root lifespans in the Community Land Model (versionmore » 4.5) increases plant production as N cycles more rapidly through the ecosystem without loss of plant function (D. M. Ricciuto, unpublished). The primary reasons for the poorer representation of roots compared with leaves in TEMs are three-fold: (1) data are much harder won, especially in the field; (2) no simple mechanistic models of root function are available; and (3) scaling root function from an individual root to a root system lags behind methods of scaling leaf function to a canopy. Here in this issue of New Phytologist, McMurtrie & Näsholm (pp. 119–130) develop a relatively simple model for root N uptake that mechanistically accounts for processes of N supply (mineralization and transport by diffusion and mass flow) and N demand (root uptake and microbial immobilization).« less

  11. A scalable multi-process model of root nitrogen uptake

    DOE PAGES

    Walker, Anthony P.

    2018-02-28

    This article is a Commentary on McMurtrie & Näsholm et al., 218: 119–130. Roots are represented in Terrestrial Ecosystem Models (TEMs) in much less detail than their equivalent above-ground resource acquisition organs – leaves. Often roots in TEMs are simply resource sinks, and below-ground resource acquisition is commonly simulated without any relationship to root dynamics at all, though there are exceptions (e.g. Zaehle & Friend, 2010). The representation of roots as carbon (C) and nitrogen (N) sinks without complementary source functions can lead to strange sensitivities in a model. For example, reducing root lifespans in the Community Land Model (versionmore » 4.5) increases plant production as N cycles more rapidly through the ecosystem without loss of plant function (D. M. Ricciuto, unpublished). The primary reasons for the poorer representation of roots compared with leaves in TEMs are three-fold: (1) data are much harder won, especially in the field; (2) no simple mechanistic models of root function are available; and (3) scaling root function from an individual root to a root system lags behind methods of scaling leaf function to a canopy. Here in this issue of New Phytologist, McMurtrie & Näsholm (pp. 119–130) develop a relatively simple model for root N uptake that mechanistically accounts for processes of N supply (mineralization and transport by diffusion and mass flow) and N demand (root uptake and microbial immobilization).« less

  12. Sparse representation based biomarker selection for schizophrenia with integrated analysis of fMRI and SNPs.

    PubMed

    Cao, Hongbao; Duan, Junbo; Lin, Dongdong; Shugart, Yin Yao; Calhoun, Vince; Wang, Yu-Ping

    2014-11-15

    Integrative analysis of multiple data types can take advantage of their complementary information and therefore may provide higher power to identify potential biomarkers that would be missed using individual data analysis. Due to different natures of diverse data modality, data integration is challenging. Here we address the data integration problem by developing a generalized sparse model (GSM) using weighting factors to integrate multi-modality data for biomarker selection. As an example, we applied the GSM model to a joint analysis of two types of schizophrenia data sets: 759,075 SNPs and 153,594 functional magnetic resonance imaging (fMRI) voxels in 208 subjects (92 cases/116 controls). To solve this small-sample-large-variable problem, we developed a novel sparse representation based variable selection (SRVS) algorithm, with the primary aim to identify biomarkers associated with schizophrenia. To validate the effectiveness of the selected variables, we performed multivariate classification followed by a ten-fold cross validation. We compared our proposed SRVS algorithm with an earlier sparse model based variable selection algorithm for integrated analysis. In addition, we compared with the traditional statistics method for uni-variant data analysis (Chi-squared test for SNP data and ANOVA for fMRI data). Results showed that our proposed SRVS method can identify novel biomarkers that show stronger capability in distinguishing schizophrenia patients from healthy controls. Moreover, better classification ratios were achieved using biomarkers from both types of data, suggesting the importance of integrative analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Abstracting and indexing guide

    USGS Publications Warehouse

    ,; ,

    1974-01-01

    These instructions have been prepared for those who abstract and index scientific and technical documents for the Water Resources Scientific Information Center (WRSIC). With the recent publication growth in all fields, information centers have undertaken the task of keeping the various scientific communities aware of current and past developments. An abstract with carefully selected index terms offers the user of WRSIC services a more rapid means for deciding whether a document is pertinent to his needs and professional interests, thus saving him the time necessary to scan the complete work. These means also provide WRSIC with a document representation or surrogate which is more easily stored and manipulated to produce various services. Authors are asked to accept the responsibility for preparing abstracts of their own papers to facilitate quick evaluation, announcement, and dissemination to the scientific community.

  14. Characterization of photomultiplier tubes with a realistic model through GPU-boosted simulation

    NASA Astrophysics Data System (ADS)

    Anthony, M.; Aprile, E.; Grandi, L.; Lin, Q.; Saldanha, R.

    2018-02-01

    The accurate characterization of a photomultiplier tube (PMT) is crucial in a wide-variety of applications. However, current methods do not give fully accurate representations of the response of a PMT, especially at very low light levels. In this work, we present a new and more realistic model of the response of a PMT, called the cascade model, and use it to characterize two different PMTs at various voltages and light levels. The cascade model is shown to outperform the more common Gaussian model in almost all circumstances and to agree well with a newly introduced model independent approach. The technical and computational challenges of this model are also presented along with the employed solution of developing a robust GPU-based analysis framework for this and other non-analytical models.

  15. Method of recommending items to a user based on user interest

    DOEpatents

    Bollen, John; Van De Sompel, Herbert

    2013-11-05

    Although recording of usage data is common in scholarly information services, its exploitation for the creation of value-added services remains limited due to concerns regarding, among others, user privacy, data validity, and the lack of accepted standards for the representation, sharing and aggregation of usage data. A technical, standards-based architecture for sharing usage information is presented. In this architecture, OpenURL-compliant linking servers aggregate usage information of a specific user community as it navigates the distributed information environment that it has access to. This usage information is made OAI-PMH harvestable so that usage information exposed by many linking servers can be aggregated to facilitate the creation of value-added services with a reach beyond that of a single community or a single information service.

  16. Usage based indicators to assess the impact of scholarly works: architecture and method

    DOEpatents

    Bollen, Johan [Santa Fe, NM; Van De Sompel, Herbert [Santa Fe, NM

    2012-03-13

    Although recording of usage data is common in scholarly information services, its exploitation for the creation of value-added services remains limited due to concerns regarding, among others, user privacy, data validity, and the lack of accepted standards for the representation, sharing and aggregation of usage data. A technical, standards-based architecture for sharing usage information is presented. In this architecture, OpenURL-compliant linking servers aggregate usage information of a specific user community as it navigates the distributed information environment that it has access to. This usage information is made OAI-PMH harvestable so that usage information exposed by many linking servers can be aggregated to facilitate the creation of value-added services with a reach beyond that of a single community or a single information service.

  17. Hierarchical Adaptive Regression Kernels for Regression with Functional Predictors.

    PubMed

    Woodard, Dawn B; Crainiceanu, Ciprian; Ruppert, David

    2013-01-01

    We propose a new method for regression using a parsimonious and scientifically interpretable representation of functional predictors. Our approach is designed for data that exhibit features such as spikes, dips, and plateaus whose frequency, location, size, and shape varies stochastically across subjects. We propose Bayesian inference of the joint functional and exposure models, and give a method for efficient computation. We contrast our approach with existing state-of-the-art methods for regression with functional predictors, and show that our method is more effective and efficient for data that include features occurring at varying locations. We apply our methodology to a large and complex dataset from the Sleep Heart Health Study, to quantify the association between sleep characteristics and health outcomes. Software and technical appendices are provided in online supplemental materials.

  18. Deep learning of joint myelin and T1w MRI features in normal-appearing brain tissue to distinguish between multiple sclerosis patients and healthy controls.

    PubMed

    Yoo, Youngjin; Tang, Lisa Y W; Brosch, Tom; Li, David K B; Kolind, Shannon; Vavasour, Irene; Rauscher, Alexander; MacKay, Alex L; Traboulsee, Anthony; Tam, Roger C

    2018-01-01

    Myelin imaging is a form of quantitative magnetic resonance imaging (MRI) that measures myelin content and can potentially allow demyelinating diseases such as multiple sclerosis (MS) to be detected earlier. Although focal lesions are the most visible signs of MS pathology on conventional MRI, it has been shown that even tissues that appear normal may exhibit decreased myelin content as revealed by myelin-specific images (i.e., myelin maps). Current methods for analyzing myelin maps typically use global or regional mean myelin measurements to detect abnormalities, but ignore finer spatial patterns that may be characteristic of MS. In this paper, we present a machine learning method to automatically learn, from multimodal MR images, latent spatial features that can potentially improve the detection of MS pathology at early stage. More specifically, 3D image patches are extracted from myelin maps and the corresponding T1-weighted (T1w) MRIs, and are used to learn a latent joint myelin-T1w feature representation via unsupervised deep learning. Using a data set of images from MS patients and healthy controls, a common set of patches are selected via a voxel-wise t -test performed between the two groups. In each MS image, any patches overlapping with focal lesions are excluded, and a feature imputation method is used to fill in the missing values. A feature selection process (LASSO) is then utilized to construct a sparse representation. The resulting normal-appearing features are used to train a random forest classifier. Using the myelin and T1w images of 55 relapse-remitting MS patients and 44 healthy controls in an 11-fold cross-validation experiment, the proposed method achieved an average classification accuracy of 87.9% (SD = 8.4%), which is higher and more consistent across folds than those attained by regional mean myelin (73.7%, SD = 13.7%) and T1w measurements (66.7%, SD = 10.6%), or deep-learned features in either the myelin (83.8%, SD = 11.0%) or T1w (70.1%, SD = 13.6%) images alone, suggesting that the proposed method has strong potential for identifying image features that are more sensitive and specific to MS pathology in normal-appearing brain tissues.

  19. [Time perceptions and representations].

    PubMed

    Tordjman, S

    2015-09-01

    Representations of time and time measurements depend on subjective constructs that vary according to changes in our concepts, beliefs, societal needs and technical advances. Similarly, the past, the future and the present are subjective representations that depend on each individual's psychic time and biological time. Therefore, there is no single, one-size-fits-all time for everyone, but rather a different, subjective time for each individual. We need to acknowledge the existence of different inter-individual times but also intra-individual times, to which different functions and different rhythms are attached, depending on the system of reference. However, the construction of these time perceptions and representations is influenced by objective factors (physiological, physical and cognitive) related to neuroscience which will be presented and discussed in this article. Thus, studying representation and perception of time lies at the crossroads between neuroscience, human sciences and philosophy. Furthermore, it is possible to identify several constants among the many and various representations of time and their corresponding measures, regardless of the system of time reference. These include the notion of movements repeated in a stable rhythmic pattern involving the recurrence of the same interval of time, which enables us to define units of time of equal and invariable duration. This rhythmicity is also found at a physiological level and contributes through circadian rhythms, in particular the melatonin rhythm, to the existence of a biological time. Alterations of temporality in mental disorders will be also discussed in this article illustrated by certain developmental disorders such as autism spectrum disorders. In particular, the hypothesis will be developed that children with autism would need to create discontinuity out of continuity through stereotyped behaviors and/or interests. This discontinuity repeated at regular intervals could have been fundamentally lacking in their physiological development due to possibly altered circadian rhythms, including arhythmy and asynchrony. Time measurement, based on the repetition of discontinuity at regular intervals, involves also a spatial representation. It is our own trajectory through space-time, and thus our own motion, including the physiological process of aging, that affords us a representation of the passing of time, just as the countryside seems to be moving past us when we travel in a vehicle. Chinese and Indian societies actually have circular representations of time, and linear representations of time and its trajectory through space-time are currently a feature of Western societies. Circular time is collective time, and its metaphysical representations go beyond the life of a single individual, referring to the cyclical, or at least nonlinear, nature of time. Linear time is individual time, in that it refers to the scale of a person's lifetime, and it is physically represented by an arrow flying ineluctably from the past to the future. An intermediate concept can be proposed that acknowledges the existence of linear time involving various arrows of time corresponding to different lifespans (human, animal, plant, planet lifespans, etc.). In fact, the very notion of time would depend on the trajectory of each arrow of time, like shooting stars in the sky with different trajectory lengths which would define different time scales. The time scale of these various lifespans are very different (for example, a few decades for humans and a few days or hours for insects). It would not make sense to try to understand the passage of time experienced by an insect which may live only a few hours based on a human time scale. One hour in an insect's life cannot be compared to one experienced by a human. Yet again, it appears that there is a coexistence of different clocks based here on different lifespans. Finally, the evolution of our society focused on the present moment and choosing the cesium atom as the international reference unit of time measurement (cesium has a transition frequency of 9.192.631.77000 oscillations per second), will be questioned. We can consider that focusing on the present moment, in particular on instantaneity rather than infinity, prevents us from facing our own finitude. In conclusion, the question is raised that the current representation of time might be a means of managing our fear of death, giving us the illusion of controlling the uncontrollable, in particular the passage of time, and a means of avoiding to represent what many regard as non-representable, namely our own demise. Copyright © 2015 L’Encéphale. Published by Elsevier Masson SAS.. All rights reserved.

  20. Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes

    PubMed Central

    Johnstone, Daniel M.; Riveros, Carlos; Heidari, Moones; Graham, Ross M.; Trinder, Debbie; Berretta, Regina; Olynyk, John K.; Scott, Rodney J.; Moscato, Pablo; Milward, Elizabeth A.

    2013-01-01

    While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation—if not adequately minimized by effective normalization—may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes. PMID:27605185

  1. Structural prediction and analysis of VIH-related peptides from selected crustacean species

    PubMed Central

    Nagaraju, Ganji Purna Chandra; Kumari, Nunna Siva; Prasad, Ganji Lakshmi Vara; Rajitha, Balney; Meenu, Madan; Rao, Manam Sreenivasa; Naik, Bannoth Reddya

    2009-01-01

    The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous extra technical aspects. As a result, no structural information is available for VIH peptide sequences registered in the Genbank. In this situation, it is not surprising that predictive methods have achieved great interest. Here, in this study the molt-inhibiting hormone (MIH) of the kuruma prawn (Marsupenaeus japonicus) is used, to predict the structure of four VIHrelated peptides in the crustacean species. The high similarity of the 3D-structures and the calculated physiochemical characteristics of these peptides suggest a common fold for the entire family. PMID:20011146

  2. A new method to improve network topological similarity search: applied to fold recognition

    PubMed Central

    Lhota, John; Hauptman, Ruth; Hart, Thomas; Ng, Clara; Xie, Lei

    2015-01-01

    Motivation: Similarity search is the foundation of bioinformatics. It plays a key role in establishing structural, functional and evolutionary relationships between biological sequences. Although the power of the similarity search has increased steadily in recent years, a high percentage of sequences remain uncharacterized in the protein universe. Thus, new similarity search strategies are needed to efficiently and reliably infer the structure and function of new sequences. The existing paradigm for studying protein sequence, structure, function and evolution has been established based on the assumption that the protein universe is discrete and hierarchical. Cumulative evidence suggests that the protein universe is continuous. As a result, conventional sequence homology search methods may be not able to detect novel structural, functional and evolutionary relationships between proteins from weak and noisy sequence signals. To overcome the limitations in existing similarity search methods, we propose a new algorithmic framework—Enrichment of Network Topological Similarity (ENTS)—to improve the performance of large scale similarity searches in bioinformatics. Results: We apply ENTS to a challenging unsolved problem: protein fold recognition. Our rigorous benchmark studies demonstrate that ENTS considerably outperforms state-of-the-art methods. As the concept of ENTS can be applied to any similarity metric, it may provide a general framework for similarity search on any set of biological entities, given their representation as a network. Availability and implementation: Source code freely available upon request Contact: lxie@iscb.org PMID:25717198

  3. Intrauterine growth restriction and placental gene expression in severe preeclampsia, comparing early-onset and late-onset forms.

    PubMed

    Nevalainen, Jaana; Skarp, Sini; Savolainen, Eeva-Riitta; Ryynänen, Markku; Järvenpää, Jouko

    2017-10-26

    To evaluate placental gene expression in severe early- or late-onset preeclampsia with intrauterine growth restriction compared to controls. Chorionic villus sampling was conducted after cesarean section from the placentas of five women with early- or late-onset severe preeclampsia and five controls for each preeclampsia group. Microarray analysis was performed to identify gene expression differences between the groups. Pathway analysis showed over-representation of gene ontology (GO) biological process terms related to inflammatory and immune response pathways, platelet development, vascular development, female pregnancy and reproduction in early-onset preeclampsia. Pathways related to immunity, complement and coagulation cascade were overrepresented in the hypergeometric test for the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Ten genes (ABI3BP, C7, HLA-G, IL2RB, KRBOX1, LRRC15, METTL7B, MPP5, RFLNB and SLC20A) had a ≥±1 fold expression difference in severe early-onset preeclampsia group compared to early controls. There were 362 genes that had a ≥±1 fold expression difference in severe early-onset preeclampsia group compared to late-onset preeclampsia group including ABI3BP, C7, HLA-G and IL2RB. There are significant differences in placental gene expression between severe early- and late-onset preeclampsia when both are associated with intrauterine growth restriction. ABI3BP, C7, HLA-G and IL2RB might contribute to the development of early form of severe preeclampsia.

  4. Development of a Bayesian model to estimate health care outcomes in the severely wounded

    PubMed Central

    Stojadinovic, Alexander; Eberhardt, John; Brown, Trevor S; Hawksworth, Jason S; Gage, Frederick; Tadaki, Douglas K; Forsberg, Jonathan A; Davis, Thomas A; Potter, Benjamin K; Dunne, James R; Elster, E A

    2010-01-01

    Background: Graphical probabilistic models have the ability to provide insights as to how clinical factors are conditionally related. These models can be used to help us understand factors influencing health care outcomes and resource utilization, and to estimate morbidity and clinical outcomes in trauma patient populations. Study design: Thirty-two combat casualties with severe extremity injuries enrolled in a prospective observational study were analyzed using step-wise machine-learned Bayesian belief network (BBN) and step-wise logistic regression (LR). Models were evaluated using 10-fold cross-validation to calculate area-under-the-curve (AUC) from receiver operating characteristics (ROC) curves. Results: Our BBN showed important associations between various factors in our data set that could not be developed using standard regression methods. Cross-validated ROC curve analysis showed that our BBN model was a robust representation of our data domain and that LR models trained on these findings were also robust: hospital-acquired infection (AUC: LR, 0.81; BBN, 0.79), intensive care unit length of stay (AUC: LR, 0.97; BBN, 0.81), and wound healing (AUC: LR, 0.91; BBN, 0.72) showed strong AUC. Conclusions: A BBN model can effectively represent clinical outcomes and biomarkers in patients hospitalized after severe wounding, and is confirmed by 10-fold cross-validation and further confirmed through logistic regression modeling. The method warrants further development and independent validation in other, more diverse patient populations. PMID:21197361

  5. The cyclic-AMP receptor protein (CRP) regulon in Aggregatibacter actinomycetemcomitans includes leukotoxin

    PubMed Central

    Feuerbacher, Leigh A.; Burgum, Alex; Kolodrubetz, David

    2011-01-01

    The cyclic-AMP receptor protein (CRP) acts as a global regulatory protein among bacteria. Here, the CRP regulon has been defined in Aggregatibacter actinomycetemcomitans using microarray analysis of A. actinomycetemcomitans strain JP2 wild type cells compared to an isogenic crp deletion mutant. Genes whose expression levels changed at least 2-fold with p ≤ 0.05 were considered significant. Of the 300 genes identified as being CRP-regulated, 139 were CRP-activated, including leukotoxin, with the remaining being CRP-repressed. The 300 genes represent 14.2% of ORFs probed which is significantly higher than what has been reported for CRP regulons in other bacteria. If the CRP-regulated genes are put into 17 functional classes, all 17 categories had at least 1 CRP-regulated gene. Several functional categories, mainly transport and binding proteins and energy metabolism proteins, were disproportionately represented in the CRP-regulated subset of genes relative to their overall representation in the genome. This is similar to the patterns seen in other bacteria. Finally, quantitative RT-PCR was used to show that the leukotoxin RNA levels were repressed 16-fold in the CRP mutant indicating that CRP activates leukotoxin transcription. However, this regulation appears to be acting through another regulatory protein since the leukotoxin promoter, unlike ~129 other promoters of CRP-regulated genes, does not have a match to the consensus CRP binding site. Several candidate genes for this intermediary transcription factor have been identified in the CRP-regulon. PMID:21575705

  6. Palaeogeographical peculiarities of the Pabdeh Formation (Paleogene) in Iran: New evidence of global diversity-determined geological heritage

    NASA Astrophysics Data System (ADS)

    Habibi, Tahereh; Nielsen, Jan K.; Ponedelnik, Alena A.; Ruban, Dmitry A.

    2017-11-01

    Unique palaeogeographical peculiarities of sedimentary formations are important for geological heritage conservation and use for the purposes of tourism. The heritage value of the Pabdeh Formation (Paleocene-Oligocene) of the Zagros Fold-Thrust Belt in Iran has been investigated. The uniqueness of its palaeogeographical peculiarities has been assessed on the basis of the literature, field studies of three representative sections in the Fars Province (Kavar, Zanjiran, and Shahneshin sections), and comparison with the similar features known in Iran and globally. The Pabdeh Formation reflects the process of mixed siliciclastic-carbonate ramp progradation and the onset of a typical carbonate platform. The other unique features include representation of mesopelagic palaeohabitat, specific trace fossil assemblages, prehistoric bituminous artefacts (production of which was linked to the Pabdeh deposits), etc. It is established that the palaeogeographical type of geological heritage of the Pabdeh Formation is represented by all known subtypes, namely facies, palaeoecosystem, ichnological, taphonomical, event, and geoarchaeological subtypes. Their rank varies between regional and global. The very fact of co-occurrence of these subtypes determines the global importance of the entire palaeogeographical type in the case of this formation. The establishment of geopark in the Zagros Fold-Thrust Belt will facilitate adequate use of the Pabdeh Formation for the purpose of geotourism development. The aesthetic properties (rocks of different colour and striped patterns of outcrops) increase the attractiveness of this geological body to visitors.

  7. Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

    PubMed Central

    Wang, Minglei; Yafremava, Liudmila S.; Caetano-Anollés, Derek; Mittenthal, Jay E.; Caetano-Anollés, Gustavo

    2007-01-01

    The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya. PMID:17908824

  8. BEAM web server: a tool for structural RNA motif discovery.

    PubMed

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  9. Contrast-Enhanced Magnetic Resonance Cholangiography: Practical Tips and Clinical Indications for Biliary Disease Management.

    PubMed

    Palmucci, Stefano; Roccasalva, Federica; Piccoli, Marina; Fuccio Sanzà, Giovanni; Foti, Pietro Valerio; Ragozzino, Alfonso; Milone, Pietro; Ettorre, Giovanni Carlo

    2017-01-01

    Since its introduction, MRCP has been improved over the years due to the introduction of several technical advances and innovations. It consists of a noninvasive method for biliary tree representation, based on heavily T2-weighted images. Conventionally, its protocol includes two-dimensional single-shot fast spin-echo images, acquired with thin sections or with multiple thick slabs. In recent years, three-dimensional T2-weighted fast-recovery fast spin-echo images have been added to the conventional protocol, increasing the possibility of biliary anatomy demonstration and leading to a significant benefit over conventional 2D imaging. A significant innovation has been reached with the introduction of hepatobiliary contrasts, represented by gadoxetic acid and gadobenate dimeglumine: they are excreted into the bile canaliculi, allowing the opacification of the biliary tree. Recently, 3D interpolated T1-weighted spoiled gradient echo images have been proposed for the evaluation of the biliary tree, obtaining images after hepatobiliary contrast agent administration. Thus, the acquisition of these excretory phases improves the diagnostic capability of conventional MRCP-based on T2 acquisitions. In this paper, technical features of contrast-enhanced magnetic resonance cholangiography are briefly discussed; main diagnostic tips of hepatobiliary phase are showed, emphasizing the benefit of enhanced cholangiography in comparison with conventional MRCP.

  10. Sparse gammatone signal model optimized for English speech does not match the human auditory filters.

    PubMed

    Strahl, Stefan; Mertins, Alfred

    2008-07-18

    Evidence that neurosensory systems use sparse signal representations as well as improved performance of signal processing algorithms using sparse signal models raised interest in sparse signal coding in the last years. For natural audio signals like speech and environmental sounds, gammatone atoms have been derived as expansion functions that generate a nearly optimal sparse signal model (Smith, E., Lewicki, M., 2006. Efficient auditory coding. Nature 439, 978-982). Furthermore, gammatone functions are established models for the human auditory filters. Thus far, a practical application of a sparse gammatone signal model has been prevented by the fact that deriving the sparsest representation is, in general, computationally intractable. In this paper, we applied an accelerated version of the matching pursuit algorithm for gammatone dictionaries allowing real-time and large data set applications. We show that a sparse signal model in general has advantages in audio coding and that a sparse gammatone signal model encodes speech more efficiently in terms of sparseness than a sparse modified discrete cosine transform (MDCT) signal model. We also show that the optimal gammatone parameters derived for English speech do not match the human auditory filters, suggesting for signal processing applications to derive the parameters individually for each applied signal class instead of using psychometrically derived parameters. For brain research, it means that care should be taken with directly transferring findings of optimality for technical to biological systems.

  11. Design and Development of a Sharable Clinical Decision Support System Based on a Semantic Web Service Framework.

    PubMed

    Zhang, Yi-Fan; Gou, Ling; Tian, Yu; Li, Tian-Chang; Zhang, Mao; Li, Jing-Song

    2016-05-01

    Clinical decision support (CDS) systems provide clinicians and other health care stakeholders with patient-specific assessments or recommendations to aid in the clinical decision-making process. Despite their demonstrated potential for improving health care quality, the widespread availability of CDS systems has been limited mainly by the difficulty and cost of sharing CDS knowledge among heterogeneous healthcare information systems. The purpose of this study was to design and develop a sharable clinical decision support (S-CDS) system that meets this challenge. The fundamental knowledge base consists of independent and reusable knowledge modules (KMs) to meet core CDS needs, wherein each KM is semantically well defined based on the standard information model, terminologies, and representation formalisms. A semantic web service framework was developed to identify, access, and leverage these KMs across diverse CDS applications and care settings. The S-CDS system has been validated in two distinct client CDS applications. Model-level evaluation results confirmed coherent knowledge representation. Application-level evaluation results reached an overall accuracy of 98.66 % and a completeness of 96.98 %. The evaluation results demonstrated the technical feasibility and application prospect of our approach. Compared with other CDS engineering efforts, our approach facilitates system development and implementation and improves system maintainability, scalability and efficiency, which contribute to the widespread adoption of effective CDS within the healthcare domain.

  12. Detailed clinical models: a review.

    PubMed

    Goossen, William; Goossen-Baremans, Anneke; van der Zel, Michael

    2010-12-01

    Due to the increasing use of electronic patient records and other health care information technology, we see an increase in requests to utilize these data. A highly level of standardization is required during the gathering of these data in the clinical context in order to use it for analyses. Detailed Clinical Models (DCM) have been created toward this purpose and several initiatives have been implemented in various parts of the world to create standardized models. This paper presents a review of DCM. Two types of analyses are presented; one comparing DCM against health care information architectures and a second bottom up approach from concept analysis to representation. In addition core parts of the draft ISO standard 13972 on DCM are used such as clinician involvement, data element specification, modeling, meta information, and repository and governance. SIX INITIATIVES WERE SELECTED: Intermountain Healthcare, 13606/OpenEHR Archetypes, Clinical Templates, Clinical Contents Models, Health Level 7 templates, and Dutch Detailed Clinical Models. Each model selected was reviewed for their overall development, involvement of clinicians, use of data types, code bindings, expressing semantics, modeling, meta information, use of repository and governance. Using both a top down and bottom up approach to comparison reveals many commonalties and differences between initiatives. Important differences include the use of or lack of a reference model and expressiveness of models. Applying clinical data element standards facilitates the use of conceptual DCM models in different technical representations.

  13. Can physics help to explain embryonic development? An overview.

    PubMed

    Fleury, V

    2013-10-01

    Recent technical advances including digital imaging and particle image velocimetry can be used to extract the full range of embryonic movements that constitute the instantaneous 'morphogenetic fields' of a developing animal. The final shape of the animal results from the sum over time (integral) of the movements that make up the velocity fields of all the tissue constituents. In vivo microscopy can be used to capture the details of vertebrate development at the earliest embryonic stages. The movements thus observed can be quantitatively compared to physical models that provide velocity fields based on simple hypotheses about the nature of living matter (a visco-elastic gel). This approach has cast new light on the interpretation of embryonic movement, folding, and organisation. It has established that several major discontinuities in development are simple physical changes in boundary conditions. In other words, with no change in biology, the physical consequences of collisions between folds largely explain the morphogenesis of the major structures (such as the head). Other discontinuities result from changes in physical conditions, such as bifurcations (changes in physical behaviour beyond specific yield points). For instance, beyond a certain level of stress, a tissue folds, without any new gene being involved. An understanding of the physical features of movement provides insights into the levers that drive evolution; the origin of animals is seen more clearly when viewed under the light of the fundamental physical laws (Newton's principle, action-reaction law, changes in symmetry breaking scale). This article describes the genesis of a vertebrate embryo from the shapeless stage (round mass of tissue) to the development of a small, elongated, bilaterally symmetric structure containing vertebral precursors, hip and shoulder enlarges, and a head. Copyright © 2013. Published by Elsevier Masson SAS.

  14. Transsclera Drug Delivery by Pulsed High-Intensity Focused Ultrasound (HIFU): An Ex Vivo Study.

    PubMed

    Murugappan, Suresh Kanna; Zhou, Yufeng

    2015-01-01

    PURPOSE/AIM OF STUDY: Drug delivery to the ocular posterior segment is of importance, but it is a challenge in the treatment of irreversible blindness disease, such as age-related macular degeneration. Although some methods (i.e. intraocular injection, sustained release by polymer and iontophoresis) have been applied, some technical drawbacks, such as slow rate and damage to the eye, need to be overcome for wide use. In this study, the feasibility of high-intensity focused ultrasound (HIFU) to enhance the transsclera drug delivery was tested for the first time. One-hundred HIFU pulses with the driving frequency of 1.1 MHz, acoustic power of 105.6 W, pulse duration of 10-50 ms and pulse repetition frequency of 1 Hz were delivered to the fresh ex vivo porcine sclera specimen. In comparison to the passive diffusion (control), 50-ms HIFU can increase the penetration depth by 2.0 folds (501.7 ± 126.4 µm versus 252.4 ± 29.2 µm) using bicinchoninic acid assay and Rhodamine 6 G fluorescence intensity by 3.1 folds (22.4 ± 12.3 versus 7.1 ± 4.1) and coverage area by 2.6 folds (40.4 ± 9.1% versus 15.8 ± 2.9%). No morphological changes on the sonicated sclera samples were found using a surface electron microscope. In summary, pulsed-HIFU may be an effective modality in the transsclera drug delivery with a high transporting rate and depth. In vivo studies are necessary to further evaluate its performance, including the drug penetration and its possible side effects.

  15. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction.

    PubMed

    Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

    2016-09-01

    Recently, new RNA secondary structure probing techniques have been developed, including Next Generation Sequencing based methods capable of probing transcriptome-wide. These techniques hold great promise for improving structure prediction accuracy. However, each new data type comes with its own signal properties and biases, which may even be experiment specific. There is therefore a growing need for RNA structure prediction methods that can be automatically trained on new data types and readily extended to integrate and fully exploit multiple types of data. Here, we develop and explore a modular probabilistic approach for integrating probing data in RNA structure prediction. It can be automatically trained given a set of known structures with probing data. The approach is demonstrated on SHAPE datasets, where we evaluate and selectively model specific correlations. The approach often makes superior use of the probing data signal compared to other methods. We illustrate the use of ProbFold on multiple data types using both simulations and a small set of structures with both SHAPE, DMS and CMCT data. Technically, the approach combines stochastic context-free grammars (SCFGs) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically compiled binaries for x86 Linux machines, C ++ programs, example datasets and a tutorial is available from http://moma.ki.au.dk/prj/probfold/ : jakob.skou@clin.au.dk Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Kinetics during the redox biotransformation of pollutants mediated by immobilized and soluble humic acids.

    PubMed

    Cervantes, Francisco J; Martínez, Claudia M; Gonzalez-Estrella, Jorge; Márquez, Arturo; Arriaga, Sonia

    2013-03-01

    The aim of this study was to elucidate the kinetic constraints during the redox biotransformation of the azo dye, Reactive Red 2 (RR2), and carbon tetrachloride (CT) mediated by soluble humic acids (HAs) and immobilized humic acids (HAi), as well as by the quinoid model compounds, anthraquinone-2,6-disulfonate (AQDS) and 1,2-naphthoquinone-4-sulfonate (NQS). The microbial reduction of both HAs and HAi by anaerobic granular sludge (AGS) was the rate-limiting step during decolorization of RR2 since the reduction of RR2 by reduced HAi proceeded at more than three orders of magnitute faster than the electron-transferring rate observed during the microbial reduction of HAi by AGS. Similarly, the reduction of RR2 by reduced AQDS proceeded 1.6- and 1.9-fold faster than the microbial reduction of AQDS by AGS when this redox mediator (RM) was supplied in soluble and immobilized form, respectively. In contrast, the reduction of NQS by AGS occurred 1.6- and 19.2-fold faster than the chemical reduction of RR2 by reduced NQS when this RM was supplied in soluble and immobilized form, respectively. The microbial reduction of HAs and HAi by a humus-reducing consortium proceeded 1,400- and 790-fold faster than the transfer of electrons from reduced HAs and HAi, respectively, to achieve the reductive dechlorination of CT to chloroform. Overall, the present study provides elucidation on the rate-limiting steps involved in the redox biotransformation of priority pollutants mediated by both HAs and HAi and offers technical suggestions to overcome the kinetic restrictions identified in the redox reactions evaluated.

  17. Landsat analysis of the Yangjiatan tungsten district, Hunan Province, People's Republic of China

    USGS Publications Warehouse

    Carter, W.D.; Kiilsgaard, T.H.

    1983-01-01

    The Yangjiatan tungsten district at latitude 27??28??? N. and longitude 111??54???E. is located about 140 km southwest of the city of Changsha and 35 km northeast of the town of Shaoyang, southeast Hunan Province, People's Republic of China. The deposits, consisting largely of scheelite in veins (Wang, 1975), are contained in highly folded and faulted sedimentary rocks of Paleozoic, Mesozoic, and Cenozoic age intruded by granitic plutons that are circular in plan view. The major faults and folds trend in a northeasterly direction; whereas, the plutons are clustered in a more easterly trending band across the Landsat image. Landsat image E-2338-02202, acquired December 26, 1975, is number 470 in the "Landsat Image Atlas of the People's Republic of China" printed by the Publishing House of Geology in 1979. A computer-compatible tape of the image was analyzed and used as a demonstration project under a United Nations technical assistance program. Supervised classification of soils, rocks, and vegetation; band ratioing to detect limonite alteration; and edge enhancement were all conducted to demonstrate the flexibility and capability of interactive computer systems. Field evaluation of the results of this work will be conducted by colleagues of the Remote Sensing Center for Geology, Ministry of Geology, in China. ?? 1983.

  18. Integration of Motor Learning Principles Into Real-Time Ambulatory Voice Biofeedback and Example Implementation Via a Clinical Case Study With Vocal Fold Nodules.

    PubMed

    Van Stan, Jarrad H; Mehta, Daryush D; Petit, Robert J; Sternad, Dagmar; Muise, Jason; Burns, James A; Hillman, Robert E

    2017-02-01

    Ambulatory voice biofeedback (AVB) has the potential to significantly improve voice therapy effectiveness by targeting one of the most challenging aspects of rehabilitation: carryover of desired behaviors outside of the therapy session. Although initial evidence indicates that AVB can alter vocal behavior in daily life, retention of the new behavior after biofeedback has not been demonstrated. Motor learning studies repeatedly have shown retention-related benefits when reducing feedback frequency or providing summary statistics. Therefore, novel AVB settings that are based on these concepts are developed and implemented. The underlying theoretical framework and resultant implementation of innovative AVB settings on a smartphone-based voice monitor are described. A clinical case study demonstrates the functionality of the new relative frequency feedback capabilities. With new technical capabilities, 2 aspects of feedback are directly modifiable for AVB: relative frequency and summary feedback. Although reduced-frequency AVB was associated with improved carryover of a therapeutic vocal behavior (i.e., reduced vocal intensity) in a patient post-excision of vocal fold nodules, causation cannot be assumed. Timing and frequency of AVB schedules can be manipulated to empirically assess generalization of motor learning principles to vocal behavior modification and test the clinical effectiveness of AVB with various feedback schedules.

  19. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.

    PubMed

    Khan, Zia; Wang, Yu-Chiun; Wieschaus, Eric F; Kaschube, Matthias

    2014-07-01

    Understanding the cellular and mechanical processes that underlie the shape changes of individual cells and their collective behaviors in a tissue during dynamic and complex morphogenetic events is currently one of the major frontiers in developmental biology. The advent of high-speed time-lapse microscopy and its use in monitoring the cellular events in fluorescently labeled developing organisms demonstrate tremendous promise in establishing detailed descriptions of these events and could potentially provide a foundation for subsequent hypothesis-driven research strategies. However, obtaining quantitative measurements of dynamic shapes and behaviors of cells and tissues in a rapidly developing metazoan embryo using time-lapse 3D microscopy remains technically challenging, with the main hurdle being the shortage of robust imaging processing and analysis tools. We have developed EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data. Our results demonstrate that EDGE4D enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo. We expect this tool to be broadly useful for the analysis of epithelial cell geometries and movements in a wide variety of developmental contexts. © 2014. Published by The Company of Biologists Ltd.

  20. Lengthening temporalis myoplasty: a surgical tool for dynamic labial commissure reanimation.

    PubMed

    Guerreschi, Pierre; Labbe, Daniel

    2015-04-01

    Lengthening temporalis myoplasty (LTM), first described by Labbé in 1997, ensures the transfers of the entire temporal muscle from the coronoid process to the upper half of the lip without interposition of aponeurotic tissue. The temporal muscle changes function because it is entirely mobilized toward another effector: the labial commissure. Thanks to brain plasticity, the muscle loses its chewing function, and after 6 months of speech rehabilitation it acquires its new smiling function. We describe technical points especially the coronoid process approaches both through an upper temporal fossa approach and a lower nasolabial fold approach. Rehabilitation starts 3 weeks after the surgery following a standardized protocol to move from a mandibular smile to a voluntary, then spontaneous, smile in three steps. The LTM is the main part of a one-stage global treatment of the paralyzed face. It constitutes a dynamic palliative treatment usually started at the sequelae stage, 18 month after the outcome of a peripheral facial paralysis. This one-stage procedure is a reproducible and relevant surgical technique in the difficult treatment of peripheral facial paralysis. It allows implementing an active muscle transfer to reanimate the labial commissure and re-create a mobile nasolabial fold. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  1. Integration of Motor Learning Principles Into Real-Time Ambulatory Voice Biofeedback and Example Implementation Via a Clinical Case Study With Vocal Fold Nodules

    PubMed Central

    Mehta, Daryush D.; Petit, Robert J.; Sternad, Dagmar; Muise, Jason; Burns, James A.; Hillman, Robert E.

    2017-01-01

    Purpose Ambulatory voice biofeedback (AVB) has the potential to significantly improve voice therapy effectiveness by targeting one of the most challenging aspects of rehabilitation: carryover of desired behaviors outside of the therapy session. Although initial evidence indicates that AVB can alter vocal behavior in daily life, retention of the new behavior after biofeedback has not been demonstrated. Motor learning studies repeatedly have shown retention-related benefits when reducing feedback frequency or providing summary statistics. Therefore, novel AVB settings that are based on these concepts are developed and implemented. Method The underlying theoretical framework and resultant implementation of innovative AVB settings on a smartphone-based voice monitor are described. A clinical case study demonstrates the functionality of the new relative frequency feedback capabilities. Results With new technical capabilities, 2 aspects of feedback are directly modifiable for AVB: relative frequency and summary feedback. Although reduced-frequency AVB was associated with improved carryover of a therapeutic vocal behavior (i.e., reduced vocal intensity) in a patient post-excision of vocal fold nodules, causation cannot be assumed. Conclusions Timing and frequency of AVB schedules can be manipulated to empirically assess generalization of motor learning principles to vocal behavior modification and test the clinical effectiveness of AVB with various feedback schedules. PMID:28124070

  2. Occupational risk factors for Parkinson's disease: a case-control study in Japan

    PubMed Central

    2011-01-01

    Background The evidence for associations between occupational factors and the risk of Parkinson's disease (PD) is inconsistent. We assessed the risk of PD associated with various occupational factors in Japan. Methods We examined 249 cases within 6 years of onset of PD. Control subjects were 369 inpatients and outpatients without neurodegenerative disease. Information on occupational factors was obtained from a self-administered questionnaire. Relative risks of PD were estimated using odds ratios (ORs) and 95% confidence intervals (CIs) based on logistic regression. Adjustments were made for gender, age, region of residence, educational level, and pack-years of smoking. Results Working in a professional or technical occupation tended to be inversely related to the risk of PD: adjusted OR was 0.59 (95% CI: 0.32-1.06, P = 0.08). According to a stratified analysis by gender, the decreased risk of PD for persons in professional or technical occupations was statistically significant only for men. Adjusted ORs for a professional or technical occupation among men and women were 0.22 (95% CI: 0.06-0.67) and 0.99 (0.47-2.07), respectively, and significant interaction was observed (P = 0.048 for homogeneity of OR). In contrast, risk estimates for protective service occupations and transport or communications were increased, although the results were not statistically significant: adjusted ORs were 2.73 (95% CI: 0.56-14.86) and 1.74 (95% CI: 0.65-4.74), respectively. No statistical significance was seen in data concerning exposure to occupational agents and the risk of PD, although roughly a 2-fold increase in OR was observed for workers exposed to stone or sand. Conclusion The results of our study suggest that occupational factors do not play a substantial etiologic role in this population. However, among men, professional or technical occupations may decrease the risk of PD. PMID:21733194

  3. [Low-field magnetic resonance imaging for rheumatoid arthritis].

    PubMed

    Ostendorf, B; Edelmann, E; Kellner, H; Scherer, A

    2010-02-01

    Magnetic resonance imaging (MRI) as a cross-sectional imaging procedure allows a three-dimensional representation of musculature, ligaments, tendons, capsules, synovial membranes, bones and cartilage with high resolution quality. An activity assessment is further possible by application of a contrast medium (gadolinium-DTPA) to differentiate between active and chronic inflammatory processes. Evidence of a bone marrow edema detected by MRI in patients with rheumatoid arthritis (RA) can be interpreted as a prognostic and predictive factor for the development of bone erosions. On the basis of these advantages MRI is being employed more and more in the early diagnosis of inflammatory joint diseases. Semi-quantitative scores for analysis and grading of findings have already been developed and are in clinical use. Because MRI technical performances are invariably reproducible they can be practically retrieved in the course of examination which is particularly relevant in rheumatology. Therapy response or progression can thus be adequately displayed. Open, dedicated low-field MRI with a low signal strength of 0.2 Tesla (T) has been known since the 90s and now represents new MRI examination options in rheumatology. Smaller devices with lower acquisition and maintenance expenses as well as considerably more convenience due to the device itself result in a higher subjective acceptability by the patients as well as objectively more data records of low-field MRI scans of RA, which underline the significance of this new technical method. The German Society for Rheumatology (DGRh), represented by the Committee for "Diagnostic Imaging", meets this development with the release of recommendations and standards for the procedures of low-field MRI and their scoring and summarizes the most important technical data and information on clinical indications.

  4. A Functional Central Limit Theorem for the Becker-Döring Model

    NASA Astrophysics Data System (ADS)

    Sun, Wen

    2018-04-01

    We investigate the fluctuations of the stochastic Becker-Döring model of polymerization when the initial size of the system converges to infinity. A functional central limit problem is proved for the vector of the number of polymers of a given size. It is shown that the stochastic process associated to fluctuations is converging to the strong solution of an infinite dimensional stochastic differential equation (SDE) in a Hilbert space. We also prove that, at equilibrium, the solution of this SDE is a Gaussian process. The proofs are based on a specific representation of the evolution equations, the introduction of a convenient Hilbert space and several technical estimates to control the fluctuations, especially of the first coordinate which interacts with all components of the infinite dimensional vector representing the state of the process.

  5. Summer Research Experiences with a Laboratory Tokamak

    NASA Astrophysics Data System (ADS)

    Farley, N.; Mauel, M.; Navratil, G.; Cates, C.; Maurer, D.; Mukherjee, S.; Shilov, M.; Taylor, E.

    1998-11-01

    Columbia University's Summer Research Program for Secondary School Science Teachers seeks to improve middle and high school student understanding of science. The Program enhances science teachers' understanding of the practice of science by having them participate for two consecutive summers as members of laboratory research teams led by Columbia University faculty. In this poster, we report the research and educational activities of two summer internships with the HBT-EP research tokamak. Research activities have included (1) computer data acquisition and the representation of complex plasma wave phenomena as audible sounds, and (2) the design and construction of pulsed microwave systems to experience the design and testing of special-purpose equipment in order to achieve a specific technical goal. We also present an overview of the positive impact this type of plasma research involvement has had on high school science teaching.

  6. Production Functions for Water Delivery Systems: Analysis and Estimation Using Dual Cost Function and Implicit Price Specifications

    NASA Astrophysics Data System (ADS)

    Teeples, Ronald; Glyer, David

    1987-05-01

    Both policy and technical analysis of water delivery systems have been based on cost functions that are inconsistent with or are incomplete representations of the neoclassical production functions of economics. We present a full-featured production function model of water delivery which can be estimated from a multiproduct, dual cost function. The model features implicit prices for own-water inputs and is implemented as a jointly estimated system of input share equations and a translog cost function. Likelihood ratio tests are performed showing that a minimally constrained, full-featured production function is a necessary specification of the water delivery operations in our sample. This, plus the model's highly efficient and economically correct parameter estimates, confirms the usefulness of a production function approach to modeling the economic activities of water delivery systems.

  7. Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata).

    PubMed

    Ferraresso, Serena; Vitulo, Nicola; Mininni, Alba N; Romualdi, Chiara; Cardazzo, Barbara; Negrisolo, Enrico; Reinhardt, Richard; Canario, Adelino V M; Patarnello, Tomaso; Bargelloni, Luca

    2008-12-03

    Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great importance for aquaculture. A public data base was constructed, consisting of 19,734 unique clusters (3,563 contigs and 16,171 singletons). Functional annotation was obtained for 8,021 clusters. Over 4,000 sequences were also associated with a GO entry. Two 60mer probes were designed for each gene and in-situ synthesized on glass slides using Agilent SurePrint technology. Platform reproducibility and accuracy were assessed on two early stages of sea bream development (one-day and four days old larvae). Correlation between technical replicates was always > 0.99, with strong positive correlation between paired probes. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. Functional analysis suggested that down-regulated transcripts (407) in older larvae are mostly essential/housekeeping genes, whereas tissue-specific genes are up-regulated in parallel with the formation of key organs (eye, digestive system). Cross-validation of microarray data was carried out using quantitative qRT-PCR on 11 target genes, selected to reflect the whole range of fold-change and both up-regulated and down-regulated genes. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates. Good concordance between qRT-PCR and microarray data was observed between 2- and 7-fold change, while fold-change compression in the microarray was present for differences greater than 10-fold in the qRT-PCR. A highly reliable oligo-microarray platform was developed and validated for the gilthead sea bream despite the presently limited knowledge of the species transcriptome. Because of the flexible design this array will be able to accommodate additional probes as soon as novel unique transcripts are available.

  8. Addressing security issues related to virtual institute distributed activities

    NASA Astrophysics Data System (ADS)

    Stytz, Martin R.; Banks, Sheila B.

    2008-03-01

    One issue confounding the development and experimentation of distributed modeling and simulation environments is the inability of the project team to identify and collaborate with resources, both human and technical, from outside the United States. This limitation is especially significant within the human behavior representation area where areas such as cultural effects research and joint command team behavior modeling require the participation of various cultural and national representatives. To address this limitation, as well as other human behavior representation research issues, NATO Research and Technology Organization initiated a project to develop a NATO virtual institute that enables more effective and more collaborative research into human behavior representation. However, in building and operating a virtual institute one of the chief concerns must be the cyber security of the institute. Because the institute "exists" in cyberspace, all of its activities are susceptible to cyberattacks, subterfuge, denial of service and all of the vulnerabilities that networked computers must face. In our opinion, for the concept of virtual institutes to be successful and useful, their operations and services must be protected from the threats in the cyber environment. A key to developing the required protection is the development and promulgation of standards for cyber security. In this paper, we discuss the types of cyber standards that are required, how new internet technologies can be exploited and can benefit the promulgation, development, maintenance, and robustness of the standards. This paper is organized as follows. Section One introduces the concept of the virtual institutes, the expected benefits, and the motivation for our research and for research in this area. Section Two presents background material and a discussion of topics related to VIs, uman behavior and cultural modeling, and network-centric warfare. Section Three contains a discussion of the security challenges that face the virtual institute and the characteristics of the standards that must be employed. Section Four contains our proposal for documentation of the cybersecurity standards. Section Five contains the conclusion and suggestions for further work.

  9. A statistical survey of heat input parameters into the cusp thermosphere

    NASA Astrophysics Data System (ADS)

    Moen, J. I.; Skjaeveland, A.; Carlson, H. C.

    2017-12-01

    Based on three winters of observational data, we present those ionosphere parameters deemed most critical to realistic space weather ionosphere and thermosphere representation and prediction, in regions impacted by variability in the cusp. The CHAMP spacecraft revealed large variability in cusp thermosphere densities, measuring frequent satellite drag enhancements, up to doublings. The community recognizes a clear need for more realistic representation of plasma flows and electron densities near the cusp. Existing average-value models produce order of magnitude errors in these parameters, resulting in large under estimations of predicted drag. We fill this knowledge gap with statistics-based specification of these key parameters over their range of observed values. The EISCAT Svalbard Radar (ESR) tracks plasma flow Vi , electron density Ne, and electron, ion temperatures Te, Ti , with consecutive 2-3 minute windshield-wipe scans of 1000x500 km areas. This allows mapping the maximum Ti of a large area within or near the cusp with high temporal resolution. In magnetic field-aligned mode the radar can measure high-resolution profiles of these plasma parameters. By deriving statistics for Ne and Ti , we enable derivation of thermosphere heating deposition under background and frictional-drag-dominated magnetic reconnection conditions. We separate our Ne and Ti profiles into quiescent and enhanced states, which are not closely correlated due to the spatial structure of the reconnection foot point. Use of our data-based parameter inputs can make order of magnitude corrections to input data driving thermosphere models, enabling removal of previous two fold drag errors.

  10. What basic number processing measures in kindergarten explain unique variability in first-grade arithmetic proficiency?

    PubMed

    Bartelet, Dimona; Vaessen, Anniek; Blomert, Leo; Ansari, Daniel

    2014-01-01

    Relations between children's mathematics achievement and their basic number processing skills have been reported in both cross-sectional and longitudinal studies. Yet, some key questions are currently unresolved, including which kindergarten skills uniquely predict children's arithmetic fluency during the first year of formal schooling and the degree to which predictors are contingent on children's level of arithmetic proficiency. The current study assessed kindergarteners' non-symbolic and symbolic number processing efficiency. In addition, the contribution of children's underlying magnitude representations to differences in arithmetic achievement was assessed. Subsequently, in January of Grade 1, their arithmetic proficiency was assessed. Hierarchical regression analysis revealed that children's efficiency to compare digits, count, and estimate numerosities uniquely predicted arithmetic differences above and beyond the non-numerical factors included. Moreover, quantile regression analysis indicated that symbolic number processing efficiency was consistently a significant predictor of arithmetic achievement scores regardless of children's level of arithmetic proficiency, whereas their non-symbolic number processing efficiency was not. Finally, none of the task-specific effects indexing children's representational precision was significantly associated with arithmetic fluency. The implications of the results are 2-fold. First, the findings indicate that children's efficiency to process symbols is important for the development of their arithmetic fluency in Grade 1 above and beyond the influence of non-numerical factors. Second, the impact of children's non-symbolic number processing skills does not depend on their arithmetic achievement level given that they are selected from a nonclinical population. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Artificial limb representation in amputees

    PubMed Central

    van den Heiligenberg, Fiona M Z; Orlov, Tanya; Macdonald, Scott N; Duff, Eugene P; Henderson Slater, David; Beckmann, Christian F; Johansen-Berg, Heidi; Culham, Jody C; Makin, Tamar R

    2018-01-01

    Abstract The human brain contains multiple hand-selective areas, in both the sensorimotor and visual systems. Could our brain repurpose neural resources, originally developed for supporting hand function, to represent and control artificial limbs? We studied individuals with congenital or acquired hand-loss (hereafter one-handers) using functional MRI. We show that the more one-handers use an artificial limb (prosthesis) in their everyday life, the stronger visual hand-selective areas in the lateral occipitotemporal cortex respond to prosthesis images. This was found even when one-handers were presented with images of active prostheses that share the functionality of the hand but not necessarily its visual features (e.g. a ‘hook’ prosthesis). Further, we show that daily prosthesis usage determines large-scale inter-network communication across hand-selective areas. This was demonstrated by increased resting state functional connectivity between visual and sensorimotor hand-selective areas, proportional to the intensiveness of everyday prosthesis usage. Further analysis revealed a 3-fold coupling between prosthesis activity, visuomotor connectivity and usage, suggesting a possible role for the motor system in shaping use-dependent representation in visual hand-selective areas, and/or vice versa. Moreover, able-bodied control participants who routinely observe prosthesis usage (albeit less intensively than the prosthesis users) showed significantly weaker associations between degree of prosthesis observation and visual cortex activity or connectivity. Together, our findings suggest that altered daily motor behaviour facilitates prosthesis-related visual processing and shapes communication across hand-selective areas. This neurophysiological substrate for prosthesis embodiment may inspire rehabilitation approaches to improve usage of existing substitutionary devices and aid implementation of future assistive and augmentative technologies. PMID:29534154

  12. Artificial limb representation in amputees.

    PubMed

    van den Heiligenberg, Fiona M Z; Orlov, Tanya; Macdonald, Scott N; Duff, Eugene P; Henderson Slater, David; Beckmann, Christian F; Johansen-Berg, Heidi; Culham, Jody C; Makin, Tamar R

    2018-05-01

    The human brain contains multiple hand-selective areas, in both the sensorimotor and visual systems. Could our brain repurpose neural resources, originally developed for supporting hand function, to represent and control artificial limbs? We studied individuals with congenital or acquired hand-loss (hereafter one-handers) using functional MRI. We show that the more one-handers use an artificial limb (prosthesis) in their everyday life, the stronger visual hand-selective areas in the lateral occipitotemporal cortex respond to prosthesis images. This was found even when one-handers were presented with images of active prostheses that share the functionality of the hand but not necessarily its visual features (e.g. a 'hook' prosthesis). Further, we show that daily prosthesis usage determines large-scale inter-network communication across hand-selective areas. This was demonstrated by increased resting state functional connectivity between visual and sensorimotor hand-selective areas, proportional to the intensiveness of everyday prosthesis usage. Further analysis revealed a 3-fold coupling between prosthesis activity, visuomotor connectivity and usage, suggesting a possible role for the motor system in shaping use-dependent representation in visual hand-selective areas, and/or vice versa. Moreover, able-bodied control participants who routinely observe prosthesis usage (albeit less intensively than the prosthesis users) showed significantly weaker associations between degree of prosthesis observation and visual cortex activity or connectivity. Together, our findings suggest that altered daily motor behaviour facilitates prosthesis-related visual processing and shapes communication across hand-selective areas. This neurophysiological substrate for prosthesis embodiment may inspire rehabilitation approaches to improve usage of existing substitutionary devices and aid implementation of future assistive and augmentative technologies.

  13. Arraying proteins by cell-free synthesis.

    PubMed

    He, Mingyue; Wang, Ming-Wei

    2007-10-01

    Recent advances in life science have led to great motivation for the development of protein arrays to study functions of genome-encoded proteins. While traditional cell-based methods have been commonly used for generating protein arrays, they are usually a time-consuming process with a number of technical challenges. Cell-free protein synthesis offers an attractive system for making protein arrays, not only does it rapidly converts the genetic information into functional proteins without the need for DNA cloning, but also presents a flexible environment amenable to production of folded proteins or proteins with defined modifications. Recent advancements have made it possible to rapidly generate protein arrays from PCR DNA templates through parallel on-chip protein synthesis. This article reviews current cell-free protein array technologies and their proteomic applications.

  14. Observing Exoplanetary Ozone In The Mid-Ultraviolet

    NASA Technical Reports Server (NTRS)

    Heap, S.

    2008-01-01

    There are good reasons for pushing the spectral range of observation to shorter wavelengths than currently envisaged for terrestrial planet-finding missions utilizing with a 4-rn, diffraction-limited, optical telescope: (1) The angular resolution is higher, so that the image of an exoplanet is better separated from that of the much brighter star. (2) Due to the higher resolution, the exozodiacal background per resolution element is smaller, so exposure times are reduced for the same incident flux. (3) Most importantly, the sensitivity to the presence of life on habitable exoplanets is increased by a hundred-fold by access to the ozone biomarker at 250-300 nm. These benefits must be weighed against challenges arising from the faintness of exoplanets in the mid-UV. We will describe the benefits and the technical and cost challenges.

  15. MM T for linear resonant cooler. Volume 1. Final report, October 1984-September 1986

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Narayan, R.; Silvestro, J.

    1988-02-16

    The three-fold objectives of this contract were to: (1) enhance the producibility and performance of the prototype cooler design developed in a prior contract, (b) qualify the design to the target specification in the contract (basically the HD1045/UA B2 specification amended for 2,500 hour MTTF and low audible noise), and (c) develop and demonstrate a pilot production facility for the cooler. Technical difficulties and cost growth related to objectives (a) and (b) above precluded accomplishing (c) as part of this contract's activities. Nevertheless, performance within or exceeding all major requirements has been demonstrated, and the company is currently producing themore » cooler for use on a U.S. Air Force airborne IR system.« less

  16. Evolution of robot-assisted orthotopic ileal neobladder formation: a step-by-step update to the University of Southern California (USC) technique.

    PubMed

    Chopra, Sameer; de Castro Abreu, Andre Luis; Berger, Andre K; Sehgal, Shuchi; Gill, Inderbir; Aron, Monish; Desai, Mihir M

    2017-01-01

    To describe our, step-by-step, technique for robotic intracorporeal neobladder formation. The main surgical steps to forming the intracorporeal orthotopic ileal neobladder are: isolation of 65 cm of small bowel; small bowel anastomosis; bowel detubularisation; suture of the posterior wall of the neobladder; neobladder-urethral anastomosis and cross folding of the pouch; and uretero-enteral anastomosis. Improvements have been made to these steps to enhance time efficiency without compromising neobladder configuration. Our technical improvements have resulted in an improvement in operative time from 450 to 360 min. We describe an updated step-by-step technique of robot-assisted intracorporeal orthotopic ileal neobladder formation. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

  17. Uncertainty Quantification given Discontinuous Climate Model Response and a Limited Number of Model Runs

    NASA Astrophysics Data System (ADS)

    Sargsyan, K.; Safta, C.; Debusschere, B.; Najm, H.

    2010-12-01

    Uncertainty quantification in complex climate models is challenged by the sparsity of available climate model predictions due to the high computational cost of model runs. Another feature that prevents classical uncertainty analysis from being readily applicable is bifurcative behavior in climate model response with respect to certain input parameters. A typical example is the Atlantic Meridional Overturning Circulation. The predicted maximum overturning stream function exhibits discontinuity across a curve in the space of two uncertain parameters, namely climate sensitivity and CO2 forcing. We outline a methodology for uncertainty quantification given discontinuous model response and a limited number of model runs. Our approach is two-fold. First we detect the discontinuity with Bayesian inference, thus obtaining a probabilistic representation of the discontinuity curve shape and location for arbitrarily distributed input parameter values. Then, we construct spectral representations of uncertainty, using Polynomial Chaos (PC) expansions on either side of the discontinuity curve, leading to an averaged-PC representation of the forward model that allows efficient uncertainty quantification. The approach is enabled by a Rosenblatt transformation that maps each side of the discontinuity to regular domains where desirable orthogonality properties for the spectral bases hold. We obtain PC modes by either orthogonal projection or Bayesian inference, and argue for a hybrid approach that targets a balance between the accuracy provided by the orthogonal projection and the flexibility provided by the Bayesian inference - where the latter allows obtaining reasonable expansions without extra forward model runs. The model output, and its associated uncertainty at specific design points, are then computed by taking an ensemble average over PC expansions corresponding to possible realizations of the discontinuity curve. The methodology is tested on synthetic examples of discontinuous model data with adjustable sharpness and structure. This work was supported by the Sandia National Laboratories Seniors’ Council LDRD (Laboratory Directed Research and Development) program. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

  18. Multimodal Wavelet Embedding Representation for data Combination (MaWERiC): Integrating Magnetic Resonance Imaging and Spectroscopy for Prostate Cancer Detection

    PubMed Central

    Tiwari, Pallavi; Kurhanewicz, John; Viswanath, Satish; Sridhar, Akshay; Madabhushi, Anant

    2011-01-01

    Rationale and Objectives To develop a computerized data integration framework (MaWERiC) for quantitatively combining structural and metabolic information from different Magnetic Resonance (MR) imaging modalities. Materials and Methods In this paper, we present a novel computerized support system that we call Multimodal Wavelet Embedding Representation for data Combination (MaWERiC) which (1) employs wavelet theory and dimensionality reduction for providing a common, uniform representation of the different imaging (T2-w) and non-imaging (spectroscopy) MRI channels, and (2) leverages a random forest classifier for automated prostate cancer detection on a per voxel basis from combined 1.5 Tesla in vivo MRI and MRS. Results A total of 36 1.5 T endorectal in vivo T2-w MRI, MRS patient studies were evaluated on a per-voxel via MaWERiC, using a three-fold cross validation scheme across 25 iterations. Ground truth for evaluation of the results was obtained via ex-vivo whole-mount histology sections which served as the gold standard for expert radiologist annotations of prostate cancer on a per-voxel basis. The results suggest that MaWERiC based MRS-T2-w meta-classifier (mean AUC, μ = 0.89 ± 0.02) significantly outperformed (i) a T2-w MRI (employing wavelet texture features) classifier (μ = 0.55± 0.02), (ii) a MRS (employing metabolite ratios) classifier (μ= 0.77 ± 0.03), (iii) a decision-fusion classifier, obtained by combining individual T2-w MRI and MRS classifier outputs (μ = 0.85 ± 0.03) and (iv) a data combination scheme involving combination of metabolic MRS and MR signal intensity features (μ = 0.66± 0.02). Conclusion A novel data integration framework, MaWERiC, for combining imaging and non-imaging MRI channels was presented. Application to prostate cancer detection via combination of T2-w MRI and MRS data demonstrated significantly higher AUC and accuracy values compared to the individual T2-w MRI, MRS modalities and other data integration strategies. PMID:21960175

  19. Semiotics and agents for integrating and navigating through multimedia representations of concepts

    NASA Astrophysics Data System (ADS)

    Joyce, Dan W.; Lewis, Paul H.; Tansley, Robert H.; Dobie, Mark R.; Hall, Wendy

    1999-12-01

    The purpose of this paper is two-fold. We begin by exploring the emerging trend to view multimedia information in terms of low-level and high-level components; the former being feature-based and the latter the 'semantics' intrinsic to what is portrayed by the media object. Traditionally, this has been viewed by employing analogies with generative linguistics. Recently, a new perceptive based on the semiotic tradition has been alluded to in several papers. We believe this to be a more appropriate approach. From this, we propose an approach for tackling this problem which uses an associative data structure expressing authored information together with intelligent agents acting autonomously over this structure. We then show how neural networks can be used to implement such agents. The agents act as 'vehicles' for bridging the gap between multimedia semantics and concrete expressions of high-level knowledge, but we suggest that traditional neural network techniques for classification are not architecturally adequate.

  20. 3D chromosome rendering from Hi-C data using virtual reality

    NASA Astrophysics Data System (ADS)

    Zhu, Yixin; Selvaraj, Siddarth; Weber, Philip; Fang, Jennifer; Schulze, Jürgen P.; Ren, Bing

    2015-01-01

    Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intrachromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regions are distant in one dimension but could be spatially proximal when mapped to three-dimensional space. For example, the visualization of enhancers folding over genes is only fully expressed in three-dimensional space. Thus, to accurately understand DNA behavior during gene expression, a means to model chromosomes is essential. Using coordinates generated from Hi-C interaction frequency data, we have created interactive 3D models of whole chromosome structures and its respective domains. We have also rendered information on genomic features such as genes, CTCF binding sites, and enhancers. The goal of this article is to present the procedure, findings, and conclusions of our models and renderings.

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