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Sample records for adaptive zero-tree structure

  1. Adaptive zero-tree structure for curved wavelet image coding

    NASA Astrophysics Data System (ADS)

    Zhang, Liang; Wang, Demin; Vincent, André

    2006-02-01

    We investigate the issue of efficient data organization and representation of the curved wavelet coefficients [curved wavelet transform (WT)]. We present an adaptive zero-tree structure that exploits the cross-subband similarity of the curved wavelet transform. In the embedded zero-tree wavelet (EZW) and the set partitioning in hierarchical trees (SPIHT), the parent-child relationship is defined in such a way that a parent has four children, restricted to a square of 2×2 pixels, the parent-child relationship in the adaptive zero-tree structure varies according to the curves along which the curved WT is performed. Five child patterns were determined based on different combinations of curve orientation. A new image coder was then developed based on this adaptive zero-tree structure and the set-partitioning technique. Experimental results using synthetic and natural images showed the effectiveness of the proposed adaptive zero-tree structure for encoding of the curved wavelet coefficients. The coding gain of the proposed coder can be up to 1.2 dB in terms of peak SNR (PSNR) compared to the SPIHT coder. Subjective evaluation shows that the proposed coder preserves lines and edges better than the SPIHT coder.

  2. Myoelectric signal compression using zero-trees of wavelet coefficients.

    PubMed

    Norris, Jason A; Englehart, Kevin B; Lovely, Dennis F

    2003-11-01

    Recent progress in the diagnostic use of the myoelectric signal for neuromuscular diseases, coupled with increasing interests in telemedicine applications, mandate the need for an effective compression technique. The efficacy of the embedded zero-tree wavelet compression algorithm is examined with respect to some important analysis parameters (the length of the analysis segment and wavelet type) and measurement conditions (muscle type and contraction type). It is shown that compression performance improves with segment length, and that good choices of wavelet type include the Meyer wavelet and the fifth order biorthogonal wavelet. The effects of different muscle sites and contraction types on compression performance are less conclusive.A comparison of a number of lossy compression techniques has revealed that the EZW algorithm exhibits superior performance to a hard thresholding wavelet approach, but falls short of adaptive differential pulse code modulation. The bit prioritization capability of the EZW algorithm allows one to specify the compression factor online, making it an appealing technique for streaming data applications, as often encountered in telemedicine.

  3. Steady-State and Dynamic Myoelectric Signal Compression Using Embedded Zero-Tree Wavelets

    DTIC Science & Technology

    2001-10-25

    MES compression. This research investigates static and dynamic MES compression using the embedded zero- tree wavelet ( EZW ) compression algorithm and...compression using a modified version of Shapiro’s [5] embedded zero-tree wavelet ( EZW ) compression algorithm. This research investigates static...and transient MES compression using the EZW compression algorithm and compares its performance to a standard wavelet compression technique. For

  4. 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…

  5. Adaptive building skin structures

    NASA Astrophysics Data System (ADS)

    Del Grosso, A. E.; Basso, P.

    2010-12-01

    The concept of adaptive and morphing structures has gained considerable attention in the recent years in many fields of engineering. In civil engineering very few practical applications are reported to date however. Non-conventional structural concepts like deployable, inflatable and morphing structures may indeed provide innovative solutions to some of the problems that the construction industry is being called to face. To give some examples, searches for low-energy consumption or even energy-harvesting green buildings are amongst such problems. This paper first presents a review of the above problems and technologies, which shows how the solution to these problems requires a multidisciplinary approach, involving the integration of architectural and engineering disciplines. The discussion continues with the presentation of a possible application of two adaptive and dynamically morphing structures which are proposed for the realization of an acoustic envelope. The core of the two applications is the use of a novel optimization process which leads the search for optimal solutions by means of an evolutionary technique while the compatibility of the resulting configurations of the adaptive envelope is ensured by the virtual force density method.

  6. 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.

  7. 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.

  8. Adaptive structures to enable ground test validation of precision structures

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.; Fanson, James F.; Chen, Gun-Shing; Kuo, Chin-Po

    1990-01-01

    The use of analytical models and ground-based experimental validation of precision space structures is addressed. The application of adaptive structures to such validation of precision space structures is addressed, with the focus on adaptive truss structures.

  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. Adaptive structures - Test hardware and experimental results

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.; Fanson, James L.; Chen, Gun-Shing; Kuo, Chin-Po

    1990-01-01

    The facilities and procedures used at JPL to test adaptive structures such as the large deployable reflector (LDR) are described and preliminary results are reported. The applications of adaptive structures in future NASA missions are outlined, and the techniques which are employed to modify damping, stiffness, and isolation characteristics, as well as geometric changes, are listed. The development of adaptive structures is shown to be effective as a result of new actuators and sensors, and examples are listed for categories such as fiber optics, shape-memory materials, piezoelectrics, and electrorheological fluids. Some ground test results are described for laboratory truss structures and truss test beds, which are shown to be efficient and easy to assemble in space. Adaptive structures are shown to be important for precision space structures such as the LDR, and can alleviate ground test requirements.

  11. Adaptive structures for deployment/construction of structures in space

    NASA Technical Reports Server (NTRS)

    Wada, Ben K.; Utku, Senol

    1992-01-01

    The application of adaptive structures to the structural design of space structures is examined with attention given to facilitating their construction in space and enhancing reliability. A modified approach based on traditional techniques is presented which incorporates the loads analysis by Wada (1979) and the application of adaptive structures to control structural motion. An analytical technique is described for the deployment/construction of the structure in which each step of the assembly sequence is analyzed. The use of adaptive structures is shown to permit the static adjustment of the structure after assembly in its operational environment. The concepts presented to incorporate adaptive structures in the deployment of large space structures are expected to improve the reliability and reduce the cost of the total systems.

  12. Adaptive Control Of Large Vibrating, Rotating Structures

    NASA Technical Reports Server (NTRS)

    Bayard, David S.

    1991-01-01

    Globally convergent theoretical method provides for adaptive set-point control of orientation of, along with suppression of the vibrations of, large structure. Method utilizes inherent passivity properties of structure to attain mathematical condition essential to adaptive convergence on commanded set point. Maintains stability and convergence in presence of errors in mathematical model of dynamics of structure and actuators. Developed for controlling attitudes of large, somewhat flexible spacecraft, also useful in such terrestrial applications as controlling movable bridges or suppressing earthquake vibrations in bridges, buildings, and other large structures.

  13. A modular approach to adaptive structures.

    PubMed

    Pagitz, Markus; Pagitz, Manuel; Hühne, Christian

    2014-10-07

    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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Adaptive Control Techniques for Large Space Structures.

    DTIC Science & Technology

    1986-09-15

    Adaptive Systems: A Ji . Fixed-Point Analysis", submitted, IEEE Trans. on Circuits and Systems; Special Issue on Adaptive Systems, Sept. 1987. I.M.Y...Shaped Cost Functionals: Extensions of LQG Methods," *.. AIAA J. of Guidance and Control, pp. 529-535, Nov-Dec. 1980. [81 C.A. Desoer , R.W. Liu, J. Murray...for Parameter Conver- gence in Adaptive Control," Memo No. UCB/ERL M84/25, Univ. of California, Berke- ley, 1984. [19] C.A. Desoer and M. Vidyasagar

  19. Adaptive Control Techniques for Large Space Structures

    DTIC Science & Technology

    1989-01-06

    Point Analy- sis", submitted, IEEE Trans. on Circuits and Systems; Special Issue on Adaptive Systems, Sept. 1987. I.M.Y. Mareels, R.R. Bitmead, M. Gevers...adaptive system with unmodelled dynamics," Proc. IFAC Workshop on Adaptive Systems, San Francisco, CA. C.A. Desoer , R.W. Liu, J. Murray and R. Sacks...June 1980. C.A. Desoer and M. Vidyasagar, Feedback Systems: Input-Output Properties, Academic Press, * 1975. J.C. Doyle and G. Stein (1981

  20. 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.

  1. Flexilevel Adaptive Testing Paradigm: Hierarchical Concept Structures.

    DTIC Science & Technology

    1977-07-01

    items . In reference to the psychometric outcomes, Table 3 presents the mean item difficulties by subtest plus a Kuder - Richardson reliability index. A...leas~: 50percent of the subject population , an adaptive Kuder - Richardson index was calculated . This was found to be r = . 701 for Block II test and r...whole correlations between adaptive test and total test scores (r ’s = .95). Descriptive test indices and test reliabilities were also essentially

  2. Kinematics and computation of workspace for adaptive geometry structures

    NASA Astrophysics Data System (ADS)

    Pourki, Forouza; Sosa, Horacio

    1993-09-01

    A new feature in the design of smart structures is the capability of the structure to respond autonomously to undesirable phenomena and environment. This capability is often synonymous to the requirement that the structure should assume a set of different geometric shapes or adapt to a set of kinematic constraints to accomplish a maneuver. Systems with these characteristics have been referred to as `shape adaptive' or `variable geometry' structures. The present paper introduces a basis for the kinematics and work space studies of statically deterministic truss structures which are shape adaptive. The difference between these structures and the traditional truss structures, which are merely built to support the weight and may be modelled by finite element methods, is the fact that these variable geometry structures allow for large (and nonlinear) deformations. On the other hand, these structures unlike structures composed of well investigated `four bar mechanisms,' are statically deterministic.

  3. 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.

  4. Adaptive Control Techniques for Large Space Structures

    DTIC Science & Technology

    1987-12-23

    2500 Mizssion. CoV~ege Boulevard Sar-ta Clara, Califorr-Iia 950541-1215 P--epared for: AFOSR, O irectcorate of Aerospace Sciences Bolling Air Force...formulated in late 1982 in re- sponse to the increasing concern that performance robustness of Air Force LSS type system would be inadequate to meet...Reducing the effects of on-board disturbance rejection) is particularly important for planned Air Force missions. For these cases, adaptive control

  5. Rapid adaptation in visual cortex to the structure of images.

    PubMed

    Müller, J R; Metha, A B; Krauskopf, J; Lennie, P

    1999-08-27

    Complex cells in striate cortex of macaque showed a rapid pattern-specific adaptation. Adaptation made cells more sensitive to orientation change near the adapting orientation. It reduced correlations among the responses of populations of cells, thereby increasing the information transmitted by each action potential. These changes were brought about by brief exposures to stationary patterns, on the time scale of a single fixation. Thus, if successive fixations expose neurons' receptive fields to images with similar but not identical structure, adaptation will remove correlations and improve discriminability.

  6. Control of sound radiation with active/adaptive structures

    NASA Technical Reports Server (NTRS)

    Fuller, C. R.; Rogers, C. A.; Robertshaw, H. H.

    1992-01-01

    Recent research is discussed in the area of active structural acoustic control with active/adaptive structures. Progress in the areas of structural acoustics, actuators, sensors, and control approaches is presented. Considerable effort has been given to the interaction of these areas with each other due to the coupled nature of the problem. A discussion is presented on actuators bonded to or embedded in the structure itself. The actuators discussed are piezoceramic actuators and shape memory alloy actuators. The sensors discussed are optical fiber sensors, Nitinol fiber sensors, piezoceramics, and polyvinylidene fluoride sensors. The active control techniques considered are state feedback control techniques and least mean square adaptive algorithms. Results presented show that significant progress has been made towards controlling structurally radiated noise by active/adaptive means applied directly to the structure.

  7. 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.

  8. Adaptive neuro-control for large flexible structures

    NASA Astrophysics Data System (ADS)

    Krishna Kumar, K.; Montgomery, L.

    1992-12-01

    Special problems related to control system design for large flexible structures include the inherent low damping, wide range of modal frequencies, unmodeled dynamics, and possibility of system failures. Neuro-control, which combines concepts from artificial neural networks and adaptive control is investigated as a solution to some of these problems. Specifically, the roles of neutro-controllers in learning unmodeled dynamics and adaptive control for system failures are investigated. The neuro-controller synthesis procedure and its capabilities in adaptively controlling the structure are demonstrated using a mathematical model of an existing structure, the advanced control evaluation for systems test article located at NASA/Marshall Space Flight Center. Also, the real-time adaptive capability of neuro-controllers is demonstrated via an experiment utilizing a flexible clamped-free beam equipped with an actuator that uses a bang-bang controller.

  9. 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.

  10. 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.

  11. Adaptive Origami for Efficiently Folded Structures

    DTIC Science & Technology

    2016-02-01

    4 3.2 Design of 2D-to- 3D Actuating Mechanisms...printing, lithography) to convert surface patterns on substrates into stable 3D objects. The design and fabrication of structures based on folding...Nafion, where prescribed 3D geometric information can be encoded as a spatially patterned composite of discrete shape-memory and locked-shape-memory

  12. 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.

  13. Adaptive neuro-control for large flexible structures

    NASA Astrophysics Data System (ADS)

    Krishankumar, K.; Montgomery, L.

    Special problems related to control system design for large flexible structures include the inherent low structural damping, wide range of modal frequencies, unmodeled dynamics, and possibility of system failures. Neuro-control, which combines concepts from artificial neural networks and adaptive control is investigated as a solution to some of these problems. Specifically, the roles of neuro-controllers in learning unmodeled dynamics and adaptive control for system failures are investigated. Satisfying these objectives requires training a neural network model (neuro-model) to simulate the actual structure, and then training a neural network controller (neuro-controller) to minimize structural response resulting from an arbitrary disturbance. The neuro-controller synthesis procedure and its capabilities in adaptively controlling the structure are demonstrated using a mathematical model of an existing structure, the Advanced Control Evaluation for Systems test article located at NASA/Marshall Space Flight Center, Huntsville, Alabama. Also, the real-time adaptive capability of neuro-controllers is demonstrated via an experiment utilizing a flexible clamped-free beam equipped with an actuator that uses a bang-bang controller.

  14. Residual mode filters and adaptive control in large space structures

    NASA Technical Reports Server (NTRS)

    Davidson, Roger A.; Balas, Mark J.

    1989-01-01

    One of the most difficult problems in controlling large systems and structures is compensating for the destructive interaction which can occur between the reduced-order model (ROM) of the plant, which is used by the controller, and the unmodeled dynamics of the plant, often called the residual modes. The problem is more significant in the case of large space structures because their naturally light damping and high performance requirements lead to more frequent, destructive residual mode interaction (RMI). Using the design/compensation technique of residual mode filters (RMF's), effective compensation of RMI can be accomplished in a straightforward manner when using linear controllers. The use of RMF's has been shown to be effective for a variety of large structures, including a space-based laser and infinite dimensional systems. However, the dynamics of space structures is often uncertain and may even change over time due to on-orbit erosion from space debris and corrosive chemicals in the upper atmosphere. In this case, adaptive control can be extremely beneficial in meeting the performance requirements of the structure. Adaptive control for large structures is also based on ROM's and so destructive RMI may occur. Unfortunately, adaptive control is inherently nonlinear, and therefore the known results of RMF's cannot be applied. The purpose is to present the results of new research showing the effects of RMI when using adaptive control and the work which will hopefully lead to RMF compensation of this problem.

  15. 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.

  16. 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.

  17. Computerized Adaptive Testing with Multiple-Form Structures

    ERIC Educational Resources Information Center

    Armstrong, Ronald D.; Jones, Douglas H.; Koppel, Nicole B.; Pashley, Peter J.

    2004-01-01

    A multiple-form structure (MFS) is an ordered collection or network of testlets (i.e., sets of items). An examinee's progression through the network of testlets is dictated by the correctness of an examinee's answers, thereby adapting the test to his or her trait level. The collection of paths through the network yields the set of all possible…

  18. 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…

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Adaptive state estimation for control of flexible structures

    NASA Technical Reports Server (NTRS)

    Chen, Chung-Wen; Huang, Jen-Kuang

    1990-01-01

    This paper proposes a new approach of obtaining adaptive state estimation of a system in the presence of unknown system disturbances and measurement noise. In the beginning, a non-optimal Kalman filter with arbitrary initial guess for the process and measurement noises is implemented. At the same time, an adaptive transversal predictor (ATP) based on the recursive least-squares (RLS) algorithm is used to yield optimal one- to p- step-ahead output predictions using the previous input/output data. Referring to these optimal predictions the Kalman filter gain is updated and the performance of the state estimation is thus improved. If forgetting factor is implemented in the recursive least-squares algorithm, this method is also capable of dealing with the situation when the noise statistics are slowly time-varying. This feature makes this new approach especially suitable for the control of flexible structures. A numerical example demonstrates the feasibility of this real time adaptive state estimation method.

  6. 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.

  7. 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.

  8. Morphology operators construction by adaptive elliptical structuring elements based on nonlinear structure tensor

    NASA Astrophysics Data System (ADS)

    Tang, Chunming; Liu, Xinlei; Li, Yanjie; Zhao, Hongbo

    2017-01-01

    As the linear structure tensor is tending to inaccurately or even wrong estimate the gradient direction of a gray-level image, we present a novel algorithm to construct adaptive elliptical structuring elements via estimating the local anisotropy of an image based on the nonlinear structure tensor. Erosion, dilation, opening, closing and Hit-or-Miss transform are redefined according to the presented structuring elements, which have been applied to some representative images. The processed results and the quantitative analysis show that the novel morphological operators have more advantages in structure adaptation, corner protection, filtering and targets extraction than the others.

  9. Structural adaptations to diverse fighting styles in sexually selected weapons

    PubMed Central

    McCullough, Erin L.; Tobalske, Bret W.; Emlen, Douglas J.

    2014-01-01

    The shapes of sexually selected weapons differ widely among species, but the drivers of this diversity remain poorly understood. Existing explanations suggest weapon shapes reflect structural adaptations to different fighting styles, yet explicit tests of this hypothesis are lacking. We constructed finite element models of the horns of different rhinoceros beetle species to test whether functional specializations for increased performance under species-specific fighting styles could have contributed to the diversification of weapon form. We find that horns are both stronger and stiffer in response to species-typical fighting loads and that they perform more poorly under atypical fighting loads, which suggests weapons are structurally adapted to meet the functional demands of fighting. Our research establishes a critical link between weapon form and function, revealing one way male–male competition can drive the diversification of animal weapons. PMID:25201949

  10. Adaptivity demonstration of inflatable rigidized integrated structures (IRIS)

    NASA Astrophysics Data System (ADS)

    Natori, M. C.; Higuchi, Ken; Sekine, Koji; Okazaki, Kakuma

    1995-10-01

    An inflatable rigidized integrated structure (IRIS), which is composed of membrane elements and cable networks, and whose structural accuracy is decided by mainly cable networks, has various design adaptivity, since it is a high performance deployable structure for future space applications. In order to keep some stiffness after deployment, materials of membrane are assumed to be rigidized in space, and sometimes the cable network is also rigidized. The concept can cover various structural elements and structure systems. The accuracy analysis of reflector surface constrained by inside hard points and the manufacturing of a simple reflector model is introduced. Test results of rigidized cable columns to show many variations of IRIS to be feasible are also reported.

  11. 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.

  12. Load-Adapted Design of Generative Manufactured Lattice Structures

    NASA Astrophysics Data System (ADS)

    Reinhart, Gunther; Teufelhart, Stefan

    Additive layer manufacturing offers many opportunities for the production of lightweight components, because of the high geometrical freedom that can be realized in comparison to conventional manufacturing processes. This potential gets demonstrated at the example of a bending beam. Therefore, a topology optimization is performed as well as the use of periodically arranged lattice structures. The latter ones show the constraint, that shear forces in the struts reduce the stiffness of the lattice. To avoid this, the structure has to be adapted to the flux of force. This thesis is supported by studies on a torqueloaded shaft.

  13. Experimental studies of adaptive structures for precision performance

    NASA Technical Reports Server (NTRS)

    Chen, G.-S.; Lurie, B. J.; Wada, B. K.

    1989-01-01

    An experimental study was made of the adaptive structure concept. Experimental data were obtained for a three-longeron, thirteen-bay truss-type test structure. This test structure can be softly suspended as well as rigidly clamped at the central bay. The load-carrying active member consists of a stack of concentric piezoelectric wafers, an eddy current displacement sensor, and a strain gage force sensor. A bridge (or compound) feedback technique developed in communication engineering is applied to the problem of active damping augmentation in adaptive structures. Using collocated force and velocity feedback around the active member, a desired output mechanical impedance can be implemented to maximize energy absorption by the active members. In addition, large gains can be implemented to linearize the active member's nonlinear behavior. Good agreements with linear finite element analysis was found for both static and dynamic structural responses. An 11 percent damping in the first bending mode was demonstrated in the closed-loop damping experiment.

  14. 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.

  15. 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.

  16. 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.

  17. Residual vibration suppression of flexible arms using ER adaptive structures

    NASA Astrophysics Data System (ADS)

    Wei, Kexiang; Meng, Guang; Tang, Huanqing; Liu, Yingchun

    2007-07-01

    In the past decades, there have been a number of research activities to control unwanted vibration of flexible robot arms. The electrorheological (ER) adaptive structures, which behave as viscoelastic damping structures with controllable shear modulus, are used to suppress the residual vibrations of the rotating flexible arm in this study. The flexible arm is designed as an ER sandwich structures, in which ER fluids is sandwiched between two elastic surface layers. Experimental tests are conducted. The vibration response performances of the beam subjected to different electric field intensity and motion conditions are demonstrated and evaluated. The experimental results obtained indicate that significant vibration attenuation is achieved at different operating conditions by applying an electric field to the rotating flexible arm.

  18. Narcissistic Personality Inventory: structure of the adapted Dutch version.

    PubMed

    Barelds, Dick P H; Dijkstra, Pieternel

    2010-04-01

    The present study examined the structure of a Dutch adaptation of the 40-item Narcissistic Personality Inventory (Raskin & Terry, 1988) in a community sample (n = 460) and a student sample (n = 515). Altering the response format of the NPI to a Likert-scale had no apparent effect on the responses. Confirmatory factor analyses supported neither the four-factor structure reported by Emmons (1984), nor the seven-factor structure reported by Raskin and Terry (1988). Instead, exploratory factor analyses supported either a single-factor solution (general narcissism), or a two-factor solution (Authority/Power and Self-Admiration). The validity of the NPI was supported by its relations with sex, age, personality, self-esteem, shame, guilt and social desirability.

  19. 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.

  20. 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.

  1. Rapid Structured Volume Grid Smoothing and Adaption Technique

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.

    2004-01-01

    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 reduction 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.

  2. The Electronically Steerable Flash Lidar Adaptability for Characterizing Forest Structure

    NASA Astrophysics Data System (ADS)

    Ramond, T.; Weimer, C. S.; Lefsky, M. A.; Ruppert, L.; Donley, B.; Delker, T.; Applegate, J.

    2010-12-01

    The Electronically Steerable Flash Lidar (ESFL) instrument developed at Ball Aerospace is one that provides unprecedented flexibility to adapt to the scene of the moment. For probing the structure of forests, ESFL provides several features that can be changed shot-to-shot, enabling real time adaptability. The number of beams transmitted to the scene can vary. The spacing of the beams can be changed from a contiguous configuration suited to probing smaller scale forest structure to a sparse configuration to sample larger scale variations over the maximum possible swath. Variation of the oscillator rate can provide multiple range sampling resolutions. Data will be presented illustrating these capabilities during flight from a Twin Otter aircraft. The poster will discuss how this instrument could be used to design studies intended to quantify exactly what is the minimum sampling structure needed to measure a given scientific parameter with the desired accuracy. Such a result could allow for maximum efficiency of precious observation time in the world of remote sensing from airplane or from space.

  3. 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.

  4. Adaptive and learning control of large space structures

    NASA Technical Reports Server (NTRS)

    Montgomery, R. C.; Thau, F. J.

    1980-01-01

    The paper describes the adaptive learning system for space operations which assumes that structural testing can be conducted during deployment and assembly. Simulation results using the solar electric propulsion array and a novel remote sensor are presented; they involve faster scan television coverage of the motions of the array from four cameras on the corners of the Space Shuttle payload bay. The description of the simulation, the filtering algorithm for processing the TV data, the parameter extraction algorithm, and the simulation results are presented.

  5. Novel pathogenetic mechanisms and structural adaptations in ischemic mitral regurgitation.

    PubMed

    Silbiger, Jeffrey J

    2013-10-01

    Ischemic mitral regurgitation (MR) is a common complication of myocardial infarction thought to result from leaflet tethering caused by displacement of the papillary muscles that occurs as the left ventricle remodels. The author explores the possibility that left atrial remodeling may also play a role in the pathogenesis of ischemic MR, through a novel mechanism: atriogenic leaflet tethering. When ischemic MR is hemodynamically significant, the left ventricle compensates by dilating to preserve forward output using the Starling mechanism. Left ventricular dilatation, however, worsens MR by increasing the mitral valve regurgitant orifice, leading to a vicious cycle in which MR begets more MR. The author proposes that several structural adaptations play a role in reducing ischemic MR. In contrast to the compensatory effects of left ventricular enlargement, these may reduce, rather than increase, its severity. The suggested adaptations involve the mitral valve leaflets, the papillary muscles, the mitral annulus, and the left ventricular false tendons. This review describes the potential role each may play in reducing ischemic MR. Therapies that exploit these adaptations are also discussed.

  6. 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

  7. Multivariable feedback active structural acoustic control using adaptive piezoelectric sensoriactuators.

    PubMed

    Vipperman, J S; Clark, R L

    1999-01-01

    An experimental implementation of a multivariable feedback active structural acoustic control system is demonstrated on a piezostructure plate with pinned boundary conditions. Four adaptive piezoelectric sensoriactuators provide an array of truly colocated actuator/sensor pairs to be used as control transducers. Radiation filters are developed based on the self- and mutual-radiation efficiencies of the structure and are included into the performance cost of an H2 control law which minimizes total radiated sound power. In the cost function, control effort is balanced with reductions in radiated sound power. A similarity transform which produces generalized velocity states that are required as inputs to the radiation filters is presented. Up to 15 dB of attenuation in radiated sound power was observed at the resonant frequencies of the piezostructure.

  8. Algorithms and data structures for adaptive multigrid elliptic solvers

    NASA Technical Reports Server (NTRS)

    Vanrosendale, J.

    1983-01-01

    Adaptive refinement and the complicated data structures required to support it are discussed. These data structures must be carefully tuned, especially in three dimensions where the time and storage requirements of algorithms are crucial. Another major issue is grid generation. The options available seem to be curvilinear fitted grids, constructed on iterative graphics systems, and unfitted Cartesian grids, which can be constructed automatically. On several grounds, including storage requirements, the second option seems preferrable for the well behaved scalar elliptic problems considered here. A variety of techniques for treatment of boundary conditions on such grids are reviewed. A new approach, which may overcome some of the difficulties encountered with previous approaches, is also presented.

  9. 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.

  10. 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.

  11. 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.

  12. Hyperspectral image compression: adapting SPIHT and EZW to anisotropic 3-D wavelet coding.

    PubMed

    Christophe, Emmanuel; Mailhes, Corinne; Duhamel, Pierre

    2008-12-01

    Hyperspectral images present some specific characteristics that should be used by an efficient compression system. In compression, wavelets have shown a good adaptability to a wide range of data, while being of reasonable complexity. Some wavelet-based compression algorithms have been successfully used for some hyperspectral space missions. This paper focuses on the optimization of a full wavelet compression system for hyperspectral images. Each step of the compression algorithm is studied and optimized. First, an algorithm to find the optimal 3-D wavelet decomposition in a rate-distortion sense is defined. Then, it is shown that a specific fixed decomposition has almost the same performance, while being more useful in terms of complexity issues. It is shown that this decomposition significantly improves the classical isotropic decomposition. One of the most useful properties of this fixed decomposition is that it allows the use of zero tree algorithms. Various tree structures, creating a relationship between coefficients, are compared. Two efficient compression methods based on zerotree coding (EZW and SPIHT) are adapted on this near-optimal decomposition with the best tree structure found. Performances are compared with the adaptation of JPEG 2000 for hyperspectral images on six different areas presenting different statistical properties.

  13. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    PubMed

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  14. Cloud Structures on Neptune Observed with Keck Telescope Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Max, C. E.; Macintosh, B. A.; Gibbard, S. G.; Gavel, D. T.; Roe, H. G.; de Pater, I.; Ghez, A. M.; Acton, D. S.; Lai, O.; Stomski, P.; Wizinowich, P. L.

    2003-01-01

    We report on observations obtained with the adaptive optics system at the 10 m Keck II Telescope during engineering validation and early science observing time for the adaptive optics system. We observed Neptune at near-infrared wavelengths. Angular resolution was 0.05"-0.06", corresponding to a spatial scale of approximately 1000 km at Neptune. We discuss the latitudinal structure of circumferential cloud bands and of compact infrared-bright features seen in the southern hemisphere, as well as their variation with wavelength. We determine the values of I/F (proportional to the ratio of reflected intensity to incident solar flux) in the J and H infrared-wavelength bands, including narrowband filters where there is strong methane absorption. We use the I/F values inside and outside of methane bands to estimate the altitude of clouds responsible for the brightest compact features in the infrared. Our data show that, on two of our four observing dates, the brightest region on Neptune contained highly reflective haze layers located below the tropopause but not deeper than a few bars.

  15. A simulated force generator with an adaptive command structure

    NASA Astrophysics Data System (ADS)

    Hanes, P. Jeff

    2006-05-01

    The Force Laydown Automated Generator (FLAG) is a script-driven behavior model that automatically creates military formations from the platoon level up to division level for use in simulations built on the FLAMES simulation framework. The script allows users to define formation command structure, command relationships, vehicle type and equipment, and behaviors. We have used it to automatically generate more than 3000 units in a single simulation. Currently, FLAG is used in the Air Force Research Laboratory Munitions Directorate (AFRL/MN) to assist their Comprehensive Analysis Process (CAP). It produces a reasonable threat laydown of red forces for testing their blue concept weapons. Our success in the application of FLAG leads us to believe that it offers an invaluable potential for use in training environments and other applications that need a large number of reactive, adaptive forces - red or blue.

  16. 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.

  17. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  18. 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.

  19. 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.

  20. A novel tree structure based watermarking algorithm

    NASA Astrophysics Data System (ADS)

    Lin, Qiwei; Feng, Gui

    2008-03-01

    In this paper, we propose a new blind watermarking algorithm for images which is based on tree structure. The algorithm embeds the watermark in wavelet transform domain, and the embedding positions are determined by significant coefficients wavelets tree(SCWT) structure, which has the same idea with the embedded zero-tree wavelet (EZW) compression technique. According to EZW concepts, we obtain coefficients that are related to each other by a tree structure. This relationship among the wavelet coefficients allows our technique to embed more watermark data. If the watermarked image is attacked such that the set of significant coefficients is changed, the tree structure allows the correlation-based watermark detector to recover synchronously. The algorithm also uses a visual adaptive scheme to insert the watermark to minimize watermark perceptibility. In addition to the watermark, a template is inserted into the watermarked image at the same time. The template contains synchronization information, allowing the detector to determine the geometric transformations type applied to the watermarked image. Experimental results show that the proposed watermarking algorithm is robust against most signal processing attacks, such as JPEG compression, median filtering, sharpening and rotating. And it is also an adaptive method which shows a good performance to find the best areas to insert a stronger watermark.

  1. Exploring the Structure of Adaptive Behavior: Project Report Number 87-1.

    ERIC Educational Resources Information Center

    Bruininks, Robert H.; McGrew, Kevin

    This report presents results from three research studies that were designed to explore both the definition and the structure of the adaptive behavior construct. The first study investigated the structure of adaptive behavior as a function of age, developmental level, and type of handicap through an exploratory factor analysis of both the…

  2. 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.

  3. 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

  4. 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.

  5. Top-down determinants of niche structure and adaptation among African Acacias.

    PubMed

    Staver, A Carla; Bond, William J; Cramer, Michael D; Wakeling, Julia L

    2012-07-01

    The role of top-down factors like herbivory and fire in structuring species' niches, even in disturbance-dependent biomes like savanna, remains poorly understood. Interactions between herbivory and fire may set up a potential tradeoff axis, along which unique adaptations contribute to structuring communities and determining species distributions. We examine the role of herbivory and fire in structuring distributions of Acacia saplings in Hluhluwe iMfolozi Park in South Africa, and the relationship of species' niche structure to traits that help them survive herbivory or fire. Results suggest that (1) fire and herbivory form a single trade-off axis, (2) Acacia sapling distributions are constrained by fire and herbivory, and (3) Acacia saplings have adaptations that are structured by the tradeoff axis. Herbivory-adapted species tend to have 'cage'-like architecture, thicker bark, and less starch storage, while fire-adapted species tend to have 'pole'-like architecture, relatively thinner bark, and more starch storage.

  6. Adaptability in Crisis Management: The Role of Organizational Structure

    DTIC Science & Technology

    2013-06-01

    and hindrance stress : Relationships with exhaustion, motivation to learn, and learning performance. Journal of Applied Psychology , 89, 883-891...The notion of EOs is not new. Indeed, in organizational psychology and management sciences very similar concepts – for example, empowered self...role and implications of adaptability in relation to other aspects of teamwork and team effectiveness, for instance team cognition (e.g., shared

  7. Adaptive Techniques for Control of Large Space Structures.

    DTIC Science & Technology

    1984-12-01

    S1 a ) remais oiniall teruine the robt imss propertie% of adaptive stable. 1 hts. h\\ iheoi-cin 2. an) -regionl of local algorithms Ni oreose, . input...that Vg¢R ev + .[Hev(Jw)] 4 y and 1 He(iw) + Hey • ’I (4.8a) Then, bounds on lei 2 and 1o. can be obtained from: le-e~2 1 112*2 l~ 2 ’eo 12 [ie.* 2

  8. 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.

  9. Adaptation paths to novel motor tasks are shaped by prior structure learning.

    PubMed

    Kobak, Dmitry; Mehring, Carsten

    2012-07-18

    After extensive practice with motor tasks sharing structural similarities (e.g., different dancing movements, or different sword techniques), new tasks of the same type can be learned faster. According to the recent "structure learning" hypothesis (Braun et al., 2009a), such rapid generalization of related motor skills relies on learning the dynamic and kinematic relationships shared by this set of skills. As a consequence, motor adaptation becomes constrained, effectively leading to a dimensionality reduction of the learning problem; at the same time, adaptation to tasks lying outside the structure becomes biased toward the structure. We tested these predictions by investigating how previously learned structures influence subsequent motor adaptation. Human subjects were making reaching movements in 3D virtual reality, experiencing perturbations either in the vertical or in the horizontal plane. Perturbations were either visuomotor rotations of varying angle or velocity-dependent forces of varying strength. We found that, after extensive training with both kinematic or dynamic perturbations, adaptation to unpracticed, diagonal, perturbations happened along the previously learned structure (vertical or horizontal), and resulting adaptation trajectories were curved. This effect is robust, can be observed on the single-subject level, and occurs during adaptation both within and across trials. Additionally, we demonstrate that structure learning changes involuntary visuomotor reflexes and therefore is not exclusively a high-level cognitive phenomenon.

  10. Fundamental Advances in Inverse Mechanics Towards Self-Aware and Intrinsically Adaptable Structural Systems

    DTIC Science & Technology

    2014-11-30

    AFRL-OSR-VA-TR-2015-0007 FUNDAMENTAL ADVANCES IN INVERSE MECHANICS TOWARDS SELF-AWARE JOHN BRIGHAM UNIVERSITY OF PITTSBURGH Final Report 12/04/2014...TITLE AND SUBTITLE Fundamental Advances in Inverse Mechanics Towards Self-Aware and Intrinsically Adaptable Structural Systems 5a. CONTRACT NUMBER...methods for solving inverse problems related to smart morphable structures that can evaluate their current environment and then adapt accordingly to

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

    PubMed

    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.

  12. 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

  13. A hierarchical structure for automatic meshing and adaptive FEM analysis

    NASA Technical Reports Server (NTRS)

    Kela, Ajay; Saxena, Mukul; Perucchio, Renato

    1987-01-01

    A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.

  14. Application of adaptive trusses to vibration isolation in flexible structures

    NASA Technical Reports Server (NTRS)

    Clark, William W.; Robertshaw, Harry H.

    1992-01-01

    It is shown through analysis that force feedback can be used to provide complete vibration isolation in two directions. Simultations were carried out to demonstrate the use of two control methods applied to an adaptive truss as an active mount. The first technique was simple force feedback with a gain. This method has the potential to provide excellent vibration isolation performance. It requires no model of the system and no knowledge of the applied disturbance, and is easily implemented in an adaptive truss. There is some question as to how high the gain can be allowed to go but the experimental results have shown performance advantages over passive techniques even for small gains. The second technique presented is the LQR method, with disturbance modeling. A method is presented for using the LQR method for vibration isolation with the intention of achieving performance with guaranteed stability and relatively lower loop gains. The overhead for those benefits is an accurate system model. It was shown analytically that this method works; however, the performance is not as good as expected. It is believed that the difference in performance is partly due to an increase in active damping which is inadvertently provided by the LQR method.

  15. Adaptive Neural Control for Space Structure Vibration Suppression.

    DTIC Science & Technology

    1996-08-01

    Hierarchy of Modular Nebular Structures Progressing from Basic Constituents to Higher-Level Modules...Systems Replicator Networks Dynamic Ganglia & Toeplitz Synapses Individual Neurons Figure 2-2: Hierarchy of Modular Nebular Structures Progressing from...significant portion of the low frequency drift was traced to the round-off problems with ARMA replicators discovered in ANC 10. Our next hypothesis was

  16. A conforming to interface structured adaptive mesh refinement technique for modeling fracture problems

    NASA Astrophysics Data System (ADS)

    Soghrati, Soheil; Xiao, Fei; Nagarajan, Anand

    2016-12-01

    A Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) technique is introduced for the automated transformation of a structured grid into a conforming mesh with appropriate element aspect ratios. The CISAMR algorithm is composed of three main phases: (i) Structured Adaptive Mesh Refinement (SAMR) of the background grid; (ii) r-adaptivity of the nodes of elements cut by the crack; (iii) sub-triangulation of the elements deformed during the r-adaptivity process and those with hanging nodes generated during the SAMR process. The required considerations for the treatment of crack tips and branching cracks are also discussed in this manuscript. Regardless of the complexity of the problem geometry and without using iterative smoothing or optimization techniques, CISAMR ensures that aspect ratios of conforming elements are lower than three. Multiple numerical examples are presented to demonstrate the application of CISAMR for modeling linear elastic fracture problems with intricate morphologies.

  17. A conforming to interface structured adaptive mesh refinement technique for modeling fracture problems

    NASA Astrophysics Data System (ADS)

    Soghrati, Soheil; Xiao, Fei; Nagarajan, Anand

    2017-04-01

    A Conforming to Interface Structured Adaptive Mesh Refinement (CISAMR) technique is introduced for the automated transformation of a structured grid into a conforming mesh with appropriate element aspect ratios. The CISAMR algorithm is composed of three main phases: (i) Structured Adaptive Mesh Refinement (SAMR) of the background grid; (ii) r-adaptivity of the nodes of elements cut by the crack; (iii) sub-triangulation of the elements deformed during the r-adaptivity process and those with hanging nodes generated during the SAMR process. The required considerations for the treatment of crack tips and branching cracks are also discussed in this manuscript. Regardless of the complexity of the problem geometry and without using iterative smoothing or optimization techniques, CISAMR ensures that aspect ratios of conforming elements are lower than three. Multiple numerical examples are presented to demonstrate the application of CISAMR for modeling linear elastic fracture problems with intricate morphologies.

  18. 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.

  19. Structured estimation - Sample size reduction for adaptive pattern classification

    NASA Technical Reports Server (NTRS)

    Morgera, S.; Cooper, D. B.

    1977-01-01

    The Gaussian two-category classification problem with known category mean value vectors and identical but unknown category covariance matrices is considered. The weight vector depends on the unknown common covariance matrix, so the procedure is to estimate the covariance matrix in order to obtain an estimate of the optimum weight vector. The measure of performance for the adapted classifier is the output signal-to-interference noise ratio (SIR). A simple approximation for the expected SIR is gained by using the general sample covariance matrix estimator; this performance is both signal and true covariance matrix independent. An approximation is also found for the expected SIR obtained by using a Toeplitz form covariance matrix estimator; this performance is found to be dependent on both the signal and the true covariance matrix.

  20. An Adaptive Mesh Algorithm: Mesh Structure and Generation

    SciTech Connect

    Scannapieco, Anthony J.

    2016-06-21

    The purpose of Adaptive Mesh Refinement is to minimize spatial errors over the computational space not to minimize the number of computational elements. The additional result of the technique is that it may reduce the number of computational elements needed to retain a given level of spatial accuracy. Adaptive mesh refinement is a computational technique used to dynamically select, over a region of space, a set of computational elements designed to minimize spatial error in the computational model of a physical process. The fundamental idea is to increase the mesh resolution in regions where the physical variables are represented by a broad spectrum of modes in k-space, hence increasing the effective global spectral coverage of those physical variables. In addition, the selection of the spatially distributed elements is done dynamically by cyclically adjusting the mesh to follow the spectral evolution of the system. Over the years three types of AMR schemes have evolved; block, patch and locally refined AMR. In block and patch AMR logical blocks of various grid sizes are overlaid to span the physical space of interest, whereas in locally refined AMR no logical blocks are employed but locally nested mesh levels are used to span the physical space. The distinction between block and patch AMR is that in block AMR the original blocks refine and coarsen entirely in time, whereas in patch AMR the patches change location and zone size with time. The type of AMR described herein is a locally refi ned AMR. In the algorithm described, at any point in physical space only one zone exists at whatever level of mesh that is appropriate for that physical location. The dynamic creation of a locally refi ned computational mesh is made practical by a judicious selection of mesh rules. With these rules the mesh is evolved via a mesh potential designed to concentrate the nest mesh in regions where the physics is modally dense, and coarsen zones in regions where the physics is modally

  1. Complex Adaptive Systems and the Origins of Adaptive Structure: What Experiments Can Tell Us

    ERIC Educational Resources Information Center

    Cornish, Hannah; Tamariz, Monica; Kirby, Simon

    2009-01-01

    Language is a product of both biological and cultural evolution. Clues to the origins of key structural properties of language can be found in the process of cultural transmission between learners. Recent experiments have shown that iterated learning by human participants in the laboratory transforms an initially unstructured artificial language…

  2. Successive Cambia: A Developmental Oddity or an Adaptive Structure?

    PubMed Central

    Robert, Elisabeth M. R.; Schmitz, Nele; Boeren, Ilse; Driessens, Tess; Herremans, Kristof; De Mey, Johan; Van de Casteele, Elke; Beeckman, Hans; Koedam, Nico

    2011-01-01

    Background Secondary growth by successive cambia is a rare phenomenon in woody plant species. Only few plant species, within different phylogenetic clades, have secondary growth by more than one vascular cambium. Often, these successive cambia are organised concentrically. In the mangrove genus Avicennia however, the successive cambia seem to have a more complex organisation. This study aimed (i) at understanding the development of successive cambia by giving a three-dimensional description of the hydraulic architecture of Avicennia and (ii) at unveiling the possible adaptive nature of growth by successive cambia through a study of the ecological distribution of plant species with concentric internal phloem. Results Avicennia had a complex network of non-cylindrical wood patches, the complexity of which increased with more stressful ecological conditions. As internal phloem has been suggested to play a role in water storage and embolism repair, the spatial organisation of Avicennia wood could provide advantages in the ecologically stressful conditions species of this mangrove genus are growing in. Furthermore, we could observe that 84.9% of the woody shrub and tree species with concentric internal phloem occurred in either dry or saline environments strengthening the hypothesis that successive cambia provide the necessary advantages for survival in harsh environmental conditions. Conclusions Successive cambia are an ecologically important characteristic, which seems strongly related with water-limited environments. PMID:21304983

  3. Robust adaptive self-structuring fuzzy control design for nonaffine, nonlinear systems

    NASA Astrophysics Data System (ADS)

    Chen, Pin-Cheng; Wang, Chi-Hsu; Lee, Tsu-Tian

    2011-01-01

    In this article, a robust adaptive self-structuring fuzzy control (RASFC) scheme for the uncertain or ill-defined nonlinear, nonaffine systems is proposed. The RASFC scheme is composed of a robust adaptive controller and a self-structuring fuzzy controller. In the self-structuring fuzzy controller design, a novel self-structuring fuzzy system (SFS) is used to approximate the unknown plant nonlinearity, and the SFS can automatically grow and prune fuzzy rules to realise a compact fuzzy rule base. The robust adaptive controller is designed to achieve an L 2 tracking performance to stabilise the closed-loop system. This L 2 tracking performance can provide a clear expression of tracking error in terms of the sum of lumped uncertainty and external disturbance, which has not been shown in previous works. Finally, five examples are presented to show that the proposed RASFC scheme can achieve favourable tracking performance, yet heavy computational burden is relieved.

  4. Teacher Observation of Classroom Adaptation--Checklist: Development and Factor Structure

    ERIC Educational Resources Information Center

    Koth, Christine W.; Bradshaw, Catherine P.; Leaf, Philip J.

    2009-01-01

    Two studies examined the validity and factor structure of the Teacher Observation of Classroom Adaptation-Checklist, an instrument used to evaluate school-based programs. The checklist is a cost-effective alternative to the original interview format, and the factor structure is consistent across gender, race, age, and time of administration.…

  5. 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…

  6. 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…

  7. 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.

  8. 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.

  9. Electromagnetic Modeling and Measurement of Adaptive Metamaterial Structural Elements

    DTIC Science & Technology

    2011-03-01

    via electrodes , the permittivity is shifted, thereby shifting the resonance of the device [24]. Figure 35. Geometry of a tunable FSS structure that...2.5.6 Series SRR Particles. Nicholson and Ghorbani present a series SRR design with interdigital capacitors patterned on a barium strontium titanate

  10. 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.

  11. Cooperation in networked populations of selfish adaptive agents: Sensitivity to network structure

    NASA Astrophysics Data System (ADS)

    Gulyás, László

    2007-05-01

    This paper investigates the adaptation of cooperating strategies in an iterated prisoner's dilemma (IPD) game with individually learning agents, subject to the structure of the interaction network. In particular, we study how cooperation or defection comes to dominate the population on Watts-Strogatz networks, under varying average path lengths. Our results are in good agreement with previous works on discrete choice dynamics on networks, but are in stark contrast with results from the evolution of cooperation literature. We argue that the latter is because the different adaptation method used (i.e., adaptive learning instead of ‘evolutionary’ strategy switching).

  12. Structural correlates of mechanosensory transduction and adaptation in identified neurons of spider slit sensilla.

    PubMed

    Höger, U; Seyfarth, E A

    2001-11-01

    We used isolated but functionally intact preparations of the lyriform slit-sense organ VS-3 from the leg of the spider, Cupiennius salei Keys, to examine the role of prominent fine-structural elements for mechanosensory transduction and adaptation. Slit sensilla act as strain sensors in the cuticular exoskeleton; each slit is innervated by two mechanosensitive neurons. Punctate mechanical deformation at four points along the dendrites demonstrated that mechanical excitability is confined to membrane sites at the extreme dendrite tips that are enclosed by cuticular slit structures. Depletion of microtubules in VS-3 neurons by prolonged mechanical stimulation and application of 5 mmol l(-1) colchicine did not disrupt the generation of a receptor potential. Hence, putative gating mechanisms of the mechanically activated membrane channels at the dendrite tips appear to be largely independent of microtubular structures. The discrete adaptation pattern in each of the two partner neurons, rapidly adapting versus slowly adapting, did not depend on the distinct mode of dendrite attachment to cuticular slit structures, and even persisted in isolated neurons after their dendrite tips and auxiliary structures were lost. We suggest that the two discrete adaptation patterns are based on intrinsic differences in the action potential encoding process rather than differences in stimulus transformation or mechanotransduction.

  13. Stabilizing Spatially-Structured Populations through Adaptive Limiter Control

    PubMed Central

    Sah, Pratha; Dey, Sutirth

    2014-01-01

    Stabilizing the dynamics of complex, non-linear systems is a major concern across several scientific disciplines including ecology and conservation biology. Unfortunately, most methods proposed to reduce the fluctuations in chaotic systems are not applicable to real, biological populations. This is because such methods typically require detailed knowledge of system specific parameters and the ability to manipulate them in real time; conditions often not met by most real populations. Moreover, real populations are often noisy and extinction-prone, which can sometimes render such methods ineffective. Here, we investigate a control strategy, which works by perturbing the population size, and is robust to reasonable amounts of noise and extinction probability. This strategy, called the Adaptive Limiter Control (ALC), has been previously shown to increase constancy and persistence of laboratory populations and metapopulations of Drosophila melanogaster. Here, we present a detailed numerical investigation of the effects of ALC on the fluctuations and persistence of metapopulations. We show that at high migration rates, application of ALC does not require a priori information about the population growth rates. We also show that ALC can stabilize metapopulations even when applied to as low as one-tenth of the total number of subpopulations. Moreover, ALC is effective even when the subpopulations have high extinction rates: conditions under which another control algorithm had previously failed to attain stability. Importantly, ALC not only reduces the fluctuation in metapopulation sizes, but also the global extinction probability. Finally, the method is robust to moderate levels of noise in the dynamics and the carrying capacity of the environment. These results, coupled with our earlier empirical findings, establish ALC to be a strong candidate for stabilizing real biological metapopulations. PMID:25153073

  14. Adaptive Structures Programs for the Strategic Defense Initiative Organization

    DTIC Science & Technology

    2007-11-02

    to address this difficult problem. A PZT device is being used to isolate the motion of a cryocooler cold finger on an existing, advanced Stirling ...Suppression for Cryocoolers Advanced Materials Applications for Space Structures (AMASS) Advanced Composites with Embedded Sensors and Actuators (ACESA...One of the greatest sources of sensor jitter, given a quiescent spacecraft, is the cryocooler itself1 ’• 12. A project was initiated by M&S with JPL

  15. Materials for Adaptive Structural Acoustic Control. Volume 1

    DTIC Science & Technology

    1993-04-06

    unusual response of thin film BaTiO3 is discussed in Appendix 49, which shows that for small grains (6-8 nm) the structure is cubic nonferroelectric, but...smart dental braces made from shape memory alloys Smart hulls and propulsion systems for navy ships and submarines that detect flow noise, remove... zirconia are a good example. Here the tetragonal-monoclinic phase change accompanied by ferroelastic twin wail motion are the stand-by phenomena capable of

  16. 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

  17. Materials for Adaptive Structural Acoustic Control. Volume 3

    DTIC Science & Technology

    1993-04-06

    3 Nanocomposites," Materials Letters 1., 26 (1992). 22. C. A. Randall, S. F . Wang, D. Laubscher, J. P. Dougherty and W. Huebner, "Structure Property ...1955). 4. G. W. Taylor. "Electric Properties of Niobium- doped Ferroelectric Pb(Zr,Sn,Ti)0 3 Ceramics", J. Appl. Phys., 38, 4697-4706(1967). 5 W. C...I Forrii Approved REPORT DOCUMENTATION PAGE 10M4 No 07040788 Vuioh, -Domogln utwd-n to, th, -c.lietl•on , f ,-~~i~m ,I -&lem d I*. -cr•=I•uf gow,DO3t

  18. Adaptive Damping and Positioning Using Intelligent Composite Active Structures (ADPICAS)

    DTIC Science & Technology

    2005-10-01

    previous applications for optimal actuator placement were based on structures themselves and overlooked the effects of the applied control law . In fact, the...optimal gain matrix K such that the state-feedback law u = -Kx minimizes the quadratic cost function, J(u), as: J(u) = f(xTQx + uTRu)dt (4.46) 0 where Q...account. The second improvement lays in the combination of the optimization technique (i.e. GAs) with the control law in the entire optimization process

  19. Stochastic stage-structured modeling of the adaptive immune system

    SciTech Connect

    Chao, D. L.; Davenport, M. P.; Forrest, S.; Perelson, Alan S.,

    2003-01-01

    We have constructed a computer model of the cytotoxic T lymphocyte (CTL) response to antigen and the maintenance of immunological memory. Because immune responses often begin with small numbers of cells and there is great variation among individual immune systems, we have chosen to implement a stochastic model that captures the life cycle of T cells more faithfully than deterministic models. Past models of the immune response have been differential equation based, which do not capture stochastic effects, or agent-based, which are computationally expensive. We use a stochastic stage-structured approach that has many of the advantages of agent-based modeling but is more efficient. Our model can provide insights into the effect infections have on the CTL repertoire and the response to subsequent infections.

  20. Self-adaptive asymmetric on-line boosting for detecting anatomical structures

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Tajbakhsh, Nima; Xue, Wenzhe; Liang, Jianming

    2012-03-01

    In this paper, we propose a self-adaptive, asymmetric on-line boosting (SAAOB) method for detecting anatomical structures in CT pulmonary angiography (CTPA). SAAOB is novel in that it exploits a new asymmetric loss criterion with self-adaptability according to the ratio of exposed positive and negative samples and in that it has an advanced rule to update sample's importance weight taking account of both classification result and sample's label. Our presented method is evaluated by detecting three distinct thoracic structures, the carina, the pulmonary trunk and the aortic arch, in both balanced and imbalanced conditions.

  1. 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.

  2. 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

  3. 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).

  4. 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.

  5. Effects of community structure on epidemic spread in an adaptive network

    NASA Astrophysics Data System (ADS)

    Tunc, Ilker; Shaw, Leah B.

    2014-08-01

    When an epidemic spreads in a population, individuals may adaptively change the structure of their social contact network to reduce risk of infection. Here we study the spread of an epidemic on an adaptive network with community structure. We model two communities with different average degrees. The disease model is susceptible-infected-susceptible (SIS), and adaptation is rewiring of links between susceptibles and infectives. Locations of rewired links are selected so that the community structure will be preserved if susceptible-infective links are homogeneously distributed. The bifurcation structure is obtained, and a mean field model is developed that accurately predicts the steady-state behavior of the system. In a static network, weakly connected heterogeneous communities can have significantly different infection levels. In contrast, adaptation promotes similar infection levels and alters the network structure so that communities have more similar average degrees. We estimate the time for network restructuring to allow infection incursion from one community to another and show that it is inversely proportional to the number of cross-links between communities. In extremely heterogeneous systems, periodic oscillations in infection level can occur due to repeated infection incursions.

  6. 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.

  7. 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.

  8. Adaptive potential of genomic structural variation in human and mammalian evolution.

    PubMed

    Radke, David W; Lee, Charles

    2015-09-01

    Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.

  9. 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…

  10. Adaptive Piezoelectric Circuitry Sensor Network with High-Frequency Harmonics Interrogation for Structural Damage Detection

    DTIC Science & Technology

    2014-09-17

    Harmonics Interrogation for Structural Damage Detection FA9550-11-1-0072 Kon-Well Wang and Jiong Tang The Regents of the University of Michigan, 3003...Well Wang 734-764-8464 1    Adaptive Piezoelectric Circuitry Sensor Network with High-Frequency Harmonics Interrogation for Structural Damage Detection...limitations. This research explores damage identification via advancing a third type of approach: high-frequency harmonic excitation-based self

  11. 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.

  12. 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.

  13. A low-complexity adaptive beamformer for ultrasound imaging using structured covariance matrix.

    PubMed

    Asl, Babak Mohammadzadeh; Mahloojifar, Ali

    2012-04-01

    In recent years, adaptive beamforming methods have been successfully applied to medical ultrasound imaging, resulting in simultaneous improvement in imaging resolution and contrast. These improvements have been achieved at the expense of higher computational complexity, with respect to the conventional non-adaptive delay-and-sum (DAS) beamformer, in which computational complexity is proportional to the number of elements, O(M). The computational overhead results from the covariance matrix inversion needed for computation of the adaptive weights, the complexity of which is cubic with the subarray size, O(L(3)). This is a computationally intensive procedure, which makes the implementation of adaptive beamformers less attractive in spite of their advantages. Considering that, in medical ultrasound applications, most of the energy is scattered from angles close to the steering angle, assuming spatial stationarity is a good approximation, allowing us to assume the Toeplitz structure for the estimated covariance matrix. Based on this idea, in this paper, we have applied the Toeplitz structure to the spatially smoothed covariance matrix by averaging the entries along all subdiagonals. Because the inverse of the resulting Toeplitz covariance matrix can be computed in O(L(2)) operations, this technique results in a greatly reduced computational complexity. By using simulated and experimental RF data-point targets as well as cyst phantoms-we show that the proposed low-complexity adaptive beamformer significantly outperforms the DAS and its performance is comparable to that of the minimum variance beamformer, with reduced computational complexity.

  14. [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.

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

    PubMed

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

    2016-08-09

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Physiological adaptation along environmental gradients and replicated hybrid zone structure in swordtails (Teleostei: Xiphophorus).

    PubMed

    Culumber, Z W; Shepard, D B; Coleman, S W; Rosenthal, G G; Tobler, M

    2012-09-01

    Local adaptation is often invoked to explain hybrid zone structure, but empirical evidence of this is generally rare. Hybrid zones between two poeciliid fishes, Xiphophorus birchmanni and X. malinche, occur in multiple tributaries with independent replication of upstream-to-downstream gradients in morphology and allele frequencies. Ecological niche modelling revealed that temperature is a central predictive factor in the spatial distribution of pure parental species and their hybrids and explains spatial and temporal variation in the frequency of neutral genetic markers in hybrid populations. Among populations of parentals and hybrids, both thermal tolerance and heat-shock protein expression vary strongly, indicating that spatial and temporal structure is likely driven by adaptation to local thermal environments. Therefore, hybrid zone structure is strongly influenced by interspecific differences in physiological mechanisms for coping with the thermal environment.

  2. 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.

  3. An adaptive piezoelectric vibration absorber enhanced by a negative capacitance applied to a shell structure

    NASA Astrophysics Data System (ADS)

    Gripp, J. A. B.; Góes, L. C. S.; Heuss, O.; Scinocca, F.

    2015-12-01

    Piezoelectric shunt damping is a well-known technique to damp mechanical vibrations of a structure, using a piezoelectric transducer to convert mechanical vibration energy into electrical energy, which is dissipated in an electrical resistance. Resonant shunts consisting of a resistance and an inductance connected to a piezoelectric transducer are used to damp structural vibrations in narrow frequency bands, but their performance is very sensitive to variations in structural modal frequencies and transducer capacitance. In order to overcome this drawback, a piezoelectric shunt damping technique with improved performance and robustness is presented in this paper. The design of the adaptive circuit considers the variation of the host structure’s natural frequency as a project parameter. This paper describes an adaptive resonant piezoelectric vibration absorber enhanced by a synthetic negative capacitance applied to a shell structure. The resonant shunt circuit autonomously adapts its inductance value by comparing the phase difference of the vibration velocity and the current flowing through the shunt circuit. Moreover, a synthetic negative capacitance is added to the shunt circuit to enhance the vibration attenuation provided by the piezoelectric absorber. The circuitry is implemented using analog components. Validation of the proposed method is done by bonding the piezoelectric absorber on a free-formed metallic shell.

  4. Adaptive variable structure hierarchical fuzzy control for a class of high-order nonlinear dynamic systems.

    PubMed

    Mansouri, Mohammad; Teshnehlab, Mohammad; Aliyari Shoorehdeli, Mahdi

    2015-05-01

    In this paper, a novel adaptive hierarchical fuzzy control system based on the variable structure control is developed for a class of SISO canonical nonlinear systems in the presence of bounded disturbances. It is assumed that nonlinear functions of the systems be completely unknown. Switching surfaces are incorporated into the hierarchical fuzzy control scheme to ensure the system stability. A fuzzy soft switching system decides the operation area of the hierarchical fuzzy control and variable structure control systems. All the nonlinearly appeared parameters of conclusion parts of fuzzy blocks located in different layers of the hierarchical fuzzy control system are adjusted through adaptation laws deduced from the defined Lyapunov function. The proposed hierarchical fuzzy control system reduces the number of rules and consequently the number of tunable parameters with respect to the ordinary fuzzy control system. Global boundedness of the overall adaptive system and the desired precision are achieved using the proposed adaptive control system. In this study, an adaptive hierarchical fuzzy system is used for two objectives; it can be as a function approximator or a control system based on an intelligent-classic approach. Three theorems are proven to investigate the stability of the nonlinear dynamic systems. The important point about the proposed theorems is that they can be applied not only to hierarchical fuzzy controllers with different structures of hierarchical fuzzy controller, but also to ordinary fuzzy controllers. Therefore, the proposed algorithm is more general. To show the effectiveness of the proposed method four systems (two mechanical, one mathematical and one chaotic) are considered in simulations. Simulation results demonstrate the validity, efficiency and feasibility of the proposed approach to control of nonlinear dynamic systems.

  5. Adaptive active vibration control to improve the fatigue life of a carbon-epoxy smart structure

    NASA Astrophysics Data System (ADS)

    Ripamonti, Francesco; Cazzulani, Gabriele; Cinquemani, Simone; Resta, Ferruccio; Torti, Alessandro

    2015-04-01

    Active vibration controls are helpful in improving fatigue life of structures through limitation of absolute displacements. However, control algorithms are usually designed without explicitly taking into account the fatigue phenomenon. In this paper, an adaptive vibration controller is proposed to increase the fatigue life of a smart structure made of composite material and actuated with piezoelectric patches. The main innovation with respect to the most common solutions is that the control laws are directly linked to a damage driving force, which is correlated to a fatigue damage model for the specific material. The control logic is different depending on the damage state of the structure. If no significant damage affects the structure, the controller decreases the crack nucleation probability by limiting the driving forces in the overall structure. On the contrary, if initiated cracks are present, their further propagation is prevented by controlling the damage driving forces in the already damaged areas. The structural diagnostics is performed through a vibration-based health monitoring technique, while periodical adaptation of the controller is adopted to consider damage-induced changes on the structure state-space model and to give emphasis to the most excited modes. The control algorithm has been numerically validated on the finite element model of a cantilever plate.

  6. Shape adaptation of long bone structures using a contour based approach.

    PubMed

    Roberts, M D; Hart, R T

    2005-06-01

    In this work, an approach for mechanically driven shape adaptation of long bone structures is presented which utilizes contour descriptions to track morphological changes at different bone cross sections. A script-based procedure is used to iteratively generate a solid geometry and finite element (FE) model from these contours, perform a stress analysis, and then update the contour shapes using the results of the stress analysis using a prescribed remodeling rule. Because a remeshing operation is performed at each timestep the method is able to effectively simulate large changes in geometry. Several examples of shape adaptation of idealized and geometrically accurate long-bone structures are presented using a variety of remodeling signals and parameters.

  7. [Structural and functional reorganization of photosynthetic apparatus in cold adaptation of wheat plants].

    PubMed

    Venzhik, Ju V; Titov, D F; Talanova, V V; Miroslavov, E D; Koteeva, N K

    2012-01-01

    The structural and functional characteristics of the photosynthetic apparatus (PSA) and the cold resistance of wheat seedlings were studied during low-temperature adaptation. It has been established that large chloroplasts with thylakoid system of "sun type" forme in the mesophyll cells in the early hours of plants hardening. At the same time the functional reorganization of the PSA in the leaves of wheat occurs: content of pigments changes, stabilization of the pigment-protein complexes is observed, non-photochemical quenching of excess energy increases. The stabilization of photosynthesis during cold adaptation occurs due to structural and functional reorganization of the PSA. It is assumed that the reorganization of the PSA is a prerequisite for formation of increased cold resistance of leaf cells, and this, along with other physiological and biochemical changes occurring in cells and tissues of plants, allows the plants to survive in chilling.

  8. Effect of joint imperfections on static control of adaptive structures as space cranes

    NASA Technical Reports Server (NTRS)

    Ramesh, A. V.; Utku, Senol; Wada, B. K.; Chen, G. S.

    1990-01-01

    Effect of imperfections in the joints of an adaptive structure on its slow (no inertia forces) motion along a prescribed trajectory as a space crane is studied. Two mathematical models to predict the effect of joint imperfections are proposed. The two models are used to obtain estimates of the deviations of the node of the space crane to which the end-effector is attached, from its prescribed trajectory. An application of the models to a two-section space crane is given.

  9. Structural and Functional Mechanisms of Adaptations of WrbA in Extremophilic Organisms

    DTIC Science & Technology

    2010-05-11

    Archaeoglobus fulgidus and the mesophile Escherichia coli were investigated to gain an understanding of the mechanisms by which proteins in extremophilic...hypcrthcrmoph’tieArchaeoglohns fidgidus and the mesophile EMiwruhia coli were investigated to gain an understanding of the mechanisms by which proteins in...extremophilic organisms adapt to high temperature. A model of the thermophilic enzyme was constructed based on the crystal structure of the mesophilic

  10. Adapting to Reductions in Team Size: An Examination of Three Structural Alternatives

    DTIC Science & Technology

    2005-06-01

    Std Z39-18 Reductions in Team Size 2 Abstract Research on downsizing in organizations has traditionally focused on the affective- based reactions...of survivors or the reactions of financial markets to downsizing announcements. Very little research has examined how organizational units adapt to... downsizing . This paper investigates three structural approaches to downsizing in teams and directly tests the general proposition that the

  11. 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

  12. 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.

  13. 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

    2016-09-06

    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.

  14. Adaptive fuzzy logic controller with direct action type structures for InnoSAT attitude control system

    NASA Astrophysics Data System (ADS)

    Bakri, F. A.; Mashor, M. Y.; Sharun, S. M.; Bibi Sarpinah, S. N.; Abu Bakar, Z.

    2016-10-01

    This study proposes an adaptive fuzzy controller for attitude control system (ACS) of Innovative Satellite (InnoSAT) based on direct action type structure. In order to study new methods used in satellite attitude control, this paper presents three structures of controllers: Fuzzy PI, Fuzzy PD and conventional Fuzzy PID. The objective of this work is to compare the time response and tracking performance among the three different structures of controllers. The parameters of controller were tuned on-line by adjustment mechanism, which was an approach similar to a PID error that could minimize errors between actual and model reference output. This paper also presents a Model References Adaptive Control (MRAC) as a control scheme to control time varying systems where the performance specifications were given in terms of the reference model. All the controllers were tested using InnoSAT system under some operating conditions such as disturbance, varying gain, measurement noise and time delay. In conclusion, among all considered DA-type structures, AFPID controller was observed as the best structure since it outperformed other controllers in most conditions.

  15. Hybrid Self-Adaptive Evolution Strategies Guided by Neighborhood Structures for Combinatorial Optimization Problems.

    PubMed

    Coelho, V N; Coelho, I M; Souza, M J F; Oliveira, T A; Cota, L P; Haddad, M N; Mladenovic, N; Silva, R C P; Guimarães, F G

    2016-01-01

    This article presents an Evolution Strategy (ES)--based algorithm, designed to self-adapt its mutation operators, guiding the search into the solution space using a Self-Adaptive Reduced Variable Neighborhood Search procedure. In view of the specific local search operators for each individual, the proposed population-based approach also fits into the context of the Memetic Algorithms. The proposed variant uses the Greedy Randomized Adaptive Search Procedure with different greedy parameters for generating its initial population, providing an interesting exploration-exploitation balance. To validate the proposal, this framework is applied to solve three different [Formula: see text]-Hard combinatorial optimization problems: an Open-Pit-Mining Operational Planning Problem with dynamic allocation of trucks, an Unrelated Parallel Machine Scheduling Problem with Setup Times, and the calibration of a hybrid fuzzy model for Short-Term Load Forecasting. Computational results point out the convergence of the proposed model and highlight its ability in combining the application of move operations from distinct neighborhood structures along the optimization. The results gathered and reported in this article represent a collective evidence of the performance of the method in challenging combinatorial optimization problems from different application domains. The proposed evolution strategy demonstrates an ability of adapting the strength of the mutation disturbance during the generations of its evolution process. The effectiveness of the proposal motivates the application of this novel evolutionary framework for solving other combinatorial optimization problems.

  16. Three-dimensional structural representation of the sleep-wake adaptability.

    PubMed

    Putilov, Arcady A

    2016-01-01

    Various characteristics of the sleep-wake cycle can determine the success or failure of individual adjustment to certain temporal conditions of the today's society. However, it remains to be explored how many such characteristics can be self-assessed and how they are inter-related one to another. The aim of the present report was to apply a three-dimensional structural representation of the sleep-wake adaptability in the form of "rugby cake" (scalene or triaxial ellipsoid) to explain the results of analysis of the pattern of correlations of the responses to the initial 320-item list of a new inventory with scores on the six scales designed for multidimensional self-assessment of the sleep-wake adaptability (Morning and Evening Lateness, Anytime and Nighttime Sleepability, and Anytime and Daytime Wakeability). The results obtained for sample consisting of 149 respondents were confirmed by the results of similar analysis of earlier collected responses of 139 respondents to the same list of 320 items and responses of 1213 respondents to the 72 items of one of the earlier established questionnaire tools. Empirical evidence was provided in support of the model-driven prediction of the possibility to identify items linked to as many as 36 narrow (6 core and 30 mixed) adaptabilities of the sleep-wake cycle. The results enabled the selection of 168 items for self-assessment of all these adaptabilities predicted by the rugby cake model.

  17. Adaptability of protein structures to enable functional interactions and evolutionary implications.

    PubMed

    Haliloglu, Turkan; Bahar, Ivet

    2015-12-01

    Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even before protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence→structure→dynamics→function where 'dynamics' bridges structure and function.

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

    NASA Astrophysics Data System (ADS)

    Wada, Ben K.; Fanson, James L.; Miura, Koryo

    1991-11-01

    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.

  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. 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

  1. 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.

  2. Local Adaptation and Vector-Mediated Population Structure in Plasmodium vivax Malaria

    PubMed Central

    Gonzalez-Ceron, Lilia; Carlton, Jane M.; Gueye, Amy; Fay, Michael; McCutchan, Thomas F.; Su, Xin-zhuan

    2008-01-01

    Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control. PMID:18385220

  3. 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.

  4. Global References, Local Translation: Adaptation of the Bologna Process Degree Structure and Credit System at Universities in Cameroon

    ERIC Educational Resources Information Center

    Eta, Elizabeth Agbor; Vubo, Emmanuel Yenshu

    2016-01-01

    This article uses temporal comparison and thematic analytical approaches to analyse text documents and interviews, examining the adaptation of the Bologna Process degree structure and credit system in two sub-systems of education in Cameroon: the Anglo-Saxon and the French systems. The central aim is to verify whether such adaptation has replaced,…

  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. 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.

  7. 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.

  8. 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.

  9. Adaptive comb filtering for motion artifact reduction from PPG with a structure of adaptive lattice IIR notch filter.

    PubMed

    Lee, Boreom; Kee, Youngwook; Han, Jonghee; Yi, Won Jin

    2011-01-01

    Photoplethysmographic (PPG) signal can provide important information about cardiovascular and respiratory conditions of individuals in a hospital or daily life. However, PPG can be distorted by motion artifacts significantly. Therefore, the reduction of the effects of motion artifacts is very important procedure for monitoring cardio-respiratory system by PPG. There have been many adaptive techniques to reduce motion artifacts from PPG signal including normalized least mean squares (NLMS) method, recursive least squares (RLS) filter, and Kalman filter. In the present study, we propose the adaptive comb filter (ACF) for reducing the effects of motion artifacts from PPG signal. ACF with adaptive lattice infinite impulse response (IIR) notch filter (ALNF) successfully reduced the motion artifacts from the quasi-periodic PPG signal.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Cold adaptation: structural and functional characterizations of psychrophilic and mesophilic acetate kinase.

    PubMed

    Tang, Md Abul Kashem; Motoshima, Hiroyuki; Watanabe, Keiichi

    2014-08-01

    Acetate kinase catalyzes the reversible magnesium-dependent phosphoryl transfer from ATP to acetate to form acetyl phosphate and ADP. Here, we report functional and some structural properties of cold-adapted psychrotrophic enzyme; acetate kinase with those from mesophilic counterpart in Escherichia coli K-12. Recombinant acetate kinase from Shewanella sp. AS-11 (SAK) and E. coli K-12 (EAK) were purified to homogeneity following affinity chromatography and followed by Super Q column chromatography as reported before [44]. Both purified enzymes are shared some of the common properties such as (similar molecular mass, amino acid sequence and similar optimum pH), but characterized shift in the apparent optimum temperature of specific activity to lower temperature as well as by a lower thermal stability compared with EAK. The functional comparisons reveal that SAK is a cold adapted enzyme, having a higher affinity to acetate than EAK. In the acetyl phosphate and ADP-forming direction, the catalytic efficiency (k(cat)/K(m)) for acetate was 8.0 times higher for SAK than EAK at 10 °C. The activity ratio of SAK to EAK was increased with decreasing temperature in both of the forward and backward reactions. Furthermore, the activation energy, enthalpy and entropy in both reaction directions that catalyzed by SAK were lower than those catalyzed by EAK. The model structure of SAK showed the significantly reduced numbers of salt bridges and cation-pi interactions as compared with EAK. These results suggest that weakening of intramolecular electrostatic interactions of SAK is involved in a more flexible structure which is likely to be responsible for its cold adaptation.

  15. Vibrational behavior of adaptive aircraft wing structures modelled as composite thin-walled beams

    NASA Technical Reports Server (NTRS)

    Song, O.; Librescu, L.; Rogers, C. A.

    1992-01-01

    The vibrational behavior of cantilevered aircraft wings modeled as thin-walled beams and incorporating piezoelectric effects is studied. Based on the converse piezoelectric effect, the system of piezoelectric actuators conveniently located on the wing yield the control of its associated vertical and lateral bending eigenfrequencies. The possibility revealed by this study enabling one to increase adaptively the eigenfrequencies of thin-walled cantilevered beams could play a significant role in the control of the dynamic response and flutter of wing and rotor blade structures.

  16. The prediction of EEG signals using a feedback-structured adaptive rational function filter.

    PubMed

    Kim, H S; Kim, T S; Choi, Y H; Park, S H

    2000-08-01

    In this article, we present a feedback-structured adaptive rational function filter based on a recursive modified Gram-Schmidt algorithm and apply it to the prediction of an EEG signal that has nonlinear and nonstationary characteristics. For the evaluation of the prediction performance, the proposed filter is compared with other methods, where a single-step prediction and a multi-step prediction are considered for a short-term prediction, and the prediction performance is assessed in normalized mean square error. The experimental results show that the proposed filter shows better performance than other methods considered for the short-term prediction of EEG signals.

  17. 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.

  18. An innovations-based noise cancelling technique on inverse kepstrum whitening filter and adaptive FIR filter in beamforming structure.

    PubMed

    Jeong, Jinsoo

    2011-01-01

    This paper presents an acoustic noise cancelling technique using an inverse kepstrum system as an innovations-based whitening application for an adaptive finite impulse response (FIR) filter in beamforming structure. The inverse kepstrum method uses an innovations-whitened form from one acoustic path transfer function between a reference microphone sensor and a noise source so that the rear-end reference signal will then be a whitened sequence to a cascaded adaptive FIR filter in the beamforming structure. By using an inverse kepstrum filter as a whitening filter with the use of a delay filter, the cascaded adaptive FIR filter estimates only the numerator of the polynomial part from the ratio of overall combined transfer functions. The test results have shown that the adaptive FIR filter is more effective in beamforming structure than an adaptive noise cancelling (ANC) structure in terms of signal distortion in the desired signal and noise reduction in noise with nonminimum phase components. In addition, the inverse kepstrum method shows almost the same convergence level in estimate of noise statistics with the use of a smaller amount of adaptive FIR filter weights than the kepstrum method, hence it could provide better computational simplicity in processing. Furthermore, the rear-end inverse kepstrum method in beamforming structure has shown less signal distortion in the desired signal than the front-end kepstrum method and the front-end inverse kepstrum method in beamforming structure.

  19. 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

  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. Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.

    PubMed

    Shirai, T; Ishida, H; Noda, J; Yamane, T; Ozaki, K; Hakamada, Y; Ito, S

    2001-07-27

    The crystal structure of the catalytic domain of alkaline cellulase K was determined at 1.9 A resolution. Because of the most alkaliphilic nature and it's highest activity at pH 9.5, it is used commercially in laundry detergents. An analysis of the structural bases of the alkaliphilic character of the enzyme suggested a mechanism similar to that previously proposed for alkaline proteases, that is, an increase in the number of Arg, His, and Gln residues, and a decrease in Asp and Lys residues. Some ion pairs were formed by the gained Arg residues, which is similar to what has been found in the alkaline proteases. Lys-Asp ion pairs are disfavored and partly replaced with Arg-Asp ion pairs. The alkaline adaptation appeared to be a remodeling of ion pairs so that the charge balance is kept in the high pH range.

  2. [Night sleep structural alteration as a function of individual strategy of adapting to 520-isolation].

    PubMed

    Zavalko, I M; Boritko, Ya S; Kovrov, G V; Vinokhodova, A G; Chekalina, A I; Smoleevsky, A E

    2014-01-01

    Purpose of the work was to establish a relationship between trends in sleep alteration and individual adaptation to the stress-factors in the 520-day isolation study. Psychological evaluations using a battery of motivation tests and L. Sobchik's modification of the Luscher personality test, and Mirror coordinograph enabled to differentiate groups reacting to the stress on the pattern of "control" (G-1) or "search" (G-2) manifested in individual styles of behavior and operator's activity. The 2 groups showed different dynamics of the night sleep structure. Difficulties with falling asleep in G-1 arose on the eve of "landing onto Mars" and end of the experiment, whereas in G-2 they were evident prior to the end only. Besides, the micro- and segmental sleep structures were more stable in G-1 suggesting the integrity of somnogenic mechanisms despite difficult sleep initiation.

  3. Carbon fiber-ZnO nanowire hybrid structures for flexible and adaptable strain sensors.

    PubMed

    Liao, Qingliang; Mohr, Markus; Zhang, Xiaohui; Zhang, Zheng; Zhang, Yue; Fecht, Hans-Jörg

    2013-12-21

    We report the flexible piezotronic strain sensors fabricated using carbon fiber-ZnO nanowire hybrid structures by a novel and reliable method. The I-V characteristic of the sensor shows high sensitivity to external strain due to the change in Schottky barrier height (SBH), which has a linear relationship with strain. This fabricated strain sensor has a quick, real-time current response under both static and dynamic mechanical loads. The change in SBH resulted from the strain-induced piezoelectric potential is investigated by band gap theory. In this work we develop a new feasible method to fabricate a flexible strain sensor within the fabric adapted to textile structures, able to measure their strain.

  4. 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.

  5. Auto-adaptive statistical procedure for tracking structural health monitoring data

    NASA Astrophysics Data System (ADS)

    Smith, R. Lowell; Jannarone, Robert J.

    2004-07-01

    Whatever specific methods come to be preferred in the field of structural health/integrity monitoring, the associated raw data will eventually have to provide inputs for appropriate damage accumulation models and decision making protocols. The status of hardware under investigation eventually will be inferred from the evolution in time of the characteristics of this kind of functional figure of merit. Irrespective of the specific character of raw and processed data, it is desirable to develop simple, practical procedures to support damage accumulation modeling, status discrimination, and operational decision making in real time. This paper addresses these concerns and presents an auto-adaptive procedure developed to process data output from an array of many dozens of correlated sensors. These represent a full complement of information channels associated with typical structural health monitoring applications. What the algorithm does is learn in statistical terms the normal behavior patterns of the system, and against that backdrop, is configured to recognize and flag departures from expected behavior. This is accomplished using standard statistical methods, with certain proprietary enhancements employed to address issues of ill conditioning that may arise. Examples have been selected to illustrate how the procedure performs in practice. These are drawn from the fields of nondestructive testing, infrastructure management, and underwater acoustics. The demonstrations presented include the evaluation of historical electric power utilization data for a major facility, and a quantitative assessment of the performance benefits of net-centric, auto-adaptive computational procedures as a function of scale.

  6. Densified network glasses and liquids with thermodynamically reversible and structurally adaptive behaviour.

    PubMed

    Bauchy, M; Micoulaut, M

    2015-03-09

    If crystallization can be avoided during cooling, a liquid will display a substantial increase of its viscosity, and will form a glass that behaves as a solid with a relaxation time that grows exponentially with decreasing temperature. Given this 'off-equilibrium' nature, a hysteresis loop appears when a cooling/heating cycle is performed across the glass transition. Here we report on molecular dynamics simulations of densified glass-forming liquids that follow this kind of cycle. Over a finite pressure interval, minuscule thermal changes are found, revealing glasses of 'thermally reversible' character with optimal volumetric or enthalpic recovery. By analysing the topology of the atomic network structure, we find that corresponding liquids adapt under the pressure-induced increasing stress by experiencing larger bond-angle excursions. The analysis of the dynamic behaviour reveals that the structural relaxation time is substantially reduced in these adaptive liquids, and also drives the reversible character of the glass transition. Ultimately, the results substantiate the notion of stress-free (Maxwell isostatic) rigidity in disordered molecular systems, while also revealing new implications for the topological engineering of complex materials.

  7. Densified network glasses and liquids with thermodynamically reversible and structurally adaptive behaviour

    NASA Astrophysics Data System (ADS)

    Bauchy, M.; Micoulaut, M.

    2015-03-01

    If crystallization can be avoided during cooling, a liquid will display a substantial increase of its viscosity, and will form a glass that behaves as a solid with a relaxation time that grows exponentially with decreasing temperature. Given this ‘off-equilibrium’ nature, a hysteresis loop appears when a cooling/heating cycle is performed across the glass transition. Here we report on molecular dynamics simulations of densified glass-forming liquids that follow this kind of cycle. Over a finite pressure interval, minuscule thermal changes are found, revealing glasses of ‘thermally reversible’ character with optimal volumetric or enthalpic recovery. By analysing the topology of the atomic network structure, we find that corresponding liquids adapt under the pressure-induced increasing stress by experiencing larger bond-angle excursions. The analysis of the dynamic behaviour reveals that the structural relaxation time is substantially reduced in these adaptive liquids, and also drives the reversible character of the glass transition. Ultimately, the results substantiate the notion of stress-free (Maxwell isostatic) rigidity in disordered molecular systems, while also revealing new implications for the topological engineering of complex materials.

  8. 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.

  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. Adaptability of Protein Structures to Enable Functional Interactions and Evolutionary Implications

    PubMed Central

    Haliloglu, Turkan; Bahar, Ivet

    2015-01-01

    Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even prior to protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence → structure → dynamics → function where ‘dynamics’ bridges structure and function. PMID:26254902

  11. 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.

  12. 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

  13. Structural adaptation of tooth enamel protein amelogenin in the presence of SDS micelles

    PubMed Central

    Chandrababu, Karthik Balakrishna; Dutta, Kaushik; Lokappa, Sowmya Bekshe; Ndao, Moise; Evans, John Spencer; Moradian-Oldak, Janet

    2014-01-01

    Amelogenin, the major extracellular matrix protein of developing tooth enamel is intrinsically disordered. Through its interaction with other proteins and mineral, amelogenin assists enamel biomineralization by controlling the formation of highly organized enamel crystal arrays. We used circular dichroism (CD), dynamic light scattering (DLS), fluorescence and NMR spectroscopy to investigate the folding propensity of recombinant porcine amelogenin rP172 following its interaction with SDS, at levels above critical micelle concentration. The rP172-SDS complex formation was confirmed by DLS, while an increase in the structure moiety of rP172 was noted through CD and fluorescence experiments. Fluorescence quenching analyses performed on several rP172 mutants where all but one Trp was replaced by Tyr at different sequence regions confirmed that the interaction of amelogenin with SDS micelles occurs via the N-terminal region close to Trp25 where helical segments can be detected by NMR. NMR spectroscopy and structural refinement calculations using CS-Rosetta modelling confirm that the highly conserved N-terminal domain is prone to form helical structure when bound to SDS micelles. Our findings reported here reveal interactions leading to significant changes in the secondary structure of rP172 upon treatment with SDS. These interactions may reflect the physiological relevance of the flexible nature of amelogenin and its sequence specific helical propensity that might enable it to structurally adapt with charged and potential targets such as cell surface, mineral, and other proteins during enamel biomineralization. PMID:24114119

  14. 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.

  15. Geographic distribution and adaptive significance of genomic structural variants: an anthropological genetics perspective.

    PubMed

    Eaaswarkhanth, Muthukrishnan; Pavlidis, Pavlos; Gokcumen, Omer

    2014-01-01

    Anthropological geneticists have successfully used single-nucleotide and short tandem repeat variations across human genomes to reconstruct human history. These markers have also been used extensively to identify adaptive and phenotypic variation. The recent advent of high-throughput genomic technologies revealed an overlooked type of genomic variation: structural variants (SVs). In fact, some SVs may contribute to human adaptation in substantial and previously unexplored ways. SVs include deletions, insertions, duplications, inversions, and translocations of genomic segments that vary among individuals from the same species. SVs are much less numerous than single-nucleotide variants but account for at least seven times more variable base pairs than do single-nucleotide variants when two human genomes are compared. Moreover, recent studies have shown that SVs have higher mutation rates than single-nucleotide variants when the affected base pairs are considered, especially in certain parts of the genome. The null hypothesis for the evolution of SVs, as for single-nucleotide variants, is neutrality. Hence, drift is the primary force that shapes the current allelic distribution of most SVs. However, due to their size, a larger proportion of SVs appear to evolve under nonneutral forces (mostly purifying selection) than do single-nucleotide variants. In fact, as exemplified by several groundbreaking studies, SVs contribute to anthropologically relevant phenotypic variation and local adaptation among humans. In this review, we argue that with the advent of affordable genomic technologies, anthropological scrutiny of genomic structural variation emerges as a fertile area of inquiry to better understand human phenotypic variation. To motivate potential studies, we discuss scenarios through which structural variants (SVs) affect phenotypic variation among humans within an anthropological context. We further provide a methodological workflow in which we analyzed 1000 Genomes

  16. 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

  17. 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.

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

    PubMed

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

    2016-09-01

    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.

  19. 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

  20. Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure.

    PubMed

    Galinsky, Kevin J; Loh, Po-Ru; Mallick, Swapan; Patterson, Nick J; Price, Alkes L

    2016-11-03

    Analyzing genetic differences between closely related populations can be a powerful way to detect recent adaptation. The very large sample size of the UK Biobank is ideal for using population differentiation to detect selection and enables an analysis of the UK population structure at fine resolution. In this study, analyses of 113,851 UK Biobank samples showed that population structure in the UK is dominated by five principal components (PCs) spanning six clusters: Northern Ireland, Scotland, northern England, southern England, and two Welsh clusters. Analyses of ancient Eurasians revealed that populations in the northern UK have higher levels of Steppe ancestry and that UK population structure cannot be explained as a simple mixture of Celts and Saxons. A scan for unusual population differentiation along the top PCs identified a genome-wide-significant signal of selection at the coding variant rs601338 in FUT2 (p = 9.16 × 10(-9)). In addition, by combining evidence of unusual differentiation within the UK with evidence from ancient Eurasians, we identified genome-wide-significant (p = 5 × 10(-8)) signals of recent selection at two additional loci: CYP1A2-CSK and F12. We detected strong associations between diastolic blood pressure in the UK Biobank and both the variants with selection signals at CYP1A2-CSK (p = 1.10 × 10(-19)) and the variants with ancient Eurasian selection signals at the ATXN2-SH2B3 locus (p = 8.00 × 10(-33)), implicating recent adaptation related to blood pressure.

  1. 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

  2. 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.

  3. 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.

  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 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.

  6. Adaptive neural network control for a class of low-triangular-structured nonlinear systems.

    PubMed

    Du, Hongbin; Shao, Huihe; Yao, Pingjing

    2006-03-01

    In this paper, a class of unknown perturbed nonlinear systems is theoretically stabilized by using adaptive neural network control. The systems, with disturbances and nonaffine unknown functions, have low triangular structure, which generalizes both strict-feedback uncertain systems and pure-feedback ones. There do not exist any effective methods to stabilize this kind of systems. With some new conclusions for Nussbaum-Gain functions (NGF) and the idea of backstepping, semiglobal, uniformal, and ultimate boundedness of all the signals in the closed-loop is proved at equilibrium point. The two problems, control directions and control singularity, are well dealt with. The effectiveness of proposed scheme is shown by simulation on a proper nonlinear system.

  7. Nonlinear structural response using adaptive dynamic relaxation on a massively-parallel-processing system

    NASA Technical Reports Server (NTRS)

    Oakley, David R.; Knight, Norman F., Jr.

    1994-01-01

    A parallel adaptive dynamic relaxation (ADR) algorithm has been developed for nonlinear structural analysis. This algorithm has minimal memory requirements, is easily parallelizable and scalable to many processors, and is generally very reliable and efficient for highly nonlinear problems. Performance evaluations on single-processor computers have shown that the ADR algorithm is reliable and highly vectorizable, and that it is competitive with direct solution methods for the highly nonlinear problems considered. The present algorithm is implemented on the 512-processor Intel Touchstone DELTA system at Caltech, and it is designed to minimize the extent and frequency of interprocessor communication. The algorithm has been used to solve for the nonlinear static response of two and three dimensional hyperelastic systems involving contact. Impressive relative speedups have been achieved and demonstrate the high scalability of the ADR algorithm. For the class of problems addressed, the ADR algorithm represents a very promising approach for parallel-vector processing.

  8. 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.

  9. Adaptive support for aircraft panel testing: New method and its experimental verification on a beam structure

    NASA Astrophysics Data System (ADS)

    Sachau, Delf; Baschke, Manuel

    2017-04-01

    Acoustic transmissibility of aircraft panels is measured in full-scale test rigs. The panels are supported at their frames. These boundary conditions do not take into account the dynamic influence of the fuselage, which is significant in the frequency range below 300 Hz. This paper introduces a new adaptive boundary system (ABS). It combines accelerometers and electrodynamic shakers with real-time signal processing. The ABS considers the dynamic effect of the fuselage on the panel. The frames are dominating the dynamic behaviour of a fuselage in the low-frequency range. Therefore, the new method is applied to a beam representing a frame of the aircraft structure. The experimental results are evaluated and the precision of the ABS is discussed. The theoretical apparent mass representing the cut-off part of a frame is calculated and compared with the apparent mass, as provided by the ABS. It is explained how the experimental set-up limits the precision of the ABS.

  10. Control of a slow moving space crane as an adaptive structure

    NASA Technical Reports Server (NTRS)

    Utku, S.; Ramesh, A. V.; Das, S. K.; Wada, B. K.; Chen, G. S.

    1989-01-01

    Assuming that the space crane is an adaptive structure with length-adjustable bars and taking as controls the length-adjustments of these bars, the computation of the incremental controls corresponding to the motion of a payload along its minimum-energy trajectory is given in terms of the inverse-transpose of matrix B of the joint equilibrium equations Bs = p, where s lists the bar forces and p lists the nodal loads. The compensation of the controls for elastic deformations and support movements are shown. It is also shown that the computations may be done automatically and in real time by an attached processor once the characteristics of the crane's maneuver are keyed in.

  11. Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments

    SciTech Connect

    Seshagiri, Lakshminarasimhan; Sosonkina, Masha; Zhang, Zhao

    2009-05-20

    Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmark the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.

  12. Both epidermal growth factor and insulin-like growth factor receptors are dispensable for structural intestinal adaptation

    PubMed Central

    Sun, Raphael C.; Diaz-Miron, Jose L.; Choi, Pamela M.; Sommovilla, Joshua; Guo, Jun; Erwin, Christopher R.; Warner, Brad W.

    2015-01-01

    Purpose Intestinal adaptation structurally represents increases in crypt depth and villus height in response to small bowel resection (SBR). Previously, we found that neither epidermal growth factor receptor (EGFR) nor insulin-like growth factor 1 receptor (IGF1R) function was individually required for normal adaptation. In this study, we sought to determine the effect of disrupting both EGFR and IGF1R expression on resection-induced adaptation. Methods Intestinal-specific EGFR and IGF1R double knockout mice (EGFR/IGF1R-IKO) (n=6) and wild-type (WT) control mice (n=7) underwent 50% proximal SBR. On postoperative day (POD) 7, structural adaptation was scored by measuring crypt depth and villus height. Rates of crypt cell proliferation, apoptosis, and submucosal capillary density were also compared. Results After 50% SBR, normal adaptation occurred in both WT and EGFR/IGF1R-IKO. Rates of proliferation and apoptosis were no different between the two groups. The angiogenic response was less in the EGFR/IGF1R-IKO compared to WT mice. Conclusion Disrupted expression of EGFR and IGF1R in the intestinal epithelial cells does not affect resection-induced structural adaptation but attenuates angiogenesis after SBR. These findings suggest that villus growth is driven by receptors and pathways that occur outside the epithelial cell component, while angiogenic responses may be influenced by epithelial-endothelial crosstalk. PMID:25818318

  13. 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.

  14. 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

  15. Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.

    PubMed

    Wild, Klemens; Bange, Gert; Motiejunas, Domantas; Kribelbauer, Judith; Hendricks, Astrid; Segnitz, Bernd; Wade, Rebecca C; Sinning, Irmgard

    2016-07-17

    The signal recognition particle (SRP) is a ribonucleoprotein complex with a key role in targeting and insertion of membrane proteins. The two SRP GTPases, SRP54 (Ffh in bacteria) and FtsY (SRα in eukaryotes), form the core of the targeting complex (TC) regulating the SRP cycle. The architecture of the TC and its stimulation by RNA has been described for the bacterial SRP system while this information is lacking for other domains of life. Here, we present the crystal structures of the GTPase heterodimers of archaeal (Sulfolobus solfataricus), eukaryotic (Homo sapiens), and chloroplast (Arabidopsis thaliana) SRP systems. The comprehensive structural comparison combined with Brownian dynamics simulations of TC formation allows for the description of the general blueprint and of specific adaptations of the quasi-symmetric heterodimer. Our work defines conserved external nucleotide-binding sites for SRP GTPase activation by RNA. Structural analyses of the GDP-bound, post-hydrolysis states reveal a conserved, magnesium-sensitive switch within the I-box. Overall, we provide a general model for SRP cycle regulation by RNA.

  16. 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.; ...

    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

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

    PubMed

    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.

  18. 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

  19. Joint Japan/U.S. Conference on Adaptive Structures, 2nd, Nagoya, Japan, Nov. 12-14, 1991, Collection of Papers

    NASA Technical Reports Server (NTRS)

    Matsuzaki, Yuji (Editor); Wada, Ben K. (Editor)

    1992-01-01

    The present conference discusses the development status of adaptive structures in Europe and in Japan, the 'Cosmo-Lab' structures/robotics cooperation concept, active-adhesion concepts for in-orbit structural assembly, adaptively controlled truss structures, object-oriented modeling in structural analysis, the control effectiveness and energy efficiency of an active mass damper, a space truss with experimental tendon control, and piezoelectric actuator-based space trusses. Also discussed is the control of resonant frequencies in adaptive structures through prestressing, active control of vortex-excited vibrations of flexible cylindrical structures, shape adjustment of a flexible space antenna reflector, the SDIO Adaptive Structures Program, optimal trajectories of iterative manipulation for space robots, a docking device as an adaptive structure, shape-memory polymers and their hybrid composites, and fuzzy control methods for structural dynamics.

  20. 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.

  1. Structural and functional characterization of a cold adapted TPM-domain with ATPase/ADPase activity.

    PubMed

    Cerutti, María L; Otero, Lisandro H; Smal, Clara; Pellizza, Leonardo; Goldbaum, Fernando A; Klinke, Sebastián; Aran, Martín

    2016-11-01

    The Pfam PF04536 TPM_phosphatase family is a broadly conserved family of domains found across prokaryotes, plants and invertebrates. Despite having a similar protein fold, members of this family have been implicated in diverse cellular processes and found in varied subcellular localizations. Very recently, the biochemical characterization of two evolutionary divergent TPM domains has shown that they are able to hydrolyze phosphate groups from different substrates. However, there are still incorrect functional annotations and uncertain relationships between the structure and function of this family of domains. BA41 is an uncharacterized single-pass transmembrane protein from the Antarctic psychrotolerant bacterium Bizionia argentinensis with a predicted compact extracytoplasmic TPM domain and a C-terminal cytoplasmic low complexity region. To shed light on the structural properties that enable TPM domains to adopt divergent roles, we here accomplish a comprehensive structural and functional characterization of the central TPM domain of BA41 (BA41-TPM). Contrary to its predicted function as a beta-propeller methanol dehydrogenase, light scattering and crystallographic studies showed that BA41-TPM behaves as a globular monomeric protein and adopts a conserved Rossmann fold, typically observed in other TPM domain structures. Although the crystal structure reveals the conservation of residues involved in substrate binding, no putative catalytic or intramolecular metal ions were detected. Most important, however, extensive biochemical studies demonstrated that BA41-TPM has hydrolase activity against ADP, ATP, and other di- and triphosphate nucleotides and shares properties of cold-adapted enzymes. The role of BA41 in extracellular ATP-mediated signaling pathways and its occurrence in environmental and pathogenic microorganisms is discussed.

  2. 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

  3. 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

  4. Structure identification of an uncertain network coupled with complex-variable chaotic systems via adaptive impulsive control

    NASA Astrophysics Data System (ADS)

    Liu, Dan-Feng; Wu, Zhao-Yan; Ye, Qing-Ling

    2014-04-01

    In this paper, structure identification of an uncertain network coupled with complex-variable chaotic systems is investigated. Both the topological structure and the system parameters can be unknown and need to be identified. Based on impulsive stability theory and the Lyapunov function method, an impulsive control scheme combined with an adaptive strategy is adopted to design effective and universal network estimators. The restriction on the impulsive interval is relaxed by adopting an adaptive strategy. Further, the proposed method can monitor the online switching topology effectively. Several numerical simulations are provided to illustrate the effectiveness of the theoretical results.

  5. Different molecular and structural adaptations with eccentric and conventional strength training in elderly men and women.

    PubMed

    Mueller, Matthias; Breil, Fabio Andreas; Lurman, Glenn; Klossner, Stephan; Flück, Martin; Billeter, Rudolf; Däpp, Christoph; Hoppeler, Hans

    2011-01-01

    Reprogramming of gene expression contributes to structural and functional adaptation of muscle tissue in response to altered use. The aim of this study was to investigate mechanisms for observed improvements in leg extension strength, gain in relative thigh muscle mass and loss of body and thigh fat content in response to eccentric and conventional strength training in elderly men (n = 14) and women (n = 14; average age of the men and women: 80.1 ± 3.7 years) by means of structural and molecular analyses. Biopsies were collected from m. vastus lateralis in the resting state before and after 12 weeks of training with two weekly resistance exercise sessions (RET) or eccentric ergometer sessions (EET). Gene expression was analyzed using custom-designed low-density PCR arrays. Muscle ultrastructure was evaluated using EM morphometry. Gain in thigh muscle mass was paralleled by an increase in muscle fiber cross-sectional area (hypertrophy) with RET but not with EET, where muscle growth is likely occurring by the addition of sarcomeres in series or by hyperplasia. The expression of transcripts encoding factors involved in muscle growth, repair and remodeling (e.g., IGF-1, HGF, MYOG, MYH3) was increased to a larger extent after EET than RET. MicroRNA 1 expression was decreased independent of the training modality, and was paralleled by an increased expression of IGF-1 representing a potential target. IGF-1 is a potent promoter of muscle growth, and its regulation by microRNA 1 may have contributed to the gain of muscle mass observed in our subjects. EET depressed genes encoding mitochondrial and metabolic transcripts. The changes of several metabolic and mitochondrial transcripts correlated significantly with changes in mitochondrial volume density. Intramyocellular lipid content was decreased after EET concomitantly with total body fat. Changes in intramyocellular lipid content correlated with changes in body fat content with both RET and EET. In the elderly, RET and

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Epidemic threshold and topological structure of susceptible-infectious-susceptible epidemics in adaptive networks

    NASA Astrophysics Data System (ADS)

    Guo, Dongchao; Trajanovski, Stojan; van de Bovenkamp, Ruud; Wang, Huijuan; Van Mieghem, Piet

    2013-10-01

    The interplay between disease dynamics on a network and the dynamics of the structure of that network characterizes many real-world systems of contacts. A continuous-time adaptive susceptible-infectious-susceptible (ASIS) model is introduced in order to investigate this interaction, where a susceptible node avoids infections by breaking its links to its infected neighbors while it enhances the connections with other susceptible nodes by creating links to them. When the initial topology of the network is a complete graph, an exact solution to the average metastable-state fraction of infected nodes is derived without resorting to any mean-field approximation. A linear scaling law of the epidemic threshold τc as a function of the effective link-breaking rate ω is found. Furthermore, the bifurcation nature of the metastable fraction of infected nodes of the ASIS model is explained. The metastable-state topology shows high connectivity and low modularity in two regions of the τ,ω plane for any effective infection rate τ>τc: (i) a “strongly adaptive” region with very high ω and (ii) a “weakly adaptive” region with very low ω. These two regions are separated from the other half-open elliptical-like regions of low connectivity and high modularity in a contour-line-like way. Our results indicate that the adaptation of the topology in response to disease dynamics suppresses the infection, while it promotes the network evolution towards a topology that exhibits assortative mixing, modularity, and a binomial-like degree distribution.

  12. 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.

  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

    DOE PAGES

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

    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

  15. 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

  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. Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

    PubMed

    Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

    2016-10-01

    Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available.

  18. Biological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus

    PubMed Central

    Yamada, Shinya; Hatta, Masato; Staker, Bart L.; Watanabe, Shinji; Imai, Masaki; Shinya, Kyoko; Sakai-Tagawa, Yuko; Ito, Mutsumi; Ozawa, Makoto; Watanabe, Tokiko; Sakabe, Saori; Li, Chengjun; Kim, Jin Hyun; Myler, Peter J.; Phan, Isabelle; Raymond, Amy; Smith, Eric; Stacy, Robin; Nidom, Chairul A.; Lank, Simon M.; Wiseman, Roger W.; Bimber, Benjamin N.; O'Connor, David H.; Neumann, Gabriele; Stewart, Lance J.; Kawaoka, Yoshihiro

    2010-01-01

    Two amino acids (lysine at position 627 or asparagine at position 701) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals. However, the recently emerged pandemic H1N1 viruses lack these amino acids. Here, we report that a basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals. Moreover, a basic amino acid at position 591 of PB2 substantially increased the lethality of an avian H5N1 virus in mice. We also present the X-ray crystallographic structure of the C-terminus of a pandemic H1N1 virus PB2 protein. Arginine at position 591 fills the cleft found in H5N1 PB2 proteins in this area, resulting in differences in surface shape and charge for H1N1 PB2 proteins. These differences may affect the protein's interaction with viral and/or cellular factors, and hence its ability to support virus replication in mammals. PMID:20700447

  19. Structural break detection method based on the Adaptive Regression Splines technique

    NASA Astrophysics Data System (ADS)

    Kucharczyk, Daniel; Wyłomańska, Agnieszka; Zimroz, Radosław

    2017-04-01

    For many real data, long term observation consists of different processes that coexist or occur one after the other. Those processes very often exhibit different statistical properties and thus before the further analysis the observed data should be segmented. This problem one can find in different applications and therefore new segmentation techniques have been appeared in the literature during last years. In this paper we propose a new method of time series segmentation, i.e. extraction from the analysed vector of observations homogeneous parts with similar behaviour. This method is based on the absolute deviation about the median of the signal and is an extension of the previously proposed techniques also based on the simple statistics. In this paper we introduce the method of structural break point detection which is based on the Adaptive Regression Splines technique, one of the form of regression analysis. Moreover we propose also the statistical test which allows testing hypothesis of behaviour related to different regimes. First, the methodology we apply to the simulated signals with different distributions in order to show the effectiveness of the new technique. Next, in the application part we analyse the real data set that represents the vibration signal from a heavy duty crusher used in a mineral processing plant.

  20. 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.

  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. Hyperspectral imaging-based credit card verifier structure with adaptive learning.

    PubMed

    Sumriddetchkajorn, Sarun; Intaravanne, Yuttana

    2008-12-10

    We propose and experimentally demonstrate a hyperspectral imaging-based optical structure for verifying a credit card. Our key idea comes from the fact that the fine detail of the embossed hologram stamped on the credit card is hard to duplicate, and therefore its key color features can be used for distinguishing between the real and counterfeit ones. As the embossed hologram is a diffractive optical element, we shine a number of broadband light sources one at a time, each at a different incident angle, on the embossed hologram of the credit card in such a way that different color spectra per incident angle beam are diffracted and separated in space. In this way, the center of mass of the histogram on each color plane is investigated by using a feed-forward backpropagation neural-network configuration. Our experimental demonstration using two off-the-shelf broadband white light emitting diodes, one digital camera, and a three-layer neural network can effectively identify 38 genuine and 109 counterfeit credit cards with false rejection rates of 5.26% and 0.92%, respectively. Key features include low cost, simplicity, no moving parts, no need of an additional decoding key, and adaptive learning.

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

    PubMed

    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.

  4. Neighborhood and school ethnic structuring and cultural adaptations among Mexican-origin adolescents.

    PubMed

    White, Rebecca M B; Updegraff, Kimberly A; Umaña-Taylor, Adriana J; Zeiders, Katharine H; Perez-Brena, Norma; Burleson, Elizabeth

    2017-03-01

    The ethnic and racial structuring of U.S. neighborhoods may have important implications for developmental competencies during adolescence, including the development of heritage and mainstream cultural orientations. In particular, living in highly concentrated Latino neighborhoods during early adolescence-which channels adolescents into related school environments-may promote retention of the ethnic or heritage culture, but it also may constrain adaptation to the mainstream U.S. culture. We tested these hypotheses longitudinally in a sample of 246 Mexican origin adolescents (50.8% girls) and their parents. Data were collected 4 times over 8 years, with adolescents averaging 12.5 (SD = .58) to 19.6 (SD = .66) years of age across the period of the study. Latino ethnic concentration in early adolescents' neighborhoods promoted the retention of Mexican cultural orientations; Latino ethnic concentration in middle schools undermined the development of mainstream U.S cultural orientations. Findings are discussed in terms of integrating cultural-developmental theory with mainstream neighborhood theory to improve understandings of neighborhood and school ethnic concentration effects on adolescent development. (PsycINFO Database Record

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Comparing model-based adaptive LMS filters and a model-free hysteresis loop analysis method for structural health monitoring

    NASA Astrophysics Data System (ADS)

    Zhou, Cong; Chase, J. Geoffrey; Rodgers, Geoffrey W.; Xu, Chao

    2017-02-01

    The model-free hysteresis loop analysis (HLA) method for structural health monitoring (SHM) has significant advantages over the traditional model-based SHM methods that require a suitable baseline model to represent the actual system response. This paper provides a unique validation against both an experimental reinforced concrete (RC) building and a calibrated numerical model to delineate the capability of the model-free HLA method and the adaptive least mean squares (LMS) model-based method in detecting, localizing and quantifying damage that may not be visible, observable in overall structural response. Results clearly show the model-free HLA method is capable of adapting to changes in how structures transfer load or demand across structural elements over time and multiple events of different size. However, the adaptive LMS model-based method presented an image of greater spread of lesser damage over time and story when the baseline model is not well defined. Finally, the two algorithms are tested over a simpler hysteretic behaviour typical steel structure to quantify the impact of model mismatch between the baseline model used for identification and the actual response. The overall results highlight the need for model-based methods to have an appropriate model that can capture the observed response, in order to yield accurate results, even in small events where the structure remains linear.

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

    PubMed Central

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

    2011-01-01

    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

  12. Structural insights into the cold adaptation of the photosynthetic pigment-protein C-phycocyanin from an Arctic cyanobacterium.

    PubMed

    Su, Hai-Nan; Wang, Qian-Min; Li, Chun-Yang; Li, Kang; Luo, Wei; Chen, Bo; Zhang, Xi-Ying; Qin, Qi-Long; Zhou, Bai-Cheng; Chen, Xiu-Lan; Zhang, Yu-Zhong; Xie, Bin-Bin

    2017-04-01

    The cold adaptation mechanism of phycobiliproteins, the major photosynthetic pigment-proteins in cyanobacteria and red algae, has rarely been studied. Here we reported the biochemical, structural, and molecular dynamics simulation study of the C-phycocyanin from Arctic cyanobacterial strain Pseudanabaena sp. LW0831. We characterized the phycobilisome components of LW0831 and obtained their gene sequences. Compared to the mesophilic counterpart from Arthrospira platensis (Ar-C-PC), LW0831 C-phycocyanin (Ps-C-PC) has a decreased thermostability (∆Tm of -16°C), one of the typical features of cold-adapted enzymes. To uncover its structural basis, we resolved the crystal structure of Ps-C-PC 1 at 2.04Å. Consistent with the decrease in thermostability, comparative structural analyses revealed decreased intra-trimer and inter-trimer interactions in Ps-C-PC 1, compared to Ar-C-PC. However, comparative molecular dynamics simulations indicated that Ps-C-PC 1 shows similar flexibilities to Ar-C-PC for both the (αβ)3 trimer and (αβ)6 hexamer. Therefore, the optimization mode is clearly different from cold-adapted enzymes, which usually have increased flexibilities. Detailed analyses demonstrated different optimization modes for the α and β subunits and it was revealed that hydrophobic interactions are key to this difference, though salt bridges, hydrogen bonds, and surface hydrophobicity are also involved. This study is the first report of the structure of cold-adapted phycobiliproteins and provides insights into the cold-adaptation strategies of non-enzyme proteins.

  13. 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

  14. Pregnancy-induced adaptations in the intrinsic structure of rat pelvic floor muscles

    PubMed Central

    Alperin, Marianna; Lawley, Danielle M.; Esparza, Mary C.; Lieber, Richard L.

    2016-01-01

    , but continued to be significantly elevated in coccygeus (P < .0001). CONCLUSION This study demonstrates that pregnancy induces unique adaptations in the structure of the PFMs, which adjust their architectural design by adding sarcomeres in series to increase fiber length as well as mounting a substantial synthesis of collagen in intramuscular ECM. PMID:25979618

  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. 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…

  17. Experimental study of adaptive pointing and tracking for large flexible space structures

    NASA Technical Reports Server (NTRS)

    Boussalis, D.; Bayard, D. S.; Ih, C.; Wang, S. J.; Ahmed, A.

    1991-01-01

    This paper describes an experimental study of adaptive pointing and tracking control for flexible spacecraft conducted on a complex ground experiment facility. The algorithm used in this study is based on a multivariable direct model reference adaptive control law. Several experimental validation studies were performed earlier using this algorithm for vibration damping and robust regulation, with excellent results. The current work extends previous studies by addressing the pointing and tracking problem. As is consistent with an adaptive control framework, the plant is assumed to be poorly known to the extent that only system level knowledge of its dynamics is available. Explicit bounds on the steady-state pointing error are derived as functions of the adaptive controller design parameters. It is shown that good tracking performance can be achieved in an experimental setting by adjusting adaptive controller design weightings according to the guidelines indicated by the analytical expressions for the error.

  18. 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

  19. 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

  20. 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

  1. Structural and Function Correlation of Cone Packing Utilizing Adaptive Optics and Microperimetry

    PubMed Central

    Supriya, Dabir; Shwetha, Mangalesh; Kiran Anupama, Kumar; Kummelil Mathew, Kurian; Berendschot, Tos T. J. M.; Schouten, Jan S. A. G.; Bharamshetter, Roopa; Naresh, Yadav K.; Rohit, Shetty; Hegde, Bharath

    2015-01-01

    Aim. To assess the functional aspects of cone mosaic and correlate cone packing with retinal sensitivity utilizing microperimetry in emmetropes at different eccentricities. Methods. Twenty-four healthy volunteers underwent microperimetry (MAIA Centervue, Italy) and assessment of photoreceptors using adaptive optics retinal camera, rtx1 (Imagine Eyes, Orsay, France), at 2 and 3 degrees from the foveal centre in 4 quadrants: superior, inferior, temporal, and nasal. Data was analyzed using SPSS version 17 (IBM). Spearman's correlation tests were used to establish correlation between mean cone packing density and retinal sensitivity at different quadrants. Results. Thirteen females and 11 males (age range 20–40 years) were included. The cone density was found to be significantly different among all quadrants (temporal = 25786.68/mm2 ± 4367.07/mm2, superior = 23009.35/mm2 ± 5415.81/mm2, nasal = 22838.09/mm2 ± 4166.22/mm2, and inferior = 21097.53/mm2 ± 4235.84/mm2). A statistical significance (P < 0.008) was found between orthogonal meridians, that is, temporal, nasal (48624.77/mm2)> superior, inferior (44106.88/mm2). A drop in retinal sensitivity was observed as the eccentricity increased (P < 0.05). It was also found that as cone packing density decreased retinal sensitivity also decreased (P < 0.05) in all quadrants. This was observed at both 2 and 3 degrees. Conclusion. It is of crucial importance to establish normative variations in cone structure-function correlation. This may help in detection of subtle pathology and its early intervention. PMID:26167509

  2. MAPPING THE CLUMPY STRUCTURES WITHIN SUBMILLIMETER GALAXIES USING LASER-GUIDE STAR ADAPTIVE OPTICS SPECTROSCOPY

    SciTech Connect

    Menendez-Delmestre, Karin; Goncalves, Thiago S.; Blain, Andrew W.; Swinbank, Mark; Smail, Ian; Ivison, Rob J.; Chapman, Scott C.

    2013-04-20

    We present the first integral-field spectroscopic observations of high-redshift submillimeter-selected galaxies (SMGs) using Laser-Guide Star Adaptive Optics. We target H{alpha} emission of three SMGs at redshifts z {approx} 1.4-2.4 with the OH-Suppressing Infrared Imaging Spectrograph on Keck. The spatially resolved spectroscopy of these galaxies reveals unresolved broad-H{alpha} line regions (FWHM >1000 km s{sup -1}) likely associated with an active galactic nucleus (AGN) and regions of diffuse star formation traced by narrow-line H{alpha} emission (FWHM {approx}< 500 km s{sup -1}) dominated by multiple H{alpha}-bright stellar clumps, each contributing 1%-30% of the total clump-integrated H{alpha} emission. We find that these SMGs host high star formation rate surface densities, similar to local extreme sources, such as circumnuclear starbursts and luminous infrared galaxies. However, in contrast to these local environments, SMGs appear to be undergoing such intense activity on significantly larger spatial scales as revealed by extended H{alpha} emission over 4-16 kpc. H{alpha} kinematics show no evidence of ordered global motion as would be found in a disk, but rather large velocity offsets ({approx}few Multiplication-Sign 100 km s{sup -1}) between the distinct stellar clumps. Together with the asymmetric distribution of the stellar clumps around the AGN in these objects, it is unlikely that we are unveiling a clumpy disk structure as has been suggested in other high-redshift populations of star-forming galaxies. The SMG clumps in this sample may correspond to remnants of originally independent gas-rich systems that are in the process of merging, hence triggering the ultraluminous SMG phase.

  3. Building a conceptual framework to culturally adapt health promotion and prevention programs at the deep structural level.

    PubMed

    Wang-Schweig, Meme; Kviz, Frederick J; Altfeld, Susan J; Miller, Arlene M; Miller, Brenda A

    2014-07-01

    The debate on the effectiveness and merit for the amount of time, effort, and resources to culturally adapt health promotion and prevention programs continues. This may be due, in large part, to the lack of theory in commonly used methods to match programmatic content and delivery to the culture of a population, particularly at the deep structural level. This paper asserts that prior to the cultural adaptation of prevention programs, it is necessary to first develop a conceptual framework. We propose a multiphase approach to address key challenges in the science of cultural adaptation by first identifying and exploring relevant cultural factors that may affect the targeted health-related behavior prior to proceeding through steps of a stage model. The first phase involves developing an underlying conceptual framework that integrates cultural factors to ground this process. The second phase employs the different steps of a stage model. For Phase I of our approach, we offer four key steps and use our research study as an example of how these steps were applied to build a framework for the cultural adaptation of a family-based intervention to prevent adolescent alcohol use, Guiding Good Choices (GGC), to Chinese American families. We then provide a summary of the preliminary evidence from a few key relationships that were tested among our sample with the greater purpose of discussing how these findings might be used to culturally adapt GGC.

  4. [The possible role of the elements of protein secondary structure in adaptation to the action of ionizing radiation].

    PubMed

    Kharchenko, L I; Pavlovskaia, T E

    1997-01-01

    Changes in the secondary structure of enzymes induced by gamma-rays 60Co at doses not exceeding one ionization per macromolecule were studied to elucidate a possible role of radiation-chemical processes in the evolution of proteins. The data on the comparative radioresistance of various types of secondary protein structures, alpha-helix, parallel and anti-parallel beta-structures, and beta-turn, were obtained by the method of circular dichroism. It was shown that beta-turns were resistant against radiation, alpha-helix was relatively stable, and beta-layer underwent significant changes. The importance of these structural types in the evolution of proteins is discussed. A special role of beta-turn as structural elements fixing the confirmation of macromolecules and therefore responsible for adaptation of the protein structure against a constant radiation background is proposed.

  5. Adaptation of yellow fever virus 17D to Vero cells is associated with mutations in structural and non-structural protein genes.

    PubMed

    Beasley, David W C; Morin, Merribeth; Lamb, Ashley R; Hayman, Edward; Watts, Douglas M; Lee, Cynthia K; Trent, Dennis W; Monath, Thomas P

    2013-09-01

    Serial passaging of yellow fever virus 17D in Vero cells was employed to derive seed material for a novel inactivated vaccine, XRX-001. Two independent passaging series identified a novel lysine to arginine mutation at amino acid 160 of the envelope protein, a surface-exposed residue in structural domain I. A third passage series resulted in an isoleucine to methionine mutation at residue 113 of the NS4B protein, a central membrane spanning region of the protein which has previously been associated with Vero cell adaptation of other mosquito-borne flaviviruses. These studies confirm that flavivirus adaptation to growth in Vero cells can be mediated by structural or non-structural protein mutations.

  6. 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

  7. Based on ground station adaptive optics for laser communications demonstration platform structures

    NASA Astrophysics Data System (ADS)

    Zhang, Lei; Tong, Shoufeng; Wang, Haozeng; Yang, Hongkun

    2013-08-01

    With the rapid development of modern science and technology in astronomical imaging, optical communications, optical radar, optical information processing, high-precision ranging, tracking, guidance, and remote sensing, light waves propagating in the medium, especially in the turbulent atmosphere spread more and more important. Atmospheric turbulence is one of the main factors which have influence on the performance of a laser communication system. Adaptive optics technology is an important means to solve the problem of atmospheric turbulence. This paper states how adaptive optics technique can be used in space laser communication system to compensate atmospheric turbulence when laser beam transmission through it. The core content of adaptive optics is correct laser beam wave-front disturbance in real-time,with it to enhance optical system imaging quality and the next aim is reach the level of diffraction limitation. Adaptive optics system consists of wave-front detection, wave-front control and wave-front correction . The demo platform including: atmospheric turbulence simulation unit、adaptive correction unit、signal transmitting and receiving unit. Liquid crystal spatial light modulator applications in adaptive optics system and the turbulence simulation system introduced. And used zernike polynomials method to produce atmospheric turbulence phase screen simulation analysis. Simulation results show that: in the low spatial frequency components, the atmospheric turbulence phase screen generated by Zernike polynomial method consistent with the theoretical values, but in the high spatial frequency components, the simulation results with large difference between the theoretical values. In addition, the simulation results also show that: we can change the distribution of turbulence in the atmospheric turbulence phase screen by increasing the Zernike polynomials of orders or change the receiving apertures, but to calculate the large calculate the complex and

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. The use of recurrent signals about adaptation for subsequent saccade programming depends on object structure.

    PubMed

    Doré-Mazars, Karine; Vergilino-Perez, Dorine; Collins, Thérèse; Bohacova, Katarina; Beauvillain, Cécile

    2006-10-03

    Executing sequences of accurate saccadic eye movements supposes the use of signals carrying information about the first saccade for updating the predetermined motor plan of the subsequent saccades. The present study examines the signals used in planning a second saccade when subjects made two successive saccades towards one long or two short peripheral objects displayed before the first saccade execution. Different first eye movement signals could be used: desired eye movement signals, representing the movement necessary for attaining the intended target, or actual eye movement signals, representing the movement actually executed. Experimental dissociation of desired and actual eye movement signals is made possible by adaptive modifications of the first saccade, obtained by transfer of single saccade adaptation, during which the motor vector was progressively modified in response to the systematic intra-saccadic step of a single target. Whether the second saccade used the actual eye movement signal to compensate or not for the adaptive changes in the first saccade depended on which object properties were relevant for saccade planning. Compensation was observed for saccades that aimed for a new object (between-object saccades) because adaptation modifies relative object location. No compensation was observed for saccades that explored an extended object (within-object saccades). Implications for the on-line control of subsequent eye movements are discussed.

  13. Default Accentuation and Foot Structure in Japanese: Evidence from Japanese Adaptations of French Words.

    ERIC Educational Resources Information Center

    Shinohara, Shigeko

    2000-01-01

    Examined accentuation patterns that appear in Japanese adaptation of French words. Argues that these patterns reflect the default accentuation of Japanese grammar; they correspond to accent patterns found in some marginal sectors of Japanese vocabulary where the accent is predictable. (Author/VWL)

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

    PubMed Central

    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. PMID:24917883

  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. 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

  17. Structural Insight into and Mutational Analysis of Family 11 Xylanases: Implications for Mechanisms of Higher pH Catalytic Adaptation

    PubMed Central

    Bai, Wenqin; Zhou, Cheng; Zhao, Yueju; Wang, Qinhong; Ma, Yanhe

    2015-01-01

    To understand the molecular basis of higher pH catalytic adaptation of family 11 xylanases, we compared the structures of alkaline, neutral, and acidic active xylanases and analyzed mutants of xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5. It was revealed that alkaline active xylanases have increased charged residue content, an increased ratio of negatively to positively charged residues, and decreased Ser, Thr, and Tyr residue content relative to non-alkaline active counterparts. Between strands β6 and β7, alkaline xylanases substitute an α-helix for a coil or turn found in their non-alkaline counterparts. Compared with non-alkaline xylanases, alkaline active enzymes have an inserted stretch of seven amino acids rich in charged residues, which may be beneficial for xylanase function in alkaline conditions. Positively charged residues on the molecular surface and ionic bonds may play important roles in higher pH catalytic adaptation of family 11 xylanases. By structure comparison, sequence alignment and mutational analysis, six amino acids (Glu16, Trp18, Asn44, Leu46, Arg48, and Ser187, numbering based on Xyn11A-LC) adjacent to the acid/base catalyst were found to be responsible for xylanase function in higher pH conditions. Our results will contribute to understanding the molecular mechanisms of higher pH catalytic adaptation in family 11 xylanases and engineering xylanases to suit industrial applications. PMID:26161643

  18. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus).

    PubMed

    Benestan, Laura; Quinn, Brady K; Maaroufi, Halim; Laporte, Martin; Clark, Fraser K; Greenwood, Spencer J; Rochette, Rémy; Bernatchez, Louis

    2016-10-01

    Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using bayescan, arlequin and outflank) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current-mediated larval connectivity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adaptive genetic variation. Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.

  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. 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…

  1. 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

    2014-05-07

    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.

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

    PubMed

    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.

  4. 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.

  5. Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics’ and structural biology’s lenses

    PubMed Central

    Cicconardi, Francesco; Di Marino, Daniele; Olimpieri, Pier Paolo; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.; Steiner, Florian M.

    2017-01-01

    Chemoreception is essential for survival. Some chemicals signal the presence of nutrients or toxins, others the proximity of mating partners, competitors, or predators. Chemical signal transduction has therefore been studied in multiple organisms. In Drosophila species, a number of odorant receptor genes and various other types of chemoreceptors were found. Three main gene families encode for membrane receptors and one for globular proteins that shuttle compounds with different degrees of affinity and specificity towards receptors. By sequencing the genome of Drosophila nigrosparsa, a habitat specialist restricted to montane/alpine environment, and combining genomics and structural biology techniques, we characterised odorant, gustatory, ionotropic receptors and odorant binding proteins, annotating 189 loci and modelling the protein structure of two ionotropic receptors and one odorant binding protein. We hypothesise that the D. nigrosparsa genome experienced gene loss and various evolutionary pressures (diversifying positive selection, relaxation, and pseudogenisation), as well as structural modification in the geometry and electrostatic potential of the two ionotropic receptor binding sites. We discuss possible trajectories in chemosensory adaptation processes, possibly enhancing compound affinity and mediating the evolution of more specialized food, and a fine-tuned mechanism of adaptation. PMID:28256589

  6. M4ARC: multi-model multi-mode adaptive resonant control for dynamically loaded flexible beam structures

    NASA Astrophysics Data System (ADS)

    Tjahyadi, H.; He, F.; Sammut, K.

    2008-08-01

    A hybrid multi-model-multi-mode adaptive resonant control (M4ARC) approach is proposed for dynamically loaded flexible beam structures to provide superior vibration damping performance as compared to its fixed-model and adaptive counterparts. The proposed approach uses a configurable controller, the parameters of which are updated using a fast and accurate on-line frequency identification method for N modes of interest. This method incorporates a simple supervision scheme that selects between the output of an N-mode filter bank (representing the multiple-fixed-model set) and the output of an estimator bank (representing the accurate model of the plant). The estimator bank comprises a multi-rate set of parallel N second-order recursive-least-squares estimators to achieve rapid parameter convergence. While the estimators are still in transition, the supervisor provides the configurable controller with an intermediate set of frequencies that correspond to the closest fixed model. Once the estimators converge, the supervisor selects the estimated frequency set to provide the configurable controller with an accurate representation of the current plant. This supervisor scheme significantly reduces the computational complexity as compared with existing counterparts. Experiments reveal that the proposed M4ARC approach offers the best compromise in terms of adapting to sudden and highly variable loading condition changes (within a bounded domain) while, at the same time, achieving fast transient performance.

  7. Adaptive mesh refinement for singular structures in incompressible MHD and compressible Hall-MHD with electron and ion inertia

    NASA Astrophysics Data System (ADS)

    Grauer, R.; Germaschewski, K.

    The goal of this presentation is threefold. First, the role of singular structures like shocks, vortex tubes and current sheets for understanding intermittency in small scale turbulence is demonstrated. Secondly, in order to investigate the time evolution of singular structures, effective numerical techniques have to be applied, like block structured adaptive mesh refinement combined with recent advances in treating hyperbolic equations. And thirdly, the developed numerical techniques can perfectly be applied to the question of fast reconnection demonstrated by the example of compressible Hall-MHD including electron and ion inertia. 1 Why is it worth studying singular structures? The motivation for studying singular structures has several sources. In turbulent fluid and plasma flows the formation of nearly singular structures like shocks, vortex tubes or current sheets provide an effective mechanism to transport energy from large to small scales. In the last years it has become clear that the nature of the singular structures is a key feature of small scale intermittency. In a phenomenological way this is established in She-Leveque like models (She and Leveque, 1994; Grauer, Krug and Marliani, 1994; Politano and Pouquet, 1995; M¨uller and Biskamp, 2000), which are able to describe some of the scaling properties of high order structure functions. An additional source which highlights the importance of singular structures originates from studies of a toy model of turbulence, the so-called Burgers turbulence. The very left tail of the probability distribution of velocity increments can be calculated using the instanton approach (Balkovsky, Falkovich, Kolokolov and Lebedev, 1997). Here it is interesting to note that the main contribution in the relevant path integral stems from the the singular structures which are shocks in the burgers turbulence. From a mathematical point of view the question whether

  8. 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

  9. Adaptations for the Oxidation of Polycyclic Aromatic Hydrocarbons Exhibited By the Structure of Human 450 1a2

    SciTech Connect

    Sansen, S.; Yano, J.K.; Reynald, R.L.; Schoch, G.A.; Griffin, K.J.; Stout, C.D.; Johnson, E.F.

    2007-07-12

    Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidations. This enzyme is also of great importance in the bioactivation of mutagens, including the N-hydroxylation of arylamines. P450-catalyzed reactions involve a wide range of substrates, and this versatility is reflected in a structural diversity evident in the active sites of available P450 structures. Here, we present the structure of human P450 1A2 in complex with the inhibitor alpha-naphthoflavone, determined to a resolution of 1.95 A. alpha-Naphthoflavone is bound in the active site above the distal surface of the heme prosthetic group. The structure reveals a compact, closed active site cavity that is highly adapted for the positioning and oxidation of relatively large, planar substrates. This unique topology is clearly distinct from known active site architectures of P450 family 2 and 3 enzymes and demonstrates how P450 family 1 enzymes have evolved to catalyze efficiently polycyclic aromatic hydrocarbon oxidation. This report provides the first structure of a microsomal P450 from family 1 and offers a template to study further structure-function relationships of alternative substrates and other cytochrome P450 family 1 members.

  10. 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

  11. 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

  12. Performance analysis of structured gradient algorithm. [for adaptive beamforming linear arrays

    NASA Technical Reports Server (NTRS)

    Godara, Lal C.

    1990-01-01

    The structured gradient algorithm uses a structured estimate of the array correlation matrix (ACM) to estimate the gradient required for the constrained least-mean-square (LMS) algorithm. This structure reflects the structure of the exact array correlation matrix for an equispaced linear array and is obtained by spatial averaging of the elements of the noisy correlation matrix. In its standard form the LMS algorithm does not exploit the structure of the array correlation matrix. The gradient is estimated by multiplying the array output with the receiver outputs. An analysis of the two algorithms is presented to show that the covariance of the gradient estimated by the structured method is less sensitive to the look direction signal than that estimated by the standard method. The effect of the number of elements on the signal sensitivity of the two algorithms is studied.

  13. 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.

  14. 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.

  15. 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.

  16. 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…

  17. 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.

  18. Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding.

    PubMed

    Lafuente, Maria; Atcher, Joan; Solà, Jordi; Alfonso, Ignacio

    2015-11-16

    The hierarchical self-assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide-based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error-check and error-correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed.

  19. [Histology of the living eye : Noninvasive microscopic structure and functional analysis of the retina with adaptive optics].

    PubMed

    Domdei, N; Reiniger, J L; Pfau, M; Charbel Issa, P; Holz, F G; Harmening, W M

    2017-03-01

    Equipping an ophthalmoscope with adaptive optics (AO) offers access to the living human retina with unprecedented spatial resolution. With AO, cellular structures such as the nerve fiber layer, the microvasculature of the smallest retinal capillaries, rod and cone photoreceptors and the mosaic of the retinal pigment epithelium are directly observable. A large number of studies in the normal and diseased retina have already shown that this level of detail offers new insights into disease mechanisms and progression, and promises to identify early disease markers. In conjunction with functional testing of single photoreceptors that is possible with AO microstimulation, a structure-function relationship on the cellular scale is within reach. These technological advances offer new avenues for clinical ophthalmology, interventional efforts, and basic research of the function and dysfunction of vision.

  20. 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.

  1. Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis.

    PubMed

    Segovia, Nicolás I; Gallardo-Escárate, Cristian; Poulin, Elie; Haye, Pilar A

    2017-03-16

    Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°-42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors.

  2. Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis

    PubMed Central

    Segovia, Nicolás I.; Gallardo-Escárate, Cristian; Poulin, Elie; Haye, Pilar A.

    2017-01-01

    Marine benthic organisms inhabit a heterogeneous environment in which connectivity between populations occurs mainly through dispersive larval stages, while local selective pressures acting on early life history stages lead to non-random mortality, shaping adaptive genetic structure. In order to test the influence of local adaptation and neutral processes in a marine benthic species with low dispersal, in this study we used Genotyping by Sequencing technology to compare the neutral and putatively selected signals (neutral and outlier loci, respectively) in SNPs scattered throughout the genome in six local populations of the commercially exploited ascidian Pyura chilensis along the southeast Pacific coast (24°–42°S). This species is sessile as an adult, has a short-lived larval stage, and may also be dispersed by artificial transport as biofouling. We found that the main signal in neutral loci was a highly divergent lineage present at 39°S, and a subjacent signal that indicated a separation at 30°S (north/south), widely reported in the area. North/south separation was the main signal in outlier loci, and the linage divergence at 39°S was subjacent. We conclude that the geographic structure of the genetic diversity of outlier and neutral loci was established by different strengths of environmental, historical and anthropogenic factors. PMID:28300177

  3. Coherent structure extraction in turbulent channel flow using boundary adapted wavelets

    NASA Astrophysics Data System (ADS)

    Sakurai, Teluo; Yoshimatsu, Katsunori; Schneider, Kai; Farge, Marie; Morishita, Koji; Ishihara, Takashi

    2017-04-01

    We present a construction of isotropic boundary adapted wavelets, which are orthogonal and yield a multi-resolution analysis. We analyze direct numerical simulation data of turbulent channel flow computed at a friction Reynolds number of 395, and investigate the role of coherent vorticity. Thresholding of the vorticity wavelet coefficients allows to split the flow into two parts, coherent and incoherent vorticity. The coherent vorticity is reconstructed from their few intense wavelet coefficients. The statistics of the coherent part, i.e., energy and enstrophy spectra, are close to the statistics of the total flow, and moreover, the nonlinear energy budgets are very well preserved. The remaining incoherent part, represented by the large majority of the weak wavelet coefficients, corresponds to a structureless, i.e., noise-like, background flow whose energy is equidistributed.

  4. Adaptivity via mesh movement with three-dimensional block-structured grids

    SciTech Connect

    Catherall, D.

    1996-12-31

    The method described here is one in which grid nodes are redistributed so that they are attracted towards regions of high solution activity. The major difficulty in attempting this arises from the degree of grid smoothness and orthogonality required by the flow solver. These requirements are met by suitable choice of grid equations, to be satisfied by the adapted grid, and by the inclusion of certain source terms, for added control in regions where grid movement is limited by the local geometry. The method has been coded for multiblock grids, so that complex configurations may be treated. It is demonstrated here for inviscid supercritical flow with two test cases: an ONERA M6 wing with a rounded tip, and a forward-swept wing/fuselage configuration (M151).

  5. 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.

  6. 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.

  7. 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.

  8. Enhancing the flexibility and adaptability of the DARC structural representation for computer-aided drug design.

    PubMed

    Sobel, Y; Vizet, P; Chemtob, S; Barbieux, F; Mercier, C

    1998-01-01

    Noticeable progress has been achieved in the determination of dynamic topochromatic variables for the structural representation of compounds and their situation in a given population. These independent structural variables can be further combined into more complex variables. Their contributions to the evolution of an associated property can therefore be evaluated with certainty. The risk of having correlated variables is avoided while the structural description remains exhaustive. In order to enhance the interpretative ability of the QSAR model, one or several physicochemical properties can be taken with these structural parameters as explanatory variables. Typically, partition coefficients, 3-D and quantum mechanical data are used for this purpose. The structural aspects not taken into account by the physicochemical parameters are reflected in the remaining topochromatic variables. The use of these new concepts is presented in a study of carbazole mutagenicity. The model explains 99% of the total variance with one external property and four additional topochromatic variables. The modulation of the heat of formation of an intermediate by two topochromatic variables suggests a much more precise interpretation than a simple combination of the usual external variables.

  9. Structured light 3D depth map enhancement and gesture recognition using image content adaptive filtering

    NASA Astrophysics Data System (ADS)

    Ramachandra, Vikas; Nash, James; Atanassov, Kalin; Goma, Sergio

    2013-03-01

    A structured-light system for depth estimation is a type of 3D active sensor that consists of a structured-light projector that projects an illumination pattern on the scene (e.g. mask with vertical stripes) and a camera which captures the illuminated scene. Based on the received patterns, depths of different regions in the scene can be inferred. In this paper, we use side information in the form of image structure to enhance the depth map. This side information is obtained from the received light pattern image reflected by the scene itself. The processing steps run real time. This post-processing stage in the form of depth map enhancement can be used for better hand gesture recognition, as is illustrated in this paper.

  10. Exploring the Structural Complexity of Intermetallic Compounds by an Adaptive Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Zhao, X.; Nguyen, M. C.; Zhang, W. Y.; Wang, C. Z.; Kramer, M. J.; Sellmyer, D. J.; Li, X. Z.; Zhang, F.; Ke, L. Q.; Antropov, V. P.; Ho, K. M.

    2014-01-01

    Solving the crystal structures of novel phases with nanoscale dimensions resulting from rapid quenching is difficult due to disorder and competing polymorphic phases. Advances in computer speed and algorithm sophistication have now made it feasible to predict the crystal structure of an unknown phase without any assumptions on the Bravais lattice type, atom basis, or unit cell dimensions, providing a novel approach to aid experiments in exploring complex materials with nanoscale grains. This approach is demonstrated by solving a long-standing puzzle in the complex crystal structures of the orthorhombic, rhombohedral, and hexagonal polymorphs close to the Zr2Co11 intermetallic compound. From our calculations, we identified the hard magnetic phase and the origin of high coercivity in this compound, thus guiding further development of these materials for use as high performance permanent magnets without rare-earth elements.

  11. 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.

  12. 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

    2013-03-05

    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.

  13. 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.

  14. 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...

  15. 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)…

  16. 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

  17. 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

  18. Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

    PubMed Central

    Cui, Liying; Leebens-Mack, Jim; Wang, Li-San; Tang, Jijun; Rymarquis, Linda; Stern, David B; dePamphilis, Claude W

    2006-01-01

    Background Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes. Results Ancestral gene orders were inferred and then subjected to simulated rearrangement events under the random breakage model with varying ratios of inversions and transpositions. We found that adjacent chloroplast genes in C. reinhardtii were located on the same strand much more frequently than in simulated genomes that were generated under a random rearrangement processes (increased sidedness; p < 0.0001). In addition, functionally related genes were found to be more clustered than those evolved under random rearrangements (p < 0.0001). We report evidence of co-transcription of neighboring genes, which may be responsible for the observed gene clusters in C. reinhardtii cpDNA. Conclusion Simulations and experimental evidence suggest that both selective maintenance and directional selection for gene clusters are determinants of chloroplast gene order. PMID:16469102

  19. Unattenuated structural and biochemical alterations in the rat lung during functional adaptation to ozone

    SciTech Connect

    Tepper, J.S.; Costa, D.L.; Lehmann, J.R.; Weber, M.F.; Hatch, G.E. )

    1989-08-01

    Acute ozone (O{sub 3}) exposure in humans produces changes in pulmonary function that attenuate with repeated exposure. This phenomenon, termed adaptation, has been produced in unanesthetized rats. Rats exposed to O3 (0, 0.35, 0.5, or 1.0 ppm) for 2.25 h for 5 consecutive days showed an increased frequency of breathing and a decreased tidal volume on Days 1 and 2 of exposure at all O{sub 3} concentrations. However, by Day 5 these breathing responses to O{sub 3} were diminished in rats exposed to 0.35 and 0.5 ppm, but not in rats exposed to 1.0 ppm. In addition, a flow limitation in smaller airways was observed after the second day of exposure to 0.5 ppm O{sub 3} that initially attenuated and then disappeared by the fifth day of exposure. In contrast to these findings, a light microscopic examination of fixed lung tissue sections from rats exposed to 0.5 ppm indicated a 5-day progressive pattern of epithelial damage and inflammation in the terminal bronchiolar region. A sustained 37% increase in lavageable protein was also observed over the course of the 5-day exposure regimen to 0.5 ppm. Lung glutathione increased initially, but it was within the control range on Days 4 and 5. Lung ascorbate was significantly elevated above control levels on Days 3 and 5. These data suggest that attenuation of the pulmonary function response to O{sub 3} occurs in laboratory rats with repeated exposure while biochemical and morphologic aspects of the tissue response continue to progress.

  20. 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

  1. 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

  2. The Impact of Hybrid Team Structures on Performance and Adaptation: Beyond Mechanistic and Organic Prototypes

    DTIC Science & Technology

    2004-06-01

    1961; Lawrence & Lorsch , 1967; Pennings, 1992) advocate an “if/then” approach to structuring organizations based on the current task environment...rhythm in organizational behavior. In L. L. Cummings & B. M. Staw (Eds.), Research in Organizational Behavior (Vol. 18, pp. 251-284). Greenwich, CT: JAI ...A meta- analytic review. Journal of Applied Psychology, 87, 797-807. Lawrence. P. R., & Lorsch , J. W. (1967). Organization and environment. Boston

  3. "Adapted Linear Interaction Energy": A Structure-Based LIE Parametrization for Fast Prediction of Protein-Ligand Affinities.

    PubMed

    Linder, Mats; Ranganathan, Anirudh; Brinck, Tore

    2013-02-12

    We present a structure-based parametrization of the Linear Interaction Energy (LIE) method and show that it allows for the prediction of absolute protein-ligand binding energies. We call the new model "Adapted" LIE (ALIE) because the α and β coefficients are defined by system-dependent descriptors and do therefore not require any empirical γ term. The best formulation attains a mean average deviation of 1.8 kcal/mol for a diverse test set and depends on only one fitted parameter. It is robust with respect to additional fitting and cross-validation. We compare this new approach with standard LIE by Åqvist and co-workers and the LIE + γSASA model (initially suggested by Jorgensen and co-workers) against in-house and external data sets and discuss their applicabilities.

  4. Coupled Flow-Structure-Biochemistry Simulations of Dynamic Systems of Blood Cells Using an Adaptive Surface Tracking Method.

    PubMed

    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.

  5. 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.

  6. Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52.

    PubMed

    Erler, Axel; Wegmann, Susanne; Elie-Caille, Celine; Bradshaw, Charles Richard; Maresca, Marcello; Seidel, Ralf; Habermann, Bianca; Muller, Daniel J; Stewart, A Francis

    2009-08-21

    Single-strand annealing proteins, such as Redbeta from lambda phage or eukaryotic Rad52, play roles in homologous recombination. Here, we use atomic force microscopy to examine Redbeta quaternary structure and Redbeta-DNA complexes. In the absence of DNA, Redbeta forms a shallow right-handed helix. The presence of single-stranded DNA (ssDNA) disrupts this structure. Upon addition of a second complementary ssDNA, annealing generates a left-handed helix that incorporates 14 Redbeta monomers per helical turn, with each Redbeta monomer annealing approximately 11 bp of DNA. The smallest stable annealing intermediate requires 20 bp DNA and two Redbeta monomers. Hence, we propose that Redbeta promotes base pairing by first increasing the number of transient interactions between ssDNAs. Then, annealing is promoted by the binding of a second Redbeta monomer, which nucleates the formation of a stable annealing intermediate. Using threading, we identify sequence similarities between the RecT/Redbeta and the Rad52 families, which strengthens previous suggestions, based on similarities of their quaternary structures, that they share a common mode of action. Hence, our findings have implications for a common mechanism of DNA annealing mediated by single-strand annealing proteins including Rad52.

  7. Evolutionary adaptation of plant annexins has diversified their molecular structures, interactions and functional roles.

    PubMed

    Clark, Greg B; Morgan, Reginald O; Fernandez, Maria-Pilar; Roux, Stanley J

    2012-11-01

    Annexins are an homologous, structurally related superfamily of proteins known to associate with membrane lipid and cytoskeletal components. Their involvement in membrane organization, vesicle trafficking and signaling is fundamental to cellular processes such as growth, differentiation, secretion and repair. Annexins exist in some prokaryotes and all eukaryotic phyla within which plant annexins represent a monophyletic clade of homologs descended from green algae. Genomic, proteomic and transcriptomic approaches have provided data on the diversity, cellular localization and expression patterns of different plant annexins. The availability of 35 complete plant genomes has enabled systematic comparative analysis to determine phylogenetic relationships, characterize structures and observe functional specificity between and within individual subfamilies. Short amino termini and selective erosion of the canonical type 2 calcium coordinating sites in domains 2 and 3 are typical of plant annexins. The convergent evolution of alternate functional motifs such as 'KGD', redox-sensitive Cys and hydrophobic Trp/Phe residues argues for their functional relevance and contribution to mechanistic diversity in plant annexins. This review examines recent findings and advances in plant annexin research with special focus on their structural diversity, cellular and molecular interactions and their potential integrated functions in the broader context of physiological responses.

  8. 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

  9. Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

    PubMed Central

    Kemppainen, Petri; Knight, Christopher G; Sarma, Devojit K; Hlaing, Thaung; Prakash, Anil; Maung Maung, Yan Naung; Somboon, Pradya; Mahanta, Jagadish; Walton, Catherine

    2015-01-01

    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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. Adaptive equalization

    NASA Astrophysics Data System (ADS)

    Qureshi, S. U. H.

    1985-09-01

    Theoretical work which has been effective in improving data transmission by telephone and radio links using adaptive equalization (AE) techniques is reviewed. AE has been applied to reducing the temporal dispersion effects, such as intersymbol interference, caused by the channel accessed. Attention is given to the Nyquist telegraph transmission theory, least mean square error adaptive filtering and the theory and structure of linear receive and transmit filters for reducing error. Optimum nonlinear receiver structures are discussed in terms of optimality criteria as a function of error probability. A suboptimum receiver structure is explored in the form of a decision-feedback equalizer. Consideration is also given to quadrature amplitude modulation and transversal equalization for receivers.

  17. Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure

    PubMed Central

    Yoo, Yun Joo; Sun, Lei; Poirier, Julia G.; Paterson, Andrew D.

    2016-01-01

    ABSTRACT By jointly analyzing multiple variants within a gene, instead of one at a time, gene‐based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive. It combines variant effects within the same cluster linearly, and aggregates cluster‐specific effects in a quadratic sum of squares and cross‐products, producing a test statistic with reduced degrees of freedom (df) equal to the number of clusters. By simulation studies of 1000 genes from across the genome, we demonstrate that MLC is a well‐powered and robust choice among existing methods across a broad range of gene structures. Compared to minimum P‐value, variance‐component, and principal‐component methods, the mean power of MLC is never much lower than that of other methods, and can be higher, particularly with multiple causal variants. Moreover, the variation in gene‐specific MLC test size and power across 1000 genes is less than that of other methods, suggesting it is a complementary approach for discovery in genome‐wide analysis. The cluster construction of the MLC test statistics helps reveal within‐gene LD structure, allowing interpretation of clustered variants as haplotypic effects, while multiple regression helps to distinguish direct and indirect associations. PMID:27885705

  18. Self-adapting peripherally heterofunctionalized hyperbranched polymers: formation of Janus and tripodal structures.

    PubMed

    Samuel, Ashok Zachariah; Ramakrishnan, S

    2013-01-29

    A peripherally clickable hyperbranched polyester carrying numerous propargyl terminal groups was prepared by a simple melt transesterification polycondensation of a suitably designed AB(2) monomer; this clickable hyperscaffold was then transformed into a variety of different derivatives by using the Cu-catalyzed azide-yne click reaction. Functionalization of the periphery with equimolar quantities of mutually immiscible segments, such as hydrocarbon, fluorocarbon, and PEG, yielded frustrated molecular systems that readapt and form structures wherein the immiscible segments appear to self-segregate to generate either Janus structures (when two immiscible segments are present) or tripodal structures (when three immiscible segments are present). Evidence for such self-segregation was obtained from a variety of studies, such as differential scanning calorimetry, Langmuir isotherms, AFM imaging, and small-angle X-ray scattering measurements. Crystallization of one or more of the peripheral segments reinforced this self-segregation; the weight-fraction-normalized enthalpies of melting associated with the different domains revealed a competition between the segments to optimize their crystalline organization. When one or more of the segments are amorphous, the remaining segments crystallize more effectively and consequently exhibit a higher melting enthalpy. AFM images of monolayers, transferred from the Langmuir trough, revealed that the thickness matches the expected values; furthermore, contact angle measurements clearly demonstrated that the monolayer films are fairly hydrophobic, and in the case of the tripodal hybramers, the presence of domains of hydrocarbon and fluorocarbon appears to impart nanoscale chemical heterogeneity that is reflected in the strong hysteresis in the advancing and receding contact angles.

  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. Adaptive beamforming for array imaging of plate structures using lamb waves.

    PubMed

    Engholm, Marcus; Stepinski, Tadeusz

    2010-12-01

    Lamb waves are considered a promising tool for the monitoring of plate structures. Large areas of plate structures can be monitored using active arrays employing beamforming techniques. Dispersion and multiple propagating modes are issues that need to be addressed when working with Lamb waves. Previous work has mainly focused on standard delay-and-sum (DAS) beamforming while reducing the effects of multiple modes through frequency selectivity and transducer design. This paper presents a minimum variance distortionless response (MVDR) approach for Lamb waves using a uniform rectangular array (URA) and a single transmitter. Theoretically calculated dispersion curves are used to compensate for dispersion. The combination of the MVDR approach and the two-dimensional array improves the suppression of interfering Lamb modes. The proposed approach is evaluated on simulated and experimental data and compared with the standard DAS beamformer. It is shown that the MVDR algorithm performs better in terms of higher resolution and better side lobe and mode suppression capabilities. Known issues of the MVDR approach, such as signal cancellation in highly correlated environments and poor robustness, are addressed using methods that have proven effective for the purpose in other fields of active imaging.

  2. Adaptation of roll-to-roll imprint lithography: from flexible electronics to structural templates

    NASA Astrophysics Data System (ADS)

    Holland, Edward R.; Jeans, Albert; Mei, Ping; Taussig, Carl P.; Elder, Richard E.; Bell, Cynthia; Howard, Emmett; Stowell, John

    2011-04-01

    HP has previously demonstrated the roll-to-roll (R2R) fabrication of active-matrix display backplanes using the Self-Aligned Imprint Lithography (SAIL) process. This approach permits a single imprint step to create a multi level mask comprising all patterns required for subsequent etching steps, obviating the need for multiple alignment steps. In this paper the imprint lithography technique and aspects of SAIL are reviewed. New work using imprint processing to generate structural templates, with aspect ratios approaching 6:1, for fluid containment will be presented. Arrays of transparent well structures, formed on a flexible transparent substrate provide the basis for a color display filter matrix that is filled by inkjet deposition of pigmented resins. A primary benefit of this approach is precise color pattern definition. A separation between primary color fields of 4 microns is realized without risk of color mixing or overlap. Components patterned with high absolute precision by imprint lithography were readily integrated with parts from other sources to yield flexible color reflective display demonstrator panels. This work highlights the flexibility of imprint processing and its suitability for use with a wide variety of materials and in differing applications.

  3. 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.

  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. Mechanical adaptability of the Bouligand-type structure in natural dermal armour

    NASA Astrophysics Data System (ADS)

    Zimmermann, Elizabeth A.; Gludovatz, Bernd; Schaible, Eric; Dave, Neil K. N.; Yang, Wen; Meyers, Marc A.; Ritchie, Robert O.

    2013-10-01

    Arapaima gigas, a fresh water fish found in the Amazon Basin, resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armour. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils arranged in distinct lamellae. Here we show how the Bouligand-type (twisted plywood) arrangement of collagen fibril lamellae has a key role in developing their unique protective properties, by using in situ synchrotron small-angle X-ray scattering during mechanical tensile tests to observe deformation mechanisms in the fibrils. Specifically, the Bouligand-type structure allows the lamellae to reorient in response to the loading environment; remarkably, most lamellae reorient towards the tensile axis and deform in tension through stretching/sliding mechanisms, whereas other lamellae sympathetically rotate away from the tensile axis and compress, thereby enhancing the scale’s ductility and toughness to prevent fracture.

  6. Structural and Thermal Adaptations in Polyaniline Emeraldine Salt Composites with Ferrous Oxalate

    NASA Astrophysics Data System (ADS)

    Bhardwaj, Ekta; Prasher, Sangeeta; Kumar, Mukesh; Kaur, Updesh; Sahni, Manju

    2017-02-01

    We report on the modifications induced in the structural, optical and electrical properties of polyaniline onto the ferrous oxalate composites of the polymer. Fourier transform infrared spectra, x-ray diffraction patterns and digital thermal analysis studies have been employed to associate the modifications induced in the polymer due to the enhanced dopant concentration. The studies revealed that the cation dopant may bond with the lone pair of N- of the polymer, making the polymer stretched and crystalline. The polymer has been greatly influenced at the maximum dopant concentration. It seems that the dopant has modified the initial conformation of the polymer, whereas the main chain has remained unchanged. The thermal studies also indicate that the polymer has been stabilized to a greater extent on doping.

  7. 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

  8. 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.

  9. 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.

  10. A Block-Structured Adaptive Mesh Refinement Technique with a Finite-Difference-Based Lattice Boltzmann Method

    NASA Astrophysics Data System (ADS)

    Fakhari, Abbas; Lee, Taehun

    2013-11-01

    A novel adaptive mesh refinement (AMR) algorithm for the numerical solution of fluid flow problems is presented in this study. The proposed AMR algorithm can be used to solve partial differential equations including, but not limited to, the Navier-Stokes equations using an AMR technique. Here, the lattice Boltzmann method (LBM) is employed as a substitute of the nearly incompressible Navier-Stokes equations. Besides its simplicity, the proposed AMR algorithm is straightforward and yet efficient. The idea is to remove the need for a tree-type data structure by using the pointer attributes in a unique way, along with an appropriate adjustment of the child block's IDs, to determine the neighbors of a certain block. Thanks to the unique way of invoking pointers, there is no need to construct a quad-tree (in 2D) or oct-tree (in 3D) data structure for maintaining the connectivity data between different blocks. As a result, the memory and time required for tree traversal are completely eliminated, leaving us with a clean and efficient algorithm that is easier to implement and use on parallel machines. Several benchmark studies are carried out to assess the accuracy and efficiency of the proposed AMR-LBM, including lid-driven cavity flow, vortex shedding past a square cylinder, and Kelvin-Helmholtz instability for single-phase and multiphase fluids.

  11. CSBB-ConeExclusion, adapting structure based solution virtual screening to libraries on solid support.

    PubMed

    Shave, Steven; Auer, Manfred

    2013-12-23

    Combinatorial chemical libraries produced on solid support offer fast and cost-effective access to a large number of unique compounds. If such libraries are screened directly on-bead, the speed at which chemical space can be explored by chemists is much greater than that addressable using solution based synthesis and screening methods. Solution based screening has a large supporting body of software such as structure-based virtual screening tools which enable the prediction of protein-ligand complexes. Use of these techniques to predict the protein bound complexes of compounds synthesized on solid support neglects to take into account the conjugation site on the small molecule ligand. This may invalidate predicted binding modes, the linker may be clashing with protein atoms. We present CSBB-ConeExclusion, a methodology and computer program which provides a measure of the applicability of solution dockings to solid support. Output is given in the form of statistics for each docking pose, a unique 2D visualization method which can be used to determine applicability at a glance, and automatically generated PyMol scripts allowing visualization of protein atom incursion into a defined exclusion volume. CSBB-ConeExclusion is then exemplarically used to determine the optimum attachment point for a purine library targeting cyclin-dependent kinase 2 CDK2.

  12. Structural adaptations for ram ventilation: gill fusions in scombrids and billfishes.

    PubMed

    Wegner, Nicholas C; Sepulveda, Chugey A; Aalbers, Scott A; Graham, Jeffrey B

    2013-01-01

    For ram-gill ventilators such as tunas and mackerels (family Scombridae) and billfishes (families Istiophoridae, Xiphiidae), fusions binding the gill lamellae and filaments prevent gill deformation by a fast and continuous ventilatory stream. This study examines the gills from 28 scombrid and seven billfish species in order to determine how factors such as body size, swimming speed, and the degree of dependence upon ram ventilation influence the site of occurrence and type of fusions. In the family Scombridae there is a progressive increase in the reliance on ram ventilation that correlates with the elaboration of gill fusions. This ranges from mackerels (tribe Scombrini), which only utilize ram ventilation at fast cruising speeds and lack gill fusions, to tunas (tribe Thunnini) of the genus Thunnus, which are obligate ram ventilators and have two distinct fusion types (one binding the gill lamellae and a second connecting the gill filaments). The billfishes appear to have independently evolved gill fusions that rival those of tunas in terms of structural complexity. Examination of a wide range of body sizes for some scombrids and billfishes shows that gill fusions begin to develop at lengths as small as 2.0 cm fork length. In addition to securing the spatial configuration of the gill sieve, gill fusions also appear to increase branchial resistance to slow the high-speed current produced by ram ventilation to distribute flow evenly and optimally to the respiratory exchange surfaces.

  13. Adaptive radiations, ecological specialization, and the evolutionary integration of complex morphological structures.

    PubMed

    Monteiro, Leandro R; Nogueira, Marcelo R

    2010-03-01

    The evolutionary integration of complex morphological structures is a macroevolutionary pattern in which morphogenetic components evolve in a coordinated fashion, which can result from the interplay among processes of developmental, genetic integration, and different types of selection. We tested hypotheses of ecological versus developmental factors underlying patterns of within-species and evolutionary integration in the mandible of phyllostomid bats, during the most impressive ecological and morphological radiation among mammals. Shape variation of mandibular morphogenetic components was associated with diet, and the transition of integration patterns from developmental to within-species to evolutionary was examined. Within-species (as a proxy to genetic) integration in different lineages resembled developmental integration regardless of diet specialization, however, evolutionary integration patterns reflected selection in different mandibular components. For dietary specializations requiring extensive functional changes in mastication patterns or biting, such as frugivores and sanguivores, the evolutionary integration pattern was not associated with expected within-species or developmental integration. On the other hand, specializations with lower mastication demands or without major functional reorganization (such as nectarivores and carnivores), presented evolutionary integration patterns similar to the expected developmental pattern. These results show that evolutionary integration patterns are largely a result of independent selection on specific components regardless of developmental modules.

  14. Efficient global wave propagation adapted to 3-D structural complexity: a pseudospectral/spectral-element approach

    NASA Astrophysics Data System (ADS)

    Leng, Kuangdai; Nissen-Meyer, Tarje; van Driel, Martin

    2016-12-01

    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 34 s down to 11 s. 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.

  15. The population dynamics of bacteria in physically structured habitats and the adaptive virtue of random motility.

    PubMed

    Wei, Yan; Wang, Xiaolin; Liu, Jingfang; Nememan, Ilya; Singh, Amoolya H; Weiss, Howie; Levin, Bruce R

    2011-03-08

    Why is motility so common in bacteria? An obvious answer to this ecological and evolutionary question is that in almost all habitats, bacteria need to go someplace and particularly in the direction of food. Although the machinery required for motility and chemotaxis (acquiring and processing the information needed to direct movement toward nutrients) are functionally coupled in contemporary bacteria, they are coded for by different sets of genes. Moreover, information that resources are more abundant elsewhere in a habitat would be of no value to a bacterium unless it already had the means to get there. Thus, motility must have evolved before chemotaxis, and bacteria with flagella and other machinery for propulsion in random directions must have an advantage over bacteria relegated to moving at the whim of external forces alone. However, what are the selection pressures responsible for the evolution and maintenance of undirected motility in bacteria? Here we use a combination of mathematical modeling and experiments with Escherichia coli to generate and test a parsimonious and ecologically general hypothesis for the existence of undirected motility in bacteria: it enables bacteria to move away from each other and thereby obtain greater individual shares of resources in physically structured environments. The results of our experiments not only support this hypothesis, but are quantitatively and qualitatively consistent with the predictions of our model.

  16. The masticatory system under varying functional load. Part 1: Structural adaptation of rabbit jaw muscles to reduced masticatory load.

    PubMed

    Vreeke, Marloes; Langenbach, Geerling E J; Korfage, Joannes A M; Zentner, Andrej; Grünheid, Thorsten

    2011-08-01

    Skeletal muscle fibres can change their myosin heavy-chain (MyHC) isoform and cross-sectional area, which determine their contraction velocity and maximum force generation, respectively, to adapt to varying functional loads. In general, reduced muscle activity induces transition towards faster fibres and a decrease in fibre cross-sectional area. In order to investigate the effect of a reduction in masticatory load on three functionally different jaw muscles, the MyHC composition and the corresponding cross-sectional area of fibres were determined in the superficial masseter, superficial temporalis, and digastric muscles of male juvenile New Zealand White rabbits that had been raised on a soft diet (n=8) from 8 to 20 weeks of age and in those of normal diet controls (n=8). Differences between groups were tested for statistical significance using a Mann-Whitney rank sum test. The proportion and cross-sectional area of fibres co-expressing MyHC-I and MyHC-cardiac alpha were significantly smaller in the masseter muscles of the animals that had been fed soft food than in those of the controls. In contrast, the proportions and cross-sectional areas of the various fibre types in the temporalis and digastric muscles did not differ significantly between the groups. The results suggest that reducing the masticatory load during development affects the contraction velocity and maximum force generation of the jaw-closing muscles that are primarily responsible for force generation during chewing. These muscles adapt structurally to the reduced functional load with changes in the MyHC composition and cross-sectional area mainly within their slow fibre compartment.

  17. Population genomic structure and adaptation in the zoonotic malaria parasite Plasmodium knowlesi.

    PubMed

    Assefa, Samuel; Lim, Caeul; Preston, Mark D; Duffy, Craig W; Nair, Mridul B; Adroub, Sabir A; Kadir, Khamisah A; Goldberg, Jonathan M; Neafsey, Daniel E; Divis, Paul; Clark, Taane G; Duraisingh, Manoj T; Conway, David J; Pain, Arnab; Singh, Balbir

    2015-10-20

    Malaria cases caused by the zoonotic parasite Plasmodium knowlesi are being increasingly reported throughout Southeast Asia and in travelers returning from the region. To test for evidence of signatures of selection or unusual population structure in this parasite, we surveyed genome sequence diversity in 48 clinical isolates recently sampled from Malaysian Borneo and in five lines maintained in laboratory rhesus macaques after isolation in the 1960s from Peninsular Malaysia and the Philippines. Overall genomewide nucleotide diversity (π = 6.03 × 10(-3)) was much higher than has been seen in worldwide samples of either of the major endemic malaria parasite species Plasmodium falciparum and Plasmodium vivax. A remarkable substructure is revealed within P. knowlesi, consisting of two major sympatric clusters of the clinical isolates and a third cluster comprising the laboratory isolates. There was deep differentiation between the two clusters of clinical isolates [mean genomewide fixation index (FST) = 0.21, with 9,293 SNPs having fixed differences of FST = 1.0]. This differentiation showed marked heterogeneity across the genome, with mean FST values of different chromosomes ranging from 0.08 to 0.34 and with further significant variation across regions within several chromosomes. Analysis of the largest cluster (cluster 1, 38 isolates) indicated long-term population growth, with negatively skewed allele frequency distributions (genomewide average Tajima's D = -1.35). Against this background there was evidence of balancing selection on particular genes, including the circumsporozoite protein (csp) gene, which had the top Tajima's D value (1.57), and scans of haplotype homozygosity implicate several genomic regions as being under recent positive selection.

  18. The Relationship of Organizational Structure to Organizational Adaptiveness in Elementary Schools. Report from the Project on Organization for Instruction and Administrative Arrangements.

    ERIC Educational Resources Information Center

    Walter, James Ellsworth

    This study attempted to examine the organizational structures of elementary schools in terms of complexity, centralization, formalization, stratification, and job satisfaction; and to analyze the relationship of these variables to the adaptiveness of elementary schools. More specifically, it compared the Multiunit School-Elementary (MUS-E) type of…

  19. 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

  20. The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monoxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation.

    PubMed

    Hsu, Mei-Hui; Baer, Brian R; Rettie, Allan E; Johnson, Eric F

    2017-02-06

    P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for ω-hydroxylation. The structure indicated that octane is bound in a narrow active site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for ω-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized E310 contributes to substrate positioning. The preference for ω-hydroxylation was decreased in a E310A mutant having a shorter side-chain, but overall rates of metabolism were retained. E310D and E310Q substitutions having longer side-chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane ω-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for ω-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for ω-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of un-activated primary C-H bonds.

  1. 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

  2. Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7

    NASA Astrophysics Data System (ADS)

    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

    2016-03-01

    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.

  3. Oligomerization as a strategy for cold adaptation: Structure and dynamics of the GH1 β-glucosidase from Exiguobacterium antarcticum B7.

    PubMed

    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

    2016-03-31

    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.

  4. Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine.

    PubMed

    Epelde, Lur; Lanzén, Anders; Blanco, Fernando; Urich, Tim; Garbisu, Carlos

    2015-01-01

    Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.

  5. Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models.

    PubMed

    Sugden, Isaac; Adjiman, Claire S; Pantelides, Constantinos C

    2016-12-01

    The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015). J. Chem. Theory Comput. 11, 1957-1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule's conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016). Acta Cryst. B72, 439-459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.

  6. Structure, function and molecular adaptations of haemoglobins of the polar cartilaginous fish Bathyraja eatonii and Raja hyperborea.

    PubMed

    Verde, Cinzia; De Rosa, M Cristina; Giordano, Daniela; Mosca, Donato; De Pascale, Donatella; Raiola, Luca; Cocca, Ennio; Carratore, Vitale; Giardina, Bruno; Di Prisco, Guido

    2005-07-15

    Cartilaginous fish are very ancient organisms. In the Antarctic sea, the modern chondrichthyan genera are poorly represented, with only three species of sharks and eight species of skates; the paucity of chondrichthyans is probably an ecological consequence of unusual trophic or habitat conditions in the Southern Ocean. In the Arctic, there are 26 species belonging to the class Chondrichthyes. Fish in the two polar regions have been subjected to different regional histories that have influenced the development of diversity: Antarctic marine organisms are highly stenothermal, in response to stable water temperatures, whereas the Arctic communities are exposed to seasonal temperature variations. The structure and function of the oxygen-transport haem protein from the Antarctic skate Bathyraja eatonii and from the Arctic skate Raja hyperborea (both of the subclass Elasmobranchii, order Rajiformes, family Rajidae) is reported in the present paper. These species have a single major haemoglobin (Hb 1; over 80% of the total). The Bohr-proton and the organophosphate-binding sites are absent. Thus the haemoglobins of northern and southern polar skates appear functionally similar, whereas differences were observed with several temperate elasmobranchs. Such evidence suggests that, in temperate and polar habitats, physiological adaptations have evolved along distinct pathways, whereas, in this case, the effect of the differences characterizing the two polar environments is negligible.

  7. Repercussion of geometric and dynamic constraints on the 3D rendering quality in structurally adaptive multi-view shooting systems

    NASA Astrophysics Data System (ADS)

    Ali-Bey, Mohamed; Moughamir, Saïd; Manamanni, Noureddine

    2011-12-01

    in this paper a simulator of a multi-view shooting system with parallel optical axes and structurally variable configuration is proposed. The considered system is dedicated to the production of 3D contents for auto-stereoscopic visualization. The global shooting/viewing geometrical process, which is the kernel of this shooting system, is detailed and the different viewing, transformation and capture parameters are then defined. An appropriate perspective projection model is afterward derived to work out a simulator. At first, this latter is used to validate the global geometrical process in the case of a static configuration. Next, the simulator is used to show the limitations of a static configuration of this shooting system type by considering the case of dynamic scenes and then a dynamic scheme is achieved to allow a correct capture of this kind of scenes. After that, the effect of the different geometrical capture parameters on the 3D rendering quality and the necessity or not of their adaptation is studied. Finally, some dynamic effects and their repercussions on the 3D rendering quality of dynamic scenes are analyzed using error images and some image quantization tools. Simulation and experimental results are presented throughout this paper to illustrate the different studied points. Some conclusions and perspectives end the paper. [Figure not available: see fulltext.

  8. Imaging the Antarctic mantle using adaptively parameterized P-wave tomography: Evidence for heterogeneous structure beneath West Antarctica

    NASA Astrophysics Data System (ADS)

    Hansen, Samantha E.; Graw, Jordan H.; Kenyon, Lindsey M.; Nyblade, Andrew A.; Wiens, Douglas A.; Aster, Richard C.; Huerta, Audrey D.; Anandakrishnan, Sridhar; Wilson, Terry

    2014-12-01

    Previously developed continental-scale surface wave models for Antarctica provide only broad interpretations of the mantle structure, and the best resolved features in recent regional-scale seismic models are restricted above ∼300-400 km depth. We have developed the first continental-scale P-wave velocity model beneath Antarctica using an adaptively parameterized tomography approach that includes data from many new seismic networks. Our model shows considerable, previously unrecognized mantle heterogeneity, especially beneath West Antarctica. A pronounced slow velocity anomaly extends between Ross Island and Victoria Land, further grid south than previous studies indicate. However, at least for mantle depths ≥∼200 km, this anomaly does not extend grid north along the Transantarctic Mountains (TAMs) and beneath the West Antarctic Rift System. The boundary between these slow velocities and fast velocities underlying East Antarctica is ∼100-150 km beneath the front of the TAMs, consistent with flexural uplift models. The lateral extent of the low velocity anomaly is best explained by focused, rift-related decompression melting. In West Antarctica, Marie Byrd Land is underlain by a deep (∼800 km) low velocity anomaly. Synthetic tests illustrate that the low velocities also extend laterally below the transition zone, consistent with a mantle plume ponded below the 660 km discontinuity. The slow anomalies beneath Ross Island and Marie Byrd Land are separate features, highlighting the heterogeneous upper mantle of West Antarctica.

  9. 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.

  10. European Phaseolus coccineus L. landraces: Population Structure and Adaptation, as Revealed by cpSSRs and Phenotypic Analyses

    PubMed Central

    Rodriguez, Monica; Rau, Domenico; Angioi, Simonetta A.; Bellucci, Elisa; Bitocchi, Elena; Nanni, Laura; Knüpffer, Helmut; Negri, Valeria; Papa, Roberto; Attene, Giovanna

    2013-01-01

    Relatively few studies have extensively analysed the genetic diversity of the runner bean through molecular markers. Here, we used six chloroplast microsatellites (cpSSRs) to investigate the cytoplasmic diversity of 331 European domesticated accessions of the scarlet runner bean (Phaseolus coccineus L.), including the botanical varieties albiflorus, bicolor and coccineus, and a sample of 49 domesticated and wild accessions from Mesoamerica. We further explored the pattern of diversity of the European landraces using 12 phenotypic traits on 262 individuals. For 158 European accessions, we studied the relationships between cpSSR polymorphisms and phenotypic traits. Additionally, to gain insights into the role of gene flow and migration, for a subset of 115 accessions, we compared and contrasted the results obtained by cpSSRs and phenotypic traits with those obtained in a previous study with 12 nuclear microsatellites (nuSSRs). Our results suggest that both demographic and selective factors have roles in the shaping of the population genetic structure of the European runner bean. In particular, we infer the existence of a moderate-to-strong cytoplasmic bottleneck that followed the expansion of the crop into Europe, and we deduce multiple domestication events for this species. We also observe an adaptive population differentiation in the phenology across a latitudinal gradient, which suggests that selection led to the diversification of the runner bean in Europe. The botanical varieties albiflorus, bicolor and coccineus, which are based solely on flower colour, cannot be distinguished based on these cpSSRs and nuSSRs, nor according to the 12 quantitative traits. PMID:23451209

  11. The structural rigidity of the cranium of Australopithecus africanus: implications for diet, dietary adaptations, and the allometry of feeding biomechanics.

    PubMed

    Strait, David S; Grosse, Ian R; Dechow, Paul C; Smith, Amanda L; Wang, Qian; Weber, Gerhard W; Neubauer, Simon; Slice, Dennis E; Chalk, Janine; Richmond, Brian G; Lucas, Peter W; Spencer, Mark A; Schrein, Caitlin; Wright, Barth W; Byron, Craig; Ross, Callum F

    2010-04-01

    Australopithecus africanus is an early hominin (i.e., human relative) believed to exhibit stress-reducing adaptations in its craniofacial skeleton that may be related to the consumption of resistant food items using its premolar teeth. Finite element analyses simulating molar and premolar biting were used to test the hypothesis that the cranium of A. africanus is structurally more rigid than that of Macaca fascicularis, an Old World monkey that lacks derived australopith facial features. Previously generated finite element models of crania of these species were subjected to isometrically scaled loads, permitting a direct comparison of strain magnitudes. Moreover, strain energy (SE) in the models was compared after results were scaled to account for differences in bone volume and muscle forces. Results indicate that strains in certain skeletal regions below the orbits are higher in M. fascicularis than in A. africanus. Moreover, although premolar bites produce von Mises strains in the rostrum that are elevated relative to those produced by molar biting in both species, rostral strains are much higher in the macaque than in the australopith. These data suggest that at least the midface of A. africanus is more rigid than that of M. fascicularis. Comparisons of SE reveal that the A. africanus cranium is, overall, more rigid than that of M. fascicularis during premolar biting. This is consistent with the hypothesis that this hominin may have periodically consumed large, hard food items. However, the SE data suggest that the A. africanus cranium is marginally less rigid than that of the macaque during molar biting. It is hypothesized that the SE results are being influenced by the allometric scaling of cranial cortical bone thickness.

  12. Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge Variability.

    PubMed

    Ochoa-Leyva, Adrián; Barona-Gómez, Francisco; Saab-Rincón, Gloria; Verdel-Aranda, Karina; Sánchez, Filiberto; Soberón, Xavier

    2011-08-05

    Evolution of proteins involves sequence changes that are frequently localized at loop regions, revealing their important role in natural evolution. However, the development of strategies to understand and imitate such events constitutes a challenge to design novel enzymes in the laboratory. In this study, we show how to adapt loop swapping as semiautonomous units of functional groups in an enzyme with the (β/α)(8)-barrel and how this functional adaptation can be measured in vivo. To mimic the natural mechanism providing loop variability in antibodies, we developed an overlap PCR strategy. This includes introduction of sequence diversity at two hinge residues, which connect the new loops with the rest of the protein scaffold, and we demonstrate that this is necessary for a successful exploration of functional sequence space. This design allowed us to explore the sequence requirements to functional adaptation of each loop replacement that may not be sampled otherwise. Libraries generated following this strategy were evaluated in terms of their folding competence and their functional proficiency, an observation that was formalized as a Structure-Function Loop Adaptability value. Molecular details about the function and structure of some variants were obtained by enzyme kinetics and circular dichroism. This strategy yields functional variants that retain the original activity at higher frequencies, suggesting a new strategy for protein engineering that incorporates a more divergent sequence exploration beyond that limited to point mutations. We discuss how this approach may provide insights into the mechanism of enzyme evolution and function.

  13. 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

  14. 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

  15. A new type of color-coded light structures for an adapted and rapid determination of point correspondences for 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Caulier, Yannick; Bernhard, Luc; Spinnler, Klaus

    2011-05-01

    This paper proposes a new type of color coded light structures for the inspection of complex moving objects. The novelty of the methods relies on the generation of free-form color patterns permitting the projection of color structures adapted to the geometry of the surfaces to be characterized. The point correspondence determination algorithm consists of a stepwise procedure involving simple and computationally fast methods. The algorithm is therefore robust against varying recording conditions typically arising in real-time quality control environments and can be further integrated for industrial inspection purposes. The proposed approach is validated and compared on the basis of different experimentations concerning the 3D surface reconstruction by projecting adapted spatial color coded patterns. It is demonstrated that in case of certain inspection requirements, the method permits to code more reference points that similar color coded matrix methods.

  16. 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

  17. 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

  18. Structural Adaptation of Cold-Active RTX Lipase from Pseudomonas sp. Strain AMS8 Revealed via Homology and Molecular Dynamics Simulation Approaches

    PubMed Central

    Mohamad Ali, Mohd. Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

    2013-01-01

    The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future. PMID:23738333

  19. Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

    PubMed

    Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

    2013-01-01

    The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

  20. 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...

  1. 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.

  2. 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.

  3. Visual Adaptation

    PubMed Central

    Webster, Michael A.

    2015-01-01

    Sensory systems continuously mold themselves to the widely varying contexts in which they must operate. Studies of these adaptations have played a long and central role in vision science. In part this is because the specific adaptations remain a powerful tool for dissecting vision, by exposing the mechanisms that are adapting. That is, “if it adapts, it's there.” Many insights about vision have come from using adaptation in this way, as a method. A second important trend has been the realization that the processes of adaptation are themselves essential to how vision works, and thus are likely to operate at all levels. That is, “if it's there, it adapts.” This has focused interest on the mechanisms of adaptation as the target rather than the probe. Together both approaches have led to an emerging insight of adaptation as a fundamental and ubiquitous coding strategy impacting all aspects of how we see. PMID:26858985

  4. 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.

  5. Internal skeletal analysis of the colonial azooxanthellate scleractinian Dendrophyllia cribrosa using microfocus X-ray CT images: underlying basis for its rigid and highly adaptive colony structure.

    PubMed

    Sentoku, Asuka; Morisaki, Hitomi; Masumoto, Shinji; Ohno, Rie; Tomiyama, Takayuki; Ezaki, Yoichi

    2015-01-01

    Dendrophyllid Scleractinia exhibit a variety of colonial morphologies, formed under the strict constraints on (1) budding sites, (2) orientations of the directive septa of offsets, (3) inclination of budding direction, and (4) those constraints in every generation. Dendrophyllia cribrosa exhibits a sympodial dendroid form, characteristically large coralla, and occasional fusions of adjacent branches within the same colony. Adjacent corallites are bound and supported by coenosteum skeleton. This study examined the inner skeletal structures at the junctions of fused branches using a non-destructive microfocus X-ray computed tomography (CT) imaging approach, and considered the reasons for the large colonial sizes and their adaptive significance. Three-dimensional reconstructions of two-dimensional X-ray CT images reveal that individual corallites are not directly connected in fused parts. Additionally, no completely buried individuals were found within fused skeleton. When adjacent branches approach one another, constituent corallites change their growth directions to avoid collisions between the branches. The adjacent branches fuse without a reduction in the number of constituent corallites, leading to the establishment of reticular and rigid colonial structures. In addition, a nearly even distribution of individuals on the colony surface facilitates efficient intake of nutrients. Thus, the growth of large D. cribrosa colonies involves avoidance of collision between constituent individuals, the reinforcement of colonial structure, and efficient uptake of nutrients. These observations provide insights on the dynamics of interrelationships between colony-making mechanisms and the adaptive strategies required under habitat conditions such as specific current activities.

  6. The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance.

    PubMed

    Lee, Dong-Keun; Chung, Pil Joong; Jeong, Jin Seo; Jang, Geupil; Bang, Seung Woon; Jung, Harin; Kim, Youn Shic; Ha, Sun-Hwa; Choi, Yang Do; Kim, Ju-Kon

    2016-11-28

    Drought has a serious impact on agriculture worldwide. A plant's ability to adapt to rhizosphere drought stress requires reprogramming of root growth and development. Although physiological studies have documented the root adaption for tolerance to the drought stress, underlying molecular mechanisms is still incomplete, which is essential for crop engineering. Here, we identified OsNAC6-mediated root structural adaptations, including increased root number and root diameter, which enhanced drought tolerance. Multiyear drought field tests demonstrated that the grain yield of OsNAC6 root-specific overexpressing transgenic rice lines was less affected by drought stress than were nontransgenic controls. Genome-wide analyses of loss- and gain-of-function mutants revealed that OsNAC6 up-regulates the expression of direct target genes involved in membrane modification, nicotianamine (NA) biosynthesis, glutathione relocation, 3'-phophoadenosine 5'-phosphosulphate accumulation and glycosylation, which represent multiple drought tolerance pathways. Moreover, overexpression of NICOTIANAMINE SYNTHASE genes, direct targets of OsNAC6, promoted the accumulation of the metal chelator NA and, consequently, drought tolerance. Collectively, OsNAC6 orchestrates novel molecular drought tolerance mechanisms and has potential for the biotechnological development of high-yielding crops under water-limiting conditions.

  7. 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...

  8. 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

  9. Adaptive microclimatic structural and expressional dehydrin 1 evolution in wild barley, Hordeum spontaneum, at 'Evolution Canyon', Mount Carmel, Israel.

    PubMed

    Yang, Zujun; Zhang, Tao; Bolshoy, Alexander; Beharav, Alexander; Nevo, Eviatar

    2009-05-01

    'Evolution Canyon' (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unravelling evolution in action highlighting the twin evolutionary processes of adaptation and speciation. A major model organism in ECI is wild barley, Hordeum spontaneum, the progenitor of cultivated barley, which displays dramatic interslope adaptive and speciational divergence on the 'African' dry slope (AS) and the 'European' humid slope (ES), separated on average by 200 m. Here we examined interslope single nucleotide polymorphism (SNP) sequences and the expression diversity of the drought resistant dehydrin 1 gene (Dhn1) between the opposite slopes. We analysed 47 plants (genotypes), 4-10 individuals in each of seven stations (populations) in an area of 7000 m(2), for Dhn1 sequence diversity located in the 5' upstream flanking region of the gene. We found significant levels of Dhn1 genic diversity represented by 29 haplotypes, derived from 45 SNPs in a total of 708 bp sites. Most of the haplotypes, 25 out of 29 (= 86.2%), were represented by one genotype; hence, unique to one population. Only a single haplotype was common to both slopes. Genetic divergence of sequence and haplotype diversity was generally and significantly different among the populations and slopes. Nucleotide diversity was higher on the AS, whereas haplotype diversity was higher on the ES. Interslope divergence was significantly higher than intraslope divergence. The applied Tajima D rejected neutrality of the SNP diversity. The Dhn1 expression under dehydration indicated interslope divergent expression between AS and ES genotypes, reinforcing Dhn1 associated with drought resistance of wild barley at 'Evolution Canyon'. These results are inexplicable by mutation, gene flow, or chance effects, and support adaptive natural microclimatic selection as the major evolutionary divergent driving force.

  10. Adaptation of the dermal collagen structure of human skin and scar tissue in response to stretch: an experimental study.

    PubMed

    Verhaegen, Pauline D; Schouten, Hennie J; Tigchelaar-Gutter, Wikky; van Marle, Jan; van Noorden, Cornelis J; Middelkoop, Esther; van Zuijlen, Paul P

    2012-01-01

    Surgeons are often faced with large defects that are difficult to close. Stretching adjacent skin can facilitate wound closure. In clinical practice, intraoperative stretching is performed in a cyclical or continuous fashion. However, exact mechanisms of tissue adaptation to stretch remain unclear. Therefore, we investigated collagen and elastin orientation and morphology of stretched and nonstretched healthy skin and scars. Tissue samples were stretched, fixed in stretched-out position, and processed for histology. Objective methods were used to quantify the collagen orientation index (COI), bundle thickness, and bundle spacing. Also sections were analyzed for elastin orientation and quantity. Significantly more parallel aligned collagen bundles were found after cyclical (COI = 0.57) and continuous stretch (COI = 0.57) compared with nonstretched skin (COI = 0.40). Similarly, more parallel aligned elastin was found after stretch. Also, significantly thicker collagen bundles and more bundle spacing were found after stretch. For stretched scars, significantly more parallel aligned collagen was found (COI = 0.61) compared with nonstretched scars (COI = 0.49). In conclusion, both elastin and collagen realign in a parallel fashion in response to stretch. For healthy skin, thicker bundles and more space between the bundles were found. Rapid changes in extension, alignment, and collagen morphology appear to be the underlying mechanisms of adaptation to stretching.

  11. 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.

  12. 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.

  13. Structural 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...

  14. 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.

  15. 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.

  16. IIR algorithms for adaptive line enhancement

    SciTech Connect

    David, R.A.; Stearns, S.D.; Elliott, G.R.; Etter, D.M.

    1983-01-01

    We introduce a simple IIR structure for the adaptive line enhancer. Two algorithms based on gradient-search techniques are presented for adapting the structure. Results from experiments which utilized real data as well as computer simulations are provided.

  17. 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

  18. Validation of the factor structure of the Greek adaptation of the Sociocultural Attitudes Towards Appearance Questionnaire (SATAQ-3).

    PubMed

    Argyrides, Marios; Kkeli, Natalie; Kendeou, Panayiota

    2014-06-01

    The current study aimed to confirm the factor structure and reliability of the newly translated Greek version of the Sociocultural Attitudes Towards Appearance Questionnaire-3 (SATAQ-3) among 1753 Greek-Cypriot high school students. Results of the structural equation modeling indicated a very good fit with the original four-factor structure of the SATAQ-3 for both males and females. The Cronbach's alpha coefficients for the four subscales were .92 for 'Internalization-General', .82 for 'Internalization-Athlete', .94 for 'Pressure' and .88 for 'Information'. Further analyses showed no significant differences between BMI categories with respect to the Internalization-General, Internalization-Athlete and Information factors but there were significant differences on the Pressure factor. The findings of the current study support the existence of the original four-factor structure of the SATAQ-3. The validity and reliability results of the Greek version of the SATAQ-3 support its use in Greek-speaking countries or populations.

  19. 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.

  20. Structural analysis of alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline conditions.

    PubMed

    Zhao, Yueju; Zhang, Yunhua; Cao, Yang; Qi, Jianxun; Mao, Liangwei; Xue, Yanfen; Gao, Feng; Peng, Hao; Wang, Xiaowei; Gao, George F; Ma, Yanhe

    2011-01-28

    Significant progress has been made in isolating novel alkaline β-mannanases, however, there is a paucity of information concerning the structural basis for alkaline tolerance displayed by these β-mannanases. We report the catalytic domain structure of an industrially important β-mannanase from the alkaliphilic Bacillus sp. N16-5 (BSP165 MAN) at a resolution of 1.6 Å. This enzyme, classified into subfamily 8 in glycosyl hydrolase family 5 (GH5), has a pH optimum of enzymatic activity at pH 9.5 and folds into a classic (β/α)(8)-barrel. In order to gain insight into molecular features for alkaline adaptation, we compared BSP165 MAN with previously reported GH5 β-mannanases. It was revealed that BSP165 MAN and other subfamily 8 β-mannanases have significantly increased hydrophobic and Arg residues content and decreased polar residues, comparing to β-mannanases of subfamily 7 or 10 in GH5 which display optimum activities at lower pH. Further, extensive structural comparisons show alkaline β-mannanases possess a set of distinctive features. Position and length of some helices, strands and loops of the TIM barrel structures are changed, which contributes, to a certain degree, to the distinctly different shaped (β/α)(8)-barrels, thus affecting the catalytic environment of these enzymes. The number of negatively charged residues is increased on the molecular surface, and fewer polar residues are exposed to the solvent. Two amino acid substitutions in the vicinity of the acid/base catalyst were proposed to be possibly responsible for the variation in pH optimum of these homologous enzymes in subfamily 8 of GH5, identified by sequence homology analysis and pK(a) calculations of the active site residues. Mutational analysis has proved that Gln91 and Glu226 are important for BSP165 MAN to function at high pH. These findings are proposed to be possible factors implicated in the alkaline adaptation of GH5 β-mannanases and will help to further understanding of

  1. 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.

  2. 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

  3. 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

  4. Crystal structure of eta-crystallin: adaptation of a class 1 aldehyde dehydrogenase for a new role in the eye lens.

    PubMed

    Bateman, O A; Purkiss, A G; van Montfort, R; Slingsby, C; Graham, C; Wistow, G

    2003-04-22

    Eta-crystallin is a retinal dehydrogenase that has acquired a role as a structural protein in the eye lens of elephant shrews, members of an ancient order of mammals. While it retains some activity toward retinal, which is oxidized to retinoic acid, the protein has acquired a number of specific sequence changes that have presumably been selected to enhance the lens role. The crystal structure of eta-crystallin, in common with class 1 and 2 ALDHs, is a dimer of dimers. It has a better-defined NAD binding site than those of related mammalian ALDH1 enzymes with the cofactor bound in the "hydride transfer" position in all four monomers with small differences about the dimer dyads. Although the active site is well conserved, the substrate-binding site is larger in eta-crystallin, and there are some mutations to the substrate access tunnel that might affect binding or release of substrate and product. It is possible that eta-crystallin has lost flexibility to improve its role in the lens. Enhanced binding of cofactor could enable it to act as a UV/blue light filter in the lens, improving visual acuity. The structure not only gives a view of a "natural mutant" of ALDH1 illustrating the adaptive conflict that can arise in multifunctional proteins, but also provides a well-ordered NAD binding site structure for this class of enzymes with important roles in development and health.

  5. 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.

  6. 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…

  7. 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

  8. Adaptively Forward Modelling the Spatial Magnetic Effects Due to a Magnetized Structure by Tesseroids in Spherical Coordinate System

    NASA Astrophysics Data System (ADS)

    Du, Jinsong; Chen, Chao

    2015-04-01

    GLQI when nodes are ones. The RP method shows a better accuracy when the computing point nears the source located in the low latitude but worse in the high latitude where the RP fails to depict the actual geometric shape of the tesseroid. Because the error decays most quickly as the distance between the source and the computing point increasing, the 3D GLQI with higher than first-order Gaussian nodes is most efficiently combined with the reasonable subdivision technique. Investigation of computational efficiency indicates that, in practical applications, combination of different methods and reasonable choices for the number of subdivision and the Gaussian nodes of the GLQI can produce the most accurate results in an acceptable computational time. The calculated magnetic effects of the global lithospheric magnetization model show that there are little differences between the results at the satellite altitude by the MD method and by the 3D GLQI method but very large differences at the low altitude, which means that the MD method will introduce large errors and become worse and worse as the altitude decreasing. However, the corresponding computation is very time-consuming, especially when the geometric size of the source is large or the DSO is short. Because the error decays most quickly as the DSO increasing, the 3D GLQI with higher than first-order Gaussian nodes is most efficiently combined with the reasonable subdivision technique. Therefore, in order to reduce the computing time while maintaining the desired accuracy, an adaptive forward modeling scheme that consists of using a fixed Gaussian order and recursively subdivision is employed. As a key point in this approach, the relationships between the accuracy of the magnetic effects and the size-to-DSO ratio are focused and investigated. Numerical test shows that this adaptive approach improves the computational efficiency significantly.

  9. Hot Very Small dust Grains in NGC 1068 seen in jet induced structures thanks to VLT/NACO adaptive optics

    NASA Astrophysics Data System (ADS)

    Rouan, D.; Lacombe, F.; Gendron, E.; Gratadour, D.; Clénet, Y.; Lagrange, A.-M.; Mouillet, D.; Boisson, C.; Rousset, G.; Fusco, T.; Mugnier, L.; Séchaud, M.; Thatte, N.; Genzel, R.; Gigan, P.; Arsenault, R.; Kern, P.

    2004-04-01

    We present K, L and M diffraction-limited images of NGC 1068, obtained with NAOS+CONICA at VLT/YEPUN over a 3.5 arcsec × 3.5 arcsec region around the central engine. Hot dust (T_col = 550-650 K) is found to be distributed in three main structurally different regions: (a) in the true nucleus, seen as a quasi-spherical, however slightly NS elongated, core of extremely hot dust, resolved in K and L with respective diameters of ≈5 pc and 8.5 pc; (b) along the North-South direction, according to a spiral arm like structure and a southern tongue; (c) as a set of parallel elongated nodules (wave-like) on each side, albeit mainly at north, of the jet, at a distance of 50 to 70 pc from the central engine. The IR images reveal several structures also clearly observed on either radio maps, mid-IR or HST UV-visible maps, so that a very precise registration of the respective emissions can be done for the first time from UV to 6 cm. These results do support the current interpretion that source (a) corresponds to emission from dust near sublimation temperature delimiting the walls of the cavity in the central obscuring torus. Structure (b) is thought to be a mixture of hot dust and active star forming regions along a micro spiral structure that could trace the tidal mechanism bringing matter to the central engine. Structure c) which was not known, exhibits too high a temperature for ``classical'' grains; it is most probably the signature of transiently heated very small dust grains (VSG): nano-diamonds, which are resistant and can form in strong UV field or in shocks, are very attractive candidates. The ``waves'' can be condensations triggered by jet induced shocks, as predicted by recent models. First estimates, based on a simple VSG model and on a detailed radiative transfer model, do agree with those interpretations, both qualitatively and quantitatively. Based on observations collected at the ESO/Paranal YEPUN telescope, Proposal 70.B-0307(A).

  10. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.

    PubMed

    Edwards, Thomas E; Ferré-D'Amaré, Adrian R

    2006-09-01

    Riboswitches are noncoding mRNA elements that bind small-molecule metabolites with high affinity and specificity, and they regulate the expression of associated genes. The thi-box riboswitch can exhibit a 1000-fold higher affinity for thiamine pyrophosphate over closely related noncognate compounds such as thiamine monophosphate. To understand the chemical basis of thi-box pyrophosphate specificity, we have determined crystal structures of an E. coli thi-box bound to thiamine pyrophosphate, thiamine monophosphate, and the structural analogs benfotiamine and pyrithiamine. When bound to monophosphorylated compounds, the RNA elements that recognize the thiamine and phosphate moieties of the ligand move closer together. This allows the riboswitch to recognize the monophosphate in a manner similar to how it recognizes the beta-phosphate of thiamine pyrophosphate. In the pyrithiamine complex, the pyrophosphate binding site is largely unstructured. These results show how the riboswitch can bind to various metabolites, and why the thi-box preferentially binds thiamine pyrophosphate.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Intestinal adaptation following resection.

    PubMed

    Tappenden, Kelly A

    2014-05-01

    Intestinal adaptation is a natural compensatory process that occurs following extensive intestinal resection, whereby structural and functional changes in the intestine improve nutrient and fluid absorption in the remnant bowel. In animal studies, postresection structural adaptations include bowel lengthening and thickening and increases in villus height and crypt depth. Functional changes include increased nutrient transporter expression, accelerated crypt cell differentiation, and slowed transit time. In adult humans, data regarding adaptive changes are sparse, and the mechanisms underlying intestinal adaptation remain to be fully elucidated. Several factors influence the degree of intestinal adaptation that occurs post resection, including site and extent of resection, luminal stimulation with enteral nutrients, and intestinotrophic factors. Two intestinotrophic growth factors, the glucagon-like peptide 2 analog teduglutide and recombinant growth hormone (somatropin), are now approved for clinical use in patients with short bowel syndrome (SBS). Both agents enhance fluid absorption and decrease requirements for parenteral nutrition (PN) and/or intravenous fluid. Intestinal adaptation has been thought to be limited to the first 1-2 years following resection in humans. However, recent data suggest that a significant proportion of adult patients with SBS can achieve enteral autonomy, even after many years of PN dependence, particularly with trophic stimulation.

  17. Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure

    PubMed Central

    Sillo, Fabiano; Garbelotto, Matteo; Friedman, Maria; Gonthier, Paolo

    2015-01-01

    It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34–41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are incongruent; and 4) test the previously formulated hypothesis that genes involved in pathogenicity may be less divergent between the two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies. Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naïve hosts. PMID:26527650

  18. Telescope Adaptive Optics Code

    SciTech Connect

    Phillion, D.

    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 default 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

  19. 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.

  20. 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

  1. Evolution at ‘Sutures’ and ‘Centers’: Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes

    PubMed Central

    Cooper, Jacob D.; Kerr, Benjamin

    2016-01-01

    Epistatic interactions among genes can give rise to rugged fitness landscapes, in which multiple “peaks” of high-fitness allele combinations are separated by “valleys” of low-fitness genotypes. How populations traverse rugged fitness landscapes is a long-standing question in evolutionary biology. Sexual reproduction may affect how a population moves within a rugged fitness landscape. Sex may generate new high-fitness genotypes by recombination, but it may also destroy high-fitness genotypes by shuffling the genes of a fit parent with a genetically distinct mate, creating low-fitness offspring. Either of these opposing aspects of sex require genotypic diversity in the population. Spatially structured populations may harbor more diversity than well-mixed populations, potentially amplifying both positive and negative effects of sex. On the other hand, spatial structure leads to clumping in which mating is more likely to occur between like types, diminishing the effects of recombination. In this study, we use computer simulations to investigate the combined effects of recombination and spatial structure on adaptation in rugged fitness landscapes. We find that spatially restricted mating and offspring dispersal may allow multiple genotypes inhabiting suboptimal peaks to coexist, and recombination at the “sutures” between the clusters of these genotypes can create genetically novel offspring. Sometimes such an offspring genotype inhabits a new peak on the fitness landscape. In such a case, spatially restricted mating allows this fledgling subpopulation to avoid recombination with distinct genotypes, as mates are more likely to be the same genotype. Such population “centers” can allow nascent peaks to establish despite recombination. Spatial structure may therefore allow an evolving population to enjoy the creative side of sexual recombination while avoiding its destructive side. PMID:27973606

  2. 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.

  3. 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)

  4. Integron-associated mobile gene cassettes code for folded proteins: the structure of Bal32a, a new member of the adaptable alpha+beta barrel family.

    PubMed

    Robinson, Andrew; Wu, Peter S-C; Harrop, Stephen J; Schaeffer, Patrick M; Dosztányi, Zsuzsanna; Gillings, Michael R; Holmes, Andrew J; Nevalainen, K M Helena; Stokes, H W; Otting, Gottfried; Dixon, Nicholas E; Curmi, Paul M G; Mabbutt, Bridget C

    2005-03-11

    The wide-ranging physiology and large genetic variability observed for prokaryotes is largely attributed, not to the prokaryotic genome itself, but rather to mechanisms of lateral gene transfer. Cassette PCR has been used to sample the integron/gene cassette metagenome from different natural environments without laboratory cultivation of the host organism, and without prior knowledge of any target protein sequence. Since over 90% of cassette genes are unrelated to any sequence in the current databases, it is not clear whether these genes code for folded functional proteins. We have selected a sample of eight cassette-encoded genes with no known homologs; five have been isolated as soluble protein products and shown by biophysical techniques to be folded. In solution, at least three of these proteins organise as stable oligomeric assemblies. The tertiary structure of one of these, Bal32a derived from a contaminated soil site, has been solved by X-ray crystallography to 1.8 A resolution. From the three-dimensional structure, Bal32a is found to be a member of the highly adaptable alpha+beta barrel family of transport proteins and enzymes. In Bal32a, the barrel cavity is unusually deep and inaccessible to solvent. Polar side-chains in its interior are reminiscent of catalytic sites of limonene-1,2-epoxide hydrolase and nogalonic acid methyl ester cyclase. These studies demonstrate the viability of direct sampling of mobile DNA as a route for the discovery of novel proteins.

  5. Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis.

    PubMed

    Ramli, Aizi Nor Mazila; Azhar, Mohd Akmal; Shamsir, Mohd Shahir; Rabu, Amir; Murad, Abdul Munir Abdul; Mahadi, Nor Muhammad; Illias, Rosli Md

    2013-08-01

    A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica PI12 has yet to be studied in detail. A 3D model of AmyPI12 was built using a homology modelling approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9.9. Analysis of the AmyPI12 model revealed the presence of binding sites for a conserved calcium ion (CaI), non-conserved calcium ions (CaII and CaIII) and a sodium ion (Na). Compared with its template-the thermostable α-amylase from Bacillus stearothermophilus (BSTA)-the binding of CaII, CaIII and Na ions in AmyPI12 was observed to be looser, which suggests that the low stability of AmyPI12 allows the protein to work at different temperature scales. The AmyPI12 amino acid sequence and model were compared with thermophilic α-amylases from Bacillus species that provided the highest structural similarities with AmyPI12. These comparative studies will enable identification of possible determinants of cold adaptation.

  6. Adaptation of the distal convoluted tubule of the rat. Structural and functional effects of dietary salt intake and chronic diuretic infusion.

    PubMed Central

    Ellison, D H; Velázquez, H; Wright, F S

    1989-01-01

    We studied the effects of dietary NaCl intake on the renal distal tubule by feeding rats high or low NaCl chow or by chronically infusing furosemide. Furosemide-treated animals were offered saline as drinking fluid to replace urinary losses. Effects of naCl intake were evaluated using free-flow micropuncture, in vivo microperfusion, and morphometric techniques. Dietary NaCl restriction did not affect NaCl delivery to the early distal tubule but markedly increased the capacity of the distal convoluted tubule to transport Na and Cl. Chronic furosemide infusion increased NaCl delivery to the early distal tubule and also increased the rates of Na and Cl transport above the rates observed in low NaCl diet rats. When compared with high NaCl intake alone, chronic furosemide infusion with saline ingestion increased the fractional volume of distal convoluted tubule cells by nearly 100%, whereas dietary NaCl restriction had no effect. The results are consistent with the hypotheses that (a) chronic NaCl restriction increases the transport ability of the distal convoluted tubule independent of changes in tubule structure, (b) high rates of ion delivery to the distal nephron cause tubule hypertrophy, and (c) tubule hypertrophy is associated with increases in ion transport capacity. They indicate that the distal tubule adapts functionally and structurally to perturbations in dietary Na and Cl intake. Images PMID:2910903

  7. 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.

  8. Local adaptation to soil hypoxia determines the structure of an arbuscular mycorrhizal fungal community in roots from natural CO₂ springs.

    PubMed

    Maček, Irena; Dumbrell, Alex J; Nelson, Michaela; Fitter, Alastair H; Vodnik, Dominik; Helgason, Thorunn

    2011-07-01

    The processes responsible for producing and maintaining the diversity of natural arbuscular mycorrhizal (AM) fungal communities remain largely unknown. We used natural CO(2) springs (mofettes), which create hypoxic soil environments, to determine whether a long-term, directional, abiotic selection pressure could change AM fungal community structure and drive the selection of particular AM fungal phylotypes. We explored whether those phylotypes that appear exclusively in hypoxic soils are local specialists or widespread generalists able to tolerate a range of soil conditions. AM fungal community composition was characterized by cloning, restriction fragment length polymorphism typing, and the sequencing of small subunit rRNA genes from roots of four plant species growing at high (hypoxic) and low (control) geological CO(2) exposure. We found significant levels of AM fungal community turnover (β diversity) between soil types and the numerical dominance of two AM fungal phylotypes in hypoxic soils. Our results strongly suggest that direct environmental selection acting on AM fungi is a major factor regulating AM fungal communities and their phylogeographic patterns. Consequently, some AM fungi are more strongly associated with local variations in the soil environment than with their host plant's distribution.

  9. ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

    PubMed

    Vishnepolsky, Boris; Pirtskhalava, Malak

    2009-06-01

    The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.

  10. 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.

  11. 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…

  12. 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...

  13. 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.

  14. 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.

  15. Seasonal adaptations of the tuberous roots of Ranunculus asiaticus to desiccation and resurrection by changes in cell structure and protein content.

    PubMed

    Kamenetsky, Rina; Peterson, R Larry; Melville, Lewis H; Machado, Cibele F; Bewley, J Derek

    2005-04-01

    The annual developmental cycle of tuberous roots of Ranunculus asiaticus was studied with respect to structure and content of their cells, to understand how these roots are adapted to desiccation, high temperature and rehydration. Light microscopy, histochemical analysis, and protein analyses by SDS-PAGE were employed at eight stages of annual root development. During growth and maturation of the roots, cortical cells increased in size and their cell walls accumulated pectin materials in a distinct layer to the inside of the primary walls, with pits between adjoining cells. The number of starch granules and protein bodies also increased within the cells. Several discrete proteins accumulated. Following quiescence and rehydration of the roots there was a loss of starch and proteins from the cells, and cell walls decreased in thickness. The resurrection geophyte R. asiaticus possesses desiccation-tolerant annual roots. They store carbon and nitrogen reserves within their cells, and pectin within the walls to support growth of the plant following summer quiescence and rehydration.

  16. Accurate and efficient representation of intra­molecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models

    PubMed Central

    Sugden, Isaac; Adjiman, Claire S.; Pantelides, Constantinos C.

    2016-01-01

    The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput. 11, 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B72, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions. PMID:27910837

  17. History of adaptation determines short-term shifts in performance and community structure of hydrogen-producing microbial communities degrading wheat straw.

    PubMed

    Valdez-Vazquez, Idania; Morales, Ana L; Escalante, Ana E

    2017-03-14

    This study addresses the question of ecological interest for the determination of structure and diversity of microbial communities that degrade lignocellulosic biomasses to produce biofuels. Two microbial consortia with different history, native of wheat straw (NWS) and from a methanogenic digester (MD) fed with cow manure, were contrasted in terms of hydrogen performance, substrate disintegration and microbial diversity. NWS outperformed the hydrogen production rate of MD. Microscopic images revealed that NWS acted on the cuticle and epidermis, generating cellulose strands with high crystallinity, while MD degraded deeper layers, equally affecting all polysaccharides. The bacterial composition markedly differed according to the inocula origin. NWS almost solely comprised hydrogen producers of the phyla Firmicutes and Proteobacteria, with 38% members of Enterococcus. After hydrogen fermentation, NWS comprised 8% Syntrophococcus, an acetogen that cleaves aryl ethers of constituent groups on the aromatic components of lignin. Conversely, MD comprised thirteen phyla, primarily including Firmicutes with H2 -producing members, and Bacteroidetes with non-H2 -producing members, which reduced the hydrogen performance. Overall, the results of this study provide clear evidence that the history of adaptation of NWS enhanced the hydrogen performance from untreated wheat straw. Further, native wheat straw communities have the potential to refine cellulose fibers and produce biofuels simultaneously.

  18. 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

  19. Adaptation to low body temperature influences pulmonary surfactant composition thereby increasing fluidity while maintaining appropriately ordered membrane structure and surface activity.

    PubMed

    Suri, Lakshmi N M; McCaig, Lynda; Picardi, Maria V; Ospina, Olga L; Veldhuizen, Ruud A W; Staples, James F; Possmayer, Fred; Yao, Li-Juan; Perez-Gil, Jesus; Orgeig, Sandra

    2012-07-01

    The interfacial surface tension of the lung is regulated by phospholipid-rich pulmonary surfactant films. Small changes in temperature affect surfactant structure and function in vitro. We compared the compositional, thermodynamic and functional properties of surfactant from hibernating and summer-active 13-lined ground squirrels (Ictidomys tridecemlineatus) with porcine surfactant to understand structure-function relationships in surfactant membranes and films. Hibernating squirrels had more surfactant large aggregates with more fluid monounsaturated molecular species than summer-active animals. The latter had more unsaturated species than porcine surfactant. Cold-adapted surfactant membranes displayed gel-to-fluid transitions at lower phase transition temperatures with reduced enthalpy. Both hibernating and summer-active squirrel surfactants exhibited lower enthalpy than porcine surfactant. LAURDAN fluorescence and DPH anisotropy revealed that surfactant bilayers from both groups of squirrels possessed similar ordered phase characteristics at low temperatures. While ground squirrel surfactants functioned well during dynamic cycling at 3, 25, and 37 degrees C, porcine surfactant demonstrated poorer activity at 3 degrees C but was superior at 37 degrees C. Consequently the surfactant composition of ground squirrels confers a greater thermal flexibility relative to homeothermic mammals, while retaining tight lipid packing at low body temperatures. This may represent the most critical feature contributing to sustained stability of the respiratory interface at low lung volumes. Thus, while less effective than porcine surfactant at 37 degrees C, summer-active surfactant functions adequately at both 37 degrees C and 3 degrees C allowing these animals to enter hibernation. Here further compositional alterations occur which improve function at low temperatures by maintaining adequate stability at low lung volumes and when temperature increases during arousal from

  20. 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.

  1. 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.

  2. 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.

  3. 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…

  4. Adaptation of adaptive optics systems.

    NASA Astrophysics Data System (ADS)

    Xin, Yu; Zhao, Dazun; Li, Chen

    1997-10-01

    In the paper, a concept of an adaptation of adaptive optical system (AAOS) is proposed. The AAOS has certain real time optimization ability against the variation of the brightness of detected objects m, atmospheric coherence length rO and atmospheric time constant τ by means of changing subaperture number and diameter, dynamic range, and system's temporal response. The necessity of AAOS using a Hartmann-Shack wavefront sensor and some technical approaches are discussed. Scheme and simulation of an AAOS with variable subaperture ability by use of both hardware and software are presented as an example of the system.

  5. Toward reflexive climate adaptation research

    DOE PAGES

    Preston, Benjamin L.; Rickards, Lauren; Fünfgeld, Hartmut; ...

    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

  6. 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.

  7. 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: new insights into relationship between conformational flexibility and hydrogen bonding.

    PubMed

    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

    2009-04-03

    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, k(cat)/K(m) (10-40 degrees C), followed the order pseudolysin < MCP-02 < E495 with a ratio of approximately 1:2:4. MCP-02 and E495 have the same optimal temperature (T(opt), 57 degrees C, 5 degrees C lower than pseudolysin) and apparent melting temperature (T(m) = 64 degrees C, approximately 10 degrees 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.

  8. Solar Adaptive Optics.

    PubMed

    Rimmele, Thomas R; Marino, Jose

    Adaptive optics (AO) has become an indispensable tool at ground-based solar telescopes. AO enables the ground-based observer to overcome the adverse effects of atmospheric seeing and obtain diffraction limited observations. Over the last decade adaptive optics systems have been deployed at major ground-based solar telescopes and revitalized ground-based solar astronomy. The relatively small aperture of solar telescopes and the bright source make solar AO possible for visible wavelengths where the majority of solar observations are still performed. Solar AO systems enable diffraction limited observations of the Sun for a significant fraction of the available observing time at ground-based solar telescopes, which often have a larger aperture than equivalent space based observatories, such as HINODE. New ground breaking scientific results have been achieved with solar adaptive optics and this trend continues. New large aperture telescopes are currently being deployed or are under construction. With the aid of solar AO these telescopes will obtain observations of the highly structured and dynamic solar atmosphere with unprecedented resolution. This paper reviews solar adaptive optics techniques and summarizes the recent progress in the field of solar adaptive optics. An outlook to future solar AO developments, including a discussion of Multi-Conjugate AO (MCAO) and Ground-Layer AO (GLAO) will be given.

  9. 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.

  10. 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.

  11. Adaptive multifunctional composites

    NASA Astrophysics Data System (ADS)

    Wang, Ya; Inman, Daniel J.

    2013-05-01

    The adaptive multifunctional composite structure studied here is to address two issues remaining in lightweight structural composites required by many engineering applications. The first is to add additional functionality to multifunctional composites and the second is to provide adaptive damping in structures that cover a wide range of frequencies and temperatures. Because of its potential for practical payoffs, passive structural damping can find wide application through the use of high-damping viscoelastic polymers or elastomers. However, all passive damping using these damping materials suffer from failing at certain temperatures and in certain frequency ranges. The extreme environments often seen by engineering systems provide high temperature, which is exactly where damping levels in structures reduce causing unacceptable vibrations. In addition, as loading frequencies reduce damping levels also fall off, and many loads experienced by large structures are low frequency. The proposed research addresses increasing the range of effectiveness of damping by addressing the temperature and frequency dependence of material damping by using a multifunctional composite system containing an active element. Previous research has yielded a finite element model of linear viscoelastic material and structural behavior that captures characteristic frequency-dependent behavior, continuing research has addressed the accommodation of temperature dependence, and the examination of the new concept of `electronic damping' or `e-damping'. The resulting modeling approach is validated through experimental validation.

  12. 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.

  13. 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.

  14. 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

  15. Adaptive manifold learning.

    PubMed

    Zhang, Zhenyue; Wang, Jing; Zha, Hongyuan

    2012-02-01

    Manifold learning algorithms seek to find a low-dimensional parameterization of high-dimensional data. They heavily rely on the notion of what can be considered as local, how accurately the manifold can be approximated locally, and, last but not least, how the local structures can be patched together to produce the global parameterization. In this paper, we develop algorithms that address two key issues in manifold learning: 1) the adaptive selection of the local neighborhood sizes when imposing a connectivity structure on the given set of high-dimensional data points and 2) the adaptive bias reduction in the local low-dimensional embedding by accounting for the variations in the curvature of the manifold as well as its interplay with the sampling density of the data set. We demonstrate the effectiveness of our methods for improving the performance of manifold learning algorithms using both synthetic and real-world data sets.

  16. 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.

  17. A hybrid wavelet-based adaptive immersed boundary finite-difference lattice Boltzmann method for two-dimensional fluid-structure interaction

    NASA Astrophysics Data System (ADS)

    Cui, Xiongwei; Yao, Xiongliang; Wang, Zhikai; Liu, Minghao

    2017-03-01

    A second generation wavelet-based adaptive finite-difference Lattice Boltzmann method (FD-LBM) is developed in this paper. In this approach, the adaptive wavelet collocation method (AWCM) is firstly, to the best of our knowledge, incorporated into the FD-LBM. According to the grid refinement criterion based on the wavelet amplitudes of density distribution functions, an adaptive sparse grid is generated by the omission and addition of collocation points. On the sparse grid, the finite differences are used to approximate the derivatives. To eliminate the special treatments in using the FD-based derivative approximation near boundaries, the immersed boundary method (IBM) is also introduced into FD-LBM. By using the adaptive technique, the adaptive code requires much less grid points as compared to the uniform-mesh code. As a consequence, the computational efficiency can be improved. To justify the proposed method, a series of test cases, including fixed boundary cases and moving boundary cases, are invested. A good agreement between the present results and the data in previous literatures is obtained, which demonstrates the accuracy and effectiveness of the present AWCM-IB-LBM.

  18. Stasis and adaptation.

    PubMed

    Coiera, Enrico

    2013-01-01

    Many of our most pressing societal challenges arise from our inability to move on from present practices and structures and do what is needed. Healthcare struggles to improve safety and quality. It resists adoption of best practices and persists in high levels of unwarranted variation in care delivery, and clings to financially unsustainable models of care. One explanation for this state of affairs is not a lack of will, but that we are experiencing system inertia--a consequence of the increasing complexity of our human systems. In this paper I explore three possible system level interventions that may help design systems that are less likely to approach inertia, as well as help change our current systems so that they again become adaptive, and move to the outcomes we desire. Firstly, I question our religious belief in the power of standards, an intervention designed to minimise adaptation and almost from first principles designed to lead to inertia. Next I explore the power of apoptosis, a process that sees existing structures and practices programmatically removed to free up resource for adaptation. Finally I explore a flexible but controversial approach to system management called market-based control. Whether any of these, together or in tandem, are a way out of inertia is an open question. However, it is time for us to engage with the challenge of system inertia, and find a way out.

  19. 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…

  20. Relationship of Non-Structural Forms of Social Interaction with Problems of Social and Psychological Adaptation of Students Prone to Chemical Addictions

    ERIC Educational Resources Information Center

    Gilemkhanova, Elvira N.

    2016-01-01

    The changes in contemporary social and cultural environment determine the necessity to increase the efficiency of adaptive mechanisms, especially for those categories of people who are subject to social risks. One of those categories is students prone to chemical addictions. To study the relationship of forms of social interaction with problems of…

  1. Retroelements: propagation and adaptation.

    PubMed

    Hull, R; Covey, S N

    1995-01-01

    Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.

  2. 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.

  3. 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…

  4. Award 1 Title: Acoustic Communications 2011 Experiment: Deployment Support and Post Experiment Data Handling and Analysis. Award 2 Title: Exploiting Structured Dependencies in the Design of Adaptive Algorithms for Underwater Communication Award. 3 Title: Coupled Research in Ocean Acoustics and Signal Processing for the Next Generation of Underwater Acoustic Communication Systems

    DTIC Science & Technology

    2015-09-30

    Exploiting Structured Dependencies in the Design of Adaptive Algorithms for Underwater Communication Award #3 Title Coupled Research in Ocean Acoustics...depend on the physical oceanography and pushing the state of the art in our understanding of adaptive signal processing algorithms relevant to...deployable VHF acoustic data transmission and acquisition system. 3. Develop signal models and processing algorithms that reduce to the extent

  5. 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.

  6. Adaptation Forestry in Minnesota's Northwoods

    NASA Astrophysics Data System (ADS)

    Cornett, M.; White, M.; Etterson, J.; Kavajecz, L.; Mead, J.; Handler, S.; Swanston, C.; Hall, K.

    2014-12-01

    Forest restoration and management goals are shifting in northern Minnesota in light of new information on climate trends. Adaptation forestry encompasses a combination of practices designed to favor native populations and species likely to persist under warmer, drier conditions. The overarching project goal is to increase the adaptive capacity of northern forests such that they continue to sustain a variety of services, including carbon sequestration, fiber production, watershed protection, and wildlife habitat. We are currently testing the feasibility and efficacy of adaptation forestry in the northern Great Lakes region in three common forest types: Boreal-Mixed, Pine, and Hardwoods. 12 sites (2,000 acres total) recently subjected to a range of structural treatments (gap creation, shelterwood, and clear-cut with reserves) were coupled with "adaptation plantings" of species that are likely to thrive under changed climate conditions (e.g., red oak, bur oak, white pine). Seedlings, ~110,000 total, originated from two source locations, one that reflects current adaptation to the climate of northern Minnesota and another from a more southern source in central Minnesota. To date, we have assessed results from two growing seasons by tracking survival, growth and phenological characteristics of planted seedlings. This project is a first step in determining whether adaptation management can be used as a tool to help northern forests transition to an uncertain future. Cooperation with state, federal, and academic partners may ultimately influence the adaptive capacity across millions of acres in the Great Lakes region.

  7. 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.

  8. 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.

  9. Cardiovascular adaptation in athletes.

    PubMed

    Kovacs, Richard; Baggish, Aaron L

    2016-01-01

    Millions of athletes train for and participate in competitive athletics each year. Many of these athletes will present to a cardiovascular specialist with signs or symptoms that might indicate heart disease and these athletes/patients will ask for advice on their ability to continue to train and compete safely. By virtue of their training, athletes׳ hearts may undergo significant structural and electrical change, presenting a special challenge for the cardiovascular specialist. It is important to understand normal adaptive changes in order to separate normal physiology from pathology.

  10. Countermeasures to Enhance Sensorimotor Adaptability

    NASA Technical Reports Server (NTRS)

    Bloomberg, J. J.; Peters, B. T.; Mulavara, A. P.; Brady, R. A.; Batson, C. C.; Miller, C. A.; Cohen, H. S.

    2011-01-01

    During exploration-class missions, sensorimotor disturbances may lead to disruption in the ability to ambulate and perform functional tasks during the initial introduction to a novel gravitational environment following a landing on a planetary surface. The goal of our current project is to develop a sensorimotor adaptability (SA) training program to facilitate rapid adaptation to novel gravitational environments. We have developed a unique training system comprised of a treadmill placed on a motion-base facing a virtual visual scene that provides an unstable walking surface combined with incongruent visual flow designed to enhance sensorimotor adaptability. We have conducted a series of studies that have shown: Training using a combination of modified visual flow and support surface motion during treadmill walking enhances locomotor adaptability to a novel sensorimotor environment. Trained individuals become more proficient at performing multiple competing tasks while walking during adaptation to novel discordant sensorimotor conditions. Trained subjects can retain their increased level of adaptability over a six months period. SA training is effective in producing increased adaptability in a more complex over-ground ambulatory task on an obstacle course. This confirms that for a complex task like walking, treadmill training contains enough of the critical features of overground walking to be an effective training modality. The structure of individual training sessions can be optimized to promote fast/strategic motor learning. Training sessions that each contain short-duration exposures to multiple perturbation stimuli allows subjects to acquire a greater ability to rapidly reorganize appropriate response strategies when encountering a novel sensory environment. Individual sensory biases (i.e. increased visual dependency) can predict adaptive responses to novel sensory environments suggesting that customized training prescriptions can be developed to enhance

  11. 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

  12. 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.

  13. Topologies for perfect adaptation in gene transcription

    NASA Astrophysics Data System (ADS)

    Shi, Wenjia; Tang, Chao

    2014-03-01

    Adaptation is commonly used in sensory systems and signaling networks to allow the detection of further stimuli. Despite enzymatic network topologies for adaptation have been investigated systematically, the topology of transcriptional network that could perform adaptation still remains unclear, due to the complexity of transcriptional regulation. Here, we systematically investigated all three-node transcriptional networks, and found the topologies of transcriptional networks for adaptation are different from that of enzymatic ones. While both negative feedback loop (NFBL) and incoherent feed forward loop (IFFL) are capable of performing adaptation analytically, a positive self-regulation on buffer node is necessary for NFBL topology and more flexible structures emerge for IFFL than that of enzymatic networks. Most of the simulation results agree with analytical predictions. This study may explain the mechanism of adapted gene regulation behavior and supply a design table for gene regulatory adaptation.

  14. 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.

  15. Adaptive Image Denoising by Mixture Adaptation.

    PubMed

    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. The 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.

  16. 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

  17. 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.

  18. 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…

  19. Consensus formation on adaptive networks

    NASA Astrophysics Data System (ADS)

    Kozma, Balazs; Barrat, Alain

    2008-01-01

    The structure of a network can significantly influence the properties of the dynamical processes that take place on them. While many studies have been paid to this influence, much less attention has been devoted to the interplay and feedback mechanisms between dynamical processes and network topology on adaptive networks. Adaptive rewiring of links can happen in real life systems such as acquaintance networks, where people are more likely to maintain a social connection if their views and values are similar. In our study, we consider different variants of a model for consensus formation. Our investigations reveal that the adaptation of the network topology fosters cluster formation by enhancing communication between agents of similar opinion, although it also promotes the division of these clusters. The temporal behavior is also strongly affected by adaptivity: while, on static networks, it is influenced by percolation properties, on adaptive networks, both the early and late time evolutions of the system are determined by the rewiring process. The investigation of a variant of the model reveals that the scenarios of transitions between consensus and polarized states are more robust on adaptive networks.

  20. Legal and Institutional Foundations of Adaptive Environmental Governance

    EPA Science Inventory

    Legal and institutional structures fundamentally shape opportunities for adaptive governance of environmental resources at multiple ecological and societal scales. Properties of adaptive governance are widely studied. However, these studies have not resulted in consolidated frame...

  1. Cartesian-cell based grid generation and adaptive mesh refinement

    NASA Technical Reports Server (NTRS)

    Coirier, William J.; Powell, Kenneth G.

    1993-01-01

    Viewgraphs on Cartesian-cell based grid generation and adaptive mesh refinement are presented. Topics covered include: grid generation; cell cutting; data structures; flow solver formulation; adaptive mesh refinement; and viscous flow.

  2. 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…

  3. Habituation of visual adaptation

    PubMed Central

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  4. Adaptive Beamforming with Inadequate Snapshots

    NASA Astrophysics Data System (ADS)

    YU, Jing; LI, Yaan

    2017-01-01

    In array signal processing, the covariance matrix used to calculate the adaptive weights is often poor estimated when the snapshot number is inadequate. The prior environmental knowledge can be used to make the estimation more accuracy. In this paper, an alternative knowledge-aided adaptive beamforming approach that is robust to low sample support environment is proposed. In this algorithm the covariance matrix used to calculate the optimum weights is constructed by blending a sample covariance matrix and a priori structured covariance matrix. Numerical simulations demonstrate the proposed algorithm has the potential for substantial performance improvement.

  5. 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…

  6. Exploring the coordinative adaptation and molecular shapes of trinuclear CuM(II) (M = Zn/Cd) complexes derived from salen type Schiff bases: structural and theoretical studies.

    PubMed

    Hazari, Alokesh; Das, Lakshmi Kanta; Bauzá, Antonio; Frontera, Antonio; Ghosh, Ashutosh

    2016-04-07

    Three new trinuclear hetero-metallic complexes [(CuL)2Zn(NCS)2] (1), [(CuL(R))2Zn(NCS)(μ1,1-NCS)] (2) and [(CuL(R))2Cd(μ1,3-NCS)2] (4) have been synthesized using [CuL] and [CuL(R)] as "metalloligands" (where H2L = N,N'-bis(salicylidene)-1,3-propanediamine and H2L(R) = N,N'-bis(2-hydroxybenzyl)-1,3-propanediamine). All three complexes are characterized by elemental analysis, spectroscopic methods and single crystal XRD. Complex 1 is an angular trinuclear species, in which two terminal four-coordinate square planar "metalloligands" [CuL] are coordinated to a central Zn(ii) through double phenoxido bridges along with two mutually cis nitrogen atoms of terminal isothiocyanate ions as is usually found in such complexes. In contrast, in complex 2, the two terminal "metalloligands" [CuL(R)] are square pyramidal, as one of the SCN(-) ions makes an unusual μ1,1-NCS bridge between copper centers while the other one coordinates to Zn(ii) through a N atom in a usual fashion making its geometry also square pyramidal. For 4 which possesses an angular trinuclear structure, in addition to double phenoxido bridges from two terminal [CuL(R)], both the SCN(-) ions are S-bonded to Cd(ii) and form a bridge (cis-μ1,3-SCN) between Cd(ii) and each of the terminal Cu(ii) ions. This structure is different from its unreduced analogue in which NCS(-) was N-terminal coordinated to Cd(ii) (3/3'). All the structures have been optimized using density functional theory (DFT) calculations. It has been found that for H2L, optimized structures like 1 and 2 differ only by 0.4 kcal mol(-1) but the H2L(R) structure 2 is more stable by 5.5 kcal mol(-1) than the structure resembling 1. For Cd(ii) complexes also, H2L optimized structures such as 3 and 4 do not differ significantly in energy (1.0 kcal mol(-1)) but the H2L(R) structure 4 is more stable than that of 3 by 4.6 kcal mol(-1). In fact, structure 4 has been found to be the most stable one among the other possible isomers of H2L(R).

  7. 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

  8. 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.

  9. Imaging an Adapted Dentoalveolar Complex

    PubMed Central

    Herber, Ralf-Peter; Fong, Justine; Lucas, Seth A.; Ho, Sunita P.

    2012-01-01

    Adaptation of a rat dentoalveolar complex was illustrated using various imaging modalities. Micro-X-ray computed tomography for 3D modeling, combined with complementary techniques, including image processing, scanning electron microscopy, fluorochrome labeling, conventional histology (H&E, TRAP), and immunohistochemistry (RANKL, OPN) elucidated the dynamic nature of bone, the periodontal ligament-space, and cementum in the rat periodontium. Tomography and electron microscopy illustrated structural adaptation of calcified tissues at a higher resolution. Ongoing biomineralization was analyzed using fluorochrome labeling, and by evaluating attenuation profiles using virtual sections from 3D tomographies. Osteoclastic distribution as a function of anatomical location was illustrated by combining histology, immunohistochemistry, and tomography. While tomography and SEM provided past resorption-related events, future adaptive changes were deduced by identifying matrix biomolecules using immunohistochemistry. Thus, a dynamic picture of the dentoalveolar complex in rats was illustrated. PMID:22567314

  10. 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…

  11. Host selection and adaptation are major driving forces shaping ALS Xylella fastidiosa population structure in the San Joaquin Valley of California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Xylella fastidiosa (Xf) causes disease in many commercial crops including almond leaf scorch (ALS) disease in susceptible almond (Prunus dulcis). In this study, genetic diversity and population structure of Xf associated with ALS disease were evaluated. Strains from two almond production sites in th...

  12. The Periplasmic Bacterial Molecular Chaperone SurA Adapts Its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues

    SciTech Connect

    Xu, X.; Wang, S.; Hu, Y.-X.; McKay, D.B.

    2009-06-04

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

  13. Halophilic adaptation of enzymes.

    PubMed

    Madern, D; Ebel, C; Zaccai, G

    2000-04-01

    It is now clear that the understanding of halophilic adaptation at a molecular level requires a strategy of complementary experiments, combining molecular biology, biochemistry, and cellular approaches with physical chemistry and thermodynamics. In this review, after a discussion of the definition and composition of halophilic enzymes, the effects of salt on their activity, solubility, and stability are reviewed. We then describe how thermodynamic observations, such as parameters pertaining to solvent-protein interactions or enzyme-unfolding kinetics, depend strongly on solvent composition and reveal the important role played by water and ion binding to halophilic proteins. The three high-resolution crystal structures now available for halophilic proteins are analyzed in terms of haloadaptation, and finally cellular response to salt stress is discussed briefly.

  14. Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer

    PubMed Central

    Brouwer, Paul; Bräutigam, Andrea; Buijs, Valerie A.; Tazelaar, Anne O. E.; van der Werf, Adrie; Schlüter, Urte; Reichart, Gert-Jan; Bolger, Anthony; Usadel, Björn; Weber, Andreas P. M.; Schluepmann, Henriette

    2017-01-01

    Sustainable agriculture demands reduced input of man-made nitrogen (N) fertil