Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Methedology for designing, observing and computing external geodetic networks of long lengths tunnels

RESUMEN La realización de túneles de gran longitud para ferrocarriles ha adquirido un gran auge en los últimos años. En España se han abordado proyectos de estas características, no existiendo para su ejecución una metodología completa y contrastada de actuación. Las características geométricas, de observación y de trabajo en túneles hace que las metodologías que se aplican en otros proyectos de ingeniería no sean aplicables por las siguientes causas: separación de las redes exteriores e interiores de los túneles debido a la diferente naturaleza de los observables, geometría en el interior siempre desfavorable a los requerimientos de observación clásica, mala visibilidad dentro del túnel, aumento de errores conforme avanza la perforación, y movimientos propios del túnel durante su ejecución por la propia geodinámica activa. Los patrones de observación geodésica usados deben revisarse cuando se ejecutan túneles de gran longitud. Este trabajo establece una metodología para el diseño de redes exteriores. ABSTRACT: The realization of long railway tunnels has acquired a great interest in recent years. In Spain it is necessary to address projects of this nature, but ther is no corresponding methodological framework supporting them. The tunnel observational and working geometrical properties, make that former methodologies used may be unuseful in this case: the observation of the exterior and interior geodetical networks of the tunnel is different in nature. Conditions of visibility in the interior of the tunnels, regardless of the geometry, are not the most advantageous for observation due to the production system and the natural conditions of the tunnels. Errors increase as the drilling of the tunnel progresses, as it becomes problematical to perform continuous verifications along the itinerary itself. Moreover, inherent tunnel movements due to active geodynamics must also be considered. Therefore patterns for geodetic and topographic observations have to be reviewed when very long tunnels are constructed.

A temperature-based thermodynamically consistent integration scheme for discrete thermo-elastodynamics

The formulation of thermodynamically consistent (TC) time integration methods was introduced by a general procedure based on the GENERIC form of the evolution equations for thermo-mechanical problems. The use of the entropy was reported to be the best choice for the thermodynamical variable to easily provide TC integrators. Also the employment of the internal energy was proved to not involve excessive complications. However, attempts towards the use of the temperature in the design of GENERIC-based TC schemes have so far been unfruitful. This paper complements the said procedure to attain TC integrators by presenting a TC scheme based on the temperature as thermodynamical state variable. As a result, the problems which arise due to the use of the entropy are overcome, mainly the definition of boundary conditions. What is more, the newly proposed method exhibits the general enhanced numerical stability and robustness properties of the entropy formulation.

Energy-entropy-momentum time integration methods for coupled smooth dissipative problems

Esta tesis aborda la formulación, análisis e implementación de métodos numéricos de integración temporal para la solución de sistemas disipativos suaves de dimensión finita o infinita de manera que su estructura continua sea conservada. Se entiende por dichos sistemas aquellos que involucran acoplamiento termo-mecánico y/o efectos disipativos internos modelados por variables internas que siguen leyes continuas, de modo que su evolución es considerada suave. La dinámica de estos sistemas está gobernada por las leyes de la termodinámica y simetrías, las cuales constituyen la estructura que se pretende conservar de forma discreta. Para ello, los sistemas disipativos se describen geométricamente mediante estructuras metriplécticas que identifican claramente las partes reversible e irreversible de la evolución del sistema. Así, usando una de estas estructuras conocida por las siglas (en inglés) de GENERIC, la estructura disipativa de los sistemas es identificada del mismo modo que lo es la Hamiltoniana para sistemas conservativos. Con esto, métodos (EEM) con precisión de segundo orden que conservan la energía, producen entropía y conservan los impulsos lineal y angular son formulados mediante el uso del operador derivada discreta introducido para asegurar la conservación de la Hamiltoniana y las simetrías de sistemas conservativos. Siguiendo estas directrices, se formulan dos tipos de métodos EEM basados en el uso de la temperatura o de la entropía como variable de estado termodinámica, lo que presenta importantes implicaciones que se discuten a lo largo de esta tesis. Entre las cuales cabe destacar que las condiciones de contorno de Dirichlet son naturalmente impuestas con la formulación basada en la temperatura. Por último, se validan dichos métodos y se comprueban sus mejores prestaciones en términos de la estabilidad y robustez en comparación con métodos estándar. This dissertation is concerned with the formulation, analysis and implementation of structure-preserving time integration methods for the solution of the initial(-boundary) value problems describing the dynamics of smooth dissipative systems, either finite- or infinite-dimensional ones. Such systems are understood as those involving thermo-mechanical coupling and/or internal dissipative effects modeled by internal state variables considered to be smooth in the sense that their evolutions follow continuos laws. The dynamics of such systems are ruled by the laws of thermodynamics and symmetries which constitutes the structure meant to be preserved in the numerical setting. For that, dissipative systems are geometrically described by metriplectic structures which clearly identify the reversible and irreversible parts of their dynamical evolution. In particular, the framework known by the acronym GENERIC is used to reveal the systems' dissipative structure in the same way as the Hamiltonian is for conserving systems. Given that, energy-preserving, entropy-producing and momentum-preserving (EEM) second-order accurate methods are formulated using the discrete derivative operator that enabled the formulation of Energy-Momentum methods ensuring the preservation of the Hamiltonian and symmetries for conservative systems. Following these guidelines, two kind of EEM methods are formulated in terms of entropy and temperature as a thermodynamical state variable, involving important implications discussed throughout the dissertation. Remarkably, the formulation in temperature becomes central to accommodate Dirichlet boundary conditions. EEM methods are finally validated and proved to exhibit enhanced numerical stability and robustness properties compared to standard ones.

On representations of finite type

Representations of the (infinite) canonical anticommutation relations and the associated operator algebra, the fermion algebra, are studied. A “coupling constant” (in (0,1]) is defined for primary states of “finite type” of that algebra. Primary, faithful states of finite type with arbitrary coupling are constructed and classified. Their physical significance for quantum thermodynamical systems at high temperatures is discussed. The scope of this study is broadened to include a large class of operator algebras sharing some of the structural properties of the fermion algebra.

Evidence for nonrandom hydrophobicity structures in protein chains.

The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along the protein chains. Theoretical expectations of these variables from random distributions of hydrophobicities are compared with those obtained from functional proteins. The results, which are based upon proteins in the SWISS-PROT data base, convincingly show that the amino acid sequences in proteins differ from what is expected from random sequences in a statistically significant way. By performing Fourier transforms on the random walks, one obtains additional evidence for nonrandomness of the distributions. We have also analyzed results from a synthetic model containing only two amino acid types, hydrophobic and hydrophilic. With reasonable criteria on good folding properties in terms of thermodynamical and kinetic behavior, sequences that fold well are isolated. Performing the same statistical analysis on the sequences that fold well indicates similar deviations from randomness as for the functional proteins. The deviations from randomness can be interpreted as originating from anticorrelations in terms of an Ising spin model for the hydrophobicities. Our results, which differ from some previous investigations using other methods, might have impact on how permissive with respect to sequence specificity protein folding process is-only sequences with nonrandom hydrophobicity distributions fold well. Other distributions give rise to energy landscapes with poor folding properties and hence did not survive the evolution.

Gravidade de Lovelock e a correspondência AdS/CFT

A correspondência AdS/CFT é uma notável ferramenta no estudo de teorias de gauge fortemente acopladas que podem ser mapeadas em uma descrição gravitacional dual fracamente acoplada. A correspondência é melhor entendida no limite em que ambos $N$ e $\\lambda$, o rank do grupo de gauge e o acoplamento de \'t Hooft da teoria de gauge, respectivamente, são infinitos. Levar em consideração interações com termos de curvatura de ordem superior nos permite considerar correções de $\\lambda$ finito. Por exemplo, a primeira correção de acoplamento finito para supergravidade tipo IIB surge como um termo de curvatura com forma esquemática $\\alpha\'^3 R^4$. Neste trabalho investigamos correções de curvatura no contexto da gravidade de Lovelock, que é um cenário simples para investigar tais correções pois as suas equações de movimento ainda são de segunda ordem em derivadas. Esse cenário também é particularmente interessante do ponto de vista da correspondência AdS/CFT devido a sua grande classe de soluções de buracos negros assintoticamente AdS. Consideramos um sistema de gravidade AdS-axion-dilaton em cinco dimensões com um termo de Gauss-Bonnet e encontramos uma solução das equações de movimento, o que corresponde a uma black brane exibindo uma anisotropia espacial, onde a fonte da anisotropia é um campo escalar linear em uma das coordenadas espaciais. Estudamos suas propriedades termodinâmicas e realizamos a renormalização holográfica usando o método de Hamilton-Jacobi. Finalmente, usamos a solução obtida como dual gravitacional de um plasma anisotrópico fortemente acoplado com duas cargas centrais independentes, $a eq c$. Calculamos vários observáveis relevantes para o estudo do plasma, a saber, a viscosidade de cisalhamento sobre densidade de entropia, a força de arrasto, o parâmetro de jet quenching, o potencial entre um par quark-antiquark e a taxa de produção de fótons.

Static versus dynamic heterogeneities in the D=3 Edwards-Anderson-ising spin glass

We numerically study the aging properties of the dynamical heterogeneities in the Ising spin glass. We find that a phase transition takes place during the aging process. Statics-dynamics correspondence implies that systems of finite size in equilibrium have static heterogeneities that obey finite-size scaling, thus signaling an analogous phase transition in the thermodynamical limit. We compute the critical exponents and the transition point in the equilibrium setting, and use them to show that aging in dynamic heterogeneities can be described by a finite-time scaling ansatz, with potential implications for experimental work.

Nature of the spin-glass phase at experimental length scales

We present a massive equilibrium simulation of the three-dimensional Ising spin glass at low temperatures. The Janus special-purpose computer has allowed us to equilibrate, using parallel tempering, L = 32 lattices down to T ≈ 0.64Tc. We demonstrate the relevance of equilibrium finite-size simulations to understand experimental non-equilibrium spin glasses in the thermodynamical limit by establishing a time-length dictionary. We conclude that non-equilibrium experiments performed on a time scale of one hour can be matched with equilibrium results on L ≈ 110 lattices. A detailed investigation of the probability distribution functions of the spin and link overlap, as well as of their correlation functions, shows that Replica Symmetry Breaking is the appropriate theoretical framework for the physically relevant length scales. Besides, we improve over existing methodologies to ensure equilibration in parallel tempering simulations.

Tethered Monte Carlo: computing the effective potential without critical slowing down

We present Tethered Monte Carlo, a simple, general purpose method of computing the effective potential of the order parameter (Helmholtz free energy). This formalism is based on a new statistical ensemble, closely related to the micromagnetic one, but with an extended configuration space (through Creutz-like demons). Canonical averages for arbitrary values of the external magnetic field are computed without additional simulations. The method is put to work in the two-dimensional Ising model, where the existence of exact results enables us to perform high precision checks. A rather peculiar feature of our implementation, which employs a local Metropolis algorithm, is the total absence, within errors, of critical slowing down for magnetic observables. Indeed, high accuracy results are presented for lattices as large as L = 1024.

Tethered Monte Carlo: computing the effective potential without critical slowing down

We present Tethered Monte Carlo, a simple, general purpose method of computing the effective potential of the order parameter (Helmholtz free energy). This formalism is based on a new statistical ensemble, closely related to the micromagnetic one, but with an extended configuration space (through Creutz-like demons). Canonical averages for arbitrary values of the external magnetic field are computed without additional simulations. The method is put to work in the two-dimensional Ising model, where the existence of exact results enables us to perform high precision checks. A rather peculiar feature of our implementation, which employs a local Metropolis algorithm, is the total absence, within errors, of critical slowing down for magnetic observables. Indeed, high accuracy results are presented for lattices as large as L = 1024.

Nonclassical light revealed by the joint statistics of simultaneous measurements

Nonclassicality cannot be a single-observable property, since the statistics of any quantum observable is compatible with classical physics. We develop a general procedure to reveal nonclassical behavior of light states from the joint statistics arising in the practical measurement of multiple observables. Beside embracing previous approaches, this protocol can disclose nonclassical features for standard examples of classical-like behavior, such as SU(2) and Glauber coherent states. When combined with other criteria, this would imply that every light state is nonclassical.

Emission-line galaxy surveys with GTC: The Hα Universe

Emission line galaxies are the most easily detected and studied objects in the high redshift Universe. They are being used to trace the evolution of critical observables of the Universe such as Star Formation Rate densities, starburst properties and abundances. Most of the research is being done using [OII]3727 and UV lines, but Hα is still one the best tracers for Star Formation Rate and physical properties of current star-forming galaxies. As a complementary contribution to studies of galaxy evolution, our team has focused into a long-term project to study the population of Hα-selected star-forming galaxies of the Universe at different redshifts. In 1995 we first determined the local Hα luminosity function, and from it the Star Formation Rate density (SFRd) of the local Universe. We then, using narrow-band imaging in the optical, extended this measurement to z ≃ 0.24 and z ≃ 0.4. Working in the near-infrared, GTC will be a very powerful tool to study the evolution of the Hα emission-line galaxy populations at different redshifts. We will both quantify the SFRd evolution and characterize the star-forming galaxy populations by directly comparing the same observables at all redshifts up to z ≃ 2.5.

Desarrollo cultural en las organizaciones: un modelo de estudio basado en la Grounded Theory

La cultura organizacional se configura a partir de la interrelación de los procesos de apropiación de la filosofía, la pertenencia, la adaptación, la satisfacción y el liderazgo compartidos por un grupo. Este conjunto de categorías puede ser reconocido mediante el uso de una matriz que incluye en su estructura subcategorías o conceptos y un conjunto de propiedades observables en el público interno. El presente artículo tiene por objetivo describir un modelo de estudio construido a partir de la Grounded Theory o Teoría Fundamentada que nos permita comprender el desarrollo cultural de las organizaciones. El estudio de caso se realizó en una compañía líder en Europa del sector de la distribución.

Polarimetric Response of Rice Fields at C-Band: Analysis and Phenology Retrieval

A set of ten RADARSAT-2 images acquired in fully polarimetric mode over a test site with rice fields in Seville, Spain, has been analyzed to extract the main features of the C-band radar backscatter as a function of rice phenology. After observing the evolutions versus phenology of different polarimetric observables and explaining their behavior in terms of scattering mechanisms present in the scene, a simple retrieval approach has been proposed. This algorithm is based on three polarimetric observables and provides estimates from a set of four relevant intervals of phenological stages. The validation against ground data, carried out at parcel level for a set of six stands and up to nine dates per stand, provides a 96% rate of coincidence. Moreover, an equivalent compact-pol retrieval algorithm has been also proposed and validated, providing the same performance at parcel level. In all cases, the inversion is carried out by exploiting a single satellite acquisition, without any other auxiliary information.