Interactions and structural analysis of the zinc -binding motif in decorin, a small leucine rich proteoglycan in extracellular matrix

Decorin, a dermatan/chondroitin sulfate proteoglycan, is ubiquitously distributed in the extracellular matrix (ECM) of mammals. Decorin belongs to the small leucine rich proteoglycan (SLRP) family, a proteoglycan family characterized by a core protein dominated by Leucine Rich Repeat motifs. The decorin core protein appears to mediate the binding of decorin to ECM molecules, such as collagens and fibronectin. It is believed that the interactions of decorin with these ECM molecules contribute to the regulation of ECM assembly, cell adhesions, and cell proliferation. These basic biological processes play critical roles during embryonic development and wound healing and are altered in pathological conditions such as fibrosis and tumorgenesis. ^ In this dissertation, we discover that decorin core protein can bind to Zn2+ ions with high affinity. Zinc is an essential trace element in mammals. Zn2+ ions play a catalytic role in the activation of many enzymes and a structural role in the stabilization of protein conformation. By examining purified recombinant decorin and its core protein fragments for Zn2+ binding activity using Zn2+-chelating column chromatography and Zn2+-equilibrium dialysis approaches, we have located the Zn2+ binding domain to the N-terminal sequence of the decorin core protein. The decorin N-terminal domain appears to contain two Zn2+ binding sites with similar high binding affinity. The sequence of the decorin N-terminal domain does not resemble any other reported zinc-binding motifs and, therefore, represents a novel Zn 2+ binding motif. By investigating the influence of Zn2+ ions on decorin binding interactions, we found a novel Zn2+ dependent interaction with fibrinogen, the major plasma protein in blood clots. Furthermore, a recombinant peptide (MD4) consisting of a 41 amino acid sequence of mouse decorin N-terminal domain can prolong thrombin induced fibrinogen/fibrin clot formation. This suggests that in the presence of Zn2+ the decorin N-terminal domain has an anticoagulation activity. The changed Zn2+-binding activities of the truncated MD4 peptides and site-directed mutagenesis generated mutant peptides revealed that the functional MD4 peptide might contain both a structural zinc-binding site in the cysteine cluster region and a catalytic zinc site that could be created by the flanking sequences of the cysteine cluster region. A model of a loop-like structure for MD4 peptide is proposed. ^

Structural conservations and diversities of dsRNA viruses: Structural studies of the cytoplasmic polyhedrosis virus by electron cryomicroscopy and 3D reconstruction

The Reoviridae virus family is a group of economically and pathologically important viruses that have either single-, double-, or triple-shelled protein layers enclosing a segmented double stranded RNA genome. Each virus particle in this family has its own viral RNA dependent RNA polymerase and the enzymatic activities necessary for the mature RNA synthesis. Based on the structure of the inner most cores of the viruses, the Reoviridae viruses can be divided into two major groups. One group of viruses has a smooth surfaced inner core, surrounded by complete outer shells of one or two protein layers. The other group has an inner core decorated with turrets on the five-fold vertices, and could either completely lack or have incomplete outer protein layers. The structural difference is one of the determinant factors for their biological differences during the infection. ^ Cytoplasmic polyhedrosis virus (CPV) is a single-shelled, turreted virus and the structurally simplest member in Reoviridae. It causes specific chronic infections in the insect gut epithelial cells. Due to its wide range of insect hosts, CPV has been engineered as a potential insecticide for use in fruit and vegetable farming. Its unique structural simplicity, unparalleled capsid stability and ease of purification make CPV an ideal model system for studying the structural basis of dsRNA virus assembly at the highest possible resolution by electron cryomicroscopy (cryoEM) and three-dimensional (3D) reconstruction. ^ In this thesis work, I determined the first 3D structure of CPV capsids using 100 kV cryoEM. At an effective resolution of 17 Å, the full capsid reveals a 600-Å diameter, T = 1 icosahedral shell decorated with A and B spikes at the 5-fold vertices. The internal space of the empty CPV is unoccupied except for 12 mushroom-shaped densities that are attributed to the transcriptional enzyme complexes. The inside of the full capsid is packed with icosahedrally-ordered viral genomic RNA. The interactions of viral RNA with the transcriptional enzyme complexes and other capsid proteins suggest a mechanism for RNA transcription and subsequent release. ^ Second, the interactions between the turret proteins (TPs) and the major capsid shell protein (CSPs) have been identified through 3D structural comparisons of the intact CPV capsids with the spikeless CPV capsids, which were generated by chemical treatments. The differential effects of these chemical treatment experiments also indicated that CPV has a significantly stronger structural integrity than other dsRNA viruses, such as the orthoreovirus subcores, which are normally enclosed within outer protein shells. ^ Finally, we have reconstructed the intact CPV to an unprecendented 8 Å resolution from several thousand of 400kV cryoEM images. The 8 Å structure reveals interactions among the 120 molecules of each of the capsid shell protein (CSP), the large protrusion protein (LPP), and 60 molecules of the turret protein (TP). A total of 1980 α-helices and 720 β-sheets have been identified in these capsid proteins. The CSP structure is largely conserved, with the majority of the secondary structures homologous to those observed in the x-ray structures of corresponding proteins of other reoviruses, such as orthoreovirus and bluetongue virus. The three domains of TP are well positioned to play multifunctional roles during viral transcription. The completely non-equivalent interactions between LPP and CSP and those between the anchoring domain of TP and CSP account for the unparalleled stability of this structurally simplest member of the Reoviridae. ^

Nd, Sr and Sm isotopic composition and model ages of rocks from the Anginskaya and Talanchanskaya formations, Lake Baikal

The paper presents data on the Nd-Sr systematics of magmatic rocks of the Khaidaiskii Series of the Anginskaya Formation in the Ol'khon region, western Baikal area, and rocks of the Talanchanskaya Formation on the eastern shore of Lake Baikal. Geochemical characteristics of these rocks are identical and testify to their arc provenance. At the same time, the epsilon(t)Nd of rocks of the Khaidaiskii Series in the Ol'khon area has positive values, and the data points of these rocks plot near the mantle succession line in the epsilon(t)Nd-87Sr/86Sr diagram, whereas the epsilon(t)Nd values of rocks of the Talanchanskaya Formation are negative, and the data points of these rocks fall into the fourth quadrant in the epsilon(t)Nd -87Sr/86Sr diagram. This testifies to a mantle genesis of the parental magmas of the Khaidaiskii Series and to the significant involvement of older crustal material in the generation of the melts that produced the orthorocks on the eastern shore of the lake. These conclusions are corroborated by model ages of magmatic rocks in the Ol'khon area (close to 1 Ga) and of rocks of the Talanchanskaya Formation (approximately 2 Ga). The comparison of our data with those obtained by other researchers on the Nd-Sr isotopic age of granulites of the Ol'khon Group and metavolcanics in various structural zones in the northern Baikal area suggests, with regard for the geochemistry of these rocks, the accretion of tectonic nappes that had different isotopic histories: some of them were derived from the mantle wedge and localized in the island arc itself (magmatic rocks of the Anginskaya Formation) or backarc spreading zone (mafic metamagmatic rocks of the Ol'khon Group), while others were partial melts derived, with the participation of crustal material, from sources of various age (metagraywackes in the backarc basin in the Ol'khon Group and the ensialic basement of the island arc in the Talanchanskaya Formation).

Prioritization of Policies: A Prototype Model of a Flowchart Method

This paper builds a prototype model of how to prioritize policies by using a flowchart. We presented the following six steps to decide priorities of policies: Step 1 is to attain the social subsistence level (primary education, health care, and food sufficiency); Step 2 is to attain macroeconomic stability; Step 3 is to liberalize the economy by structural adjustment programs; Step 4 is capacity building specific to a growth strategy by facilitating sufficient infrastructure (physical infrastructure and institutions); Step 5 is to initiate a growth strategy; and Step 6 is to narrow income inequalities. We illustrated the effectiveness of our "flowchart method" in case studies of Morocco, Laos, Vietnam, and China. The first priority of reforms in Morocco was given to social sectors of primary education and health care, particularly in the rural areas at Step 1. Laos should not put much emphasis on growth strategy before educational reform, attainment of macroeconomic stability, and institutional capacity building at Steps 1, 2, and 3. Vietnam can focus on reforming the state-run enterprises and developing the stock markets at Step 5 of growth strategies. We found that we should apply our flowchart method to China not nation-wide but province-wide.

Discussion of "Simplified Model of Low Cycle Fatigue for RC Frames"

To model strength degradation due to low cycle fatigue, at least three different approaches can be considered. One possibility is based on the formulation of a new free energy function and damage energy release rate, as was proposed by Ju(1989). The second approach uses the notion of bounding surface introduced in cyclic plasticity by Dafalias and Popov (1975). From this concept, some models have been proposed to quantify damage in concrete or RC (Suaris et al. 1990). The model proposed by the author to include fatigue effects is based essentially in Marigo (1985) and can be included in this approach.

A damage model for seismic retrofitting of structures

Numerous damage models have been developed in order to analyse the seismic behavior. Among the different possibilities existing in the literature, it is very clear that models developed along the lines of Continuum Damage Mechanics are more consistent with the definition of damage like a phenomenon with mechanical consequences as they include explicitly the coupling between damage and mechanical behavior. On the other hand, for seismic processes, phenomena such as low cycle fatigue may have a pronounced effect on the overall behavior of the frames and, therefore, its consideration turns out to be very important. However, many of existing models evaluate the damage only as a function of the maximum amplitude of cyclic deformation without considering the number of cycles. In this paper, a generalization of the simplified model proposed by Flórez is made in order to include the low cycle fatigue. Such model employs in its formulation irreversible thermodynamics and internal state variable theory.

A simplified model for evaluation of fatigue damage in frames

Many studies have been developed to analyze the structural seismic behavior through the damage index concept. The evaluation of this index has been employed to quantify the safety of new and existing structures and, also, to establish a framework for seismic retrofitting decision making of structures. Most proposed models are based in a posterthquake evaluation in such a way they uncouple the structural response from the damage evaluation. In this paper, a generalization of the model by Flórez-López (1995) is proposed. The formulation employs irreversible thermodynamics and internal state variable theory applied to the study of beams and frames and it allows and explicit coupling between the degradation and the structural mechanical behavior. A damage index es defined in order to model elastoplasticity coupled with damage and fatigue damage.

Structural challenges in multijunction solar cells for ultra-high CPV

The paths towards high efficiency multijunction solar cells operating inside real concentrators at ultra high concentration (>1000 suns) are described. The key addressed factors comprehend: 1) the development of an optimized tunnel junction with a high peak current density (240 A/cm2) to mitigate the non-uniform light profiles created by concentrators, 2) the inclusion of highly conductive semiconductor lateral layers to minimize the effects of the non-uniform light profiles in general, and the chromatic aberration in particular; and 3) an adequate design of reliability studies to test multijunction solar cells for real operation conditions in order to determine the fragile parts in the device and improve them. These challenges are faced by means of experimental and theoretical investigation using a quasi-3D distributed circuital model.

A critical force constant of the structural phase transition in quartz

Long wavelength optical phonons of quartz were analyzed by a Born-Von Karman model not previously used. It was found that only one force constant associated with the turning of the Si-O bonds has a critical effect on the soft-mode frequency and the α-β transition in quartz. The square of the soft-mode frequency was found to depend linearly on this force constant which has the temperature dependence K(T)= -5.33+225.3x10-4(851-T)2/3 in units of 104 dyn/cm2.

A stochastic model updating method for parameter variability quantification based on response surface models and Monte Carlo simulation

Stochastic model updating must be considered for quantifying uncertainties inherently existing in real-world engineering structures. By this means the statistical properties,instead of deterministic values, of structural parameters can be sought indicating the parameter variability. However, the implementation of stochastic model updating is much more complicated than that of deterministic methods particularly in the aspects of theoretical complexity and low computational efficiency. This study attempts to propose a simple and cost-efficient method by decomposing a stochastic updating process into a series of deterministic ones with the aid of response surface models and Monte Carlo simulation. The response surface models are used as surrogates for original FE models in the interest of programming simplification, fast response computation and easy inverse optimization. Monte Carlo simulation is adopted for generating samples from the assumed or measured probability distributions of responses. Each sample corresponds to an individual deterministic inverse process predicting the deterministic values of parameters. Then the parameter means and variances can be statistically estimated based on all the parameter predictions by running all the samples. Meanwhile, the analysis of variance approach is employed for the evaluation of parameter variability significance. The proposed method has been demonstrated firstly on a numerical beam and then a set of nominally identical steel plates tested in the laboratory. It is found that compared with the existing stochastic model updating methods, the proposed method presents similar accuracy while its primary merits consist in its simple implementation and cost efficiency in response computation and inverse optimization.

Development of FEM/BEM and SEA models from experimental results for structural elements with attached equipment

This work focuses on the analysis of a structural element of MetOP-A satellite. Given the special interest in the influence of equipment installed on structural elements, the paper studies one of the lateral faces on which the Advanced SCATterometer (ASCAT) is installed. The work is oriented towards the modal characterization of the specimen, describing the experimental set-up and the application of results to the development of a Finite Element Method (FEM) model to study the vibro-acoustic response. For the high frequency range, characterized by a high modal density, a Statistical Energy Analysis (SEA) model is considered, and the FEM model is used when modal density is low. The methodology for developing the SEA model and a compound FEM and Boundary Element Method (BEM) model to provide continuity in the medium frequency range is presented, as well as the necessary updating, characterization and coupling between models required to achieve numerical models that match experimental results.

Model-based Self-awareness Patterns for Autonomy

Los sistemas técnicos son cada vez más complejos, incorporan funciones más avanzadas, están más integrados con otros sistemas y trabajan en entornos menos controlados. Todo esto supone unas condiciones más exigentes y con mayor incertidumbre para los sistemas de control, a los que además se demanda un comportamiento más autónomo y fiable. La adaptabilidad de manera autónoma es un reto para tecnologías de control actualmente. El proyecto de investigación ASys propone abordarlo trasladando la responsabilidad de la capacidad de adaptación del sistema de los ingenieros en tiempo de diseño al propio sistema en operación. Esta tesis pretende avanzar en la formulación y materialización técnica de los principios de ASys de cognición y auto-consciencia basadas en modelos y autogestión de los sistemas en tiempo de operación para una autonomía robusta. Para ello el trabajo se ha centrado en la capacidad de auto-conciencia, inspirada en los sistemas biológicos, y se ha explorado la posibilidad de integrarla en la arquitectura de los sistemas de control. Además de la auto-consciencia, se han explorado otros temas relevantes: modelado funcional, modelado de software, tecnología de los patrones, tecnología de componentes, tolerancia a fallos. Se ha analizado el estado de la técnica en los ámbitos pertinentes para las cuestiones de la auto-consciencia y la adaptabilidad en sistemas técnicos: arquitecturas cognitivas, control tolerante a fallos, y arquitecturas software dinámicas y computación autonómica. El marco teórico de ASys existente de sistemas autónomos cognitivos ha sido adaptado para servir de base para este análisis de autoconsciencia y adaptación y para dar sustento conceptual al posterior desarrollo de la solución. La tesis propone una solución general de diseño para la construcción de sistemas autónomos auto-conscientes. La idea central es la integración de un meta-controlador en la arquitectura de control del sistema autónomo, capaz de percibir la estado funcional del sistema de control y, si es necesario, reconfigurarlo en tiempo de operación. Esta solución de metacontrol se ha formalizado en cuatro patrones de diseño: i) el Patrón Metacontrol, que define la integración de un subsistema de metacontrol, responsable de controlar al propio sistema de control a través de la interfaz proporcionada por su plataforma de componentes, ii) el patrón Bucle de Control Epistémico, que define un bucle de control cognitivo basado en el modelos y que se puede aplicar al diseño del metacontrol, iii) el patrón de Reflexión basada en Modelo Profundo propone una solución para construir el modelo ejecutable utilizado por el meta-controlador mediante una transformación de modelo a modelo a partir del modelo de ingeniería del sistema, y, finalmente, iv) el Patrón Metacontrol Funcional, que estructura el meta-controlador en dos bucles, uno para el control de la configuración de los componentes del sistema de control, y otro sobre éste, controlando las funciones que realiza dicha configuración de componentes; de esta manera las consideraciones funcionales y estructurales se desacoplan. La Arquitectura OM y el metamodelo TOMASys son las piezas centrales del marco arquitectónico desarrollado para materializar la solución compuesta de los patrones anteriores. El metamodelo TOMASys ha sido desarrollado para la representación de la estructura y su relación con los requisitos funcionales de cualquier sistema autónomo. La Arquitectura OM es un patrón de referencia para la construcción de una metacontrolador integrando los patrones de diseño propuestos. Este meta-controlador se puede integrar en la arquitectura de cualquier sistema control basado en componentes. El elemento clave de su funcionamiento es un modelo TOMASys del sistema decontrol, que el meta-controlador usa para monitorizarlo y calcular las acciones de reconfiguración necesarias para adaptarlo a las circunstancias en cada momento. Un proceso de ingeniería, complementado con otros recursos, ha sido elaborado para guiar la aplicación del marco arquitectónico OM. Dicho Proceso de Ingeniería OM define la metodología a seguir para construir el subsistema de metacontrol para un sistema autónomo a partir del modelo funcional del mismo. La librería OMJava proporciona una implementación del meta-controlador OM que se puede integrar en el control de cualquier sistema autónomo, independientemente del dominio de la aplicación o de su tecnología de implementación. Para concluir, la solución completa ha sido validada con el desarrollo de un robot móvil autónomo que incorpora un meta-controlador con la Arquitectura OM. Las propiedades de auto-consciencia y adaptación proporcionadas por el meta-controlador han sido validadas en diferentes escenarios de operación del robot, en los que el sistema era capaz de sobreponerse a fallos en el sistema de control mediante reconfiguraciones orquestadas por el metacontrolador. ABSTRACT Technical systems are becoming more complex, they incorporate more advanced functionalities, they are more integrated with other systems and they are deployed in less controlled environments. All this supposes a more demanding and uncertain scenario for control systems, which are also required to be more autonomous and dependable. Autonomous adaptivity is a current challenge for extant control technologies. The ASys research project proposes to address it by moving the responsibility for adaptivity from the engineers at design time to the system at run-time. This thesis has intended to advance in the formulation and technical reification of ASys principles of model-based self-cognition and having systems self-handle at runtime for robust autonomy. For that it has focused on the biologically inspired capability of self-awareness, and explored the possibilities to embed it into the very architecture of control systems. Besides self-awareness, other themes related to the envisioned solution have been explored: functional modeling, software modeling, patterns technology, components technology, fault tolerance. The state of the art in fields relevant for the issues of self-awareness and adaptivity has been analysed: cognitive architectures, fault-tolerant control, and software architectural reflection and autonomic computing. The extant and evolving ASys Theoretical Framework for cognitive autonomous systems has been adapted to provide a basement for this selfhood-centred analysis and to conceptually support the subsequent development of our solution. The thesis proposes a general design solution for building self-aware autonomous systems. Its central idea is the integration of a metacontroller in the control architecture of the autonomous system, capable of perceiving the functional state of the control system and reconfiguring it if necessary at run-time. This metacontrol solution has been formalised into four design patterns: i) the Metacontrol Pattern, which defines the integration of a metacontrol subsystem, controlling the domain control system through an interface provided by its implementation component platform, ii) the Epistemic Control Loop pattern, which defines a modelbased cognitive control loop that can be applied to the design of such a metacontroller, iii) the Deep Model Reflection pattern proposes a solution to produce the online executable model used by the metacontroller by model-to-model transformation from the engineering model, and, finally, iv) the Functional Metacontrol pattern, which proposes to structure the metacontroller in two loops, one for controlling the configuration of components of the controller, and another one on top of the former, controlling the functions being realised by that configuration; this way the functional and structural concerns become decoupled. The OM Architecture and the TOMASys metamodel are the core pieces of the architectural framework developed to reify this patterned solution. The TOMASys metamodel has been developed for representing the structure and its relation to the functional requirements of any autonomous system. The OM architecture is a blueprint for building a metacontroller according to the patterns. This metacontroller can be integrated on top of any component-based control architecture. At the core of its operation lies a TOMASys model of the control system. An engineering process and accompanying assets have been constructed to complete and exploit the architectural framework. The OM Engineering Process defines the process to follow to develop the metacontrol subsystem from the functional model of the controller of the autonomous system. The OMJava library provides a domain and application-independent implementation of an OM Metacontroller than can be used in the implementation phase of OMEP. Finally, the complete solution has been validated in the development of an autonomous mobile robot that incorporates an OM metacontroller. The functional selfawareness and adaptivity properties achieved thanks to the metacontrol system have been validated in different scenarios. In these scenarios the robot was able to overcome failures in the control system thanks to reconfigurations performed by the metacontroller.

Estimating the modal parameters from multiple measurement setups using a joint state space model

Computing the modal parameters of structural systems often requires processing data from multiple non-simultaneously recorded setups of sensors. These setups share some sensors in common, the so-called reference sensors, which are fixed for all measurements, while the other sensors change their position from one setup to the next. One possibility is to process the setups separately resulting in different modal parameter estimates for each setup. Then, the reference sensors are used to merge or glue the different parts of the mode shapes to obtain global mode shapes, while the natural frequencies and damping ratios are usually averaged. In this paper we present a new state space model that processes all setups at once. The result is that the global mode shapes are obtained automatically, and only a value for the natural frequency and damping ratio of each mode is estimated. We also investigate the estimation of this model using maximum likelihood and the Expectation Maximization algorithm, and apply this technique to simulated and measured data corresponding to different structures.

Computational model for local damage assesment of structures

In the last years many studies have been developed to analyze the seismic behavior throug the damage concept. In fact, the evaluation of the structural damage is important in order to quantify the safety of new and existing structures and, also, to establish a framework for seismic retrofitting decision making of structures. Most proposed models are based on a post-earthquake evaluation in such a way they uncouple the computation of the structural response from that of damage. However, there are other models which include explicity the existing coupling between the degradation and the structural mechanical beaviour. Those models are closer to the physical reality and its formulation is based on the principles of Continuum Damage Mechanics. In the present work, a coupled model is formulated using a simplified application of the Continuum Damage Mechanics to the analysis of frames and allows its representation in standard finite element programs. This work is part of the activities developed by the Structural Mechanics Department (UPM) within ICONS (European Research Project on Innovative Seismic Design Concepts for New and Existing Structures).

A computational model coupling mechanics and electrophysiology in spinal cord injury

Traumatic brain injury and spinal cord injury have recently been put under the spotlight as major causes of death and disability in the developed world. Despite the important ongoing experimental and modeling campaigns aimed at understanding the mechanics of tissue and cell damage typically observed in such events, the differenti- ated roles of strain, stress and their corresponding loading rates on the damage level itself remain unclear. More specif- ically, the direct relations between brain and spinal cord tis- sue or cell damage, and electrophysiological functions are still to be unraveled. Whereas mechanical modeling efforts are focusing mainly on stress distribution and mechanistic- based damage criteria, simulated function-based damage cri- teria are still missing. Here, we propose a new multiscale model of myelinated axon associating electrophysiological impairment to structural damage as a function of strain and strain rate. This multiscale approach provides a new framework for damage evaluation directly relating neuron mechanics and electrophysiological properties, thus provid- ing a link between mechanical trauma and subsequent func- tional deficits.