Sensitivity, specificity and predictive values of linear and nonlinear indices of heart rate variability in stable angina patients

Abstract Background Decreased heart rate variability (HRV) is related to higher morbidity and mortality. In this study we evaluated the linear and nonlinear indices of the HRV in stable angina patients submitted to coronary angiography. Methods We studied 77 unselected patients for elective coronary angiography, which were divided into two groups: coronary artery disease (CAD) and non-CAD groups. For analysis of HRV indices, HRV was recorded beat by beat with the volunteers in the supine position for 40 minutes. We analyzed the linear indices in the time (SDNN [standard deviation of normal to normal], NN50 [total number of adjacent RR intervals with a difference of duration greater than 50ms] and RMSSD [root-mean square of differences]) and frequency domains ultra-low frequency (ULF) ≤ 0,003 Hz, very low frequency (VLF) 0,003 – 0,04 Hz, low frequency (LF) (0.04–0.15 Hz), and high frequency (HF) (0.15–0.40 Hz) as well as the ratio between LF and HF components (LF/HF). In relation to the nonlinear indices we evaluated SD1, SD2, SD1/SD2, approximate entropy (−ApEn), α1, α2, Lyapunov Exponent, Hurst Exponent, autocorrelation and dimension correlation. The definition of the cutoff point of the variables for predictive tests was obtained by the Receiver Operating Characteristic curve (ROC). The area under the ROC curve was calculated by the extended trapezoidal rule, assuming as relevant areas under the curve ≥ 0.650. Results Coronary arterial disease patients presented reduced values of SDNN, RMSSD, NN50, HF, SD1, SD2 and -ApEn. HF ≤ 66 ms2, RMSSD ≤ 23.9 ms, ApEn ≤−0.296 and NN50 ≤ 16 presented the best discriminatory power for the presence of significant coronary obstruction. Conclusion We suggest the use of Heart Rate Variability Analysis in linear and nonlinear domains, for prognostic purposes in patients with stable angina pectoris, in view of their overall impairment.

Infinite dimensional Lie algebra associated with conformal transformations of the two-point velocity correlation tensor from isotropic turbulence

We deal with homogeneous isotropic turbulence and use the two-point velocity correlation tensor field (parametrized by the time variable t) of the velocity fluctuations to equip an affine space K3 of the correlation vectors by a family of metrics. It was shown in Grebenev and Oberlack (J Nonlinear Math Phys 18:109–120, 2011) that a special form of this tensor field generates the so-called semi-reducible pseudo-Riemannian metrics ds2(t) in K3. This construction presents the template for embedding the couple (K3, ds2(t)) into the Euclidean space R3 with the standard metric. This allows to introduce into the consideration the function of length between the fluid particles, and the accompanying important problem to address is to find out which transformations leave the statistic of length to be invariant that presents a basic interest of the paper. Also we classify the geometry of the particles configuration at least locally for a positive Gaussian curvature of this configuration and comment the case of a negative Gaussian curvature.

Diffusion in polymer systems studied by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a powerful technique to determine the diffusion of fluorescence molecules in various environments. The technique is based on detecting and analyzing the fluctuation of fluorescence light emitted by fluorescence species diffusing through a small and fixed observation volume, formed by a laser focused into the sample. Because of its great potential and high versatility in addressing the diffusion and transport properties in complex systems, FCS has been successfully applied to a great variety of systems. In my thesis, I focused on the application of FCS to study the diffusion of fluorescence molecules in organic environments, especially in polymer melts. In order to examine our FCS setup and a developed measurement protocol, I first utilized FCS to measure tracer diffusion in polystyrene (PS) solutions, for which abundance data exist in the literature. I studied molecular and polymeric tracer diffusion in polystyrene solutions over a broad range of concentrations and different tracer and matrix molecular weights (Mw). Then FCS was further established to study tracer dynamics in polymer melts. In this part I investigated the diffusion of molecular tracers in linear flexible polymer melts [polydimethylsiloxane (PDMS), polyisoprene (PI)], a miscible polymer blend [PI and poly vinyl ethylene (PVE)], and star-shaped polymer [3-arm star polyisoprene (SPI)]. The effects of tracer sizes, polymer Mw, polymer types, and temperature on the diffusion coefficients of small tracers were discussed. The distinct topology of the host polymer, i.e. star polymer melt, revealed the notably different motion of the small tracer, as compared to its linear counterpart. Finally, I emphasized the advantage of the small observation volume which allowed FCS to investigate the tracer diffusions in heterogeneous systems; a swollen cross-linked PS bead and silica inverse opals, where high spatial resolution technique was required.

Tracer diffusion at water-oil interfaces studied by fluorescence correlation spectroscopy

The adsorption of particles and surfactants at water-oil interfaces has attracted continuous attention because of its emulsion stabilizing effect and the possibility to form two-dimensional materials. Herein, I studied the interfacial diffusion of single molecules and nanoparticles at water-oil interfaces using fluorescence correlation spectroscopy. rnrnFluorescence correlation spectroscopy (FCS) is a promising technique to study diffusion of fluorescent tracers in diverse conditions. This technique monitors and analyzes the fluorescence fluctuation caused by single fluorescent tracers coming in and out of a diffraction-limited observation volume “one at a time”. Thus, this technique allows a combination of high precision, high spatial resolution and low tracer concentration. rnrnIn chapter 1, I discussed some controversial questions regarding the properties of water-hydrophobic interfaces and also introduced the current progress on the stability and dynamic of single nanoparticles at water-oil interfaces. The materials and setups I used in this thesis were summarized in chapter 2. rnrnIn chapter 3, I presented a new strategy to study the properties of water-oil interfaces. The two-dimensional diffusion of isolated molecular tracers at water/n-alkane interfaces was measured using fluorescence correlation spectroscopy. The diffusion coefficients of larger tracers with a hydrodynamic radius of 4.0 nm agreed well with the values calculated from the macroscopic viscosities of the two bulk phases. However, for small molecule tracers with hydrodynamic radii of only 1.0 and 0.6 nm, notable deviations were observed, indicating the existence of an interfacial region with a reduced effective viscosity. rnrnIn chapter 4, the interfacial diffusion of nanoparticles at water-oil interfaces was investigated using FCS. In stark contrast to the interfacial diffusion of molecular tracers, that of nanoparticles at any conditions is slower than the values calculated in accordance to the surrounding viscosity. The diffusion of nanoparticles at water-oil interfaces depended on the interfacial tension of liquid-liquid interfaces, the surface properties of nanoparticles, the particle sizes and the viscosities of surrounding liquid phases. In addition, the interfacial diffusion of nanoparticles with Janus motif is even slower than that of their symmetric counterparts. Based on the experimental results I obtained, I drew some possibilities to describe the origin of nanoparticle slowdown at water-oil interfaces.

Uniform approach to linear and nonlinear interrelation patterns in multivariate time series

Currently, a variety of linear and nonlinear measures is in use to investigate spatiotemporal interrelation patterns of multivariate time series. Whereas the former are by definition insensitive to nonlinear effects, the latter detect both nonlinear and linear interrelation. In the present contribution we employ a uniform surrogate-based approach, which is capable of disentangling interrelations that significantly exceed random effects and interrelations that significantly exceed linear correlation. The bivariate version of the proposed framework is explored using a simple model allowing for separate tuning of coupling and nonlinearity of interrelation. To demonstrate applicability of the approach to multivariate real-world time series we investigate resting state functional magnetic resonance imaging (rsfMRI) data of two healthy subjects as well as intracranial electroencephalograms (iEEG) of two epilepsy patients with focal onset seizures. The main findings are that for our rsfMRI data interrelations can be described by linear cross-correlation. Rejection of the null hypothesis of linear iEEG interrelation occurs predominantly for epileptogenic tissue as well as during epileptic seizures.

Hydrodynamic correlation functions of a driven granular fluid in steady state

We study a homogeneously driven granular fluid of hard spheres at intermediate volume fractions and focus on time-delayed correlation functions in the stationary state. Inelastic collisions are modeled by incomplete normal restitution, allowing for efficient simulations with an event-driven algorithm. The incoherent scattering function Fincoh(q,t ) is seen to follow time-density superposition with a relaxation time that increases significantly as the volume fraction increases. The statistics of particle displacements is approximately Gaussian. For the coherent scattering function S(q,ω), we compare our results to the predictions of generalized fluctuating hydrodynamics, which takes into account that temperature fluctuations decay either diffusively or with a finite relaxation rate, depending on wave number and inelasticity. For sufficiently small wave number q we observe sound waves in the coherent scattering function S(q,ω) and the longitudinal current correlation function Cl(q,ω). We determine the speed of sound and the transport coefficients and compare them to the results of kinetic theory.

A Bayesian approach to estimating the regression coefficients of a multinomial logit model

A Bayesian approach to estimation of the regression coefficients of a multinominal logit model with ordinal scale response categories is presented. A Monte Carlo method is used to construct the posterior distribution of the link function. The link function is treated as an arbitrary scalar function. Then the Gauss-Markov theorem is used to determine a function of the link which produces a random vector of coefficients. The posterior distribution of the random vector of coefficients is used to estimate the regression coefficients. The method described is referred to as a Bayesian generalized least square (BGLS) analysis. Two cases involving multinominal logit models are described. Case I involves a cumulative logit model and Case II involves a proportional-odds model. All inferences about the coefficients for both cases are described in terms of the posterior distribution of the regression coefficients. The results from the BGLS method are compared to maximum likelihood estimates of the regression coefficients. The BGLS method avoids the nonlinear problems encountered when estimating the regression coefficients of a generalized linear model. The method is not complex or computationally intensive. The BGLS method offers several advantages over Bayesian approaches. ^

Artificial oxygen fluxes measured by the eddy correlation method using stirring-sensitive oxygen microsensor and oxygen optodes in a flume experiment

In the last decade, the aquatic eddy correlation (EC) technique has proven to be a powerful approach for non-invasive measurements of oxygen fluxes across the sediment water interface. Fundamental to the EC approach is the correlation of turbulent velocity and oxygen concentration fluctuations measured with high frequencies in the same sampling volume. Oxygen concentrations are commonly measured with fast responding electrochemical microsensors. However, due to their own oxygen consumption, electrochemical microsensors are sensitive to changes of the diffusive boundary layer surrounding the probe and thus to changes in the ambient flow velocity. The so-called stirring sensitivity of microsensors constitutes an inherent correlation of flow velocity and oxygen sensing and thus an artificial flux which can confound the benthic flux determination. To assess the artificial flux we measured the correlation between the turbulent flow velocity and the signal of oxygen microsensors in a sealed annular flume without any oxygen sinks and sources. Experiments revealed significant correlations, even for sensors designed to have low stirring sensitivities of ~0.7%. The artificial fluxes depended on ambient flow conditions and, counter intuitively, increased at higher velocities because of the nonlinear contribution of turbulent velocity fluctuations. The measured artificial fluxes ranged from 2 - 70 mmol m**-2 d**-1 for weak and very strong turbulent flow, respectively. Further, the stirring sensitivity depended on the sensor orientation towards the flow. Optical microsensors (optodes) that should not exhibit a stirring sensitivity were tested in parallel and did not show any significant correlation between O2 signals and turbulent flow. In conclusion, EC data obtained with electrochemical sensors can be affected by artificial flux and we recommend using optical microsensors in future EC-studies. Flume experiments were conducted in February 2013 at the Institute for Environmental Sciences, University of Koblenz-Landau Landau. Experiments were performed in a closed oval-shaped acrylic glass flume with cross-sectional width of 4 cm and height of 10 cm and total length of 54 cm. The fluid flow was induced by a propeller driven by a motor and mean flow velocities of up to 20 cm s-1 were generated by applying voltages between 0 V and 4 V DC. The flume was completely sealed with an acrylic glass cover. Oxygen sensors were inserted through rubber seal fittings and allowed positioning the sensors with inclinations to the main flow direction of ~60°, ~95° and ~135°. A Clark type electrochemical O2 microsensor with a low stirring sensitivity (0.7%) was tested and a fast-responding needle-type O2 optode (PyroScience GmbH, Germany) was used as reference as optodes should not be stirring sensitive. Instantaneous three-dimensional flow velocities were measured at 7.4 Hz using stereoscopic particle image velocimetry (PIV). The velocity at the sensor tip was extracted. The correlation of the fluctuating O2 sensor signals and the fluctuating velocities was quantified with a cross-correlation analysis. A significant cross-correlation is equivalent to a significant artificial flux. For a total of 18 experiments the flow velocity was adjusted between 1.7 and 19.2 cm s**-1, and 3 different orientations of the electrochemical sensor were tested with inclination angles of ~60°, ~95° and ~135° with respect to the main flow direction. In experiments 16-18, wavelike flow was induced, whereas in all other experiments the motor was driven by constant voltages. In 7 experiments, O2 was additionally measured by optodes. Although performed simultaneously with the electrochemical sensor, optode measurements are listed as separate experiments (denoted by the attached 'op' in the filename), because the velocity time series was extracted at the optode tip, located at a different position in the flume.

Trade Coefficients and the Role of Elasticity in a Spatial CGE Model Based on the Armington Assumption

The Armington Assumption in the context of multi-regional CGE models is commonly interpreted as follows: Same commodities with different origins are imperfect substitutes for each other. In this paper, a static spatial CGE model that is compatible with this assumption and explicitly considers the transport sector and regional price differentials is formulated. Trade coefficients, which are derived endogenously from the optimization behaviors of firms and households, are shown to take the form of a potential function. To investigate how the elasticity of substitutions affects equilibrium solutions, a simpler version of the model that incorporates three regions and two sectors (besides the transport sector) is introduced. Results indicate: (1) if commodities produced in different regions are perfect substitutes, regional economies will be either autarkic or completely symmetric and (2) if they are imperfect substitutes, the impact of elasticity on the price equilibrium system as well as trade coefficients will be nonlinear and sometimes very sensitive.

Ion-Ion correlations effect on nonlinear high-frequency plasma conductivity. AT(30-1)-1238-MATT-675

On the basis of the BBGKY hierarchy of equations an expression is derived for the response of a fully ionized plasma to a strong, high-frequency electric field in the limit of infinite ion mass. It is found that even in this limit the ionion correlation function is substantially affected by the field. The corrections to earlier nonlinear results for the current density appear to be quite ssential. The validity of the model introduced by Dawson and Oberman to study the response to a vanishingly small field is confirmed for larger values of the field when the eorrect expression for the ion-ion correlations i s introduced; the model by itself does not yield such an expression. The results have interest for the heating of the plasma and for the propagation of a strong electromagnetic wave through the plasma. The theory seems to be valid for any field intensity for which the plasma is stable.

Hydrodynamic forces on heave plates for offshore systems oscillating close to the seabed or the free surface

La energía eólica marina es uno de los recursos energéticos con mayor proyección pudiendo contribuir a reducir el consumo de combustibles fósiles y a cubrir la demanda de energía en todo el mundo. El concepto de aerogenerador marino está basado en estructuras fijas como jackets o en plataformas flotantes, ya sea una semisumergible o una TLP. Se espera que la energía eólica offshore juegue un papel importante en el perfil de producción energética de los próximos años; por tanto, las turbinas eólicas deben hacerse más fables y rentables para ser competitivas frente a otras fuentes de energía. Las estructuras flotantes pueden experimentar movimientos resonantes en estados de la mar con largos períodos de oleaje. Estos movimientos disminuyen su operatividad y pueden causar daños en los componentes eléctricos de las turbinas y en las palas, también en los risers y moorings. La respuesta de la componente vertical del movimiento puede reducirse mediante diferentes actuaciones: (1) aumentando la amortiguación del sistema, (2) manteniendo el período del movimiento vertical fuera del rango de la energía de la ola, y (3) reduciendo las fuerzas de excitación verticales. Un ejemplo típico para llevar a cabo esta reducción son las "Heave Plates". Las heave plates son placas que se utilizan en la industria offshore debido a sus características hidrodinámicas, ya que aumentan la masa añadida y la amortiguación del sistema. En un análisis hidrodinámico convencional, se considera una estructura sometida a un oleaje con determinadas características y se evalúan las cargas lineales usando la teoría potencial. El amortiguamiento viscoso, que juega un papel crucial en la respuesta en resonancia del sistema, es un dato de entrada para el análisis. La tesis se centra principalmente en la predicción del amortiguamiento viscoso y de la masa añadida de las heave plates usadas en las turbinas eólicas flotantes. En los cálculos, las fuerzas hidrodinámicas se han obtenido con el f n de estudiar cómo los coeficientes hidrodinámicos de masa añadida5 y amortiguamiento varían con el número de KC, que caracteriza la amplitud del movimiento respecto al diámetro del disco. Por otra parte, se ha investigado la influencia de la distancia media de la ‘heave plate’ a la superficie libre o al fondo del mar, sobre los coeficientes hidrodinámicos. En este proceso, un nuevo modelo que describe el trabajo realizado por la amortiguación en función de la enstrofía, es descrito en el presente documento. Este nuevo enfoque es capaz de proporcionar una correlación directa entre el desprendimiento local de vorticidad y la fuerza de amortiguación global. El análisis también incluye el estudio de los efectos de la geometría de la heave plate, y examina la sensibilidad de los coeficientes hidrodinámicos al incluir porosidad en ésta. Un diseño novedoso de una heave plate, basado en la teoría fractal, también fue analizado experimentalmente y comparado con datos experimentales obtenidos por otros autores. Para la resolución de las ecuaciones de Navier Stokes se ha usado un solver basado en el método de volúmenes finitos. El solver usa las librerías de OpenFOAM (Open source Field Operation And Manipulation), para resolver un problema multifásico e incompresible, usando la técnica VOF (volume of fluid) que permite capturar el movimiento de la superficie libre. Los resultados numéricos han sido comparados con resultados experimentales llevados a cabo en el Canal del Ensayos Hidrodinámicos (CEHINAV) de la Universidad Politécnica de Madrid y en el Canal de Experiencias Hidrodinámicas (CEHIPAR) en Madrid, al igual que con otros experimentos realizados en la Escuela de Ingeniería Mecánica de la Universidad de Western Australia. Los principales resultados se presentan a continuación: 1. Para pequeños valores de KC, los coeficientes hidrodinámicos de masa añadida y amortiguamiento incrementan su valor a medida que el disco se aproxima al fondo marino. Para los casos cuando el disco oscila cerca de la superficie libre, la dependencia de los coeficientes hidrodinámicos es más fuerte por la influencia del movimiento de la superficie libre. 2. Los casos analizados muestran la existencia de un valor crítico de KC, donde la tendencia de los coeficientes hidrodinámicos se ve alterada. Dicho valor crítico depende de la distancia al fondo marino o a la superficie libre. 3. El comportamiento físico del flujo, para valores de KC cercanos a su valor crítico ha sido estudiado mediante el análisis del campo de vorticidad. 4. Introducir porosidad al disco, reduce la masa añadida para los valores de KC estudiados, pero se ha encontrado que la porosidad incrementa el valor del coeficiente de amortiguamiento cuando se incrementa la amplitud del movimiento, logrando un máximo de damping para un disco con 10% de porosidad. 5. Los resultados numéricos y experimentales para los discos con faldón, muestran que usar este tipo de geometrías incrementa la masa añadida cuando se compara con el disco sólido, pero reduce considerablemente el coeficiente de amortiguamiento. 6. Un diseño novedoso de heave plate basado en la teoría fractal ha sido experimentalmente estudiado a diferentes calados y comparado con datos experimentales obtenidos por otro autores. Los resultados muestran un comportamiento incierto de los coeficientes y por tanto este diseño debería ser estudiado más a fondo. ABSTRACT Offshore wind energy is one of the promising resources which can reduce the fossil fuel energy consumption and cover worldwide energy demands. Offshore wind turbine concepts are based on either a fixed structure as a jacket or a floating offshore platform like a semisubmersible, spar or tension leg platform. Floating offshore wind turbines have the potential to be an important part of the energy production profile in the coming years. In order to accomplish this wind integration, these wind turbines need to be made more reliable and cost efficient to be competitive with other sources of energy. Floating offshore artifacts, such oil rings and wind turbines, may experience resonant heave motions in sea states with long peak periods. These heave resonances may increase the system downtime and cause damage on the system components and as well as on risers and mooring systems. The heave resonant response may be reduced by different means: (1) increasing the damping of the system, (2) keeping the natural heave period outside the range of the wave energy, and (3) reducing the heave excitation forces. A typical example to accomplish this reduction are “Heave Plates”. Heave plates are used in the offshore industry due to their hydrodynamic characteristics, i.e., increased added mass and damping. Conventional offshore hydrodynamic analysis considers a structure in waves, and evaluates the linear and nonlinear loads using potential theory. Viscous damping, which is expected to play a crucial role in the resonant response, is an empirical input to the analysis, and is not explicitly calculated. The present research has been mainly focused on the prediction of viscous damping and added mass of floating offshore wind turbine heave plates. In the calculations, the hydrodynamic forces have been measured in order to compute how the hydrodynamic coefficients of added mass1 and damping vary with the KC number, which characterises the amplitude of heave motion relative to the diameter of the disc. In addition, the influence on the hydrodynamic coefficients when the heave plate is oscillating close to the free surface or the seabed has been investigated. In this process, a new model describing the work done by damping in terms of the flow enstrophy, is described herein. This new approach is able to provide a direct correlation between the local vortex shedding processes and the global damping force. The analysis also includes the study of different edges geometry, and examines the sensitivity of the damping and added mass coefficients to the porosity of the plate. A novel porous heave plate based on fractal theory has also been proposed, tested experimentally and compared with experimental data obtained by other authors for plates with similar porosity. A numerical solver of Navier Stokes equations, based on the finite volume technique has been applied. It uses the open-source libraries of OpenFOAM (Open source Field Operation And Manipulation), to solve 2 incompressible, isothermal immiscible fluids using a VOF (volume of fluid) phase-fraction based interface capturing approach, with optional mesh motion and mesh topology changes including adaptive re-meshing. Numerical results have been compared with experiments conducted at Technical University of Madrid (CEHINAV) and CEHIPAR model basins in Madrid and with others performed at School of Mechanical Engineering in The University of Western Australia. A brief summary of main results are presented below: 1. At low KC numbers, a systematic increase in added mass and damping, corresponding to an increase in the seabed proximity, is observed. Specifically, for the cases when the heave plate is oscillating closer to the free surface, the dependence of the hydrodynamic coefficients is strongly influenced by the free surface. 2. As seen in experiments, a critical KC, where the linear trend of the hydrodynamic coefficients with KC is disrupted and that depends on the seabed or free surface distance, has been found. 3. The physical behavior of the flow around the critical KC has been explained through an analysis of the flow vorticity field. 4. The porosity of the heave plates reduces the added mass for the studied porosity at all KC numbers, but the porous heave plates are found to increase the damping coefficient with increasing amplitude of oscillation, achieving a maximum damping coefficient for the heave plate with 10% porosity in the entire KC range. 5. Another concept taken into account in this work has been the heave plates with flaps. Numerical and experimental results show that using discs with flaps will increase added mass when compared to the plain plate but may also significantly reduce damping. 6. A novel heave plate design based on fractal theory has tested experimentally for different submergences and compared with experimental data obtained by other authors for porous plates. Results show an unclear behavior in the coefficients and should be studied further. Future work is necessary in order to address a series of open questions focusing on 3D effects, optimization of the heave plates shapes, etc.

Automated wordlength optimization framework for multi-source statistical interval-based analysis of nonlinear systems with control-flow structures

El uso de aritmética de punto fijo es una opción de diseño muy extendida en sistemas con fuertes restricciones de área, consumo o rendimiento. Para producir implementaciones donde los costes se minimicen sin impactar negativamente en la precisión de los resultados debemos llevar a cabo una asignación cuidadosa de anchuras de palabra. Encontrar la combinación óptima de anchuras de palabra en coma fija para un sistema dado es un problema combinatorio NP-hard al que los diseñadores dedican entre el 25 y el 50 % del ciclo de diseño. Las plataformas hardware reconfigurables, como son las FPGAs, también se benefician de las ventajas que ofrece la aritmética de coma fija, ya que éstas compensan las frecuencias de reloj más bajas y el uso más ineficiente del hardware que hacen estas plataformas respecto a los ASICs. A medida que las FPGAs se popularizan para su uso en computación científica los diseños aumentan de tamaño y complejidad hasta llegar al punto en que no pueden ser manejados eficientemente por las técnicas actuales de modelado de señal y ruido de cuantificación y de optimización de anchura de palabra. En esta Tesis Doctoral exploramos distintos aspectos del problema de la cuantificación y presentamos nuevas metodologías para cada uno de ellos: Las técnicas basadas en extensiones de intervalos han permitido obtener modelos de propagación de señal y ruido de cuantificación muy precisos en sistemas con operaciones no lineales. Nosotros llevamos esta aproximación un paso más allá introduciendo elementos de Multi-Element Generalized Polynomial Chaos (ME-gPC) y combinándolos con una técnica moderna basada en Modified Affine Arithmetic (MAA) estadístico para así modelar sistemas que contienen estructuras de control de flujo. Nuestra metodología genera los distintos caminos de ejecución automáticamente, determina las regiones del dominio de entrada que ejercitarán cada uno de ellos y extrae los momentos estadísticos del sistema a partir de dichas soluciones parciales. Utilizamos esta técnica para estimar tanto el rango dinámico como el ruido de redondeo en sistemas con las ya mencionadas estructuras de control de flujo y mostramos la precisión de nuestra aproximación, que en determinados casos de uso con operadores no lineales llega a tener tan solo una desviación del 0.04% con respecto a los valores de referencia obtenidos mediante simulación. Un inconveniente conocido de las técnicas basadas en extensiones de intervalos es la explosión combinacional de términos a medida que el tamaño de los sistemas a estudiar crece, lo cual conlleva problemas de escalabilidad. Para afrontar este problema presen tamos una técnica de inyección de ruidos agrupados que hace grupos con las señales del sistema, introduce las fuentes de ruido para cada uno de los grupos por separado y finalmente combina los resultados de cada uno de ellos. De esta forma, el número de fuentes de ruido queda controlado en cada momento y, debido a ello, la explosión combinatoria se minimiza. También presentamos un algoritmo de particionado multi-vía destinado a minimizar la desviación de los resultados a causa de la pérdida de correlación entre términos de ruido con el objetivo de mantener los resultados tan precisos como sea posible. La presente Tesis Doctoral también aborda el desarrollo de metodologías de optimización de anchura de palabra basadas en simulaciones de Monte-Cario que se ejecuten en tiempos razonables. Para ello presentamos dos nuevas técnicas que exploran la reducción del tiempo de ejecución desde distintos ángulos: En primer lugar, el método interpolativo aplica un interpolador sencillo pero preciso para estimar la sensibilidad de cada señal, y que es usado después durante la etapa de optimización. En segundo lugar, el método incremental gira en torno al hecho de que, aunque es estrictamente necesario mantener un intervalo de confianza dado para los resultados finales de nuestra búsqueda, podemos emplear niveles de confianza más relajados, lo cual deriva en un menor número de pruebas por simulación, en las etapas iniciales de la búsqueda, cuando todavía estamos lejos de las soluciones optimizadas. Mediante estas dos aproximaciones demostramos que podemos acelerar el tiempo de ejecución de los algoritmos clásicos de búsqueda voraz en factores de hasta x240 para problemas de tamaño pequeño/mediano. Finalmente, este libro presenta HOPLITE, una infraestructura de cuantificación automatizada, flexible y modular que incluye la implementación de las técnicas anteriores y se proporciona de forma pública. Su objetivo es ofrecer a desabolladores e investigadores un entorno común para prototipar y verificar nuevas metodologías de cuantificación de forma sencilla. Describimos el flujo de trabajo, justificamos las decisiones de diseño tomadas, explicamos su API pública y hacemos una demostración paso a paso de su funcionamiento. Además mostramos, a través de un ejemplo sencillo, la forma en que conectar nuevas extensiones a la herramienta con las interfaces ya existentes para poder así expandir y mejorar las capacidades de HOPLITE. ABSTRACT Using fixed-point arithmetic is one of the most common design choices for systems where area, power or throughput are heavily constrained. In order to produce implementations where the cost is minimized without negatively impacting the accuracy of the results, a careful assignment of word-lengths is required. The problem of finding the optimal combination of fixed-point word-lengths for a given system is a combinatorial NP-hard problem to which developers devote between 25 and 50% of the design-cycle time. Reconfigurable hardware platforms such as FPGAs also benefit of the advantages of fixed-point arithmetic, as it compensates for the slower clock frequencies and less efficient area utilization of the hardware platform with respect to ASICs. As FPGAs become commonly used for scientific computation, designs constantly grow larger and more complex, up to the point where they cannot be handled efficiently by current signal and quantization noise modelling and word-length optimization methodologies. In this Ph.D. Thesis we explore different aspects of the quantization problem and we present new methodologies for each of them: The techniques based on extensions of intervals have allowed to obtain accurate models of the signal and quantization noise propagation in systems with non-linear operations. We take this approach a step further by introducing elements of MultiElement Generalized Polynomial Chaos (ME-gPC) and combining them with an stateof- the-art Statistical Modified Affine Arithmetic (MAA) based methodology in order to model systems that contain control-flow structures. Our methodology produces the different execution paths automatically, determines the regions of the input domain that will exercise them, and extracts the system statistical moments from the partial results. We use this technique to estimate both the dynamic range and the round-off noise in systems with the aforementioned control-flow structures. We show the good accuracy of our approach, which in some case studies with non-linear operators shows a 0.04 % deviation respect to the simulation-based reference values. A known drawback of the techniques based on extensions of intervals is the combinatorial explosion of terms as the size of the targeted systems grows, which leads to scalability problems. To address this issue we present a clustered noise injection technique that groups the signals in the system, introduces the noise terms in each group independently and then combines the results at the end. In this way, the number of noise sources in the system at a given time is controlled and, because of this, the combinato rial explosion is minimized. We also present a multi-way partitioning algorithm aimed at minimizing the deviation of the results due to the loss of correlation between noise terms, in order to keep the results as accurate as possible. This Ph.D. Thesis also covers the development of methodologies for word-length optimization based on Monte-Carlo simulations in reasonable times. We do so by presenting two novel techniques that explore the reduction of the execution times approaching the problem in two different ways: First, the interpolative method applies a simple but precise interpolator to estimate the sensitivity of each signal, which is later used to guide the optimization effort. Second, the incremental method revolves on the fact that, although we strictly need to guarantee a certain confidence level in the simulations for the final results of the optimization process, we can do it with more relaxed levels, which in turn implies using a considerably smaller amount of samples, in the initial stages of the process, when we are still far from the optimized solution. Through these two approaches we demonstrate that the execution time of classical greedy techniques can be accelerated by factors of up to ×240 for small/medium sized problems. Finally, this book introduces HOPLITE, an automated, flexible and modular framework for quantization that includes the implementation of the previous techniques and is provided for public access. The aim is to offer a common ground for developers and researches for prototyping and verifying new techniques for system modelling and word-length optimization easily. We describe its work flow, justifying the taken design decisions, explain its public API and we do a step-by-step demonstration of its execution. We also show, through an example, the way new extensions to the flow should be connected to the existing interfaces in order to expand and improve the capabilities of HOPLITE.

Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells

Fluorescein-labeled oligodeoxynucleotides (oligos) were introduced into cultured rat myoblasts, and their molecular movements inside the nucleus were studied by fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). FCS revealed that a large fraction of both intranuclear oligo(dT) (43%) and oligo(dA) (77%) moves rapidly with a diffusion coefficient of 4 × 10−7 cm2/s. Interestingly, this rate of intranuclear oligo movement is similar to their diffusion rates measured in aqueous solution. In addition, we detected a large fraction (45%) of the intranuclear oligo(dT), but not oligo(dA), diffusing at slower rates (≤1 × 10−7 cm2/s). The amount of this slower-moving oligo(dT) was greatly reduced if the oligo(dT) was prehybridized in solution with (unlabeled) oligo(dA) prior to introduction to cells, presumably because the oligo(dT) was then unavailable for subsequent hybridization to endogenous poly(A) RNA. The FCS-measured diffusion rate for much of the slower oligo(dT) population approximated the diffusion rate in aqueous solution of oligo(dT) hybridized to a large polyadenylated RNA (1.0 × 10−7 cm2/s). Moreover, this intranuclear movement rate falls within the range of calculated diffusion rates for an average-sized heterogeneous nuclear ribonucleoprotein particle in aqueous solution. A subfraction of oligo(dT) (15%) moved over 10-fold more slowly, suggesting it was bound to very large macromolecular complexes. Average diffusion coefficients obtained from FRAP experiments were in agreement with the FCS data. These results demonstrate that oligos can move about within the nucleus at rates comparable to those in aqueous solution and further suggest that this is true for large ribonucleoprotein complexes as well.

Impact of vaccination on the spatial correlation and persistence of measles dynamics.

The onset of measles vaccination in England and Wales in 1968 coincided with a marked drop in the temporal correlation of epidemic patterns between major cities. We analyze a variety of hypotheses for the mechanisms driving this change. Straightforward stochastic models suggest that the interaction between a lowered susceptible population (and hence increased demographic noise) and nonlinear dynamics is sufficient to cause the observed drop in correlation. The decorrelation of epidemics could potentially lessen the chance of global extinction and so inhibit attempts at measles eradication.