Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimate their parameters are an essential issue for studying dynamic behaviors of biological systems which include metabolic networks, genetic regulatory networks and signal transduction pathways, under perturbation of external stimuli. In general, biological dynamic systems are partially observed. Therefore, a natural way to model dynamic biological systems is to employ nonlinear state-space equations. Although statistical methods for parameter estimation of linear models in biological dynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamic systems remains a challenging task. In this report, we apply extended Kalman Filter (EKF) to the estimation of both states and parameters of nonlinear state-space models. To evaluate the performance of the EKF for parameter estimation, we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signaling transduction pathways datasets. The preliminary results show that EKF can accurately estimate the parameters and predict states in nonlinear state-space equations for modeling dynamic biochemical networks.

From school to work: A comprehensive model of work-related motivation in the transition to working life.

Motivation is a core concept to understand work related outcomes and vocational pursuits. However, existing research mostly focused on specific aspects of motivation, such as goals or self-efficacy beliefs, while falling short of adequately addressing more complex and integrative notions of motivation. Advancing the current state of research, we draw from Motivational Systems Theory and a model of proactive motivation to propose a comprehensive model of work-related motivation. Specifically, we define motivation as a system of mutually related factors consisting of goals, emotions, and personal agency beliefs, comprised by capability beliefs and context evaluations. Adapting this model of motivation to the school-to-work transition, we postulate that this motivational system is affected by different social, personal, and environmental variables, for example social support, the presence of role-models, personality traits, and scholastic achievement. We further expect that students with more autonomous work-related goals, expectations of more positive emotional experiences in their future working life, fewer perceived barriers to their career development, and higher work-related self-efficacy beliefs would be more successful in their transition from school to work. We also propose that goal-directed engagement acts as a partial mediator in the relationship between motivation and a successful transition. Finally, we hypothesize that work-related motivation while in school will have meaningful effects on positive outcomes while in vocational training, as represented by more work engagement, higher career commitment, job satisfaction, and lower intentions to quit training. In sum, we advance the point that the adaptation of a broader concept of work-related motivation in the school-to-work transition would result in more powerful predictions of success in this transition and would enhance scientific research and interventions in career development and counselling practice.

Adaptive Algorithms for Personalized Diabetes Treatment

Dynamic systems, especially in real-life applications, are often determined by inter-/intra-variability, uncertainties and time-varying components. Physiological systems are probably the most representative example in which population variability, vital signal measurement noise and uncertain dynamics render their explicit representation and optimization a rather difficult task. Systems characterized by such challenges often require the use of adaptive algorithmic solutions able to perform an iterative structural and/or parametrical update process towards optimized behavior. Adaptive optimization presents the advantages of (i) individualization through learning of basic system characteristics, (ii) ability to follow time-varying dynamics and (iii) low computational cost. In this chapter, the use of online adaptive algorithms is investigated in two basic research areas related to diabetes management: (i) real-time glucose regulation and (ii) real-time prediction of hypo-/hyperglycemia. The applicability of these methods is illustrated through the design and development of an adaptive glucose control algorithm based on reinforcement learning and optimal control and an adaptive, personalized early-warning system for the recognition and alarm generation against hypo- and hyperglycemic events.

Career adaptability development in adolescence: Multiple prdictors and effect on sense of power and life satisfaction

This longitudinal panel study investigated predictors of career adaptability development and its effect on development of sense of power and experience of life satisfaction among 330 Swiss eighth graders. A multivariate measure of career adaptability consisting of career choice readiness, planning, exploration, and confidence was applied. Based on Motivational Systems Theory four groups of predictors were assessed: positive emotional disposition, goal decidedness, capability beliefs and social context beliefs. Influence of gender, age, immigration background, parental educational level, and college-bound or vocational education plans were also assessed. Perceived social support and positive emotional disposition, non-immigration background, and continuing to vocational education were single significant predictors of more career adaptability development over the school year. Supporting the connection of career adaptability and positive youth development, increase in career adaptability over time predicted increase in sense of power and experience of life satisfaction.

Dichotomous Hamiltonians with unbounded entries and solutions of Riccati equations

An operator Riccati equation from systems theory is considered in the case that all entries of the associated Hamiltonian are unbounded. Using a certain dichotomy property of the Hamiltonian and its symmetry with respect to two different indefinite inner products, we prove the existence of nonnegative and nonpositive solutions of the Riccati equation. Moreover, conditions for the boundedness and uniqueness of these solutions are established.

A Dynamical Tool to Study the Cultural Context of Conflict Escalation

The present article describes research in progress which is developing a simple, replicable methodology aimed at identifying the regularities and specificity of human behavior in conflict escalation and de-escalation prooesses. These research efforts will ultimately be used to study conflict dynamics across cultures. The experimental data collected through this methodology, together with case studies and aggregated, time-series macro data are key for identifying relevant parameters, systems' properties, and micromechanisms defining the behavior of naturally occurring conflict escalation and de-escalation dynamics. This, in turn, is critical for the development of realistic, empirically supported computational models. The article outlines the theoretical assumptions of Dynamical Systems Theory with regard to conflict dynamics, with an emphasis on the process of conflict escalation and de-escalation. Next, work on a methodology for empirical study of escalation processes from a DST perspective is outlined. Specifically, the development of a progressive scenario methodology designed to map escalation sequences, together with anexample of a preliminary study based on the proposed researcb paradigm, is presented. Implications of the approach for the study of culture are discussed.

The utility of rapid participatory appraisal for community assessment, diagnosis, and policy development

The selection of a model to guide the understanding and resolution of community problems is an important issue relating to the foundation of public health practice: assessment, policy development, and assurance. Many assessment models produce a diagnosis of community weaknesses, but fail to promote planning and interventions. Rapid Participatory Appraisal (RPA) is a participatory action research model which regards assessment as the first step in the problem solving process, and claims to achieve assessment and policy development within limited resources of time and money. Literature documenting the fulfillment of these claims, and thereby supporting the utility of the model, is relatively sparse and difficult to obtain. Very few articles discuss the changes resulting from RPA assessments in urban areas, and those that do describe studies conducted outside the U.S.A. ^ This study examines the utility of the RPA model and its underlying theories: systems theory, grounded theory, and principles of participatory change, as illustrated by the case study of a community assessment conducted for the Texas Diabetes Institute (TDI), San Antonio, Texas, and subsequent outcomes. Diabetes has a high prevalence and is a major issue in San Antonio. Faculty and students conducted the assessment by informal collaboration between two nursing and public health assessment courses, providing practical student experiences. The study area was large, and the flexibility of the model tested by its use in contiguous sub-regions, reanalyzing aggregated results for the study area. Official TDI reports, and a mail survey of agency employees, described policy development resulting from community diagnoses revealed by the assessment. ^ The RPA model met the criteria for utility from the perspectives of merit, worth, efficiency, and effectiveness. The RPA model best met the agencies' criteria (merit), met the data needs of TDI in this particular situation (worth), provided valid results within budget, time, and personnel constraints (efficiency), and stimulated policy development by TDI (effectiveness). ^ The RPA model appears to have utility for community assessment, diagnosis, and policy development in circumstances similar to the TDI diabetes study. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Los vínculos de intercambio entre el noreste de Africa y el Levante (ca.3400 - 3000 a.C.)

El estudio de los vínculos entre distintas comunidades generó diversos modelos teóricos e interpretaciones que fueron desarrollados para el estudio de las relaciones de intercambio existentes entre las poblaciones antiguas. En general, estas posturas teóricas se pueden diferenciar entre las que se concentran específicamente en los vínculos de intercambio establecidos entre distintas comunidades y diferentes áreas, y las que analizan el efecto de ellos en los procesos internos de una comunidad. En este trabajo nos enfocamos en el primer aspecto, ya que nuestro objeto es abordar las relaciones de intercambio existentes desde la Alta Nubia hasta el Levante, atravesando Baja Nubia, Alto Egipto y Bajo Egipto durante el período que se extiende desde el 3400 a.C al 3000 a.C., aplicando la teoría sistema-mundo y los análisis de los sistemas-mundo

Los vínculos de intercambio entre el noreste de Africa y el Levante (ca.3400 - 3000 a.C.)

El estudio de los vínculos entre distintas comunidades generó diversos modelos teóricos e interpretaciones que fueron desarrollados para el estudio de las relaciones de intercambio existentes entre las poblaciones antiguas. En general, estas posturas teóricas se pueden diferenciar entre las que se concentran específicamente en los vínculos de intercambio establecidos entre distintas comunidades y diferentes áreas, y las que analizan el efecto de ellos en los procesos internos de una comunidad. En este trabajo nos enfocamos en el primer aspecto, ya que nuestro objeto es abordar las relaciones de intercambio existentes desde la Alta Nubia hasta el Levante, atravesando Baja Nubia, Alto Egipto y Bajo Egipto durante el período que se extiende desde el 3400 a.C al 3000 a.C., aplicando la teoría sistema-mundo y los análisis de los sistemas-mundo

Los vínculos de intercambio entre el noreste de Africa y el Levante (ca.3400 - 3000 a.C.)

El estudio de los vínculos entre distintas comunidades generó diversos modelos teóricos e interpretaciones que fueron desarrollados para el estudio de las relaciones de intercambio existentes entre las poblaciones antiguas. En general, estas posturas teóricas se pueden diferenciar entre las que se concentran específicamente en los vínculos de intercambio establecidos entre distintas comunidades y diferentes áreas, y las que analizan el efecto de ellos en los procesos internos de una comunidad. En este trabajo nos enfocamos en el primer aspecto, ya que nuestro objeto es abordar las relaciones de intercambio existentes desde la Alta Nubia hasta el Levante, atravesando Baja Nubia, Alto Egipto y Bajo Egipto durante el período que se extiende desde el 3400 a.C al 3000 a.C., aplicando la teoría sistema-mundo y los análisis de los sistemas-mundo

Artificial Neural Nets with Interaction of Afferents

The aim is to obtain computationally more powerful, neuro physiologically founded, artificial neurons and neural nets. Artificial Neural Nets (ANN) of the Perceptron type evolved from the original proposal by McCulloch an Pitts classical paper [1]. Essentially, they keep the computing structure of a linear machine followed by a non linear operation. The McCulloch-Pitts formal neuron (which was never considered by the author’s to be models of real neurons) consists of the simplest case of a linear computation of the inputs followed by a threshold. Networks of one layer cannot compute anylogical function of the inputs, but only those which are linearly separable. Thus, the simple exclusive OR (contrast detector) function of two inputs requires two layers of formal neurons

Dendritic-Like Reliable Computation in Artificial Neurons

Dendritic computation is a term that has been in neuro physiological research for a long time [1]. It is still controversial and far for been clarified within the concepts of both computation and neurophysiology [2], [3]. In any case, it hasnot been integrated neither in a formal computational scheme or structure, nor into formulations of artificial neural nets. Our objective here is to formulate a type of distributed computation that resembles dendritic trees, in such a way that it shows the advantages of neural network distributed computation, mostly the reliability that is shown under the existence of holes (scotomas) in the computing net, without ?blind spots?.

On-board and Ground Visual Pose Estimation Techniques for UAV Control

In this paper, two techniques to control UAVs (Unmanned Aerial Vehicles), based on visual information are presented. The first one is based on the detection and tracking of planar structures from an on-board camera, while the second one is based on the detection and 3D reconstruction of the position of the UAV based on an external camera system. Both strategies are tested with a VTOL (Vertical take-off and landing) UAV, and results show good behavior of the visual systems (precision in the estimation and frame rate) when estimating the helicopter¿s position and using the extracted information to control the UAV.

Sobre los aeropuertos verdes: marco para la evaluación ambiental suficiente de una construcción bajo interpretación transversal

En el estudio buscamos caracterizar el análisis de la SOSTENIBILIDAD (Suficiencia) del CICLO DE VIDA de una INFRAESTRUCTURA AEROPORTUARIA centrándonos en la evaluación de los aspectos SOCIALES (de forma Interdisciplinaria o Transversal) que le afectan y considerando todos los AGENTES involucrados (ingenieros/ operadores/ mantenedores/ usuarios/ stakeholders/ etc.). La complejidad de las interacciones entre los edificios y su entorno hace que sea difícil definir y evaluar con precisión la sostenibilidad de un edificio. Las NORMAS AMBIENTALES para la construcción (unas pocas existentes y algunos en fase de desarrollo) se centran en la sostenibilidad ECONÓMICA, SOCIAL Y AMBIENTAL que caracteriza a un edificio, siendo los aspectos socio-económicos difíciles de evaluar. En consecuencia, los métodos existentes para la evaluación de la construcción sostenible (por ejemplo, LEED, BREEAM, SBTool) tienden a superar los aspectos ambientales pues son más fáciles de evaluar de manera cuantitativa. Así desde el punto de vista holístico (global) y utilizando la teoría de sistemas complejos, la sostenibilidad debe ser evaluada, en parte, utilizando los INDICADORES DE SOSTENIBILIDAD SOCIALES Y ECONÓMICOS para cubrir todos los factores de Sostenibilidad. El estudio propone una metodología para valorar la sostenibilidad en la construcción aeroportuaria a través de la evaluación de los indicadores sostenibles de la construcción (SKPIs) sin y superando las carencias presentadas. Para ello hemos implementado una herramienta de evaluación de la sostenibilidad, donde: Puede evaluar, en primer aproximación e independientemente, la sostenibilidad del CICLO DE VIDA de la INFRAESTRUCTURA AEROPORTUARIA Puede COMPLETAR otras herramientas comerciales disponibles (ej. BREEAM, LEED), bajo un enfoque ECONÓMICO-SOCIAL y complementando el enfoque ambiental La evaluación de los KPIs se realiza por medio de TECNOLOGÍAS Y ESTRATEGIAS SOSTENIBLES, cuya aplicación supondría un aumento de la sostenibilidad del edificio La herramienta propuesta considera la complejidad y transdisciplinariedad del problema, fundada en un SISTEMA DE CRÉDITOS fácil de usar. Así el programa diseñado permite el análisis y la comparación del CICLO DE VIDA de la INFRAESTRUCTURA AEROPORTUARIA: Abarcando las etapas de construcción (diseño, operación, mantenimiento, etc.) Incluyendo a todos los agentes de construcción (ocupantes, stakeholders, constructores, etc.) Finalmente, se aporta un ejemplo teórico de una INFRAESTRUCTURA AEROPORTUARIA (Terminal Aeroportuaria) para fijar, demostrar y discutir el estudio presentado Abstract We seek to characterize the sustainability analysis of the life cycle of a building focus us on the evaluation of social aspect. From a holistic point of view and using complex systems theory, sustainability must be evaluated, in part, using social key performance indicator (KPI) to cover all factors of sustainability. The most remarkable of the proposed framework is to provide a methodology to achieve the sustainability in construction through the assessment of social KPIs. Besides we implement a tool to assess sustainability, where this tool could complete other commercial tools available (e.g. BREEAM, LEED). The proposed tool considers the complexity and trans-disciplinary of the problem. The procedure is based on a credit system easy to use. It also allows analysis and comparison of the boundary conditions of the building, embracing construction stages (design, operation), involving all the building agents (occupants, stakeholders, etc.)