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Sample records for adaptive zero-tree structure

  1. Structural Adaptation

    ERIC Educational Resources Information Center

    Crowley, Julianne; Titmus, Morgan

    2016-01-01

    This article explores an alternative conception held by high school and first-year university biology students regarding the structure of the left and right ventricles of the heart and the significance of the left ventricular wall being thicker than the right. The left ventricular wall of the heart is thicker than the right ventricular wall due to…

  2. Intelligent adaptive structures

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.

    1990-01-01

    'Intelligent Adaptive Structures' (IAS) refers to structural systems whose geometric and intrinsic structural characteristics can be automatically changed to meet mission requirements with changing operational scenarios. An IAS is composed of actuators, sensors, and a control logic; these are integrated in a distributed fashion within the elements of the structure. The IAS concepts thus far developed for space antennas and other precision structures should be applicable to civil, marine, automotive, and aeronautical structural systems.

  3. Adaptive structures. [for space applications

    NASA Technical Reports Server (NTRS)

    Wada, B. K.; Fanson, J. L.; Crawley, E. F.

    1990-01-01

    Current research in the field of advanced adaptive structures for space applications is reviewed. A classification of adaptive structures is proposed whereby such structures are subdivided into adaptive, sensory, controlled, active, and intelligent structures. The definition and properties of each type of adaptive structures are presented, and methods of structure control are discussed.

  4. Adaptive structures in space

    NASA Technical Reports Server (NTRS)

    Wada, B. K.; Fanson, J. L.; Chen, G. S.; Kuo, C.-P.

    1990-01-01

    Future NASA missions will need large (20 to 100m) structural systems with precision position (few microns to submicron) requirements. Data are presented which indicate the technology deficiencies of previous programs and analyses in current state-of-the-art structural design approaches, analytical prediction capabilities, control of structure capabilities, and ground test technologies to meet the performance requirements of future large precision structural systems. Test results on laboratory truss structures that demonstrate static displacement control, active damping, and on-orbit system identification are described. It is shown that for large precision structures, adaptive structures provide not only a means to achieve the precision and characteristics required in space, but can also significantly alleviate the ground test requirements for flight-validating the hardware.

  5. Study on the application of embedded zero-tree wavelet algorithm in still images compression

    NASA Astrophysics Data System (ADS)

    Zhang, Jing; Lu, Yanhe; Li, Taifu; Lei, Gang

    2005-12-01

    An image has directional selection capability with high frequency through wavelet transformation. It is coincident with the visual characteristics of human eyes. The most important visual characteristic in human eyes is the visual covering effect. The embedded Zero-tree Wavelet (EZW) coding method completes the same level coding for a whole image. In an image, important regions (regions of interest) and background regions (indifference regions) are coded through the same levels. On the basis of studying the human visual characteristics, that is, the visual covering effect, this paper employs an image-compressing method with regions of interest, i.e., an algorithm of Embedded Zero-tree Wavelet with Regions of Interest (EZWROI Algorism) to encode the regions of interest and regions of non-interest separately. In this way, the lost important information in the image is much less. It makes full use of channel resource and memory space, and improves the image quality in the regions of interest. Experimental study showed that a resumed image using an EZW_ROI algorithm is better in visual effects than that of EZW on condition of high compression ratio.

  6. A symbol-map wavelet zero-tree image coding algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Xiaodong; Liu, Wenyao; Peng, Xiang; Liu, Xiaoli

    2008-03-01

    A improved SPIHT image compression algorithm called symbol-map zero-tree coding algorithm (SMZTC) is proposed in this paper based on wavelet transform. The SPIHT algorithm is a high efficiency wavelet coefficients coding method and have good image compressing effect, but it has more complexity and need too much memory. The algorithm presented in this paper utilizes two small symbol-maps Mark and FC to store the status of coefficients and zero tree sets during coding procedure so as to reduce the memory requirement. By this strategy, the memory cost is reduced distinctly as well as the scanning speed of coefficients is improved. Those comparison experiments for 512 by 512 images are done with some other zerotree coding algorithms, such as SPIHT, NLS method. During the experiments, the biorthogonal 9/7 lifting wavelet transform is used to image transform. The results of coding experiments show that this algorithm speed of codec is improved significantly, and compression-ratio is almost uniformed with SPIHT algorithm.

  7. Adaptive Control For Flexible Structures

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Ih, Che-Hang Charles; Wang, Shyh Jong

    1988-01-01

    Paper discusses ways to cope with measurement noise in adaptive control system for large, flexible structure in outer space. System generates control signals for torque and thrust actuators to turn all or parts of structure to desired orientations while suppressing torsional and other vibrations. Main result of paper is general theory for introduction of filters to suppress measurement noise while preserving stability.

  8. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  9. Conical isogrid adapter structural test results

    NASA Technical Reports Server (NTRS)

    Dyer, J. E.; Slysh, P.

    1974-01-01

    The structural characteristics of isogrid composite structures are discussed. To demonstrate the feasibility of applying isogrid to conical structures, a full scale flanged isogrid conical adapter similar to the configuration of the D-1 Centaur equipment module was constructed. The adapter was tested to evaluate the response of the conical isogrid structure to various combinations of bending and axial compression loading. The analysis techniques for predicting conical isogrid structural capability are examined.

  10. Dynamic adaptivity of "smart" piezoelectric structures

    NASA Astrophysics Data System (ADS)

    Tzou, Horn-Sen; Zhong, Jianping P.

    1990-10-01

    Active smart" space and machine structures with adaptive dynamic characteristics have long been interested in a variety of high-performance systems, e.g., flexible robots, flexible space structures, "smart" machines, etc. In this paper, an active adaptive structure made of piezoelectric materials is proposed and evaluated. The structural adaptivity is achieved by a voltage feedback (open or closed loops) utilizing the converse piezoelectric effect. A mathematical model is proposed and the electrodynamic equations of motion and the generalized boundary conditions of a generic piezoelectric shell subjected to mechanical and electrical excitations are derived using Hamilton's principle and the linear piezoelectric theory. The dynamic adaptivity of the structure is introduced using a feedback control system. The theory is demonstrated in a case study in which the structural adaptivity (natural frequency) is investigated.

  11. Guideline For Design Of Adaptive Structures

    NASA Technical Reports Server (NTRS)

    Utku, Senol; Wada, Ben K.

    1994-01-01

    Guideline for design of adaptive structures specifies active members should be located at positions of maximum strain energy. Equations of motion of flexible structures formulated in terms of kinetic energies, strain energies, and direct measurements of forces. Maintaining precise dimensional control during assembly essential to assembly without large external loads or to prevent jamming of substructure preventing successful deployment. Active members used to prevent "binding" during deployment of structure. Then structure adjusted to precision shape requirement and adjusted during operation as required.

  12. A modular approach to adaptive structures.

    PubMed

    Pagitz, Markus; Pagitz, Manuel; Hühne, Christian

    2014-01-01

    A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized for a given set of target shapes and stiffness requirements. An advantage of such a fusion is that cell walls are prestressed by cell pressures which increases, decreases the overall structural stiffness, weight. Inspired by the nastic movement of plants, Pagitz et al (2012 Bioinspir. Biomim. 7) published a novel concept for pressure actuated cellular structures. This article extends previous work by introducing a modular approach to adaptive structures. An algorithm that breaks down any continuous target shapes into a small number of standardized modules is presented. Furthermore it is shown how cytoskeletons within each cell enhance the properties of adaptive modules. An adaptive passenger seat and an aircrafts leading, trailing edge is used to demonstrate the potential of a modular approach. PMID:25289521

  13. Adaptive piezoelectric shell structures: theory and experiments

    NASA Astrophysics Data System (ADS)

    Tzou, H. S.; Zhong, J. P.

    1993-07-01

    Active "smart" space and mechanical structures with adaptive dynamic characteristics have long been interested in a variety of high-performance systems, e.g. flexible space structures, flexible robots, "smart" machines etc. In this paper, an active adaptive structure made of piezoelectric materials is proposed and evaluated. Electromechanical equations of motion and generalised boundary conditions of a generic piezoelectric shell subjected to mechanical and electrical excitations are derived using Hamilton's principle and the linear piezoelectric theory. The structural adaptivity is achieved by a voltage feedback (open or closed loops) utilising the converse piezoelectric effect. Applications of the theory is demonstrated in a bimorph beam case and a cylindrical shell case. Frequency manipulation of the bimorph beam is studied theoretically and experimentally. Damping control of the cylindrical shell via in-plane membrane forces is also investigated.

  14. Adaptive GOP structure based on motion coherence

    NASA Astrophysics Data System (ADS)

    Ma, Yanzhuo; Wan, Shuai; Chang, Yilin; Yang, Fuzheng; Wang, Xiaoyu

    2009-08-01

    Adaptive Group of Pictures (GOP) is helpful for increasing the efficiency of video encoding by taking account of characteristics of video content. This paper proposes a method for adaptive GOP structure selection for video encoding based on motion coherence, which extracts key frames according to motion acceleration, and assigns coding type for each key and non-key frame correspondingly. Motion deviation is then used instead of motion magnitude in the selection of the number of B frames. Experimental results show that the proposed method for adaptive GOP structure selection achieves performance gain of 0.2-1dB over the fixed GOP, and has the advantage of better transmission resilience. Moreover, this method can be used in real-time video coding due to its low complexity.

  15. Adaptive finite element strategies for shell structures

    NASA Technical Reports Server (NTRS)

    Stanley, G.; Levit, I.; Stehlin, B.; Hurlbut, B.

    1992-01-01

    The present paper extends existing finite element adaptive refinement (AR) techniques to shell structures, which have heretofore been neglected in the AR literature. Specific challenges in applying AR to shell structures include: (1) physical discontinuities (e.g., stiffener intersections); (2) boundary layers; (3) sensitivity to geometric imperfections; (4) the sensitivity of most shell elements to mesh distortion, constraint definition and/or thinness; and (5) intrinsic geometric nonlinearity. All of these challenges but (5) are addressed here.

  16. Parallel computations and control of adaptive structures

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alvin, Kenneth F.; Belvin, W. Keith; Chong, K. P. (Editor); Liu, S. C. (Editor); Li, J. C. (Editor)

    1991-01-01

    The equations of motion for structures with adaptive elements for vibration control are presented for parallel computations to be used as a software package for real-time control of flexible space structures. A brief introduction of the state-of-the-art parallel computational capability is also presented. Time marching strategies are developed for an effective use of massive parallel mapping, partitioning, and the necessary arithmetic operations. An example is offered for the simulation of control-structure interaction on a parallel computer and the impact of the approach presented for applications in other disciplines than aerospace industry is assessed.

  17. Advances in adaptive structures at Jet Propulsion Laboratory

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.; Garba, John A.

    1993-01-01

    Future proposed NASA missions with the need for large deployable or erectable precision structures will require solutions to many technical problems. The Jet Propulsion Laboratory (JPL) is developing new technologies in Adaptive Structures to meet these challenges. The technology requirements, approaches to meet the requirements using Adaptive Structures, and the recent JPL research results in Adaptive Structures are described.

  18. Adaptive vibration damping of fin structures

    NASA Astrophysics Data System (ADS)

    Stuwing, Michael; Sachau, Delf; Breitbach, Elmar J.

    1999-07-01

    Modern military aircraft are characterized by employment of optimized structural components. New demands on exploitation of lightweight construction technology will arise because even greater flexibility with increased maneuverability is desired. The structural integration of multifunctional, often called 'smart' elements, properly activated to e.g. reduce structural loading, offers great potential to necessary advances in military aircraft design. One major problem of modern military aircraft is the buffet loading on the fin structures. Flying the aircraft at high angles of attack allows vortices, evolving from the leading edge of the wing, to hit the fin and excite structural vibrations. This leads to structural attrition as well as a reduced aircraft maneuverability. With the aim to reduce these fin vibrations, an adaptive structure has been developed which is presented in this paper. A concept is discussed with which the vibrational loads are reduced by introduction of counteracting forces using an 'active interface'. This interface concept is characterized by the integration of active, piezoelectric elements directly into the bending support of the fin structure. To validate the stability of the interface FE calculations and extensive measurements on piezoceramic stack actuators have been performed. The manufactured interface was integrate in an existing test structure and realistically loaded. The result will be given in this presentation.

  19. Structured adaptive grid generation using algebraic methods

    NASA Technical Reports Server (NTRS)

    Yang, Jiann-Cherng; Soni, Bharat K.; Roger, R. P.; Chan, Stephen C.

    1993-01-01

    The accuracy of the numerical algorithm depends not only on the formal order of approximation but also on the distribution of grid points in the computational domain. Grid adaptation is a procedure which allows optimal grid redistribution as the solution progresses. It offers the prospect of accurate flow field simulations without the use of an excessively timely, computationally expensive, grid. Grid adaptive schemes are divided into two basic categories: differential and algebraic. The differential method is based on a variational approach where a function which contains a measure of grid smoothness, orthogonality and volume variation is minimized by using a variational principle. This approach provided a solid mathematical basis for the adaptive method, but the Euler-Lagrange equations must be solved in addition to the original governing equations. On the other hand, the algebraic method requires much less computational effort, but the grid may not be smooth. The algebraic techniques are based on devising an algorithm where the grid movement is governed by estimates of the local error in the numerical solution. This is achieved by requiring the points in the large error regions to attract other points and points in the low error region to repel other points. The development of a fast, efficient, and robust algebraic adaptive algorithm for structured flow simulation applications is presented. This development is accomplished in a three step process. The first step is to define an adaptive weighting mesh (distribution mesh) on the basis of the equidistribution law applied to the flow field solution. The second, and probably the most crucial step, is to redistribute grid points in the computational domain according to the aforementioned weighting mesh. The third and the last step is to reevaluate the flow property by an appropriate search/interpolate scheme at the new grid locations. The adaptive weighting mesh provides the information on the desired concentration

  20. Probabilistic structural analysis of adaptive/smart/intelligent space structures

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.

    1991-01-01

    A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

  1. Probabilistic structural analysis of adaptive/smart/intelligent space structures

    NASA Technical Reports Server (NTRS)

    Pai, Shantaram S.; Chamis, Christos C.

    1992-01-01

    A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.

  2. Active isolation of vibrations with adaptive structures

    NASA Technical Reports Server (NTRS)

    Guigou, C.; Fuller, C. R.; Wagstaff, P. R.

    1991-01-01

    Vibration transmission in structures is controlled by means of a technique which employs distributed arrays of piezoelectric transducers bonded to the supporting structure. Distributed PVDF piezoelectric strips are employed as error sensors, and a two-channel feedforward adaptive LMS algorithm is used for minimizing error signals and thereby controlling the structure. A harmonic force input excites a thick plate, and a receiving plate is configured with three pairs of piezoelectric actuators. Modal analyses are performed to determine the resonant frequencies of the system, and a scanning laser vibrometer is used to study the shape of the response of the receiving plate during excitation with and without the control algorithm. Efficient active isolation of the vibrations is achieved with modal suppression, and good control is noted in the on-resonance cases in which increased numbers of PVDF sensors and piezoelectric actuators are employed.

  3. Anisotropic mesh adaptation on Lagrangian Coherent Structures

    NASA Astrophysics Data System (ADS)

    Miron, Philippe; Vétel, Jérôme; Garon, André; Delfour, Michel; Hassan, Mouhammad El

    2012-08-01

    The finite-time Lyapunov exponent (FTLE) is extensively used as a criterion to reveal fluid flow structures, including unsteady separation/attachment surfaces and vortices, in laminar and turbulent flows. However, for large and complex problems, flow structure identification demands computational methodologies that are more accurate and effective. With this objective in mind, we propose a new set of ordinary differential equations to compute the flow map, along with its first (gradient) and second order (Hessian) spatial derivatives. We show empirically that the gradient of the flow map computed in this way improves the pointwise accuracy of the FTLE field. Furthermore, the Hessian allows for simple interpolation error estimation of the flow map, and the construction of a continuous optimal and multiscale Lp metric. The Lagrangian particles, or nodes, are then iteratively adapted on the flow structures revealed by this metric. Typically, the L1 norm provides meshes best suited to capturing small scale structures, while the L∞ norm provides meshes optimized to capture large scale structures. This means that the mesh density near large scale structures will be greater with the L∞ norm than with the L1 norm for the same mesh complexity, which is why we chose this technique for this paper. We use it to optimize the mesh in the vicinity of LCS. It is found that Lagrangian Coherent Structures are best revealed with the minimum number of vertices with the L∞ metric.

  4. Structural features determining thermal adaptation of esterases.

    PubMed

    Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich

    2016-02-01

    The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.

  5. Structural dynamic health monitoring of adaptive CFRP structures

    NASA Astrophysics Data System (ADS)

    Kaiser, Stephan; Melcher, Joerg; Breitbach, Elmar J.; Sachau, Delf

    1999-07-01

    The DLR Institute of Structural Mechanics is engaged in the construction and optimization of adaptive structures for aerospace and terrestrial applications. Due to the FFS- Project, one of the recent works of the Institute is the reduction of buffet induced vibration loads at a fin. The construction of modern aircrafts is influenced b the increasing use of fiber composites. They have more specific stiffness and strength properties than metals. On the other hand the layered structure leads to new kinds of damages like delaminations. In the fin interface there are actuators and sensors integrated. Therefore the fin is connected with a controller. For the extension of this adaptive system towards an on-line tool for health monitoring this controller can be used as an identifier of the structure's modal parameters. The most promising procedure is based on MX filters. These filters constitute the filter coefficients from which a fast transformation procedure extracts the modal parameters. The changes of these parameters are related to the location and extent of the damage. So when using the already integrate controller for system identification, one can have a low-cost on-line damage detection for dynamic adaptive structures. First off-line test at CFRP plates have shown the ability to detect delaminations.

  6. Adaptive momentum management for large space structures

    NASA Technical Reports Server (NTRS)

    Hahn, E.

    1987-01-01

    Momentum management is discussed for a Large Space Structure (LSS) with the structure selected configuration being the Initial Orbital Configuration (IOC) of the dual keel space station. The external forces considered were gravity gradient and aerodynamic torques. The goal of the momentum management scheme developed is to remove the bias components of the external torques and center the cyclic components of the stored angular momentum. The scheme investigated is adaptive to uncertainties of the inertia tensor and requires only approximate knowledge of principle moments of inertia. Computational requirements are minimal and should present no implementation problem in a flight type computer and the method proposed is shown to be effective in the presence of attitude control bandwidths as low as .01 radian/sec.

  7. Adaptive Control of Flexible Structures Using Residual Mode Filters

    NASA Technical Reports Server (NTRS)

    Balas, Mark J.; Frost, Susan

    2010-01-01

    Flexible structures containing a large number of modes can benefit from adaptive control techniques which are well suited to applications that have unknown modeling parameters and poorly known operating conditions. In this paper, we focus on a direct adaptive control approach that has been extended to handle adaptive rejection of persistent disturbances. We extend our adaptive control theory to accommodate troublesome modal subsystems of a plant that might inhibit the adaptive controller. In some cases the plant does not satisfy the requirements of Almost Strict Positive Realness. Instead, there maybe be a modal subsystem that inhibits this property. This section will present new results for our adaptive control theory. We will modify the adaptive controller with a Residual Mode Filter (RMF) to compensate for the troublesome modal subsystem, or the Q modes. Here we present the theory for adaptive controllers modified by RMFs, with attention to the issue of disturbances propagating through the Q modes. We apply the theoretical results to a flexible structure example to illustrate the behavior with and without the residual mode filter. We have proposed a modified adaptive controller with a residual mode filter. The RMF is used to accommodate troublesome modes in the system that might otherwise inhibit the adaptive controller, in particular the ASPR condition. This new theory accounts for leakage of the disturbance term into the Q modes. A simple three-mode example shows that the RMF can restore stability to an otherwise unstable adaptively controlled system. This is done without modifying the adaptive controller design.

  8. Parallel adaptive mesh refinement for electronic structure calculations

    SciTech Connect

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1996-12-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradients with multigrid preconditioning. We have parallelized our solver using an object-oriented adaptive mesh refinement framework.

  9. Community Structure and Vietnamese Refugee Adaptation: The Significance of Context.

    ERIC Educational Resources Information Center

    Starr, Paul D.; Roberts, Alden E.

    1982-01-01

    Describes research investigating the effects of community structure on the adjustment of Vietnamese refugees in America. Emphasizes how congruence between individual characteristics and characteristics of the receiving community determine successful refugee adaptation to a new environment. (MJL)

  10. Structural Probability Concepts Adapted to Electrical Engineering

    NASA Technical Reports Server (NTRS)

    Steinberg, Eric P.; Chamis, Christos C.

    1994-01-01

    Through the use of equivalent variable analogies, the authors demonstrate how an electrical subsystem can be modeled by an equivalent structural subsystem. This allows the electrical subsystem to be probabilistically analyzed by using available structural reliability computer codes such as NESSUS. With the ability to analyze the electrical subsystem probabilistically, we can evaluate the reliability of systems that include both structural and electrical subsystems. Common examples of such systems are a structural subsystem integrated with a health-monitoring subsystem, and smart structures. Since these systems have electrical subsystems that directly affect the operation of the overall system, probabilistically analyzing them could lead to improved reliability and reduced costs. The direct effect of the electrical subsystem on the structural subsystem is of secondary order and is not considered in the scope of this work.

  11. Gradient-based adaptation of continuous dynamic model structures

    NASA Astrophysics Data System (ADS)

    La Cava, William G.; Danai, Kourosh

    2016-01-01

    A gradient-based method of symbolic adaptation is introduced for a class of continuous dynamic models. The proposed model structure adaptation method starts with the first-principles model of the system and adapts its structure after adjusting its individual components in symbolic form. A key contribution of this work is its introduction of the model's parameter sensitivity as the measure of symbolic changes to the model. This measure, which is essential to defining the structural sensitivity of the model, not only accommodates algebraic evaluation of candidate models in lieu of more computationally expensive simulation-based evaluation, but also makes possible the implementation of gradient-based optimisation in symbolic adaptation. The proposed method is applied to models of several virtual and real-world systems that demonstrate its potential utility.

  12. Adaptive structures for fixed and rotary wing aircraft

    NASA Astrophysics Data System (ADS)

    Martin, Willi; Jänker, Peter; Siemetzki, Markus; Lorkowski, Thomas; Grohmann, Boris; Maier, Rudolf; Maucher, Christoph; Klöppel, Valentin; Enenkl, Bernhard; Roth, Dieter; Hansen, Heinz

    2007-07-01

    Since more than 10 years EADS Innovation Works, which is the corporate research centre of EADS (European Aeronautic Defence and Space Company), is investigating smart materials and adaptive structures for aircraft in cooperation with EADS business units. Focus of research efforts are adaptive systems for shape control, noise reduction and vibration control of both fixed and rotary wing aircraft as well as for lift optimisation of fixed wing aircraft. Two outstanding adaptive systems which have been pushed ahead in cooperation with Airbus Germany and Eurocopter Germany are adaptive servo flaps for helicopter rotor blades and innovative high lift devices for fixed wing aircraft which both were tested in flight for the first time representing world premieres. In this paper various examples of adaptive systems are presented which were developed and realized by EADS in recent years.

  13. Adaptive Crystal Structures: CuAu and NiPt

    NASA Astrophysics Data System (ADS)

    Sanati, M.; Wang, L. G.; Zunger, Alex

    2003-01-01

    We discover that Au-rich Cu1-xAux and Pt-rich Ni1-xPtx contain a composition range in which there is a quasicontinuum of stable, ordered “adaptive structures” made of (001) repeat units of simple structural motifs. This is found by searching ˜3×106 different fcc configurations whose energies are parametrized via a “cluster expansion” of first-principles-calculated total energies of just a few structures. This structural adaptivity is explained in terms of an anisotropic, long-range strain energy.

  14. Dynamics of adaptive structures: Design through simulations

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alexander, S.

    1993-01-01

    The use of a helical bi-morph actuator/sensor concept by mimicking the change of helical waveform in bacterial flagella is perhaps the first application of bacterial motions (living species) to longitudinal deployment of space structures. However, no dynamical considerations were analyzed to explain the waveform change mechanisms. The objective is to review various deployment concepts from the dynamics point of view and introduce the dynamical considerations from the outset as part of design considerations. Specifically, the impact of the incorporation of the combined static mechanisms and dynamic design considerations on the deployment performance during the reconfiguration stage is studied in terms of improved controllability, maneuvering duration, and joint singularity index. It is shown that intermediate configurations during articulations play an important role for improved joint mechanisms design and overall structural deployability.

  15. Structured Adaptive Mesh Refinement Application Infrastructure

    SciTech Connect

    2010-07-15

    SAMRAI is an object-oriented support library for structured adaptice mesh refinement (SAMR) simulation of computational science problems, modeled by systems of partial differential equations (PDEs). SAMRAI is developed and maintained in the Center for Applied Scientific Computing (CASC) under ASCI ITS and PSE support. SAMRAI is used in a variety of application research efforts at LLNL and in academia. These applications are developed in collaboration with SAMRAI development team members.

  16. Adaptive structural vibration control of acoustic deflector

    NASA Astrophysics Data System (ADS)

    Ostasevicius, Vytautas; Palevicius, Arvydas; Ragulskis, Minvydas; Dagys, Donatas; Janusas, Giedrius

    2004-06-01

    Vehicle interior acoustics became an important design criterion. Both legal restrictions and the growing demand for comfort, force car manufacturers to optimize the vibro-acoustic behavior of their products. The main source of noise is, of course, the engine, but sometimes some ill-designed cover or other shell structure inside the car resonates and makes unpredicted noise. To avoid this, we must learn the genesis mechanism of such vibrations, having as subject complex 3D shells. The swift development of computer technologies opens the possibility to numerically predict and optimize the vibrations and noises.

  17. Block-structured adaptive mesh refinement - theory, implementation and application

    SciTech Connect

    Deiterding, Ralf

    2011-01-01

    Structured adaptive mesh refinement (SAMR) techniques can enable cutting-edge simulations of problems governed by conservation laws. Focusing on the strictly hyperbolic case, these notes explain all algorithmic and mathematical details of a technically relevant implementation tailored for distributed memory computers. An overview of the background of commonly used finite volume discretizations for gas dynamics is included and typical benchmarks to quantify accuracy and performance of the dynamically adaptive code are discussed. Large-scale simulations of shock-induced realistic combustion in non-Cartesian geometry and shock-driven fluid-structure interaction with fully coupled dynamic boundary motion demonstrate the applicability of the discussed techniques for complex scenarios.

  18. Adaptive Control of Truss Structures for Gossamer Spacecraft

    NASA Technical Reports Server (NTRS)

    Yang Bong-Jun; Calise, anthony J.; Craig, James I.; Whorton, Mark S.

    2007-01-01

    Neural network-based adaptive control is considered for active control of a highly flexible truss structure which may be used to support solar sail membranes. The objective is to suppress unwanted vibrations in SAFE (Solar Array Flight Experiment) boom, a test-bed located at NASA. Compared to previous tests that restrained truss structures in planar motion, full three dimensional motions are tested. Experimental results illustrate the potential of adaptive control in compensating for nonlinear actuation and modeling error, and in rejecting external disturbances.

  19. Parallel computation of geometry control in adaptive truss structures

    NASA Technical Reports Server (NTRS)

    Ramesh, A. V.; Utku, S.; Wada, B. K.

    1992-01-01

    The fast computation of geometry control in adaptive truss structures involves two distinct parts: the efficient integration of the inverse kinematic differential equations that govern the geometry control and the fast computation of the Jacobian, which appears on the right-hand-side of the inverse kinematic equations. This paper present an efficient parallel implementation of the Jacobian computation on an MIMD machine. Large speedup from the parallel implementation is obtained, which reduces the Jacobian computation to an O(M-squared/n) procedure on an n-processor machine, where M is the number of members in the adaptive truss. The parallel algorithm given here is a good candidate for on-line geometry control of adaptive structures using attached processors.

  20. An Adaptive Evaluation Structure for Computer-Based Instruction.

    ERIC Educational Resources Information Center

    Welsh, William A.

    Adaptive Evaluation Structure (AES) is a set of linked computer programs designed to increase the effectiveness of interactive computer-assisted instruction at the college level. The package has four major features, the first of which is based on a prior cognitive inventory and on the accuracy and pace of student responses. AES adjusts materials…

  1. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  2. Coarse-node computations with an adaptive node structure

    SciTech Connect

    Tzanos, C.P.

    1988-01-01

    The analysis with COMMIX of liquid metal reactor (LMR) intermediate heat exchanger (IHX) transients that are characterized by low flows, and especially imbalanced low flows, shows that if a coarse-node structure is used the predicted temperatures are significantly different than those given by a fine-node structure. If a fine-node structure is used, for problems that involve a large part of the plant, the computation time becomes excessive. This paper presents an improved version of an adaptive node structure. At this stage this version has been applied only to one-dimensional problems.

  3. Adaptive-Control Experiments On A Large Flexible Structure

    NASA Technical Reports Server (NTRS)

    Ih, Che-Hang C.; Bayard, David S.; Wang, Shyh J.; Eldred, Daniel B.

    1990-01-01

    Antennalike flexible structure built for research in advanced technology including suppression of vibrations and control of initial deflections. Structure instrumented with sensors and actuators connected to digital electronic control system, programmed with control algorithms to be tested. Particular attention in this research focused on direct model-reference adaptive-control algorithm based on command generator tracker theory. Built to exhibit multiple vibrational modes, low modal frequencies, and low structural damping. Made three-dimensional so complicated interactions among components of structure and control system investigated.

  4. Structural disorder provides increased adaptability for vesicle trafficking pathways.

    PubMed

    Pietrosemoli, Natalia; Pancsa, Rita; Tompa, Peter

    2013-01-01

    Vesicle trafficking systems play essential roles in the communication between the organelles of eukaryotic cells and also between cells and their environment. Endocytosis and the late secretory route are mediated by clathrin-coated vesicles, while the COat Protein I and II (COPI and COPII) routes stand for the bidirectional traffic between the ER and the Golgi apparatus. Despite similar fundamental organizations, the molecular machinery, functions, and evolutionary characteristics of the three systems are very different. In this work, we compiled the basic functional protein groups of the three main routes for human and yeast and analyzed them from the structural disorder perspective. We found similar overall disorder content in yeast and human proteins, confirming the well-conserved nature of these systems. Most functional groups contain highly disordered proteins, supporting the general importance of structural disorder in these routes, although some of them seem to heavily rely on disorder, while others do not. Interestingly, the clathrin system is significantly more disordered (~23%) than the other two, COPI (~9%) and COPII (~8%). We show that this structural phenomenon enhances the inherent plasticity and increased evolutionary adaptability of the clathrin system, which distinguishes it from the other two routes. Since multi-functionality (moonlighting) is indicative of both plasticity and adaptability, we studied its prevalence in vesicle trafficking proteins and correlated it with structural disorder. Clathrin adaptors have the highest capability for moonlighting while also comprising the most highly disordered members. The ability to acquire tissue specific functions was also used to approach adaptability: clathrin route genes have the most tissue specific exons encoding for protein segments enriched in structural disorder and interaction sites. Overall, our results confirm the general importance of structural disorder in vesicle trafficking and suggest

  5. Adaptive control experiment with a large flexible structure

    NASA Technical Reports Server (NTRS)

    Ih, Che-Hang Charles; Bayard, David S.; Wang, Shyh Jong; Eldred, Daniel B.

    1988-01-01

    A large space antenna-like ground experiment structure has been developed for conducting research and validation of advanced control technology. A set of proof-of-concept adaptive control experiments for transient and initial deflection regulation with a small set of sensors and actuators were conducted. Very limited knowledge of the plant dynamics and its environment was used in the design of the adaptive controller so that performance could be demonstrated under conditions of gross underlying uncertainties. High performance has been observed under such stringent conditions. These experiments have established a baseline for future studies involving more complex hardware and environmental conditions, and utilizing additional sets of sensors and actuators.

  6. Adaptive control of large space structures using recursive lattice filters

    NASA Technical Reports Server (NTRS)

    Sundararajan, N.; Goglia, G. L.

    1985-01-01

    The use of recursive lattice filters for identification and adaptive control of large space structures is studied. Lattice filters were used to identify the structural dynamics model of the flexible structures. This identification model is then used for adaptive control. Before the identified model and control laws are integrated, the identified model is passed through a series of validation procedures and only when the model passes these validation procedures is control engaged. This type of validation scheme prevents instability when the overall loop is closed. Another important area of research, namely that of robust controller synthesis, was investigated using frequency domain multivariable controller synthesis methods. The method uses the Linear Quadratic Guassian/Loop Transfer Recovery (LQG/LTR) approach to ensure stability against unmodeled higher frequency modes and achieves the desired performance.

  7. Structured near-optimal channel-adapted quantum error correction

    NASA Astrophysics Data System (ADS)

    Fletcher, Andrew S.; Shor, Peter W.; Win, Moe Z.

    2008-01-01

    We present a class of numerical algorithms which adapt a quantum error correction scheme to a channel model. Given an encoding and a channel model, it was previously shown that the quantum operation that maximizes the average entanglement fidelity may be calculated by a semidefinite program (SDP), which is a convex optimization. While optimal, this recovery operation is computationally difficult for long codes. Furthermore, the optimal recovery operation has no structure beyond the completely positive trace-preserving constraint. We derive methods to generate structured channel-adapted error recovery operations. Specifically, each recovery operation begins with a projective error syndrome measurement. The algorithms to compute the structured recovery operations are more scalable than the SDP and yield recovery operations with an intuitive physical form. Using Lagrange duality, we derive performance bounds to certify near-optimality.

  8. Adaptive control of large space structures using recursive lattice filters

    NASA Technical Reports Server (NTRS)

    Goglia, G. L.

    1985-01-01

    The use of recursive lattice filters for identification and adaptive control of large space structures was studied. Lattice filters are used widely in the areas of speech and signal processing. Herein, they are used to identify the structural dynamics model of the flexible structures. This identified model is then used for adaptive control. Before the identified model and control laws are integrated, the identified model is passed through a series of validation procedures and only when the model passes these validation procedures control is engaged. This type of validation scheme prevents instability when the overall loop is closed. The results obtained from simulation were compared to those obtained from experiments. In this regard, the flexible beam and grid apparatus at the Aerospace Control Research Lab (ACRL) of NASA Langley Research Center were used as the principal candidates for carrying out the above tasks. Another important area of research, namely that of robust controller synthesis, was investigated using frequency domain multivariable controller synthesis methods.

  9. Recent Developments in Smart Adaptive Structures for Solar Sailcraft

    NASA Technical Reports Server (NTRS)

    Worton, M. S.; Kim, Y. K.; Oakley, J.; Adetona, O.; Keel, L. H.

    2007-01-01

    The "Smart Adaptive Structures for Solar Sailcraft" development activity at MSFC has investigated issues associated with understanding how to model and scale the subsystem and multi-body system dynamics of a gossamer solar sailcraft with the objective of designing sailcraft attitude control systems. This research and development activity addressed three key tasks that leveraged existing facilities and core competencies of MSFC to investigate dynamics and control issues of solar sails. Key aspects of this effort included modeling and testing of a 30 m deployable boom; modeling of the multi-body system dynamics of a gossamer sailcraft; investigation of control-structures interaction for gossamer sailcraft; and development and experimental demonstration of adaptive control technologies to mitigate control-structures interaction.

  10. An adaptive learning control system for large flexible structures

    NASA Technical Reports Server (NTRS)

    Thau, F. E.

    1985-01-01

    The objective of the research has been to study the design of adaptive/learning control systems for the control of large flexible structures. In the first activity an adaptive/learning control methodology for flexible space structures was investigated. The approach was based on using a modal model of the flexible structure dynamics and an output-error identification scheme to identify modal parameters. In the second activity, a least-squares identification scheme was proposed for estimating both modal parameters and modal-to-actuator and modal-to-sensor shape functions. The technique was applied to experimental data obtained from the NASA Langley beam experiment. In the third activity, a separable nonlinear least-squares approach was developed for estimating the number of excited modes, shape functions, modal parameters, and modal amplitude and velocity time functions for a flexible structure. In the final research activity, a dual-adaptive control strategy was developed for regulating the modal dynamics and identifying modal parameters of a flexible structure. A min-max approach was used for finding an input to provide modal parameter identification while not exceeding reasonable bounds on modal displacement.

  11. Software abstractions and computational issues in parallel structure adaptive mesh methods for electronic structure calculations

    SciTech Connect

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1997-05-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.

  12. Adaptations in Electronic Structure Calculations in Heterogeneous Environments

    SciTech Connect

    Talamudupula, Sai

    2011-01-01

    Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model is limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.

  13. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations. PMID:15446426

  14. Comparative population genetic structures and local adaptation of two mutualists.

    PubMed

    Anderson, Bruce; Olivieri, Isabelle; Lourmas, Mathieu; Stewart, Barbara A

    2004-08-01

    Similar patterns of dispersal and gene flow between closely associated organisms may promote local adaptation and coevolutionary processes. We compare the genetic structures of the two species of a plant genus (Roridula gorgonias and R. dentata) and their respective obligately associated hemipteran mutualists (Pameridea roridulae and P. marlothi) using allozymes. In addition, we determine whether genetic structure is related to differences in host choice by Pameridea. Allozyme variation was found to be very structured among plant populations but less so among hemipteran populations. Strong genetic structuring among hemipteran populations was only evident when large distances isolated the plant populations on which they live. Although genetic distances among plant populations were correlated with genetic distances among hemipteran populations, genetic distances of both plants and hemipterans were better correlated with geographic distance. Because Roridula and Pameridea have different scales of gene flow, adaptation at the local population level is unlikely. However, the restricted gene flow of both plants and hemipterans could enable adaptation to occur at a regional level. In choice experiments, the hemipteran (Pameridea) has a strong preference for its carnivorous host plant (Roridula) above unrelated host plants. Pameridea also prefers its host species to its closely related sister species. Specialization at the specific level is likely to reinforce cospeciation processes in this mutualism. However, Pameridea does not exhibit intraspecific preferences toward plants from their natal populations above plants from isolated, non-natal populations.

  15. Adaptive sensor array algorithm for structural health monitoring of helmet

    NASA Astrophysics Data System (ADS)

    Zou, Xiaotian; Tian, Ye; Wu, Nan; Sun, Kai; Wang, Xingwei

    2011-04-01

    The adaptive neural network is a standard technique used in nonlinear system estimation and learning applications for dynamic models. In this paper, we introduced an adaptive sensor fusion algorithm for a helmet structure health monitoring system. The helmet structure health monitoring system is used to study the effects of ballistic/blast events on the helmet and human skull. Installed inside the helmet system, there is an optical fiber pressure sensors array. After implementing the adaptive estimation algorithm into helmet system, a dynamic model for the sensor array has been developed. The dynamic response characteristics of the sensor network are estimated from the pressure data by applying an adaptive control algorithm using artificial neural network. With the estimated parameters and position data from the dynamic model, the pressure distribution of the whole helmet can be calculated following the Bazier Surface interpolation method. The distribution pattern inside the helmet will be very helpful for improving helmet design to provide better protection to soldiers from head injuries.

  16. Engaging stakeholders for adaptive management using structured decision analysis

    USGS Publications Warehouse

    Irwin, Elise R.; Kathryn, D.; Kennedy, Mickett

    2009-01-01

    Adaptive management is different from other types of management in that it includes all stakeholders (versus only policy makers) in the process, uses resource optimization techniques to evaluate competing objectives, and recognizes and attempts to reduce uncertainty inherent in natural resource systems. Management actions are negotiated by stakeholders, monitored results are compared to predictions of how the system should respond, and management strategies are adjusted in a “monitor-compare-adjust” iterative routine. Many adaptive management projects fail because of the lack of stakeholder identification, engagement, and continued involvement. Primary reasons for this vary but are usually related to either stakeholders not having ownership (or representation) in decision processes or disenfranchisement of stakeholders after adaptive management begins. We present an example in which stakeholders participated fully in adaptive management of a southeastern regulated river. Structured decision analysis was used to define management objectives and stakeholder values and to determine initial flow prescriptions. The process was transparent, and the visual nature of the modeling software allowed stakeholders to see how their interests and values were represented in the decision process. The development of a stakeholder governance structure and communication mechanism has been critical to the success of the project.

  17. Temporal and structural heterogeneities emerging in adaptive temporal networks

    NASA Astrophysics Data System (ADS)

    Aoki, Takaaki; Rocha, Luis E. C.; Gross, Thilo

    2016-04-01

    We introduce a model of adaptive temporal networks whose evolution is regulated by an interplay between node activity and dynamic exchange of information through links. We study the model by using a master equation approach. Starting from a homogeneous initial configuration, we show that temporal and structural heterogeneities, characteristic of real-world networks, spontaneously emerge. This theoretically tractable model thus contributes to the understanding of the dynamics of human activity and interaction networks.

  18. A general framework for adaptive processing of data structures.

    PubMed

    Frasconi, P; Gori, M; Sperduti, A

    1998-01-01

    A structured organization of information is typically required by symbolic processing. On the other hand, most connectionist models assume that data are organized according to relatively poor structures, like arrays or sequences. The framework described in this paper is an attempt to unify adaptive models like artificial neural nets and belief nets for the problem of processing structured information. In particular, relations between data variables are expressed by directed acyclic graphs, where both numerical and categorical values coexist. The general framework proposed in this paper can be regarded as an extension of both recurrent neural networks and hidden Markov models to the case of acyclic graphs. In particular we study the supervised learning problem as the problem of learning transductions from an input structured space to an output structured space, where transductions are assumed to admit a recursive hidden statespace representation. We introduce a graphical formalism for representing this class of adaptive transductions by means of recursive networks, i.e., cyclic graphs where nodes are labeled by variables and edges are labeled by generalized delay elements. This representation makes it possible to incorporate the symbolic and subsymbolic nature of data. Structures are processed by unfolding the recursive network into an acyclic graph called encoding network. In so doing, inference and learning algorithms can be easily inherited from the corresponding algorithms for artificial neural networks or probabilistic graphical model.

  19. Segmentation of branching vascular structures using adaptive subdivision surface fitting

    NASA Astrophysics Data System (ADS)

    Kitslaar, Pieter H.; van't Klooster, Ronald; Staring, Marius; Lelieveldt, Boudewijn P. F.; van der Geest, Rob J.

    2015-03-01

    This paper describes a novel method for segmentation and modeling of branching vessel structures in medical images using adaptive subdivision surfaces fitting. The method starts with a rough initial skeleton model of the vessel structure. A coarse triangular control mesh consisting of hexagonal rings and dedicated bifurcation elements is constructed from this skeleton. Special attention is paid to ensure a topological sound control mesh is created around the bifurcation areas. Then, a smooth tubular surface is obtained from this coarse mesh using a standard subdivision scheme. This subdivision surface is iteratively fitted to the image. During the fitting, the target update locations of the subdivision surface are obtained using a scanline search along the surface normals, finding the maximum gradient magnitude (of the imaging data). In addition to this surface fitting framework, we propose an adaptive mesh refinement scheme. In this step the coarse control mesh topology is updated based on the current segmentation result, enabling adaptation to varying vessel lumen diameters. This enhances the robustness and flexibility of the method and reduces the amount of prior knowledge needed to create the initial skeletal model. The method was applied to publicly available CTA data from the Carotid Bifurcation Algorithm Evaluation Framework resulting in an average dice index of 89.2% with the ground truth. Application of the method to the complex vascular structure of a coronary artery tree in CTA and to MRI images were performed to show the versatility and flexibility of the proposed framework.

  20. Model of adaptive temporal development of structured finite systems

    NASA Astrophysics Data System (ADS)

    Patera, Jiri; Shaw, Gordon L.; Slansky, Richard; Leng, Xiaodan

    1989-07-01

    The weight systems of level-zero representations of affine Kac-Moody algebras provide an appropriate kinematical framework for studying structured finite systems with adaptive temporal development. Much of the structure is determined by Lie algebra theory, so it is possible to restrict greatly the connection space and analytic results are possible. The time development of these systems often evolves to cyclic temporal-spatial patterns, depending on the definition of the dynamics. The purpose of this paper is to set up the mathematical formalism for this ``memory in Lie algebras'' class of models. An illustration is used to show the kinds of complex behavior that occur in simple cases.

  1. Passively Adaptive Inflatable Structure for the Shooting Star Experiment

    NASA Technical Reports Server (NTRS)

    Tinker, Michael L..

    1998-01-01

    An inflatable structural system is described for the Shooting Star Experiment that is a technology demonstrator flight for solar thermal propulsion. The inflatable structure is a pressurized assembly used in orbit to support a fresnel lens for focusing sunlight into a thermal storage engine. When the engine temperature reaches a preset level, the propellant is injected into the storage engine, absorbs heat from a heat exchanger, and is expanded through the nozzle to produce thrust. The inflatable structure is an adaptive system in that a regulator and relief valve are utilized to maintain pressure within design limits during the full range of orbital conditions. Further, the polyimide film material used for construction of the inflatable is highly nonlinear, with modulus varying as a function of frequency, temperature, and level of excitation. A series of tests is described for characterizing the structure in response to various operating conditions.

  2. Decentralized adaptive control designs and microstrip antennas for smart structures

    NASA Astrophysics Data System (ADS)

    Khorrami, Farshad; Jain, Sandeep; Das, Nirod K.

    1996-05-01

    Smart structures lend themselves naturally to a decentralized control design framework, especially with adaptation mechanisms. The main reason being that it is highly undesirable to connect all the sensors and actuators in a large structure to a central processor. It is rather desirable to have local decision-making at each smart patch. Furthermore, this local controllers should be easily `expandable' to `contractible.' This corresponds to the fact that addition/deletion of several smart patches should not require a total redesign of the control system. The decentralized control strategies advocated in this paper are of expandable/contractible type. On another front, we are considering utilization of micro-strip antennas for power transfer to and from smart structures. We have made preliminary contributions in this direction and further developments are underway. These approaches are being pursued for active vibration damping and noise cancellation via piezoelectric ceramics although the methodology is general enough to be applicable to other type of active structures.

  3. Structural basis for adaptation of lactobacilli to gastrointestinal mucus.

    PubMed

    Etzold, Sabrina; Kober, Olivia I; Mackenzie, Donald A; Tailford, Louise E; Gunning, A Patrick; Walshaw, John; Hemmings, Andrew M; Juge, Nathalie

    2014-03-01

    The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the underpinning mechanisms of these interactions are not understood. Here, we provide structural and functional insights into the canonical mucus-binding protein (MUB), a multi-repeat cell-surface adhesin found in Lactobacillus inhabitants of the GI tract. X-ray crystallography together with small-angle X-ray scattering demonstrated a 'beads on a string' arrangement of repeats, generating 174 nm long protein fibrils, as shown by atomic force microscopy. Each repeat consists of tandemly arranged Ig- and mucin-binding protein (MucBP) modules. The binding of full-length MUB was confined to mucus via multiple interactions involving terminal sialylated mucin glycans. While individual MUB domains showed structural similarity to fimbrial proteins from Gram-positive pathogens, the particular organization of MUB provides a structural explanation for the mechanisms in which lactobacilli have adapted to their host niche by maximizing interactions with the mucus receptors, potentiating the retention of bacteria within the mucus layer. Together, this study reveals functional and structural features which may affect tropism of microbes across mucus and along the GI tract, providing unique insights into the mechanisms adopted by commensals and probiotics to adapt to the mucosal environment. PMID:24373178

  4. Direct Adaptive Aircraft Control Using Dynamic Cell Structure Neural Networks

    NASA Technical Reports Server (NTRS)

    Jorgensen, Charles C.

    1997-01-01

    A Dynamic Cell Structure (DCS) Neural Network was developed which learns topology representing networks (TRNS) of F-15 aircraft aerodynamic stability and control derivatives. The network is integrated into a direct adaptive tracking controller. The combination produces a robust adaptive architecture capable of handling multiple accident and off- nominal flight scenarios. This paper describes the DCS network and modifications to the parameter estimation procedure. The work represents one step towards an integrated real-time reconfiguration control architecture for rapid prototyping of new aircraft designs. Performance was evaluated using three off-line benchmarks and on-line nonlinear Virtual Reality simulation. Flight control was evaluated under scenarios including differential stabilator lock, soft sensor failure, control and stability derivative variations, and air turbulence.

  5. Strategic Defense Initiative Organization adaptive structures program overview

    NASA Astrophysics Data System (ADS)

    Obal, Michael; Sater, Janet M.

    In the currently envisioned architecture none of the Strategic Defense System (SDS) elements to be deployed will receive scheduled maintenance. Assessments of performance capability due to changes caused by the uncertain effects of environments will be difficult, at best. In addition, the system will have limited ability to adjust in order to maintain its required performance levels. The Materials and Structures Office of the Strategic Defense Initiative Organization (SDIO) has begun to address solutions to these potential difficulties via an adaptive structures technology program that combines health and environment monitoring with static and dynamic structural control. Conceivable system benefits include improved target tracking and hit-to-kill performance, on-orbit system health monitoring and reporting, and threat attack warning and assessment.

  6. Adaptivity and smart algorithms for fluid-structure interaction

    NASA Technical Reports Server (NTRS)

    Oden, J. Tinsley

    1990-01-01

    This paper reviews new approaches in CFD which have the potential for significantly increasing current capabilities of modeling complex flow phenomena and of treating difficult problems in fluid-structure interaction. These approaches are based on the notions of adaptive methods and smart algorithms, which use instantaneous measures of the quality and other features of the numerical flowfields as a basis for making changes in the structure of the computational grid and of algorithms designed to function on the grid. The application of these new techniques to several problem classes are addressed, including problems with moving boundaries, fluid-structure interaction in high-speed turbine flows, flow in domains with receding boundaries, and related problems.

  7. Self-Adaptive Stepsize Search Applied to Optimal Structural Design

    NASA Astrophysics Data System (ADS)

    Nolle, L.; Bland, J. A.

    Structural engineering often involves the design of space frames that are required to resist predefined external forces without exhibiting plastic deformation. The weight of the structure and hence the weight of its constituent members has to be as low as possible for economical reasons without violating any of the load constraints. Design spaces are usually vast and the computational costs for analyzing a single design are usually high. Therefore, not every possible design can be evaluated for real-world problems. In this work, a standard structural design problem, the 25-bar problem, has been solved using self-adaptive stepsize search (SASS), a relatively new search heuristic. This algorithm has only one control parameter and therefore overcomes the drawback of modern search heuristics, i.e. the need to first find a set of optimum control parameter settings for the problem at hand. In this work, SASS outperforms simulated-annealing, genetic algorithms, tabu search and ant colony optimization.

  8. Finite element simulation of adaptive aerospace structures with SMA actuators

    NASA Astrophysics Data System (ADS)

    Frautschi, Jason; Seelecke, Stefan

    2003-07-01

    The particular demands of aerospace engineering have spawned many of the developments in the field of adaptive structures. Shape memory alloys are particularly attractive as actuators in these types of structures due to their large strains, high specific work output and potential for structural integration. However, the requisite extensive physical testing has slowed development of potential applications and highlighted the need for a simulation tool for feasibility studies. In this paper we present an implementation of an extended version of the M'ller-Achenbach SMA model into a commercial finite element code suitable for such studies. Interaction between the SMA model and the solution algorithm for the global FE equations is thoroughly investigated with respect to the effect of tolerances and time step size on convergence, computational cost and accuracy. Finally, a simulation of a SMA-actuated flexible trailing edge of an aircraft wing modeled with beam elements is presented.

  9. Rapid Structured Volume Grid Smoothing and Adaption Technique

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.

    2006-01-01

    A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reductions in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.

  10. Controller-structure interaction compensation using adaptive residual mode filters

    NASA Technical Reports Server (NTRS)

    Davidson, Roger A.; Balas, Mark J.

    1990-01-01

    It is not feasible to construct controllers for large space structures or large scale systems (LSS's) which are of the same order as the structures. The complexity of the dynamics of these systems is such that full knowledge of its behavior cannot by processed by today's controller design methods. The controller for system performance of such a system is therefore based on a much smaller reduced-order model (ROM). Unfortunately, the interaction between the LSS and the ROM-based controller can produce instabilities in the closed-loop system due to the unmodeled dynamics of the LSS. Residual mode filters (RMF's) allow the systematic removal of these instabilities in a matter which does not require a redesign of the controller. In addition RMF's have a strong theoretical basis. As simple first- or second-order filters, the RMF CSI compensation technique is at once modular, simple and highly effective. RMF compensation requires knowledge of the dynamics of the system modes which resulted in the previous closed-loop instabilities (the residual modes), but this information is sometimes known imperfectly. An adaptive, self-tuning RMF design, which compensates for uncertainty in the frequency of the residual mode, has been simulated using continuous-time and discrete-time models of a flexible robot manipulator. Work has also been completed on the discrete-time experimental implementation on the Martin Marietta flexible robot manipulator experiment. This paper will present the results of that work on adaptive, self-tuning RMF's, and will clearly show the advantage of this adaptive compensation technique for controller-structure interaction (CSI) instabilities in actively-controlled LSS's.

  11. An adaptive identification and control scheme for large space structures

    NASA Technical Reports Server (NTRS)

    Carroll, J. V.

    1988-01-01

    A unified identification and control scheme capable of achieving space at form performance objectives under nominal or failure conditions is described. Preliminary results are also presented, showing that the methodology offers much promise for effective robust control of large space structures. The control method is a multivariable, adaptive, output predictive controller called Model Predictive Control (MPC). MPC uses a state space model and input reference trajectories of set or tracking points to adaptively generate optimum commands. For a fixed model, MPC processes commands with great efficiency, and is also highly robust. A key feature of MPC is its ability to control either nonminimum phase or open loop unstable systems. As an output controller, MPC does not explicitly require full state feedback, as do most multivariable (e.g., Linear Quadratic) methods. Its features are very useful in LSS operations, as they allow non-collocated actuators and sensors. The identification scheme is based on canonical variate analysis (CVA) of input and output data. The CVA technique is particularly suited for the measurement and identification of structural dynamic processes - that is, unsteady transient or dynamically interacting processes such as between aerodynamics and structural deformation - from short, noisy data. CVA is structured so that the identification can be done in real or near real time, using computationally stable algorithms. Modeling LSS dynamics in 1-g laboratories has always been a major impediment not only to understanding their behavior in orbit, but also to controlling it. In cases where the theoretical model is not confirmed, current methods provide few clues concerning additional dynamical relationships that are not included in the theoretical models. CVA needs no a priori model data, or structure; all statistically significant dynamical states are determined using natural, entropy-based methods. Heretofore, a major limitation in applying adaptive

  12. Protein structure refinement with adaptively restrained homologous replicas.

    PubMed

    Della Corte, Dennis; Wildberg, André; Schröder, Gunnar F

    2016-09-01

    A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail. Proteins 2016; 84(Suppl 1):302-313. © 2015 Wiley Periodicals, Inc. PMID:26441154

  13. Phylogenetic constraints and adaptation explain food-web structure.

    PubMed

    Cattin, Marie-France; Bersier, Louis-Félix; Banasek-Richter, Carolin; Baltensperger, Richard; Gabriel, Jean-Pierre

    2004-02-26

    Food webs are descriptions of who eats whom in an ecosystem. Although extremely complex and variable, their structure possesses basic regularities. A fascinating question is to find a simple model capturing the underlying processes behind these repeatable patterns. Until now, two models have been devised for the description of trophic interactions within a natural community. Both are essentially based on the concept of ecological niche, with the consumers organized along a single niche dimension; for example, prey size. Unfortunately, they fail to describe adequately recent and high-quality data. Here, we propose a new model built on the hypothesis that any species' diet is the consequence of phylogenetic constraints and adaptation. Simple rules incorporating both concepts yield food webs whose structure is very close to real data. Consumers are organized in groups forming a nested hierarchy, which better reflects the complexity and multidimensionality of most natural systems.

  14. Novel MRE/CFRP sandwich structures for adaptive vibration control

    NASA Astrophysics Data System (ADS)

    Kozlowska, J.; Boczkowska, A.; Czulak, A.; Przybyszewski, B.; Holeczek, K.; Stanik, R.; Gude, M.

    2016-03-01

    The aim of this work was the development of sandwich structures formed by embedding magnetorheological elastomers (MRE) between constrained layers of carbon fibre-reinforced plastic (CFRP) laminates. The MREs were obtained by mechanical stirring of a reactive mixture of substrates with carbonyl-iron particles, followed by orienting the particles into chains under an external magnetic field. Samples with particle volume fractions of 11.5% and 33% were examined. The CFRP/MRE sandwich structures were obtained by compressing MREs samples between two CFRP laminates composed. The used A.S.SET resin was in powder form and the curing process was carried out during pressing with MRE. The microstructure of the manufactured sandwich beams was inspected using SEM. Moreover, the rheological and damping properties of the examined materials with and without a magnetic field were experimentally investigated. In addition, the free vibration responses of the adaptive three-layered MR beams were studied at different fixed magnetic field levels. The free vibration tests revealed that an applied non-homogeneous magnetic field causes a shift in natural frequency values and a reduction in the vibration amplitudes of the CFRP/MRE adaptive beams. The reduction in vibration amplitude was attributed mainly to the stiffening effect of the MRE core and only a minor contribution was made by the enhanced damping capacity, which was evidenced by the variation in damping ratio values.

  15. Adaptation of Block-Structured Adaptive Mesh Refinement to Particle-In-Cell simulations

    NASA Astrophysics Data System (ADS)

    Vay, Jean-Luc; Colella, Phillip; McCorquodale, Peter; Friedman, Alex; Grote, Dave

    2001-10-01

    Particle-In-Cell (PIC) methods which solve the Maxwell equations (or a simplification) on a regular Cartesian grid are routinely used to simulate plasma and particle beam systems. Several techniques have been developed to accommodate irregular boundaries and scale variations. We describe here an ongoing effort to adapt the block-structured Adaptive Mesh Refinement (AMR) algorithm (http://seesar.lbl.gov/AMR/) to the Particle-In-Cell method. The AMR technique connects grids having different resolutions, using interpolation. Special care has to be taken to avoid the introduction of spurious forces close to the boundary of the inner, high-resolution grid, or at least to reduce such forces to an acceptable level. The Berkeley AMR library CHOMBO has been modified and coupled to WARP3d (D.P. Grote et al., Fusion Engineering and Design), 32-33 (1996), 193-200, a PIC code which is used for the development of high current accelerators for Heavy Ion Fusion. The methods and preliminary results will be presented.

  16. Distributed adaptive diagnosis of sensor faults using structural response data

    NASA Astrophysics Data System (ADS)

    Dragos, Kosmas; Smarsly, Kay

    2016-10-01

    The reliability and consistency of wireless structural health monitoring (SHM) systems can be compromised by sensor faults, leading to miscalibrations, corrupted data, or even data loss. Several research approaches towards fault diagnosis, referred to as ‘analytical redundancy’, have been proposed that analyze the correlations between different sensor outputs. In wireless SHM, most analytical redundancy approaches require centralized data storage on a server for data analysis, while other approaches exploit the on-board computing capabilities of wireless sensor nodes, analyzing the raw sensor data directly on board. However, using raw sensor data poses an operational constraint due to the limited power resources of wireless sensor nodes. In this paper, a new distributed autonomous approach towards sensor fault diagnosis based on processed structural response data is presented. The inherent correlations among Fourier amplitudes of acceleration response data, at peaks corresponding to the eigenfrequencies of the structure, are used for diagnosis of abnormal sensor outputs at a given structural condition. Representing an entirely data-driven analytical redundancy approach that does not require any a priori knowledge of the monitored structure or of the SHM system, artificial neural networks (ANN) are embedded into the sensor nodes enabling cooperative fault diagnosis in a fully decentralized manner. The distributed analytical redundancy approach is implemented into a wireless SHM system and validated in laboratory experiments, demonstrating the ability of wireless sensor nodes to self-diagnose sensor faults accurately and efficiently with minimal data traffic. Besides enabling distributed autonomous fault diagnosis, the embedded ANNs are able to adapt to the actual condition of the structure, thus ensuring accurate and efficient fault diagnosis even in case of structural changes.

  17. Design, realization and structural testing of a compliant adaptable wing

    NASA Astrophysics Data System (ADS)

    Molinari, G.; Quack, M.; Arrieta, A. F.; Morari, M.; Ermanni, P.

    2015-10-01

    This paper presents the design, optimization, realization and testing of a novel wing morphing concept, based on distributed compliance structures, and actuated by piezoelectric elements. The adaptive wing features ribs with a selectively compliant inner structure, numerically optimized to achieve aerodynamically efficient shape changes while simultaneously withstanding aeroelastic loads. The static and dynamic aeroelastic behavior of the wing, and the effect of activating the actuators, is assessed by means of coupled 3D aerodynamic and structural simulations. To demonstrate the capabilities of the proposed morphing concept and optimization procedure, the wings of a model airplane are designed and manufactured according to the presented approach. The goal is to replace conventional ailerons, thus to achieve controllability in roll purely by morphing. The mechanical properties of the manufactured components are characterized experimentally, and used to create a refined and correlated finite element model. The overall stiffness, strength, and actuation capabilities are experimentally tested and successfully compared with the numerical prediction. To counteract the nonlinear hysteretic behavior of the piezoelectric actuators, a closed-loop controller is implemented, and its capability of accurately achieving the desired shape adaptation is evaluated experimentally. Using the correlated finite element model, the aeroelastic behavior of the manufactured wing is simulated, showing that the morphing concept can provide sufficient roll authority to allow controllability of the flight. The additional degrees of freedom offered by morphing can be also used to vary the plane lift coefficient, similarly to conventional flaps. The efficiency improvements offered by this technique are evaluated numerically, and compared to the performance of a rigid wing.

  18. Augmented mandibular bone structurally adapts to functional loading.

    PubMed

    Verhoeven, J W; Ruijter, J M; Koole, R; de Putter, C; Terlou, M; Cune, M S

    2013-12-01

    Long-term changes in trabecular bone structure during the 10 years following onlay grafting with simultaneous mandibular implant placement were studied. Extraoral radiographs of both mandibular sides in eight patients were taken regularly. Bone structure was analysed using a custom-written image analysis program. Parameters studied were trabecular area and perimeter and marrow cavity area and perimeter. After skeletonisation of the trabecular network, the number of end points and branching points, skeleton length, and branch angle were determined. The observed structural changes agree with the development of a more complex and more delicate or fine osseous structure. The bone shows more trabecular branching. All changes are most pronounced in the graft spongiosa, but are also found in the graft cortex and in the original mandible. The mean trabecular branch angle becomes more horizontal. The applied technique can be used to analyse long-term changes in the architecture of bone grafts. Changes found in the graft architecture correspond to changes expected after functional adaptation to loading. PMID:23791249

  19. On Cognition, Structured Sequence Processing, and Adaptive Dynamical Systems

    NASA Astrophysics Data System (ADS)

    Petersson, Karl Magnus

    2008-11-01

    Cognitive neuroscience approaches the brain as a cognitive system: a system that functionally is conceptualized in terms of information processing. We outline some aspects of this concept and consider a physical system to be an information processing device when a subclass of its physical states can be viewed as representational/cognitive and transitions between these can be conceptualized as a process operating on these states by implementing operations on the corresponding representational structures. We identify a generic and fundamental problem in cognition: sequentially organized structured processing. Structured sequence processing provides the brain, in an essential sense, with its processing logic. In an approach addressing this problem, we illustrate how to integrate levels of analysis within a framework of adaptive dynamical systems. We note that the dynamical system framework lends itself to a description of asynchronous event-driven devices, which is likely to be important in cognition because the brain appears to be an asynchronous processing system. We use the human language faculty and natural language processing as a concrete example through out.

  20. Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

    PubMed

    Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

    2011-11-01

    The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

  1. Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

    PubMed

    Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

    2011-11-01

    The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures. PMID:21827423

  2. Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation

    PubMed Central

    Mboup, Mamadou; Bahri, Bochra; Leconte, Marc; De Vallavieille-Pope, Claude; Kaltz, Oliver; Enjalbert, Jérôme

    2012-01-01

    Environmental heterogeneity influences coevolution and local adaptation in host–parasite systems. This also concerns applied issues, because the geographic range of parasites may depend on their capacity to adapt to abiotic conditions. We studied temperature-specific adaptation in the wheat yellow/stripe rust pathogen, Puccinia striiformis f.sp. tritici (PST). Using laboratory experiments, PST isolates from northern and southern France were studied for their ability to germinate and to infect bread and durum wheat cultivars over a temperature gradient. Pathogen origin × temperature interactions for infectivity and germination rate suggest local adaptation to high- versus low-temperature regimes in south and north. Competition experiments in southern and northern field sites showed a general competitive advantage of southern over northern isolates. This advantage was particularly pronounced in the southern ‘home’ site, consistent with a model integrating laboratory infectivity and field temperature variation. The stable PST population structure in France likely reflects adaptation to ecological and genetic factors: persistence of southern PST may be due to adaptation to the warmer Mediterranean climate; and persistence of northern PST can be explained by adaptation to commonly used cultivars, for which southern isolates are lacking the relevant virulence genes. Thus, understanding the role of temperature-specific adaptations may help to improve forecast models or breeding programmes. PMID:25568055

  3. Robust adaptive vibration control of a flexible structure.

    PubMed

    Khoshnood, A M; Moradi, H M

    2014-07-01

    Different types of L1 adaptive control systems show that using robust theories with adaptive control approaches has produced high performance controllers. In this study, a model reference adaptive control scheme considering robust theories is used to propose a practical control system for vibration suppression of a flexible launch vehicle (FLV). In this method, control input of the system is shaped from the dynamic model of the vehicle and components of the control input are adaptively constructed by estimating the undesirable vibration frequencies. Robust stability of the adaptive vibration control system is guaranteed by using the L1 small gain theorem. Simulation results of the robust adaptive vibration control strategy confirm that the effects of vibration on the vehicle performance considerably decrease without the loss of the phase margin of the system.

  4. Real-time control of geometry and stiffness in adaptive structures

    NASA Technical Reports Server (NTRS)

    Ramesh, A. V.; Utku, S.; Wada, B. K.

    1991-01-01

    The basic theory is presented for the geometry, stiffness, and damping control of adaptive structures, with emphasis on adaptive truss structures. Necessary and sufficient conditions are given for stress-free geometry control in statically determinate and indeterminate adaptive discrete structures. Two criteria for selecting the controls are proposed, and their use in real-time control is illustrated by numerical simulation results. It is shown that the stiffness and damping control of adaptive truss structures for vibration suppression is possible by elongation and elongation rate dependent feedback forces from the active elements.

  5. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  6. Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

    SciTech Connect

    Beckingsale, D. A.; Gaudin, W. P.; Hornung, R. D.; Gunney, B. T.; Gamblin, T.; Herdman, J. A.; Jarvis, S. A.

    2014-11-17

    Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

  7. Adaptations of motor neural structures' activity to lapses in attention.

    PubMed

    Derosière, Gérard; Billot, Maxime; Ward, E Tomas; Perrey, Stéphane

    2015-01-01

    Sustained attention is fundamental for cognition and when impaired, impacts negatively on important contemporary living skills. Degradation in sustained attention is characterized by the time-on-task (TOT) effect, which manifests as a gradual increase in reaction time (RT). The TOT effect is accompanied by changes in relative brain activity patterns in attention-related areas, most noticeably in the prefrontal cortex (PFC) and the right parietal areas. However, activity changes in task-relevant motor structures have not been confirmed to date. This article describes an investigation of such motor-related activity changes as measured with 1) the time course of corticospinal excitability (CSE) through single-pulse transcranial magnetic stimulation; and 2) the changes in activity of premotor (PMC), primary motor (M1), PFC, and right parietal areas by means of near-infrared spectroscopy, during a sustained attention RT task exhibiting the TOT effect. Our results corroborate established findings such as a significant increase (P < 0.05) in lateral prefrontal and right parietal areas activity after the emergence of the TOT effect but also reveal adaptations in the form of motor activity changes--in particular, a significant increase in CSE (P < 0.01) and in primary motor area (M1) activity (P < 0.05).

  8. Parallel architectures for iterative methods on adaptive, block structured grids

    NASA Technical Reports Server (NTRS)

    Gannon, D.; Vanrosendale, J.

    1983-01-01

    A parallel computer architecture well suited to the solution of partial differential equations in complicated geometries is proposed. Algorithms for partial differential equations contain a great deal of parallelism. But this parallelism can be difficult to exploit, particularly on complex problems. One approach to extraction of this parallelism is the use of special purpose architectures tuned to a given problem class. The architecture proposed here is tuned to boundary value problems on complex domains. An adaptive elliptic algorithm which maps effectively onto the proposed architecture is considered in detail. Two levels of parallelism are exploited by the proposed architecture. First, by making use of the freedom one has in grid generation, one can construct grids which are locally regular, permitting a one to one mapping of grids to systolic style processor arrays, at least over small regions. All local parallelism can be extracted by this approach. Second, though there may be a regular global structure to the grids constructed, there will be parallelism at this level. One approach to finding and exploiting this parallelism is to use an architecture having a number of processor clusters connected by a switching network. The use of such a network creates a highly flexible architecture which automatically configures to the problem being solved.

  9. Adapt

    NASA Astrophysics Data System (ADS)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  10. Brain: a complex adaptive structure at multiple levels

    NASA Astrophysics Data System (ADS)

    Klein, Bradley G.

    2001-10-01

    The human brain is comprised of over 100 billion neurons organized into tracts, nuclei, circuits and systems. This provides innumerable elegant abilities that rely on the nervous system to act as a complex adaptive structure (CAS). This property is apparent with respect to overall function, the function of individual neurons and the function of sensory and motor systems. At the overall functional level, the nervous system monitors the environments and can alter that environment. Alterations such as turning on a light switch or changing the diameter of neural vasculature, can improve the performance or chance for survival of the nervous system. Individual neurons can alter the activity of their electrogenic pumps, their rate of transmitter synthesis, their neurotransmitter release and their receptor density in order to maintain optimal functioning in a circuit following changes in their micro-environment. At the systems level, the visual system adjusts the orientation of the eyes or pupillary diameter to receive the highest quality visual information. In the motor system, the myotatic reflex maintains muscle position in the face of changing load, and the gain of the muscle organ responsible for the myotatic reflex can also be automatically adjusted. Internal homeostasis, essential for optimal performance of the nervous system, can be achieved through complex behavioral actions such as feeding. The hypothalamus plays an important role in such behaviors and in the type of sensorimotor integration responsible for the CAS nature of overall nervous system function. Thinking about the CAS characteristics of the nervous system may lead to development of non-biological CAS prostheses for the brain.

  11. Parallel adaptive fluid-structure interaction simulation of explosions impacting on building structures

    SciTech Connect

    Deiterding, Ralf; Wood, Stephen L

    2013-01-01

    We pursue a level set approach to couple an Eulerian shock-capturing fluid solver with space-time refinement to an explicit solid dynamics solver for large deformations and fracture. The coupling algorithms considering recursively finer fluid time steps as well as overlapping solver updates are discussed in detail. Our ideas are implemented in the AMROC adaptive fluid solver framework and are used for effective fluid-structure coupling to the general purpose solid dynamics code DYNA3D. Beside simulations verifying the coupled fluid-structure solver and assessing its parallel scalability, the detailed structural analysis of a reinforced concrete column under blast loading and the simulation of a prototypical blast explosion in a realistic multistory building are presented.

  12. A more efficient anisotropic mesh adaptation for the computation of Lagrangian coherent structures

    NASA Astrophysics Data System (ADS)

    Fortin, A.; Briffard, T.; Garon, A.

    2015-03-01

    The computation of Lagrangian coherent structures is more and more used in fluid mechanics to determine subtle fluid flow structures. We present in this paper a new adaptive method for the efficient computation of Finite Time Lyapunov Exponent (FTLE) from which the coherent Lagrangian structures can be obtained. This new adaptive method considerably reduces the computational burden without any loss of accuracy on the FTLE field.

  13. A Study of Structure in M33 Using Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Wittman, David Michael

    1997-08-01

    FASTTRAC (Fast Adaptive Secondary for Tip-Tilt Removal by Automatic Centroiding) is a tip-tilt secondary system which increases the angular resolution of images taken at Steward Observatory's 90' Bok and 61' Bigelow telescopes. K band imagery is gathered with the facility infrared camera and wavefront sensing is done with a small format charge-coupled device (CCD). I examine desirable characteristics of wavefront-sensing CCDs and evaluate the performance of the device used in FASTTRAC according to those criteria. The main drawback of the device is its low quantum efficiency due to frontside illumination. The read noise of the system is adequate, particularly for FASTTRAC which is generally assigned to bright time. The increased angular resolution provided by FASTTRAC is desirable for imaging crowded fields, such as those found in Local Group galaxies. Stellar photometry is a more powerful tool for studying the structure of these galaxies than is surface photometry, in which the light from all types of stars is mixed together. In particular, the distribution of old stars is representative of the underlying mass distribution, so these stars may be used to measure the overdensity in the arms of spiral galaxies. FASTTRAC was used to observe fields in M33, the nearest spiral which is not seen edge-on. These fields were observed in a range of seeing conditions and with guide stars of varying magnitudes and positions relative to the fields of interest. I analyze the performance of FASTTRAC in these varying conditions and offer some advice to future FASTTRAC observers. I also analyze the crowding in the M33 fields and conclude that, to K~16.5, it does not vary significantly with placement in or outside of a spiral arm. Therefore a coarsely-sampled, wide field survey of the populations of M33 will not be systematically biased by crowding. Therefore a survey covering 35' by 25' was conducted in I and K bands, covering all of M33 out to a deprojected radius of 16 prime. The

  14. Biomimetic rules for design of complex adaptive structures

    NASA Astrophysics Data System (ADS)

    Dry, Carolyn M.

    2001-10-01

    Nature builds by 1) use of local, inexpensive, available often recycled materials which 2) are self-ordering or growing by attributes shared between the material and environment, 3) repair themselves, 4) sense and adapt to changes in the environment daily, seasonally, and yearly; 5) easily disintegrate and recycle back into the material sink when their usefulness is at an end; and 6) do not harm the environment, but perhaps enhance it or resolve problems.

  15. Spatial structure enhanced cooperation in dissatisfied adaptive snowdrift game

    NASA Astrophysics Data System (ADS)

    Zhang, Wen; Xu, Chen; Hui, Pak Ming

    2013-05-01

    The dissatisfied adaptive snowdrift game (DASG) describes the adaptive actions driven by the level of dissatisfaction when two connected agents interact. We study the DASG in static networks both numerically and analytically. In a random network of uniform degree k, the system evolves into a homogeneous state consisting only of cooperators when the cost-to-benefit ratio r < r 0 and a mixed phase with the coexistence of cooperators and defectors when r > r 0, where r 0 is a threshold. For an infinite population, the large k limit corresponding to the well-mixed case is solved analytically. A theory is developed based on the pair approximation. It gives the frequency of cooperation f c and the densities of different pairs that are in good agreement with simulation results. The results revealed that f c is enhanced in networked populations with a finite k, when compared with the well-mixed case. The reasons that the theory works well for the present model are traced back to the weak spatial correlation implied by the random network and the fact that the adaptive actions in DASG are driven only by the strategy pairs. The results shed light on the class of models that the pair approximation is applicable.

  16. Adaptive control of robotic manipulators with structural flexibility

    NASA Astrophysics Data System (ADS)

    Wu, Sijun

    The control problem of mechanically flexible systems was an important issue for the past decade due mainly to the growing needs for fast, precise manipulators in industry and space applications. In this thesis, stable, high precision, and high-bandwidth closed-loop tip position control of a one-link flexible robot was investigated. Two adaptive control methods are developed and studied. A non-dimensionalized dynamic model for the flexible robot arm is developed. Payload mass and moment of inertia are also considered in the modeling. It can be shown that with a set of strain gauge measurements, the payload mass and moment of inertia could be estimated. This provides a convenient tool to detect the variations of the payload, which is crucial for precision control. The lattice filter used in the tip position control of a flexible arm proves to be a good parameter identifier in the on-line identification of the robot due to its high convergence rate and noise rejection capability. Although the lattice filter is usualy designed for auto-regressive or moving-average processes, its applications are extended to include auto-regressive and moving-average processes. The proposed model reference adaptive inverse controller is in the form of a series type of model reference system. It differs from other model reference controller in that the forward controller is the identified systems inverse. Moreover, an additional control signal is applied which comes from a signal synthesis block to compensate the output tracking and parameter identification errors. Compared with other control techniques such as stable factorization and linear quadratic Gaussian, the predictive adaptive controller could provide faster control with reasonably low input energy level.

  17. A Structure-Adaptive Hybrid RBF-BP Classifier with an Optimized Learning Strategy

    PubMed Central

    Wen, Hui; Xie, Weixin; Pei, Jihong

    2016-01-01

    This paper presents a structure-adaptive hybrid RBF-BP (SAHRBF-BP) classifier with an optimized learning strategy. SAHRBF-BP is composed of a structure-adaptive RBF network and a BP network of cascade, where the number of RBF hidden nodes is adjusted adaptively according to the distribution of sample space, the adaptive RBF network is used for nonlinear kernel mapping and the BP network is used for nonlinear classification. The optimized learning strategy is as follows: firstly, a potential function is introduced into training sample space to adaptively determine the number of initial RBF hidden nodes and node parameters, and a form of heterogeneous samples repulsive force is designed to further optimize each generated RBF hidden node parameters, the optimized structure-adaptive RBF network is used for adaptively nonlinear mapping the sample space; then, according to the number of adaptively generated RBF hidden nodes, the number of subsequent BP input nodes can be determined, and the overall SAHRBF-BP classifier is built up; finally, different training sample sets are used to train the BP network parameters in SAHRBF-BP. Compared with other algorithms applied to different data sets, experiments show the superiority of SAHRBF-BP. Especially on most low dimensional and large number of data sets, the classification performance of SAHRBF-BP outperforms other training SLFNs algorithms. PMID:27792737

  18. Adaptive filters of stationary-noise compensation which correspond to a Toeplitz correlation-matrix structure

    NASA Astrophysics Data System (ADS)

    Abramovich, Iu. I.; Arov, D. Z.; Kachur, V. G.

    1987-12-01

    The paper considers the problem of finding the vector of an adaptive filter of stationary-noise compensation which corresponds to a Toeplitz correlation-matrix structure. The existence of a Toeplitz solution is demonstrated. Lower-bound estimates are obtained for the gain in noise-compensation efficiency using a priori information about the Toeplitz matrix structure. Constructive methods for obtaining adaptive solutions corresponding to these estimates are indicated.

  19. Structured adaptive mesh refinement on the connection machine

    SciTech Connect

    Berger, M.J. . Courant Inst. of Mathematical Sciences); Saltzman, J.S. )

    1993-01-01

    Adaptive mesh refinement has proven itself to be a useful tool in a large collection of applications. By refining only a small portion of the computational domain, computational savings of up to a factor of 80 in 3 dimensional calculations have been obtained on serial machines. A natural question is, can this algorithm be used on massively parallel machines and still achieve the same efficiencies We have designed a data layout scheme for mapping grid points to processors that preserves locality and minimizes global communication for the CM-200. The effect of the data layout scheme is that at the finest level nearby grid points from adjacent grids in physical space are in adjacent memory locations. Furthermore, coarse grid points are arranged in memory to be near their associated fine grid points. We show applications of the algorithm to inviscid compressible fluid flow in two space dimensions.

  20. Evolution of collective action in adaptive social structures.

    PubMed

    Moreira, João A; Pacheco, Jorge M; Santos, Francisco C

    2013-01-01

    Many problems in nature can be conveniently framed as a problem of evolution of collective cooperative behaviour, often modelled resorting to the tools of evolutionary game theory in well-mixed populations, combined with an appropriate N-person dilemma. Yet, the well-mixed assumption fails to describe the population dynamics whenever individuals have a say in deciding which groups they will participate. Here we propose a simple model in which dynamical group formation is described as a result of a topological evolution of a social network of interactions. We show analytically how evolutionary dynamics under public goods games in finite adaptive networks can be effectively transformed into a N-Person dilemma involving both coordination and co-existence. Such dynamics would be impossible to foresee from more conventional 2-person interactions as well as from descriptions based on infinite, well-mixed populations. Finally, we show how stochastic effects help rendering cooperation viable, promoting polymorphic configurations in which cooperators prevail.

  1. Cooperation of a Dissatisfied Adaptive Prisoner's Dilemma in Spatial Structures

    NASA Astrophysics Data System (ADS)

    Zhang, Wen; Li, Yao-Sheng; Du, Peng; Xu, Chen

    2013-10-01

    We study the cooperative behavior of a dissatisfied adaptive prisoner's dilemma via a pair updating rule. We compare two kinds of relationship among the competing agents, one is the well-mixed population and the other is the two-dimensional square lattice. It is found that the cooperation emerges in both the cases and the frequency of cooperation is enhanced in the square lattice. Though it is impossible for the cooperators to have a higher average payoff than that of the defectors in the well-mixed case, the cooperators in the spatial square lattice could have higher average payoffs in certain regions of the game parameters. We theoretically analyze the well-mixed case exactly and the square lattice by pair approximation. The theoretic results are in agreement with the simulation data.

  2. An object-oriented approach for parallel self adaptive mesh refinement on block structured grids

    NASA Technical Reports Server (NTRS)

    Lemke, Max; Witsch, Kristian; Quinlan, Daniel

    1993-01-01

    Self-adaptive mesh refinement dynamically matches the computational demands of a solver for partial differential equations to the activity in the application's domain. In this paper we present two C++ class libraries, P++ and AMR++, which significantly simplify the development of sophisticated adaptive mesh refinement codes on (massively) parallel distributed memory architectures. The development is based on our previous research in this area. The C++ class libraries provide abstractions to separate the issues of developing parallel adaptive mesh refinement applications into those of parallelism, abstracted by P++, and adaptive mesh refinement, abstracted by AMR++. P++ is a parallel array class library to permit efficient development of architecture independent codes for structured grid applications, and AMR++ provides support for self-adaptive mesh refinement on block-structured grids of rectangular non-overlapping blocks. Using these libraries, the application programmers' work is greatly simplified to primarily specifying the serial single grid application and obtaining the parallel and self-adaptive mesh refinement code with minimal effort. Initial results for simple singular perturbation problems solved by self-adaptive multilevel techniques (FAC, AFAC), being implemented on the basis of prototypes of the P++/AMR++ environment, are presented. Singular perturbation problems frequently arise in large applications, e.g. in the area of computational fluid dynamics. They usually have solutions with layers which require adaptive mesh refinement and fast basic solvers in order to be resolved efficiently.

  3. Adaptability to changes in temporal structure is fornix-dependent.

    PubMed

    Kwok, Sze Chai; Mitchell, Anna S; Buckley, Mark J

    2015-08-01

    Recognition memory deficits, even after short delays, are sometimes observed following hippocampal damage. One hypothesis links the hippocampus with processes in updating contextual memory representation. Here, we used fornix transection, which partially disconnects the hippocampal system, and compares the performance of fornix-transected monkeys with normal monkeys on two versions of a delayed-matching-to-position task with short delays. Spatial recognition memory was affected by fornix transection only when the temporal structure of the task changed across trials, while differences in motor control, motivation, perception, or short-term memory were not critical. We attributed the deficit to a compromised ability in tracking changes in task temporal structure. PMID:26179228

  4. Adapting to test structure: letting testing teach what to learn.

    PubMed

    Garcia-Marques, Leonel; Nunes, Ludmila D; Marques, Pedro; Carneiro, Paula; Weinstein, Yana

    2015-01-01

    We propose that we encode and store information as a function of the particular ways we have used similar information in the past. More specifically, we contend that the experience of retrieval can serve as a powerful cue to the most effective ways to encode similar information in comparable future learning episodes. To explore these ideas, we did two studies in which all participants went through study-test cycles of single category lists while we manipulated the nature of the recognition tests. The recognition tests either included only same-category lures or only different-category lures. The experience of repeated testing leads participants to avoid conceptual-based strategies but only when conceptual knowledge was poorly diagnostic for recognition (i.e., in the same-category lures condition). In a second study with a similar manipulation, we showed that repeated testing with lures from the same category as study items improved performance in a final recall surprise test compared to conditions in which different-category lures were used. Such a difference is akin to the one obtained when encoding instructions focus on distinctive item features compared to cases in which the focus is on relational processing. We suggest that testing requirements lead to adaptive changes at encoding.

  5. The structural, functional, and nutritional adaptation of college basketball players over a season.

    PubMed

    Bolonchuk, W W; Lukaski, H C; Siders, W A

    1991-06-01

    The purpose of this study was to determine the structural, functional and nutritional adaptation of college basketball players over a season. Structure was determined by somatotype and body composition, function was determined by peak work capacity and work efficiency, and nutrition was determined by plasma metals analysis. The tests were performed twice on each of the eight subjects, one preseason (PRS) and one postseason (PST). A small structural adaptation was indicated by a mean decrease (less than 1 kg) in fat free weight and an increase in ectomorphy (less than 0.03). Body weight and skinfolds did not change significantly. Functional adaptation was indicated by a one minute decrease in running time for the work capacity test (p less than 0.002), and an increase (p less than 0.02) in VO2 for the work efficiency test. Nutritional adaptation was indicated by a greater mobilization of plasma Zn after exercise during PST than PRS. Plasma Cu apparently was mobilized during exercise in PST but the change during the season (-10 to -6.6%) was not statistically significant because of the large interindividual variability in response. Structural and functional adaptation to basketball training over a collegiate season is small; however, the change in Zn mobility and the tendency for a concomitant change in Cu mobilization offers a unique finding to help explain the nutritional adaptation to training.

  6. Adapting Computational Data Structures Technology to Reason about Infinity

    ERIC Educational Resources Information Center

    Goldberg, Robert; Hammerman, Natalie

    2004-01-01

    The NCTM curriculum states that students should be able to "compare and contrast the real number system and its various subsystems with regard to their structural characteristics." In evaluating overall conformity to the 1989 standard, the National Council of Teachers of Mathematics (NCTM) requires that "teachers must value and encourage the use…

  7. Recursive dynamic programming for adaptive sequence and structure alignment

    SciTech Connect

    Thiele, R.; Zimmer, R.; Lengauer, T.

    1995-12-31

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.

  8. Spiders in Motion: Demonstrating Adaptation, Structure-Function Relationships, and Trade-Offs in Invertebrates

    ERIC Educational Resources Information Center

    Bowlin, Melissa S.; McLeer, Dorothy F.; Danielson-Francois, Anne M.

    2014-01-01

    Evolutionary history and structural considerations constrain all aspects of animal physiology. Constraints on invertebrate locomotion are especially straightforward for students to observe and understand. In this exercise, students use spiders to investigate the concepts of adaptation, structure-function relationships, and trade-offs. Students…

  9. Adaptation to a Changing Environment by Modifications in Organizational Decision Unit Structure.

    ERIC Educational Resources Information Center

    Duncan, Robert B.

    This paper presents a model of how organizations adapt to the uncertainty in their environment by making changes in the way they structure themselves for decisionmaking. The research reported here indicates that it is not just a single change in organizational structure, but rather a shifting between a more rigid and more flexible decision…

  10. A structured multi-block solution-adaptive mesh algorithm with mesh quality assessment

    NASA Technical Reports Server (NTRS)

    Ingram, Clint L.; Laflin, Kelly R.; Mcrae, D. Scott

    1995-01-01

    The dynamic solution adaptive grid algorithm, DSAGA3D, is extended to automatically adapt 2-D structured multi-block grids, including adaption of the block boundaries. The extension is general, requiring only input data concerning block structure, connectivity, and boundary conditions. Imbedded grid singular points are permitted, but must be prevented from moving in space. Solutions for workshop cases 1 and 2 are obtained on multi-block grids and illustrate both increased resolution of and alignment with the solution. A mesh quality assessment criteria is proposed to determine how well a given mesh resolves and aligns with the solution obtained upon it. The criteria is used to evaluate the grid quality for solutions of workshop case 6 obtained on both static and dynamically adapted grids. The results indicate that this criteria shows promise as a means of evaluating resolution.

  11. Application of flexure structures to active and adaptive opto-mechanical mechanisms

    NASA Astrophysics Data System (ADS)

    Zago, Lorenzo; Genequand, Pierre M.; Kjelberg, Ivar; Morschel, Joseph

    1997-03-01

    Active and adaptive structures, also commonly called 'smart' structures, combine in one integrated system various functions such as load carrying and structural function, mechanical (cinematic) functions, sensing, control and actuating. Originally developed for high accuracy opto-mechanical applications, CSEM's technology of flexure structures and flexible mechanisms is particularly suited to solve many structural and mechanical issues found in such active/adaptive mechanisms. The paper illustrates some recent flexure structures developments at CSEM and outlines the comprehensive know-how involved in this technology. This comprises in particular the elaboration of optimal design guidelines, related to the geometry, kinematics and dynamics issues (for instance, the minimization of spurious high frequency effects), the evaluation and predictability of all performance quantities relevant to the utilization of flexure structures in space (reliability, fatigue, static and dynamic modeling, etc.). material issues and manufacturing procedures.

  12. Structural adaptations of proteins to different biological membranes

    PubMed Central

    Pogozheva, Irina D.; Tristram-Nagle, Stephanie; Mosberg, Henry I.; Lomize, Andrei L.

    2013-01-01

    To gain insight into adaptations of proteins to their membranes, intrinsic hydrophobic thicknesses, distributions of different chemical groups and profiles of hydrogen-bonding capacities (α and β) and the dipolarity/polarizability parameter (π*) were calculated for lipid-facing surfaces of 460 integral α-helical, β-barrel and peripheral proteins from eight types of biomembranes. For comparison, polarity profiles were also calculated for ten artificial lipid bilayers that have been previously studied by neutron and X-ray scattering. Estimated hydrophobic thicknesses are 30-31 Å for proteins from endoplasmic reticulum, thylakoid, and various bacterial plasma membranes, but differ for proteins from outer bacterial, inner mitochondrial and eukaryotic plasma membranes (23.9, 28.6 and 33.5 Å, respectively). Protein and lipid polarity parameters abruptly change in the lipid carbonyl zone that matches the calculated hydrophobic boundaries. Maxima of positively charged protein groups correspond to the location of lipid phosphates at 20-22 Å distances from the membrane center. Locations of Tyr atoms coincide with hydrophobic boundaries, while distributions maxima of Trp rings are shifted by 3-4 Å toward the membrane center. Distributions of Trp atoms indicate the presence of two 5-8 Å-wide midpolar regions with intermediate π* values within the hydrocarbon core, whose size and symmetry depend on the lipid composition of membrane leaflets. Midpolar regions are especially asymmetric in outer bacterial membranes and cell membranes of mesophilic but not hyperthermophilic archaebacteria, indicating the larger width of the central nonpolar region in the later case. In artificial lipid bilayers, midpolar regions are observed up to the level of acyl chain double bonds. PMID:23811361

  13. Cortical structure of hallucal metatarsals and locomotor adaptations in hominoids.

    PubMed

    Jashashvili, Tea; Dowdeswell, Mark R; Lebrun, Renaud; Carlson, Kristian J

    2015-01-01

    Diaphyseal morphology of long bones, in part, reflects in vivo loads experienced during the lifetime of an individual. The first metatarsal, as a cornerstone structure of the foot, presumably expresses diaphyseal morphology that reflects loading history of the foot during stance phase of gait. Human feet differ substantially from those of other apes in terms of loading histories when comparing the path of the center of pressure during stance phase, which reflects different weight transfer mechanisms. Here we use a novel approach for quantifying continuous thickness and cross-sectional geometric properties of long bones in order to test explicit hypotheses about loading histories and diaphyseal structure of adult chimpanzee, gorilla, and human first metatarsals. For each hallucal metatarsal, 17 cross sections were extracted at regularly-spaced intervals (2.5% length) between 25% and 65% length. Cortical thickness in cross sections was measured in one degree radially-arranged increments, while second moments of area were measured about neutral axes also in one degree radially-arranged increments. Standardized thicknesses and second moments of area were visualized using false color maps, while penalized discriminant analyses were used to evaluate quantitative species differences. Humans systematically exhibit the thinnest diaphyseal cortices, yet the greatest diaphyseal rigidities, particularly in dorsoplantar regions. Shifts in orientation of maximum second moments of area along the diaphysis also distinguish human hallucal metatarsals from those of chimpanzees and gorillas. Diaphyseal structure reflects different loading regimes, often in predictable ways, with human versus non-human differences probably resulting both from the use of arboreal substrates by non-human apes and by differing spatial relationships between hallux position and orientation of the substrate reaction resultant during stance. The novel morphological approach employed in this study offers the

  14. Cortical Structure of Hallucal Metatarsals and Locomotor Adaptations in Hominoids

    PubMed Central

    Jashashvili, Tea; Dowdeswell, Mark R.; Lebrun, Renaud; Carlson, Kristian J.

    2015-01-01

    Diaphyseal morphology of long bones, in part, reflects in vivo loads experienced during the lifetime of an individual. The first metatarsal, as a cornerstone structure of the foot, presumably expresses diaphyseal morphology that reflects loading history of the foot during stance phase of gait. Human feet differ substantially from those of other apes in terms of loading histories when comparing the path of the center of pressure during stance phase, which reflects different weight transfer mechanisms. Here we use a novel approach for quantifying continuous thickness and cross-sectional geometric properties of long bones in order to test explicit hypotheses about loading histories and diaphyseal structure of adult chimpanzee, gorilla, and human first metatarsals. For each hallucal metatarsal, 17 cross sections were extracted at regularly-spaced intervals (2.5% length) between 25% and 65% length. Cortical thickness in cross sections was measured in one degree radially-arranged increments, while second moments of area were measured about neutral axes also in one degree radially-arranged increments. Standardized thicknesses and second moments of area were visualized using false color maps, while penalized discriminant analyses were used to evaluate quantitative species differences. Humans systematically exhibit the thinnest diaphyseal cortices, yet the greatest diaphyseal rigidities, particularly in dorsoplantar regions. Shifts in orientation of maximum second moments of area along the diaphysis also distinguish human hallucal metatarsals from those of chimpanzees and gorillas. Diaphyseal structure reflects different loading regimes, often in predictable ways, with human versus non-human differences probably resulting both from the use of arboreal substrates by non-human apes and by differing spatial relationships between hallux position and orientation of the substrate reaction resultant during stance. The novel morphological approach employed in this study offers the

  15. Cortical structure of hallucal metatarsals and locomotor adaptations in hominoids.

    PubMed

    Jashashvili, Tea; Dowdeswell, Mark R; Lebrun, Renaud; Carlson, Kristian J

    2015-01-01

    Diaphyseal morphology of long bones, in part, reflects in vivo loads experienced during the lifetime of an individual. The first metatarsal, as a cornerstone structure of the foot, presumably expresses diaphyseal morphology that reflects loading history of the foot during stance phase of gait. Human feet differ substantially from those of other apes in terms of loading histories when comparing the path of the center of pressure during stance phase, which reflects different weight transfer mechanisms. Here we use a novel approach for quantifying continuous thickness and cross-sectional geometric properties of long bones in order to test explicit hypotheses about loading histories and diaphyseal structure of adult chimpanzee, gorilla, and human first metatarsals. For each hallucal metatarsal, 17 cross sections were extracted at regularly-spaced intervals (2.5% length) between 25% and 65% length. Cortical thickness in cross sections was measured in one degree radially-arranged increments, while second moments of area were measured about neutral axes also in one degree radially-arranged increments. Standardized thicknesses and second moments of area were visualized using false color maps, while penalized discriminant analyses were used to evaluate quantitative species differences. Humans systematically exhibit the thinnest diaphyseal cortices, yet the greatest diaphyseal rigidities, particularly in dorsoplantar regions. Shifts in orientation of maximum second moments of area along the diaphysis also distinguish human hallucal metatarsals from those of chimpanzees and gorillas. Diaphyseal structure reflects different loading regimes, often in predictable ways, with human versus non-human differences probably resulting both from the use of arboreal substrates by non-human apes and by differing spatial relationships between hallux position and orientation of the substrate reaction resultant during stance. The novel morphological approach employed in this study offers the

  16. A structural model of the adaptive human pilot

    NASA Technical Reports Server (NTRS)

    Hess, R. A.

    1979-01-01

    A compensatory tracking model of the human pilot is offered which attempts to provide a more realistic representation of the human's signal processing structure than that which is exhibited by pilot models currently in use. Two features of the model distinguish it from other representations of the human pilot. First, proprioceptive information from the control stick or manipulator constitutes one of the major feedback paths in the model, providing feedback of vehicle output rate due to control activity. Implicit in this feedback loop is a model of the vehicle dynamics which is valid in and beyond the region of crossover. Second, error-rate information is continuously derived and independently but intermittently controlled. An output injected remnant model is offered and qualitatively justified on the basis of providing a measure of the effect of inaccuracies such as time variations in the pilot's internal model of the controlled element dynamics. The data from experimental tracking tasks involving five different controlled element dynamics and one nonideal viewing condition were matched with model generated describing functions and remnant power spectral densities.

  17. Structural and Psycho-Social Limits to Climate Change Adaptation in the Great Barrier Reef Region.

    PubMed

    Evans, Louisa S; Hicks, Christina C; Adger, W Neil; Barnett, Jon; Perry, Allison L; Fidelman, Pedro; Tobin, Renae

    2016-01-01

    Adaptation, as a strategy to respond to climate change, has limits: there are conditions under which adaptation strategies fail to alleviate impacts from climate change. Research has primarily focused on identifying absolute bio-physical limits. This paper contributes empirical insight to an emerging literature on the social limits to adaptation. Such limits arise from the ways in which societies perceive, experience and respond to climate change. Using qualitative data from multi-stakeholder workshops and key-informant interviews with representatives of the fisheries and tourism sectors of the Great Barrier Reef region, we identify psycho-social and structural limits associated with key adaptation strategies, and examine how these are perceived as more or less absolute across levels of organisation. We find that actors experience social limits to adaptation when: i) the effort of pursuing a strategy exceeds the benefits of desired adaptation outcomes; ii) the particular strategy does not address the actual source of vulnerability, and; iii) the benefits derived from adaptation are undermined by external factors. We also find that social limits are not necessarily more absolute at higher levels of organisation: respondents perceived considerable opportunities to address some psycho-social limits at the national-international interface, while they considered some social limits at the local and regional levels to be effectively absolute. PMID:26960200

  18. Structural and Psycho-Social Limits to Climate Change Adaptation in the Great Barrier Reef Region.

    PubMed

    Evans, Louisa S; Hicks, Christina C; Adger, W Neil; Barnett, Jon; Perry, Allison L; Fidelman, Pedro; Tobin, Renae

    2016-01-01

    Adaptation, as a strategy to respond to climate change, has limits: there are conditions under which adaptation strategies fail to alleviate impacts from climate change. Research has primarily focused on identifying absolute bio-physical limits. This paper contributes empirical insight to an emerging literature on the social limits to adaptation. Such limits arise from the ways in which societies perceive, experience and respond to climate change. Using qualitative data from multi-stakeholder workshops and key-informant interviews with representatives of the fisheries and tourism sectors of the Great Barrier Reef region, we identify psycho-social and structural limits associated with key adaptation strategies, and examine how these are perceived as more or less absolute across levels of organisation. We find that actors experience social limits to adaptation when: i) the effort of pursuing a strategy exceeds the benefits of desired adaptation outcomes; ii) the particular strategy does not address the actual source of vulnerability, and; iii) the benefits derived from adaptation are undermined by external factors. We also find that social limits are not necessarily more absolute at higher levels of organisation: respondents perceived considerable opportunities to address some psycho-social limits at the national-international interface, while they considered some social limits at the local and regional levels to be effectively absolute.

  19. Structural and Psycho-Social Limits to Climate Change Adaptation in the Great Barrier Reef Region

    PubMed Central

    Evans, Louisa S.; Hicks, Christina C.; Adger, W. Neil; Barnett, Jon; Perry, Allison L.; Fidelman, Pedro; Tobin, Renae

    2016-01-01

    Adaptation, as a strategy to respond to climate change, has limits: there are conditions under which adaptation strategies fail to alleviate impacts from climate change. Research has primarily focused on identifying absolute bio-physical limits. This paper contributes empirical insight to an emerging literature on the social limits to adaptation. Such limits arise from the ways in which societies perceive, experience and respond to climate change. Using qualitative data from multi-stakeholder workshops and key-informant interviews with representatives of the fisheries and tourism sectors of the Great Barrier Reef region, we identify psycho-social and structural limits associated with key adaptation strategies, and examine how these are perceived as more or less absolute across levels of organisation. We find that actors experience social limits to adaptation when: i) the effort of pursuing a strategy exceeds the benefits of desired adaptation outcomes; ii) the particular strategy does not address the actual source of vulnerability, and; iii) the benefits derived from adaptation are undermined by external factors. We also find that social limits are not necessarily more absolute at higher levels of organisation: respondents perceived considerable opportunities to address some psycho-social limits at the national-international interface, while they considered some social limits at the local and regional levels to be effectively absolute. PMID:26960200

  20. U.S. perspective on technology demonstration experiments for adaptive structures

    NASA Technical Reports Server (NTRS)

    Aswani, Mohan; Wada, Ben K.; Garba, John A.

    1991-01-01

    Evaluation of design concepts for adaptive structures is being performed in support of several focused research programs. These include programs such as Precision Segmented Reflector (PSR), Control Structure Interaction (CSI), and the Advanced Space Structures Technology Research Experiment (ASTREX). Although not specifically designed for adaptive structure technology validation, relevant experiments can be performed using the Passive and Active Control of Space Structures (PACOSS) testbed, the Space Integrated Controls Experiment (SPICE), the CSI Evolutionary Model (CEM), and the Dynamic Scale Model Test (DSMT) Hybrid Scale. In addition to the ground test experiments, several space flight experiments have been planned, including a reduced gravity experiment aboard the KC-135 aircraft, shuttle middeck experiments, and the Inexpensive Flight Experiment (INFLEX).

  1. Adaptive Filtering for Large Space Structures: A Closed-Form Solution

    NASA Technical Reports Server (NTRS)

    Rauch, H. E.; Schaechter, D. B.

    1985-01-01

    In a previous paper Schaechter proposes using an extended Kalman filter to estimate adaptively the (slowly varying) frequencies and damping ratios of a large space structure. The time varying gains for estimating the frequencies and damping ratios can be determined in closed form so it is not necessary to integrate the matrix Riccati equations. After certain approximations, the time varying adaptive gain can be written as the product of a constant matrix times a matrix derived from the components of the estimated state vector. This is an important savings of computer resources and allows the adaptive filter to be implemented with approximately the same effort as the nonadaptive filter. The success of this new approach for adaptive filtering was demonstrated using synthetic data from a two mode system.

  2. The Impact of Spatial Structure on Viral Genomic Diversity Generated during Adaptation to Thermal Stress

    PubMed Central

    Ally, Dilara; Wiss, Valorie R.; Deckert, Gail E.; Green, Danielle; Roychoudhury, Pavitra; Wichman, Holly A.; Brown, Celeste J.; Krone, Stephen M.

    2014-01-01

    Background Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially. Methodology/Principal Findings We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved. Conclusions/Significance Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide

  3. Modified Adaptive Control for Region 3 Operation in the Presence of Wind Turbine Structural Modes

    NASA Technical Reports Server (NTRS)

    Frost, Susan Alane; Balas, Mark J.; Wright, Alan D.

    2010-01-01

    Many challenges exist for the operation of wind turbines in an efficient manner that is reliable and avoids component fatigue and failure. Turbines operate in highly turbulent environments resulting in aerodynamic loads that can easily excite turbine structural modes, possibly causing component fatigue and failure. Wind turbine manufacturers are highly motivated to reduce component fatigue and failure that can lead to loss of revenue due to turbine down time and maintenance costs. The trend in wind turbine design is toward larger, more flexible turbines that are ideally suited to adaptive control methods due to the complexity and expense required to create accurate models of their dynamic characteristics. In this paper, we design an adaptive collective pitch controller for a high-fidelity simulation of a utility-scale, variable-speed horizontal axis wind turbine operating in Region 3. The objective of the adaptive pitch controller is to regulate generator speed, accommodate wind gusts, and reduce the excitation of structural modes in the wind turbine. The control objective is accomplished by collectively pitching the turbine blades. The adaptive collective pitch controller for Region 3 was compared in simulations with a baseline classical Proportional Integrator (PI) collective pitch controller. The adaptive controller will demonstrate the ability to regulate generator speed in Region 3, while accommodating gusts, and reducing the excitation of certain structural modes in the wind turbine.

  4. Augmented Adaptive Control of a Wind Turbine in the Presence of Structural Modes

    NASA Technical Reports Server (NTRS)

    Frost, Susan A.; Balas, Mark J.; Wright, Alan D.

    2010-01-01

    Wind turbines operate in highly turbulent environments resulting in aerodynamic loads that can easily excite turbine structural modes, potentially causing component fatigue and failure. Two key technology drivers for turbine manufacturers are increasing turbine up time and reducing maintenance costs. Since the trend in wind turbine design is towards larger, more flexible turbines with lower frequency structural modes, manufacturers will want to develop methods to operate in the presence of these modes. Accurate models of the dynamic characteristics of new wind turbines are often not available due to the complexity and expense of the modeling task, making wind turbines ideally suited to adaptive control. In this paper, we develop theory for adaptive control with rejection of disturbances in the presence of modes that inhibit the controller. We use this method to design an adaptive collective pitch controller for a high-fidelity simulation of a utility-scale, variable-speed wind turbine operating in Region 3. The objective of the adaptive pitch controller is to regulate generator speed, accommodate wind gusts, and reduce the interference of certain structural modes in feedback. The control objective is accomplished by collectively pitching the turbine blades. The adaptive pitch controller for Region 3 is compared in simulations with a baseline classical Proportional Integrator (PI) collective pitch controller.

  5. Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae).

    PubMed

    Batista, Philip D; Janes, Jasmine K; Boone, Celia K; Murray, Brent W; Sperling, Felix A H

    2016-09-01

    Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism. PMID:27648243

  6. Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae).

    PubMed

    Batista, Philip D; Janes, Jasmine K; Boone, Celia K; Murray, Brent W; Sperling, Felix A H

    2016-09-01

    Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

  7. Ways and Means of Adapting Culture and Structure: Case Studies. Support Document 1

    ERIC Educational Resources Information Center

    Clayton, Berwyn; Fisher, Thea; Harris, Roger; Bateman, Andrea; Brown, Mike

    2008-01-01

    The resource in this support document is a set of small case studies, offering insights into how a range of organisations have gone about adapting their organisational structure and/or culture to enhance their capability. Key elements of each case are presented with a particular emphasis on: (1) the principles that have underpinned each approach…

  8. Adaptive structures; Proceedings of the ASME Winter Annual Meeting, San Francisco, CA, Dec. 10-15, 1989

    NASA Technical Reports Server (NTRS)

    Wada, Ben K. (Editor)

    1989-01-01

    The present conference on adaptive structures discusses piezoelectric and electrostrictive sensors and actuators for adaptive structures and smart materials, real-time control for composite structures with embedded actuators and sensors, a laminated-shell theory incorporating embedded distributed actuators, traveling-wave power flow techniques, uncertainty modeling for the control of an active structure, and active vibration isolation in the presence of unmodeled structural dynamic response. Also discussed are the control of flexible beams via free-free active truss, truss structure control using member actuators with latch mechanism, neural processors for smart-structure control, the effect of imperfections on the static control of adaptive structures, adaptive structures for segmented optical systems, and the shape-control of flexible structures.

  9. Conceptual study of the damping of large space structures using large-stroke adaptive stiffness cables

    NASA Technical Reports Server (NTRS)

    Thorwald, Gregory; Mikulas, Martin M., Jr.

    1992-01-01

    The concept of a large-stroke adaptive stiffness cable-device for damping control of space structures with large mass is introduced. The cable is used to provide damping in several examples, and its performance is shown through numerical simulation results. Displacement and velocity information of how the structure moves is used to determine when to modify the cable's stiffness in order to provide a damping force.

  10. An adaptive inverse iteration algorithm using interpolating multiwavelets for structural eigenvalue problems

    NASA Astrophysics Data System (ADS)

    Wang, Youming; Chen, Xuefeng; He, Zhengjia

    2011-02-01

    Structural eigenvalues have been broadly applied in modal analysis, damage detection, vibration control, etc. In this paper, the interpolating multiwavelets are custom designed based on stable completion method to solve structural eigenvalue problems. The operator-orthogonality of interpolating multiwavelets gives rise to highly sparse multilevel stiffness and mass matrices of structural eigenvalue problems and permits the incremental computation of the eigenvalue solution in an efficient manner. An adaptive inverse iteration algorithm using the interpolating multiwavelets is presented to solve structural eigenvalue problems. Numerical examples validate the accuracy and efficiency of the proposed algorithm.

  11. Structure of the GAT domain of the endosomal adapter protein Tom1.

    PubMed

    Xiao, Shuyan; Ellena, Jeffrey F; Armstrong, Geoffrey S; Capelluto, Daniel G S

    2016-06-01

    Cellular homeostasis requires correct delivery of cell-surface receptor proteins (cargo) to their target subcellular compartments. The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain's association to Tollip's Tom1-binding domain (TBD). In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. The estimated protein structure exhibits a bundle of three helical elements. We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states. PMID:26977434

  12. Block-structured adaptive meshes and reduced grids for atmospheric general circulation models.

    PubMed

    Jablonowski, Christiane; Oehmke, Robert C; Stout, Quentin F

    2009-11-28

    Adaptive mesh refinement techniques offer a flexible framework for future variable-resolution climate and weather models since they can focus their computational mesh on certain geographical areas or atmospheric events. Adaptive meshes can also be used to coarsen a latitude-longitude grid in polar regions. This allows for the so-called reduced grid setups. A spherical, block-structured adaptive grid technique is applied to the Lin-Rood finite-volume dynamical core for weather and climate research. This hydrostatic dynamics package is based on a conservative and monotonic finite-volume discretization in flux form with vertically floating Lagrangian layers. The adaptive dynamical core is built upon a flexible latitude-longitude computational grid and tested in two- and three-dimensional model configurations. The discussion is focused on static mesh adaptations and reduced grids. The two-dimensional shallow water setup serves as an ideal testbed and allows the use of shallow water test cases like the advection of a cosine bell, moving vortices, a steady-state flow, the Rossby-Haurwitz wave or cross-polar flows. It is shown that reduced grid configurations are viable candidates for pure advection applications but should be used moderately in nonlinear simulations. In addition, static grid adaptations can be successfully used to resolve three-dimensional baroclinic waves in the storm-track region.

  13. Scale-adaptive tensor algebra for local many-body methods of electronic structure theory

    SciTech Connect

    Liakh, Dmitry I

    2014-01-01

    While the formalism of multiresolution analysis (MRA), based on wavelets and adaptive integral representations of operators, is actively progressing in electronic structure theory (mostly on the independent-particle level and, recently, second-order perturbation theory), the concepts of multiresolution and adaptivity can also be utilized within the traditional formulation of correlated (many-particle) theory which is based on second quantization and the corresponding (generally nonorthogonal) tensor algebra. In this paper, we present a formalism called scale-adaptive tensor algebra (SATA) which exploits an adaptive representation of tensors of many-body operators via the local adjustment of the basis set quality. Given a series of locally supported fragment bases of a progressively lower quality, we formulate the explicit rules for tensor algebra operations dealing with adaptively resolved tensor operands. The formalism suggested is expected to enhance the applicability and reliability of local correlated many-body methods of electronic structure theory, especially those directly based on atomic orbitals (or any other localized basis functions).

  14. Highly phosphorylated core oligosaccharide structures from cold-adapted Psychromonas arctica.

    PubMed

    Corsaro, Maria M; Pieretti, Giuseppina; Lindner, Buko; Lanzetta, Rosa; Parrilli, Ermenegilda; Tutino, Maria L; Parrilli, Michelangelo

    2008-01-01

    Many cold habitats contain plenty of microorganisms that represent the most abundant cold-adapted life forms on earth. These organisms have developed a wide range of adaptations that involve the cell wall of the microorganism. In particular, bacteria enhance the synthesis of unsaturated fatty acids of membrane lipids to maintain the membrane fluidity, but very little is known about the adaptational changes in the structure of the lipopolysaccharides (LPSs), the main constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. The aim of this study was to investigate the chemical structure of these LPSs for insight into the temperature-adaptation mechanism. For this objective, the cold-adapted Psychromonas arctica bacterium, which lives in the arctic sea-water near Spitzbergen (Svalbard islands, Arctic) was cultivated at 4 degrees C. The lipooligosaccharides (LOSs) were isolated and analysed by means of chemical analysis and electrospray ionisation high-resolution Fourier transform mass spectrometry. The LOS was then degraded either by mild hydrazinolysis (O-deacylation) or with hot 4 M KOH (N-deacylation). Both products were investigated in detail by using 1H and 13C NMR spectroscopy and mass spectrometry. The core consists of a mixture of species that differ because of the presence of nonstoichiometric D-fructose and/or D-galacturonic acid units.

  15. [Phospholipids and structural modification of tissues and cell membranes for adaptation in high altitude mountains].

    PubMed

    Iakovlev, V M; Vishnevskiĭ, A A; Shanazarov, A S

    2012-01-01

    The nature of the impact of physical factors of high altitudes (3200 m) on the lipids of tissues and membranes of animals was researched. It was established that the adaptation process in Wistar rats was followed by peroxide degradation and subsequent modification of the phospholipids' structure of tissues and microsomal membranes. Adaptive phospholipids reconstruction takes place in microsomal membranes in the tissues of the lungs, brain, liver and skeletal muscles. Together with this, the amount of phosphatidylinositol and phosphatidic acid accumulates, indicating that the hydrolysis of phosphatidylinositol-4, 5 biphosphate to diacylglycerol and secondary messenger--inositol triphosphate, occurs. A decrease in temperature adaptation (+10 degrees C) leads to a more noticeable shift in peroxide oxidation of lipids, phospholipid structure in the tissues and membranes rather than adaptation in thermoneutral conditions (+30 degrees C). Modification of lipid composition of tissues and cell membranes in the highlands obviously increases the adaptive capabilities of cells of the whole body: physical performance and resistance to hypoxia increases in animals. PMID:22586936

  16. [Phospholipids and structural modification of tissues and cell membranes for adaptation in high altitude mountains].

    PubMed

    Iakovlev, V M; Vishnevskiĭ, A A; Shanazarov, A S

    2012-01-01

    The nature of the impact of physical factors of high altitudes (3200 m) on the lipids of tissues and membranes of animals was researched. It was established that the adaptation process in Wistar rats was followed by peroxide degradation and subsequent modification of the phospholipids' structure of tissues and microsomal membranes. Adaptive phospholipids reconstruction takes place in microsomal membranes in the tissues of the lungs, brain, liver and skeletal muscles. Together with this, the amount of phosphatidylinositol and phosphatidic acid accumulates, indicating that the hydrolysis of phosphatidylinositol-4, 5 biphosphate to diacylglycerol and secondary messenger--inositol triphosphate, occurs. A decrease in temperature adaptation (+10 degrees C) leads to a more noticeable shift in peroxide oxidation of lipids, phospholipid structure in the tissues and membranes rather than adaptation in thermoneutral conditions (+30 degrees C). Modification of lipid composition of tissues and cell membranes in the highlands obviously increases the adaptive capabilities of cells of the whole body: physical performance and resistance to hypoxia increases in animals.

  17. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-01

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system. PMID:27332140

  18. A new adaptive mesh refinement data structure with an application to detonation

    NASA Astrophysics Data System (ADS)

    Ji, Hua; Lien, Fue-Sang; Yee, Eugene

    2010-11-01

    A new Cell-based Structured Adaptive Mesh Refinement (CSAMR) data structure is developed. In our CSAMR data structure, Cartesian-like indices are used to identify each cell. With these stored indices, the information on the parent, children and neighbors of a given cell can be accessed simply and efficiently. Owing to the usage of these indices, the computer memory required for storage of the proposed AMR data structure is only {5}/{8} word per cell, in contrast to the conventional oct-tree [P. MacNeice, K.M. Olson, C. Mobary, R. deFainchtein, C. Packer, PARAMESH: a parallel adaptive mesh refinement community toolkit, Comput. Phys. Commun. 330 (2000) 126] and the fully threaded tree (FTT) [A.M. Khokhlov, Fully threaded tree algorithms for adaptive mesh fluid dynamics simulations, J. Comput. Phys. 143 (1998) 519] data structures which require, respectively, 19 and 2{3}/{8} words per cell for storage of the connectivity information. Because the connectivity information (e.g., parent, children and neighbors) of a cell in our proposed AMR data structure can be accessed using only the cell indices, a tree structure which was required in previous approaches for the organization of the AMR data is no longer needed for this new data structure. Instead, a much simpler hash table structure is used to maintain the AMR data, with the entry keys in the hash table obtained directly from the explicitly stored cell indices. The proposed AMR data structure simplifies the implementation and parallelization of an AMR code. Two three-dimensional test cases are used to illustrate and evaluate the computational performance of the new CSAMR data structure.

  19. Development of adaptive seismic isolators for ultimate seismic protection of civil structures

    NASA Astrophysics Data System (ADS)

    Li, Jianchun; Li, Yancheng; Li, Weihua; Samali, Bijan

    2013-04-01

    Base isolation is the most popular seismic protection technique for civil engineering structures. However, research has revealed that the traditional base isolation system due to its passive nature is vulnerable to two kinds of earthquakes, i.e. the near-fault and far-fault earthquakes. A great deal of effort has been dedicated to improve the performance of the traditional base isolation system for these two types of earthquakes. This paper presents a recent research breakthrough on the development of a novel adaptive seismic isolation system as the quest for ultimate protection for civil structures, utilizing the field-dependent property of the magnetorheological elastomer (MRE). A novel adaptive seismic isolator was developed as the key element to form smart seismic isolation system. The novel isolator contains unique laminated structure of steel and MR elastomer layers, which enable its large-scale civil engineering applications, and a solenoid to provide sufficient and uniform magnetic field for energizing the field-dependent property of MR elastomers. With the controllable shear modulus/damping of the MR elastomer, the developed adaptive seismic isolator possesses a controllable lateral stiffness while maintaining adequate vertical loading capacity. In this paper, a comprehensive review on the development of the adaptive seismic isolator is present including designs, analysis and testing of two prototypical adaptive seismic isolators utilizing two different MRE materials. Experimental results show that the first prototypical MRE seismic isolator can provide stiffness increase up to 37.49%, while the second prototypical MRE seismic isolator provides amazing increase of lateral stiffness up to1630%. Such range of increase of the controllable stiffness of the seismic isolator makes it highly practical for developing new adaptive base isolation system utilizing either semi-active or smart passive controls.

  20. Adaptive unstructured meshing for thermal stress analysis of built-up structures

    NASA Technical Reports Server (NTRS)

    Dechaumphai, Pramote

    1992-01-01

    An adaptive unstructured meshing technique for mechanical and thermal stress analysis of built-up structures has been developed. A triangular membrane finite element and a new plate bending element are evaluated on a panel with a circular cutout and a frame stiffened panel. The adaptive unstructured meshing technique, without a priori knowledge of the solution to the problem, generates clustered elements only where needed. An improved solution accuracy is obtained at a reduced problem size and analysis computational time as compared to the results produced by the standard finite element procedure.

  1. Adaptive identification and control of structural dynamics systems using recursive lattice filters

    NASA Technical Reports Server (NTRS)

    Sundararajan, N.; Montgomery, R. C.; Williams, J. P.

    1985-01-01

    A new approach for adaptive identification and control of structural dynamic systems by using least squares lattice filters thar are widely used in the signal processing area is presented. Testing procedures for interfacing the lattice filter identification methods and modal control method for stable closed loop adaptive control are presented. The methods are illustrated for a free-free beam and for a complex flexible grid, with the basic control objective being vibration suppression. The approach is validated by using both simulations and experimental facilities available at the Langley Research Center.

  2. Fluidic origami: a plant-inspired adaptive structure with shape morphing and stiffness tuning

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2015-10-01

    Inspired by the physics behind the rapid plant movements and the rich topologies in origami folding, this research creates a unique class of multi-functional adaptive structure through exploring the innovation of fluidic origami. The idea is to connect multiple Miura folded sheets along their crease lines into a space-filling structure, and fill the tubular cells in-between with working fluids. The pressure and fluid flow in these cells can be strategically controlled much like in plants for nastic movements. The relationship between the internal fluid volume and the overall structure deformation is primarily determined by the kinematics of folding. This relationship can be exploited so that fluidic origami can achieve actuation/morphing by actively changing the internal fluid volume, and stiffness tuning by constraining the fluid volume. In order to characterize the working principles and performance potentials of these two adaptive functions, this research develops an equivalent truss frame model on a fluidic origami unit cell to analyze its fundamental elastic characteristics. Eigen-stiffness analysis based on this model reveals the primary modes of deformation and their relationships with initial folding configurations. Performances of the adaptive functions are correlated to the crease pattern design. In parallel to analytical studies, the feasibility of the morphing and stiffness tuning is also examined experimentally via a 3D printed multi-material prototype demonstrator. The research reported in this paper could lead to the synthesis of adaptive fluidic origami cellular metastructures or metamaterial systems for various engineering applications.

  3. Approach for Structurally Clearing an Adaptive Compliant Trailing Edge Flap for Flight

    NASA Technical Reports Server (NTRS)

    Miller, Eric J.; Lokos, William A.; Cruz, Josue; Crampton, Glen; Stephens, Craig A.; Kota, Sridhar; Ervin, Gregory; Flick, Pete

    2015-01-01

    The Adaptive Compliant Trailing Edge (ACTE) flap was flown on the National Aeronautics and Space Administration (NASA) Gulfstream GIII testbed at the NASA Armstrong Flight Research Center. This smoothly curving flap replaced the existing Fowler flaps creating a seamless control surface. This compliant structure, developed by FlexSys Inc. in partnership with the Air Force Research Laboratory, supported NASA objectives for airframe structural noise reduction, aerodynamic efficiency, and wing weight reduction through gust load alleviation. A thorough structures airworthiness approach was developed to move this project safely to flight. A combination of industry and NASA standard practice require various structural analyses, ground testing, and health monitoring techniques for showing an airworthy structure. This paper provides an overview of compliant structures design, the structural ground testing leading up to flight, and the flight envelope expansion and monitoring strategy. Flight data will be presented, and lessons learned along the way will be highlighted.

  4. Defect structure of a nematic liquid crystal around a spherical particle: adaptive mesh refinement approach.

    PubMed

    Fukuda, Jun-ichi; Yoneya, Makoto; Yokoyama, Hiroshi

    2002-04-01

    We investigate numerically the structure of topological defects close to a spherical particle immersed in a uniformly aligned nematic liquid crystal. To this end we have implemented an adaptive mesh refinement scheme in an axi-symmetric three-dimensional system, which makes it feasible to take into account properly the large length scale difference between the particle and the topological defects. The adaptive mesh refinement scheme proves to be quite efficient and useful in the investigation of not only the macroscopic properties such as the defect position but also the fine structure of defects. It can be shown that a hyperbolic hedgehog that accompanies a particle with strong homeotropic anchoring takes the structure of a ring.

  5. Adaptive cluster expansion approach for predicting the structure evolution of graphene oxide

    SciTech Connect

    Li, Xi-Bo; Guo, Pan; Wang, D.; Liu, Li-Min; Zhang, Yongsheng

    2014-12-14

    An adaptive cluster expansion (CE) method is used to explore surface adsorption and growth processes. Unlike the traditional CE method, suitable effective cluster interaction (ECI) parameters are determined, and then the selected fixed number of ECIs is continually optimized to predict the stable configurations with gradual increase of adatom coverage. Comparing with traditional CE method, the efficiency of the adaptive CE method could be greatly enhanced. As an application, the adsorption and growth of oxygen atoms on one side of pristine graphene was carefully investigated using this method in combination with first-principles calculations. The calculated results successfully uncover the structural evolution of graphene oxide for the different numbers of oxygen adatoms on graphene. The aggregation behavior of the stable configurations for different oxygen adatom coverages is revealed for increasing coverages of oxygen atoms. As a targeted method, adaptive CE can also be applied to understand the evolution of other surface adsorption and growth processes.

  6. Approach for Structurally Clearing an Adaptive Compliant Trailing Edge Flap for Flight

    NASA Technical Reports Server (NTRS)

    Miller, Eric J.; Lokos, William A.; Cruz, Josue; Crampton, Glen; Stephens, Craig A.; Kota, Sridhar; Ervin, Gregory; Flick, Pete

    2015-01-01

    The Adaptive Compliant Trailing Edge (ACTE) flap was flown on the NASA Gulfstream GIII test bed at the NASA Armstrong Flight Research Center. This smoothly curving flap replaced the existing Fowler flaps creating a seamless control surface. This compliant structure, developed by FlexSys Inc. in partnership with Air Force Research Laboratory, supported NASA objectives for airframe structural noise reduction, aerodynamic efficiency, and wing weight reduction through gust load alleviation. A thorough structures airworthiness approach was developed to move this project safely to flight.

  7. Transient thermal-structural analysis using adaptive unstructured remeshing and mesh movement

    NASA Technical Reports Server (NTRS)

    Dechaumphai, Pramote; Morgan, Kenneth

    1990-01-01

    An adaptive unstructured remeshing technique is applied to transient thermal-structural analysis. The effectiveness of the technique, together with the finite element method and an error estimation technique, is evaluated by two applications which have exact solutions: (1) the steady-state thermal analysis of a plate subjected to a highly localized surface heating, and (2) the transient thermal-structural analysis of a simulated convectively cooled leading edge subjected to a translating heat source. These applications demonstrate that the remeshing technique significantly reduces the problem size as well as the analysis solution error as compared to the results produced using standard structured meshes.

  8. Adaptation to structural modifications of the human vocal tract during speech: Electropalatographic measures

    NASA Astrophysics Data System (ADS)

    Aasland, Wendi A.; Baum, Shari R.; McFarland, David H.

    2001-05-01

    Structural modifications to the vocal tract force speakers to alter their previously learned articulatory patterns in order to produce perceptually adequate speech. Previous research has shown that acoustic output in the production of alveolar consonants changes during adaptation to structural alterations of the palate, but to date, little is known regarding exactly how these changes result kinematically. The present study examines the adjustments made to tongue-palate contact patterns, measured using electropalatography (EPG), during adaptation to a palatal perturbation for the fricative [s]. Productions of the nonsense word [asa] were elicited in nine subjects at five time intervals, 15 min apart, while speakers wore electropalates modified with a thicker-than-normal alveolar ridge. Between measurement intervals, speakers read [s]-laden passages to promote adaptation. Productions were also elicited with an unperturbed electropalate in place to characterize normal articulation. Electropalatographic analyses revealed a posterior shift in center of gravity of tongue-palate contact, alterations in the width of the medial groove necessary for [s] production, and increased variability in productions, which may reflect the instability of the new motor programs. Results are discussed in relation to the development of adaptive articulatory programs in speech motor control. [Work supported by NSERC and a FRSQ Bourse de Formation.

  9. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis.

    PubMed

    Whitlock, Raj

    2014-07-01

    Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These

  10. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

    PubMed Central

    Whitlock, Raj

    2014-01-01

    Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These

  11. Symmetry-Adapted Ab Initio Shell Model for Nuclear Structure Calculations

    NASA Astrophysics Data System (ADS)

    Draayer, J. P.; Dytrych, T.; Launey, K. D.; Langr, D.

    2012-05-01

    An innovative concept, the symmetry-adapted ab initio shell model, that capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. This framework is expected to inform the leading features of nuclear structure and reaction data for light and medium mass nuclei, which are currently inaccessible by theory and experiment and for which predictions of modern phenomenological models often diverge. We use powerful computational and group-theoretical algorithms to perform ab initio CI (configuration-interaction) calculations in a model space spanned by SU(3) symmetry-adapted many-body configurations with the JISP16 nucleon-nucleon interaction. We demonstrate that the results for the ground states of light nuclei up through A = 16 exhibit a strong dominance of low-spin and high-deformation configurations together with an evident symplectic structure. This, in turn, points to the importance of using a symmetry-adapted framework, one based on an LS coupling scheme with the associated spatial configurations organized according to deformation.

  12. Fibrin Networks Support Recurring Mechanical Loads by Adapting their Structure across Multiple Scales.

    PubMed

    Kurniawan, Nicholas A; Vos, Bart E; Biebricher, Andreas; Wuite, Gijs J L; Peterman, Erwin J G; Koenderink, Gijsje H

    2016-09-01

    Tissues and cells sustain recurring mechanical loads that span a wide range of loading amplitudes and timescales as a consequence of exposure to blood flow, muscle activity, and external impact. Both tissues and cells derive their mechanical strength from fibrous protein scaffolds, which typically have a complex hierarchical structure. In this study, we focus on a prototypical hierarchical biomaterial, fibrin, which is one of the most resilient naturally occurring biopolymers and forms the structural scaffold of blood clots. We show how fibrous networks composed of fibrin utilize irreversible changes in their hierarchical structure at different scales to maintain reversible stress stiffening up to large strains. To trace the origin of this paradoxical resilience, we systematically tuned the microstructural parameters of fibrin and used a combination of optical tweezers and fluorescence microscopy to measure the interactions of single fibrin fibers for the first time, to our knowledge. We demonstrate that fibrin networks adapt to moderate strains by remodeling at the network scale through the spontaneous formation of new bonds between fibers, whereas they adapt to high strains by plastic remodeling of the fibers themselves. This multiscale adaptation mechanism endows fibrin gels with the remarkable ability to sustain recurring loads due to shear flows and wound stretching. Our findings therefore reveal a microscopic mechanism by which tissues and cells can balance elastic nonlinearity and plasticity, and thus can provide microstructural insights into cell-driven remodeling of tissues. PMID:27602730

  13. A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

    NASA Technical Reports Server (NTRS)

    Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

    1995-01-01

    This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.

  14. Demographic History, Population Structure, and Local Adaptation in Alpine Populations of Cardamine impatiens and Cardamine resedifolia

    PubMed Central

    Ometto, Lino; Li, Mingai; Bresadola, Luisa; Barbaro, Enrico; Neteler, Markus; Varotto, Claudio

    2015-01-01

    Species evolution depends on numerous and distinct forces, including demography and natural selection. For example, local adaptation and population structure affect the evolutionary history of species living along environmental clines. This is particularly relevant in plants, which are often characterized by limited dispersal ability and the need to respond to abiotic and biotic stress factors specific to the local environment. Here we study the demographic history and the possible existence of local adaptation in two related species of Brassicaceae, Cardamine impatiens and Cardamine resedifolia, which occupy separate habitats along the elevation gradient. Previous genome-wide analyses revealed the occurrence of distinct selective pressures in the two species, with genes involved in cold response evolving particularly fast in C. resedifolia. In this study we surveyed patterns of molecular evolution and genetic variability in a set of 19 genes, including neutral and candidate genes involved in cold response, across 10 populations each of C. resedifolia and C. impatiens from the Italian Alps (Trentino). We inferred the population structure and demographic history of the two species, and tested the occurrence of signatures of local adaptation in these genes. The results indicate that, despite a slightly higher population differentiation in C. resedifolia than in C. impatiens, both species are only weakly structured and that populations sampled at high altitude experience less gene flow than low-altitude ones. None of the genes showed signatures of positive selection, suggesting that they do not seem to play relevant roles in the current evolutionary processes of adaptation to alpine environments of these species. PMID:25933225

  15. Single-pass GPU-raycasting for structured adaptive mesh refinement data

    NASA Astrophysics Data System (ADS)

    Kaehler, Ralf; Abel, Tom

    2013-01-01

    Structured Adaptive Mesh Refinement (SAMR) is a popular numerical technique to study processes with high spatial and temporal dynamic range. It reduces computational requirements by adapting the lattice on which the underlying differential equations are solved to most efficiently represent the solution. Particularly in astrophysics and cosmology such simulations now can capture spatial scales ten orders of magnitude apart and more. The irregular locations and extensions of the refined regions in the SAMR scheme and the fact that different resolution levels partially overlap, poses a challenge for GPU-based direct volume rendering methods. kD-trees have proven to be advantageous to subdivide the data domain into non-overlapping blocks of equally sized cells, optimal for the texture units of current graphics hardware, but previous GPU-supported raycasting approaches for SAMR data using this data structure required a separate rendering pass for each node, preventing the application of many advanced lighting schemes that require simultaneous access to more than one block of cells. In this paper we present the first single-pass GPU-raycasting algorithm for SAMR data that is based on a kD-tree. The tree is efficiently encoded by a set of 3D-textures, which allows to adaptively sample complete rays entirely on the GPU without any CPU interaction. We discuss two different data storage strategies to access the grid data on the GPU and apply them to several datasets to prove the benefits of the proposed method.

  16. Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations

    PubMed Central

    Desai, Michael M.; Walczak, Aleksandra M.; Fisher, Daniel S.

    2013-01-01

    Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a single genetic locus. However, in linked regions of rapidly adapting genomes, multiple beneficial mutations at different loci can segregate simultaneously within the population, an effect known as clonal interference. This leads to a subtle interplay between hitchhiking and interference effects, which leads to a unique signature of rapid adaptation on genetic variation both at the selected sites and at linked neutral loci. Here, we introduce an effective coalescent theory (a “fitness-class coalescent”) that describes how positive selection at many perfectly linked sites alters the structure of genealogies. We use this theory to calculate several simple statistics describing genetic variation within a rapidly adapting population and to implement efficient backward-time coalescent simulations, which can be used to predict how clonal interference alters the expected patterns of molecular evolution. PMID:23222656

  17. Adaptive finite element modeling of direct current resistivity in 2-D generally anisotropic structures

    NASA Astrophysics Data System (ADS)

    Yan, Bo; Li, Yuguo; Liu, Ying

    2016-07-01

    In this paper, we present an adaptive finite element (FE) algorithm for direct current (DC) resistivity modeling in 2-D generally anisotropic conductivity structures. Our algorithm is implemented on an unstructured triangular mesh that readily accommodates complex structures such as topography and dipping layers and so on. We implement a self-adaptive, goal-oriented grid refinement algorithm in which the finite element analysis is performed on a sequence of refined grids. The grid refinement process is guided by an a posteriori error estimator. The problem is formulated in terms of total potentials where mixed boundary conditions are incorporated. This type of boundary condition is superior to the Dirichlet type of conditions and improves numerical accuracy considerably according to model calculations. We have verified the adaptive finite element algorithm using a two-layered earth with azimuthal anisotropy. The FE algorithm with incorporation of mixed boundary conditions achieves high accuracy. The relative error between the numerical and analytical solutions is less than 1% except in the vicinity of the current source location, where the relative error is up to 2.4%. A 2-D anisotropic model is used to demonstrate the effects of anisotropy upon the apparent resistivity in DC soundings.

  18. Adaptive modeling, identification, and control of dynamic structural systems. I. Theory

    USGS Publications Warehouse

    Safak, Erdal

    1989-01-01

    A concise review of the theory of adaptive modeling, identification, and control of dynamic structural systems based on discrete-time recordings is presented. Adaptive methods have four major advantages over the classical methods: (1) Removal of the noise from the signal is done over the whole frequency band; (2) time-varying characteristics of systems can be tracked; (3) systems with unknown characteristics can be controlled; and (4) a small segment of the data is needed during the computations. Included in the paper are the discrete-time representation of single-input single-output (SISO) systems, models for SISO systems with noise, the concept of stochastic approximation, recursive prediction error method (RPEM) for system identification, and the adaptive control. Guidelines for model selection and model validation and the computational aspects of the method are also discussed in the paper. The present paper is the first of two companion papers. The theory given in the paper is limited to that which is necessary to follow the examples for applications in structural dynamics presented in the second paper.

  19. Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

    NASA Technical Reports Server (NTRS)

    Wada, Ben K. (Editor); Fanson, James L. (Editor); Miura, Koryo (Editor)

    1991-01-01

    The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

  20. A Unifying Framework for Adaptive Radar Detection in Homogeneous Plus Structured Interference— Part II: Detectors Design

    NASA Astrophysics Data System (ADS)

    Ciuonzo, Domenico; De Maio, Antonio; Orlando, Danilo

    2016-06-01

    This paper deals with the problem of adaptive multidimensional/multichannel signal detection in homogeneous Gaussian disturbance with unknown covariance matrix and structured (unknown) deterministic interference. The aforementioned problem extends the well-known Generalized Multivariate Analysis of Variance (GMANOVA) tackled in the open literature. In a companion paper, we have obtained the Maximal Invariant Statistic (MIS) for the problem under consideration, as an enabling tool for the design of suitable detectors which possess the Constant False-Alarm Rate (CFAR) property. Herein, we focus on the development of several theoretically-founded detectors for the problem under consideration. First, all the considered detectors are shown to be function of the MIS, thus proving their CFARness property. Secondly, coincidence or statistical equivalence among some of them in such a general signal model is proved. Thirdly, strong connections to well-known simpler scenarios found in adaptive detection literature are established. Finally, simulation results are provided for a comparison of the proposed receivers.

  1. Local Laser Strengthening of Steel Sheets for Load Adapted Component Design in Car Body Structures

    NASA Astrophysics Data System (ADS)

    Jahn, Axel; Heitmanek, Marco; Standfuss, Jens; Brenner, Berndt; Wunderlich, Gerd; Donat, Bernd

    The current trend in car body construction concerning light weight design and car safety improvement increasingly requires an adaption of the local material properties on the component load. Martensitic hardenable steels, which are typically used in car body components, show a significant hardening effect, for instance in laser welded seams. This effect can be purposefully used as a local strengthening method. For several steel grades the local strengthening, resulting from a laser remelting process was investigated. The strength in the treated zone was determined at crash relevant strain rates. A load adapted design of complex reinforcement structures was developed for compression and bending loaded tube samples, using numerical simulation of the deformation behavior. Especially for bending loaded parts, the crash energy absorption can be increased significantly by local laser strengthening.

  2. Arbitrary Lagrangian-Eulerian Method with Local Structured Adaptive Mesh Refinement for Modeling Shock Hydrodynamics

    SciTech Connect

    Anderson, R W; Pember, R B; Elliott, N S

    2001-10-22

    A new method that combines staggered grid Arbitrary Lagrangian-Eulerian (ALE) techniques with structured local adaptive mesh refinement (AMR) has been developed for solution of the Euler equations. This method facilitates the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required through dynamic adaption. Many of the core issues involved in the development of the combined ALEAMR method hinge upon the integration of AMR with a staggered grid Lagrangian integration method. The novel components of the method are mainly driven by the need to reconcile traditional AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. Numerical examples are presented which demonstrate the accuracy and efficiency of the method.

  3. [Stabilization of mauthner neuron structure in goldfish adapted to the contralateral optokinetic stimulation].

    PubMed

    Tsaplina, N Iu; Mikhaĭlova, G Z; Shtanchaev, R Sh; Moshkov, D A

    2009-01-01

    Previously we have demonstrated, that the contralateral optokinetic (visual) stimulation (COS) induces an inversion of goldfish motor asymmetry and three-fold decrease of the ventral dendrite of ipsilateral Mauthner neuron (MN) volume, whereas repetitive in training mode daily COS sessions induced a motor behavior resistance to this influence in fish. In the present investigation we have examined the effect of the training COS sessions on the structure of MN and their parts. It was found that daily visual training stabilizes the size of the ventral dendrites, significantly increasing their resistance to single prolonged COS. Thus, the adapted morpho-functional state was induced in the individual dendrite and in the whole neuron by repetitive stimulation of that dendrite. These results make it possible to investigate in more detail the role of an individual dendrite in the modification of functional activity of the whole neuron and in adaptation and memory mechanisms at the cellular level.

  4. Stabilization of mauthner neuron structure on adaptation of goldfish to contralateral optokinetic stimulation.

    PubMed

    Tsaplina, N Yu; Mikhailova, G Z; Shtanchaev, R Sh; Moshkov, D A

    2010-09-01

    We have previously shown that contralateral optokinetic (visual) stimulation (COS) evokes inversion of motor asymmetry in goldfish and three-fold reductions in the volume of the ventral dendrite of the ipsilateral Mauthner neuron (MN). A training regime consisting of repeated daily sessions of COS induced resistance of the motor behavior of the fish to this treatment. We report here our studies of the effects of training sessions of COS on the structure of MN and their components. Daily visual training was found to stabilize the sizes of the dorsal dendrites of MN, significantly increasing their resistance to single prolonged sessions of COS. Thus, repeated stimulation of an individual dendrite induces an adaptive morphological state in the dendrite and in the neuron as a whole. This allows more detailed studies of the role of the individual dendrite in modifying the functional activity of the whole neuron in the mechanisms of adaptation and memory at the cellular level to be performed.

  5. Adaptive nonlinear polynomial neural networks for control of boundary layer/structural interaction

    NASA Technical Reports Server (NTRS)

    Parker, B. Eugene, Jr.; Cellucci, Richard L.; Abbott, Dean W.; Barron, Roger L.; Jordan, Paul R., III; Poor, H. Vincent

    1993-01-01

    The acoustic pressures developed in a boundary layer can interact with an aircraft panel to induce significant vibration in the panel. Such vibration is undesirable due to the aerodynamic drag and structure-borne cabin noises that result. The overall objective of this work is to develop effective and practical feedback control strategies for actively reducing this flow-induced structural vibration. This report describes the results of initial evaluations using polynomial, neural network-based, feedback control to reduce flow induced vibration in aircraft panels due to turbulent boundary layer/structural interaction. Computer simulations are used to develop and analyze feedback control strategies to reduce vibration in a beam as a first step. The key differences between this work and that going on elsewhere are as follows: that turbulent and transitional boundary layers represent broadband excitation and thus present a more complex stochastic control scenario than that of narrow band (e.g., laminar boundary layer) excitation; and secondly, that the proposed controller structures are adaptive nonlinear infinite impulse response (IIR) polynomial neural network, as opposed to the traditional adaptive linear finite impulse response (FIR) filters used in most studies to date. The controllers implemented in this study achieved vibration attenuation of 27 to 60 dB depending on the type of boundary layer established by laminar, turbulent, and intermittent laminar-to-turbulent transitional flows. Application of multi-input, multi-output, adaptive, nonlinear feedback control of vibration in aircraft panels based on polynomial neural networks appears to be feasible today. Plans are outlined for Phase 2 of this study, which will include extending the theoretical investigation conducted in Phase 2 and verifying the results in a series of laboratory experiments involving both bum and plate models.

  6. Adaptive nonlinear polynomial neural networks for control of boundary layer/structural interaction

    NASA Astrophysics Data System (ADS)

    Parker, B. Eugene, Jr.; Cellucci, Richard L.; Abbott, Dean W.; Barron, Roger L.; Jordan, Paul R., III; Poor, H. Vincent

    1993-12-01

    The acoustic pressures developed in a boundary layer can interact with an aircraft panel to induce significant vibration in the panel. Such vibration is undesirable due to the aerodynamic drag and structure-borne cabin noises that result. The overall objective of this work is to develop effective and practical feedback control strategies for actively reducing this flow-induced structural vibration. This report describes the results of initial evaluations using polynomial, neural network-based, feedback control to reduce flow induced vibration in aircraft panels due to turbulent boundary layer/structural interaction. Computer simulations are used to develop and analyze feedback control strategies to reduce vibration in a beam as a first step. The key differences between this work and that going on elsewhere are as follows: that turbulent and transitional boundary layers represent broadband excitation and thus present a more complex stochastic control scenario than that of narrow band (e.g., laminar boundary layer) excitation; and secondly, that the proposed controller structures are adaptive nonlinear infinite impulse response (IIR) polynomial neural network, as opposed to the traditional adaptive linear finite impulse response (FIR) filters used in most studies to date. The controllers implemented in this study achieved vibration attenuation of 27 to 60 dB depending on the type of boundary layer established by laminar, turbulent, and intermittent laminar-to-turbulent transitional flows. Application of multi-input, multi-output, adaptive, nonlinear feedback control of vibration in aircraft panels based on polynomial neural networks appears to be feasible today. Plans are outlined for Phase 2 of this study, which will include extending the theoretical investigation conducted in Phase 2 and verifying the results in a series of laboratory experiments involving both bum and plate models.

  7. Active load path adaption in a simple kinematic load-bearing structure due to stiffness change in the structure's supports

    NASA Astrophysics Data System (ADS)

    Gehb, C. M.; Platz, R.; Melz, T.

    2016-09-01

    Load-bearing structures with kinematic functions enable and disable degrees of freedom and are part of many mechanical engineering applications. The relative movement between a wheel and the body of a car or a landing gear and an aircraft fuselage are examples for load-bearing systems with defined kinematics. In most cases, the load is transmitted through a predetermined load path to the structural support interfaces. However, unexpected load peaks or varying health condition of the system's supports, which means for example varying damping and stiffness characteristics, may require an active adjustment of the load path. However, load paths transmitted through damaged or weakened supports can be the reason for reduced comfort or even failure. In this paper a simplified 2D two mass oscillator with two supports is used to numerically investigate the potential of controlled adaptive auxiliary kinematic guidance elements in a load-bearing structure to adapt the load path depending on the stiffness change, representing damage of the supports. The aim is to provide additional forces in the auxiliary kinematic guidance elements for two reasons. On the one hand, one of the two supports that may become weaker through stiffness change will be relieved from higher loading. On the other hand, tilting due to different compliance in the supports will be minimized. Therefore, shifting load between the supports during operation could be an effective option.

  8. Adaptable structural synthesis using advanced analysis and optimization coupled by a computer operating system

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, J.; Bhat, R. B.

    1979-01-01

    A finite element program is linked with a general purpose optimization program in a 'programing system' which includes user supplied codes that contain problem dependent formulations of the design variables, objective function and constraints. The result is a system adaptable to a wide spectrum of structural optimization problems. In a sample of numerical examples, the design variables are the cross-sectional dimensions and the parameters of overall shape geometry, constraints are applied to stresses, displacements, buckling and vibration characteristics, and structural mass is the objective function. Thin-walled, built-up structures and frameworks are included in the sample. Details of the system organization and characteristics of the component programs are given.

  9. Self-adaptive predictor-corrector algorithm for static nonlinear structural analysis

    NASA Technical Reports Server (NTRS)

    Padovan, J.

    1981-01-01

    A multiphase selfadaptive predictor corrector type algorithm was developed. This algorithm enables the solution of highly nonlinear structural responses including kinematic, kinetic and material effects as well as pro/post buckling behavior. The strategy involves three main phases: (1) the use of a warpable hyperelliptic constraint surface which serves to upperbound dependent iterate excursions during successive incremental Newton Ramphson (INR) type iterations; (20 uses an energy constraint to scale the generation of successive iterates so as to maintain the appropriate form of local convergence behavior; (3) the use of quality of convergence checks which enable various self adaptive modifications of the algorithmic structure when necessary. The restructuring is achieved by tightening various conditioning parameters as well as switch to different algorithmic levels to improve the convergence process. The capabilities of the procedure to handle various types of static nonlinear structural behavior are illustrated.

  10. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement

  11. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors

    SciTech Connect

    Alexander, Roger P; Jouline, Igor B

    2007-01-01

    As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N- and C-terminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.

  12. Dip-separated structural filtering using seislet transform and adaptive empirical mode decomposition based dip filter

    NASA Astrophysics Data System (ADS)

    Chen, Yangkang

    2016-07-01

    The seislet transform has been demonstrated to have a better compression performance for seismic data compared with other well-known sparsity promoting transforms, thus it can be used to remove random noise by simply applying a thresholding operator in the seislet domain. Since the seislet transform compresses the seismic data along the local structures, the seislet thresholding can be viewed as a simple structural filtering approach. Because of the dependence on a precise local slope estimation, the seislet transform usually suffers from low compression ratio and high reconstruction error for seismic profiles that have dip conflicts. In order to remove the limitation of seislet thresholding in dealing with conflicting-dip data, I propose a dip-separated filtering strategy. In this method, I first use an adaptive empirical mode decomposition based dip filter to separate the seismic data into several dip bands (5 or 6). Next, I apply seislet thresholding to each separated dip component to remove random noise. Then I combine all the denoised components to form the final denoised data. Compared with other dip filters, the empirical mode decomposition based dip filter is data-adaptive. One only needs to specify the number of dip components to be separated. Both complicated synthetic and field data examples show superior performance of my proposed approach than the traditional alternatives. The dip-separated structural filtering is not limited to seislet thresholding, and can also be extended to all those methods that require slope information.

  13. KRISTINA: Kinematic rib-based structural system for innovative adaptive trailing edge

    NASA Astrophysics Data System (ADS)

    Pecora, R.; Amoroso, F.; Magnifico, M.; Dimino, I.; Concilio, A.

    2016-04-01

    Nature teaches that the flight of the birds succeeds perfectly since they are able to change the shape of their wings in a continuous manner. The careful observation of this phenomenon has re-introduced in the recent research topics the study of "metamorphic" wing structures; these innovative architectures allow for the controlled wing shape adaptation to different flight conditions with the ultimate goal of getting desirable improvements such as the increase of aerodynamic efficiency or load control effectiveness. In this framework, the European research project SARISTU aimed at combining morphing and smart ideas to the leading edge, the trailing edge and the winglet of a large commercial airplane (EASA CS25 category) while assessing integrated technologies validation through high-speed wind tunnel test on a true scale outer wing segment. The design process of the adaptive trailing edge (ATED) addressed by SARISTU is here outlined, from the conceptual definition of the camber-morphing architecture up to the assessment of the device executive layout. Rational design criteria were implemented in order to preliminarily define ATED structural layout and the general configuration of the embedded mechanisms enabling morphing under the action of aerodynamic loads. Advanced FE analyses were then carried out and the robustness of adopted structural arrangements was proven in compliance with applicable airworthiness requirements.

  14. Protein Secondary Structure Prediction Using Local Adaptive Techniques in Training Neural Networks

    NASA Astrophysics Data System (ADS)

    Aik, Lim Eng; Zainuddin, Zarita; Joseph, Annie

    2008-01-01

    One of the most significant problems in computer molecular biology today is how to predict a protein's three-dimensional structure from its one-dimensional amino acid sequence or generally call the protein folding problem and difficult to determine the corresponding protein functions. Thus, this paper involves protein secondary structure prediction using neural network in order to solve the protein folding problem. The neural network used for protein secondary structure prediction is multilayer perceptron (MLP) of the feed-forward variety. The training set are taken from the protein data bank which are 120 proteins while 60 testing set is the proteins which were chosen randomly from the protein data bank. Multiple sequence alignment (MSA) is used to get the protein similar sequence and Position Specific Scoring matrix (PSSM) is used for network input. The training process of the neural network involves local adaptive techniques. Local adaptive techniques used in this paper comprises Learning rate by sign changes, SuperSAB, Quickprop and RPROP. From the simulation, the performance for learning rate by Rprop and Quickprop are superior to all other algorithms with respect to the convergence time. However, the best result was obtained using Rprop algorithm.

  15. An adaptive structure data acquisition system using a graphical-based programming language

    NASA Technical Reports Server (NTRS)

    Baroth, Edmund C.; Clark, Douglas J.; Losey, Robert W.

    1992-01-01

    An example of the implementation of data fusion using a PC and a graphical programming language is discussed. A schematic of the data acquisition system and user interface panel for an adaptive structure test are presented. The computer programs (a series of icons 'wired' together) are also discussed. The way in which using graphical-based programming software to control a data acquisition system can simplify analysis of data, promote multidisciplinary interaction, and provide users a more visual key to understanding their data are shown.

  16. IMRT planning on adaptive volume structures--a decisive reduction in computational complexity.

    PubMed

    Scherrer, Alexander; Küfer, Karl-Heinz; Bortfeld, Thomas; Monz, Michael; Alonso, Fernando

    2005-05-01

    The objective of radiotherapy planning is to find a compromise between the contradictive goals of delivering a sufficiently high dose to the target volume while widely sparing critical structures. The search for such a compromise requires the computation of several plans, which mathematically means solving several optimization problems. In the case of intensity modulated radiotherapy (IMRT) these problems are large-scale, hence the accumulated computational expense is very high. The adaptive clustering method presented in this paper overcomes this difficulty. The main idea is to use a preprocessed hierarchy of aggregated dose-volume information as a basis for individually adapted approximations of the original optimization problems. This leads to a decisively reduced computational expense: numerical experiments on several sets of real clinical data typically show computation times decreased by a factor of about 10. In contrast to earlier work in this field, this reduction in computational complexity will not lead to a loss in accuracy: the adaptive clustering method produces the optimum of the original optimization problem.

  17. Structure-based analysis of high pressure adaptation of alpha-actin.

    PubMed

    Morita, Takami

    2003-07-25

    Deep-sea fishes occur to depths of several thousand meters, and at these abyssal depths encounter pressures that shallower living fishes cannot tolerate. Tolerance of abyssal pressures by deep-sea fish is likely to depend in part on adaptive modifications of proteins. However, the types of structural modifications to proteins that allow function at high pressure have not been discovered. To elucidate the mechanisms of protein adaptation to high pressure, we cloned the alpha-skeletal actin cDNAs from two abyssal Coryphaenoides species, C. armatus and C. yaquinae, and identified three amino acid substitutions, V54A or L67P, Q137K, and A155S, that distinguish these abyssal actins from orthologs of alpha-actin from non-abyssal Coryphaenoides. These substitutions, Q137K and A155S, prevent the dissociation reactions of ATP and Ca2+ from being influenced by high pressure. In particular, the lysine residue at position 137 results in a much smaller apparent volume change in the Ca2+ dissociation reaction. The V54A or L67P substitution reduces the volume change associated with actin polymerization and has a role in maintaining the DNase I activity of actin at high pressure. Together, these results indicate that a few amino acid substitutions in key functional positions can adaptively alter the pressure sensitivity of a protein. PMID:12740368

  18. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement

  19. Active vibration control of adaptive flexible structures using piezoelectric smart sensors and actuators

    SciTech Connect

    Hong, S.Y.

    1992-01-01

    The active control of vibrations and radiated noise from structures is studied. The emphasis is the use of a minimum number of discrete piezoelectric wafer type sensors and actuators and optimal control algorithms. One of the major objectives is to effect control without substantially changing the structural dynamics of the original system. Canonical structures such as a cantilever beam and an all-clamped square plate, as well as practical structures such as fuel tanks, are investigated. For the suppression of a single mode as well as for multi-mode structural motions, velocity feedback and coupled model steady-state quadratic optimal control methods are applied using both analog and digital control systems with the various types of PZT (Lead-Zirconate-Titanate) transducers. The advantages of circular disc type PZT wafers are explained and a uni-disc type co-located sensor and actuator system has been proposed. For more efficient filtering of the structural mode signal, a smart filtering idea was developed considering the mode shape and poling direction of the sensor. To cover the signals from a partially distributed sensor and actuator to a point displacement and forcing signal, efficient conversion methods are developed. From the experimental and theoretical studies on the optimum selection of actuator positions, a coupled mode optimal control simulations is executed. A variety of adaptive structural vibration control experiments are performed verifying the potential of PZT transducers as sensors and actuators. Single mode and multimode control of structural vibration and radiated noise has been achieved. Using at the most 1-4 small disc or ring-shaped actuators, the original vibration levels have been reduced by 12-25 dB. Successful vibration control of the automobile fuel tank indicates that the ideas in this thesis can be applied to practical structures such as passenger compartments of ground and airborne vehicles.

  20. Vibration-based structural health monitoring using adaptive statistical method under varying environmental condition

    NASA Astrophysics Data System (ADS)

    Jin, Seung-Seop; Jung, Hyung-Jo

    2014-03-01

    It is well known that the dynamic properties of a structure such as natural frequencies depend not only on damage but also on environmental condition (e.g., temperature). The variation in dynamic characteristics of a structure due to environmental condition may mask damage of the structure. Without taking the change of environmental condition into account, false-positive or false-negative damage diagnosis may occur so that structural health monitoring becomes unreliable. In order to address this problem, an approach to construct a regression model based on structural responses considering environmental factors has been usually used by many researchers. The key to success of this approach is the formulation between the input and output variables of the regression model to take into account the environmental variations. However, it is quite challenging to determine proper environmental variables and measurement locations in advance for fully representing the relationship between the structural responses and the environmental variations. One alternative (i.e., novelty detection) is to remove the variations caused by environmental factors from the structural responses by using multivariate statistical analysis (e.g., principal component analysis (PCA), factor analysis, etc.). The success of this method is deeply depending on the accuracy of the description of normal condition. Generally, there is no prior information on normal condition during data acquisition, so that the normal condition is determined by subjective perspective with human-intervention. The proposed method is a novel adaptive multivariate statistical analysis for monitoring of structural damage detection under environmental change. One advantage of this method is the ability of a generative learning to capture the intrinsic characteristics of the normal condition. The proposed method is tested on numerically simulated data for a range of noise in measurement under environmental variation. A comparative

  1. [The multistemmed structure of Juniperus thurifera: adaptive advantage in a severe environment?].

    PubMed

    Bertaudière, V; Montès, N; Badri, W; Gauquelin, T

    2001-07-01

    A comparative study of radial growth and biomass between multistemmed trees with variable number of stems and single-stemmed trees was carried out to better understand determinism and organisation of multicaulis structure of a juniper species (Juniperus thurifera L.) growing in high Mediterranean mountains (High Atlas, Morocco). It appears that all the stems of the same tree have similar ages and so simultaneous development. Their mean annual radial increments show significant differences because of probable competition for water and nutrient supply and obvious physical competition for space. The multistemmed trees characterized by low number of stems have the same mean annual radial growth as single-stemmed trees and more generally all multistemmed junipers have a higher biomass. The multicaulis structure of Juniperus thurifera thus could be considered as an adaptation to severe environment, characterized not only by hard topographical, edaphic and climatic conditions, but by strong human pressure too. PMID:11476004

  2. Vibration suppression for large scale adaptive truss structures using direct output feedback control

    NASA Technical Reports Server (NTRS)

    Lu, Lyan-Ywan; Utku, Senol; Wada, Ben K.

    1993-01-01

    In this article, the vibration control of adaptive truss structures, where the control actuation is provided by length adjustable active members, is formulated as a direct output feedback control problem. A control method named Model Truncated Output Feedback (MTOF) is presented. The method allows the control feedback gain to be determined in a decoupled and truncated modal space in which only the critical vibration modes are retained. The on-board computation required by MTOF is minimal; thus, the method is favorable for the applications of vibration control of large scale structures. The truncation of the modal space inevitably introduces spillover effect during the control process. In this article, the effect is quantified in terms of active member locations, and it is shown that the optimal placement of active members, which minimizes the spillover effect (and thus, maximizes the control performance) can be sought. The problem of optimally selecting the locations of active members is also treated.

  3. Semiactive vibration control of nonlinear structures through adaptive backstepping techniques with H ∞ performance

    NASA Astrophysics Data System (ADS)

    Zapateiro, Mauricio; Karimi, Hamid Reza; Luo, Ningsu

    2011-05-01

    This article presents a new approach to the vibration mitigation problem in structures subject to seismic motions. These kinds of structures are characterised by the uncertainties of the parameters that describe their dynamics, such as stiffness and damping coefficients. Moreover, the dampers used to mitigate the vibrations caused by earthquakes are usually nonlinear devices with frictional or hysteretic dynamics. We propose an adaptive backstepping controller to account for the uncertainties and the nonlinearities. The controller is formulated in such a way that it satisfies an H ∞ performance. It is designed for a 10-storey building whose base is isolated with a frictional damper (passive device) and a magnetorheological damper (semiactive device). Controller performance is analysed through numerical simulations.

  4. [The multistemmed structure of Juniperus thurifera: adaptive advantage in a severe environment?].

    PubMed

    Bertaudière, V; Montès, N; Badri, W; Gauquelin, T

    2001-07-01

    A comparative study of radial growth and biomass between multistemmed trees with variable number of stems and single-stemmed trees was carried out to better understand determinism and organisation of multicaulis structure of a juniper species (Juniperus thurifera L.) growing in high Mediterranean mountains (High Atlas, Morocco). It appears that all the stems of the same tree have similar ages and so simultaneous development. Their mean annual radial increments show significant differences because of probable competition for water and nutrient supply and obvious physical competition for space. The multistemmed trees characterized by low number of stems have the same mean annual radial growth as single-stemmed trees and more generally all multistemmed junipers have a higher biomass. The multicaulis structure of Juniperus thurifera thus could be considered as an adaptation to severe environment, characterized not only by hard topographical, edaphic and climatic conditions, but by strong human pressure too.

  5. Consequences of adaptive behaviour for the structure and dynamics of food webs.

    PubMed

    Valdovinos, Fernanda S; Ramos-Jiliberto, Rodrigo; Garay-Narváez, Leslie; Urbani, Pasquinell; Dunne, Jennifer A

    2010-12-01

    Species coexistence within ecosystems and the stability of patterns of temporal changes in population sizes are central topics in ecological theory. In the last decade, adaptive behaviour has been proposed as a mechanism of population stabilization. In particular, widely distributed adaptive trophic behaviour (ATB), the fitness-enhancing changes in individuals' feeding-related traits due to variation in their trophic environment, may play a key role in modulating the dynamics of feeding relationships within natural communities. In this article, we review and synthesize models and results from theoretical research dealing with the consequences of ATB on the structure and dynamics of complex food webs. We discuss current approaches, point out limitations, and consider questions ripe for future research. In spite of some differences in the modelling and analytic approaches, there are points of convergence: (1) ATB promotes the complex structure of ecological networks, (2) ATB increases the stability of their dynamics, (3) ATB reverses May's negative complexity-stability relationship, and (4) ATB provides resilience and resistance of networks against perturbations. Current knowledge supports ATB as an essential ingredient for models of community dynamics, and future research that incorporates ATB will be well positioned to address questions important for basic ecological research and its applications.

  6. Spiders in motion: demonstrating adaptation, structure-function relationships, and trade-offs in invertebrates.

    PubMed

    Bowlin, Melissa S; McLeer, Dorothy F; Danielson-Francois, Anne M

    2014-03-01

    Evolutionary history and structural considerations constrain all aspects of animal physiology. Constraints on invertebrate locomotion are especially straightforward for students to observe and understand. In this exercise, students use spiders to investigate the concepts of adaptation, structure-function relationships, and trade-offs. Students measure burst and endurance performance in several taxonomic families of spiders whose ecological niches have led to different locomotory adaptations. Based on observations of spiders in their natural habitat and prior background information, students make predictions about spider performance. Students then construct their own knowledge by performing a hands-on, inquiry-based scientific experiment where the results are not necessarily known. Depending on the specific families chosen, students can observe that web-dwelling spiders have more difficulty navigating complex terrestrial terrain than ground-dwelling spiders and that there is a trade-off between burst performance and endurance performance in spiders. Our inexpensive runway design allows for countless variations on this basic experiment; for example, we have successfully used runways to show students how the performance of heterothermic ectotherms varies with temperature. High levels of intra- and interindividual variation in performance underscore the importance of using multiple trials and statistical tests. Finally, this laboratory activity can be completely student driven or standardized, depending on the instructor's preference.

  7. Dynamic modeling, property investigation, and adaptive controller design of serial robotic manipulators modeled with structural compliance

    NASA Technical Reports Server (NTRS)

    Tesar, Delbert; Tosunoglu, Sabri; Lin, Shyng-Her

    1990-01-01

    Research results on general serial robotic manipulators modeled with structural compliances are presented. Two compliant manipulator modeling approaches, distributed and lumped parameter models, are used in this study. System dynamic equations for both compliant models are derived by using the first and second order influence coefficients. Also, the properties of compliant manipulator system dynamics are investigated. One of the properties, which is defined as inaccessibility of vibratory modes, is shown to display a distinct character associated with compliant manipulators. This property indicates the impact of robot geometry on the control of structural oscillations. Example studies are provided to illustrate the physical interpretation of inaccessibility of vibratory modes. Two types of controllers are designed for compliant manipulators modeled by either lumped or distributed parameter techniques. In order to maintain the generality of the results, neither linearization is introduced. Example simulations are given to demonstrate the controller performance. The second type controller is also built for general serial robot arms and is adaptive in nature which can estimate uncertain payload parameters on-line and simultaneously maintain trajectory tracking properties. The relation between manipulator motion tracking capability and convergence of parameter estimation properties is discussed through example case studies. The effect of control input update delays on adaptive controller performance is also studied.

  8. Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula.

    PubMed

    Oh, Dong-Ha; Hong, Hyewon; Lee, Sang Yeol; Yun, Dae-Jin; Bohnert, Hans J; Dassanayake, Maheshi

    2014-04-01

    Schrenkiella parvula (formerly Thellungiella parvula), a close relative of Arabidopsis (Arabidopsis thaliana) and Brassica crop species, thrives on the shores of Lake Tuz, Turkey, where soils accumulate high concentrations of multiple-ion salts. Despite the stark differences in adaptations to extreme salt stresses, the genomes of S. parvula and Arabidopsis show extensive synteny. S. parvula completes its life cycle in the presence of Na⁺, K⁺, Mg²⁺, Li⁺, and borate at soil concentrations lethal to Arabidopsis. Genome structural variations, including tandem duplications and translocations of genes, interrupt the colinearity observed throughout the S. parvula and Arabidopsis genomes. Structural variations distinguish homologous gene pairs characterized by divergent promoter sequences and basal-level expression strengths. Comparative RNA sequencing reveals the enrichment of ion-transport functions among genes with higher expression in S. parvula, while pathogen defense-related genes show higher expression in Arabidopsis. Key stress-related ion transporter genes in S. parvula showed increased copy number, higher transcript dosage, and evidence for subfunctionalization. This extremophyte offers a framework to identify the requisite adjustments of genomic architecture and expression control for a set of genes found in most plants in a way to support distinct niche adaptation and lifestyles. PMID:24563282

  9. PACS—Realization of an adaptive concept using pressure actuated cellular structures

    NASA Astrophysics Data System (ADS)

    Gramüller, B.; Boblenz, J.; Hühne, C.

    2014-10-01

    A biologically inspired concept is investigated which can be utilized to develop energy efficient, lightweight and applicational flexible adaptive structures. Building a real life morphing unit is an ambitious task as the numerous works in the particular field show. Summarizing fundamental demands and barriers regarding shape changing structures, the basic challenges of designing morphing structures are listed. The concept of Pressure Actuated Cellular Structures (PACS) is arranged within the recent morphing activities and it is shown that it complies with the underlying demands. Systematically divided into energy-related and structural subcomponents the working principle is illuminated and relationships between basic design parameters are expressed. The analytical background describing the physical mechanisms of PACS is presented in concentrated manner. This work focuses on the procedure of dimensioning, realizing and experimental testing of a single cell and a single row cantilever made of PACS. The experimental outcomes as well as the results from the FEM computations are used for evaluating the analytical methods. The functionality of the basic principle is thus validated and open issues are determined pointing the way ahead.

  10. Structural characterization of metal binding to a cold-adapted frataxin.

    PubMed

    Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

    2015-06-01

    Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

  11. Evaluation of an adaptive unstructured remeshing technique for integrated fluid-thermal-structural analysis

    NASA Technical Reports Server (NTRS)

    Dechaumphai, Pramote

    1990-01-01

    An adaptive unstructured remeshing technique is evaluated for integrated fluid-thermal-structural analysis. The technique is combined with the finite element method to solve: (1) the Navier-Stokes equations for high-speed compressible flow; (2) the energy equation for the structural-thermal response; and (3) the quasi-static equilibrium equations for the structural response. The remeshing technique and the analysis solution procedure are described. The effectiveness of the approach is evaluated with two application studies. The flow analysis of Mach 8 shock-shock interference on a three-inch-diameter cylinder is used as the first application study to demonstrate the capability of the remeshing technique and to examine proper remeshing indicators for the inviscid and boundary layer regions. The applicability of the approach for the thermal and structural analyses of the structure is evaluated in the second application study of a 0.25-inch-diameter convectively cooled leading edge subjected to intense aerodynamic heating. Issues associated with remeshing indicators for thermal stress problems are identified.

  12. Subversion of innate and adaptive immune activation induced by structurally modified lipopolysaccharide from Salmonella typhimurium.

    PubMed

    Pastelin-Palacios, Rodolfo; Gil-Cruz, Cristina; Pérez-Shibayama, Christian I; Moreno-Eutimio, Mario A; Cervantes-Barragán, Luisa; Arriaga-Pizano, Lourdes; Ludewig, Burkhard; Cunningham, Adam F; García-Zepeda, Eduardo A; Becker, Ingeborg; Alpuche-Aranda, Celia; Bonifaz, Laura; Gunn, John S; Isibasi, Armando; López-Macías, Constantino

    2011-08-01

    Salmonella are successful pathogens that infect millions of people every year. During infection, Salmonella typhimurium changes the structure of its lipopolysaccharide (LPS) in response to the host environment, rendering bacteria resistant to cationic peptide lysis in vitro. However, the role of these structural changes in LPS as in vivo virulence factors and their effects on immune responses and the generation of immunity are largely unknown. We report that modified LPS are less efficient than wild-type LPS at inducing pro-inflammatory responses. The impact of this LPS-mediated subversion of innate immune responses was demonstrated by increased mortality in mice infected with a non-lethal dose of an attenuated S. typhimurium strain mixed with the modified LPS moieties. Up-regulation of co-stimulatory molecules on antigen-presenting cells and CD4(+) T-cell activation were affected by these modified LPS. Strains of S. typhimurium carrying structurally modified LPS are markedly less efficient at inducing specific antibody responses. Immunization with modified LPS moiety preparations combined with experimental antigens, induced an impaired Toll-like receptor 4-mediated adjuvant effect. Strains of S. typhimurium carrying structurally modified LPS are markedly less efficient at inducing immunity against challenge with virulent S. typhimurium. Hence, changes in S. typhimurium LPS structure impact not only on innate immune responses but also on both humoral and cellular adaptive immune responses.

  13. Subversion of innate and adaptive immune activation induced by structurally modified lipopolysaccharide from Salmonella typhimurium

    PubMed Central

    Pastelin-Palacios, Rodolfo; Gil-Cruz, Cristina; Pérez-Shibayama, Christian I; Moreno-Eutimio, Mario A; Cervantes-Barragán, Luisa; Arriaga-Pizano, Lourdes; Ludewig, Burkhard; Cunningham, Adam F; García-Zepeda, Eduardo A; Becker, Ingeborg; Alpuche-Aranda, Celia; Bonifaz, Laura; Gunn, John S; Isibasi, Armando; López-Macías, Constantino

    2011-01-01

    Salmonella are successful pathogens that infect millions of people every year. During infection, Salmonella typhimurium changes the structure of its lipopolysaccharide (LPS) in response to the host environment, rendering bacteria resistant to cationic peptide lysis in vitro. However, the role of these structural changes in LPS as in vivo virulence factors and their effects on immune responses and the generation of immunity are largely unknown. We report that modified LPS are less efficient than wild-type LPS at inducing pro-inflammatory responses. The impact of this LPS-mediated subversion of innate immune responses was demonstrated by increased mortality in mice infected with a non-lethal dose of an attenuated S. typhimurium strain mixed with the modified LPS moieties. Up-regulation of co-stimulatory molecules on antigen-presenting cells and CD4+ T-cell activation were affected by these modified LPS. Strains of S. typhimurium carrying structurally modified LPS are markedly less efficient at inducing specific antibody responses. Immunization with modified LPS moiety preparations combined with experimental antigens, induced an impaired Toll-like receptor 4-mediated adjuvant effect. Strains of S. typhimurium carrying structurally modified LPS are markedly less efficient at inducing immunity against challenge with virulent S. typhimurium. Hence, changes in S. typhimurium LPS structure impact not only on innate immune responses but also on both humoral and cellular adaptive immune responses. PMID:21631497

  14. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

    PubMed Central

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  15. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  16. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer.

  17. Structure-adaptive CBCT reconstruction using weighted total variation and Hessian penalties

    PubMed Central

    Shi, Qi; Sun, Nanbo; Sun, Tao; Wang, Jing; Tan, Shan

    2016-01-01

    The exposure of normal tissues to high radiation during cone-beam CT (CBCT) imaging increases the risk of cancer and genetic defects. Statistical iterative algorithms with the total variation (TV) penalty have been widely used for low dose CBCT reconstruction, with state-of-the-art performance in suppressing noise and preserving edges. However, TV is a first-order penalty and sometimes leads to the so-called staircase effect, particularly over regions with smooth intensity transition in the reconstruction images. A second-order penalty known as the Hessian penalty was recently used to replace TV to suppress the staircase effect in CBCT reconstruction at the cost of slightly blurring object edges. In this study, we proposed a new penalty, the TV-H, which combines TV and Hessian penalties for CBCT reconstruction in a structure-adaptive way. The TV-H penalty automatically differentiates the edges, gradual transition and uniform local regions within an image using the voxel gradient, and adaptively weights TV and Hessian according to the local image structures in the reconstruction process. Our proposed penalty retains the benefits of TV, including noise suppression and edge preservation. It also maintains the structures in regions with gradual intensity transition more successfully. A majorization-minimization (MM) approach was designed to optimize the objective energy function constructed with the TV-H penalty. The MM approach employed a quadratic upper bound of the original objective function, and the original optimization problem was changed to a series of quadratic optimization problems, which could be efficiently solved using the Gauss-Seidel update strategy. We tested the reconstruction algorithm on two simulated digital phantoms and two physical phantoms. Our experiments indicated that the TV-H penalty visually and quantitatively outperformed both TV and Hessian penalties.

  18. Structure-adaptive CBCT reconstruction using weighted total variation and Hessian penalties

    PubMed Central

    Shi, Qi; Sun, Nanbo; Sun, Tao; Wang, Jing; Tan, Shan

    2016-01-01

    The exposure of normal tissues to high radiation during cone-beam CT (CBCT) imaging increases the risk of cancer and genetic defects. Statistical iterative algorithms with the total variation (TV) penalty have been widely used for low dose CBCT reconstruction, with state-of-the-art performance in suppressing noise and preserving edges. However, TV is a first-order penalty and sometimes leads to the so-called staircase effect, particularly over regions with smooth intensity transition in the reconstruction images. A second-order penalty known as the Hessian penalty was recently used to replace TV to suppress the staircase effect in CBCT reconstruction at the cost of slightly blurring object edges. In this study, we proposed a new penalty, the TV-H, which combines TV and Hessian penalties for CBCT reconstruction in a structure-adaptive way. The TV-H penalty automatically differentiates the edges, gradual transition and uniform local regions within an image using the voxel gradient, and adaptively weights TV and Hessian according to the local image structures in the reconstruction process. Our proposed penalty retains the benefits of TV, including noise suppression and edge preservation. It also maintains the structures in regions with gradual intensity transition more successfully. A majorization-minimization (MM) approach was designed to optimize the objective energy function constructed with the TV-H penalty. The MM approach employed a quadratic upper bound of the original objective function, and the original optimization problem was changed to a series of quadratic optimization problems, which could be efficiently solved using the Gauss-Seidel update strategy. We tested the reconstruction algorithm on two simulated digital phantoms and two physical phantoms. Our experiments indicated that the TV-H penalty visually and quantitatively outperformed both TV and Hessian penalties. PMID:27699100

  19. Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

    PubMed Central

    Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V.; Yang, Wei; Deacon, Ashley; Sliz, Piotr

    2012-01-01

    Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfra­structure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities. PMID:22514186

  20. Clinal resistance structure and pathogen local adaptation in a serpentine flax-flax rust interaction.

    PubMed

    Springer, Yuri P

    2007-08-01

    Because disease resistance is a hallmark signature of pathogen-mediated selection pressure on hosts, studies of resistance structure (the spatial distribution of disease resistance genes among conspecific host populations) can provide valuable insights into the influence of pathogens on host evolution and spatial variation in the magnitude of their effects. To date few studies of wild plant-pathogen interactions have characterized resistance structure by sampling across the host's biogeographic range, and only a handful have paired such investigations with studies of disease levels under natural conditions. I used a greenhouse cross-inoculation experiment to characterize genetic resistance of 16 populations of California dwarf flax (Hesperolinon californicum) to attack by multiple samples of the rust fungus Melampsora lini. I documented a latitudinal cline in resistance structure, manifest across the host's biogeographic range, which mirrored almost identically a cline in infection prevalence documented through field surveys of disease in study populations. These results provide empirical evidence for clinal patterns of antagonistic selection pressure, demonstrate that such patterns can be manifest across broad biogeographic scales, and suggest that rates of disease prevalence in wild plant populations may be tightly linked to the distribution of host resistance genes. Tests for local adaptation of the fungus revealed evidence of the phenomenon (significantly greater infection in sympatric plant-fungal pairings) as well as the potential for substantial bias to be introduced into statistical analyses by spatial patterns of host resistance structure.

  1. Tracking adaptive evolution in the structure, function and molecular phylogeny of haemoglobin in non-Antarctic notothenioid fish species

    NASA Astrophysics Data System (ADS)

    Verde, Cinzia; Parisi, Elio; di Prisco, Guido

    2006-04-01

    With the notable exception of Antarctic icefishes, haemoglobin (Hb) is present in all vertebrates. In polar fish, Hb evolution has included adaptations with implications at the biochemical, physiological and molecular levels. Cold adaptation has been shown to be also linked to small changes in primary structure and post-translational modifications in proteins, including hydrophobic remodelling and increased flexibility. A wealth of knowledge is available on the oxygen-transport system of fish inhabiting Antarctic waters, but very little is known on the structure and function of Hb of non-Antarctic notothenioid fishes. The comparison of the biochemical and physiological adaptations between cold-adapted and non-cold-adapted species is a powerful tool to understand whether (and to what extent) extreme environments require specific adaptations or simply select for phenotypically different life styles. This study focuses on structure, function and molecular phylogeny of Hb in Antarctic and non-Antarctic notothenioid fishes. The rationale is to use the primary structure of Hb as tool of choice to gain insight into the pathways of the evolution history of α and β globins of notothenioids and also as a basis for reconstructing the phylogenetic relationships among Antarctic and non-Antarctic species.

  2. Structural and functional robustness of the adaptive-sorting signaling network

    NASA Astrophysics Data System (ADS)

    Pang, Ning-Ning

    2016-06-01

    A major task of study on ligand discrimination by T cells is the construction of a mechanistic model to account for threshold setting in response to variant ligands interacting with the same T-cell receptors. Recently, Lalanne and Francois in a seminal paper (2013 Phys. Rev. Lett. 110 218102) have addressed this question by constructing minimal core circuits such that the biological outputs can satisfy the essential properties of early T-cell activation. To make this core set of network topology a valuable tool for synthetic biologists to robustly engineer biological circuits, we are motivated to ask a general question: is adaptive response encoded by the proposed circuit topology structurally stable, regardless of the values of the kinetic parameters? This has particularly relevant effects for the network reliability, since failures in ligand discrimination result in either infection or autoimmune diseases. To the best of our knowledge, a rigorous and complete mathematical proof of this issue is still lacking in the literature. In this paper, by giving a rigorous mathematical proof, we have shown that this regulatory circuitry is appropriately designed and the existence, uniqueness, and globally asymptotic attractiveness of the steady state are preserved. Moreover, we further generalize the adaptive sorting module and undertake an extensive analysis on the trade-off between antagonism and sensitivity of T-cell ligand discrimination in various cellular conditions. Notably, the optimal phosphorylation step in which to place the regulatory motif is analytically obtained and numerically confirmed. Finally, relevant experimental facts and biological implications are discussed.

  3. Adaptive AFM scan speed control for high aspect ratio fast structure tracking

    SciTech Connect

    Ahmad, Ahmad; Schuh, Andreas; Rangelow, Ivo W.

    2014-10-15

    Improved imaging rates in Atomic Force Microscopes (AFM) are of high interest for disciplines such as life sciences and failure analysis of semiconductor wafers, where the sample topology shows high aspect ratios. Also, fast imaging is necessary to cover a large surface under investigation in reasonable times. Since AFMs are composed of mechanical components, they are associated with comparably low resonance frequencies that undermine the effort to increase the acquisition rates. In particular, high and steep structures are difficult to follow, which causes the cantilever to temporarily loose contact to or crash into the sample. Here, we report on a novel approach that does not affect the scanner dynamics, but adapts the lateral scanning speed of the scanner. The controller monitors the control error signal and, only when necessary, decreases the scan speed to allow the z-piezo more time to react to changes in the sample's topography. In this case, the overall imaging rate can be significantly increased, because a general scan speed trade-off decision is not needed and smooth areas are scanned fast. In contrast to methods trying to increase the z-piezo bandwidth, our method is a comparably simple approach that can be easily adapted to standard systems.

  4. Staggered grid lagrangian method with local structured adaptive mesh refinement for modeling shock hydrodynamics

    SciTech Connect

    Anderson, R W; Pember, R B; Elliot, N S

    2000-09-26

    A new method for the solution of the unsteady Euler equations has been developed. The method combines staggered grid Lagrangian techniques with structured local adaptive mesh refinement (AMR). This method is a precursor to a more general adaptive arbitrary Lagrangian Eulerian (ALE-AMR) algorithm under development, which will facilitate the solution of problems currently at and beyond the boundary of soluble problems by traditional ALE methods by focusing computational resources where they are required. Many of the core issues involved in the development of the ALE-AMR method hinge upon the integration of AMR with a Lagrange step, which is the focus of the work described here. The novel components of the method are mainly driven by the need to reconcile traditional AMR techniques, which are typically employed on stationary meshes with cell-centered quantities, with the staggered grids and grid motion employed by Lagrangian methods. These new algorithmic components are first developed in one dimension and are then generalized to two dimensions. Solutions of several model problems involving shock hydrodynamics are presented and discussed.

  5. Adaptive Radar Detection of a Subspace Signal Embedded in Subspace Structured Plus Gaussian Interference Via Invariance

    NASA Astrophysics Data System (ADS)

    De Maio, Antonio; Orlando, Danilo

    2016-04-01

    This paper deals with adaptive radar detection of a subspace signal competing with two sources of interference. The former is Gaussian with unknown covariance matrix and accounts for the joint presence of clutter plus thermal noise. The latter is structured as a subspace signal and models coherent pulsed jammers impinging on the radar antenna. The problem is solved via the Principle of Invariance which is based on the identification of a suitable group of transformations leaving the considered hypothesis testing problem invariant. A maximal invariant statistic, which completely characterizes the class of invariant decision rules and significantly compresses the original data domain, as well as its statistical characterization are determined. Thus, the existence of the optimum invariant detector is addressed together with the design of practically implementable invariant decision rules. At the analysis stage, the performance of some receivers belonging to the new invariant class is established through the use of analytic expressions.

  6. Structural Adaptation of a Thermostable Biotin-binding Protein in a Psychrophilic Environment

    PubMed Central

    Meir, Amit; Bayer, Edward A.; Livnah, Oded

    2012-01-01

    Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive disulfide bridge were shown to account for the high affinity toward biotin. Phe-43 emulates the function and position of the critical intermonomeric Trp that characterizes the tetrameric avidins but is lacking in shwanavidin. The 18 copies of the apo-monomer revealed distinctive snapshots of L3,4 and Phe-43, providing rare insight into loop flexibility, binding site accessibility, and psychrophilic adaptation. Nevertheless, as in all avidins, shwanavidin also displays high thermostability properties. The unique features of shwanavidin may provide a platform for the design of a long sought after monovalent form of avidin, which would be ideal for novel types of biotechnological application. PMID:22493427

  7. Thermal and Structural Performance of Woven Carbon Cloth For Adaptive Deployable Entry and Placement Technology

    NASA Technical Reports Server (NTRS)

    Arnold, James O.; Peterson, Keith H.; Yount, Bryan C.; Schneider, Nigel; Chavez-Garcia, Jose

    2013-01-01

    Arcjet testing and analysis of a three-dimensional (3D) woven carbon fabric has shown that it can be used as a thermal protection system and as a load bearing structural component for a low ballistic coefficient hypersonic decelerator called ADEPT (Adaptive Deployable Entry and Placement Technology). Results of arcjet tests proved that the 3D woven carbon fabric can withstand flight-like heating while under flight-like biaxial mechanical loads representative of those encountered during shallow entry flight path angles into the atmosphere of Venus. Importantly, the arcjet test results have been used to extend a preliminary material thermal response model based on previous testing of the same 3D woven carbon fabric under uni-axial mechanical loading.

  8. Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

    PubMed Central

    Montano, Valeria; Didelot, Xavier; Foll, Matthieu; Linz, Bodo; Reinhardt, Richard; Suerbaum, Sebastian; Moodley, Yoshan; Jensen, Jeffrey D.

    2015-01-01

    Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g., transcription elongation factor NusA and tumor necrosis factor alpha-inducing protein Tipα) and hitherto unknown functional genes. PMID:25995212

  9. Adaptive technique for three-dimensional MR imaging of moving structures.

    PubMed

    Korin, H W; Felmlee, J P; Ehman, R L; Riederer, S J

    1990-10-01

    The authors describe an adaptive motion correction method for three-dimensional magnetic resonance (MR) imaging. Three-dimensional imaging offers many advantages over two-dimensional multisection imaging but is susceptible to image corruption due to motion. Thus, it has been of limited use in the imaging of mobile structures, and the relatively long imaging times required have hindered its use in patients who tend to move during imaging. The authors' technique uses interleaved "navigator" echoes to provide a measure of displacement for each image echo in the acquisition and then uses this information to allow correction of the image data. The theory for signal corruption due to motion and the correction scheme that follows from it are presented. This method can produce excellent results when the motion is correctly modeled.

  10. Resistance exercise induces region-specific adaptations in anterior pituitary gland structure and function in rats.

    PubMed

    Kraemer, William J; Flanagan, Shawn D; Volek, Jeff S; Nindl, Bradley C; Vingren, Jakob L; Dunn-Lewis, Courtenay; Comstock, Brett A; Hooper, David R; Szivak, Tunde K; Looney, David P; Maresh, Carl M; Hymer, Wesley C

    2013-12-01

    The anterior pituitary gland (AP) increases growth hormone (GH) secretion in response to resistance exercise (RE), but the nature of AP adaptations to RE is unknown. To that end, we examined the effects of RE on regional AP somatotroph GH release, structure, and relative quantity. Thirty-six Sprague-Dawley rats were assigned to one of four groups: 1) no training or acute exercise (NT-NEX); 2) no training with acute exercise (NT-EX); 3) resistance training without acute exercise (RT-NEX); 4) resistance training with acute exercise (RT-EX). RE incorporated 10, 1 m-weighted ladder climbs at an 85° angle. RT groups trained 3 days/wk for 7 wk, progressively. After death, trunk blood was collected, and each AP was divided into quadrants (ventral-dorsal and left-right). We measured: 1) trunk plasma GH; 2) somatotroph GH release; 3) somatotroph size; 4) somatotroph secretory content; and 5) percent of AP cells identified as somatotrophs. Trunk GH differed by group (NT-NEX, 8.9 ± 2.4 μg/l; RT-NEX, 9.2 ± 3.5 μg/l; NT-EX, 15.6 ± 3.4 μg/l; RT-EX, 23.4 ± 4.6 μg/l). RT-EX demonstrated greater somatotroph GH release than all other groups, predominantly in ventral regions (P < 0.05-0.10). Ventral somatotrophs were larger in NT-EX and RT-NEX compared with RT-EX (P < 0.05-0.10). RT-NEX exhibited significantly greater secretory granule content than all other groups but in the ventral-right region only (P < 0.05-0.10). Our findings indicate reproducible patterns of spatially distinct, functionally different somatotroph subpopulations in the rat pituitary gland. RE training appears to induce dynamic adaptations in somatotroph structure and function.

  11. Adaptive Modulation of Adult Brain Gray and White Matter to High Altitude: Structural MRI Studies

    PubMed Central

    Zhang, Jiaxing; Zhang, Haiyan; Li, Jinqiang; Chen, Ji; Han, Qiaoqing; Lin, Jianzhong; Yang, Tianhe; Fan, Ming

    2013-01-01

    The aim of this study was to investigate brain structural alterations in adult immigrants who adapted to high altitude (HA). Voxel-based morphometry analysis of gray matter (GM) volumes, surface-based analysis of cortical thickness, and Tract-Based Spatial Statistics analysis of white matter fractional anisotropy (FA) based on MRI images were conducted on 16 adults (20–22 years) who immigrated to the Qinghai-Tibet Plateau (2300–4400 m) for 2 years. They had no chronic mountain sickness. Control group consisted of 16 matched sea level subjects. A battery of neuropsychological tests was also conducted. HA immigrants showed significantly decreased GM volumes in the right postcentral gyrus and right superior frontal gyrus, and increased GM volumes in the right middle frontal gyrus, right parahippocampal gyrus, right inferior and middle temporal gyri, bilateral inferior ventral pons, and right cerebellum crus1. While there was some divergence in the left hemisphere, surface-based patterns of GM changes in the right hemisphere resembled those seen for VBM analysis. FA changes were observed in multiple WM tracts. HA immigrants showed significant impairment in pulmonary function, increase in reaction time, and deficit in mental rotation. Parahippocampal and middle frontal GM volumes correlated with vital capacity. Superior frontal GM volume correlated with mental rotation and postcentral GM correlated with reaction time. Paracentral lobule and frontal FA correlated with mental rotation reaction time. There might be structural modifications occurred in the adult immigrants during adaptation to HA. The changes in GM may be related to impaired respiratory function and psychological deficits. PMID:23874692

  12. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    DOE PAGES

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; Mavrici, Daniela; Waldo, Geoffrey S.; Hung, Li -Wei; Sacchettini, James C.; Terwilliger, Thomas C.; Alber, Tom; Mayer, Claudine

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows thatmore » Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.« less

  13. Shape control of structures with semi-definite stiffness matrices for adaptive wings

    NASA Astrophysics Data System (ADS)

    Austin, Fred; Van Nostrand, William C.; Rossi, Michael J.

    1993-09-01

    Maintaining an optimum-wing cross section during transonic cruise can dramatically reduce the shock-induced drag and can result in significant fuel savings and increased range. Our adaptive-wing concept employs actuators as truss elements of active ribs to reshape the wing cross section by deforming the structure. In our previous work, to derive the shape control- system gain matrix, we developed a procedure that requires the inverse of the stiffness matrix of the structure without the actuators. However, this method cannot be applied to designs where the actuators are required structural elements since the stiffness matrices are singular when the actuator are removed. Consequently, a new method was developed, where the order of the problem is reduced and only the inverse of a small nonsingular partition of the stiffness matrix is required to obtain the desired gain matrix. The procedure was experimentally validated by achieving desired shapes of a physical model of an aircraft-wing rib. The theory and test results are presented.

  14. Movement Analysis of Flexion and Extension of Honeybee Abdomen Based on an Adaptive Segmented Structure

    PubMed Central

    Zhao, Jieliang; Wu, Jianing; Yan, Shaoze

    2015-01-01

    Honeybees (Apis mellifera) curl their abdomens for daily rhythmic activities. Prior to determining this fact, people have concluded that honeybees could curl their abdomen casually. However, an intriguing but less studied feature is the possible unidirectional abdominal deformation in free-flying honeybees. A high-speed video camera was used to capture the curling and to analyze the changes in the arc length of the honeybee abdomen not only in free-flying mode but also in the fixed sample. Frozen sections and environment scanning electron microscope were used to investigate the microstructure and motion principle of honeybee abdomen and to explore the physical structure restricting its curling. An adaptive segmented structure, especially the folded intersegmental membrane (FIM), plays a dominant role in the flexion and extension of the abdomen. The structural features of FIM were utilized to mimic and exhibit movement restriction on honeybee abdomen. Combining experimental analysis and theoretical demonstration, a unidirectional bending mechanism of honeybee abdomen was revealed. Through this finding, a new perspective for aerospace vehicle design can be imitated. PMID:26223946

  15. Subfamily-Specific Adaptations in the Structures of Two Penicillin-Binding Proteins from Mycobacterium tuberculosis

    PubMed Central

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; Mavrici, Daniela; Waldo, Geoffrey S.; Hung, Li-Wei; Sacchettini, James C.; Terwilliger, Thomas C.; Alber, Tom

    2014-01-01

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis. PMID:25551456

  16. Structures and Mechanisms Design Concepts for Adaptive Deployable Entry Placement Technology

    NASA Technical Reports Server (NTRS)

    Yount, Bryan C.; Arnold, James O.; Gage, Peter J.; Mockelman, Jeffrey; Venkatapathy, Ethiraj

    2012-01-01

    System studies have shown that large deployable aerodynamic decelerators such as the Adaptive Deployable Entry and Placement Technology (ADEPT) concept can revolutionize future robotic and human exploration missions involving atmospheric entry, descent and landing by significantly reducing the maximum heating rate, total heat load, and deceleration loads experienced by the spacecraft during entry [1-3]. ADEPT and the Hypersonic Inflatable Aerodynamic Decelerator (HIAD) [4] share the approach of stowing the entry system in the shroud of the launch vehicle and deploying it to a much larger diameter prior to entry. The ADEPT concept provides a low ballistic coefficient for planetary entry by employing an umbrella-like deployable structure consisting of ribs, struts and a fabric cover that form an aerodynamic decelerator capable of undergoing hypersonic flight. The ADEPT "skin" is a 3-D woven carbon cloth that serves as a thermal protection system (TPS) and as a structural surface that transfers aerodynamic forces to the underlying ribs [5]. This paper focuses on design activities associated with integrating ADEPT components (cloth, ribs, struts and mechanisms) into a system that can function across all configurations and environments of a typical mission concept: stowed during launch, in-space deployment, entry, descent, parachute deployment and separation from the landing payload. The baseline structures and mechanisms were selected via trade studies conducted during the summer and fall of 2012. They are now being incorporated into the design of a ground test article (GTA) that will be fabricated in 2013. It will be used to evaluate retention of the stowed configuration in a launch environment, mechanism operation for release, deployment and locking, and static strength of the deployed decelerator. Of particular interest are the carbon cloth interfaces, underlying hot structure, (Advanced Carbon- Carbon ribs) and other structural components (nose cap, struts, and

  17. Adaptive Methods within a Sequential Bayesian Approach for Structural Health Monitoring

    NASA Astrophysics Data System (ADS)

    Huff, Daniel W.

    Structural integrity is an important characteristic of performance for critical components used in applications such as aeronautics, materials, construction and transportation. When appraising the structural integrity of these components, evaluation methods must be accurate. In addition to possessing capability to perform damage detection, the ability to monitor the level of damage over time can provide extremely useful information in assessing the operational worthiness of a structure and in determining whether the structure should be repaired or removed from service. In this work, a sequential Bayesian approach with active sensing is employed for monitoring crack growth within fatigue-loaded materials. The monitoring approach is based on predicting crack damage state dynamics and modeling crack length observations. Since fatigue loading of a structural component can change while in service, an interacting multiple model technique is employed to estimate probabilities of different loading modes and incorporate this information in the crack length estimation problem. For the observation model, features are obtained from regions of high signal energy in the time-frequency plane and modeled for each crack length damage condition. Although this observation model approach exhibits high classification accuracy, the resolution characteristics can change depending upon the extent of the damage. Therefore, several different transmission waveforms and receiver sensors are considered to create multiple modes for making observations of crack damage. Resolution characteristics of the different observation modes are assessed using a predicted mean squared error criterion and observations are obtained using the predicted, optimal observation modes based on these characteristics. Calculation of the predicted mean square error metric can be computationally intensive, especially if performed in real time, and an approximation method is proposed. With this approach, the real time

  18. NSF/ESF Workshop on Smart Structures and Advanced Sensors, Santorini Island, Greece, June 26-28, 2005: Structural Actuation and Adaptation Working Group

    NASA Technical Reports Server (NTRS)

    Figueroa, Fernando; Tomizuka, Masayoshi; Bergman, Lawrence; Carpenter, Bernie; Salzano, Carmine; Bairrao, rogerio; Deraemaker, Arnaud; Magonette, Georges; Rodellar, Jose; Kadirkamanathan, Visaken

    2005-01-01

    This document is a result of discussions that took place during the workshop. It describes current state of research and development (R&D) in the areas of structural actuation and adaptation in the context of smart structures and advanced sensors (SS&AS), and provides an outlook to guide future R&D efforts to develop technologies needed to build SS&AS. The discussions took place among the members of the Structural Actuation and Adaptation Working Group, as well as in general sessions including all four working groups. Participants included members of academia, industry, and government from the US and Europe, and representatives from China, Japan, and Korea.

  19. Exploration of the factor structure of the Kirton Adaption-Innovation Inventory using bootstrapping estimation.

    PubMed

    Im, Subin; Min, Soonhong

    2013-04-01

    Exploratory factor analyses of the Kirton Adaption-Innovation Inventory (KAI), which serves to measure individual cognitive styles, generally indicate three factors: sufficiency of originality, efficiency, and rule/group conformity. In contrast, a 2005 study by Im and Hu using confirmatory factor analysis supported a four-factor structure, dividing the sufficiency of originality dimension into two subdimensions, idea generation and preference for change. This study extends Im and Hu's (2005) study of a derived version of the KAI by providing additional evidence of the four-factor structure. Specifically, the authors test the robustness of the parameter estimates to the violation of normality assumptions in the sample using bootstrap methods. A bias-corrected confidence interval bootstrapping procedure conducted among a sample of 356 participants--members of the Arkansas Household Research Panel, with middle SES and average age of 55.6 yr. (SD = 13.9)--showed that the four-factor model with two subdimensions of sufficiency of originality fits the data significantly better than the three-factor model in non-normality conditions. PMID:23833873

  20. Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef

    SciTech Connect

    Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie; Yang, Haitao; Guatelli, John; Xiong, Yong

    2012-10-24

    The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the {mu}1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-{mu}1 interface, which encompasses the cargo-recognition site of {mu}1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in {mu}1, whereas the N terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on {mu}1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity.

  1. Design Process of Flight Vehicle Structures for a Common Bulkhead and an MPCV Spacecraft Adapter

    NASA Technical Reports Server (NTRS)

    Aggarwal, Pravin; Hull, Patrick V.

    2015-01-01

    Design and manufacturing space flight vehicle structures is a skillset that has grown considerably at NASA during that last several years. Beginning with the Ares program and followed by the Space Launch System (SLS); in-house designs were produced for both the Upper Stage and the SLS Multipurpose crew vehicle (MPCV) spacecraft adapter. Specifically, critical design review (CDR) level analysis and flight production drawing were produced for the above mentioned hardware. In particular, the experience of this in-house design work led to increased manufacturing infrastructure for both Marshal Space Flight Center (MSFC) and Michoud Assembly Facility (MAF), improved skillsets in both analysis and design, and hands on experience in building and testing (MSA) full scale hardware. The hardware design and development processes from initiation to CDR and finally flight; resulted in many challenges and experiences that produced valuable lessons. This paper builds on these experiences of NASA in recent years on designing and fabricating flight hardware and examines the design/development processes used, as well as the challenges and lessons learned, i.e. from the initial design, loads estimation and mass constraints to structural optimization/affordability to release of production drawing to hardware manufacturing. While there are many documented design processes which a design engineer can follow, these unique experiences can offer insight into designing hardware in current program environments and present solutions to many of the challenges experienced by the engineering team.

  2. Inspiratory muscle training in patients with chronic obstructive pulmonary disease: structural adaptation and physiologic outcomes.

    PubMed

    Ramirez-Sarmiento, Alba; Orozco-Levi, Mauricio; Guell, Rosa; Barreiro, Esther; Hernandez, Nuria; Mota, Susana; Sangenis, Merce; Broquetas, Joan M; Casan, Pere; Gea, Joaquim

    2002-12-01

    The present study was aimed at evaluating the effects of a specific inspiratory muscle training protocol on the structure of inspiratory muscles in patients with chronic obstructive pulmonary disease. Fourteen patients (males, FEV1, 24 +/- 7% predicted) were randomized to either inspiratory muscle or sham training groups. Supervised breathing using a threshold inspiratory device was performed 30 minutes per day, five times a week, for 5 consecutive weeks. The inspiratory training group was subjected to inspiratory loading equivalent to 40 to 50% of their maximal inspiratory pressure. Biopsies from external intercostal muscles and vastus lateralis (control muscle) were taken before and after the training period. Muscle samples were processed for morphometric analyses using monoclonal antibodies against myosin heavy chain isoforms I and II. Increases in both the strength and endurance of the inspiratory muscles were observed in the inspiratory training group. This improvement was associated with increases in the proportion of type I fibers (by approximately 38%, p < 0.05) and in the size of type II fibers (by approximately 21%, p < 0.05) in the external intercostal muscles. No changes were observed in the control muscle. The study demonstrates that inspiratory training induces a specific functional improvement of the inspiratory muscles and adaptive changes in the structure of external intercostal muscles. PMID:12406842

  3. Structural Basis of Evasion of Cellular Adaptive Immunity by HIV-1 Nef

    PubMed Central

    Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie; Yang, Haitao; Guatelli, John; Xiong, Yong

    2012-01-01

    The HIV-1 protein Nef inhibits antigen presentation by class I MHC (MHC-I). Here the mechanism of this activity is revealed by the crystal structure of a protein complex consisting of Nef, the MHC-I cytoplasmic domain (MHC-I CD), and the μ1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-μ1 interface encompassing the cargo-recognition site of μ1 and the proline rich strand of Nef. The Nef C-terminus induces a novel conformational change in μ1, while the N-terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on μ1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity. PMID:22705789

  4. Nonlocal sparse model with adaptive structural clustering for feature extraction of aero-engine bearings

    NASA Astrophysics Data System (ADS)

    Zhang, Han; Chen, Xuefeng; Du, Zhaohui; Li, Xiang; Yan, Ruqiang

    2016-04-01

    Fault information of aero-engine bearings presents two particular phenomena, i.e., waveform distortion and impulsive feature frequency band dispersion, which leads to a challenging problem for current techniques of bearing fault diagnosis. Moreover, although many progresses of sparse representation theory have been made in feature extraction of fault information, the theory also confronts inevitable performance degradation due to the fact that relatively weak fault information has not sufficiently prominent and sparse representations. Therefore, a novel nonlocal sparse model (coined NLSM) and its algorithm framework has been proposed in this paper, which goes beyond simple sparsity by introducing more intrinsic structures of feature information. This work adequately exploits the underlying prior information that feature information exhibits nonlocal self-similarity through clustering similar signal fragments and stacking them together into groups. Within this framework, the prior information is transformed into a regularization term and a sparse optimization problem, which could be solved through block coordinate descent method (BCD), is formulated. Additionally, the adaptive structural clustering sparse dictionary learning technique, which utilizes k-Nearest-Neighbor (kNN) clustering and principal component analysis (PCA) learning, is adopted to further enable sufficient sparsity of feature information. Moreover, the selection rule of regularization parameter and computational complexity are described in detail. The performance of the proposed framework is evaluated through numerical experiment and its superiority with respect to the state-of-the-art method in the field is demonstrated through the vibration signals of experimental rig of aircraft engine bearings.

  5. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

    SciTech Connect

    Fogarty, Aoife C. Potestio, Raffaello Kremer, Kurt

    2015-05-21

    A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

  6. Osmotic activation of phospholipase C triggers structural adaptation in osmosensitive rat supraoptic neurons.

    PubMed

    Shah, Love; Bansal, Vimal; Rye, Peter L; Mumtaz, Naima; Taherian, Amir; Fisher, Thomas E

    2014-10-01

    The magnocellular neurosecretory cells of the hypothalamus (MNCs) synthesize and secrete vasopressin or oxytocin. A stretch-inactivated cation current mediated by TRPV1 channels rapidly transduces increases in external osmolality into a depolarization of the MNCs leading to an increase in action potential firing and thus hormone release. Prolonged increases in external osmolality, however, trigger a reversible structural and functional adaptation that may enable the MNCs to sustain high levels of hormone release. One poorly understood aspect of this adaptation is somatic hypertrophy. We demonstrate that hypertrophy can be evoked in acutely isolated rat MNCs by exposure to hypertonic solutions lasting tens of minutes. Osmotically evoked hypertrophy requires activation of the stretch-inactivated cation channel, action potential firing, and the influx of Ca(2+). Hypertrophy is prevented by pretreatment with a cell-permeant inhibitor of exocytotic fusion and is associated with an increase in total membrane capacitance. Recovery is disrupted by an inhibitor of dynamin function, suggesting that it requires endocytosis. We also demonstrate that hypertonic solutions cause a decrease in phosphatidylinositol 4,5-bisphosphate in the plasma membranes of MNCs that is prevented by an inhibitor of phospholipase C (PLC). Inhibitors of PLC or protein kinase C (PKC) prevent osmotically evoked hypertrophy, and treatment with a PKC-activating phorbol ester can elicit hypertrophy in the absence of changes in osmolality. These studies suggest that increases in osmolality cause fusion of internal membranes with the plasma membrane of the MNCs and that this process is mediated by activity-dependent activation of PLC and PKC.

  7. Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations

    SciTech Connect

    Carson, James P.; Kuprat, Andrew P.; Jiao, Xiangmin; Dyedov, Volodymyr; del Pin, Facundo; Guccione, Julius M.; Ratcliffe, Mark B.; Einstein, Daniel R.

    2010-04-01

    Spatial discretization of complex imaging-derived fluid-solid geometries, such as the cardiac environment, is a critical but often overlooked challenge in biomechanical computations. This is particularly true in problems with Lagrangian interfaces, where, the fluid and solid phases must match geometrically. For simplicity and better accuracy, it is also highly desirable for the two phases to share the same surface mesh at the interface between them. We outline a method for solving this problem, and illustrate the approach with a 3D fluid-solid mesh of the mouse heart. An MRI perfusion-fixed dataset of a mouse heart with 50μm isotropic resolution was semi-automatically segmented using a customized multimaterial connected-threshold approach that divided the volume into non-overlapping regions of blood, tissue and background. Subsequently, a multimaterial marching cubes algorithm was applied to the segmented data to produce two detailed, compatible isosurfaces, one for blood and one for tissue. Both isosurfaces were simultaneously smoothed with a multimaterial smoothing algorithm that exactly conserves the volume for each phase. Using these two isosurfaces, we developed and applied novel automated meshing algorithms to generate anisotropic hybrid meshes on arbitrary biological geometries with the number of layers and the desired element anisotropy for each phase as the only input parameters. Since our meshes adapt to the local feature sizes and include boundary layer prisms, they are more efficient and accurate than non-adaptive, isotropic meshes, and the fluid-structure interaction computations will tend to have relative error equilibrated over the whole mesh.

  8. Adaptive Generation of Multimaterial Grids from Imaging Data for Biomedical Lagrangian Fluid-Structure Simulations

    PubMed Central

    Carson, J.P.; Kuprat, A.P; Jiao, X.; Dyedov, V.; del Pin, F.; Johnson, G.A.; Guccione, J.M.; Ratcliffe, M.B.; Einstein, D.R.

    2009-01-01

    Spatial discretization of complex imaging-derived fluid-solid geometries, such as the cardiac environment, is a critical but often overlooked challenge in biomechanical computations. This is particularly true in problems with Lagrangian interfaces, where the fluid and solid phases share a common interface geometrically. For simplicity and better accuracy, it is also highly desirable for the two phases to have a matching surface mesh at the interface between them. We outline a method for solving this problem, and illustrate the approach with a 3D fluid-solid mesh of the mouse heart. An MRI perfusion-fixed dataset of a mouse heart with 50μm isotropic resolution was semi-automatically segmented using a customized multimaterial connected-threshold approach that divided the volume into non-overlapping regions of blood, tissue and background. Subsequently, a multimaterial marching cubes algorithm was applied to the segmented data to produce two detailed, compatible isosurfaces, one for blood and one for tissue. Both isosurfaces were simultaneously smoothed with a multimaterial smoothing algorithm that exactly conserves the volume for each phase. Using these two isosurfaces, we developed and applied novel automated meshing algorithms to generate anisotropic hybrid meshes on arbitrary biological geometries with the number of layers and the desired element anisotropy for each phase as the only input parameters. Since our meshes adapt to the local feature sizes and include boundary layer prisms, they are more efficient and accurate than non-adaptive, isotropic meshes, and the fluid-structure interaction computations will tend to have relative error equilibrated over the whole mesh. PMID:19727874

  9. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

    PubMed Central

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M. D.; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  10. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community.

    PubMed

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M D; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  11. Interactions between concentric form-from-structure and face perception revealed by visual masking but not adaptation

    PubMed Central

    Feczko, Eric; Shulman, Gordon L.; Petersen, Steven E.; Pruett, John R.

    2014-01-01

    Findings from diverse subfields of vision research suggest a potential link between high-level aspects of face perception and concentric form-from-structure perception. To explore this relationship, typical adults performed two adaptation experiments and two masking experiments to test whether concentric, but not nonconcentric, Glass patterns (a type of form-from-structure stimulus) utilize a processing mechanism shared by face perception. For the adaptation experiments, subjects were presented with an adaptor for 5 or 20 s, prior to discriminating a target. In the masking experiments, subjects saw a mask, then a target, and then a second mask. Measures of discriminability and bias were derived and repeated measures analysis of variance tested for pattern-specific masking and adaptation effects. Results from Experiment 1 show no Glass pattern-specific effect of adaptation to faces; results from Experiment 2 show concentric Glass pattern masking, but not adaptation, may impair upright/inverted face discrimination; results from Experiment 3 show concentric and radial Glass pattern masking impaired subsequent upright/inverted face discrimination more than translational Glass pattern masking; and results from Experiment 4 show concentric and radial Glass pattern masking impaired subsequent face gender discrimination more than translational Glass pattern masking. Taken together, these findings demonstrate interactions between concentric form-from-structure and face processing, suggesting a possible common processing pathway. PMID:24563526

  12. Structural and functional adaptation of vancomycin resistance VanT serine racemases

    DOE PAGES

    Meziane-Cherif, Djalal; Stogios, Peter J.; Evdokimova, Elena; Egorova, Olga; Savchenko, Alexei; Courvalin, Patrice

    2015-08-11

    Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl–D-alanine target of peptidoglycan precursors with D-alanyl–D-lactate or D-alanyl–D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 wasmore » determined. The structure showed significant similarity to type III pyridoxal 5'-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for theL-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of D-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria.« less

  13. Structural and functional adaptation of vancomycin resistance VanT serine racemases

    SciTech Connect

    Meziane-Cherif, Djalal; Stogios, Peter J.; Evdokimova, Elena; Egorova, Olga; Savchenko, Alexei; Courvalin, Patrice

    2015-08-11

    Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl–D-alanine target of peptidoglycan precursors with D-alanyl–D-lactate or D-alanyl–D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5'-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for theL-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of D-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria.

  14. Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases

    PubMed Central

    Meziane-Cherif, Djalal; Stogios, Peter J.; Evdokimova, Elena; Egorova, Olga

    2015-01-01

    ABSTRACT Vancomycin resistance in Gram-positive bacteria results from the replacement of the d-alanyl–d-alanine target of peptidoglycan precursors with d-alanyl–d-lactate or d-alanyl–d-serine (d-Ala-d-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of d-Ala-d-Ser-terminating precursors by converting l-Ser to d-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in l-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5′-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the l-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against l-Ser versus l-Ala implied that this enzyme relies on its membrane-bound domain for l-Ser transport to increase the overall rate of d-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria. PMID:26265719

  15. Nonlinear fitness space structure adaptation and principal component analysis in genetic algorithms: an application to x-ray reflectivity analysis

    NASA Astrophysics Data System (ADS)

    Tiilikainen, J.; Tilli, J.-M.; Bosund, V.; Mattila, M.; Hakkarainen, T.; Airaksinen, V.-M.; Lipsanen, H.

    2007-01-01

    Two novel genetic algorithms implementing principal component analysis and an adaptive nonlinear fitness-space-structure technique are presented and compared with conventional algorithms in x-ray reflectivity analysis. Principal component analysis based on Hessian or interparameter covariance matrices is used to rotate a coordinate frame. The nonlinear adaptation applies nonlinear estimates to reshape the probability distribution of the trial parameters. The simulated x-ray reflectivity of a realistic model of a periodic nanolaminate structure was used as a test case for the fitting algorithms. The novel methods had significantly faster convergence and less stagnation than conventional non-adaptive genetic algorithms. The covariance approach needs no additional curve calculations compared with conventional methods, and it had better convergence properties than the computationally expensive Hessian approach. These new algorithms can also be applied to other fitting problems where tight interparameter dependence is present.

  16. Using Structural Equation Modeling to Validate Online Game Players' Motivations Relative to Self-Concept and Life Adaptation

    ERIC Educational Resources Information Center

    Yang, Shu Ching; Huang, Chiao Ling

    2013-01-01

    This study aimed to validate a systematic instrument to measure online players' motivations for playing online games (MPOG) and examine how the interplay of differential motivations impacts young gamers' self-concept and life adaptation. Confirmatory factor analysis determined that a hierarchical model with a two-factor structure of…

  17. A memory structure adapted simulated annealing algorithm for a green vehicle routing problem.

    PubMed

    Küçükoğlu, İlker; Ene, Seval; Aksoy, Aslı; Öztürk, Nursel

    2015-03-01

    Currently, reduction of carbon dioxide (CO2) emissions and fuel consumption has become a critical environmental problem and has attracted the attention of both academia and the industrial sector. Government regulations and customer demands are making environmental responsibility an increasingly important factor in overall supply chain operations. Within these operations, transportation has the most hazardous effects on the environment, i.e., CO2 emissions, fuel consumption, noise and toxic effects on the ecosystem. This study aims to construct vehicle routes with time windows that minimize the total fuel consumption and CO2 emissions. The green vehicle routing problem with time windows (G-VRPTW) is formulated using a mixed integer linear programming model. A memory structure adapted simulated annealing (MSA-SA) meta-heuristic algorithm is constructed due to the high complexity of the proposed problem and long solution times for practical applications. The proposed models are integrated with a fuel consumption and CO2 emissions calculation algorithm that considers the vehicle technical specifications, vehicle load, and transportation distance in a green supply chain environment. The proposed models are validated using well-known instances with different numbers of customers. The computational results indicate that the MSA-SA heuristic is capable of obtaining good G-VRPTW solutions within a reasonable amount of time by providing reductions in fuel consumption and CO2 emissions. PMID:25056743

  18. Integrity of medial temporal structures may predict better improvement of spatial neglect with prism adaptation treatment

    PubMed Central

    Goedert, Kelly M.; Shah, Priyanka; Foundas, Anne L.; Barrett, A. M.

    2013-01-01

    Prism adaptation treatment (PAT) is a promising rehabilitative method for functional recovery in persons with spatial neglect. Previous research suggests that PAT improves motor-intentional “aiming” deficits that frequently occur with frontal lesions. To test whether presence of frontal lesions predicted better improvement of spatial neglect after PAT, the current study evaluated neglect-specific improvement in functional activities (assessment with the Catherine Bergego Scale) over time in 21 right-brain-damaged stroke survivors with left-sided spatial neglect. The results demonstrated that neglect patients' functional activities improved after two weeks of PAT and continued improving for four weeks. Such functional improvement did not occur equally in all of the participants: Neglect patients with lesions involving the frontal cortex (n=13) experienced significantly better functional improvement than did those without frontal lesions (n=8). More importantly, voxel-based lesion-behavior mapping (VLBM) revealed that in comparison to the group of patients without frontal lesions, the frontal-lesioned neglect patients had intact regions in the medial temporal areas, the superior temporal areas, and the inferior longitudinal fasciculus. The medial cortical and subcortical areas in the temporal lobe were especially distinguished in the “frontal lesion” group. The findings suggest that the integrity of medial temporal structures may play an important role in supporting functional improvement after PAT. PMID:22941243

  19. Relativistic Flows Using Spatial And Temporal Adaptive Structured Mesh Refinement. I. Hydrodynamics

    SciTech Connect

    Wang, Peng; Abel, Tom; Zhang, Weiqun; /KIPAC, Menlo Park

    2007-04-02

    Astrophysical relativistic flow problems require high resolution three-dimensional numerical simulations. In this paper, we describe a new parallel three-dimensional code for simulations of special relativistic hydrodynamics (SRHD) using both spatially and temporally structured adaptive mesh refinement (AMR). We used method of lines to discrete SRHD equations spatially and used a total variation diminishing (TVD) Runge-Kutta scheme for time integration. For spatial reconstruction, we have implemented piecewise linear method (PLM), piecewise parabolic method (PPM), third order convex essentially non-oscillatory (CENO) and third and fifth order weighted essentially non-oscillatory (WENO) schemes. Flux is computed using either direct flux reconstruction or approximate Riemann solvers including HLL, modified Marquina flux, local Lax-Friedrichs flux formulas and HLLC. The AMR part of the code is built on top of the cosmological Eulerian AMR code enzo, which uses the Berger-Colella AMR algorithm and is parallel with dynamical load balancing using the widely available Message Passing Interface library. We discuss the coupling of the AMR framework with the relativistic solvers and show its performance on eleven test problems.

  20. Finite-difference lattice Boltzmann method with a block-structured adaptive-mesh-refinement technique.

    PubMed

    Fakhari, Abbas; Lee, Taehun

    2014-03-01

    An adaptive-mesh-refinement (AMR) algorithm for the finite-difference lattice Boltzmann method (FDLBM) is presented in this study. The idea behind the proposed AMR is to remove the need for a tree-type data structure. Instead, pointer attributes are used to determine the neighbors of a certain block via appropriate adjustment of its children identifications. As a result, the memory and time required for tree traversal are completely eliminated, leaving us with an efficient algorithm that is easier to implement and use on parallel machines. To allow different mesh sizes at separate parts of the computational domain, the Eulerian formulation of the streaming process is invoked. As a result, there is no need for rescaling the distribution functions or using a temporal interpolation at the fine-coarse grid boundaries. The accuracy and efficiency of the proposed FDLBM AMR are extensively assessed by investigating a variety of vorticity-dominated flow fields, including Taylor-Green vortex flow, lid-driven cavity flow, thin shear layer flow, and the flow past a square cylinder.

  1. Using high-order methods on adaptively refined block-structured meshes - discretizations, interpolations, and filters.

    SciTech Connect

    Ray, Jaideep; Lefantzi, Sophia; Najm, Habib N.; Kennedy, Christopher A.

    2006-01-01

    Block-structured adaptively refined meshes (SAMR) strive for efficient resolution of partial differential equations (PDEs) solved on large computational domains by clustering mesh points only where required by large gradients. Previous work has indicated that fourth-order convergence can be achieved on such meshes by using a suitable combination of high-order discretizations, interpolations, and filters and can deliver significant computational savings over conventional second-order methods at engineering error tolerances. In this paper, we explore the interactions between the errors introduced by discretizations, interpolations and filters. We develop general expressions for high-order discretizations, interpolations, and filters, in multiple dimensions, using a Fourier approach, facilitating the high-order SAMR implementation. We derive a formulation for the necessary interpolation order for given discretization and derivative orders. We also illustrate this order relationship empirically using one and two-dimensional model problems on refined meshes. We study the observed increase in accuracy with increasing interpolation order. We also examine the empirically observed order of convergence, as the effective resolution of the mesh is increased by successively adding levels of refinement, with different orders of discretization, interpolation, or filtering.

  2. Exchange repulsive potential adaptable for electronic structure changes during chemical reactions

    SciTech Connect

    Yokogawa, D.

    2015-04-28

    Hybrid methods combining quantum mechanical (QM) and classical calculations are becoming important tools in chemistry. The popular approach to calculate the interaction between QM and classical calculations employs interatomic potentials. In most cases, the interatomic potential is constructed of an electrostatic (ES) potential and a non-ES potential. Because QM treatment is employed in the calculation of the ES potential, the electronic change can be considered in this ES potential. However, QM treatment of the non-ES potential is difficult because of high computational cost. To overcome this difficulty of evaluating the non-ES potential, we proposed an exchange repulsive potential as the main part of the non-ES potential on the basis of a QM approach. This potential is independent of empirical parameters and adaptable for electronic structure. We combined this potential with the reference interaction site model self-consistent field explicitly including spatial electron density distribution and successfully applied it to the chemical reactions in aqueous phase.

  3. Electrically-controlled polymeric gels as active materials in adaptive structures

    SciTech Connect

    Segalman, D.; Witkowski, W.; Adolf, D. ); Shahinpoor, M. . Dept. of Mechanical Engineering)

    1991-01-01

    This paper presents several applications of ionizable polymeric gels that are capable of undergoing substantial expansions and contractions when subjected to changing pH environments, temperature, or solvent. Conceptual designs for smart, electrically activated devices exploiting this phenomenon are discussed. These devices have the possibility of being manipulated via active computer control as large displacement actuators for use in adaptive structures. The enabling technology of these novel devices is the use of compliant containers for the gels and their solvents, removing the difficulties associated with maintaining a bath for the gels. Though most of these devices are designed using properties well discussed in the literature, some presented near the end of this paper make use of conclusions that the authors have drawn form the literature and their own experimental work. Those conclusions about the basic mechanisms of electromechanical gels are discussed in the third part of this paper and a complete set of governing equations describing these mechanisms are presented in the fourth section. This paper concludes with a discussion of some of the ramifications of the above system of equations and a discussion on gel-driven devices and on the control of such devices. 24 refs., 6 figs., 1 tab.

  4. 120nm resolution in thick samples with structured illumination and adaptive optics

    NASA Astrophysics Data System (ADS)

    Thomas, Benjamin; Sloan, Megan; Wolstenholme, Adrian J.; Kner, Peter

    2014-03-01

    μLinear Structured Illumination Microscopy (SIM) provides a two-fold increase over the diffraction limited resolution. SIM produces excellent images with 120nm resolution in tissue culture cells in two and three dimensions. For SIM to work correctly, the point spread function (PSF) and optical transfer function (OTF) must be known, and, ideally, should be unaberrated. When imaging through thick samples, aberrations will be introduced into the optical system which will reduce the peak intensity and increase the width of the PSF. This will lead to reduced resolution and artifacts in SIM images. Adaptive optics can be used to correct the optical wavefront restoring the PSF to its unaberrated state, and AO has been used in several types of fluorescence microscopy. We demonstrate that AO can be used with SIM to achieve 120nm resolution through 25m of tissue by imaging through the full thickness of an adult C. elegans roundworm. The aberrations can be corrected over a 25μm × 45μm field of view with one wavefront correction setting, demonstrating that AO can be used effectively with widefield superresolution techniques.

  5. Imaging microscopic structures in pathological retinas using a flood-illumination adaptive optics retinal camera

    NASA Astrophysics Data System (ADS)

    Viard, Clément; Nakashima, Kiyoko; Lamory, Barbara; Pâques, Michel; Levecq, Xavier; Château, Nicolas

    2011-03-01

    This research is aimed at characterizing in vivo differences between healthy and pathological retinal tissues at the microscopic scale using a compact adaptive optics (AO) retinal camera. Tests were performed in 120 healthy eyes and 180 eyes suffering from 19 different pathological conditions, including age-related maculopathy (ARM), glaucoma and rare diseases such as inherited retinal dystrophies. Each patient was first examined using SD-OCT and infrared SLO. Retinal areas of 4°x4° were imaged using an AO flood-illumination retinal camera based on a large-stroke deformable mirror. Contrast was finally enhanced by registering and averaging rough images using classical algorithms. Cellular-resolution images could be obtained in most cases. In ARM, AO images revealed granular contents in drusen, which were invisible in SLO or OCT images, and allowed the observation of the cone mosaic between drusen. In glaucoma cases, visual field was correlated to changes in cone visibility. In inherited retinal dystrophies, AO helped to evaluate cone loss across the retina. Other microstructures, slightly larger in size than cones, were also visible in several retinas. AO provided potentially useful diagnostic and prognostic information in various diseases. In addition to cones, other microscopic structures revealed by AO images may also be of interest in monitoring retinal diseases.

  6. Computation identifies structural features that govern neuronal firing properties in slowly adapting touch receptors

    PubMed Central

    Lesniak, Daine R; Marshall, Kara L; Wellnitz, Scott A; Jenkins, Blair A; Baba, Yoshichika; Rasband, Matthew N; Gerling, Gregory J; Lumpkin, Ellen A

    2014-01-01

    Touch is encoded by cutaneous sensory neurons with diverse morphologies and physiological outputs. How neuronal architecture influences response properties is unknown. To elucidate the origin of firing patterns in branched mechanoreceptors, we combined neuroanatomy, electrophysiology and computation to analyze mouse slowly adapting type I (SAI) afferents. These vertebrate touch receptors, which innervate Merkel cells, encode shape and texture. SAI afferents displayed a high degree of variability in touch-evoked firing and peripheral anatomy. The functional consequence of differences in anatomical architecture was tested by constructing network models representing sequential steps of mechanosensory encoding: skin displacement at touch receptors, mechanotransduction and action-potential initiation. A systematic survey of arbor configurations predicted that the arrangement of mechanotransduction sites at heminodes is a key structural feature that accounts in part for an afferent’s firing properties. These findings identify an anatomical correlate and plausible mechanism to explain the driver effect first described by Adrian and Zotterman. DOI: http://dx.doi.org/10.7554/eLife.01488.001 PMID:24448409

  7. Sparse and Adaptive Diffusion Dictionary (SADD) for recovering intra-voxel white matter structure.

    PubMed

    Aranda, Ramon; Ramirez-Manzanares, Alonso; Rivera, Mariano

    2015-12-01

    On the analysis of the Diffusion-Weighted Magnetic Resonance Images, multi-compartment models overcome the limitations of the well-known Diffusion Tensor model for fitting in vivo brain axonal orientations at voxels with fiber crossings, branching, kissing or bifurcations. Some successful multi-compartment methods are based on diffusion dictionaries. The diffusion dictionary-based methods assume that the observed Magnetic Resonance signal at each voxel is a linear combination of the fixed dictionary elements (dictionary atoms). The atoms are fixed along different orientations and diffusivity profiles. In this work, we present a sparse and adaptive diffusion dictionary method based on the Diffusion Basis Functions Model to estimate in vivo brain axonal fiber populations. Our proposal overcomes the following limitations of the diffusion dictionary-based methods: the limited angular resolution and the fixed shapes for the atom set. We propose to iteratively re-estimate the orientations and the diffusivity profile of the atoms independently at each voxel by using a simplified and easier-to-solve mathematical approach. As a result, we improve the fitting of the Diffusion-Weighted Magnetic Resonance signal. The advantages with respect to the former Diffusion Basis Functions method are demonstrated on the synthetic data-set used on the 2012 HARDI Reconstruction Challenge and in vivo human data. We demonstrate that improvements obtained in the intra-voxel fiber structure estimations benefit brain research allowing to obtain better tractography estimations. Hence, these improvements result in an accurate computation of the brain connectivity patterns.

  8. Classification and assessment of water bodies as adaptive structural measures for flood risk management planning.

    PubMed

    McMinn, William R; Yang, Qinli; Scholz, Miklas

    2010-09-01

    Severe rainfall events have become increasingly common in Europe. Flood defence engineering works are highly capital intensive and can be limited by land availability, leaving land and communities exposed to repeated flooding. Any adaptive drainage structure must have engineered inlets and outlets that control the water level and the rate of release. In Scotland, there are a relatively high number of drinking water reservoirs (operated by Scottish Water), which fall within this defined category and could contribute to flood management control. Reducing the rate of runoff from the upper reaches of a catchment will reduce the volume and peak flows of flood events downstream, thus allowing flood defences to be reduced in size, decreasing the corresponding capital costs. A database of retention basins with flood control potential has been developed for Scotland. The research shows that the majority of small and former drinking water reservoirs are kept full and their spillways are continuously in operation. Utilising some of the available capacity to contribute to flood control could reduce the costs of complying with the EU Flood Directive. Furthermore, the application of a previously developed classification model for Baden in Germany for the Scottish data set showed a lower diversity for basins in Scotland due to less developed infrastructure. The principle value of this approach is a clear and unambiguous categorisation, based on standard variables, which can help to promote communication and understanding between stakeholders.

  9. A memory structure adapted simulated annealing algorithm for a green vehicle routing problem.

    PubMed

    Küçükoğlu, İlker; Ene, Seval; Aksoy, Aslı; Öztürk, Nursel

    2015-03-01

    Currently, reduction of carbon dioxide (CO2) emissions and fuel consumption has become a critical environmental problem and has attracted the attention of both academia and the industrial sector. Government regulations and customer demands are making environmental responsibility an increasingly important factor in overall supply chain operations. Within these operations, transportation has the most hazardous effects on the environment, i.e., CO2 emissions, fuel consumption, noise and toxic effects on the ecosystem. This study aims to construct vehicle routes with time windows that minimize the total fuel consumption and CO2 emissions. The green vehicle routing problem with time windows (G-VRPTW) is formulated using a mixed integer linear programming model. A memory structure adapted simulated annealing (MSA-SA) meta-heuristic algorithm is constructed due to the high complexity of the proposed problem and long solution times for practical applications. The proposed models are integrated with a fuel consumption and CO2 emissions calculation algorithm that considers the vehicle technical specifications, vehicle load, and transportation distance in a green supply chain environment. The proposed models are validated using well-known instances with different numbers of customers. The computational results indicate that the MSA-SA heuristic is capable of obtaining good G-VRPTW solutions within a reasonable amount of time by providing reductions in fuel consumption and CO2 emissions.

  10. Tendon structural adaptations to load exercise are inhibited by anabolic androgenic steroids.

    PubMed

    Marqueti, R C; Paulino, M G; Fernandes, M N; de Oliveira, E M; Selistre-de-Araujo, H S

    2014-02-01

    The present study investigated the structural changes in the rat calcaneal tendon (CT), superficial flexor tendon (SFT), and deep flexor tendon (DFT) in response to jump exercises and anabolic androgenic steroids (AAS). Animals were divided into four groups: sedentary, trained, AAS-treated sedentary rats, and AAS-treated trained animals. Training increased the volume density (Vv%) of blood vessels in all regions of the CT and DFT, cell Vv% in the peritendinous sheath of the proximal and distal regions of the SFT and proximal region of DFT, and cell Vv% in the tendon proper of the proximal and distal regions of the SFT and DFT. The combination of AAS and load exercises showed little increased blood vessel Vv% at the proximal region of the CT, intermediate region of the SFT, and all regions of the DFT as opposed to an increase in adipose cell Vv% in the CT proximal region. The AAS reduced the levels of hydroxyproline in the proximal region of the DFT and in the distal region of the STF. In conclusion, exercise promoted benefits to the adaptation of the tendons to overload. These effects were absent when load exercise was combined with AAS. The abusive consumption of AAS contributes to tendon inertness and rigidity, and increases the potential risk of injury.

  11. Adaptive acquisition and modeling for free-form surface with structured-light vision sensor

    NASA Astrophysics Data System (ADS)

    Chen, Kangning; Chen, Hang; Liu, Zhigang

    2000-10-01

    Rapid and high precision data acquisition methodology from coordinate components with free-form surface and geometrical model can be implemented widely. Typical application covers part localization, automatic calibration and reverse engineering. Integrated structured light vision sensor with Cmm (Coordinate Measurement Machine) enhances the high- precision coordinate measurement capability. In this paper a curvature-based adaptive sampling approach and the evaluating index for the sampling precision are presented. The matching and subdividing algorithm for generating matrix-type mesh data from sample points is described. The methodology to register and merge the measured data from multiple viewpoints to model the free-form surface is also presented. Based on the given initial coordinate rotation matrix R and transformation vector T, the different viewpoints can be translated into a unique frame of reference. By introducing special coordinate of 3D space, the registered data is divided into mesh, which cover the whole surface of object. An application example for shoe modeling is described to illustrate the advantages.

  12. Integrity of medial temporal structures may predict better improvement of spatial neglect with prism adaptation treatment.

    PubMed

    Chen, Peii; Goedert, Kelly M; Shah, Priyanka; Foundas, Anne L; Barrett, A M

    2014-09-01

    Prism adaptation treatment (PAT) is a promising rehabilitative method for functional recovery in persons with spatial neglect. Previous research suggests that PAT improves motor-intentional "aiming" deficits that frequently occur with frontal lesions. To test whether presence of frontal lesions predicted better improvement of spatial neglect after PAT, the current study evaluated neglect-specific improvement in functional activities (assessment with the Catherine Bergego Scale) over time in 21 right-brain-damaged stroke survivors with left-sided spatial neglect. The results demonstrated that neglect patients' functional activities improved after two weeks of PAT and continued improving for four weeks. Such functional improvement did not occur equally in all of the participants: Neglect patients with lesions involving the frontal cortex (n = 13) experienced significantly better functional improvement than did those without frontal lesions (n = 8). More importantly, voxel-based lesion-behavior mapping (VLBM) revealed that in comparison to the group of patients without frontal lesions, the frontal-lesioned neglect patients had intact regions in the medial temporal areas, the superior temporal areas, and the inferior longitudinal fasciculus. The medial cortical and subcortical areas in the temporal lobe were especially distinguished in the "frontal lesion" group. The findings suggest that the integrity of medial temporal structures may play an important role in supporting functional improvement after PAT.

  13. Adaptations for economical bipedal running: the effect of limb structure on three-dimensional joint mechanics.

    PubMed

    Rubenson, Jonas; Lloyd, David G; Heliams, Denham B; Besier, Thor F; Fournier, Paul A

    2011-05-01

    The purpose of this study was to examine the mechanical adaptations linked to economical locomotion in cursorial bipeds. We addressed this question by comparing mass-matched humans and avian bipeds (ostriches), which exhibit marked differences in limb structure and running economy. We hypothesized that the nearly 50 per cent lower energy cost of running in ostriches is a result of: (i) lower limb-swing mechanical power, (ii) greater stance-phase storage and release of elastic energy, and (iii) lower total muscle power output. To test these hypotheses, we used three-dimensional joint mechanical measurements and a simple model to estimate the elastic and muscle contributions to joint work and power. Contradictory to our first hypothesis, we found that ostriches and humans generate the same amounts of mechanical power to swing the limbs at a similar self-selected running speed, indicating that limb swing probably does not contribute to the difference in energy cost of running between these species. In contrast, we estimated that ostriches generate 120 per cent more stance-phase mechanical joint power via release of elastic energy compared with humans. This elastic mechanical power occurs nearly exclusively at the tarsometatarso-phalangeal joint, demonstrating a shift of mechanical power generation to distal joints compared with humans. We also estimated that positive muscle fibre power is 35 per cent lower in ostriches compared with humans, and is accounted for primarily by higher capacity for storage and release of elastic energy. Furthermore, our analysis revealed much larger frontal and internal/external rotation joint loads during ostrich running than in humans. Together, these findings support the hypothesis that a primary limb structure specialization linked to economical running in cursorial species is an elevated storage and release of elastic energy in tendon. In the ostrich, energy-saving specializations may also include passive frontal and internal

  14. Evaluating Knowledge Structure-Based Adaptive Testing Algorithms and System Development

    ERIC Educational Resources Information Center

    Wu, Huey-Min; Kuo, Bor-Chen; Yang, Jinn-Min

    2012-01-01

    In recent years, many computerized test systems have been developed for diagnosing students' learning profiles. Nevertheless, it remains a challenging issue to find an adaptive testing algorithm to both shorten testing time and precisely diagnose the knowledge status of students. In order to find a suitable algorithm, four adaptive testing…

  15. A Knowledge-Structure-Based Adaptive Dynamic Assessment System for Calculus Learning

    ERIC Educational Resources Information Center

    Ting, M.-Y.; Kuo, B.-C.

    2016-01-01

    The purpose of this study was to investigate the effect of a calculus system that was designed using an adaptive dynamic assessment (DA) framework on performance in the "finding an area using an integral". In this study, adaptive testing and dynamic assessment were combined to provide different test items depending on students'…

  16. Parallelization of an Adaptive Multigrid Algorithm for Fast Solution of Finite Element Structural Problems

    SciTech Connect

    Crane, N K; Parsons, I D; Hjelmstad, K D

    2002-03-21

    Adaptive mesh refinement selectively subdivides the elements of a coarse user supplied mesh to produce a fine mesh with reduced discretization error. Effective use of adaptive mesh refinement coupled with an a posteriori error estimator can produce a mesh that solves a problem to a given discretization error using far fewer elements than uniform refinement. A geometric multigrid solver uses increasingly finer discretizations of the same geometry to produce a very fast and numerically scalable solution to a set of linear equations. Adaptive mesh refinement is a natural method for creating the different meshes required by the multigrid solver. This paper describes the implementation of a scalable adaptive multigrid method on a distributed memory parallel computer. Results are presented that demonstrate the parallel performance of the methodology by solving a linear elastic rocket fuel deformation problem on an SGI Origin 3000. Two challenges must be met when implementing adaptive multigrid algorithms on massively parallel computing platforms. First, although the fine mesh for which the solution is desired may be large and scaled to the number of processors, the multigrid algorithm must also operate on much smaller fixed-size data sets on the coarse levels. Second, the mesh must be repartitioned as it is adapted to maintain good load balancing. In an adaptive multigrid algorithm, separate mesh levels may require separate partitioning, further complicating the load balance problem. This paper shows that, when the proper optimizations are made, parallel adaptive multigrid algorithms perform well on machines with several hundreds of processors.

  17. Broad scale agreement between intertidal habitats and adaptive traits on a basis of contrasting population genetic structure

    NASA Astrophysics Data System (ADS)

    Zardi, G. I.; Nicastro, K. R.; Ferreira Costa, J.; Serrão, E. A.; Pearson, G. A.

    2013-10-01

    Understanding the extent to which neutral processes and adaptive divergence shape the spatial structure of natural populations is a major goal in evolutionary biology and is especially important for the identification of significant levels of biodiversity. Our results identified replicated habitat-specific (adaptive) phenotypic divergence in the brown macroalga Fucus vesiculosus that is independent of population (neutral) genetic structure. F. vesiculosus inhabits contiguous and contrasting marine to estuarine intertidal habitats. Combining analyses of genetic and phenotypic traits of populations living under differential selective regimes (estuaries and open coast), we investigated levels of neutral genetic differentiation and adaptive physiological responses to emersion stress. In southwest England (SW UK) and northern Iberia (N. Iberia), populations living in estuaries and marine coastal habitats were genetically characterized at six microsatellite loci. In N. Iberia, two clades with limited admixture were recovered, each including one open coast site and the adjacent estuarine location. In contrast, SW UK samples clustered according to habitat and formed three distinct groups of genotypes; one including the two open coast locations and the other two representing each of the estuarine sites. Temperature loggers revealed distinct emersion regimes that characterized each habitat type independently of the region, while water and air temperature profiles showed site-specific trends. Despite acclimation under usual conditions, trait means of emersion stress resilience showed a strong phenotypic divergence between habitats, consistent with environmental clines in exposure time observed in the different habitats. We demonstrate that neutral genetic clusters do not reflect locally adapted population units. Our results identified replicated habitat-specific (adaptive) phenotypic divergence that is independent of population (neutral) genetic structure in F. vesiculosus

  18. A multilevel structural equation modeling analysis of vulnerabilities and resilience resources influencing affective adaptation to chronic pain.

    PubMed

    Sturgeon, John A; Zautra, Alex J; Arewasikporn, Anne

    2014-02-01

    The processes of individual adaptation to chronic pain are complex and occur across multiple domains. We examined the social, cognitive, and affective context of daily pain adaptation in individuals with fibromyalgia and osteoarthritis. By using a sample of 260 women with fibromyalgia or osteoarthritis, we examined the contributions of pain catastrophizing, negative interpersonal events, and positive interpersonal events to daily negative and positive affect across 30days of daily diary data. Individual differences and daily fluctuations in predictor variables were estimated simultaneously by utilizing multilevel structural equation modeling techniques. The relationships between pain and negative and positive affect were mediated by stable and day-to-day levels of pain catastrophizing as well as day-to-day positive interpersonal events, but not negative interpersonal events. There were significant and independent contributions of pain catastrophizing and positive interpersonal events to adaptation to pain and pain-related affective dysregulation. These effects occur both between persons and within a person's everyday life.

  19. Multiclass Classification by Adaptive Network of Dendritic Neurons with Binary Synapses Using Structural Plasticity

    PubMed Central

    Hussain, Shaista; Basu, Arindam

    2016-01-01

    The development of power-efficient neuromorphic devices presents the challenge of designing spike pattern classification algorithms which can be implemented on low-precision hardware and can also achieve state-of-the-art performance. In our pursuit of meeting this challenge, we present a pattern classification model which uses a sparse connection matrix and exploits the mechanism of nonlinear dendritic processing to achieve high classification accuracy. A rate-based structural learning rule for multiclass classification is proposed which modifies a connectivity matrix of binary synaptic connections by choosing the best “k” out of “d” inputs to make connections on every dendritic branch (k < < d). Because learning only modifies connectivity, the model is well suited for implementation in neuromorphic systems using address-event representation (AER). We develop an ensemble method which combines several dendritic classifiers to achieve enhanced generalization over individual classifiers. We have two major findings: (1) Our results demonstrate that an ensemble created with classifiers comprising moderate number of dendrites performs better than both ensembles of perceptrons and of complex dendritic trees. (2) In order to determine the moderate number of dendrites required for a specific classification problem, a two-step solution is proposed. First, an adaptive approach is proposed which scales the relative size of the dendritic trees of neurons for each class. It works by progressively adding dendrites with fixed number of synapses to the network, thereby allocating synaptic resources as per the complexity of the given problem. As a second step, theoretical capacity calculations are used to convert each neuronal dendritic tree to its optimal topology where dendrites of each class are assigned different number of synapses. The performance of the model is evaluated on classification of handwritten digits from the benchmark MNIST dataset and compared with other

  20. Multiclass Classification by Adaptive Network of Dendritic Neurons with Binary Synapses Using Structural Plasticity.

    PubMed

    Hussain, Shaista; Basu, Arindam

    2016-01-01

    The development of power-efficient neuromorphic devices presents the challenge of designing spike pattern classification algorithms which can be implemented on low-precision hardware and can also achieve state-of-the-art performance. In our pursuit of meeting this challenge, we present a pattern classification model which uses a sparse connection matrix and exploits the mechanism of nonlinear dendritic processing to achieve high classification accuracy. A rate-based structural learning rule for multiclass classification is proposed which modifies a connectivity matrix of binary synaptic connections by choosing the best "k" out of "d" inputs to make connections on every dendritic branch (k < < d). Because learning only modifies connectivity, the model is well suited for implementation in neuromorphic systems using address-event representation (AER). We develop an ensemble method which combines several dendritic classifiers to achieve enhanced generalization over individual classifiers. We have two major findings: (1) Our results demonstrate that an ensemble created with classifiers comprising moderate number of dendrites performs better than both ensembles of perceptrons and of complex dendritic trees. (2) In order to determine the moderate number of dendrites required for a specific classification problem, a two-step solution is proposed. First, an adaptive approach is proposed which scales the relative size of the dendritic trees of neurons for each class. It works by progressively adding dendrites with fixed number of synapses to the network, thereby allocating synaptic resources as per the complexity of the given problem. As a second step, theoretical capacity calculations are used to convert each neuronal dendritic tree to its optimal topology where dendrites of each class are assigned different number of synapses. The performance of the model is evaluated on classification of handwritten digits from the benchmark MNIST dataset and compared with other spike

  1. Multiclass Classification by Adaptive Network of Dendritic Neurons with Binary Synapses Using Structural Plasticity.

    PubMed

    Hussain, Shaista; Basu, Arindam

    2016-01-01

    The development of power-efficient neuromorphic devices presents the challenge of designing spike pattern classification algorithms which can be implemented on low-precision hardware and can also achieve state-of-the-art performance. In our pursuit of meeting this challenge, we present a pattern classification model which uses a sparse connection matrix and exploits the mechanism of nonlinear dendritic processing to achieve high classification accuracy. A rate-based structural learning rule for multiclass classification is proposed which modifies a connectivity matrix of binary synaptic connections by choosing the best "k" out of "d" inputs to make connections on every dendritic branch (k < < d). Because learning only modifies connectivity, the model is well suited for implementation in neuromorphic systems using address-event representation (AER). We develop an ensemble method which combines several dendritic classifiers to achieve enhanced generalization over individual classifiers. We have two major findings: (1) Our results demonstrate that an ensemble created with classifiers comprising moderate number of dendrites performs better than both ensembles of perceptrons and of complex dendritic trees. (2) In order to determine the moderate number of dendrites required for a specific classification problem, a two-step solution is proposed. First, an adaptive approach is proposed which scales the relative size of the dendritic trees of neurons for each class. It works by progressively adding dendrites with fixed number of synapses to the network, thereby allocating synaptic resources as per the complexity of the given problem. As a second step, theoretical capacity calculations are used to convert each neuronal dendritic tree to its optimal topology where dendrites of each class are assigned different number of synapses. The performance of the model is evaluated on classification of handwritten digits from the benchmark MNIST dataset and compared with other spike

  2. Ultrastructural and biochemical characterization of mechanically adaptable collagenous structures in the edible sea urchin Paracentrotus lividus.

    PubMed

    Barbaglio, Alice; Tricarico, Serena; Ribeiro, Ana R; Di Benedetto, Cristiano; Barbato, Marta; Dessì, Desirèe; Fugnanesi, Valeria; Magni, Stefano; Mosca, Fabio; Sugni, Michela; Bonasoro, Francesco; Barbosa, Mario A; Wilkie, Iain C; Candia Carnevali, M Daniela

    2015-06-01

    The viscoelastic properties of vertebrate connective tissues rarely undergo significant changes within physiological timescales, the only major exception being the reversible destiffening of the mammalian uterine cervix at the end of pregnancy. In contrast to this, the connective tissues of echinoderms (sea urchins, starfish, sea cucumbers, etc.) can switch reversibly between stiff and compliant conditions in timescales of around a second to minutes. Elucidation of the molecular mechanism underlying such mutability has implications for the zoological, ecological and evolutionary field. Important information could also arise for veterinary and biomedical sciences, particularly regarding the pathological plasticization or stiffening of connective tissue structures. In the present investigation we analyzed aspects of the ultrastructure and biochemistry in two representative models, the compass depressor ligament and the peristomial membrane of the edible sea urchin Paracentrotus lividus, compared in three different mechanical states. The results provide further evidence that the mechanical adaptability of echinoderm connective tissues does not necessarily imply changes in the collagen fibrils themselves. The higher glycosaminoglycan (GAG) content registered in the peristomial membrane with respect to the compass depressor ligament suggests a diverse role of these molecules in the two mutable collagenous tissues. The possible involvement of GAG in the mutability phenomenon will need further clarification. During the shift from a compliant to a standard condition, significant changes in GAG content were detected only in the compass depressor ligament. Similarities in terms of ultrastructure (collagen fibrillar assembling) and biochemistry (two alpha chains) were found between the two models and mammalian collagen. Nevertheless, differences in collagen immunoreactivity, alpha chain migration on SDS-PAGE and BLAST alignment highlighted the uniqueness of sea urchin

  3. New Approach for IIR Adaptive Lattice Filter Structure Using Simultaneous Perturbation Algorithm

    NASA Astrophysics Data System (ADS)

    Martinez, Jorge Ivan Medina; Nakano, Kazushi; Higuchi, Kohji

    Adaptive infinite impulse response (IIR), or recursive, filters are less attractive mainly because of the stability and the difficulties associated with their adaptive algorithms. Therefore, in this paper the adaptive IIR lattice filters are studied in order to devise algorithms that preserve the stability of the corresponding direct-form schemes. We analyze the local properties of stationary points, a transformation achieving this goal is suggested, which gives algorithms that can be efficiently implemented. Application to the Steiglitz-McBride (SM) and Simple Hyperstable Adaptive Recursive Filter (SHARF) algorithms is presented. Also a modified version of Simultaneous Perturbation Stochastic Approximation (SPSA) is presented in order to get the coefficients in a lattice form more efficiently and with a lower computational cost and complexity. The results are compared with previous lattice versions of these algorithms. These previous lattice versions may fail to preserve the stability of stationary points.

  4. Caracterisation de la cohesion de l'interface AMF/polymere dans une structure deformable adaptative

    NASA Astrophysics Data System (ADS)

    Fischer-Rousseau, Charles

    Les structures déformables adaptatives (SDA) sont appelées à jouer un rôle important en aéronautique entre autres. Les alliages à mémoire de forme (AMF) sont un des candidats les plus prometteurs. Beaucoup de travail reste toutefois à faire avant que ces structures rencontrent les exigences élevées reliées à leur intégration dans un contexte aéronautique. Des travaux de recherche ont montré que la résistance à la décohésion de l’interface AMF/polymère peut être un élément limitant dans la performance des SDA. Dans ce travail, l’effet sur la résistance à la décohésion de l’interface AMF/polymère de divers traitements de surface, géométries de fil et types de polymère est évalué. La géométrie du fil est modifiée par une combinaison spécifique de laminage à froid et de recuit postdéformation qui maintient les propriétés de mémoire de forme tout en permettant de réduire l’aire de la section transversale du fil. Le traitement thermomécanique le plus prometteur est proposé. Une nouvelle méthode d’évaluation de la résistance à la décohésion est développée. Plutôt que de tester les fils en arrachement et de mesurer la force maximale, les tests en contraction sont basés sur la capacité des fils d’AMF à se contracter s’ils ont été encastrés dans un état tiré et qu’ils sont chauffés par effet Joule. L’hypothèse qu’on pose est que ces tests sont une meilleure approximation des conditions rencontrées dans une SDA, où les fils se contractent plutôt qu’ils sont arrachés par une force externe à la structure. Bien qu’une décohésion partielle ait été observée pour tous les échantillons, l’aire de la surface où il y a décohésion tait plus grande pour les échantillons avec une pré-déformation plus grande. Le front de décohésion a semblé cesser de progresser après les cycles de chauffage initiaux lorsque la vitesse de chauffage était faible. Un modèle numérique simulant la

  5. Improving the textural characterization of trabecular bone structure to quantify its changes: the locally adapted scaling vector method

    NASA Astrophysics Data System (ADS)

    Raeth, Christoph W.; Mueller, Dirk; Boehm, Holger F.; Rummeny, Ernst J.; Link, Thomas M.; Monetti, Roberto

    2005-04-01

    We extend the recently introduced scaling vector method (SVM) to improve the textural characterization of oriented trabecular bone structures in the context of osteoporosis. Using the concept of scaling vectors one obtains non-linear structural information from data sets, which can account for global anisotropies. In this work we present a method which allows us to determine the local directionalities in images by using scaling vectors. Thus it becomes possible to better account for local anisotropies and to implement this knowledge in the calculation of the scaling properties of the image. By applying this adaptive technique, a refined quantification of the image structure is possible: we test and evaluate our new method using realistic two-dimensional simulations of bone structures, which model the effect of osteoblasts and osteoclasts on the local change of relative bone density. The partial differential equations involved in the model are solved numerically using cellular automata (CA). Different realizations with slightly varying control parameters are considered. Our results show that even small changes in the trabecular structures, which are induced by variation of a control parameters of the system, become discernible by applying the locally adapted scaling vector method. The results are superior to those obtained by isotropic and/or bulk measures. These findings may be especially important for monitoring the treatment of patients, where the early recognition of (drug-induced) changes in the trabecular structure is crucial.

  6. Enhanced oxygen vacancy diffusion in Ta2O5 resistive memory devices due to infinitely adaptive crystal structure

    NASA Astrophysics Data System (ADS)

    Jiang, Hao; Stewart, Derek A.

    2016-04-01

    Metal oxide resistive memory devices based on Ta2O5 have demonstrated high switching speed, long endurance, and low set voltage. However, the physical origin of this improved performance is still unclear. Ta2O5 is an important archetype of a class of materials that possess an adaptive crystal structure that can respond easily to the presence of defects. Using first principles nudged elastic band calculations, we show that this adaptive crystal structure leads to low energy barriers for in-plane diffusion of oxygen vacancies in λ phase Ta2O5. Identified diffusion paths are associated with collective motion of neighboring atoms. The overall vacancy diffusion is anisotropic with higher diffusion barriers found for oxygen vacancy movement between Ta-O planes. Coupled with the fact that oxygen vacancy formation energy in Ta2O5 is relatively small, our calculated low diffusion barriers can help explain the low set voltage in Ta2O5 based resistive memory devices. Our work shows that other oxides with adaptive crystal structures could serve as potential candidates for resistive random access memory devices. We also discuss some general characteristics for ideal resistive RAM oxides that could be used in future computational material searches.

  7. Structural self-assembly and avalanchelike dynamics in locally adaptive networks

    NASA Astrophysics Data System (ADS)

    Gräwer, Johannes; Modes, Carl D.; Magnasco, Marcelo O.; Katifori, Eleni

    2015-07-01

    Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli, damage, and other environmental changes. We model these adapting network architectures using a generic dynamical system on weighted graphs and find in simulation that these networks ultimately develop a hierarchical organization of the final weighted architecture accompanied by the formation of a system-spanning backbone. In addition, we find that the long term equilibration dynamics exhibit behavior reminiscent of glassy systems characterized by long periods of slow changes punctuated by bursts of reorganization events.

  8. Structural self-assembly and avalanchelike dynamics in locally adaptive networks.

    PubMed

    Gräwer, Johannes; Modes, Carl D; Magnasco, Marcelo O; Katifori, Eleni

    2015-07-01

    Transport networks play a key role across four realms of eukaryotic life: slime molds, fungi, plants, and animals. In addition to the developmental algorithms that build them, many also employ adaptive strategies to respond to stimuli, damage, and other environmental changes. We model these adapting network architectures using a generic dynamical system on weighted graphs and find in simulation that these networks ultimately develop a hierarchical organization of the final weighted architecture accompanied by the formation of a system-spanning backbone. In addition, we find that the long term equilibration dynamics exhibit behavior reminiscent of glassy systems characterized by long periods of slow changes punctuated by bursts of reorganization events. PMID:26274219

  9. A tortoise-hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria.

    PubMed

    Nahum, Joshua R; Godfrey-Smith, Peter; Harding, Brittany N; Marcus, Joseph H; Carlson-Stevermer, Jared; Kerr, Benjamin

    2015-06-16

    In the context of Wright's adaptive landscape, genetic epistasis can yield a multipeaked or "rugged" topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such "smooth" topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise-hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise-hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright's shifting balance process.

  10. Individuals with medial knee osteoarthritis show neuromuscular adaptation when perturbed during walking despite functional and structural impairments.

    PubMed

    Kumar, Deepak; Swanik, Charles Buz; Reisman, Darcy S; Rudolph, Katherine S

    2014-01-01

    Neuromuscular control relies on sensory feedback that influences responses to changing external demands, and the normal response is for movement and muscle activation patterns to adapt to repeated perturbations. People with knee osteoarthritis (OA) are known to have pain, quadriceps weakness, and neuromotor deficits that could affect adaption to external perturbations. The aim of this study was to analyze neuromotor adaptation during walking in people with knee OA (n = 38) and controls (n = 23). Disability, quadriceps strength, joint space width, malalignment, and proprioception were assessed. Kinematic and EMG data were collected during undisturbed walking and during perturbations that caused lateral translation of the foot at initial contact. Knee excursions and EMG magnitudes were analyzed. Subjects with OA walked with less knee motion and higher muscle activation and had greater pain, limitations in function, quadriceps weakness, and malalignment, but no difference was observed in proprioception. Both groups showed increased EMG and decreased knee motion in response to the first perturbation, followed by progressively decreased EMG activity and increased knee motion during midstance over the first five perturbations, but no group differences were observed. Over 30 trials, EMG levels returned to those of normal walking. The results illustrate that people with knee OA respond similarly to healthy individuals when exposed to challenging perturbations during functional weight-bearing activities despite structural, functional, and neuromotor impairments. Mechanisms underlying the adaptive response in people with knee OA need further study. PMID:24072409

  11. Integrated Flight/Structural Mode Control for Very Flexible Aircraft Using L1 Adaptive Output Feedback Controller

    NASA Technical Reports Server (NTRS)

    Che, Jiaxing; Cao, Chengyu; Gregory, Irene M.

    2012-01-01

    This paper explores application of adaptive control architecture to a light, high-aspect ratio, flexible aircraft configuration that exhibits strong rigid body/flexible mode coupling. Specifically, an L(sub 1) adaptive output feedback controller is developed for a semi-span wind tunnel model capable of motion. The wind tunnel mount allows the semi-span model to translate vertically and pitch at the wing root, resulting in better simulation of an aircraft s rigid body motion. The control objective is to design a pitch control with altitude hold while suppressing body freedom flutter. The controller is an output feedback nominal controller (LQG) augmented by an L(sub 1) adaptive loop. A modification to the L(sub 1) output feedback is proposed to make it more suitable for flexible structures. The new control law relaxes the required bounds on the unmatched uncertainty and allows dependence on the state as well as time, i.e. a more general unmatched nonlinearity. The paper presents controller development and simulated performance responses. Simulation is conducted by using full state flexible wing models derived from test data at 10 different dynamic pressure conditions. An L(sub 1) adaptive output feedback controller is designed for a single test point and is then applied to all the test cases. The simulation results show that the L(sub 1) augmented controller can stabilize and meet the performance requirements for all 10 test conditions ranging from 30 psf to 130 psf dynamic pressure.

  12. Photoreceptor fine structure in light- and dark-adaptation in the butterfly fish (Pantodon buchholzi).

    PubMed

    Braekevelt, C R

    1990-01-01

    The morphology of the retinal photoreceptors of the butterfly fish Pantodon buchholzi has been studied by electron microscopy in both light- and dark-adaptation. The photoreceptors in this species are readily divisible into rods and cones based on morphological criteria. No double or twin cones are present. The rod photoreceptors show marked retinomotor movements. In light-adaptation they are extremely elongate cells while in the dark-adapted state they are much shorter. Cones seem to respond but minimally to the circadian cycle. Rod outer segments are composed of membranous discs of uniform diameter displaying several incisures. The inner segment has a small distal ellipsoid and a thin myoid region which is lost in dark-adaptation. The nuclei of rods are condensed and always located vitread to the external limiting membrane. The rod synaptic spherule displays 2 or 3 invaginated sites. The single cones display a tapering outer segment. The wider inner segment contains a large electron-dense ellipsoid with small glycogen deposits located peripherally. The cone nuclei are large and vesicular and usually located sclerad to the external limiting membrane. The synaptic pedicle of cones is larger and more electron-lucent and contains more synaptic sites than do the rods. No mosaic pattern of arrangement of the photoreceptors is apparent. Except for the obvious lengthening or shortening of the rods, the morphology of the photoreceptors changes but little during the circadian cycle.

  13. Does foraging adaptation create the positive complexity-stability relationship in realistic food-web structure?

    PubMed

    Kondoh, Michio

    2006-02-01

    The adaptive food-web hypothesis suggests that an adaptive foraging switch inverses the classically negative complexity-stability relationships of food webs into positive ones, providing a possible resolution for the long-standing paradox of how populations persist in a complex natural food web. However, its applicability to natural ecosystems has been questioned, because the positive relationship does not emerge when a niche model, a realistic "benchmark" of food-web models, is used. I hypothesize that, in the niche model, increasing connectance influences the fraction of basal species to destabilize the system and this masks the inversion of the negative complexity-stability relationship in the presence of adaptive foraging. A model analysis shows that, if this confounding effect is eliminated, then, even in a niche model, a population is more likely to persist in a more complex food web. This result supports the robustness of adaptive food-web hypothesis and reveals the condition in which the hypothesis should be tested.

  14. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica

    PubMed Central

    Deacon, Nicholas John; Cavender-Bares, Jeannine

    2015-01-01

    Background Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses. Results High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation. Conclusion Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic

  15. Prevalent structural disorder carries signature of prokaryotic adaptation to oxic atmosphere.

    PubMed

    Panda, Arup; Ghosh, Tapash Chandra

    2014-09-10

    Microbes have adopted efficient mechanisms to contend with environmental changes. The emergence of oxygen was a major event that led to an abrupt change in Earth's atmosphere. To adjust with this shift in environmental condition ancient microbes must have undergone several modifications. Although some proteomic and genomic attributes were proposed to facilitate survival of microorganisms in the presence of oxygen, the process of adaptation still remains elusive. Recent studies have focused that intrinsically disordered proteins play crucial roles in adaptation to a wide range of ecological conditions. Therefore, it is likely that disordered proteins could also play indispensable roles in microbial adaptation to the aerobic environment. To test this hypothesis we measured the disorder content of 679 prokaryotes from four oxygen requirement groups. Our result revealed that aerobic proteomes are endowed with the highest protein disorder followed by facultative microbes. Minimal disorder was observed in anaerobic and microaerophilic microbes with no significant difference in their disorder content. Considering all the potential confounding factors that can modulate protein disorder, here we established that the high protein disorder in aerobic microbe is not a by-product of adaptation to any other selective pressure. On the functional level, we found that the high disorder in aerobic proteomes has been utilized for processes that are important for their aerobic lifestyle. Moreover, aerobic proteomes were found to be enriched with disordered binding sites and to contain transcription factors with high disorder propensity. Based on our results, here we proposed that the high protein disorder is an adaptive opportunity for aerobic microbes to fit with the genomic and functional complexities of the aerobic lifestyle.

  16. Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes.

    PubMed

    Fan, Shaohua; Meyer, Axel

    2014-01-01

    African cichlid fishes are an ideal system for studying explosive rates of speciation and the origin of diversity in adaptive radiation. Within the last few million years, more than 2000 species have evolved in the Great Lakes of East Africa, the largest adaptive radiation in vertebrates. These young species show spectacular diversity in their coloration, morphology and behavior. However, little is known about the genomic basis of this astonishing diversity. Recently, five African cichlid genomes were sequenced, including that of the Nile Tilapia (Oreochromis niloticus), a basal and only relatively moderately diversified lineage, and the genomes of four representative endemic species of the adaptive radiations, Neolamprologus brichardi, Astatotilapia burtoni, Metriaclima zebra, and Pundamila nyererei. Using the Tilapia genome as a reference genome, we generated a high-resolution genomic variation map, consisting of single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), inversions and deletions. In total, around 18.8, 17.7, 17.0, and 17.0 million SNPs, 2.3, 2.2, 1.4, and 1.9 million indels, 262, 306, 162, and 154 inversions, and 3509, 2705, 2710, and 2634 deletions were inferred to have evolved in N. brichardi, A. burtoni, P. nyererei, and M. zebra, respectively. Many of these variations affected the annotated gene regions in the genome. Different patterns of genetic variation were detected during the adaptive radiation of African cichlid fishes. For SNPs, the highest rate of evolution was detected in the common ancestor of N. brichardi, A. burtoni, P. nyererei, and M. zebra. However, for the evolution of inversions and deletions, we found that the rates at the terminal taxa are substantially higher than the rates at the ancestral lineages. The high-resolution map provides an ideal opportunity to understand the genomic bases of the adaptive radiation of African cichlid fishes.

  17. Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

    PubMed Central

    Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

    2014-01-01

    Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

  18. Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates.

    PubMed

    Pasam, Raj K; Sharma, Rajiv; Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

    2014-01-01

    Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type - and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

  19. Relations between Classroom Goal Structures and Students' Goal Orientations in Mathematics Classes: When Is a Mastery Goal Structure Adaptive?

    ERIC Educational Resources Information Center

    Skaalvik, Einar M.; Federici, Roger A.

    2016-01-01

    The purpose of this study was to test possible interactions between mastery and performance goal structures in mathematics classrooms when predicting students' goal orientations. More specifically, we tested if the degree of performance goal structure moderated the associations between mastery goal structure and students' goal orientations.…

  20. Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation.

    PubMed

    Dionne, Mélanie; Caron, François; Dodson, Julian J; Bernatchez, Louis

    2008-05-01

    Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar. A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.

  1. Impulse noise removal using 1-D switching median filter with adaptive scanning order based on structural context of image

    NASA Astrophysics Data System (ADS)

    Koga, Takanori; Suetake, Noriaki

    2015-02-01

    This paper describes the detail-preserving impulse noise removal performance of a one-dimensional (1-D) switching median filter (SMF) applied along an adaptive space-filling curve. Usually, a SMF with a two-dimensional (2-D) filter window is widely used for impulse noise removal while still preserving detailed parts in an input image. However, the noise detector of the 2-D filter does not always distinguish between the original pixels and the noise-corrupted ones perfectly. In particular, pixels constituting thin lines in an input image tend to be incorrectly detected as noise-corrupted pixels, and such pixels are filtered regardless of the necessity of the filtering. To cope with this problem, we propose a new impulse noise removal method based on a 1-D SMF and a space-filling curve which is adaptively drawn using a minimum spanning tree reflecting structural context of an input image.

  2. Gradual adaptation of bone structure to aquatic lifestyle in extinct sloths from Peru

    PubMed Central

    Amson, Eli; de Muizon, Christian; Laurin, Michel; Argot, Christine; de Buffrénil, Vivian

    2014-01-01

    Non-pathological densification (osteosclerosis) and swelling (pachyostosis) of bones are the main modifications affecting the skeleton of land vertebrates (tetrapods) that returned to water. However, a precise temporal calibration of the acquisition of such adaptations is still wanting. Here, we assess the timing of such acquisition using the aquatic sloth Thalassocnus, from the Neogene of the Pisco Formation, Peru. This genus is represented by five species occurring in successive vertebrate-bearing horizons of distinct ages. It yields the most detailed data about the gradual acquisition of aquatic adaptations among tetrapods, in displaying increasing osteosclerosis and pachyostosis through time. Such modifications, reflecting a shift in the habitat from terrestrial to aquatic, occurred over a short geological time span (ca 4 Myr). Otherwise, the bones of terrestrial pilosans (sloths and anteaters) are much more compact than the mean mammalian condition, which suggests that the osteosclerosis of Thalassocnus may represent an exaptation. PMID:24621950

  3. Gradual adaptation of bone structure to aquatic lifestyle in extinct sloths from Peru.

    PubMed

    Amson, Eli; de Muizon, Christian; Laurin, Michel; Argot, Christine; de Buffrénil, Vivian

    2014-05-01

    Non-pathological densification (osteosclerosis) and swelling (pachyostosis) of bones are the main modifications affecting the skeleton of land vertebrates (tetrapods) that returned to water. However, a precise temporal calibration of the acquisition of such adaptations is still wanting. Here, we assess the timing of such acquisition using the aquatic sloth Thalassocnus, from the Neogene of the Pisco Formation, Peru. This genus is represented by five species occurring in successive vertebrate-bearing horizons of distinct ages. It yields the most detailed data about the gradual acquisition of aquatic adaptations among tetrapods, in displaying increasing osteosclerosis and pachyostosis through time. Such modifications, reflecting a shift in the habitat from terrestrial to aquatic, occurred over a short geological time span (ca 4 Myr). Otherwise, the bones of terrestrial pilosans (sloths and anteaters) are much more compact than the mean mammalian condition, which suggests that the osteosclerosis of Thalassocnus may represent an exaptation.

  4. Gradual adaptation of bone structure to aquatic lifestyle in extinct sloths from Peru.

    PubMed

    Amson, Eli; de Muizon, Christian; Laurin, Michel; Argot, Christine; de Buffrénil, Vivian

    2014-05-01

    Non-pathological densification (osteosclerosis) and swelling (pachyostosis) of bones are the main modifications affecting the skeleton of land vertebrates (tetrapods) that returned to water. However, a precise temporal calibration of the acquisition of such adaptations is still wanting. Here, we assess the timing of such acquisition using the aquatic sloth Thalassocnus, from the Neogene of the Pisco Formation, Peru. This genus is represented by five species occurring in successive vertebrate-bearing horizons of distinct ages. It yields the most detailed data about the gradual acquisition of aquatic adaptations among tetrapods, in displaying increasing osteosclerosis and pachyostosis through time. Such modifications, reflecting a shift in the habitat from terrestrial to aquatic, occurred over a short geological time span (ca 4 Myr). Otherwise, the bones of terrestrial pilosans (sloths and anteaters) are much more compact than the mean mammalian condition, which suggests that the osteosclerosis of Thalassocnus may represent an exaptation. PMID:24621950

  5. Asian International Students at an Australian University: Mapping the Paths between Integrative Motivation, Competence in L2 Communication, Cross-Cultural Adaptation and Persistence with Structural Equation Modelling

    ERIC Educational Resources Information Center

    Yu, Baohua

    2013-01-01

    This study examined the interrelationships of integrative motivation, competence in second language (L2) communication, sociocultural adaptation, academic adaptation and persistence of international students at an Australian university. Structural equation modelling demonstrated that the integrative motivation of international students has a…

  6. Locally adapted social parasite affects density, social structure, and life history of its ant hosts.

    PubMed

    Foitzik, Susanne; Achenbach, Alexandra; Brandt, Miriam

    2009-05-01

    Selection and adaptation are important processes in the coevolution between parasites and their hosts. The slave-making ant Protomognathus americanus, an obligate ant social parasite, has previously been shown to evolve morphological, behavioral, and chemical adaptations in the coevolutionary arms race with its Temnothorax hosts. Yet empirical studies have given variable results on the strength of the selection pressure this parasite exerts on its host populations. In this study, we directly investigated the pressure exerted by P. americanus and the reactions of the main host species, T. longispinosus, in two ant communities by manipulating parasite density in the field over several years. In addition, a cross-fostering design with the exchange of parasites between host populations allowed us to investigate local adaptation of parasite or host. We demonstrate a severe impact of the social parasite on the two host populations in West Virginia and New York, but also variation in host reactions between sites, as expected by the geographic mosaic theory of coevolution. Host density decreased at the West Virginia site with the presence of local slave-makers, whereas at the ecologically favorable New York site, density was unaffected. Nevertheless, social organization, colony size, and investment patterns of these host colonies at this site changed in response to our parasite manipulation. The release of P. americanus colonies led to a reduction in the number of resident queens and workers, an increase in intranest relatedness, and lower productivity, but also a higher investment in reproductives. In West Virginia, colony demography did not change, but raiding activity by New York slave-makers caused different investment patterns of host colonies. In addition, the cross-fostering element revealed local adaptation of the parasite P. americanus: slave-making colonies fared better in their sympatric host population, as they contained more slave-making ant workers and slaves

  7. [Dynamic structure of the cardiac rhythm in the process of adapting to high-altitude hypoxia].

    PubMed

    Shukurov, F A; Nidekker, I G

    1981-01-01

    On the basis of dynamic series of RR intervals of electrocardiograms of healthy male test subjects exposed for a different period of time to high altitude hypoxia, autoregression clouds were built. The patterns of distribution thus obtained were compared with physical work capacity of the test subjects. It is suggested that when selecting people to work actively at high altitudes autoregression clouds can be used as quantitative estimates of their health state and as predictions of potential adaptation failures.

  8. From epidemics to information propagation: Striking differences in structurally similar adaptive network models

    NASA Astrophysics Data System (ADS)

    Trajanovski, Stojan; Guo, Dongchao; Van Mieghem, Piet

    2015-09-01

    The continuous-time adaptive susceptible-infected-susceptible (ASIS) epidemic model and the adaptive information diffusion (AID) model are two adaptive spreading processes on networks, in which a link in the network changes depending on the infectious state of its end nodes, but in opposite ways: (i) In the ASIS model a link is removed between two nodes if exactly one of the nodes is infected to suppress the epidemic, while a link is created in the AID model to speed up the information diffusion; (ii) a link is created between two susceptible nodes in the ASIS model to strengthen the healthy part of the network, while a link is broken in the AID model due to the lack of interest in informationless nodes. The ASIS and AID models may be considered as first-order models for cascades in real-world networks. While the ASIS model has been exploited in the literature, we show that the AID model is realistic by obtaining a good fit with Facebook data. Contrary to the common belief and intuition for such similar models, we show that the ASIS and AID models exhibit different but not opposite properties. Most remarkably, a unique metastable state always exists in the ASIS model, while there an hourglass-shaped region of instability in the AID model. Moreover, the epidemic threshold is a linear function in the effective link-breaking rate in the AID model, while it is almost constant but noisy in the AID model.

  9. Sheep grazing causes shift in sex ratio and cohort structure of Brandt's vole: Implication of their adaptation to food shortage.

    PubMed

    Li, Guoliang; Hou, Xianglei; Wan, Xinrong; Zhang, Zhibin

    2016-01-01

    Livestock grazing has been demonstrated to affect the population abundance of small rodents in grasslands, but the causative mechanism of grazing on demographic parameters, particularly the age structure and sex ratio, is rarely investigated. In this study, we examined the effects of sheep grazing on the cohort structure and sex ratio of Brandt's vole (Lasiopodomys brandtii) in Inner Mongolia of China by using large manipulative experimental enclosures during 2010-2013. Our results indicated that sheep grazing significantly decreased the proportion of the spring-born cohort, but increased the proportion of the summer-born cohort. Grazing increased the proportion of males in both spring and summer cohorts. In addition, we found a negative relation between population density and the proportion of the overwinter cohort. Our results suggest that a shift in the cohort structure and the sex ratio may be an important strategy for small rodents to adapt to changes in food resources resulting from livestock grazing.

  10. Nematic liquid crystal around a spherical particle: Investigation of the defect structure and its stability using adaptive mesh refinement.

    PubMed

    Fukuda, Jun-Ichi; Yoneya, Makoto; Yokoyama, Hiroshi

    2004-01-01

    We investigate the orientation profile and the structure of topological defects of a nematic liquid crystal around a spherical particle using an adaptive mesh refinement scheme developed by us previously. The previous work [J. Fukuda et al., Phys. Rev. E 65, 041709 (2002)] was devoted to the investigation of the fine structure of a hyperbolic hedgehog defect that the particle accompanies and in this paper we present the equilibrium profile of the Saturn ring configuration. The radius of the Saturn ring r(d) in units of the particle radius R(0) increases weakly with the increase of Epsilon, the ratio of the nematic coherence length to R(0). Next we discuss the energetic stability of a hedgehog and a Saturn ring. The use of adaptive mesh refinement scheme together with a tensor orientational order parameter Q (alpha, beta) allows us to calculate the elastic energy of a nematic liquid crystal without any assumption of the structure and the energy of the defect core as in the previous similar studies. The reduced free energy of a nematic liquid crystal, F= F/L1RO, with L(1) being the elastic constant, is almost independent of Epsilon in the hedgehog configuration, while it shows a logarithmic dependence in the Saturn ring configuration. This result clearly indicates that the energetic stability of a hedgehog to a Saturn ring for a large particle is definitely attributed to the large defect energy of the Saturn ring with a large radius.

  11. A Unifying Framework for Adaptive Radar Detection in Homogeneous Plus Structured Interference— Part I: On the Maximal Invariant Statistic

    NASA Astrophysics Data System (ADS)

    Ciuonzo, D.; De Maio, A.; Orlando, D.

    2016-06-01

    This paper deals with the problem of adaptive multidimensional/multichannel signal detection in homogeneous Gaussian disturbance with unknown covariance matrix and structured deterministic interference. The aforementioned problem corresponds to a generalization of the well-known Generalized Multivariate Analysis of Variance (GMANOVA). In this first part of the work, we formulate the considered problem in canonical form and, after identifying a desirable group of transformations for the considered hypothesis testing, we derive a Maximal Invariant Statistic (MIS) for the problem at hand. Furthermore, we provide the MIS distribution in the form of a stochastic representation. Finally, strong connections to the MIS obtained in the open literature in simpler scenarios are underlined.

  12. An adaptive grid method for computing time accurate solutions on structured grids

    NASA Technical Reports Server (NTRS)

    Bockelie, Michael J.; Smith, Robert E.; Eiseman, Peter R.

    1991-01-01

    The solution method consists of three parts: a grid movement scheme; an unsteady Euler equation solver; and a temporal coupling routine that links the dynamic grid to the Euler solver. The grid movement scheme is an algebraic method containing grid controls that generate a smooth grid that resolves the severe solution gradients and the sharp transitions in the solution gradients. The temporal coupling is performed with a grid prediction correction procedure that is simple to implement and provides a grid that does not lag the solution in time. The adaptive solution method is tested by computing the unsteady inviscid solutions for a one dimensional shock tube and a two dimensional shock vortex iteraction.

  13. Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure

    NASA Astrophysics Data System (ADS)

    Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.

    2014-08-01

    Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver

  14. A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria

    PubMed Central

    Nahum, Joshua R.; Godfrey-Smith, Peter; Harding, Brittany N.; Marcus, Joseph H.; Carlson-Stevermer, Jared; Kerr, Benjamin

    2015-01-01

    In the context of Wright’s adaptive landscape, genetic epistasis can yield a multipeaked or “rugged” topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such “smooth” topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise–hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise–hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright’s shifting balance process. PMID:25964348

  15. IMAGING WITH MULTIMODAL ADAPTIVE-OPTICS OPTICAL COHERENCE TOMOGRAPHY IN MULTIPLE EVANESCENT WHITE DOT SYNDROME: THE STRUCTURE AND FUNCTIONAL RELATIONSHIP

    PubMed Central

    Legarreta, Andrew D.; Legarreta, John E.; Nadler, Zach; Gallagher, Denise; Hammer, Daniel X.; Ferguson, R. Daniel; Iftimia, Nicusor; Wollstein, Gadi; Schuman, Joel S.

    2016-01-01

    Purpose: To elucidate the location of pathological changes in multiple evanescent white dot syndrome (MEWDS) with the use of multimodal adaptive optics (AO) imaging. Methods: A 5-year observational case study of a 24-year-old female with recurrent MEWDS. Full examination included history, Snellen chart visual acuity, pupil assessment, intraocular pressures, slit lamp evaluation, dilated fundoscopic exam, imaging with Fourier-domain optical coherence tomography (FD-OCT), blue-light fundus autofluorescence (FAF), fundus photography, fluorescein angiography, and adaptive-optics optical coherence tomography. Results: Three distinct acute episodes of MEWDS occurred during the period of follow-up. Fourier-domain optical coherence tomography and adaptive-optics imaging showed disturbance in the photoreceptor outer segments (PR OS) in the posterior pole with each flare. The degree of disturbance at the photoreceptor level corresponded to size and extent of the visual field changes. All findings were transient with delineation of the photoreceptor recovery from the outer edges of the lesion inward. Hyperautofluorescence was seen during acute flares. Increase in choroidal thickness did occur with each active flare but resolved. Conclusion: Although changes in the choroid and RPE can be observed in MEWDS, Fourier-domain optical coherence tomography, and multimodal adaptive optics imaging localized the visually significant changes seen in this disease at the level of the photoreceptors. These transient retinal changes specifically occur at the level of the inner segment ellipsoid and OS/RPE line. En face optical coherence tomography imaging provides a detailed, yet noninvasive method for following the convalescence of MEWDS and provides insight into the structural and functional relationship of this transient inflammatory retinal disease. PMID:26735319

  16. New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation

    PubMed Central

    Kieft, Jeffrey S; Rabe, Jennifer L; Chapman, Erich G

    2015-01-01

    Arthropod-borne flaviviruses (FVs) are a growing world-wide health threat whose incidence and range are increasing. The pathogenicity and cytopathicity of these single-stranded RNA viruses are influenced by viral subgenomic non-protein-coding RNAs (sfRNAs) that the viruses produce to high levels during infection. To generate sfRNAs the virus co-opts the action of the abundant cellular exonuclease Xrn1, which is part of the cell's normal RNA turnover machinery. This exploitation of the cellular machinery is enabled by discrete, highly structured, Xrn1-resistant RNA elements (xrRNAs) in the 3′UTR that interact with Xrn1 to halt processive 5′ to 3′ decay of the viral genomic RNA. We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance. Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested. However, there is some variability in the structures that correlates with unexplained patterns in the viral 3′ UTRs. Finally, examination of these structures and their behavior in the context of viral infection leads to a new hypothesis linking RNA tertiary structure, overall 3′ UTR architecture, sfRNA production, and host adaptation. PMID:26399159

  17. Adaptive management

    USGS Publications Warehouse

    Allen, Craig R.; Garmestani, Ahjond S.

    2015-01-01

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

  18. Adaptation of cardiac structure by mechanical feedback in the environment of the cell: a model study.

    PubMed Central

    Arts, T; Prinzen, F W; Snoeckx, L H; Rijcken, J M; Reneman, R S

    1994-01-01

    In the cardiac left ventricle during systole mechanical load of the myocardial fibers is distributed uniformly. A mechanism is proposed by which control of mechanical load is distributed over many individual control units acting in the environment of the cell. The mechanics of the equatorial region of the left ventricle was modeled by a thick-walled cylinder composed of 6-1500 shells of myocardial fiber material. In each shell a separate control unit was simulated. The direction of the cells was varied so that systolic fiber shortening approached a given optimum of 15%. End-diastolic sarcomere length was maintained at 2.1 microns. Regional early-systolic stretch and global contractility stimulated growth of cellular mass. If systolic shortening was more than normal the passive extracellular matrix stretched. The design of the load-controlling mechanism was derived from biological experiments showing that cellular processes are sensitive to mechanical deformation. After simulating a few hundred adaptation cycles, the macroscopic anatomical arrangement of helical pathways of the myocardial fibers formed automatically. If pump load of the ventricle was changed, wall thickness and cavity volume adapted physiologically. We propose that the cardiac anatomy may be defined and maintained by a multitude of control units for mechanical load, each acting in the cellular environment. Interestingly, feedback through fiber stress is not a compelling condition for such control. PMID:8038399

  19. Compensatory structural adaptive modifications of vagina in response to functional demand in goat.

    PubMed

    Hussin, Amer M; Zaid, Nazih W; Hussain, S O

    2014-01-01

    Vaginal biopsies and smears were collected from ten adult local healthy goats. Routine histological methods were carried out on vaginal biopsies and then stained with PAS stain. The smears were stained with Methylene blue. All samples were inspected under light microscope. The present study found that many constituents of the wall of the vagina, which have an important functional role, were absent; among these were the vaginal glands, goblet cells, muscularis mucosa, and lymphatic nodules. On the other hand, vagina showed special compensatory histological mechanisms, namely, the deep epithelial folds, the well-developed germinated stratum basale, the apparent basement membrane, and the profuse defensive cells, such as neutrophils, macrophages, lymphocytes, plasma cells, and mast cells. The general stains of this study could not recognize dendritic cells although they play an important functional role. Moreover, the herein study declared also that the vaginal smears showing many adaptive cellular mechanisms among these were, the keratinization, the process of sheet formation that lines the vaginal lumen, the process of metachromasia which is related to the cellular activity in protein synthesis, keratin, and finally the presence of endogenous microorganisms. It was concluded that all the above cellular compensatory adaptive mechanisms may compensate the lacking vaginal constituents and act to raise the immune response of the vagina.

  20. Error estimation and adaptive mesh refinement for parallel analysis of shell structures

    NASA Technical Reports Server (NTRS)

    Keating, Scott C.; Felippa, Carlos A.; Park, K. C.

    1994-01-01

    The formulation and application of element-level, element-independent error indicators is investigated. This research culminates in the development of an error indicator formulation which is derived based on the projection of element deformation onto the intrinsic element displacement modes. The qualifier 'element-level' means that no information from adjacent elements is used for error estimation. This property is ideally suited for obtaining error values and driving adaptive mesh refinements on parallel computers where access to neighboring elements residing on different processors may incur significant overhead. In addition such estimators are insensitive to the presence of physical interfaces and junctures. An error indicator qualifies as 'element-independent' when only visible quantities such as element stiffness and nodal displacements are used to quantify error. Error evaluation at the element level and element independence for the error indicator are highly desired properties for computing error in production-level finite element codes. Four element-level error indicators have been constructed. Two of the indicators are based on variational formulation of the element stiffness and are element-dependent. Their derivations are retained for developmental purposes. The second two indicators mimic and exceed the first two in performance but require no special formulation of the element stiffness mesh refinement which we demonstrate for two dimensional plane stress problems. The parallelizing of substructures and adaptive mesh refinement is discussed and the final error indicator using two-dimensional plane-stress and three-dimensional shell problems is demonstrated.

  1. Error estimation and adaptive mesh refinement for parallel analysis of shell structures

    NASA Astrophysics Data System (ADS)

    Keating, Scott C.; Felippa, Carlos A.; Park, K. C.

    1994-11-01

    The formulation and application of element-level, element-independent error indicators is investigated. This research culminates in the development of an error indicator formulation which is derived based on the projection of element deformation onto the intrinsic element displacement modes. The qualifier 'element-level' means that no information from adjacent elements is used for error estimation. This property is ideally suited for obtaining error values and driving adaptive mesh refinements on parallel computers where access to neighboring elements residing on different processors may incur significant overhead. In addition such estimators are insensitive to the presence of physical interfaces and junctures. An error indicator qualifies as 'element-independent' when only visible quantities such as element stiffness and nodal displacements are used to quantify error. Error evaluation at the element level and element independence for the error indicator are highly desired properties for computing error in production-level finite element codes. Four element-level error indicators have been constructed. Two of the indicators are based on variational formulation of the element stiffness and are element-dependent. Their derivations are retained for developmental purposes. The second two indicators mimic and exceed the first two in performance but require no special formulation of the element stiffness mesh refinement which we demonstrate for two dimensional plane stress problems. The parallelizing of substructures and adaptive mesh refinement is discussed and the final error indicator using two-dimensional plane-stress and three-dimensional shell problems is demonstrated.

  2. An Adaptive Spectrally Weighted Structure Tensor Applied to Tensor Anisotropic Nonlinear Diffusion for Hyperspectral Images

    ERIC Educational Resources Information Center

    Marin Quintero, Maider J.

    2013-01-01

    The structure tensor for vector valued images is most often defined as the average of the scalar structure tensors in each band. The problem with this definition is the assumption that all bands provide the same amount of edge information giving them the same weights. As a result non-edge pixels can be reinforced and edges can be weakened…

  3. Ventricular structure, function, and mechanics at high altitude: chronic remodeling in Sherpa vs. short-term lowlander adaptation.

    PubMed

    Stembridge, Mike; Ainslie, Philip N; Hughes, Michael G; Stöhr, Eric J; Cotter, James D; Nio, Amanda Q X; Shave, Rob

    2014-08-01

    Short-term, high-altitude (HA) exposure raises pulmonary artery systolic pressure (PASP) and decreases left-ventricular (LV) volumes. However, relatively little is known of the long-term cardiac consequences of prolonged exposure in Sherpa, a highly adapted HA population. To investigate short-term adaptation and potential long-term cardiac remodeling, we studied ventricular structure and function in Sherpa at 5,050 m (n = 11; 31 ± 13 yr; mass 68 ± 10 kg; height 169 ± 6 cm) and lowlanders at sea level (SL) and following 10 ± 3 days at 5,050 m (n = 9; 34 ± 7 yr; mass 82 ± 10 kg; height 177 ± 6 cm) using conventional and speckle-tracking echocardiography. At HA, PASP was higher in Sherpa and lowlanders compared with lowlanders at SL (both P < 0.05). Sherpa had smaller right-ventricular (RV) and LV stroke volumes than lowlanders at SL with lower RV systolic strain (P < 0.05) but similar LV systolic mechanics. In contrast to LV systolic mechanics, LV diastolic, untwisting velocity was significantly lower in Sherpa compared with lowlanders at both SL and HA. After partial acclimatization, lowlanders demonstrated no change in the RV end-diastolic area; however, both RV strain and LV end-diastolic volume were reduced. In conclusion, short-term hypoxia induced a reduction in RV systolic function that was also evident in Sherpa following chronic exposure. We propose that this was consequent to a persistently higher PASP. In contrast to the RV, remodeling of LV volumes and normalization of systolic mechanics indicate structural and functional adaptation to HA. However, altered LV diastolic relaxation after chronic hypoxic exposure may reflect differential remodeling of systolic and diastolic LV function.

  4. Numerical study of self-adaptive vibration suppression for flexible structure using interior inlay viscous fluid unit method

    NASA Astrophysics Data System (ADS)

    Zhang, Xiongwen; Li, Jun; Xu, Hui; Li, Guojun

    2006-11-01

    This paper investigates the usage of an interior inlay viscous fluid unit as a new vibration suppression method for flexible structures via numerical simulations. The first and second modes of vibration for a beam have been calculated using the commercial computational fluid dynamic package Fluent6.1, together with the liquid surface distribution and the fluid force. The calculated results show that the inlay fluid unit has suppressive effects on flexible structures. The liquid converges self-adaptively to locations of larger vibrations. The fluid force varies with the beam vibration at a phase difference of more than 180°. Thus the fluid force suppresses the beam vibration at most of the time.

  5. Structural analysis of human proximal femur for the prediction of biomechanical strength in vitro: the locally adapted scaling vector method

    NASA Astrophysics Data System (ADS)

    Monetti, Roberto A.; Boehm, Holger; Mueller, Dirk; Rummeny, Ernst; Link, Thomas; Raeth, Christoph

    2005-04-01

    We introduce an image structure analysis technique suitable in cases where anisotropy plays an important role. The so-called Locally Adapted Scaling Vector Method (LSVM) comprises two steps. First, a procedure to estimate the local main orientation at every point of the image is applied. These orientations are then incorporated in a structure characterization procedure. We apply this methodology to High Resolution Magnetic Resonance Images (HRMRI) of human proximal femoral specimens IN VITRO. We extract a 3D local texture measure to establish correlations with the biomechanical properties of bone specimens quantified via the bone maximum compressive strength. The purpose is to compare our results with the prediction of bone strength using similar isotropic texture measures, bone mineral density, and standard 2D morphometric parameters. Our findings suggest that anisotropic texture measures are superior in cases where directional properties are relevant.

  6. Adapting the Structural Family Systems Rating to Assess the Patterns of Interaction in Families of Dementia Caregivers

    PubMed Central

    Mitrani, Victoria B.; Feaster, Daniel J.; McCabe, Brian E.; Czaja, Sara J.; Szapocznik, Jose

    2008-01-01

    Purpose: This study adapted the Structural Family Systems Ratings (SFSR), an observational measure of family interactions, for dementia caregivers. This article presents the development of the SFSR-Dementia Caregiver adaptation (SFSR-DC) and examines relationships between specific family-interaction patterns and caregiver distress. Design and Methods: The families of 177 Cuban American and White non-Hispanic American caregivers of dementia patients were assessed at baseline, 6, 12, and 18 months. Structural family theory and clinical experience were used to identify family interaction patterns believed to be related to caregiver emotional functioning. Factor analysis was used to refine subscales and develop a multiscale measure. Results: Six reliable subscales were related to caregiver distress and included in the SFSR-DC. There were two second-order factors. The SFSR-DC was provisionally cross-validated and showed invariance across the two ethnic groups. Implications: The SFSR-DC provides a method for examining specific and multiple interaction patterns in caregiver families and thus can advance knowledge regarding the role of the family in the stress processes of caregiving. These findings support the relevance of family interactions in caregiver distress and suggest that a treatment approach aimed at supporting family closeness and conflict resolution and reducing negativity might enhance caregiver well-being. PMID:16051907

  7. Cloning, expression and structural stability of a cold-adapted β-galactosidase from Rahnella sp. R3.

    PubMed

    Fan, Yuting; Hua, Xiao; Zhang, Yuzhu; Feng, Yinghui; Shen, Qiuyun; Dong, Juan; Zhao, Wei; Zhang, Wenbin; Jin, Zhengyu; Yang, Ruijin

    2015-11-01

    A novel gene was isolated for the first time from a psychrophilic gram-negative bacterium Rahnella sp. R3. The gene encoded a cold-adapted β-galactosidase (R-β-Gal). Recombinant R-β-Gal was expressed in Escherichia coli BL21 (DE3), purified and characterized. R-β-gal belongs to the glycosyl hydrolase family 42. Circular dichroism spectrometry of the structural stability of R-β-Gal with respect to temperature indicated that the secondary structures of the enzyme were stable to 45°C. In solution, the enzyme was a homo-trimer and was active at temperatures as low as 4°C. The enzyme did not require the presence of metal ions to be active, but Mg(2+), Mn(2+), and Ca(2+) enhanced its activity slightly, whereas Fe(3+), Zn(2+) and Al(3+) appeared to inactive it. The purified enzyme displayed K(m) values of 6.5 mM for ONPG and 2.2mM for lactose at 4°C. These values were lower than the corresponding K(m)s reported for other cold-adapted β-Gals.

  8. Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

    SciTech Connect

    Morgunova, Ekaterina; Gray, Fiona C.; MacNeill, Stuart A.; Ladenstein, Rudolf

    2009-10-01

    The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs. The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R{sub free} = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells.

  9. Adaptive Smith-Waterman residue match seeding for protein structural alignment.

    PubMed

    Topham, Christopher M; Rouquier, Mickaël; Tarrat, Nathalie; André, Isabelle

    2013-10-01

    The POLYFIT rigid-body algorithm for automated global pairwise and multiple protein structural alignment is presented. Smith-Waterman local alignment is used to establish a set of seed equivalences that are extended using Needleman-Wunsch dynamic programming techniques. Structural and functional interaction constraints provided by evolution are encoded as one-dimensional residue physical environment strings for alignment of highly structurally overlapped protein pairs. Local structure alignment of more distantly related pairs is carried out using rigid-body conformational matching of 15-residue fragments, with allowance made for less stringent conformational matching of metal-ion and small molecule ligand-contact, disulphide bridge, and cis-peptide correspondences. Protein structural plasticity is accommodated through the stepped adjustment of a single empirical distance parameter value in the calculation of the Smith-Waterman dynamic programming matrix. Structural overlap is used both as a measure of similarity and to assess alignment quality. Pairwise alignment accuracy has been benchmarked against that of 10 widely used aligners on the Sippl and Wiederstein set of difficult pairwise structure alignment problems, and more extensively against that of Matt, SALIGN, and MUSTANG in pairwise and multiple structural alignments of protein domains with low shared sequence identity in the SCOP-ASTRAL 40% compendium. The results demonstrate the advantages of POLYFIT over other aligners in the efficient and robust identification of matching seed residue positions in distantly related protein targets and in the generation of longer structurally overlapped alignment lengths. Superposition-based application areas include comparative modeling and protein and ligand design. POLYFIT is available on the Web server at http://polyfit.insa-toulouse.fr.

  10. The reduced order model problem in distributed parameter systems adaptive identification and control. [large space structures

    NASA Technical Reports Server (NTRS)

    Johnson, C. R., Jr.; Lawrence, D.

    1981-01-01

    The basic assumption that a large space structure can be decoupled preceding the application of reduced order active control was considered and alternative solutions to the control of such structures (in contrast to the strict modal control) were investigated. The transfer function matrix from the actuators to the sensors was deemed to be a reasonable candidate. More refined models from multivariable systems theory were studied and recent results in the multivariable control field were compared with respect to theoretical deficiencies and likely problems in application to large space structures.

  11. Location selection for vibration controllers in space crane as adaptive structures

    NASA Technical Reports Server (NTRS)

    Lu, L. Y.; Utku, S.; Wada, B. K.

    1990-01-01

    It is assumed that the space crane is vibrating about a known configuration which is reached at the end of some maneuver. For this configuration, r actuator locations are to be determined in order to control the first q of the structural vibration modes of the system optimizing the energy dissipation rate. A modified version of the control stratagem of Chang (1980) is applied using the structural modes of the uncontrolled crane, followed by algorithms for the actuator placement problem.

  12. An adaptive level set method for shock-driven fluid-structure interaction

    SciTech Connect

    Deiterding, Ralf

    2007-01-01

    The fluid-structure interaction simulation of shock- and detonation-loaded structures requires numerical methods that can cope with large deformations as well as local topology changes. A robust, level-set-based shock-capturing fluid solver is described that allows coupling to any solid mechanics solver. As computational example, the elastic response of a thin steel panel, modeled with both shell and beam theory, to a shock wave in air is considered.

  13. Differential adaptation to weightlessness of functional and structural characteristics of rat hindlimb muscles.

    PubMed

    Stevens, L; Picquet, F; Catinot, M P; Mounier, Y

    1996-09-01

    Soleus, vastus intermedius, tibialis anterior, and extensor digitorum longus muscles were removed from rats following space flight onboard the SLS-2 mission and from control animals. Muscle tissues were studied for their calcium and strontium activated tension characteristics and for structural changes. Muscles were also examined for myosin composition using electrophoresis. Results indicate that changes occurred in structural and functional muscle characteristics in both slow and fast muscle fiber types. These results are detailed and discussed.

  14. EDITORIAL: Adaptive and active materials: Selected papers from the ASME 2010 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 10) (Philadelphia, PA, USA, 28 September-1 October 2010) Adaptive and active materials: Selected papers from the ASME 2010 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 10) (Philadelphia, PA, USA, 28 September-1 October 2010)

    NASA Astrophysics Data System (ADS)

    Brei, Diann

    2011-09-01

    The third annual meeting of the AMSE/AIAA Smart Materials, Adaptive Structures and Intelligent Systems Conference (SMASIS) took place in the heart of historic Philadelphia's cultural district, and included a pioneer banquet in the National Constitutional Center. The applications emphasis of the 2010 conference was reflected in keynote talks by Dr Alan Taub, vice president of General Motors global research and development, 'Smart materials in the automotive industry'; Dr Charles R Farrar, engineering institute leader at Los Alamos National Laboratory, 'Future directions for structural health monitoring of civil engineering infrastructure'; and Professor Christopher S Lynch of the University of California Los Angeles, 'Ferroelectric materials and their applications'. The SMASIS conference was divided into six technical symposia each of which included basic research, applied technological design and development, and industrial and governmental integrated system and application demonstrations. The six symposia were: SYMP 1 Multifunctional Materials; SYMP 2 Active Materials, Mechanics and Behavior; SYMP 3 Modeling, Simulation and Control; SYMP 4 Enabling Technologies and Integrated System Design; SYMP 5 Structural Health Monitoring/NDE; and SYMP 6 Bio-inspired Smart Materials and Structures. In addition, the conference introduced a new student and young professional development symposium. Authors of papers in the materials areas (symposia 1, 2 and 6) were invited to write a full journal article on their presentation topic for publication in this special issue of Smart Materials and Structures. This set of papers demonstrates the exceptional quality and originality of the conference presentations. We are appreciative of their efforts in producing this collection of highly relevant articles on smart materials.

  15. Topology optimization of adaptive fluid-actuated cellular structures with arbitrary polygonal motor cells

    NASA Astrophysics Data System (ADS)

    Lv, Jun; Tang, Liang; Li, Wenbo; Liu, Lei; Zhang, Hongwu

    2016-05-01

    This paper mainly focuses on the fast and efficient design method for plant bioinspired fluidic cellular materials and structures composed of polygonal motor cells. Here we developed a novel structural optimization method with arbitrary polygonal coarse-grid elements based on multiscale finite element frameworks. The fluidic cellular structures are meshed with irregular polygonal coarse-grid elements according to their natural size and the shape of the imbedded motor cells. The multiscale base functions of solid displacement and hydraulic pressure are then constructed to bring the small-scale information of the irregular motor cells to the large-scale simulations on the polygonal coarse-grid elements. On this basis, a new topology optimization method based on the resulting polygonal coarse-grid elements is proposed to determine the optimal distributions or number of motor cells in the smart cellular structures. Three types of optimization problems are solved according to the usages of the fluidic cellular structures. Firstly, the proposed optimization method is utilized to minimize the system compliance of the load-bearing fluidic cellular structures. Second, the method is further extended to design biomimetic compliant actuators of the fluidic cellular materials due to the fact that non-uniform volume expansions of fluid in the cells can induce elastic action. Third, the optimization problem focuses on the weight minimization of the cellular structure under the constraints for the compliance of the whole system. Several representative examples are investigated to validate the effectiveness of the proposed polygon-based topology optimization method of the smart materials.

  16. The ever changing moods of calmodulin: how structural plasticity entails transductional adaptability.

    PubMed

    Villarroel, Alvaro; Taglialatela, Maurizio; Bernardo-Seisdedos, Ganeko; Alaimo, Alessandro; Agirre, Jon; Alberdi, Araitz; Gomis-Perez, Carolina; Soldovieri, Maria Virginia; Ambrosino, Paolo; Malo, Covadonga; Areso, Pilar

    2014-07-29

    The exceptional versatility of calmodulin (CaM) three-dimensional arrangement is reflected in the growing number of structural models of CaM/protein complexes currently available in the Protein Data Bank (PDB) database, revealing a great diversity of conformations, domain organization, and structural responses to Ca(2+). Understanding CaM binding is complicated by the diversity of target proteins sequences. Data mining of the structures shows that one face of each of the eight CaM helices can contribute to binding, with little overall difference between the Ca(2+) loaded N- and C-lobes and a clear prevalence of the C-lobe low Ca(2+) conditions. The structures reveal a remarkable variety of configurations where CaM binds its targets in a preferred orientation that can be reversed and where CaM rotates upon Ca(2+) binding, suggesting a highly dynamic metastable relation between CaM and its targets. Recent advances in structure-function studies and the discovery of CaM mutations being responsible for human diseases, besides expanding the role of CaM in human pathophysiology, are opening new exciting avenues for the understanding of the how CaM decodes Ca(2+)-dependent and Ca(2+)-independent signals.

  17. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets.

  18. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  19. The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida

    PubMed Central

    Pedersen, Hege Lynum; Willassen, Nils Peder; Leiros, Ingar

    2009-01-01

    Superoxide dismutases (SODs) are metalloenzymes that catalyse the dismutation of the superoxide radical anion into O2 and H2O2 in a two-step reaction. The crystal structure of the iron superoxide dismutase from the cold-adapted and fish-pathogenic bacterium Aliivibrio salmonicida (asFeSOD) has been determined and refined to 1.7 Å resolution. The protein has been characterized and compared with the closely related homologous iron superoxide dismutase from the mesophilic Escherichia coli (ecFeSOD) in an attempt to rationalize its environmental adaptation. ecFeSOD shares 75% identity with asFeSOD. Compared with the mesophilic FeSOD, the psychrophilic FeSOD has distinct temperature differences in residual activity and thermostability that do not seem to be related to structural differences such as intramolecular or intermolecular ion bonds, hydrogen bonds or cavity sizes. However, an increased net negative charge on the surface of asFeSOD may explain its lower thermostability com­­pared with ecFeSOD. Activity measurements and differential scanning calori­metry measurements revealed that the psychrophilic asFeSOD had a thermostability that was significantly higher than the optimal growth temperature of the host organism. PMID:19193992

  20. Longin and GAF domains: structural evolution and adaptation to the subcellular trafficking machinery.

    PubMed

    De Franceschi, Nicola; Wild, Klemens; Schlacht, Alexander; Dacks, Joel B; Sinning, Irmgard; Filippini, Francesco

    2014-01-01

    Endomembrane trafficking is one of the most prominent cytological features of eukaryotes. Given their widespread distribution and specialization, coiled-coil domains, coatomer domains, small GTPases and Longin domains are considered primordial 'building blocks' of the membrane trafficking machineries. Longin domains are conserved across eukaryotes and were likely to be present in the Last Eukaryotic Common Ancestor. The Longin fold is based on the α-β-α sandwich architecture and a unique topology, possibly accounting for the special adaptation to the eukaryotic trafficking machinery. The ancient Per ARNT Sim (PAS) and cGMP-specific phosphodiesterases, Adenylyl cyclases and FhlA (GAF) family domains show a similar architecture, and the identification of prokaryotic counterparts of GAF domains involved in trafficking provides an additional connection for the endomembrane system back into the pre-eukaryotic world. Proteome-wide, comparative bioinformatic analyses of the domains reveal three binding regions (A, B and C) mediating either specific or conserved protein-protein interactions. While the A region mediates intra- and inter-molecular interactions, the B region is involved in binding small GTPases, thus providing an evolutionary connection among major building blocks in the endomembrane system. Finally, we propose that the peculiar interaction surface of the C region of the Longin domain allowed it to extensively integrate into the endomembrane trafficking machinery in the earliest stages of building the eukaryotic cell.

  1. Structural studies of a cold-adapted dimeric β-D-galactosidase from Paracoccus sp. 32d.

    PubMed

    Rutkiewicz-Krotewicz, Maria; Pietrzyk-Brzezinska, Agnieszka J; Sekula, Bartosz; Cieśliński, Hubert; Wierzbicka-Woś, Anna; Kur, Józef; Bujacz, Anna

    2016-09-01

    The crystal structure of a novel dimeric β-D-galactosidase from Paracoccus sp. 32d (ParβDG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric β-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 β-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted β-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical β-D-galactosidase, the crystal structure in complex with galactose (ParβDG-Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric β-D-galactosidase reveals significant differences in comparison to other β-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 in ParβDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme. PMID:27599737

  2. Structural studies of a cold-adapted dimeric β-D-galactosidase from Paracoccus sp. 32d.

    PubMed

    Rutkiewicz-Krotewicz, Maria; Pietrzyk-Brzezinska, Agnieszka J; Sekula, Bartosz; Cieśliński, Hubert; Wierzbicka-Woś, Anna; Kur, Józef; Bujacz, Anna

    2016-09-01

    The crystal structure of a novel dimeric β-D-galactosidase from Paracoccus sp. 32d (ParβDG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric β-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 β-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted β-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical β-D-galactosidase, the crystal structure in complex with galactose (ParβDG-Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric β-D-galactosidase reveals significant differences in comparison to other β-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 in ParβDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme.

  3. Development of a generic adenovirus delivery system based on structure-guided design of bispecific trimeric DARPin adapters.

    PubMed

    Dreier, Birgit; Honegger, Annemarie; Hess, Christian; Nagy-Davidescu, Gabriela; Mittl, Peer R E; Grütter, Markus G; Belousova, Natalya; Mikheeva, Galina; Krasnykh, Victor; Plückthun, Andreas

    2013-03-01

    Adenoviruses (Ads) have shown promise as vectors for gene delivery in clinical trials. Efficient viral targeting to a tissue of choice requires both ablation of the virus' original tropism and engineering of an efficient receptor-mediated uptake by a specific cell population. We have developed a series of adapters binding to the virus with such high affinity that they remain fully bound for >10 d, block its natural receptor binding site and mediate interaction with a surface receptor of choice. The adapter contains two fused modules, both consisting of designed ankyrin repeat proteins (DARPins), one binding to the fiber knob of adenovirus serotype 5 and the other binding to various tumor markers. By solving the crystal structure of the complex of the trimeric knob with three bound DARPins at 1.95-Å resolution, we could use computer modeling to design a link to a trimeric protein of extraordinary kinetic stability, the capsid protein SHP from the lambdoid phage 21. We arrived at a module which binds the knob like a trimeric clamp. When this clamp was fused with DARPins of varying specificities, it enabled adenovirus serotype 5-mediated delivery of a transgene in a human epidermal growth factor receptor 2-, epidermal growth factor receptor-, or epithelial cell adhesion molecule-dependent manner with transduction efficiencies comparable to or even exceeding those of Ad itself. With these adapters, efficiently produced in Escherichia coli, Ad can be converted rapidly to new receptor specificities using any ligand as the receptor-binding moiety. Prefabricated Ads with different payloads thus can be retargeted readily to many cell types of choice.

  4. Applying Adaptive Swarm Intelligence Technology with Structuration in Web-Based Collaborative Learning

    ERIC Educational Resources Information Center

    Huang, Yueh-Min; Liu, Chien-Hung

    2009-01-01

    One of the key challenges in the promotion of web-based learning is the development of effective collaborative learning environments. We posit that the structuration process strongly influences the effectiveness of technology used in web-based collaborative learning activities. In this paper, we propose an ant swarm collaborative learning (ASCL)…

  5. Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

  6. Structural thermal adaptation of β-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii.

    PubMed

    Chiappori, Federica; Pucciarelli, Sandra; Merelli, Ivan; Ballarini, Patrizia; Miceli, Cristina; Milanesi, Luciano

    2012-04-01

    Tubulin dimers of psychrophilic eukaryotes can polymerize into microtubules at 4°C, a temperature at which microtubules from mesophiles disassemble. This unique capability requires changes in the primary structure and/or in post-translational modifications of the tubulin subunits. To contribute to the understanding of mechanisms responsible for microtubule cold stability, here we present a computational structural analysis based on molecular dynamics (MD) and experimental data of three β-tubulin isotypes, named EFBT2, EFBT3, and EFBT4, from the Antarctic protozoon Euplotes focardii that optimal temperature for growth and reproduction is 4°C. In comparison to the β-tubulin from E. crassus, a mesophilic Euplotes species, EFBT2, EFBT3, and EFBT4 possess unique amino acid substitutions that confer different flexible properties of the polypeptide, as well as an increased hydrophobicity of the regions involved in microtubule interdimeric contacts that may overcome the microtubule destabilizing effect of cold temperatures. The structural analysis based on MD indicated that all isotypes display different flexibility properties in the regions involved in the formation of longitudinal and lateral contacts during microtubule polymerization. We also investigated the role of E. focardii β-tubulin isotypes during the process of cilia formation. The unique characteristics of the primary and tertiary structures of psychrophilic β-tubulin isotypes seem responsible for the formation of microtubules with distinct dynamic and functional properties.

  7. Perceptual Distortions in the Adaptation of English Consonant Clusters: Syllable Structure or Consonantal Contact Constraints?

    ERIC Educational Resources Information Center

    Kabak, Baris; Idsardi, William J.

    2007-01-01

    We present the results from an experiment that tests the perception of English consonantal sequences by Korean speakers and we confirm that perceptual epenthesis in a second language (L2) arises from syllable structure restrictions of the first language (L1), rather than linear co-occurrence restrictions. Our study replicates and extends Dupoux,…

  8. Conception et exploitation d'une structure active pour une aile laminaire adaptative experimentale

    NASA Astrophysics Data System (ADS)

    Coutu, Daniel

    This doctoral research contributed to the success of the project CRIAQ 7.1, demonstrating the capability of a morphing laminar wing to reduce fuel consumption. Respectively, this thesis shows the design of the experimental wing and its operation in a subsonic wind tunnel (Mach numbers of 0.2 to 0.3 with angles of attack between -1 and 2°). First of all, the morphing wing is formed of a composite laminate linked to an actuation system to build an active structure capable of modifying the wing upper surface geometry. The design was performed using a new developed methodology to solve aero-structural problems. Using ANSYS software, the finite elements method was applied to model the different possible active structure configurations Aerodynamic loads applied over the active structure as well as targeted morphed geometries have been provided by the Ecole Polytechnique team. Next, laminar flow enhancements allowed by each active structure configuration we' re evaluated using the aerodynamic solver XFoil 6.96. A best trade-off between aerodynamic performance and energy needed for wing morphing was found using a multi-objective optimization technique. Among the retained stable configurations, a 4-ply composite laminated shell driven by 2 actuation lines was retained. Thereafter, the research effort focused on the exploitation of the morphing capabilities of the experimental wing over each given set of flow conditions. Therefore, once the prototype was built, the structural model was refined, calibrated and coupled with the aerodynamic solver to accurately predict the aero-structural behavior in the wind tunnel. Optimal morphing wing shapes were numerically calculated using a generalized pattern search algorithm and a local search routine to refine the solution. In the wind tunnel, this open-loop control approach allowed an average 25% laminar flow regime extension over the wing prototype upper surface. Consequently, an average 18.5% profile drag reduction was measured by

  9. Adapting hydrological model structure to catchment characteristics: A large-sample experiment

    NASA Astrophysics Data System (ADS)

    Addor, Nans; Clark, Martyn P.; Nijssen, Bart

    2016-04-01

    Current hydrological modeling frameworks do not offer a clear way to systematically investigate the relationship between model complexity and model fidelity. The characterization of this relationship has so far relied on comparisons of different modules within the same model or comparisons of entirely different models. This lack of granularity in the differences between the model constructs makes it difficult to pinpoint model features that contribute to good simulations and means that the number of models or modeling hypotheses evaluated is usually small. Here we use flexible modeling frameworks to comprehensively and systematically compare modeling alternatives across the continuum of model complexity. A key goal is to explore which model structures are most adequate for catchments in different hydroclimatic conditions. Starting from conceptual models based on the Framework for Understanding Structural Errors (FUSE), we progressively increase model complexity by replacing conceptual formulations by physically explicit ones (process complexity) and by refining model spatial resolution (spatial complexity) using the newly developed Structure for Unifying Multiple Modeling Alternatives (SUMMA). To investigate how to best reflect catchment characteristics using model structure, we rely on a recently released data set of 671 catchments in the continuous United States. Instead of running hydrological simulations in every catchment, we use clustering techniques to define catchment clusters, run hydrological simulations for representative members of each cluster, develop hypotheses (e.g., when specific process representations have useful explanatory power) and test these hypotheses using other members of the cluster. We thus refine our catchment clustering based on insights into dominant hydrological processes gained from our modeling approach. With this large-sample experiment, we seek to uncover trade-offs between realism and practicality, and formulate general

  10. Adaptive bimaterial lattices to mitigate thermal expansion mismatch stresses in satellite structures

    NASA Astrophysics Data System (ADS)

    Toropova, Marina M.; Steeves, Craig A.

    2015-08-01

    Earth-orbiting satellites regularly pass from sunlight to shade and back; these transitions are typically accompanied by significant temperature changes. When adjoining parts of a satellite that are made of different materials are subjected to large temperature changes, thermal mismatch stresses arise that are a function of the temperature change and the difference in coefficients of thermal expansion (CTEs) between the two materials. These thermal stresses are linked to undesirable deformation and, through long-term cycling, fatigue and failure of the structure. This paper describes a type of anisotropic lattice that can serve as a stress-free adaptor between two materials, eliminating thermal mismatch stresses and their concomitant consequences. The lattices consist of planar nonidentical anisotropic bimaterial cells, each designed based on a virtual triangle. Physically the cells consist of a triangle made of material with higher CTE surrounded by a hexagon made of material with lower CTE. Different skew angles of the hexagon make a particular cell and the whole lattice anisotropic. The cells can be designed and combined in a lattice in such a way that one edge of the lattice has CTE that coincides with the CTE of the first part of the structure (substrate 1), while the other edge of the lattice has CTE equal to the CTE of the second part of the structure (substrate 2). If all joints between the parts of each cell, neighbouring cells, and the lattice and the substrates are pinned, the whole structure will be free of thermal stresses. This paper will discuss the fundamental principles governing such lattices, their refinement for special circumstances, and opportunities for improving the structural performance of the lattices. This will be presented coupled to a rational strategy for lattice design.

  11. Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures

    SciTech Connect

    Oyama, Takuji; Toyota, Kenji; Waku, Tsuyoshi; Hirakawa, Yuko; Nagasawa, Naoko; Kasuga, Jun-ichi; Hashimoto, Yuichi; Miyachi, Hiroyuki; Morikawa, Kosuke

    2009-08-01

    The structures of the ligand-binding domains (LBDs) of human peroxisome proliferator-activated receptors (PPARα, PPARγ and PPARδ) in complexes with a pan agonist, an α/δ dual agonist and a PPARδ-specific agonist were determined. The results explain how each ligand is recognized by the PPAR LBDs at an atomic level. Peroxisome proliferator-activated receptors (PPARs) belong to the nuclear hormone receptor family, which is defined as transcriptional factors that are activated by the binding of ligands to their ligand-binding domains (LBDs). Although the three PPAR subtypes display different tissue distribution patterns and distinct pharmacological profiles, they all are essentially related to fatty-acid and glucose metabolism. Since the PPARs share similar three-dimensional structures within the LBDs, synthetic ligands which simultaneously activate two or all of the PPARs could be potent candidates in terms of drugs for the treatment of abnormal metabolic homeostasis. The structures of several PPAR LBDs were determined in complex with synthetic ligands, derivatives of 3-(4-alkoxyphenyl)propanoic acid, which exhibit unique agonistic activities. The PPARα and PPARγ LBDs were complexed with the same pan agonist, TIPP-703, which activates all three PPARs and their crystal structures were determined. The two LBD–ligand complex structures revealed how the pan agonist is adapted to the similar, but significantly different, ligand-binding pockets of the PPARs. The structures of the PPARδ LBD in complex with an α/δ-selective ligand, TIPP-401, and with a related δ-specific ligand, TIPP-204, were also determined. The comparison between the two PPARδ complexes revealed how each ligand exhibits either a ‘dual selective’ or ‘single specific’ binding mode.

  12. Spatially adaptive stochastic methods for fluid-structure interactions subject to thermal fluctuations in domains with complex geometries

    SciTech Connect

    Plunkett, Pat; Hu, Jonathan; Siefert, Christopher; Atzberger, Paul J.

    2014-08-07

    We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We also perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Furthermore, our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications.

  13. Spatially adaptive stochastic methods for fluid–structure interactions subject to thermal fluctuations in domains with complex geometries

    SciTech Connect

    Plunkett, Pat; Hu, Jonathan; Siefert, Christopher; Atzberger, Paul J.

    2014-11-15

    We develop stochastic mixed finite element methods for spatially adaptive simulations of fluid–structure interactions when subject to thermal fluctuations. To account for thermal fluctuations, we introduce a discrete fluctuation–dissipation balance condition to develop compatible stochastic driving fields for our discretization. We perform analysis that shows our condition is sufficient to ensure results consistent with statistical mechanics. We show the Gibbs–Boltzmann distribution is invariant under the stochastic dynamics of the semi-discretization. To generate efficiently the required stochastic driving fields, we develop a Gibbs sampler based on iterative methods and multigrid to generate fields with O(N) computational complexity. Our stochastic methods provide an alternative to uniform discretizations on periodic domains that rely on Fast Fourier Transforms. To demonstrate in practice our stochastic computational methods, we investigate within channel geometries having internal obstacles and no-slip walls how the mobility/diffusivity of particles depends on location. Our methods extend the applicability of fluctuating hydrodynamic approaches by allowing for spatially adaptive resolution of the mechanics and for domains that have complex geometries relevant in many applications.

  14. Monitoring in the context of structured decision-making and adaptive management

    USGS Publications Warehouse

    Lyons, J.E.; Runge, M.C.; Laskowski, H.P.; Kendall, W.L.

    2008-01-01

    In a natural resource management setting, monitoring is a crucial component of an informed process for making decisions, and monitoring design should be driven by the decision context and associated uncertainties. Monitoring itself can play >3 roles. First, it is important for state-dependent decision-making, as when managers need to know the system state before deciding on the appropriate course of action during the ensuing management cycle. Second, monitoring is critical for evaluating the effectiveness of management actions relative to objectives. Third, in an adaptive management setting, monitoring provides the feedback loop for learning about the system; learning is sought not for its own sake but primarily to better achieve management objectives. In this case, monitoring should be designed to reduce the critical uncertainties in models of the managed system. The United States Geological Survey and United States Fish and Wildlife Service are conducting a large-scale management experiment on 23 National Wildlife Refuges across the Northeast and Midwest Regions. The primary management objective is to provide habitat for migratory waterbirds, particularly during migration, using water-level manipulations in managed wetlands. Key uncertainties are related to the potential trade-offs created by management for a specific waterbird guild (e.g., migratory shorebirds) and the response of waterbirds, plant communities, and invertebrates to specific experimental hydroperiods. We reviewed the monitoring program associated with this study, and the ways that specific observations fill >1 of the roles identified above. We used observations from our monitoring to improve state-dependent decisions to control undesired plants, to evaluate management performance relative to shallow-water habitat objectives, and to evaluate potential trade-offs between waterfowl and shorebird habitat management. With limited staff and budgets, management agencies need efficient monitoring

  15. The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia.

    PubMed

    Deng, Lian; Hoh, Boon Peng; Lu, Dongsheng; Fu, Ruiqing; Phipps, Maude E; Li, Shilin; Nur-Shafawati, Ab Rajab; Hatin, Wan Isa; Ismail, Endom; Mokhtar, Siti Shuhada; Jin, Li; Zilfalil, Bin Alwi; Marshall, Christian R; Scherer, Stephen W; Al-Mulla, Fahd; Xu, Shuhua

    2014-09-01

    Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations--especially indigenous populations--inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N(e)) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000--6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration

  16. Bone Inner Structure Suggests Increasing Aquatic Adaptations in Desmostylia (Mammalia, Afrotheria)

    PubMed Central

    Hayashi, Shoji; Houssaye, Alexandra; Nakajima, Yasuhisa; Chiba, Kentaro; Ando, Tatsuro; Sawamura, Hiroshi; Inuzuka, Norihisa; Kaneko, Naotomo; Osaki, Tomohiro

    2013-01-01

    Background The paleoecology of desmostylians has been discussed controversially with a general consensus that desmostylians were aquatic or semi-aquatic to some extent. Bone microanatomy can be used as a powerful tool to infer habitat preference of extinct animals. However, bone microanatomical studies of desmostylians are extremely scarce. Methodology/Principal Findings We analyzed the histology and microanatomy of several desmostylians using thin-sections and CT scans of ribs, humeri, femora and vertebrae. Comparisons with extant mammals allowed us to better understand the mode of life and evolutionary history of these taxa. Desmostylian ribs and long bones generally lack a medullary cavity. This trait has been interpreted as an aquatic adaptation among amniotes. Behemotops and Paleoparadoxia show osteosclerosis (i.e. increase in bone compactness), and Ashoroa pachyosteosclerosis (i.e. combined increase in bone volume and compactness). Conversely, Desmostylus differs from these desmostylians in displaying an osteoporotic-like pattern. Conclusions/Significance In living taxa, bone mass increase provides hydrostatic buoyancy and body trim control suitable for poorly efficient swimmers, while wholly spongy bones are associated with hydrodynamic buoyancy control in active swimmers. Our study suggests that all desmostylians had achieved an essentially, if not exclusively, aquatic lifestyle. Behemotops, Paleoparadoxia and Ashoroa are interpreted as shallow water swimmers, either hovering slowly at a preferred depth, or walking on the bottom, and Desmostylus as a more active swimmer with a peculiar habitat and feeding strategy within Desmostylia. Therefore, desmostylians are, with cetaceans, the second mammal group showing a shift from bone mass increase to a spongy inner organization of bones in their evolutionary history. PMID:23565143

  17. Structural interplay between germline and adaptive recognition determines TCR-peptide-MHC cross-reactivity

    PubMed Central

    Adams, Jarrett J.; Narayanan, Samanthi; Birnbaum, Michael E.; Sidhu, Sachdev S.; Blevins, Sydney J.; Gee, Marvin H.; Sibener, Leah V.; Baker, Brian M.; Kranz, David M.; Garcia, K. Christopher

    2015-01-01

    The T cell receptor - peptide-MHC interface is comprised of conserved and diverse regions, yet the relative contributions of each in shaping T cell recognition remain unclear. We isolated cross-reactive peptides with limited homology, allowing us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR’s cross-reactivity is rooted in highly similar recognition of an apical ‘hotspot’ position in the peptide, while tolerating significant sequence variation at ancillary positions. Furthermore, we find a striking structural convergence onto a germline-mediated interaction between TCR CDR1α and the MHC α2 helix of twelve TCR-pMHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hotspot, may place limits on peptide antigen cross-reactivity. PMID:26523866

  18. Structural and functional adaptations of the mammalian nuclear envelope to meet the meiotic requirements

    PubMed Central

    Link, Jana; Jahn, Daniel; Alsheimer, Manfred

    2015-01-01

    Numerous studies in the past years provided definite evidence that the nuclear envelope is much more than just a simple barrier. It rather constitutes a multifunctional platform combining structural and dynamic features to fulfill many fundamental functions such as chromatin organization, regulation of transcription, signaling, but also structural duties like maintaining general nuclear architecture and shape. One additional and, without doubt, highly impressive aspect is the recently identified key function of selected nuclear envelope components in driving meiotic chromosome dynamics, which in turn is essential for accurate recombination and segregation of the homologous chromosomes. Here, we summarize the recent work identifying new key players in meiotic telomere attachment and movement and discuss the latest advances in our understanding of the actual function of the meiotic nuclear envelope. PMID:25674669

  19. Acidophilic adaptations in the structure of Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase (PurE).

    PubMed

    Settembre, Ethan C; Chittuluru, Johnathan R; Mill, Christopher P; Kappock, T Joseph; Ealick, Steven E

    2004-10-01

    The crystal structure of Acetobacter aceti PurE was determined to a resolution of 1.55 A and is compared with the known structures of the class I PurEs from a mesophile, Escherichia coli, and a thermophile, Thermotoga maritima. Analyses of the general factors that increase protein stability are examined as potential explanations for the acid stability of A. aceti PurE. Increased inter-subunit hydrogen bonding and an increased number of arginine-containing salt bridges appear to account for the bulk of the increased acid stability. A chain of histidines linking two active sites is discussed in the context of the proton transfers catalyzed by the enzyme.

  20. Actinoranone, A Cytotoxic Meroterpenoid of Unprecedented Structure from a Marine Adapted Streptomyces sp

    PubMed Central

    Nam, Sang-Jip; Kauffman, Christopher A.; Paul, Lauren A.; Jensen, Paul R.

    2014-01-01

    The isolation and structure elucidation of a new meroterpenoid, actinoranone (1), produced by a marine bacterium closely related to the genus Streptomyces is reported. Actinoranone is composed of an unprecedented dihydronaphthalenone polyketide linked to a bicyclic diterpenoid. The stereochemistry of 1 was defined by application of the advanced Mosher's method and by interpretation of spectroscopic data. Actinoranone (1) is significantly cytotoxic to HCT-116 human colon cancer cells with an LD50 = 2.0 μg/mL. PMID:24152065

  1. Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin.

    PubMed

    Szyk, Agnieszka; Deaconescu, Alexandra M; Piszczek, Grzegorz; Roll-Mecak, Antonina

    2011-11-01

    Tubulin tyrosine ligase (TTL) catalyzes the post-translational C-terminal tyrosination of α-tubulin. Tyrosination regulates recruitment of microtubule-interacting proteins. TTL is essential. Its loss causes morphogenic abnormalities and is associated with cancers of poor prognosis. We present the first crystal structure of TTL (from Xenopus tropicalis), defining the structural scaffold upon which the diverse TTL-like family of tubulin-modifying enzymes is built. TTL recognizes tubulin using a bipartite strategy. It engages the tubulin tail through low-affinity, high-specificity interactions, and co-opts what is otherwise a homo-oligomerization interface in structurally related ATP grasp-fold enzymes to form a tight hetero-oligomeric complex with the tubulin body. Small-angle X-ray scattering and functional analyses reveal that TTL forms an elongated complex with the tubulin dimer and prevents its incorporation into microtubules by capping the tubulin longitudinal interface, possibly modulating the partition of tubulin between monomeric and polymeric forms. PMID:22020298

  2. Coupled flow-structure-biochemistry simulations of dynamic systems of blood cells using an adaptive surface tracking method

    NASA Astrophysics Data System (ADS)

    Hoskins, M. H.; Kunz, R. F.; Bistline, J. E.; Dong, C.

    2009-07-01

    A method for the computation of low-Reynolds number dynamic blood cell systems is presented. The specific system of interest here is interaction between cancer cells and white blood cells in an experimental flow system. Fluid dynamics, structural mechanics, six-degree-of-freedom motion control, and surface biochemistry analysis components are coupled in the context of adaptive octree-based grid generation. Analytical and numerical verification of the quasi-steady assumption for the fluid mechanics is presented. The capabilities of the technique are demonstrated by presenting several three-dimensional cell system simulations, including the collision/interaction between a cancer cell and an endothelium adherent polymorphonuclear leukocyte (PMN) cell in a shear flow.

  3. Coupled Flow-Structure-Biochemistry Simulations of Dynamic Systems of Blood Cells Using an Adaptive Surface Tracking Method

    PubMed Central

    Hoskins, M.H.; Kunz, R.F.; Bistline, J.E.; Dong, C.

    2009-01-01

    A method for the computation of low Reynolds number dynamic blood cell systems is presented. The specific system of interest here is interaction between cancer cells and white blood cells in an experimental flow system. Fluid dynamics, structural mechanics, six-degree-of freedom motion control and surface biochemistry analysis components are coupled in the context of adaptive octree-based grid generation. Analytical and numerical verification of the quasi-steady assumption for the fluid mechanics is presented. The capabilities of the technique are demonstrated by presenting several three-dimensional cell system simulations, including the collision/interaction between a cancer cell and an endothelium adherent polymorphonuclear leukocyte (PMN) cell in a shear flow. PMID:20160939

  4. Adaptive segmentation of wavelet transform coefficients for video compression

    NASA Astrophysics Data System (ADS)

    Wasilewski, Piotr

    2000-04-01

    This paper presents video compression algorithm suitable for inexpensive real-time hardware implementation. This algorithm utilizes Discrete Wavelet Transform (DWT) with the new Adaptive Spatial Segmentation Algorithm (ASSA). The algorithm was designed to obtain better or similar decompressed video quality in compare to H.263 recommendation and MPEG standard using lower computational effort, especially at high compression rates. The algorithm was optimized for hardware implementation in low-cost Field Programmable Gate Array (FPGA) devices. The luminance and chrominance components of every frame are encoded with 3-level Wavelet Transform with biorthogonal filters bank. The low frequency subimage is encoded with an ADPCM algorithm. For the high frequency subimages the new Adaptive Spatial Segmentation Algorithm is applied. It divides images into rectangular blocks that may overlap each other. The width and height of the blocks are set independently. There are two kinds of blocks: Low Variance Blocks (LVB) and High Variance Blocks (HVB). The positions of the blocks and the values of the WT coefficients belonging to the HVB are encoded with the modified zero-tree algorithms. LVB are encoded with the mean value. Obtained results show that presented algorithm gives similar or better quality of decompressed images in compare to H.263, even up to 5 dB in PSNR measure.

  5. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

    PubMed

    Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

    2015-09-01

    Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species. PMID:25573196

  6. Structural and Mechanical Adaptations of Right Ventricular Free Wall Myocardium to Pulmonary-Hypertension Induced Pressure Overload

    PubMed Central

    Hill, Michael R.; Simon, Marc A.; Valdez-Jasso, Daniela; Zhang, Will; Champion, Hunter C.; Sacks, Michael S.

    2014-01-01

    Right ventricular (RV) failure in response to pulmonary hypertension (PH) is a severe disease that remains poorly understood. PH-induced pressure overload leads to changes in the RV free wall (RVFW) that eventually results in RV failure. While the development of computational models can benefit our understanding of the onset and progression of PH-induced pressure overload, detailed knowledge of the underlying structural and biomechanical events remains limited. The goal of the present study was to elucidate the structural and biomechanical adaptations of RV myocardium subjected to sustained pressure overload in a rat model. Hemodynamically confirmed severe chronic RV pressure overload was induced in Sprague-Dawley rats via pulmonary artery banding. Extensive tissue-level biaxial mechanical and histomorphological analyses were conducted to assess the remodeling response in the RV free wall. Simultaneous myofiber hypertrophy and longitudinal re-orientation of myo- and collagen fibers was observed, with both fiber types becoming more highly aligned. Transmural myo- and collagen fiber orientations were co-aligned in both the normal and diseased state. The overall tissue stiffness increased, with larger increases in longitudinal versus circumferential stiffness. Interestingly, estimated myofiber stiffness increased while the collagen fiber stiffness remained unchanged. The latter was attributed to longitudinal fiber re-orientation, which increased the degree of anisotropy. Increased mechanical coupling between the two axes was attributed to the increased fiber alignment. The increased myofiber stiffness was consistent with clinical results showing titin-associated increased sarcomeric stiffening observed in PH patients. These results further our understanding of the underlying adaptive and maladaptive remodeling mechanisms and may lead to improved techniques for prognosis, diagnosis, and treatment for PH. PMID:25164124

  7. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure.

    PubMed

    Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

    2015-09-01

    Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.

  8. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    SciTech Connect

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; Mavrici, Daniela; Waldo, Geoffrey S.; Hung, Li -Wei; Sacchettini, James C.; Terwilliger, Thomas C.; Alber, Tom; Mayer, Claudine

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

  9. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis).

    PubMed

    Liu, Bing-Jian; Zhang, Bai-Dong; Xue, Dong-Xiu; Gao, Tian-Xiang; Liu, Jin-Xian

    2016-01-01

    The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource. PMID:27100462

  10. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire.

    PubMed

    Blevins, Sydney J; Pierce, Brian G; Singh, Nishant K; Riley, Timothy P; Wang, Yuan; Spear, Timothy T; Nishimura, Michael I; Weng, Zhiping; Baker, Brian M

    2016-03-01

    How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs. PMID:26884163

  11. Linezolid-Dependent Function and Structure Adaptation of Ribosomes in a Staphylococcus epidermidis Strain Exhibiting Linezolid Dependence

    PubMed Central

    Kokkori, Sofia; Apostolidi, Maria; Tsakris, Athanassios; Pournaras, Spyros

    2014-01-01

    Linezolid-dependent growth was recently reported in Staphylococcus epidermidis clinical strains carrying mutations associated with linezolid resistance. To investigate this unexpected behavior at the molecular level, we isolated active ribosomes from one of the linezolid-dependent strains and we compared them with ribosomes isolated from a wild-type strain. Both strains were grown in the absence and presence of linezolid. Detailed biochemical and structural analyses revealed essential differences in the function and structure of isolated ribosomes which were assembled in the presence of linezolid. The catalytic activity of peptidyltransferase was found to be significantly higher in the ribosomes derived from the linezolid-dependent strain. Interestingly, the same ribosomes exhibited an abnormal ribosomal subunit dissociation profile on a sucrose gradient in the absence of linezolid, but the profile was restored after treatment of the ribosomes with an excess of the antibiotic. Our study suggests that linezolid most likely modified the ribosomal assembly procedure, leading to a new functional ribosomal population active only in the presence of linezolid. Therefore, the higher growth rate of the partially linezolid-dependent strains could be attributed to the functional and structural adaptations of ribosomes to linezolid. PMID:24890589

  12. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

    PubMed Central

    Blevins, Sydney J.; Pierce, Brian G.; Singh, Nishant K.; Riley, Timothy P.; Wang, Yuan; Spear, Timothy T.; Nishimura, Michael I.; Weng, Zhiping; Baker, Brian M.

    2016-01-01

    How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged “hot-spot” region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs. PMID:26884163

  13. Ultra-high resolution adaptive optics: optical coherence tomography for in vivo imaging of healthy and diseased retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Zhang, Yan; Jones, Steven M.; Choi, Stacey S.; Cense, Barry; Evans, Julia W.; Miller, Donald T.; Olivier, Scot S.; Werner, John S.

    2008-02-01

    Ultra-high isotropic resolution imaging of retinal structures was made possible with an adaptive optics system using dual deformable mirrors and a Fourier-domain optical coherence tomography (Fd-OCT) system with correction for longitudinal chromatic aberration. This system was used to image microscopic retinal structures of healthy as well as diseased retinas in vivo. The improved resolution and contrast enhanced visualization of morphological structures in the retina can be clearly seen. The benefits of this instrument are apparent from comparison of new images with those acquired using a previous generation AO-OCT instrument. Big change in the appearance of speckle field (reduction in speckle size) can be observed as well. Additionally, further improvements in volumetric data acquisition and image representation will be discussed. This includes creation of large Field of View (FOV) AO-OCT volume from multiple sub-volumes and its visualization. Also techniques and results of reducing speckle contrast by averaging multiple B-scans will be presented.

  14. Linezolid-dependent function and structure adaptation of ribosomes in a Staphylococcus epidermidis strain exhibiting linezolid dependence.

    PubMed

    Kokkori, Sofia; Apostolidi, Maria; Tsakris, Athanassios; Pournaras, Spyros; Stathopoulos, Constantinos; Dinos, George

    2014-08-01

    Linezolid-dependent growth was recently reported in Staphylococcus epidermidis clinical strains carrying mutations associated with linezolid resistance. To investigate this unexpected behavior at the molecular level, we isolated active ribosomes from one of the linezolid-dependent strains and we compared them with ribosomes isolated from a wild-type strain. Both strains were grown in the absence and presence of linezolid. Detailed biochemical and structural analyses revealed essential differences in the function and structure of isolated ribosomes which were assembled in the presence of linezolid. The catalytic activity of peptidyltransferase was found to be significantly higher in the ribosomes derived from the linezolid-dependent strain. Interestingly, the same ribosomes exhibited an abnormal ribosomal subunit dissociation profile on a sucrose gradient in the absence of linezolid, but the profile was restored after treatment of the ribosomes with an excess of the antibiotic. Our study suggests that linezolid most likely modified the ribosomal assembly procedure, leading to a new functional ribosomal population active only in the presence of linezolid. Therefore, the higher growth rate of the partially linezolid-dependent strains could be attributed to the functional and structural adaptations of ribosomes to linezolid.

  15. Structural and Functional Dissection of the Abp1 ADFH Actin-binding Domain Reveals Versatile In Vivo Adapter Functions

    SciTech Connect

    Quintero-Monzon,O.; Rodal, A.; Strokopytov, B.; Almo, S.; Goode, B.

    2005-01-01

    Abp1 is a multidomain protein that regulates the Arp2/3 complex and links proteins involved in endocytosis to the actin cytoskeleton. All of the proposed cellular functions of Abp1 involve actin filament binding, yet the actin binding site(s) on Abp1 have not been identified, nor has the importance of actin binding for Abp1 localization and function in vivo been tested. Here, we report the crystal structure of the Saccharomyces cerevisiae Abp1 actin-binding actin depolymerizing factor homology (ADFH) domain and dissect its activities by mutagenesis. Abp1-ADFH domain and ADF/cofilin structures are similar, and they use conserved surfaces to bind actin; however, there are also key differences that help explain their differential effects on actin dynamics. Using point mutations, we demonstrate that actin binding is required for localization of Abp1 in vivo, the lethality caused by Abp1 overexpression, and the ability of Abp1 to activate Arp2/3 complex. Furthermore, we genetically uncouple ABP1 functions that overlap with SAC6, SLA1, and SLA2, showing they require distinct combinations of activities and interactions. Together, our data provide the first structural and functional view of the Abp1-actin interaction and show that Abp1 has distinct cellular roles as an adapter, linking different sets of ligands for each function.

  16. Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion

    PubMed Central

    O’Brien, Darragh P.; Hernandez, Belen; Durand, Dominique; Hourdel, Véronique; Sotomayor-Pérez, Ana-Cristina; Vachette, Patrice; Ghomi, Mahmoud; Chamot-Rooke, Julia; Ladant, Daniel; Brier, Sébastien; Chenal, Alexandre

    2015-01-01

    Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a folded multi-domain protein with an anisometric shape. RTX motifs thus appear remarkably adapted to the structural and mechanistic constraints of the secretion process. In the low calcium environment of the bacterial cytosol, Apo-RD is an elongated disordered coil appropriately sized for transport through the narrow secretion machinery. The progressive folding of Holo-RD in the extracellular calcium-rich environment as it emerges form the T1SS may then favor its unidirectional export through the secretory channel. This process is relevant for hundreds of bacterial species producing virulent RTX proteins. PMID:26374675

  17. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis)

    PubMed Central

    Xue, Dong-Xiu; Gao, Tian-Xiang; Liu, Jin-Xian

    2016-01-01

    The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource. PMID:27100462

  18. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis).

    PubMed

    Liu, Bing-Jian; Zhang, Bai-Dong; Xue, Dong-Xiu; Gao, Tian-Xiang; Liu, Jin-Xian

    2016-01-01

    The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource.

  19. Development of Micro Air Vehicle Technology With In-Flight Adaptive-Wing Structure

    NASA Technical Reports Server (NTRS)

    Waszak, Martin R. (Technical Monitor); Shkarayev, Sergey; Null, William; Wagner, Matthew

    2004-01-01

    This is a final report on the research studies, "Development of Micro Air Vehicle Technology with In-Flight Adaptrive-Wing Structure". This project involved the development of variable-camber technology to achieve efficient design of micro air vehicles. Specifically, it focused on the following topics: 1) Low Reynolds number wind tunnel testing of cambered-plate wings. 2) Theoretical performance analysis of micro air vehicles. 3) Design of a variable-camber MAV actuated by micro servos. 4) Test flights of a variable-camber MAV.

  20. Persistent structural adaptation in the lungs of guinea pigs raised at high altitude.

    PubMed

    Ravikumar, Priya; Bellotto, Dennis J; Hsia, Connie C W

    2015-03-01

    Laboratory guinea pigs raised at high altitude (HA, 3800 m) for up to 6 mo exhibit enhanced alveolar growth and remodeling (Hsia et al., 2005. Resp. Physiol. Neurobiol. 147, 105-115). To determine whether initial HA-induced structural enhancement persists following return to intermediate altitude (IA), we raised weanling guinea pigs at (a) HA for 11-12 mo, (b) IA (1200 m) for 11-12 mo, and (c) HA for 4 mo followed by IA for 7-8 mo (HA-to-IA). Morphometric analysis was performed under light and electron microscopy. Body weight and lung volume were similar among groups. Prolonged HA residence increased alveolar epithelium and interstitium volumes while reducing alveolar-capillary blood volume. The HA-induced gains in type-1 epithelium volume and alveolar surface area were no longer present following return to IA whereas volume increases in type-2 epithelium and interstitium and the reduction in alveolar duct volume persisted. Results demonstrate persistent augmentation of some but not all aspects of lung structure throughout prolonged HA residence, with partial reversibility following re-acclimatization to IA.

  1. Structurally adaptive space crane concept for assembling space systems on orbit

    NASA Technical Reports Server (NTRS)

    Dorsey, John T.; Sutter, Thomas R.; Wu, K. Chauncey

    1992-01-01

    Many future human space exploration missions will probably require large vehicles that must be assembled on orbit. Thus, a device that can move, position, and assemble large and massive spacecraft components on orbit becomes essential for these missions. A concept is described for such a device: a space crane concept that uses erectable truss hardware to achieve high-stiffness and low-mass booms and uses articulating truss joints that can be assembled on orbit. The hardware has been tested and shown to have linear load-deflection response and to be structurally predictable. The hardware also permits the crane to be reconfigured into different geometries to satisfy future assembly requirements. A number of articulating and rotary joint concepts have been sized and analyzed, and the results are discussed. Two strategies were proposed to suppress motion-induced vibration: placing viscous dampers in selected truss struts and preshaping motion commands. Preliminary analyses indicate that these techniques have the potential to greatly enhance structural damping.

  2. Persistent Structural Adaptation in the Lungs of Guinea Pigs Raised at High Altitude

    PubMed Central

    Ravikumar, Priya; Bellotto, Dennis J.; Hsia, Connie C.W.

    2014-01-01

    Laboratory guinea pigs raised at high altitude (HA, 3,800m) for up to 6mo exhibit enhanced alveolar growth and remodeling. To determine whether initial HA-induced structural enhancement persists following return to intermediate altitude (IA), we raised weanling guinea pigs at a) HA for 11-12mo, b) IA (1,200m) for 11-12mo, and c) HA for 4 mo followed by IA for 7-8mo (HA-to-IA). Morphometric analysis was performed under light and electron microscopy. Body weight and lung volume were similar among groups. Prolonged HA residence increased alveolar epithelium and interstitium volumes while reducing alveolar-capillary blood volume. The HA-induced gains in type-1 epithelium volume and alveolar surface area were no longer present following return to IA whereas volume increases in type-2 epithelium and interstitium and the reduction in alveolar duct volume persisted. Results demonstrate persistent augmentation of some but not all aspects of lung structure throughout prolonged HA residence, with partial reversibility following re-acclimatization to IA. PMID:25534146

  3. Investigation on adaptive wing structure based on shape memory polymer composite hinge

    NASA Astrophysics Data System (ADS)

    Yu, Yuemin; Li, Xinbo; Zhang, Wei; Leng, Jinsong

    2007-07-01

    This paper describes the design and investigation of the SMP composite hinge and the morphing wing structure. The SMP composite hinge was based on SMP and carbon fiber fabric. The twisting recoverability of it was investigated by heating and then cooling repeatedly above and below the Tg. The twisting recoverability characterized by the twisting angle. Results show that the SMP composite hinge have good shape recoverability, Recovery time has a great influence on the twisting recoverability. The twisting recovery ratio became large with the increment of recovery time. The morphing wing can changes shape for different tasks. For the advantages of great recovery force and stable performances, we adopt SMP composite hinge as actuator to apply into the structure of the wing which can realize draw back wings to change sweep angle according to the speed and other requirements of military airplanes. Finally, a series of simulations and experiments are performed to investigate the deformations of morphing wings have been performed successfully. It can be seen that the sweep angle change became large with the increment of initial angle. The area reduction became large with the increment of initial angle, but after 75° the area reduction became smaller and smaller. The deformations of the triangle wing became large with the increment of temperature. The area and the sweep angle of wings can be controlled by adjusting the stimulate temperature and the initial twisting angle of shape memory polymer composite hinge.

  4. Evolution of the mammalian middle ear and jaw: adaptations and novel structures

    PubMed Central

    Anthwal, Neal; Joshi, Leena; Tucker, Abigail S

    2013-01-01

    Having three ossicles in the middle ear is one of the defining features of mammals. All reptiles and birds have only one middle ear ossicle, the stapes or columella. How these two additional ossicles came to reside and function in the middle ear of mammals has been studied for the last 200 years and represents one of the classic example of how structures can change during evolution to function in new and novel ways. From fossil data, comparative anatomy and developmental biology it is now clear that the two new bones in the mammalian middle ear, the malleus and incus, are homologous to the quadrate and articular, which form the articulation for the upper and lower jaws in non-mammalian jawed vertebrates. The incorporation of the primary jaw joint into the mammalian middle ear was only possible due to the evolution of a new way to articulate the upper and lower jaws, with the formation of the dentary-squamosal joint, or TMJ in humans. The evolution of the three-ossicle ear in mammals is thus intricately connected with the evolution of a novel jaw joint, the two structures evolving together to create the distinctive mammalian skull. PMID:22686855

  5. Adaptive defect and pattern detection in amplitude and phase structures via photorefractive four-wave mixing.

    PubMed

    Nehmetallah, George; Banerjee, Partha; Khoury, Jed

    2015-11-10

    This work comprises the theoretical and numerical validations of experimental work on pattern and defect detection of periodic amplitude and phase structures using four-wave mixing in photorefractive materials. The four-wave mixing optical processor uses intensity filtering in the Fourier domain. Specifically, the nonlinear transfer function describing four-wave mixing is modeled, and the theory for detection of amplitude and phase defects and dislocations are developed. Furthermore, numerical simulations are performed for these cases. The results show that this technique successfully detects the slightest defects clearly even with no prior enhancement. This technique should prove to be useful in quality control systems, production-line defect inspection, and e-beam lithography. PMID:26560795

  6. An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

    PubMed Central

    Ilgu, Muslum; Fulton, D. Bruce; Yennamalli, Ragothaman M.; Lamm, Monica H.; Sen, Taner Z.; Nilsen-Hamilton, Marit

    2014-01-01

    Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well-structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment. PMID:24757168

  7. The Structure of Carbonic Anhydrase IX Is Adapted for Low-pH Catalysis.

    PubMed

    Mahon, Brian P; Bhatt, Avni; Socorro, Lilien; Driscoll, Jenna M; Okoh, Cynthia; Lomelino, Carrie L; Mboge, Mam Y; Kurian, Justin J; Tu, Chingkuang; Agbandje-McKenna, Mavis; Frost, Susan C; McKenna, Robert

    2016-08-23

    Human carbonic anhydrase IX (hCA IX) expression in many cancers is associated with hypoxic tumors and poor patient outcome. Inhibitors of hCA IX have been used as anticancer agents with some entering Phase I clinical trials. hCA IX is transmembrane protein whose catalytic domain faces the extracellular tumor milieu, which is typically associated with an acidic microenvironment. Here, we show that the catalytic domain of hCA IX (hCA IX-c) exhibits the necessary biochemical and biophysical properties that allow for low pH stability and activity. Furthermore, the unfolding process of hCA IX-c appears to be reversible, and its catalytic efficiency is thought to be correlated directly with its stability between pH 3.0 and 8.0 but not above pH 8.0. To rationalize this, we determined the X-ray crystal structure of hCA IX-c to 1.6 Å resolution. Insights from this study suggest an understanding of hCA IX-c stability and activity in low-pH tumor microenvironments and may be applicable to determining pH-related effects on enzymes. PMID:27439028

  8. Structural adaptations of two sympatric epiphytic orchids (Orchidaceae) to a cloudy forest environment in rocky outcrops of Southeast Brazil.

    PubMed

    Moreira, Ana Silvia Franco Pinheiro; Filho, José Pires de Lemos; Isaias, Rosy Mary dos Santos

    2013-09-01

    The survival of plants in epiphytic environments depends on vegetative adaptations capable to defraud different stresses. Based on the structural diversity of the Orchidaceae, the current study has the objective of relating the anatomical structure of Dichaea cogniauxiana and Epidendrum secundum with the distinct environments where they live. It was expected that, despite structural similarities as strategies for resource acquisition, some peculiar variations related to the distinct light microenvironments (inside or in the edge of the nebular forest, near to "campo rupestre" area) might be found. Leaves and roots of both species were collected in a nebular forest located at a "campo rupestre" area at Serra da Piedade, Brazil), in January and February 2005. D. cogniauxiana is adhered to trunks, in sites with high atmospheric humidity and shaded, while E. secundum is located at the edge of the nebular forest, in more luminous sites. The leaves of E. secundum had thicker cuticle and higher number of stomata per area than those of D. cogniauxiana, characteristics coherent with their distinct pattern of exhibition to sun light. The suprastomatic chambers formed by the thicker cuticle may function as a barrier of resistance to water evaporation. The succulence of the leaves of E. secundum propitiates organic acids storage at night, and the storage of starch may be involved in PEP-carboxylase metabolism, both propitiating CAM mechanism. Roots with larger number of cell layers of the velamen, and specialized thick walled cortical cells (both in E. secundum) help water absorption and indicate better adaptation to an environment with intense solar radiation and a probable higher water deficit. The remarkable cell wall thickening of E. secundum exodermis can confer more efficient protection against the excess of transpiration at the border of the nebular forest. On the other hand, besides D. cogniauxiana be epiphyte, it is in a low position - in a shaded environment and with

  9. Functional adaptation of crustacean exoskeletal elements through structural and compositional diversity: a combined experimental and theoretical study.

    PubMed

    Fabritius, Helge-Otto; Ziegler, Andreas; Friák, Martin; Nikolov, Svetoslav; Huber, Julia; Seidl, Bastian H M; Ruangchai, Sukhum; Alagboso, Francisca I; Karsten, Simone; Lu, Jin; Janus, Anna M; Petrov, Michal; Zhu, Li-Fang; Hemzalová, Pavlína; Hild, Sabine; Raabe, Dierk; Neugebauer, Jörg

    2016-01-01

    The crustacean cuticle is a composite material that covers the whole animal and forms the continuous exoskeleton. Nano-fibers composed of chitin and protein molecules form most of the organic matrix of the cuticle that, at the macroscale, is organized in up to eight hierarchical levels. At least two of them, the exo- and endocuticle, contain a mineral phase of mainly Mg-calcite, amorphous calcium carbonate and phosphate. The high number of hierarchical levels and the compositional diversity provide a high degree of freedom for varying the physical, in particular mechanical, properties of the material. This makes the cuticle a versatile material ideally suited to form a variety of skeletal elements that are adapted to different functions and the eco-physiological strains of individual species. This review presents our recent analytical, experimental and theoretical studies on the cuticle, summarising at which hierarchical levels structure and composition are modified to achieve the required physical properties. We describe our multi-scale hierarchical modeling approach based on the results from these studies, aiming at systematically predicting the structure-composition-property relations of cuticle composites from the molecular level to the macro-scale. This modeling approach provides a tool to facilitate the development of optimized biomimetic materials within a knowledge-based design approach. PMID:27609556

  10. Adaptation of a Multi-Block Structured Solver for Effective Use in a Hybrid CPU/GPU Massively Parallel Environment

    NASA Astrophysics Data System (ADS)

    Gutzwiller, David; Gontier, Mathieu; Demeulenaere, Alain

    2014-11-01

    Multi-Block structured solvers hold many advantages over their unstructured counterparts, such as a smaller memory footprint and efficient serial performance. Historically, multi-block structured solvers have not been easily adapted for use in a High Performance Computing (HPC) environment, and the recent trend towards hybrid GPU/CPU architectures has further complicated the situation. This paper will elaborate on developments and innovations applied to the NUMECA FINE/Turbo solver that have allowed near-linear scalability with real-world problems on over 250 hybrid GPU/GPU cluster nodes. Discussion will focus on the implementation of virtual partitioning and load balancing algorithms using a novel meta-block concept. This implementation is transparent to the user, allowing all pre- and post-processing steps to be performed using a simple, unpartitioned grid topology. Additional discussion will elaborate on developments that have improved parallel performance, including fully parallel I/O with the ADIOS API and the GPU porting of the computationally heavy CPUBooster convergence acceleration module. Head of HPC and Release Management, Numeca International.

  11. Temperature Structure of the Intracluster Medium from Smoothed-particle Hydrodynamics and Adaptive-mesh Refinement Simulations

    NASA Astrophysics Data System (ADS)

    Rasia, Elena; Lau, Erwin T.; Borgani, Stefano; Nagai, Daisuke; Dolag, Klaus; Avestruz, Camille; Granato, Gian Luigi; Mazzotta, Pasquale; Murante, Giuseppe; Nelson, Kaylea; Ragone-Figueroa, Cinthia

    2014-08-01

    Analyses of cosmological hydrodynamic simulations of galaxy clusters suggest that X-ray masses can be underestimated by 10%-30%. The largest bias originates from both violation of hydrostatic equilibrium (HE) and an additional temperature bias caused by inhomogeneities in the X-ray-emitting intracluster medium (ICM). To elucidate this large dispersion among theoretical predictions, we evaluate the degree of temperature structures in cluster sets simulated either with smoothed-particle hydrodynamics (SPH) or adaptive-mesh refinement (AMR) codes. We find that the SPH simulations produce larger temperature variations connected to the persistence of both substructures and their stripped cold gas. This difference is more evident in nonradiative simulations, whereas it is reduced in the presence of radiative cooling. We also find that the temperature variation in radiative cluster simulations is generally in agreement with that observed in the central regions of clusters. Around R 500 the temperature inhomogeneities of the SPH simulations can generate twice the typical HE mass bias of the AMR sample. We emphasize that a detailed understanding of the physical processes responsible for the complex thermal structure in ICM requires improved resolution and high-sensitivity observations in order to extend the analysis to higher temperature systems and larger cluster-centric radii.

  12. Quantitative structure-activity relationship study on BTK inhibitors by modified multivariate adaptive regression spline and CoMSIA methods.

    PubMed

    Xu, A; Zhang, Y; Ran, T; Liu, H; Lu, S; Xu, J; Xiong, X; Jiang, Y; Lu, T; Chen, Y

    2015-01-01

    Bruton's tyrosine kinase (BTK) plays a crucial role in B-cell activation and development, and has emerged as a new molecular target for the treatment of autoimmune diseases and B-cell malignancies. In this study, two- and three-dimensional quantitative structure-activity relationship (2D and 3D-QSAR) analyses were performed on a series of pyridine and pyrimidine-based BTK inhibitors by means of genetic algorithm optimized multivariate adaptive regression spline (GA-MARS) and comparative molecular similarity index analysis (CoMSIA) methods. Here, we propose a modified MARS algorithm to develop 2D-QSAR models. The top ranked models showed satisfactory statistical results (2D-QSAR: Q(2) = 0.884, r(2) = 0.929, r(2)pred = 0.878; 3D-QSAR: q(2) = 0.616, r(2) = 0.987, r(2)pred = 0.905). Key descriptors selected by 2D-QSAR were in good agreement with the conclusions of 3D-QSAR, and the 3D-CoMSIA contour maps facilitated interpretation of the structure-activity relationship. A new molecular database was generated by molecular fragment replacement (MFR) and further evaluated with GA-MARS and CoMSIA prediction. Twenty-five pyridine and pyrimidine derivatives as novel potential BTK inhibitors were finally selected for further study. These results also demonstrated that our method can be a very efficient tool for the discovery of novel potent BTK inhibitors.

  13. Temperature structure of the intracluster medium from smoothed-particle hydrodynamics and adaptive-mesh refinement simulations

    SciTech Connect

    Rasia, Elena; Lau, Erwin T.; Nagai, Daisuke; Avestruz, Camille; Borgani, Stefano; Dolag, Klaus; Granato, Gian Luigi; Murante, Giuseppe; Ragone-Figueroa, Cinthia; Mazzotta, Pasquale; Nelson, Kaylea

    2014-08-20

    Analyses of cosmological hydrodynamic simulations of galaxy clusters suggest that X-ray masses can be underestimated by 10%-30%. The largest bias originates from both violation of hydrostatic equilibrium (HE) and an additional temperature bias caused by inhomogeneities in the X-ray-emitting intracluster medium (ICM). To elucidate this large dispersion among theoretical predictions, we evaluate the degree of temperature structures in cluster sets simulated either with smoothed-particle hydrodynamics (SPH) or adaptive-mesh refinement (AMR) codes. We find that the SPH simulations produce larger temperature variations connected to the persistence of both substructures and their stripped cold gas. This difference is more evident in nonradiative simulations, whereas it is reduced in the presence of radiative cooling. We also find that the temperature variation in radiative cluster simulations is generally in agreement with that observed in the central regions of clusters. Around R {sub 500} the temperature inhomogeneities of the SPH simulations can generate twice the typical HE mass bias of the AMR sample. We emphasize that a detailed understanding of the physical processes responsible for the complex thermal structure in ICM requires improved resolution and high-sensitivity observations in order to extend the analysis to higher temperature systems and larger cluster-centric radii.

  14. Adjustment to College as Measured by the Student Adaptation to College Questionnaire: A Quantitative Review of Its Structure and Relationships with Correlates and Consequences

    ERIC Educational Resources Information Center

    Crede, Marcus; Niehorster, Sarah

    2012-01-01

    This paper presents a meta-analytic review (k = 237, N = 44,668) of the adjustment to college literature. The review, based on studies using the Student Adaptation to College Questionnaire, is organized around three primary themes: (1) the structure of students' adjustment to college, (2) the relationship of adjustment to college constructs with…

  15. EDITORIAL: Adaptive and active materials: Selected papers from the ASME 2011 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 11) (Scottsdale, AZ, USA, 18-21 September 2011) Adaptive and active materials: Selected papers from the ASME 2011 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 11) (Scottsdale, AZ, USA, 18-21 September 2011)

    NASA Astrophysics Data System (ADS)

    Brei, Diann

    2012-09-01

    The fourth annual meeting of the ASME/AIAA Smart Materials, Adaptive Structures and Intelligent Systems Conference (SMASIS) took place in sunny Scottsdale, Arizona. Each year we strive to grow and offer new experiences. This year we held a special Guest Symposium on Sustainability along with two focused topic tracks on energy harvesting and active composites to encourage cross-fertilization between these important fields and our community. This cross-disciplinary emphasis was reflected in keynote talks by Dr Wayne Brown, President and founder of Dynalloy, Inc., 'Cross-Discipline Sharing'; Dr Brad Allenby, Arizona State University, 'You Want the Future? You can't Handle the Future!'; and Professor Aditi Chattopadhyay, Arizona State University, 'A Multidisciplinary Approach to Structural Health Monitoring and Prognosis'. SMASIS continues to grow our community through both social and technical interchange. The conference location, the exotic Firesky Resort and Spa, exemplified the theme of our Guest Symposium on Sustainability, being the only Green Seal certified resort in Arizona, and highlighting four elements thought to represent all that exist: fire, water, earth and air. Several special events were held around this theme including the night at the oasis reception sponsored by General Motors, sustainability bingo, smart trivia and student networking lunches, and an Arizona pow-wow with a spectacular Indian hoop dance. Our student and young professional development continues to grow strong with best paper and hardware competitions, scavenger student outing and games night. We are very proud that our students and young professionals are always seeking out ways to give back to the community, including organizing outreach to local high school talent. We thank all of our sponsors who made these special events possible. We hope that these social events provided participants with the opportunity to expand their own personal community and broaden their horizons. Our

  16. Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

    PubMed Central

    Morgunova, Ekaterina; Gray, Fiona C.; MacNeill, Stuart A.; Ladenstein, Rudolf

    2009-01-01

    The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R free = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells. PMID:19770505

  17. A new strategy for exploring the hierarchical structure of cancers by adaptively partitioning functional modules from gene expression network

    PubMed Central

    Xu, Junmei; Jing, Runyu; Liu, Yuan; Dong, Yongcheng; Wen, Zhining; Li, Menglong

    2016-01-01

    The interactions among the genes within a disease are helpful for better understanding the hierarchical structure of the complex biological system of it. Most of the current methodologies need the information of known interactions between genes or proteins to create the network connections. However, these methods meet the limitations in clinical cancer researches because different cancers not only share the common interactions among the genes but also own their specific interactions distinguished from each other. Moreover, it is still difficult to decide the boundaries of the sub-networks. Therefore, we proposed a strategy to construct a gene network by using the sparse inverse covariance matrix of gene expression data, and divide it into a series of functional modules by an adaptive partition algorithm. The strategy was validated by using the microarray data of three cancers and the RNA-sequencing data of glioblastoma. The different modules in the network exhibited specific functions in cancers progression. Moreover, based on the gene expression profiles in the modules, the risk of death was well predicted in the clustering analysis and the binary classification, indicating that our strategy can be benefit for investigating the cancer mechanisms and promoting the clinical applications of network-based methodologies in cancer researches. PMID:27349736

  18. Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7

    PubMed Central

    Zanphorlin, Leticia Maria; de Giuseppe, Priscila Oliveira; Honorato, Rodrigo Vargas; Tonoli, Celisa Caldana Costa; Fattori, Juliana; Crespim, Elaine; de Oliveira, Paulo Sergio Lopes; Ruller, Roberto; Murakami, Mario Tyago

    2016-01-01

    Psychrophilic enzymes evolved from a plethora of structural scaffolds via multiple molecular pathways. Elucidating their adaptive strategies is instrumental to understand how life can thrive in cold ecosystems and to tailor enzymes for biotechnological applications at low temperatures. In this work, we used X-ray crystallography, in solution studies and molecular dynamics simulations to reveal the structural basis for cold adaptation of the GH1 β-glucosidase from Exiguobacterium antarcticum B7. We discovered that the selective pressure of low temperatures favored mutations that redesigned the protein surface, reduced the number of salt bridges, exposed more hydrophobic regions to the solvent and gave rise to a tetrameric arrangement not found in mesophilic and thermophilic homologues. As a result, some solvent-exposed regions became more flexible in the cold-adapted tetramer, likely contributing to enhance enzymatic activity at cold environments. The tetramer stabilizes the native conformation of the enzyme, leading to a 10-fold higher activity compared to the disassembled monomers. According to phylogenetic analysis, diverse adaptive strategies to cold environments emerged in the GH1 family, being tetramerization an alternative, not a rule. These findings reveal a novel strategy for enzyme cold adaptation and provide a framework for the semi-rational engineering of β-glucosidases aiming at cold industrial processes. PMID:27029646

  19. In-Flight Suppression of a De-Stabilized F/A-18 Structural Mode Using the Space Launch System Adaptive Augmenting Control System

    NASA Technical Reports Server (NTRS)

    Wall, John; VanZwieten, Tannen; Giiligan Eric; Miller, Chris; Hanson, Curtis; Orr, Jeb

    2015-01-01

    Adaptive Augmenting Control (AAC) has been developed for NASA's Space Launch System (SLS) family of launch vehicles and implemented as a baseline part of its flight control system (FCS). To raise the technical readiness level of the SLS AAC algorithm, the Launch Vehicle Adaptive Control (LVAC) flight test program was conducted in which the SLS FCS prototype software was employed to control the pitch axis of Dryden's specially outfitted F/A-18, the Full Scale Advanced Systems Test Bed (FAST). This presentation focuses on a set of special test cases which demonstrate the successful mitigation of the unstable coupling of an F/A-18 airframe structural mode with the SLS FCS.

  20. Cold Adaptation of Zinc Metalloproteases in the Thermolysin Family from Deep Sea and Arctic Sea Ice Bacteria Revealed by Catalytic and Structural Properties and Molecular Dynamics

    PubMed Central

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-01-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, kcat/Km (10–40 °C), followed the order pseudolysin < MCP-02 < E495 with a ratio of ∼1:2:4. MCP-02 and E495 have the same optimal temperature (Topt, 57 °C, 5 °C lower than pseudolysin) and apparent melting temperature (Tm = 64 °C, ∼10 °C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  1. A motif of eleven amino acids is a structural adaptation that facilitates motor capability of eutherian prestin

    PubMed Central

    Tan, Xiaodong; Pecka, Jason L.; Tang, Jie; Lovas, Sándor; Beisel, Kirk W.; He, David Z. Z.

    2012-01-01

    Cochlear outer hair cells (OHCs) alter their length in response to transmembrane voltage changes. This so-called electromotility is the result of conformational changes of membrane-bound prestin. Prestin-based OHC motility is thought to be responsible for cochlear amplification, which contributes to the exquisite frequency selectivity and sensitivity of mammalian hearing. Prestin belongs to an anion transporter family, the solute carrier protein 26A (SLC26A). Prestin is unique in this family in that it functions as a voltage-dependent motor protein manifested by two hallmarks, nonlinear capacitance and motility. Evidence suggests that prestin orthologs from zebrafish and chicken are anion exchangers or transporters with no motor function. We identified a segment of 11 amino acid residues in eutherian prestin that is extremely conserved among eutherian species but highly variable among non-mammalian orthologs and SLC26A paralogs. To determine whether this sequence represents a motif that facilitates motor function in eutherian prestin, we utilized a chimeric approach by swapping corresponding residues from the zebrafish and chicken with those of gerbil. Motility and nonlinear capacitance were measured from chimeric prestin-transfected human embryonic kidney 293 cells using a voltage-clamp technique and photodiode-based displacement measurement system. We observed a gain of motor function with both of the hallmarks in the chimeric prestin without loss of transport function. Our results show, for the first time, that the substitution of a span of 11 amino acid residues confers the electrogenic anion transporters of zebrafish and chicken prestins with motor-like function. Thus, this motif represents the structural adaptation that assists gain of motor function in eutherian prestin. PMID:22399806

  2. EDITORIAL Smart materials, multifunctional composites, and morphing structures: selected papers from the 20th International Conference on Adaptive Structures and Technologies (ICAST 2009) Smart materials, multifunctional composites, and morphing structures: selected papers from the 20th International Conference on Adaptive Structures and Technologies (ICAST 2009)

    NASA Astrophysics Data System (ADS)

    Liao, Wei-Hsin

    2010-12-01

    The 20th International Conference on Adaptive Structures and Technologies (ICAST) was held on 20-22 October 2009 in Hong Kong. This special section of Smart Materials and Structures is derived from the research papers presented at the conference. Of the 106 papers presented at the conference, 11 papers were reviewed and accepted for this special section, following the regular review procedures of the journal. This special section is focused on smart materials, multifunctional composites, and applications on morphing structures. Smart materials. Smart materials are the foundation of adaptive structures and intelligent systems. The development of new materials will lead to significant improvement in various applications. Three articles are focused on the fabrication of new materials and investigation of their behaviors: Barium strontium zirconate titanate ((Ba1-xSrx)(ZrxTi1-x)O3; BSZT, x = 0.25 and 0.75) ceramics with a highly crystalline structure were fabricated using the combustion technique. The microstructure of BSZT powders exhibited an almost-spherical morphology and had a porous agglomerated form. Polyaniline (PANI)/clay nanoparticles with unique core-shell structure were synthesized via Pickering emulsion polymerization. By dispersing PANI/clay nanoparticles in silicone oil, the ER fluid was made. Magnetic field effects were investigated on the deposition rate and surface morphology of chromium nitride coatings deposited by magnetron sputtering for superior hardness, excellent wear and oxidation resistance. The surface morphology of chromium nitride films was also examined by a scanning electron microscope (SEM). Multifunctional composites. Composites are made from two or more constituent materials so they can combine the best properties of different materials. Five papers deal with fabrication, testing, and modeling of various multifunctional composites: A new active structural fiber (ASF) was fabricated by coating a single carbon fiber with a concentric

  3. Adaptive and active materials: selected papers from the ASME 2012 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 12) (Stone Mountain, GA, USA, 19-21 September 2012)

    NASA Astrophysics Data System (ADS)

    Seelecke, Stefan; Erturk, Alper; Ounaies, Zoubeida; Naguib, Hani; Huber, John; Turner, Travis; Anderson, Iain; Philen, Michael; Baba Sundaresan, Vishnu

    2013-09-01

    The fifth annual meeting of the ASME/AIAA Smart Materials, Adaptive Structures and Intelligent Systems Conference (SMASIS) was held in beautiful Stone Mountain near Atlanta, GA. It is the conference's objective to provide an up-to-date overview of research trends in the entire field of smart materials systems. This was reflected in keynote speeches by Professor Eduard Arzt (Institute of New Materials and Saarland University, Saarbrücken, Germany) on 'Micro-patterned artificial 'Gecko' surfaces: a path to switchable adhesive function', by Professor Ray H Baughman (The Alan G MacDiarmid NanoTech Institute, University of Texas at Dallas) on 'The diverse and growing family of carbon nanotube and related artificial muscles', and by Professor Richard James (University of Minnesota) on 'The direct conversion of heat to electricity using multiferroic materials with phase transformations'. SMASIS 2012 was divided into eight symposia which span basic research, applied technological design and development, and industrial and governmental integrated system and application demonstrations. • SYMP 1. Development and characterization of multifunctional materials. • SYMP 2. Mechanics and behavior of active materials. • SYMP 3. Modeling, simulation and control of adaptive systems. • SYMP 4. Integrated system design and implementation. • SYMP 5. Structural health monitoring/NDE. • SYMP 6. Bio-inspired materials and systems. • SYMP 7. Energy harvesting. • SYMP 8. Structural and materials logic. This year we were particularly excited to introduce a new symposium on energy harvesting, which has quickly matured from a special track in previous years to an independent symposium for the first time. The subject cuts across fields by studying different materials, ranging from piezoelectrics to electroactive polymers, as well as by emphasizing different energy sources from wind to waves and ambient vibrations. Modeling, experimental studies, and technology applications all

  4. Spatial Structure and Climatic Adaptation in African Maize Revealed by Surveying SNP Diversity in Relation to Global Breeding and Landrace Panels

    PubMed Central

    Westengen, Ola T.; Berg, Paul R.; Kent, Matthew P.; Brysting, Anne K.

    2012-01-01

    Background Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited. Methodology A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset. Conclusions The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are

  5. Adaptive and active materials: selected papers from the ASME 2013 Conference on Smart Materials, Adaptive Structures and Intelligent Systems (SMASIS 13) (Snowbird, UT, USA, 16-18 September 2013)

    NASA Astrophysics Data System (ADS)

    Johnson, Nancy; Naguib, Hani; Turner, Travis; Anderson, Iain; Bassiri-Gharb, Nazanin; Daqaq, Mohammed; Baba Sundaresan, Vishnu; Sarles, Andy

    2014-10-01

    The sixth annual meeting of the ASME Smart Materials, Adaptive Structures and Intelligent Systems Conference (SMASIS) was held in the beautiful mountain encircled Snowbird Resort and Conference Center in Little Cottonwood Canyon near Salt Lake City, Utah. It is the conference's objective to provide an up-to-date overview of research trends in the entire field of smart materials systems in a friendly casual forum conducive to the exchange of ideas and latest results. As each year we strive to grow and offer new experiences, this year we included special focused topic tracks on nanoscale multiferroic materials and origami engineering. The cross-disciplinary emphasis was reflected in keynote speeches by Professor Kaushik Bhattacharya (California Institute of Technology) on 'Cyclic Deformation and the Interplay between Phase Transformation and Plasticity in Shape Memory Alloys', by Professor Alison Flatau (University of Maryland at College Park) on 'Structural Magnetostrictive Alloys: The Other Smart Material', and by Dr Leslie Momoda (Director of the Sensors and Materials Laboratories, HRL Laboratories, LLC, Malibu, CA) on 'Architecturing New Functional Materials: An Industrial Perspective'. SMASIS 2013 was divided into seven symposia which span basic research, applied technological design and development, and industrial and governmental integrated system and application demonstrations. SYMP 1. Development and Characterization of Multifunctional Materials. SYMP 2. Mechanics and Behavior of Active Materials. SYMP 3. Modeling, Simulation and Control of Adaptive Systems. SYMP 4. Integrated System Design and Implementation. SYMP 5. Structural Health Monitoring. SYMP 6. Bioinspired Smart Materials and Systems. SYMP 7. Energy Harvesting. Authors of selected papers in the materials areas (symposia 1, 2, and 6) as well as energy harvesting (symposium 7) were invited to write a full journal article on their presentation topic for publication in this special issue of Smart

  6. Cloning, expression and structural stability of a cold-adapted ß-Galactosidase from Rahnella sp.R3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel gene was isolated for the first time from a psychrophilic gram-negative bacterium Rahnella sp.R3. It encoded a cold-adapted ß-galactosidase (R-ß-Gal). Recombinant R-ß-Gal was expressed in Escherichia coli BL21 (DE3), purified, and characterized. R-ß-Gal belongs to the glycosyl hydrolase fami...

  7. Structural insights into the acidophilic pH adaptation of a novel endo-1,4-β-xylanase from Scytalidium acidophilum.

    PubMed

    Michaux, Catherine; Pouyez, Jenny; Mayard, Aurélie; Vandurm, Pierre; Housen, Isabelle; Wouters, Johan

    2010-10-01

    In this study, the crystal structure of a novel endo-1,4-β-xylanase from Scytalidium acidophilum, XYL1, was solved at 1.9Å resolution. This is one of the few solved crystal structures of acidophilic proteins. The enzyme has the overall fold typical to family 11 xylanases. Comparison of this structure with other homologous acidophilic, neutrophilic and alkalophilic xylanases provides additional insights into the general features involved in low pH adaptation (stability and activity). Several sequence and structure modifications appeared to be responsible for the acidophilic characteristic: (a) the presence of an aspartic acid H bonded to the acid/base catalyst (b) the nature of specifically conserved residues in the active site (c) the negative potential at the surface (d) the decreased number of salt bridges and H bonds in comparison with highly alkaline enzymes.

  8. In-Flight Suppression of an Unstable F/A-18 Structural Mode Using the Space Launch System Adaptive Augmenting Control System

    NASA Technical Reports Server (NTRS)

    VanZwieten, Tannen S.; Gilligan, Eric T.; Wall, John H.; Miller, Christopher J.; Hanson, Curtis E.; Orr, Jeb S.

    2015-01-01

    NASA's Space Launch System (SLS) Flight Control System (FCS) includes an Adaptive Augmenting Control (AAC) component which employs a multiplicative gain update law to enhance the performance and robustness of the baseline control system for extreme off-nominal scenarios. The SLS FCS algorithm including AAC has been flight tested utilizing a specially outfitted F/A-18 fighter jet in which the pitch axis control of the aircraft was performed by a Non-linear Dynamic Inversion (NDI) controller, SLS reference models, and the SLS flight software prototype. This paper describes test cases from the research flight campaign in which the fundamental F/A-18 airframe structural mode was identified using post-flight frequency-domain reconstruction, amplified to result in closed loop instability, and suppressed in-flight by the SLS adaptive control system.

  9. In-Flight Suppression of a Destabilized F/A-18 Structural Mode Using the Space Launch System Adaptive Augmenting Control System

    NASA Technical Reports Server (NTRS)

    Wall, John H.; VanZwieten, Tannen S.; Gilligan, Eric T.; Miller, Christopher J.; Hanson, Curtis E.; Orr, Jeb S.

    2015-01-01

    NASA's Space Launch System (SLS) Flight Control System (FCS) includes an Adaptive Augmenting Control (AAC) component which employs a multiplicative gain update law to enhance the performance and robustness of the baseline control system for extreme off nominal scenarios. The SLS FCS algorithm including AAC has been flight tested utilizing a specially outfitted F/A-18 fighter jet in which the pitch axis control of the aircraft was performed by a Non-linear Dynamic Inversion (NDI) controller, SLS reference models, and the SLS flight software prototype. This paper describes test cases from the research flight campaign in which the fundamental F/A-18 airframe structural mode was identified using frequency-domain reconstruction of flight data, amplified to result in closed loop instability, and suppressed in-flight by the SLS adaptive control system.

  10. Performance of a Block Structured, Hierarchical Adaptive MeshRefinement Code on the 64k Node IBM BlueGene/L Computer

    SciTech Connect

    Greenough, Jeffrey A.; de Supinski, Bronis R.; Yates, Robert K.; Rendleman, Charles A.; Skinner, David; Beckner, Vince; Lijewski, Mike; Bell, John; Sexton, James C.

    2005-04-25

    We describe the performance of the block-structured Adaptive Mesh Refinement (AMR) code Raptor on the 32k node IBM BlueGene/L computer. This machine represents a significant step forward towards petascale computing. As such, it presents Raptor with many challenges for utilizing the hardware efficiently. In terms of performance, Raptor shows excellent weak and strong scaling when running in single level mode (no adaptivity). Hardware performance monitors show Raptor achieves an aggregate performance of 3:0 Tflops in the main integration kernel on the 32k system. Results from preliminary AMR runs on a prototype astrophysical problem demonstrate the efficiency of the current software when running at large scale. The BG/L system is enabling a physics problem to be considered that represents a factor of 64 increase in overall size compared to the largest ones of this type computed to date. Finally, we provide a description of the development work currently underway to address our inefficiencies.

  11. A new adaptive algorithm for automated feature extraction in exponentially damped signals for health monitoring of smart structures

    NASA Astrophysics Data System (ADS)

    Qarib, Hossein; Adeli, Hojjat

    2015-12-01

    In this paper authors introduce a new adaptive signal processing technique for feature extraction and parameter estimation in noisy exponentially damped signals. The iterative 3-stage method is based on the adroit integration of the strengths of parametric and nonparametric methods such as multiple signal categorization, matrix pencil, and empirical mode decomposition algorithms. The first stage is a new adaptive filtration or noise removal scheme. The second stage is a hybrid parametric-nonparametric signal parameter estimation technique based on an output-only system identification technique. The third stage is optimization of estimated parameters using a combination of the primal-dual path-following interior point algorithm and genetic algorithm. The methodology is evaluated using a synthetic signal and a signal obtained experimentally from transverse vibrations of a steel cantilever beam. The method is successful in estimating the frequencies accurately. Further, it estimates the damping exponents. The proposed adaptive filtration method does not include any frequency domain manipulation. Consequently, the time domain signal is not affected as a result of frequency domain and inverse transformations.

  12. Parallel Anisotropic Tetrahedral Adaptation

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Darmofal, David L.

    2008-01-01

    An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

  13. Adaptive Management

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...

  14. Structure of the Brachydanio Rerio Polo-Like Kinase 1 (Plk1) Catalytic Domain in Complex With An Extended Inhibitor Targeting the Adaptive Pocket of the Enzyme

    SciTech Connect

    Elling, R.A.; Fucini, R.V.; Hanan, E.J.; Barr, K.J.; Zhu, J.; Paulvannan, K.; Yang, W.; Romanowski, M.J.

    2009-05-18

    Polo-like kinase 1 (Plk1) is a member of the Polo-like kinase family of serine/threonine kinases involved in the regulation of cell-cycle progression and cytokinesis and is an attractive target for the development of anticancer therapeutics. The catalytic domain of this enzyme shares significant primary amino-acid homology and structural similarity with another mitotic kinase, Aurora A. While screening an Aurora A library of ATP-competitive compounds, a urea-containing inhibitor with low affinity for mouse Aurora A but with submicromolar potency for human and zebrafish Plk1 (hPlk1 and zPlk1, respectively) was identified. A crystal structure of the zebrafish Plk1 kinase domain-inhibitor complex reveals that the small molecule occupies the purine pocket and extends past the catalytic lysine into the adaptive region of the active site. Analysis of the structures of this protein-inhibitor complex and of similar small molecules cocrystallized with other kinases facilitates understanding of the specificity of the inhibitor for Plk1 and documents for the first time that Plk1 can accommodate extended ATP-competitive compounds that project toward the adaptive pocket and help the enzyme order its activation segment.

  15. Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure

    PubMed Central

    Hansal, Teresa; Krenn, Harald W.; Colville, Jonathan F.

    2016-01-01

    Although anthophilous Coleoptera are regarded to be unspecialised flower-visiting insects, monkey beetles (Scarabaeidae: Hopliini) represent one of the most important groups of pollinating insects in South Africa’s floristic hotspot of the Greater Cape Region. South African monkey beetles are known to feed on floral tissue; however, some species seem to specialise on pollen and/or nectar. The present study examined the mouthpart morphology and gut content of various hopliine species to draw conclusions on their feeding preferences. According to the specialisations of their mouthparts, the investigated species were classified into different feeding groups. Adaptations to pollen-feeding included a well-developed, toothed molar and a lobe-like, setose lacinia mobilis on the mandible as well as curled hairs or sclerotized teeth on the galea of the maxillae. Furthermore, elongated mouthparts were interpreted as adaptations for nectar feeding. Floral- and folial-tissue feeding species showed sclerotized teeth on the maxilla, but the lacinia was mostly found to be reduced to a sclerotized ledge. While species could clearly be identified as floral or folial tissue feeding, several species showed intermediate traits suggesting both pollen and nectar feeding adaptations. Mismatches found between mouthpart morphology and previously reported flower visiting behaviours across different genera and species requires alternative explanations, not necessarily associated with feeding preferences. Although detailed examinations of the mouthparts allowed conclusions about the feeding preference and flower-visiting behaviour, additional morphological and behavioural investigations, combined with greater taxon sampling and phylogenetic data, are still necessary to fully understand hopliine host plant relationships, related to monkey beetle diversity. PMID:26819850

  16. Characterization of promoter region and genomic structure of the murine and human genes encoding Src like adapter protein.

    PubMed

    Kratchmarova, I; Sosinowski, T; Weiss, A; Witter, K; Vincenz, C; Pandey, A

    2001-01-10

    Src-like adapter protein (SLAP) was identified as a signaling molecule in a yeast two-hybrid system using the cytoplasmic domain of EphA2, a receptor protein tyrosine kinase (Pandey et al., 1995. Characterization of a novel Src-like adapter protein that associates with the Eck receptor tyrosine kinase. J. Biol. Chem. 270, 19201-19204). It is very similar to members of the Src family of cytoplasmic tyrosine kinases in that it contains very homologous SH3 and SH2 domains (Abram and Courtneidge, 2000. Src family tyrosine kinases and growth factor signaling. Exp. Cell. Res. 254, 1-13.). However, instead of a kinase domain at the C-terminus, it contains a unique C-terminal region. In order to exclude the possibility that an alternative form exists, we have isolated genomic clones containing the murine Slap gene as well as the human SLA gene. The coding regions of murine Slap and human SLA genes contain seven exons and six introns. Absence of any kinase domain in the genomic region confirm its designation as an adapter protein. Additionally, we have cloned and sequenced approximately 2.6 kb of the region 5' to the initiator methionine of the murine Slap gene. When subcloned upstream of a luciferase gene, this fragment increased the transcriptional activity about 6-fold in a human Jurkat T cell line and approximately 52-fold in a murine T cell line indicating that this region contains promoter elements that dictate SLAP expression. We have also cloned the promoter region of the human SLA gene. Since SLAP is transcriptionally regulated by retinoic acid and by activation of B cells, the cloning of its promoter region will permit a detailed analysis of the elements required for its transcriptional regulation.

  17. Freshwater prokaryote and virus communities can adapt to a controlled increase in salinity through changes in their structure and interactions

    NASA Astrophysics Data System (ADS)

    Marine, Combe; Thierry, Bouvier; Olivier, Pringault; Emma, Rochelle-Newall; Corinne, Bouvier; Martin, Agis; The Thu, Pham; Jean-Pascal, Torreton; Van Thuoc, Chu; Bettarel, Yvan

    2013-11-01

    Little information exists on the ecological adaptive responses of riverine microorganisms to the salinity changes that typically occur in transitional waters. This study examined the precise effects of a gradual increase in salinity (+3 units per day for 12 days) on freshwater virus and prokaryote communities collected in the Red River Delta (northern Vietnam). The abundance, activity, morphology and diversity of both communities were examined along this simulated salinity gradient (0-36). Three main successive ecological stages were observed: (1) a continuous decline in prokaryotic and viral abundance from the start of the salinization process up to salinity 12-15 together with a strong decrease in the proportion of active cells, (2) a shift in both community compositions (salinity 9-15) and (3) a marked prevalence of lysogenic over lytic cycles up to salinity 21 followed by a collapse of both types of viral infection. Finally, after salinity 21, and up to seawater salinities (i.e. 36) the prokaryotic community showed multiple signs of recovery with their abundance and function even reaching initial levels. These results suggest that most of the physiological and phylogenetic changes that occurred within the salinity range 10-20 seemed to favor the installation of osmotically adapted prokaryotes accompanied by a specific cortege of viral parasites which might both be able to survive and even proliferate in saltwater conditions.

  18. Insect-Human Hybrid Eye (IHHE): an adaptive optofluidic lens combining the structural characteristics of insect and human eyes.

    PubMed

    Wei, Kang; Zeng, Hansong; Zhao, Yi

    2014-09-21

    Insect compound eyes and human camera eyes are two exquisite optical systems created by nature. The compound eye boasts an angle of view (AOV) up to 180° thanks to its hemispherical arrangement of hundreds of prime microscale lenses. The camera eye, on the other hand, can change shape to focus on objects at various depths, yet accepts light within a smaller AOV. Imitations of either imaging system have been abundant but with limited success. Here, we describe a reconfigurable polymeric optofluidic device that combines the architectural merits of both vision mechanisms, featuring a large AOV (up to 120°) with adaptive focusing capabilities (from 0 to 275 diopter (D)). This device consists of bi-layered microfluidics: an array of millimeter-sized fluidic lenses is integrated into the top layer and arranged on an elastomeric membrane embedded within the bottom layer. The membrane can be deformed from a planar surface into a series of dome-shaped geometries, rearranging individual fluidic lenses in desired curvilinear layouts. Meanwhile, each fluidic lens can vary its radius of curvature for a monocular depth sensation. Such a design presents a new perspective of tunable optofluidics for a broad range of applications, such as robotic vision and medical laparoendoscopy, where adaptive focalization with a large viewing angle is a clear advantage.

  19. Fireplace adapters

    SciTech Connect

    Hunt, R.L.

    1983-12-27

    An adapter is disclosed for use with a fireplace. The stove pipe of a stove standing in a room to be heated may be connected to the flue of the chimney so that products of combustion from the stove may be safely exhausted through the flue and outwardly of the chimney. The adapter may be easily installed within the fireplace by removing the damper plate and fitting the adapter to the damper frame. Each of a pair of bolts has a portion which hooks over a portion of the damper frame and a threaded end depending from the hook portion and extending through a hole in the adapter. Nuts are threaded on the bolts and are adapted to force the adapter into a tight fit with the adapter frame.

  20. Crystal structure analysis of a glycosides hydrolase family 42 cold-adapted ß-galactosidase from Rahnella sp. R3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ß-galactosidase isolated from a psychrotrophic bacterium, Rahnella sp. R3 (R-ß-Gal), exhibits high activity at low temperature. R-ß-Gal is a member of the glycoside hydrolases family 42 (GH42), and forms a 225 kDa trimeric structure in solution. The X-ray crystal structure of R-ß-Gal was determi...

  1. Quantifying the Adaptive Cycle.

    PubMed

    Angeler, David G; Allen, Craig R; Garmestani, Ahjond S; Gunderson, Lance H; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994-2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems. PMID:26716453

  2. Quantifying the adaptive cycle

    USGS Publications Warehouse

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

  3. Quantifying the Adaptive Cycle

    PubMed Central

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems. PMID:26716453

  4. Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula1[C][W][OPEN

    PubMed Central

    Oh, Dong-Ha; Hong, Hyewon; Lee, Sang Yeol; Yun, Dae-Jin; Bohnert, Hans J.; Dassanayake, Maheshi

    2014-01-01

    Schrenkiella parvula (formerly Thellungiella parvula), a close relative of Arabidopsis (Arabidopsis thaliana) and Brassica crop species, thrives on the shores of Lake Tuz, Turkey, where soils accumulate high concentrations of multiple-ion salts. Despite the stark differences in adaptations to extreme salt stresses, the genomes of S. parvula and Arabidopsis show extensive synteny. S. parvula completes its life cycle in the presence of Na+, K+, Mg2+, Li+, and borate at soil concentrations lethal to Arabidopsis. Genome structural variations, including tandem duplications and translocations of genes, interrupt the colinearity observed throughout the S. parvula and Arabidopsis genomes. Structural variations distinguish homologous gene pairs characterized by divergent promoter sequences and basal-level expression strengths. Comparative RNA sequencing reveals the enrichment of ion-transport functions among genes with higher expression in S. parvula, while pathogen defense-related genes show higher expression in Arabidopsis. Key stress-related ion transporter genes in S. parvula showed increased copy number, higher transcript dosage, and evidence for subfunctionalization. This extremophyte offers a framework to identify the requisite adjustments of genomic architecture and expression control for a set of genes found in most plants in a way to support distinct niche adaptation and lifestyles. PMID:24563282

  5. Adaptation and Latent Structure of the Swahili Version of Beck Depression Inventory-II in a Low Literacy Population in the Context of HIV

    PubMed Central

    Abubakar, Amina; Kalu, Raphael Birya; Katana, Khamis; Kabunda, Beatrice; Hassan, Amin S.; Newton, Charles R.; Van de Vijver, Fons

    2016-01-01

    Objective We set out to adapt the Beck Depression Inventory (BDI)-II in Kenya and examine its factorial structure. Methods In the first phase we carried out in-depth interviews involving 29 adult members of the community to elicit their understanding of depression and identify aspects of the BDI-II that required adaptation. In the second phase, a modified version of BDI-II was administered to 221 adults randomly selected from the community to allow for the evaluation of its psychometric properties. In the third phase of the study we evaluated the discriminative validity of BDI-11 by comparing a randomly chosen community sample (n = 29) with caregivers of adolescents affected by HIV (n = 77). Results A considerable overlap between the BDI symptoms and those generated in the interviews was observed. Relevant idioms and symptoms such as ‘thinking too much’ and ‘Kuchoka moyo (having a tired heart)’ were identified. The administration of the BDI had to be modified to make it suitable for the low literacy levels of our participants. Fit indices for several models (one factorial, two-factor model and a three factor model) were all within acceptable range. Evidence indicated that while multidimensional models could be fitted, the strong correlations between the factors implied that a single factor model may be the best suited solution (alpha [0.89], and a significant correlation with locally identified items [r = 0.51]) confirmed the good psychometric properties of the adapted BDI-II. No evidence was found to support the hypothesis that somatization was more prevalent. Lastly, caregivers of HIV affected adolescents had significantly higher scores compared to adults randomly selected from the community F(1, 121) = 23.31, p < .001 indicating the discriminative validity of the adapted BDI = II. Conclusions With an adapted administration procedure, the BDI-II provides an adequate measure of depressive symptoms which can be used alongside other measures for proper

  6. A vision-based system for measuring the displacements of large structures: Simultaneous adaptive calibration and full motion estimation

    NASA Astrophysics Data System (ADS)

    Santos, C. Almeida; Costa, C. Oliveira; Batista, J.

    2016-05-01

    The paper describes a kinematic model-based solution to estimate simultaneously the calibration parameters of the vision system and the full-motion (6-DOF) of large civil engineering structures, namely of long deck suspension bridges, from a sequence of stereo images captured by digital cameras. Using an arbitrary number of images and assuming a smooth structure motion, an Iterated Extended Kalman Filter is used to recursively estimate the projection matrices of the cameras and the structure full-motion (displacement and rotation) over time, helping to meet the structure health monitoring fulfilment. Results related to the performance evaluation, obtained by numerical simulation and with real experiments, are reported. The real experiments were carried out in indoor and outdoor environment using a reduced structure model to impose controlled motions. In both cases, the results obtained with a minimum setup comprising only two cameras and four non-coplanar tracking points, showed a high accuracy results for on-line camera calibration and structure full motion estimation.

  7. Adaptive SPECT

    PubMed Central

    Barrett, Harrison H.; Furenlid, Lars R.; Freed, Melanie; Hesterman, Jacob Y.; Kupinski, Matthew A.; Clarkson, Eric; Whitaker, Meredith K.

    2008-01-01

    Adaptive imaging systems alter their data-acquisition configuration or protocol in response to the image information received. An adaptive pinhole single-photon emission computed tomography (SPECT) system might acquire an initial scout image to obtain preliminary information about the radiotracer distribution and then adjust the configuration or sizes of the pinholes, the magnifications, or the projection angles in order to improve performance. This paper briefly describes two small-animal SPECT systems that allow this flexibility and then presents a framework for evaluating adaptive systems in general, and adaptive SPECT systems in particular. The evaluation is in terms of the performance of linear observers on detection or estimation tasks. Expressions are derived for the ideal linear (Hotelling) observer and the ideal linear (Wiener) estimator with adaptive imaging. Detailed expressions for the performance figures of merit are given, and possible adaptation rules are discussed. PMID:18541485

  8. Dissociation as complex adaptation.

    PubMed

    Sel, R

    1997-03-01

    In this article the general theory of complex adaptive systems, substantiated by non-linear dynamics, will be used to put the dissociative disorders into a theoretical framework and clarify their genesis and presentation. When a system is far out of equilibrium, dissipative structures may be formed ('order out of chaos', as Prigogine (1) has put it). These structures provide the starting point for further evolution and co-evolution of competing groups of functional schemata divided on a bifurcation surface. Complex adaptation is almost inevitable in a complicated system (such as the brain) driven by non-linear dynamics. Dissociation is thus regarded as a consequence of adaptation to a chaotic environment rich in contrasts. In a sufficiently complex environment a person with dissociative identity disorder is more adapted and thus more likely to occur than a 'normal' monopersonality individual.

  9. Adaptive Computing.

    ERIC Educational Resources Information Center

    Harrell, William

    1999-01-01

    Provides information on various adaptive technology resources available to people with disabilities. (Contains 19 references, an annotated list of 129 websites, and 12 additional print resources.) (JOW)

  10. Contour adaptation.

    PubMed

    Anstis, Stuart

    2013-01-01

    It is known that adaptation to a disk that flickers between black and white at 3-8 Hz on a gray surround renders invisible a congruent gray test disk viewed afterwards. This is contrast adaptation. We now report that adapting simply to the flickering circular outline of the disk can have the same effect. We call this "contour adaptation." This adaptation does not transfer interocularly, and apparently applies only to luminance, not color. One can adapt selectively to only some of the contours in a display, making only these contours temporarily invisible. For instance, a plaid comprises a vertical grating superimposed on a horizontal grating. If one first adapts to appropriate flickering vertical lines, the vertical components of the plaid disappears and it looks like a horizontal grating. Also, we simulated a Cornsweet (1970) edge, and we selectively adapted out the subjective and objective contours of a Kanisza (1976) subjective square. By temporarily removing edges, contour adaptation offers a new technique to study the role of visual edges, and it demonstrates how brightness information is concentrated in edges and propagates from them as it fills in surfaces.

  11. On the synthesis of a bio-inspired dual-cellular fluidic flexible matrix composite adaptive structure based on a non-dimensional dynamics model

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2013-01-01

    A recent study investigated the dynamic characteristics of an adaptive structure concept featuring dual fluidic flexible matrix composite (F2MC) cells inspired by the configuration of plant cells and cell walls. This novel bio-inspired system consists of two F2MC cells with different fiber angles connected through internal fluid circuits. It was discovered that the dual F2MC cellular structure can be characterized as a two degree of freedom damped mass-spring oscillator, and can be utilized as a vibration absorber or an enhanced actuator under different operation conditions. These results demonstrated that the concept is promising and further investigations are needed to develop methodologies for synthesizing future multi-cellular F2MC structural systems. While interesting, the previous study focused on specific case studies and analysis. That is, the outcome did not provide insight that could be generalized, or tools for synthesizing a multiple F2MC cellular structure. This paper attempts to address this important issue by developing a non-dimensional dynamic model, which reveals good physical insights as well as identifying crucial constitutive parameters for F2MC cellular design. Working with these parameters, rather than physical variables, can greatly simplify the mathematics involved in the study. A synthesis tool is then developed for the dual-cellular structure, and it is found that for each set of achievable target poles and zero, there exist multiple F2MC cellular designs, forming a design space. The presented physical insights and synthesis tool for the dual-cellular structure will be the building blocks for future investigation on cellular structures with a larger number of cells.

  12. Adaptive expansion of the maize maternally expressed gene (Meg) family involves changes in expression patterns and protein secondary structures of its members

    PubMed Central

    2014-01-01

    Background The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of the basal endosperm transfer cell layer (BETL) and is involved in the allocation of maternal nutrients to growing seeds. Despite the important roles of Meg1 in maize seed development, the evolutionary history of the Meg cluster and the activities of the duplicate genes are not understood. Results In maize, the Meg gene cluster resides in a 2.3 Mb-long genomic region that exhibits many features of non-centromeric heterochromatin. Using phylogenetic reconstruction and syntenic alignments, we identified the pedigree of the Meg family, in which 11 of its 13 members arose in maize after allotetraploidization ~4.8 mya. Phylogenetic and population-genetic analyses identified possible signatures suggesting recent positive selection in Meg homologs. Structural analyses of the Meg proteins indicated potentially adaptive changes in secondary structure from α-helix to β-strand during the expansion. Transcriptomic analysis of the maize endosperm indicated that 6 Meg genes are selectively activated in the BETL, and younger Meg genes are more active than older ones. In endosperms from B73 by Mo17 reciprocal crosses, most Meg genes did not display parent-specific expression patterns. Conclusions Recently-duplicated Meg genes have different protein secondary structures, and their expressions in the BETL dominate over those of older members. Together with the signs of positive selections in the young Meg genes, these results suggest that the expansion of the Meg family involves potentially adaptive transitions in which new members with novel functions prevailed over older members. PMID:25084677

  13. Adaptation of the jejunal mucosa in the experimental blind loop syndrome: changes in paracellular conductance and tight junction structure.

    PubMed

    Schulzke, J D; Fromm, M; Bentzel, C J; Menge, H; Riecken, E O

    1987-01-01

    Self-filling blind loops of rat jejunum exhibit hyperregenerative transformation of the mucosa. We used this experimental model to characterise mechanisms, which may occur under similar conditions in man (stagnant loop syndrome). Epithelial and subepithelial resistance were measured in the Ussing-chamber by voltage divider ratio measurements after positioning a microelectrode between epithelium and subepithelial tissue layers. In the blind loop, epithelial resistance increased from 8 +/- 1 to 23 +/- 1 omega cm2 and subepithelial resistance from 39 +/- 4 to 86 +/- 8 omega cm2 as compared with control jejunum. The increase in the subepithelial resistance was paralleled anatomically by an increase in the thickness of the subepithelial tissue layers from 63 +/- 4 microns to 177 +/- 19 microns. Ultrastructural analysis of the tight junction area by freeze fracture electron microscopy revealed an increase in the total junctional 'depth' in the crypts from 243 +/- 9 nm in control jejunum to 396 +/- 17 nm in the blind loop, while the number of horizontally oriented 'strands' remained unchanged. Villus tight junctions did not differ between blind loop and control. We interpret the alterations in the self-filling blind loop as an adaptive response of the epithelium which reduces backleakage of already absorbed electrolytes across the tight junction into the intestinal lumen. This mechanism is suitable to support the intestine in maintaining body electrolyte and water contents during cellular electrolyte malabsorption.

  14. Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures

    SciTech Connect

    Lin, Yuchun; Beckham, Gregg T.; Himmel, Michael E.; Crowley, Michael F.; Chu, Jhih-wei

    2013-09-19

    We examine how the catalytic domain of a glycoside hydrolase family 7 endoglucanase catalytic domain (Cel7B CD) facilitates complexation of cellulose chains from a crystal surface. With direct relevance to the science of biofuel production, this problem also represents a model system of biopolymer processing by proteins in Nature. Interactions of Cel7B CD with a cellulose microfibril along different paths of complexation are characterized by mapping the atomistic fluctuations recorded in free-energy simulations onto the parameters of a coarse-grain model. The resulting patterns of protein-biopolymer couplings also uncover the sequence signatures of the enzyme in peeling off glucan chains from the microfibril substrate. We show that the semiopen active site of Cel7B CD exhibits similar barriers and free energies of complexation over two distinct routes; namely, scooping of a chain into the active-site cleft and threading from the chain end into the channel. On the other hand, the complexation energetics strongly depends on the surface packing of the targeted chain and the resulting interaction sites with the enzyme. A revealed principle is that Cel7B CD facilitates cellulose deconstruction via adaptive coupling to the emergent substrate. The flexible, peripheral segments of the protein outside of the active-site cleft are able to accommodate the varying features of cellulose along the simulated paths of complexation. The general strategy of linking physics-based molecular interactions to protein sequence could also be helpful in elucidating how other protein machines process biopolymers.

  15. An Adaptive Course Generation Framework

    ERIC Educational Resources Information Center

    Li, Frederick W. B.; Lau, Rynson W. H.; Dharmendran, Parthiban

    2010-01-01

    Existing adaptive e-learning methods are supported by student (user) profiling for capturing student characteristics, and course structuring for organizing learning materials according to topics and levels of difficulties. Adaptive courses are then generated by extracting materials from the course structure to match the criteria specified in the…

  16. Climate adaptation

    NASA Astrophysics Data System (ADS)

    Kinzig, Ann P.

    2015-03-01

    This paper is intended as a brief introduction to climate adaptation in a conference devoted otherwise to the physics of sustainable energy. Whereas mitigation involves measures to reduce the probability of a potential event, such as climate change, adaptation refers to actions that lessen the impact of climate change. Mitigation and adaptation differ in other ways as well. Adaptation does not necessarily have to be implemented immediately to be effective; it only needs to be in place before the threat arrives. Also, adaptation does not necessarily require global, coordinated action; many effective adaptation actions can be local. Some urban communities, because of land-use change and the urban heat-island effect, currently face changes similar to some expected under climate change, such as changes in water availability, heat-related morbidity, or changes in disease patterns. Concern over those impacts might motivate the implementation of measures that would also help in climate adaptation, despite skepticism among some policy makers about anthropogenic global warming. Studies of ancient civilizations in the southwestern US lends some insight into factors that may or may not be important to successful adaptation.

  17. Adapting coastal structures to a moving relative sea level: Roman Time geoarchaeological evidence from Posillipo promontory (Naples, Italy).

    NASA Astrophysics Data System (ADS)

    Aucelli, Pietro; Cinque, Aldo; Giordano, Francesco; Mattei, Gaia; Pappone, Gerardo; Rizzo, Angela

    2016-04-01

    The Posillipo promontory belongs to the southern periphery the active volcanic complex called Campi Flegrei. Especially the central caldera of CF is well known for offering a rich geoarchaeological record of the vertical ground movements it has been suffering since Roman times; which includes the ruins of Portus Julius (built in 37 BC) presently found between 10 and 5 m bsl and the Middle Ages Lithophaga perforations at about 7m asl on the marble columns of the Serapeo building (Morhange, 2006 and references therein). In order to better constraint the vertical movements suffered by the Posillipo promontory during the last two millennia, we selected three geoarcaeolgical coastal sites (Nisida Roman port, Marechiaro Roman port and Villa Robery) and we studied them by means of both geomorphological observations and geophysical surveys (Side Scan Sonar and Single Beam echo-sounder). Within the submerged Roman port of Nisida, built in the 1st AD, we found two pilae of the ancient pier. The submersion measuring of the well-preserved one provided a palaeo-sea level at 3.1±0.30 m bsl. In the submerged Roman port of Marechiaro, we recognized a still preserved breakwater connected to the tuffaceous sea cliff, and submerged foundations of a 1st century small sea-side villa. Nearby there is also a two-storeyed Roman building (Palazzo degli Spiriti), built in the 1st cent. BC and later restructured to adapt to a phase of subsidence (Gunther 1908). From our submersion measurements, two different paleo-sea levels can be deduced: one for the 1st cent. BC at -4.4 + -0.50 m and another for the 1st cent. AD at -3 + - 0.30 m. Finally, in front of the modern Villa Rosebery the sea bottom shows a sub-horizontal element at -3m to -3.5m bsl, emerged during the 1st BC century. In fact, at least three houses were erected there during said century (Gunther, 1908). As the area was very little elevated, an alignment of pilae was also constructed to protect those houses from the breakers. By

  18. The genetic and structural basis of two distinct terminal side branch residues in stewartan and amylovoran exopolysaccharides and their potential role in host adaptation.

    PubMed

    Wang, Xiaolei; Yang, Fan; von Bodman, Susanne B

    2012-01-01

    Stewartan and amylovoran exopolysaccharide (EPS) produced by the plant pathogenic bacteria Pantoea stewartii and Erwinia amylovora are virulence factors in the cause of Stewart's vascular wilt and fire blight. The biosynthesis of amylovoran and stewartan is encoded by a set of homologous operons that have been partially characterized, although some annotations are solely on the basis of sequence homology. The major distinguishing features of these two EPS forms are the presence of a terminal pyruvate in amylovoran and glucose in stewartan, even though the gene systems to account for both are conserved and present in each bacterium. This study explores the genetic, structural and functional differences of amylovoran and stewartan, and their potential role in host adaptation. We report that the pyruvyl transferase gene in P. stewartii is non-functional, while the terminal glucosyl transferase is catalytically active. Conversely, in E. amylovora, the homologous glucosyl transferase activity appears to be relatively ineffective, while the pyruvyl transferase function predominates. We also show that the terminally pyruvylated versus glucosylated EPS require specific repeating unit translocases (Wzx). We discuss the evolutionary, functional and biological implications of the terminally pyruvylated and glucosylated polymers and their potential contribution to plant and insect host adaptation.

  19. Adaptive optics and optical structures; Proceedings of the Meeting, European Congress on Optics, 3rd, The Hague, Netherlands, Mar. 12-14, 1990

    NASA Technical Reports Server (NTRS)

    Tyson, Robert K. (Editor); Schulte In Den Baeumen, J. (Editor)

    1990-01-01

    The present conference on adaptive optics (AO) and optical structures addresses AO systems and controls, AO components, nonlinear optics applications to AO, astronomical applications of AO, large telescopes and optical alignment, as well as the wavefront control experiment for the use of AO in beam propagation. Specific references are made to applications of electromagnetic theory in optics, theoretical studies of system performance and design parameters, Hartmann-Shack wavefront sensing, the use of ray-based techniques in cophasing segmented mirrors, the use of a phase-conjugating mirror for real-time phase visualization, and the absolute instability of oppositely directed waves with respect to a high-reflectivity phase-conjugate mirror. Also addressed are automatic control systems, precision segmented reflectors, AO system creation, the VLT's 8.2-m primary mirrors, an optical 12-m telescope, alignment optimization via the Talbot effect, and a combination of interferometry and ray-tracing analysis.

  20. Prevalence of psychiatric morbidity and psychological adaptation of the nurses in a structured SARS caring unit during outbreak: a prospective and periodic assessment study in Taiwan.

    PubMed

    Su, Tung-Ping; Lien, Te-Cheng; Yang, Chih-Yi; Su, Yiet Ling; Wang, Jia-Horng; Tsai, Sing-Ling; Yin, Jeo-Chen

    2007-01-01

    To assess the rapidly changing psychological status of nurses during the acute phase of the 2003 SARS outbreak, we conducted a prospective and periodic evaluation of psychiatric morbidity and psychological adaptation among nurses in SARS units and non-SARS units. Nurse participants were from two SARS units (regular SARS [N=44] and SARS ICU [N=26]) and two non-SARS units (Neurology [N=15] and CCU [N=17]). Participants periodically self-evaluated their depression, anxiety, post-traumatic stress symptoms, sleep disturbance, attitude towards SARS and family support. Results showed that depression (38.5% vs. 3.1%) and insomnia (37% vs. 9.7%) were, respectively, greater in the SARS unit nurses than the non-SARS unit nurses. No difference between these two groups was found in the prevalence of post-traumatic stress symptoms (33% vs. 18.7%), yet, three unit subjects (SARS ICU, SARS regular and Neurology) had significantly higher rate than those in CCU (29.7% vs. 11.8%, respectively) (p<0.05). For the SARS unit nurses, significant reduction in mood ratings, insomnia rate and perceived negative feelings as well as increasing knowledge and understanding of SARS at the end of the study (all p<0.001) indicated that a gradual psychological adaptation had occurred. The adjustment of nurses in the more structured SARS ICU environment, where nurses care for even more severely ill patients, may have been as good or better than that of nurses in the regular SARS unit. Occurrence of psychiatric symptoms was linked to direct exposure to SARS patient care, previous mood disorder history, younger age and perceived negative feelings. Positive coping attitude and strong social and family support may have protected against acute stress. In conclusion, the psychological impact on the caring staffs facing future bio-disaster will be minimized with lowered risk factors and a safer and more structured work environment. PMID:16460760

  1. Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

    PubMed Central

    Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

    2016-01-01

    Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

  2. Global displacement of canine parvovirus by a host-adapted variant: structural comparison between pandemic viruses with distinct host ranges.

    PubMed

    Organtini, Lindsey J; Allison, Andrew B; Lukk, Tiit; Parrish, Colin R; Hafenstein, Susan

    2015-02-01

    Canine parvovirus type 2 (CPV-2) emerged in 1978 and spread worldwide within 2 years. Subsequently, CPV-2 was completely replaced by the variant CPV-2a, which is characterized by four specific capsid (VP2) mutations. The X-ray crystal structure of the CPV-2a capsid shows that each mutation confers small local changes. The loss of a hydrogen bond and introduction of a glycine residue likely introduce flexibility to sites that control interactions with the host receptor, antibodies, and sialic acids.

  3. Mechanism of adaptability for the nano-structured TiAlCrSiYN-based hard physical vapor deposition coatings under extreme frictional conditions

    NASA Astrophysics Data System (ADS)

    Fox-Rabinovich, G. S.; Endrino, J. L.; Aguirre, M. H.; Beake, B. D.; Veldhuis, S. C.; Kovalev, A. I.; Gershman, I. S.; Yamamoto, K.; Losset, Y.; Wainstein, D. L.; Rashkovskiy, A.

    2012-03-01

    Recently, a family of hard mono- and multilayer TiAlCrSiYN-based coatings have been introduced that exhibit adaptive behavior under extreme tribological conditions (in particular during dry ultrahigh speed machining of hardened tool steels). The major feature of these coatings is the formation of the tribo-films on the friction surface which possess high protective ability under operating temperatures of 1000 °C and above. These tribo-films are generated as a result of a self-organization process during friction. But the mechanism how these films affect adaptability of the hard coating is still an open question. The major mechanism proposed in this paper is associated with a strong gradient of temperatures within the layer of nano-scaled tribo-films. This trend was outlined by the performed thermodynamic analysis of friction phenomena combined with the developing of a numerical model of heat transfer within cutting zone based on the finite element method. The results of the theoretical studies show that the major physical-chemical processes during cutting are mostly concentrated within a layer of the tribo-films. This nano-tribological phenomenon produces beneficial heat distribution at the chip/tool interface which controls the tool life and wear behavior.Results of x-ray photoelectron spectroscopy studies indicate enhanced formation of protective sapphire- and mullite-like tribo-films on the friction surface of the multilayer TiAlCrSiYN/TiAlCrN coating. Comprehensive investigations of the structure and phase transformation within the coating layer under operation have been performed, using high resolution transmission electron microscopy, synchrotron radiation technique: x-ray absorption near-edge structure and XRD methods.The data obtained show that the tribo-films efficiently perform their thermal barrier functions preventing heat to penetrate into the body of coated cutting tool. Due to this the surface damaging process as well as non-beneficial phase

  4. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.

    PubMed

    Shaytan, Alexey K; Landsman, David; Panchenko, Anna R

    2015-06-01

    Nucleosome variability is essential for their functions in compacting the chromatin structure and regulation of transcription, replication and cell reprogramming. The DNA molecule in nucleosomes is wrapped around an octamer composed of four types of core histones (H3, H4, H2A, H2B). Nucleosomes represent dynamic entities and may change their conformation, stability and binding properties by employing different sets of histone variants or by becoming post-translationally modified. There are many variants of histones H2A and H2B. Specific H2A and H2B variants may preferentially associate with each other resulting in different combinations of variants and leading to the increased combinatorial complexity of nucleosomes. In addition, the H2A-H2B dimer can be recognized and substituted by chaperones/remodelers as a distinct unit, can assemble independently and is stable during nucleosome unwinding. In this review we discuss how sequence and structural variations in H2A-H2B dimers may provide necessary complexity and confer the nucleosome functional variability.

  5. Structural adaptation to selective pressure for altered ligand specificity in the Pseudomonas aeruginosa amide receptor, amiC.

    PubMed

    O'Hara, B P; Wilson, S A; Lee, A W; Roe, S M; Siligardi, G; Drew, R E; Pearl, L H

    2000-02-01

    The AmiC protein in Pseudomonas aeruginosa is the negative regulator and ligand receptor for an amide-inducible aliphatic amidase operon. In the wild-type PAC1 strain, amidase expression is induced by acetamide or lactamide, but not by butyramide. A mutant strain of P. aeruginosa, PAC181, was selected for its sensitivity to induction by butyramide. The molecular basis for the butyramide inducible phenotype of P.aeruginosa PAC181 has now been determined, and results from a Thr-->Asn mutation at position 106 in PAC181-AmiC. In the wild-type PAC1-AmiC protein this residue forms part of the side wall of the amide-binding pocket but does not interact with the acetamide ligand directly. In the crystal structure of PAC181-AmiC complexed with butyramide, the Thr-->Asn mutation increases the size of the ligand binding site such that the mutant protein is able to close into its 'on' configuration even in the presence of butyramide. Although the mutation allows butyramide to be recognized as an inducer of amidase expression, the mutation is structurally sub-optimal, and produces a significant decrease in the stability of the mutant protein.

  6. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers

    PubMed Central

    Shaytan, Alexey K.; Landsman, David

    2015-01-01

    Nucleosome variability is essential for their functions in compacting the chromatin structure and regulation of transcription, replication and cell reprogramming. The DNA molecule in nucleosomes is wrapped around an octamer composed of four types of core histones (H3, H4, H2A, H2B). Nucleosomes represent dynamic entities and may change their conformation, stability and binding properties by employing different sets of histone variants or by becoming post-translationally modified. There are many variants of histones H2A and H2B. Specific H2A and H2B variants may preferentially associate with each other resulting in different combinations of variants and leading to the increased combinatorial complexity of nucleosomes. In addition, the H2A-H2B dimer can be recognized and substituted by chaperones/remodelers as a distinct unit, can assemble independently and is stable during nucleosome unwinding. In this review we discuss how sequence and structural variations in H2A-H2B dimers may provide necessary complexity and confer the nucleosome functional variability. PMID:25731851

  7. Adaptive management: Chapter 1

    USGS Publications Warehouse

    Allen, Craig R.; Garmestani, Ahjond S.; Allen, Craig R.; Garmestani, Ahjond S.

    2015-01-01

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

  8. An adaptive lidar

    NASA Astrophysics Data System (ADS)

    Oshlakov, V. G.; Andreev, M. I.; Malykh, D. D.

    2009-09-01

    Using the polarization characteristics of a target and its underlying surface one can change the target contrast range. As the target one can use the compact and discrete structures with different characteristics to reflect electromagnetic waves. An important problem, solved by the adaptive polarization lidar, is to determine the availability and identification of different targets based on their polarization characteristics against the background of underlying surface, which polarization characteristics are unknown. Another important problem of the adaptive polarization lidar is a search for the objects, which polarization characteristics are unknown, against the background of underlying surface, which polarization characteristics are known. The adaptive polarization lidar makes it possible to determine the presence of impurities in sea water. The characteristics of the adaptive polarization lidar undergo variations, i.e., polarization characteristics of a sensing signal and polarization characteristics of the receiver are varied depending on the problem to be solved. One of the versions of construction of the adaptive polarization lidar is considered. The increase of the contrast in the adaptive lidar has been demonstrated by the numerical experiment when sensing hydrosols on the background of the Rayleigh scattering, caused by clear water. The numerical experiment has also demonstrated the increase of the contrast in the adaptive lidar when sensing at two wavelengths of dry haze and dense haze on the background of the Rayleigh scattering, caused by the clear atmosphere. The most effective wavelength was chosen.

  9. Assessing and Adapting LiDAR-Derived Pit-Free Canopy Height Model Algorithm for Sites with Varying Vegetation Structure

    NASA Astrophysics Data System (ADS)

    Scholl, V.; Hulslander, D.; Goulden, T.; Wasser, L. A.

    2015-12-01

    Spatial and temporal monitoring of vegetation structure is important to the ecological community. Airborne Light Detection and Ranging (LiDAR) systems are used to efficiently survey large forested areas. From LiDAR data, three-dimensional models of forests called canopy height models (CHMs) are generated and used to estimate tree height. A common problem associated with CHMs is data pits, where LiDAR pulses penetrate the top of the canopy, leading to an underestimation of vegetation height. The National Ecological Observatory Network (NEON) currently implements an algorithm to reduce data pit frequency, which requires two height threshold parameters, increment size and range ceiling. CHMs are produced at a series of height increments up to a height range ceiling and combined to produce a CHM with reduced pits (referred to as a "pit-free" CHM). The current implementation uses static values for the height increment and ceiling (5 and 15 meters, respectively). To facilitate the generation of accurate pit-free CHMs across diverse NEON sites with varying vegetation structure, the impacts of adjusting the height threshold parameters were investigated through development of an algorithm which dynamically selects the height increment and ceiling. A series of pit-free CHMs were generated using three height range ceilings and four height increment values for three ecologically different sites. Height threshold parameters were found to change CHM-derived tree heights up to 36% compared to original CHMs. The extent of the parameters' influence on modelled tree heights was greater than expected, which will be considered during future CHM data product development at NEON. (A) Aerial image of Harvard National Forest, (B) standard CHM containing pits, appearing as black speckles, (C) a pit-free CHM created with the static algorithm implementation, and (D) a pit-free CHM created through varying the height threshold ceiling up to 82 m and the increment to 1 m.

  10. Adaptive Heat Engine.

    PubMed

    Allahverdyan, A E; Babajanyan, S G; Martirosyan, N H; Melkikh, A V

    2016-07-15

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where-due to feedback from the functional part-the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment.

  11. Adaptive Heat Engine.

    PubMed

    Allahverdyan, A E; Babajanyan, S G; Martirosyan, N H; Melkikh, A V

    2016-07-15

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where-due to feedback from the functional part-the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment. PMID:27472104

  12. Adaptive Heat Engine

    NASA Astrophysics Data System (ADS)

    Allahverdyan, A. E.; Babajanyan, S. G.; Martirosyan, N. H.; Melkikh, A. V.

    2016-07-01

    A major limitation of many heat engines is that their functioning demands on-line control and/or an external fitting between the environmental parameters (e.g., temperatures of thermal baths) and internal parameters of the engine. We study a model for an adaptive heat engine, where—due to feedback from the functional part—the engine's structure adapts to given thermal baths. Hence, no on-line control and no external fitting are needed. The engine can employ unknown resources; it can also adapt to results of its own functioning that make the bath temperatures closer. We determine resources of adaptation and relate them to the prior information available about the environment.

  13. Toothbrush Adaptations.

    ERIC Educational Resources Information Center

    Exceptional Parent, 1987

    1987-01-01

    Suggestions are presented for helping disabled individuals learn to use or adapt toothbrushes for proper dental care. A directory lists dental health instructional materials available from various organizations. (CB)

  14. Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125.

    PubMed

    Giordano, Daniela; Pesce, Alessandra; Boechi, Leonardo; Bustamante, Juan Pablo; Caldelli, Elena; Howes, Barry D; Riccio, Alessia; di Prisco, Guido; Nardini, Marco; Estrin, Dario; Smulevich, Giulietta; Bolognesi, Martino; Verde, Cinzia

    2015-08-01

    Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.

  15. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells.

    PubMed

    Yokoyama, Masaru; Nomaguchi, Masako; Doi, Naoya; Kanda, Tadahito; Adachi, Akio; Sato, Hironori

    2016-01-01

    Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness.

  16. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells

    PubMed Central

    Yokoyama, Masaru; Nomaguchi, Masako; Doi, Naoya; Kanda, Tadahito; Adachi, Akio; Sato, Hironori

    2016-01-01

    Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness. PMID:26903989

  17. Hybrid active focusing with adaptive dispersion for higher defect sensitivity in guided wave inspection of cylindrical structures

    NASA Astrophysics Data System (ADS)

    Lowe, P. S.; Sanderson, R.; Boulgouris, N. V.; Gan, T. H.

    2016-07-01

    Ultrasonic guided wave inspection is widely used for scanning prismatic structures such as pipes for metal loss. Recent research has investigated focusing the sound energy into predetermined regions of a pipe in order to enhance the defect sensitivity. This paper presents an active focusing technique which is based on a combination of numerical simulation and time reversal concept. The proposed technique is empirically validated using a 3D laser vibrometry measurement of the focal spot. The defect sensitivity of the proposed technique is compared with conventional active focusing, time reversal focusing and synthetic focusing through an empirically validated finite element parametric study. Based on the results, the proposed technique achieves approximately 10 dB improvement of signal-to-coherent-noise ratio compared to the conventional active focusing and time reversal focusing. It is also demonstrated that the proposed technique to have an amplitude gain of around 5 dB over synthetic focusing for defects <0.5λs. The proposed technique is shown to have the potential to improve the reliably detectable flaw size in guided wave inspection from 9% to less than 1% cross-sectional area loss.

  18. Efficient global wave propagation adapted to 3-D structural complexity: a pseudo-spectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-09-01

    We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridian equations, which is then solved by a 2-D spectral element method (SEM). Computational efficiency of such a hybrid method stems from lateral smoothness of 3-D Earth models and axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. We show novel benchmarks for global wave solutions in 3-D structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period ranging from 34s down to 11s. It turns out that our method has run up to two orders of magnitude faster than the 3-D SEM, featured by a computational advantage expanding with seismic frequency.

  19. Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition.

    PubMed Central

    Guarné, A; Tormo, J; Kirchweger, R; Pfistermueller, D; Fita, I; Skern, T

    1998-01-01

    The leader protease of foot-and-mouth disease virus, as well as cleaving itself from the nascent viral polyprotein, disables host cell protein synthesis by specific proteolysis of a cellular protein: the eukaryotic initiation factor 4G (eIF4G). The crystal structure of the leader protease presented here comprises a globular catalytic domain reminiscent of that of cysteine proteases of the papain superfamily, and a flexible C-terminal extension found intruding into the substrate-binding site of an adjacent molecule. Nevertheless, the relative disposition of this extension and the globular domain to each other supports intramolecular self-processing. The different sequences of the two substrates cleaved during viral replication, the viral polyprotein (at LysLeuLys/GlyAlaGly) and eIF4G (at AsnLeuGly/ArgThrThr), appear to be recognized by distinct features in a narrow, negatively charged groove traversing the active centre. The structure illustrates how the prototype papain fold has been adapted to the requirements of an RNA virus. Thus, the protein scaffold has been reduced to a minimum core domain, with the active site being modified to increase specificity. Furthermore, surface features have been developed which enable C-terminal self-processing from the viral polyprotein. PMID:9857201

  20. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations

    SciTech Connect

    Sun, Shengfang; Sono, Masanori; Wang, Chunxue; Du, Jing; Lebioda, Lukasz; Dawson, John H.

    2014-05-15

    Sea worm, Amphitrite ornata, has evolved its globin (an O2 carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O2 partition constant measurement method in this study, we have examined the effects of these structural factors on the O2 equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O2 affinity and increasing catalytic activity along with the increase in the distal His Nε–heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O2 affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O2 affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O2 carrier.

  1. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations.

    PubMed

    Sun, Shengfang; Sono, Masanori; Wang, Chunxue; Du, Jing; Lebioda, Lukasz; Dawson, John H

    2014-03-01

    Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O(2) partition constant measurement method in this study, we have examined the effects of these structural factors on the O(2) equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O(2) affinity and increasing catalytic activity along with the increase in the distal His N(ε)-heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O(2) affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O(2) affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O(2) carrier. PMID:24440609

  2. Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: II. AFLP analysis reflects human-aided local adaptation of a global pest species.

    PubMed

    Thaler, R; Brandstätter, A; Meraner, A; Chabicovski, M; Parson, W; Zelger, R; Dalla Via, J; Dallinger, R

    2008-09-01

    Originally resident in southeastern Europe, the codling moth (Cydia pomonella L.) (Tortricidae) has achieved a nearly global distribution, being one of the most successful pest insect species known today. As shown in our accompanying study, mitochondrial genetic markers suggest a Pleistocenic splitting of Cydia pomonella into two refugial clades which came into secondary contact after de-glaciation. The actual distribution pattern shows, however, that Central European codling moths have experienced a geographic splitting into many strains and locally adapted populations, which is not reflected by their mitochondrial haplotype distribution. We therefore have applied, in addition to mitochondrial markers, an approach with a higher resolution potential at the population level, based on the analysis of amplification fragment length polymorphisms (AFLPs). As shown in the present study, AFLP markers elucidate the genetic structure of codling moth strains and populations from different Central European apple orchard sites. While individual genetic diversity within codling moth strains and populations was small, a high degree of genetic differentiation was observed between the analyzed strains and populations, even at a small geographic scale. One of the main factors contributing to local differentiation may be limited gene flow among adjacent codling moth populations. In addition, microclimatic, ecological, and geographic constraints also may favour the splitting of Cydia pomonella into many local populations. Lastly, codling moths in Central European fruit orchards may experience considerable selective pressure due to pest control activities. As a consequence of all these selective forces, today in Central Europe we see a patchy distribution of many locally adapted codling moth populations, each of them having its own genetic fingerprint. Because of the complete absence of any correlation between insecticide resistance and geographic or genetic distances among

  3. Osmotic stress adaptation in Lactobacillus casei BL23 leads to structural changes in the cell wall polymer lipoteichoic acid.

    PubMed

    Palomino, Maria Mercedes; Allievi, Mariana C; Gründling, Angelika; Sanchez-Rivas, Carmen; Ruzal, Sandra M

    2013-11-01

    The probiotic Gram-positive bacterium Lactobacillus casei BL23 is naturally confronted with salt-stress habitats. It has been previously reported that growth in high-salt medium, containing 0.8 M NaCl, leads to modifications in the cell envelope of this bacterium. In this study, we report that L. casei BL23 has an increased ability to form biofilms and to bind cations in high-salt conditions. This behaviour correlated with modifications of surface properties involving teichoic acids, which are important cell wall components. We also showed that, in these high-salt conditions, L. casei BL23 produces less of the cell wall polymer lipoteichoic acid (LTA), and that this anionic polymer has a shorter mean chain length and a lower level of d-alanyl-substitution. Analysis of the transcript levels of the dltABCD operon, encoding the enzymes required for the incorporation of d-alanine into anionic polymers, showed a 16-fold reduction in mRNA levels, which is consistent with a decrease in d-alanine substitutions on LTA. Furthermore, a 13-fold reduction in the transcript levels was observed for the gene LCABL_09330 coding for a putative LTA synthase. To provide further experimental evidence that LCABL_09330 is a true LTA synthase (LtaS) in L. casei BL23, the enzymic domain was cloned and expressed in E. coli. The purified protein was able to hydrolyse the membrane lipid phosphatidylglycerol as expected for an LTA synthase enzyme, and hence LCABL_09330 was renamed LtaS. The purified enzyme showed Mn(2+)-ion dependent activity, and its activity was modulated by differences in NaCl concentration. The decrease in both ltaS transcript levels and enzyme activity observed in high-salt conditions might influence the length of the LTA backbone chain. A putative function of the modified LTA structure is discussed that is compatible with the growth under salt-stress conditions and with the overall envelope modifications taking place during this stress condition. PMID:24014660

  4. Adaptive Behaviour Assessment System: Indigenous Australian Adaptation Model (ABAS: IAAM)

    ERIC Educational Resources Information Center

    du Plessis, Santie

    2015-01-01

    The study objectives were to develop, trial and evaluate a cross-cultural adaptation of the Adaptive Behavior Assessment System-Second Edition Teacher Form (ABAS-II TF) ages 5-21 for use with Indigenous Australian students ages 5-14. This study introduced a multiphase mixed-method design with semi-structured and informal interviews, school…

  5. Adaptive Development

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The goal of this research is to develop and demonstrate innovative adaptive seal technologies that can lead to dramatic improvements in engine performance, life, range, and emissions, and enhance operability for next generation gas turbine engines. This work is concentrated on the development of self-adaptive clearance control systems for gas turbine engines. Researchers have targeted the high-pressure turbine (HPT) blade tip seal location for following reasons: Current active clearance control (ACC) systems (e.g., thermal case-cooling schemes) cannot respond to blade tip clearance changes due to mechanical, thermal, and aerodynamic loads. As such they are prone to wear due to the required tight running clearances during operation. Blade tip seal wear (increased clearances) reduces engine efficiency, performance, and service life. Adaptive sealing technology research has inherent impact on all envisioned 21st century propulsion systems (e.g. distributed vectored, hybrid and electric drive propulsion concepts).

  6. Insights into regional adaptations in the growing pulmonary artery using a meso-scale structural model: effects of ascending aorta impingement.

    PubMed

    Fata, Bahar; Zhang, Will; Amini, Rouzbeh; Sacks, Michael S

    2014-02-01

    As the next step in our investigations into the structural adaptations of the main pulmonary artery (PA) during postnatal growth, we utilized the extensive experimental measurements of the growing ovine PA from our previous study (Fata et al., 2013, "Estimated in vivo Postnatal Surface Growth Patterns of the Ovine Main Pulmonary Artery and Ascending Aorta," J. Biomech. Eng., 135(7), pp. 71010-71012). to develop a structural constitutive model for the PA wall tissue. Novel to the present approach was the treatment of the elastin network as a distributed fiber network rather than a continuum phase. We then utilized this model to delineate structure-function differences in the PA wall at the juvenile and adult stages. Overall, the predicted elastin moduli exhibited minor differences remained largely unchanged with age and region (in the range of 150 to 200 kPa). Similarly, the predicted collagen moduli ranged from ∼1,600 to 2700 kPa in the four regions studied in the juvenile state. Interestingly, we found for the medial region that the elastin and collagen fiber splay underwent opposite changes (collagen standard deviation juvenile = 17 deg to adult = 28 deg, elastin standard deviation juvenile = 35 deg to adult = 27 deg), along with a trend towards more rapid collagen fiber strain recruitment with age, along with a drop in collagen fiber moduli, which went from 2700 kPa for the juvenile stage to 746 kPa in the adult. These changes were likely due to the previously observed impingement of the relatively stiff ascending aorta on the growing PA medial region. Intuitively, the effects of the local impingement would be to lower the local wall stress, consistent with the observed parallel decrease in collagen modulus. These results suggest that during the postnatal somatic growth period local stresses can substantially modulate regional tissue microstructure and mechanical behaviors in the PA. We further underscore that our previous studies

  7. Insights into regional adaptations in the growing pulmonary artery using a meso-scale structural model: effects of ascending aorta impingement.

    PubMed

    Fata, Bahar; Zhang, Will; Amini, Rouzbeh; Sacks, Michael S

    2014-02-01

    As the next step in our investigations into the structural adaptations of the main pulmonary artery (PA) during postnatal growth, we utilized the extensive experimental measurements of the growing ovine PA from our previous study (Fata et al., 2013, "Estimated in vivo Postnatal Surface Growth Patterns of the Ovine Main Pulmonary Artery and Ascending Aorta," J. Biomech. Eng., 135(7), pp. 71010-71012). to develop a structural constitutive model for the PA wall tissue. Novel to the present approach was the treatment of the elastin network as a distributed fiber network rather than a continuum phase. We then utilized this model to delineate structure-function differences in the PA wall at the juvenile and adult stages. Overall, the predicted elastin moduli exhibited minor differences remained largely unchanged with age and region (in the range of 150 to 200 kPa). Similarly, the predicted collagen moduli ranged from ∼1,600 to 2700 kPa in the four regions studied in the juvenile state. Interestingly, we found for the medial region that the elastin and collagen fiber splay underwent opposite changes (collagen standard deviation juvenile = 17 deg to adult = 28 deg, elastin standard deviation juvenile = 35 deg to adult = 27 deg), along with a trend towards more rapid collagen fiber strain recruitment with age, along with a drop in collagen fiber moduli, which went from 2700 kPa for the juvenile stage to 746 kPa in the adult. These changes were likely due to the previously observed impingement of the relatively stiff ascending aorta on the growing PA medial region. Intuitively, the effects of the local impingement would be to lower the local wall stress, consistent with the observed parallel decrease in collagen modulus. These results suggest that during the postnatal somatic growth period local stresses can substantially modulate regional tissue microstructure and mechanical behaviors in the PA. We further underscore that our previous studies

  8. Flipping Adapters for Space Launch System

    NASA Video Gallery

    The structural test article adapter is flipped at Marshall testing facility Building 4705. The turnover is an important step in finishing the machining work on the adapter, which will undergo tests...

  9. Adaptation in Collaborative Governance Regimes

    NASA Astrophysics Data System (ADS)

    Emerson, Kirk; Gerlak, Andrea K.

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program.

  10. Adaptation in collaborative governance regimes.

    PubMed

    Emerson, Kirk; Gerlak, Andrea K

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program.

  11. Adaptive Thresholds

    SciTech Connect

    Bremer, P. -T.

    2014-08-26

    ADAPT is a topological analysis code that allow to compute local threshold, in particular relevance based thresholds for features defined in scalar fields. The initial target application is vortex detection but the software is more generally applicable to all threshold based feature definitions.

  12. Adaptation of methodology to select structural alternatives of one-way slab in residential building to the guidelines of the European Committee for Standardization (CEN/TC 350)

    SciTech Connect

    Fraile-Garcia, Esteban; Ferreiro-Cabello, Javier; Martinez-Camara, Eduardo; Jimenez-Macias, Emilio

    2015-11-15

    The European Committee for Standardization (CEN) through its Technical Committee CEN/TC-350 is developing a series of standards for assessing the building sustainability, at both product and building levels. The practical application of the selection (decision making) of structural alternatives made by one-way slabs leads to an intermediate level between the product and the building. Thus the present study addresses this problem of decision making, following the CEN guidelines and incorporating relevant aspects of architectural design into residential construction. A life cycle assessment (LCA) is developed in order to obtain valid information for the decision making process (the LCA was developed applying CML methodology although Ecoindicator99 was used in order to facilitate the comparison of the values); this information (the carbon footprint values) is contrasted with other databases and with the information from the Environmental Product Declaration (EPD) of one of the lightening materials (expanded polystyrene), in order to validate the results. Solutions of different column disposition and geometries are evaluated in the three pillars of sustainable construction on residential construction: social, economic and environmental. The quantitative analysis of the variables used in this study enables and facilitates an objective comparison in the design stage by a responsible technician; the application of the proposed methodology reduces the possible solutions to be evaluated by the expert to 12.22% of the options in the case of low values of the column index and to 26.67% for the highest values. - Highlights: • Methodology for selection of structural alternatives in buildings with one-way slabs • Adapted to CEN guidelines (CEN/TC-350) for assessing the building sustainability • LCA is developed in order to obtain valid information for the decision making process. • Results validated comparing carbon footprint, databases and Env. Product Declarations

  13. Adaptive EAGLE dynamic solution adaptation and grid quality enhancement

    NASA Technical Reports Server (NTRS)

    Luong, Phu Vinh; Thompson, J. F.; Gatlin, B.; Mastin, C. W.; Kim, H. J.

    1992-01-01

    In the effort described here, the elliptic grid generation procedure in the EAGLE grid code was separated from the main code into a subroutine, and a new subroutine which evaluates several grid quality measures at each grid point was added. The elliptic grid routine can now be called, either by a computational fluid dynamics (CFD) code to generate a new adaptive grid based on flow variables and quality measures through multiple adaptation, or by the EAGLE main code to generate a grid based on quality measure variables through static adaptation. Arrays of flow variables can be read into the EAGLE grid code for use in static adaptation as well. These major changes in the EAGLE adaptive grid system make it easier to convert any CFD code that operates on a block-structured grid (or single-block grid) into a multiple adaptive code.

  14. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny.

    PubMed

    Shaaf, Salar; Sharma, Rajiv; Baloch, Faheem Shehzad; Badaeva, Ekaterina D; Knüpffer, Helmut; Kilian, Benjamin; Özkan, Hakan

    2016-06-01

    Wheat belongs to the most important crops domesticated in the Fertile Crescent. In this region, fortunately, locally adapted wheat landraces are still present in farmers' fields. This material might be of immense value for future breeding programs. However, especially wheat germplasm adapted to the central part of the Fertile Crescent has been poorly characterized for allelic variation at key loci of agricultural importance. Grain hardness is an important trait influencing milling and baking quality of wheat. This trait is mainly determined by three tightly linked genes, namely, Puroindoline a (Pina), Puroindoline b (Pinb), and Grain softness protein-1 (Gsp-1), at the Hardness (Ha-D) locus on chromosome 5DS. To investigate genetic diversity and haplotype structure, we resequenced 96 diverse wheat lines at Pina-D1, Pinb-D1, Gsp-A1, Gsp-B1, and Gsp-D1. Three types of null alleles were identified using diagnostic primers: the first type was a multiple deletion of Pina-D1, Pinb-D1, and Gsp-D1 (Pina-D1k), the second was a Pina-D1 deletion (Pina-D1b); and the third type was a deletion of Gsp-D1, representing a novel null allele designated here as Gsp-D1k. Sequence analysis resulted in four allelic variants at Pinb-D1 and five at Gsp-A1, among them Gsp-A1-V was novel. Pina-D1, Gsp-B1 and Gsp-D1 sequences were monomorphic. Haplotype and phylogenetic analysis suggested that (1) bread wheat inherited its 5DS telomeric region probably from wild diploid Ae. tauschii subsp. tauschii found within an area from Transcaucasia to Caspian Iran; and that (2) the Ha-A and Ha-B homoeoloci were most closely related to sequences of wild tetraploid T. dicocco ides. This study provides a good overview of available genetic diversity at Pina-D1, Pinb-D1, and Gsp-1, which can be exploited to extend the range of grain texture traits in wheat. PMID:26898967

  15. Adaptive Behavior Assessment System-II Parent/Primary Caregiver Form: Ages 0-5--Its Factor Structure and Other Implications for Practice

    ERIC Educational Resources Information Center

    Oakland, Thomas; Algina, James

    2011-01-01

    A child's acquisition of adaptive behavior and skills may constitute his or her most important goal during infancy and early childhood. In addition, adaptive behavior data often are required when making decisions under Part C of the 2004 Individuals With Disabilities Education Improvement Act. This study reports the results of a factor analysis of…

  16. Toward reflexive climate adaptation research

    SciTech Connect

    Preston, Benjamin L.; Rickards, Lauren; Fünfgeld, Hartmut; Keenan, Rodney J.

    2015-06-22

    Climate adaptation research is expanding very quickly within an increasingly reflexive society where the relationship between academia and other social institutions is in a state of flux. Tensions exist between the two dominant research orientations of research about and research for adaptation. In particular, the research community is challenged to develop processes for successfully executing transdisciplinary research for adaptation when academic institutions and researchers are largely structured around traditional, disciplinary expertise and funding models. One tool for helping to manage this tension is a third, more reflexive, orientation toward adaptation research that is emerging in the literature. Finally, this new ‘research on adaptation research’ promises to help enhance understanding of the research enterprise itself and how it can become more adaptive.

  17. Toward reflexive climate adaptation research

    DOE PAGES

    Preston, Benjamin L.; Rickards, Lauren; Fünfgeld, Hartmut; Keenan, Rodney J.

    2015-06-22

    Climate adaptation research is expanding very quickly within an increasingly reflexive society where the relationship between academia and other social institutions is in a state of flux. Tensions exist between the two dominant research orientations of research about and research for adaptation. In particular, the research community is challenged to develop processes for successfully executing transdisciplinary research for adaptation when academic institutions and researchers are largely structured around traditional, disciplinary expertise and funding models. One tool for helping to manage this tension is a third, more reflexive, orientation toward adaptation research that is emerging in the literature. Finally, this newmore » ‘research on adaptation research’ promises to help enhance understanding of the research enterprise itself and how it can become more adaptive.« less

  18. Femoral bone structural geometry adapts to mechanical loading and is influenced by sex steroids: the Penn State Young Women's Health Study.

    PubMed

    Petit, Moira A; Beck, Thomas J; Lin, Hung-Mo; Bentley, Christy; Legro, Richard S; Lloyd, Tom

    2004-09-01

    .48). Results were similar for each geometric variable at the shaft site. These data suggest that bone adapts its bending strength primarily to mechanical loading (represented by lean mass and sports exercise score) and that sex steroids are associated with bone geometric structure.

  19. Connector adapter

    NASA Technical Reports Server (NTRS)

    Hacker, Scott C. (Inventor); Dean, Richard J. (Inventor); Burge, Scott W. (Inventor); Dartez, Toby W. (Inventor)

    2007-01-01

    An adapter for installing a connector to a terminal post, wherein the connector is attached to a cable, is presented. In an embodiment, the adapter is comprised of an elongated collet member having a longitudinal axis comprised of a first collet member end, a second collet member end, an outer collet member surface, and an inner collet member surface. The inner collet member surface at the first collet member end is used to engage the connector. The outer collet member surface at the first collet member end is tapered for a predetermined first length at a predetermined taper angle. The collet includes a longitudinal slot that extends along the longitudinal axis initiating at the first collet member end for a predetermined second length. The first collet member end is formed of a predetermined number of sections segregated by a predetermined number of channels and the longitudinal slot.

  20. Adaptive VFH

    NASA Astrophysics Data System (ADS)

    Odriozola, Iñigo; Lazkano, Elena; Sierra, Basi

    2011-10-01

    This paper investigates the improvement of the Vector Field Histogram (VFH) local planning algorithm for mobile robot systems. The Adaptive Vector Field Histogram (AVFH) algorithm has been developed to improve the effectiveness of the traditional VFH path planning algorithm overcoming the side effects of using static parameters. This new algorithm permits the adaptation of planning parameters for the different type of areas in an environment. Genetic Algorithms are used to fit the best VFH parameters to each type of sector and, afterwards, every section in the map is labelled with the sector-type which best represents it. The Player/Stage simulation platform has been chosen for making all sort of tests and to prove the new algorithm's adequateness. Even though there is still much work to be carried out, the developed algorithm showed good navigation properties and turned out to be softer and more effective than the traditional VFH algorithm.

  1. Adaptive sampler

    DOEpatents

    Watson, B.L.; Aeby, I.

    1980-08-26

    An adaptive data compression device for compressing data is described. The device has a frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  2. Adaptive sampler

    DOEpatents

    Watson, Bobby L.; Aeby, Ian

    1982-01-01

    An adaptive data compression device for compressing data having variable frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  3. Adaptive antennas

    NASA Astrophysics Data System (ADS)

    Barton, P.

    1987-04-01

    The basic principles of adaptive antennas are outlined in terms of the Wiener-Hopf expression for maximizing signal to noise ratio in an arbitrary noise environment; the analogy with generalized matched filter theory provides a useful aid to understanding. For many applications, there is insufficient information to achieve the above solution and thus non-optimum constrained null steering algorithms are also described, together with a summary of methods for preventing wanted signals being nulled by the adaptive system. The three generic approaches to adaptive weight control are discussed; correlation steepest descent, weight perturbation and direct solutions based on sample matrix conversion. The tradeoffs between hardware complexity and performance in terms of null depth and convergence rate are outlined. The sidelobe cancellor technique is described. Performance variation with jammer power and angular distribution is summarized and the key performance limitations identified. The configuration and performance characteristics of both multiple beam and phase scan array antennas are covered, with a brief discussion of performance factors.

  4. Adapting the McMaster-Ottawa scale and developing behavioral anchors for assessing performance in an interprofessional Team Observed Structured Clinical Encounter

    PubMed Central

    Lie, Désirée; May, Win; Richter-Lagha, Regina; Forest, Christopher; Banzali, Yvonne; Lohenry, Kevin

    2015-01-01

    Background Current scales for interprofessional team performance do not provide adequate behavioral anchors for performance evaluation. The Team Observed Structured Clinical Encounter (TOSCE) provides an opportunity to adapt and develop an existing scale for this purpose. We aimed to test the feasibility of using a retooled scale to rate performance in a standardized patient encounter and to assess faculty ability to accurately rate both individual students and teams. Methods The 9-point McMaster-Ottawa Scale developed for a TOSCE was converted to a 3-point scale with behavioral anchors. Students from four professions were trained a priori to perform in teams of four at three different levels as individuals and teams. Blinded faculty raters were trained to use the scale to evaluate individual and team performances. G-theory was used to analyze ability of faculty to accurately rate individual students and teams using the retooled scale. Results Sixteen faculty, in groups of four, rated four student teams, each participating in the same TOSCE station. Faculty expressed comfort rating up to four students in a team within a 35-min timeframe. Accuracy of faculty raters varied (38–81% individuals, 50–100% teams), with errors in the direction of over-rating individual, but not team performance. There was no consistent pattern of error for raters. Conclusion The TOSCE can be administered as an evaluation method for interprofessional teams. However, faculty demonstrate a ‘leniency error’ in rating students, even with prior training using behavioral anchors. To improve consistency, we recommend two trained faculty raters per station. PMID:26004993

  5. Globin's structure and function in vesicomyid bivalves from the Gulf of Guinea cold seeps as an adaptation to life in reduced sediments.

    PubMed

    Decker, C; Zorn, N; Potier, N; Leize-Wagner, E; Lallier, F H; Olu, K; Andersen, A C

    2014-01-01

    Vesicomyid bivalves form dense clam beds in both deep-sea cold seeps and hydrothermal vents. The species diversity within this family raises questions about niche separation and specific adaptations. To compare their abilities to withstand hypoxia, we have studied the structure and function of erythrocyte hemoglobin (Hb) and foot myoglobin (Mb) from two vesicomyid species, Christineconcha regab and Laubiericoncha chuni, collected from the Regab pockmark in the Gulf of Guinea at a depth of 3,000 m. Laubiericoncha chuni possesses three monomeric globins, G1 (15,361 Da), G2 (15,668 Da), and G3 (15,682 Da) in circulating erythrocytes (Hb), and also three globins, G1, G3, and G4 (14,786 Da) in foot muscle (Mb). Therefore, globins G2 and G4 appear to be specific for erythrocytes and muscle, respectively, but globins G1 and G3 are common. In contrast, C. regab lacks erythrocyte Hb completely and possesses only globin monomers G1' (14,941 Da), G2' (15,169 Da), and G3' (15,683 Da) in foot muscle. Thus, these two vesicomyid species, C. regab and L. chuni, show a remarkable diversity in globin expression when examined by electrospray ionization mass spectrometry. Oxygen-binding affinities reveal extremely high oxygen affinities (P50 < 1 Torr, from 5° to 15°C at pH 7.5), in particular L. chuni globins, which might be an advantage allowing L. chuni to dig deeply for sulfides and remain buried for long periods in reduced sediments.

  6. Impossible expectations: fMRI adaptation in the lateral occipital complex (LOC) is modulated by the statistical regularities of 3D structural information.

    PubMed

    Freud, Erez; Ganel, Tzvi; Avidan, Galia

    2015-11-15

    fMRI adaptation (fMRIa), the attenuation of fMRI signal which follows repeated presentation of a stimulus, is a well-documented phenomenon. Yet, the underlying neural mechanisms supporting this effect are not fully understood. Recently, short-term perceptual expectations, induced by specific experimental settings, were shown to play an important modulating role in fMRIa. Here we examined the role of long-term expectations, based on 3D structural statistical regularities, in the modulation of fMRIa. To this end, human participants underwent fMRI scanning while performing a same-different task on pairs of possible (regular, expected) objects and spatially impossible (irregular, unexpected) objects. We hypothesized that given the spatial irregularity of impossible objects in relation to real-world visual experience, the visual system would always generate a prediction which is biased to the possible version of the objects. Consistently, fMRIa effects in the lateral occipital cortex (LOC) were found for possible, but not for impossible objects. Additionally, in alternating trials the order of stimulus presentation modulated LOC activity. That is, reduced activation was observed in trials in which the impossible version of the object served as the prime object (i.e. first object) and was followed by the possible version compared to the reverse order. These results were also supported by the behavioral advantage observed for trials that were primed by possible objects. Together, these findings strongly emphasize the importance of perceptual expectations in object representation and provide novel evidence for the role of real-world statistical regularities in eliciting fMRIa.

  7. Comparative structure-toxicity relationship study of substituted benzenes to Tetrahymena pyriformis using shuffling-adaptive neuro fuzzy inference system and artificial neural networks.

    PubMed

    Jalali-Heravi, Mehdi; Kyani, Anahita

    2008-06-01

    The purpose of this study was to develop the structure-toxicity relationships for a large group of 268 substituted benzene to the ciliate Tetrahymena pyriformis using mechanistically interpretable descriptors. The shuffling-adaptive neuro fuzzy inference system (Shuffling-ANFIS) has been successfully applied to select the important factors affecting the toxicity of substituted benzenes to T. pyriformis. The results of the proposed model were compared with the model of linear-free energy response surface and also the principal component analysis Bayesian-regularized neural network (PCA-BRANN) trained using the same data. The presented model shows a better statistical parameter in comparison with the previous models. The results of the model are promising and descriptive. Five descriptors of octanol-water partition coefficient (logP), bond information content (BIC0), number of R-CX-R (C-026), eigenvalue sum from Z weighted distance matrix (SEigZ) and fragment based polar surface area (PSA) selected by Shuffling-ANFIS reveal the role of hydrophobicity, electronic and steric interactions in the mechanism of toxic action. Sequential zeroing of weights (SZW) as a sensitivity analysis method revealed that the hydrophobicity and electronic interactions play a major role in toxicity of these compounds. Satisfactory results (q(2)=0.828 and RMSE=0.348) in comparison with the previous works indicate that the Shuffling-ANFIS-ANN technique is able to model a diverse chemical class with more than one mechanism of toxicity by using simple and interpretable descriptors. Shuffling-ANFIS can be used as powerful feature selection technique, because its application in prediction of toxicity potency results in good statistical and interpretable physiochemical parameters. PMID:18499226

  8. Analyzing environmental and structural charactersitics of concrete for carbon mitigation and climate adaptation in urban areas: A case study in Rajkot, India

    NASA Astrophysics Data System (ADS)

    Solis, Andrea Valdez

    Increasing temperatures, varying rain events accompanied with flooding or droughts coupled with increasing water demands, and decreasing air quality are just some examples of stresses that urban systems face with the onset of climate change and rapid urbanization. Literature suggests that greenhouse gases are a leading cause of climate change and are of a result of anthropogenic activities such as infrastructure development. Infrastructure development is heavily dependent on the production of concrete. Yet, concrete can contribute up to 7% of total CO29 emissions globally from cement manufacturing alone. The goal of this dissertation was to evaluate current concrete technologies that could contribute to carbon mitigation and climate adaptation in cities. The objectives used to reach the goal of the study included (1) applying a material flow and life cycle analysis (MFA-LCA) to determine the environmental impacts of pervious and high volume fly ash (HVFA) concrete compared to ordinary portland cement (OPC) concrete in a developing country; (2) performing a comparative assessment of pervious concrete mixture designs for structural and environmental benefits across the U.S. and India; and (3) Determining structural and durability benefits from HVFA concrete mixtures when subjected to extreme hot weather conditions (a likely element of climate change). The study revealed that cities have a choice in reducing emissions, improving stormwater issues, and developing infrastructure that can sustain higher temperatures. Pervious and HVFA concrete mixtures reduce emissions by 21% and 47%, respectively, compared to OPC mixtures. A pervious concrete demonstration in Rajkot, India showed improvements in water quality (i.e. lower levels of nitrogen by as much as 68% from initial readings), and a reduction in material costs by 25%. HVFA and OPC concrete mixtures maintained compressive strengths above a design strength of 27.6 MPa (4000 psi), achieved low to moderate permeability

  9. [Cellular adaptation and cancerogenesis].

    PubMed

    La Torre, F; Silpigni, A; Tomasello, R; Picone, G S; La Torre, I; Aragona, M

    1998-06-01

    The paper describes the main adaptive mechanisms involved in the carcinogenic process. As a result of the action of carcinogenic agents (physical, chemical, biological), and in relation to the functional status of the affected cells, a number of systems are triggered off: detoxification and conjugation systems, the metabolisation of the said agents, DNA repairing enzymes, increased shock proteins (HSP), the induction of clonal proliferation. All these systems are valuable to the survival of the body and the species and culminate in the apoptosis of damaged cells as the last attempt at adaptation of a social kind for the good of the body. When these compensation mechanisms prove ineffective, imprecise or are exceeded by cell adaptive capacity, the resulting structural and functional alterations trigger off (induction) a very long process which often lasts between one and two thirds of the body's life, in various stages, multistep and multifactorial: this neoplastic transformation leads to a purposeless, egoistic, anarchic proliferation of cells which wish to survive at all costs, even to the detriment of the body of which they form part. Following the exhaustion of cell adaptive defences, there is an accumulation of additional genetic alterations (promotion and progression), the cells become manifestly neoplastic and continue their egoistic adaptation, according to the laws of natural selection: the cells which survive are those which adapt best to the hostile environment of the host's body, which are unaffected by proliferation control mechanisms (contact inhibition, differentiation factors, apoptosis, etc.), which make the best of the growth factors present in their microenvironment, which accomplish the so-called decathlon of the metastatization process, namely acquiring new capacities which can overcome the basal membrane, invade tissues to which they are attracted and continue to proliferate. Manifestly neoplastic cells become not self at a later stage

  10. Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus)

    PubMed Central

    Junge, C; Vøllestad, L A; Barson, N J; Haugen, T O; Otero, J; Sætre, G-P; Leder, E H; Primmer, C R

    2011-01-01

    Gene flow has the potential to both constrain and facilitate adaptation to local environmental conditions. The early stages of population divergence can be unstable because of fluctuating levels of gene flow. Investigating temporal variation in gene flow during the initial stages of population divergence can therefore provide insights to the role of gene flow in adaptive evolution. Since the recent colonization of Lake Lesjaskogsvatnet in Norway by European grayling (Thymallus thymallus), local populations have been established in over 20 tributaries. Multiple founder events appear to have resulted in reduced neutral variation. Nevertheless, there is evidence for local adaptation in early life-history traits to different temperature regimes. In this study, microsatellite data from almost a decade of sampling were assessed to infer population structuring and its temporal stability. Several alternative analyses indicated that spatial variation explained 2–3 times more of the divergence in the system than temporal variation. Over all samples and years, there was a significant correlation between genetic and geographic distance. However, decomposed pairwise regression analysis revealed differing patterns of genetic structure among local populations and indicated that migration outweighs genetic drift in the majority of populations. In addition, isolation by distance was observable in only three of the six years, and signals of population bottlenecks were observed in the majority of samples. Combined, the results suggest that habitat-specific adaptation in this system has preceded the development of consistent population substructuring in the face of high levels of gene flow from divergent environments. PMID:21224882

  11. Adaptive Dynamic Bayesian Networks

    SciTech Connect

    Ng, B M

    2007-10-26

    A discrete-time Markov process can be compactly modeled as a dynamic Bayesian network (DBN)--a graphical model with nodes representing random variables and directed edges indicating causality between variables. Each node has a probability distribution, conditional on the variables represented by the parent nodes. A DBN's graphical structure encodes fixed conditional dependencies between variables. But in real-world systems, conditional dependencies between variables may be unknown a priori or may vary over time. Model errors can result if the DBN fails to capture all possible interactions between variables. Thus, we explore the representational framework of adaptive DBNs, whose structure and parameters can change from one time step to the next: a distribution's parameters and its set of conditional variables are dynamic. This work builds on recent work in nonparametric Bayesian modeling, such as hierarchical Dirichlet processes, infinite-state hidden Markov networks and structured priors for Bayes net learning. In this paper, we will explain the motivation for our interest in adaptive DBNs, show how popular nonparametric methods are combined to formulate the foundations for adaptive DBNs, and present preliminary results.

  12. Telescope Adaptive Optics Code

    2005-07-28

    The Telescope AO Code has general adaptive optics capabilities plus specialized models for three telescopes with either adaptive optics or active optics systems. It has the capability to generate either single-layer or distributed Kolmogorov turbulence phase screens using the FFT. Missing low order spatial frequencies are added using the Karhunen-Loeve expansion. The phase structure curve is extremely dose to the theoreUcal. Secondly, it has the capability to simulate an adaptive optics control systems. The defaultmore » parameters are those of the Keck II adaptive optics system. Thirdly, it has a general wave optics capability to model the science camera halo due to scintillation from atmospheric turbulence and the telescope optics. Although this capability was implemented for the Gemini telescopes, the only default parameter specific to the Gemini telescopes is the primary mirror diameter. Finally, it has a model for the LSST active optics alignment strategy. This last model is highly specific to the LSST« less

  13. A fast tree-based method for estimating column densities in adaptive mesh refinement codes. Influence of UV radiation field on the structure of molecular clouds

    NASA Astrophysics Data System (ADS)

    Valdivia, Valeska; Hennebelle, Patrick

    2014-11-01

    Context. Ultraviolet radiation plays a crucial role in molecular clouds. Radiation and matter are tightly coupled and their interplay influences the physical and chemical properties of gas. In particular, modeling the radiation propagation requires calculating column densities, which can be numerically expensive in high-resolution multidimensional simulations. Aims: Developing fast methods for estimating column densities is mandatory if we are interested in the dynamical influence of the radiative transfer. In particular, we focus on the effect of the UV screening on the dynamics and on the statistical properties of molecular clouds. Methods: We have developed a tree-based method for a fast estimate of column densities, implemented in the adaptive mesh refinement code RAMSES. We performed numerical simulations using this method in order to analyze the influence of the screening on the clump formation. Results: We find that the accuracy for the extinction of the tree-based method is better than 10%, while the relative error for the column density can be much more. We describe the implementation of a method based on precalculating the geometrical terms that noticeably reduces the calculation time. To study the influence of the screening on the statistical properties of molecular clouds we present the probability distribution function of gas and the associated temperature per density bin and the mass spectra for different density thresholds. Conclusions: The tree-based method is fast and accurate enough to be used during numerical simulations since no communication is needed between CPUs when using a fully threaded tree. It is then suitable to parallel computing. We show that the screening for far UV radiation mainly affects the dense gas, thereby favoring low temperatures and affecting the fragmentation. We show that when we include the screening, more structures are formed with higher densities in comparison to the case that does not include this effect. We

  14. Identification of adaptive mutations in the influenza A virus non-structural 1 gene that increase cytoplasmic localization and differentially regulate host gene expression.

    PubMed

    Forbes, Nicole; Selman, Mohammed; Pelchat, Martin; Jia, Jian Jun; Stintzi, Alain; Brown, Earl G

    2013-01-01

    The NS1 protein of influenza A virus (IAV) is a multifunctional virulence factor. We have previously characterized gain-of-function mutations in the NS1 protein arising from the experimental adaptation of the human isolate A/Hong Kong/1/1968(H3N2) (HK) to the mouse. The majority of these mouse adapted NS1 mutations were demonstrated to increase virulence, viral fitness, and interferon antagonism, but differ in binding to the post-transcriptional processing factor cleavage and polyadenylation specificity factor 30 (CPSF30). Because nuclear trafficking is a major genetic determinant of influenza virus host adaptation, we assessed subcellular localization and host gene expression of NS1 adaptive mutations. Recombinant HK viruses with adaptive mutations in the NS1 gene were assessed for NS1 protein subcellular localization in mouse and human cells using confocal microscopy and cellular fractionation. In human cells the HK wild-type (HK-wt) virus NS1 protein partitioned equivalently between the cytoplasm and nucleus but was defective in cytoplasmic localization in mouse cells. Several adaptive mutations increased the proportion of NS1 in the cytoplasm of mouse cells with the greatest effects for mutations M106I and D125G. The host gene expression profile of the adaptive mutants was determined by microarray analysis of infected mouse cells to show either high or low extents of host-gene regulation (HGR or LGR) phenotypes. While host genes were predominantly down regulated for the HGR group of mutants (D2N, V23A, F103L, M106I+L98S, L98S, M106V, and M106V+M124I), the LGR phenotype mutants (D125G, M106I, V180A, V226I, and R227K) were characterized by a predominant up regulation of host genes. CPSF30 binding affinity of NS1 mutants did not predict effects on host gene expression. To our knowledge this is the first report of roles of adaptive NS1 mutations that impact intracellular localization and regulation of host gene expression.

  15. Rapid contrast gain reduction following motion adaptation.

    PubMed

    Nordström, Karin; Moyer de Miguel, Irene; O'Carroll, David C

    2011-12-01

    Neural and sensory systems adapt to prolonged stimulation to allow signaling across broader input ranges than otherwise possible with the limited bandwidth of single neurons and receptors. In the visual system, adaptation takes place at every stage of processing, from the photoreceptors that adapt to prevailing luminance conditions, to higher-order motion-sensitive neurons that adapt to prolonged exposure to motion. Recent experiments using dynamic, fluctuating visual stimuli indicate that adaptation operates on a time scale similar to that of the response itself. Further work from our own laboratory has highlighted the role for rapid motion adaptation in reliable encoding of natural image motion. Physiologically, motion adaptation can be broken down into four separate components. It is not clear from the previous studies which of these motion adaptation components are involved in the fast and dynamic response changes. To investigate the adapted response in more detail, we therefore analyzed the effect of motion adaptation using a test-adapt-test protocol with adapting durations ranging from 20 ms to 20 s. Our results underscore the very rapid rate of motion adaptation, suggesting that under free flight, visual motion-sensitive neurons continuously adapt to the changing scenery. This might help explain recent observations of strong invariance in the response to natural scenes with highly variable contrast and image structure.

  16. Bacterial surface adaptation

    NASA Astrophysics Data System (ADS)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  17. Adaptation of the Boundary Violations Scale Developed Based on Structural Family Therapy to the Turkish Context: A Study of Validity and Reliability

    ERIC Educational Resources Information Center

    Avci, Rasit; Çolakkadioglu, Oguzhan; Öz, Aysegül Sükran; Akbas, Turan

    2015-01-01

    The purpose of this study was to adapt "The Boundary Violations Scale" (Madden et al., 2002), which was created to measure the intergenerational boundary violations in families from the perspective of children, to Turkish and to test the validity and reliability of the Turkish version of this instrument. This instrument was developed…

  18. Adaptive Decision Aiding in Computer-Assisted Instruction: Adaptive Computerized Training System (ACTS).

    ERIC Educational Resources Information Center

    Hopf-Weichel, Rosemarie; And Others

    This report describes results of the first year of a three-year program to develop and evaluate a new Adaptive Computerized Training System (ACTS) for electronics maintenance training. (ACTS incorporates an adaptive computer program that learns the student's diagnostic and decision value structure, compares it to that of an expert, and adapts the…

  19. A double-loop structure in the adaptive generalized predictive control algorithm for control of robot end-point contact force.

    PubMed

    Wen, Shuhuan; Zhu, Jinghai; Li, Xiaoli; Chen, Shengyong

    2014-09-01

    Robot force control is an essential issue in robotic intelligence. There is much high uncertainty when robot end-effector contacts with the environment. Because of the environment stiffness effects on the system of the robot end-effector contact with environment, the adaptive generalized predictive control algorithm based on quantitative feedback theory is designed for robot end-point contact force system. The controller of the internal loop is designed on the foundation of QFT to control the uncertainty of the system. An adaptive GPC algorithm is used to design external loop controller to improve the performance and the robustness of the system. Two closed loops used in the design approach realize the system׳s performance and improve the robustness. The simulation results show that the algorithm of the robot end-effector contacting force control system is effective. PMID:24973336

  20. A double-loop structure in the adaptive generalized predictive control algorithm for control of robot end-point contact force.

    PubMed

    Wen, Shuhuan; Zhu, Jinghai; Li, Xiaoli; Chen, Shengyong

    2014-09-01

    Robot force control is an essential issue in robotic intelligence. There is much high uncertainty when robot end-effector contacts with the environment. Because of the environment stiffness effects on the system of the robot end-effector contact with environment, the adaptive generalized predictive control algorithm based on quantitative feedback theory is designed for robot end-point contact force system. The controller of the internal loop is designed on the foundation of QFT to control the uncertainty of the system. An adaptive GPC algorithm is used to design external loop controller to improve the performance and the robustness of the system. Two closed loops used in the design approach realize the system׳s performance and improve the robustness. The simulation results show that the algorithm of the robot end-effector contacting force control system is effective.

  1. AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 34th and AIAA/ASME Adaptive Structures Forum, La Jolla, CA, Apr. 19-22, 1993, Technical Papers. Pts. 1-6

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Topics addressed include the prediction of helicopter component loads using neural networks, spacecraft on-orbit coupled loads analysis, hypersonic flutter of a curved shallow panel with aerodynamic heating, thermal-acoustic fatigue of ceramic matrix composite materials, transition elements based on transfinite interpolation, damage progression in stiffened composite panels, a direct treatment of min-max dynamic response optimization problems, and sources of helicopter rotor hub inplane shears. Also discussed are dynamics of a layered elastic system, confidence bounds on structural reliability, mixed triangular space-time finite elements, advanced transparency development for USAF aircraft, a low-velocity impact on a graphite/PEEK, an automated mode-tracking strategy, transonic flutter suppression by a passive flap, a nonlinear response of composite panels to random excitation, an optimal placement of elastic supports on a simply supported plate, a probabilistic assessment of composite structures, a model for mode I failure of laminated composites, a residual flexibility approach to multibody dynamics,and multilayer piezoelectric actuators.

  2. AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 34th and AIAA/ASME Adaptive Structures Forum, La Jolla, CA, Apr. 19-22, 1993, Technical Papers. Pts. 1-6

    NASA Astrophysics Data System (ADS)

    Topics addressed include the prediction of helicopter component loads using neural networks, spacecraft on-orbit coupled loads analysis, hypersonic flutter of a curved shallow panel with aerodynamic heating, thermal-acoustic fatigue of ceramic matrix composite materials, transition elements based on transfinite interpolation, damage progression in stiffened composite panels, a direct treatment of min-max dynamic response optimization problems, and sources of helicopter rotor hub inplane shears. Also discussed are dynamics of a layered elastic system, confidence bounds on structural reliability, mixed triangular space-time finite elements, advanced transparency development for USAF aircraft, a low-velocity impact on a graphite/PEEK, an automated mode-tracking strategy, transonic flutter suppression by a passive flap, a nonlinear response of composite panels to random excitation, an optimal placement of elastic supports on a simply supported plate, a probabilistic assessment of composite structures, a model for mode I failure of laminated composites, a residual flexibility approach to multibody dynamics,and multilayer piezoelectric actuators.

  3. ADAPTATION AND ADAPTABILITY, THE BELLEFAIRE FOLLOWUP STUDY.

    ERIC Educational Resources Information Center

    ALLERHAND, MELVIN E.; AND OTHERS

    A RESEARCH TEAM STUDIED INFLUENCES, ADAPTATION, AND ADAPTABILITY IN 50 POORLY ADAPTING BOYS AT BELLEFAIRE, A REGIONAL CHILD CARE CENTER FOR EMOTIONALLY DISTURBED CHILDREN. THE TEAM ATTEMPTED TO GAUGE THE SUCCESS OF THE RESIDENTIAL TREATMENT CENTER IN TERMS OF THE PSYCHOLOGICAL PATTERNS AND ROLE PERFORMANCES OF THE BOYS DURING INDIVIDUAL CASEWORK…

  4. Adaptation to delayed auditory feedback

    NASA Technical Reports Server (NTRS)

    Katz, D. I.; Lackner, J. R.

    1977-01-01

    Delayed auditory feedback disrupts the production of speech, causing an increase in speech duration as well as many articulatory errors. To determine whether prolonged exposure to delayed auditory feedback (DAF) leads to adaptive compensations in speech production, 10 subjects were exposed in separate experimental sessions to both incremental and constant-delay exposure conditions. Significant adaptation occurred for syntactically structured stimuli in the form of increased speaking rates. After DAF was removed, aftereffects were apparent for all stimulus types in terms of increased speech rates. A carry-over effect from the first to the second experimental session was evident as long as 29 days after the first session. The use of strategies to overcome DAF and the differences between adaptation to DAF and adaptation to visual rearrangement are discussed.

  5. Alteration of the Physical and Chemical Structure of the Primary Cell Wall of Growth-Limited Plant Cells Adapted to Osmotic Stress 1

    PubMed Central

    Iraki, Naim M.; Bressan, Ray A.; Hasegawa, P. M.; Carpita, Nicholas C.

    1989-01-01

    Cells of tobacco (Nicotiana tabacum L.) adapted to grow in severe osmotic stress of 428 millimolar NaCl (−23 bar) or 30% polyethylene glycol 8000 (−28 bar) exhibit a drastically altered growth physiology that results in slower cell expansion and fully expanded cells with volumes only one-fifth to one-eighth those of unadapted cells. This reduced cell volume occurs despite maintenance of turgor pressures sometimes severalfold higher than those of unadapted cells. This report and others (NM Iraki et al [1989] Plant Physiol 90: 000-000 and 000-000) document physical and biochemical alterations of the cell walls which might explain how adapted cells decrease the ability of the wall to expand despite diversion of carbon used for osmotic adjustment away from synthesis of cell wall polysaccharides. Tensile strength measured by a gas decompression technique showed empirically that walls of NaCl-adapted cells are much weaker than those of unadapted cells. Correlated with this weakening was a substantial decrease in the proportion of crystalline cellulose in the primary cell wall. Even though the amount of insoluble protein associated with the wall was increased relative to other wall components, the amount of hydroxyproline in the insoluble protein of the wall was only about 10% that of unadapted cells. These results indicate that a cellulosic-extensin framework is a primary determinant of absolute wall tensile strength, but complete formation of this framework apparently is sacrificed to divert carbon to substances needed for osmotic adjustment. We propose that the absolute mass of this framework is not a principal determinant of the ability of the cell wall to extend. PMID:16667031

  6. Adaptive Image Denoising by Mixture Adaptation

    NASA Astrophysics Data System (ADS)

    Luo, Enming; Chan, Stanley H.; Nguyen, Truong Q.

    2016-10-01

    We propose an adaptive learning procedure to learn patch-based image priors for image denoising. The new algorithm, called the Expectation-Maximization (EM) adaptation, takes a generic prior learned from a generic external database and adapts it to the noisy image to generate a specific prior. Different from existing methods that combine internal and external statistics in ad-hoc ways, the proposed algorithm is rigorously derived from a Bayesian hyper-prior perspective. There are two contributions of this paper: First, we provide full derivation of the EM adaptation algorithm and demonstrate methods to improve the computational complexity. Second, in the absence of the latent clean image, we show how EM adaptation can be modified based on pre-filtering. Experimental results show that the proposed adaptation algorithm yields consistently better denoising results than the one without adaptation and is superior to several state-of-the-art algorithms.

  7. Parallel Adaptive Mesh Refinement Library

    NASA Technical Reports Server (NTRS)

    Mac-Neice, Peter; Olson, Kevin

    2005-01-01

    Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.

  8. Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae.

    PubMed

    Nagler, Christina; Haug, Joachim T

    2016-01-01

    Parasites significantly influence food webs and ecosystems and occur all over the world in almost every animal group. Within crustaceans there are numerous examples of ectoparasites; for example, representatives of the isopod group Cymothoidae. These obligatory parasitic isopods are relatively poorly studied regarding their functional morphology. Here we present new details of the morphological adaptations to parasitism of the cymothoiid ingroup Nerocila with up-to-date imaging methods (macro photography, stereo imaging, fluorescence photography, micro CT, and histology). Central aspects of the study were (1) the morphology of the mouthparts and (2) the attachment on the host, hence the morphology of the thoracopods. The mouthparts (labrum, mandibles, paragnaths, maxillulae, maxillae, maxillipeds) form a distinct mouth cone and are most likely used for true sucking. The mouthparts are tightly "folded" around each other and provide functional rails for the only two moving mouthparts, mandible and maxillula. Both are not moving in an ancestral-type median-lateral movement, but are strongly tilted to move more in a proximal-distal axis. New details concerning the attachment demonstrate that the angular arrangement of the thoracopods is differentiated to impede removal by the host. The increased understanding of morphological adaptation to parasitism of modern forms will be useful in identifying disarticulated (not attached to the host) fossil parasites. PMID:27441121

  9. Functional morphology of parasitic isopods: understanding morphological adaptations of attachment and feeding structures in Nerocila as a pre-requisite for reconstructing the evolution of Cymothoidae

    PubMed Central

    Haug, Joachim T.

    2016-01-01

    Parasites significantly influence food webs and ecosystems and occur all over the world in almost every animal group. Within crustaceans there are numerous examples of ectoparasites; for example, representatives of the isopod group Cymothoidae. These obligatory parasitic isopods are relatively poorly studied regarding their functional morphology. Here we present new details of the morphological adaptations to parasitism of the cymothoiid ingroup Nerocila with up-to-date imaging methods (macro photography, stereo imaging, fluorescence photography, micro CT, and histology). Central aspects of the study were (1) the morphology of the mouthparts and (2) the attachment on the host, hence the morphology of the thoracopods. The mouthparts (labrum, mandibles, paragnaths, maxillulae, maxillae, maxillipeds) form a distinct mouth cone and are most likely used for true sucking. The mouthparts are tightly “folded” around each other and provide functional rails for the only two moving mouthparts, mandible and maxillula. Both are not moving in an ancestral-type median-lateral movement, but are strongly tilted to move more in a proximal-distal axis. New details concerning the attachment demonstrate that the angular arrangement of the thoracopods is differentiated to impede removal by the host. The increased understanding of morphological adaptation to parasitism of modern forms will be useful in identifying disarticulated (not attached to the host) fossil parasites. PMID:27441121

  10. Making Pedagogical Adaptability Less Obvious

    ERIC Educational Resources Information Center

    Vagle, Mark D.

    2016-01-01

    In this article, I try to make pedagogical adaptability a bit less obvious. In particular, I use some post-structural philosophical ideas and some concepts at the intersections of social class and race to re-interpret Dylan Wiliam's conception of formative assessment. I suggest that this interpretation can provide opportunities to resist the urge…

  11. Flight Test Approach to Adaptive Control Research

    NASA Technical Reports Server (NTRS)

    Pavlock, Kate Maureen; Less, James L.; Larson, David Nils

    2011-01-01

    The National Aeronautics and Space Administration s Dryden Flight Research Center completed flight testing of adaptive controls research on a full-scale F-18 testbed. The validation of adaptive controls has the potential to enhance safety in the presence of adverse conditions such as structural damage or control surface failures. This paper describes the research interface architecture, risk mitigations, flight test approach and lessons learned of adaptive controls research.

  12. A comparison of the structures of lean and rich axisymmetric laminar Bunsen flames: application of local rectangular refinement solution-adaptive gridding

    NASA Astrophysics Data System (ADS)

    Bennett, Beth Anne V.; Fielding, Joseph; Mauro, Richard J.; Long, Marshall B.; Smooke, Mitchell D.

    1999-12-01

    Axisymmetric laminar methane-air Bunsen flames are computed for two equivalence ratios: lean (icons/Journals/Common/Phi" ALT="Phi" ALIGN="TOP"/> = 0.776), in which the traditional Bunsen cone forms above the burner; and rich (icons/Journals/Common/Phi" ALT="Phi" ALIGN="TOP"/> = 1.243), in which the premixed Bunsen cone is accompanied by a diffusion flame halo located further downstream. Because the extremely large gradients at premixed flame fronts greatly exceed those in diffusion flames, their resolution requires a more sophisticated adaptive numerical method than those ordinarily applied to diffusion flames. The local rectangular refinement (LRR) solution-adaptive gridding method produces robust unstructured rectangular grids, utilizes multiple-scale finite-difference discretizations, and incorporates Newton's method to solve elliptic partial differential equation systems simultaneously. The LRR method is applied to the vorticity-velocity formulation of the fully elliptic governing equations, in conjunction with detailed chemistry, multicomponent transport and an optically-thin radiation model. The computed lean flame is lifted above the burner, and this liftoff is verified experimentally. For both lean and rich flames, grid spacing greatly influences the Bunsen cone's position, which only stabilizes with adequate refinement. In the rich configuration, the oxygen-free region above the Bunsen cone inhibits the complete decay of CH4, thus indirectly initiating the diffusion flame halo where CO oxidizes to CO2. In general, the results computed by the LRR method agree quite well with those obtained on equivalently refined conventional grids, yet the former require less than half the computational resources.

  13. Human Maternal Brain Plasticity: Adaptation to Parenting

    ERIC Educational Resources Information Center

    Kim, Pilyoung

    2016-01-01

    New mothers undergo dynamic neural changes that support positive adaptation to parenting and the development of mother-infant relationships. In this article, I review important psychological adaptations that mothers experience during pregnancy and the early postpartum period. I then review evidence of structural and functional plasticity in human…

  14. Visual Cues for an Adaptive Expert System.

    ERIC Educational Resources Information Center

    Miller, Helen B.

    NCR (National Cash Register) Corporation is pursuing opportunities to make their point of sale (POS) terminals easy to use and easy to learn. To approach the goal of making the technology invisible to the user, NCR has developed an adaptive expert prototype system for a department store POS operation. The structure for the adaptive system, the…

  15. Post-natal molecular adaptations in anteromedial and posterolateral bundles of the ovine anterior cruciate ligament: one structure with two parts or two distinct ligaments?

    PubMed

    Huebner, Kyla D; O'Brien, Etienne J O; Heard, Bryan J; Chung, May; Achari, Yamini; Shrive, Nigel G; Frank, Cyril B

    2012-01-01

    The human anterior cruciate ligament (ACL) is a composite structure of two anatomically distinct bundles: an anteromedial (AM) and posterolateral (PL) bundles. Tendons are often used as autografts for surgical reconstruction of ACL following severe injury. However, despite successful surgical reconstruction, some people experience re-rupture and later development of osteoarthritis. Understanding the structure and molecular makeup of normal ACL is essential for its optimal replacement. Reportedly the two bundles display different tensions throughout joint motion and may be fundamentally different. This study assessed the similarities and differences in ultrastructure and molecular composition of the AM and PL bundles to test the hypothesis that the two bundles of the ACL develop unique characteristics with maturation. ACLs from nine mature and six immature sheep were compared. The bundles were examined for mRNA and protein levels of collagen types I, III, V, and VI, and two proteoglycans. The fibril diameter composition of the two bundles was examined with transmission electron microscopy. Maturation does alter the molecular and structural composition of the two bundles of ACL. Although the PL band appears to mature slower than the AM band, no significant differences were detected between the bundles in the mature animals. We thus reject our hypothesis that the two ACL bundles are distinct. The two anatomically distinct bundles of the sheep ACL can be considered as two parts of one structure at maturity and material that would result in a structure of similar functionality can be used to replace each ACL bundle in the sheep.

  16. New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit

    PubMed Central

    Chaurasia, Priyanka; Pratap, Shivendra; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2016-01-01

    Thus far, all solved structures of pilin-proteins comprising sortase-assembled pili are from pathogenic genera and species. Here, we present the first crystal structure of a pilin subunit (SpaA) from a non-pathogen host (Lactobacillus rhamnosus GG). SpaA consists of two tandem CnaB-type domains, each with an isopeptide bond and E-box motif. Intriguingly, while the isopeptide bond in the N-terminal domain forms between lysine and asparagine, the one in the C-terminal domain atypically involves aspartate. We also solved crystal structures of mutant proteins where residues implicated in forming isopeptide bonds were replaced. Expectedly, the E-box-substituted E139A mutant lacks an isopeptide bond in the N-terminal domain. However, the C-terminal E269A substitution gave two structures; one of both domains with their isopeptide bonds present, and another of only the N-terminal domain, but with an unformed isopeptide bond and significant conformational changes. This latter crystal structure has never been observed for any other Gram-positive pilin. Notably, the C-terminal isopeptide bond still forms in D295N-substituted SpaA, irrespective of E269 being present or absent. Although E-box mutations affect SpaA proteolytic and thermal stability, a cumulative effect perturbing normal pilus polymerization was unobserved. A model showing the polymerized arrangement of SpaA within the SpaCBA pilus is proposed. PMID:27349405

  17. Structures of Mycobacterium tuberculosis DosR and DosR-DNA Complex Involved in Gene Activation during Adaptation to Hypoxic Latency

    SciTech Connect

    Wisedchaisri, Goragot; Wu, Meiting; Rice, Adrian E; Roberts, David M; Sherman, David R; Hol, Wim G.J.

    2010-07-20

    On encountering low oxygen conditions, DosR activates the transcription of 47 genes, promoting long-term survival of Mycobacterium tuberculosis in a non-replicating state. Here, we report the crystal structures of the DosR C-terminal domain and its complex with a consensus DNA sequence of the hypoxia-induced gene promoter. The DosR C-terminal domain contains four {alpha}-helices and forms tetramers consisting of two dimers with non-intersecting dyads. In the DNA-bound structure, each DosR C-terminal domain in a dimer places its DNA-binding helix deep into the major groove, causing two bends in the DNA. DosR makes numerous protein-DNA base contacts using only three amino acid residues per subunit: Lys179, Lys182, and Asn183. The DosR tetramer is unique among response regulators with known structures.

  18. Expressing Adaptation Strategies Using Adaptation Patterns

    ERIC Educational Resources Information Center

    Zemirline, N.; Bourda, Y.; Reynaud, C.

    2012-01-01

    Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

  19. Structuralism.

    ERIC Educational Resources Information Center

    Piaget, Jean

    Provided is an overview of the analytical method known as structuralism. The first chapter discusses the three key components of the concept of a structure: the view of a system as a whole instead of so many parts; the study of the transformations in the system; and the fact that these transformations never lead beyond the system but always…

  20. Criticality of Adaptive Control Dynamics

    NASA Astrophysics Data System (ADS)

    Patzelt, Felix; Pawelzik, Klaus

    2011-12-01

    We show, that stabilization of a dynamical system can annihilate observable information about its structure. This mechanism induces critical points as attractors in locally adaptive control. It also reveals, that previously reported criticality in simple controllers is caused by adaptation and not by other controller details. We apply these results to a real-system example: human balancing behavior. A model of predictive adaptive closed-loop control subject to some realistic constraints is introduced and shown to reproduce experimental observations in unprecedented detail. Our results suggests, that observed error distributions in between the Lévy and Gaussian regimes may reflect a nearly optimal compromise between the elimination of random local trends and rare large errors.