Methods for the analysis of multi-scale cell dynamics from fluorescence microscopy images

La embriogénesis es el proceso mediante el cual una célula se convierte en un ser un vivo. A lo largo de diferentes etapas de desarrollo, la población de células va proliferando a la vez que el embrión va tomando forma y se configura. Esto es posible gracias a la acción de varios procesos genéticos, bioquímicos y mecánicos que interaccionan y se regulan entre ellos formando un sistema complejo que se organiza a diferentes escalas espaciales y temporales. Este proceso ocurre de manera robusta y reproducible, pero también con cierta variabilidad que permite la diversidad de individuos de una misma especie. La aparición de la microscopía de fluorescencia, posible gracias a proteínas fluorescentes que pueden ser adheridas a las cadenas de expresión de las células, y los avances en la física óptica de los microscopios han permitido observar este proceso de embriogénesis in-vivo y generar secuencias de imágenes tridimensionales de alta resolución espacio-temporal. Estas imágenes permiten el estudio de los procesos de desarrollo embrionario con técnicas de análisis de imagen y de datos, reconstruyendo dichos procesos para crear la representación de un embrión digital. Una de las más actuales problemáticas en este campo es entender los procesos mecánicos, de manera aislada y en interacción con otros factores como la expresión genética, para que el embrión se desarrolle. Debido a la complejidad de estos procesos, estos problemas se afrontan mediante diferentes técnicas y escalas específicas donde, a través de experimentos, pueden hacerse y confrontarse hipótesis, obteniendo conclusiones sobre el funcionamiento de los mecanismos estudiados. Esta tesis doctoral se ha enfocado sobre esta problemática intentando mejorar las metodologías del estado del arte y con un objetivo específico: estudiar patrones de deformación que emergen del movimiento organizado de las células durante diferentes estados del desarrollo del embrión, de manera global o en tejidos concretos. Estudios se han centrado en la mecánica en relación con procesos de señalización o interacciones a nivel celular o de tejido. En este trabajo, se propone un esquema para generalizar el estudio del movimiento y las interacciones mecánicas que se desprenden del mismo a diferentes escalas espaciales y temporales. Esto permitiría no sólo estudios locales, si no estudios sistemáticos de las escalas de interacción mecánica dentro de un embrión. Por tanto, el esquema propuesto obvia las causas de generación de movimiento (fuerzas) y se centra en la cuantificación de la cinemática (deformación y esfuerzos) a partir de imágenes de forma no invasiva. Hoy en día las dificultades experimentales y metodológicas y la complejidad de los sistemas biológicos impiden una descripción mecánica completa de manera sistemática. Sin embargo, patrones de deformación muestran el resultado de diferentes factores mecánicos en interacción con otros elementos dando lugar a una organización mecánica, necesaria para el desarrollo, que puede ser cuantificado a partir de la metodología propuesta en esta tesis. La metodología asume un medio continuo descrito de forma Lagrangiana (en función de las trayectorias de puntos materiales que se mueven en el sistema en lugar de puntos espaciales) de la dinámica del movimiento, estimado a partir de las imágenes mediante métodos de seguimiento de células o de técnicas de registro de imagen. Gracias a este esquema es posible describir la deformación instantánea y acumulada respecto a un estado inicial para cualquier dominio del embrión. La aplicación de esta metodología a imágenes 3D + t del pez zebra sirvió para desvelar estructuras mecánicas que tienden a estabilizarse a lo largo del tiempo en dicho embrión, y que se organizan a una escala semejante al del mapa de diferenciación celular y con indicios de correlación con patrones de expresión genética. También se aplicó la metodología al estudio del tejido amnioserosa de la Drosophila (mosca de la fruta) durante el cierre dorsal, obteniendo indicios de un acoplamiento entre escalas subcelulares, celulares y supracelulares, que genera patrones complejos en respuesta a la fuerza generada por los esqueletos de acto-myosina. En definitiva, esta tesis doctoral propone una estrategia novedosa de análisis de la dinámica celular multi-escala que permite cuantificar patrones de manera inmediata y que además ofrece una representación que reconstruye la evolución de los procesos como los ven las células, en lugar de como son observados desde el microscopio. Esta metodología por tanto permite nuevas formas de análisis y comparación de embriones y tejidos durante la embriogénesis a partir de imágenes in-vivo. ABSTRACT The embryogenesis is the process from which a single cell turns into a living organism. Through several stages of development, the cell population proliferates at the same time the embryo shapes and the organs develop gaining their functionality. This is possible through genetic, biochemical and mechanical factors that are involved in a complex interaction of processes organized in different levels and in different spatio-temporal scales. The embryogenesis, through this complexity, develops in a robust and reproducible way, but allowing variability that makes possible the diversity of living specimens. The advances in physics of microscopes and the appearance of fluorescent proteins that can be attached to expression chains, reporting about structural and functional elements of the cell, have enabled for the in-vivo observation of embryogenesis. The imaging process results in sequences of high spatio-temporal resolution 3D+time data of the embryogenesis as a digital representation of the embryos that can be further analyzed, provided new image processing and data analysis techniques are developed. One of the most relevant and challenging lines of research in the field is the quantification of the mechanical factors and processes involved in the shaping process of the embryo and their interactions with other embryogenesis factors such as genetics. Due to the complexity of the processes, studies have focused on specific problems and scales controlled in the experiments, posing and testing hypothesis to gain new biological insight. However, methodologies are often difficult to be exported to study other biological phenomena or specimens. This PhD Thesis is framed within this paradigm of research and tries to propose a systematic methodology to quantify the emergent deformation patterns from the motion estimated in in-vivo images of embryogenesis. Thanks to this strategy it would be possible to quantify not only local mechanisms, but to discover and characterize the scales of mechanical organization within the embryo. The framework focuses on the quantification of the motion kinematics (deformation and strains), neglecting the causes of the motion (forces), from images in a non-invasive way. Experimental and methodological challenges hamper the quantification of exerted forces and the mechanical properties of tissues. However, a descriptive framework of deformation patterns provides valuable insight about the organization and scales of the mechanical interactions, along the embryo development. Such a characterization would help to improve mechanical models and progressively understand the complexity of embryogenesis. This framework relies on a Lagrangian representation of the cell dynamics system based on the trajectories of points moving along the deformation. This approach of analysis enables the reconstruction of the mechanical patterning as experienced by the cells and tissues. Thus, we can build temporal profiles of deformation along stages of development, comprising both the instantaneous events and the cumulative deformation history. The application of this framework to 3D + time data of zebrafish embryogenesis allowed us to discover mechanical profiles that stabilized through time forming structures that organize in a scale comparable to the map of cell differentiation (fate map), and also suggesting correlation with genetic patterns. The framework was also applied to the analysis of the amnioserosa tissue in the drosophila’s dorsal closure, revealing that the oscillatory contraction triggered by the acto-myosin network organized complexly coupling different scales: local force generation foci, cellular morphology control mechanisms and tissue geometrical constraints. In summary, this PhD Thesis proposes a theoretical framework for the analysis of multi-scale cell dynamics that enables to quantify automatically mechanical patterns and also offers a new representation of the embryo dynamics as experienced by cells instead of how the microscope captures instantaneously the processes. Therefore, this framework enables for new strategies of quantitative analysis and comparison between embryos and tissues during embryogenesis from in-vivo images.

Applications of Formal Languages to Management of Manned and Unmanned Aircraft

En el futuro, la gestión del tráfico aéreo (ATM, del inglés air traffic management) requerirá un cambio de paradigma, de la gestión principalmente táctica de hoy, a las denominadas operaciones basadas en trayectoria. Un incremento en el nivel de automatización liberará al personal de ATM —controladores, tripulación, etc.— de muchas de las tareas que realizan hoy. Las personas seguirán siendo el elemento central en la gestión del tráfico aéreo del futuro, pero lo serán mediante la gestión y toma de decisiones. Se espera que estas dos mejoras traigan un incremento en la eficiencia de la gestión del tráfico aéreo que permita hacer frente al incremento previsto en la demanda de transporte aéreo. Para aplicar el concepto de operaciones basadas en trayectoria, el usuario del espacio aéreo (la aerolínea, piloto, u operador) y el proveedor del servicio de navegación aérea deben negociar las trayectorias mediante un proceso de toma de decisiones colaborativo. En esta negociación, es necesaria una forma adecuada de compartir dichas trayectorias. Compartir la trayectoria completa requeriría un gran ancho de banda, y la trayectoria compartida podría invalidarse si cambiase la predicción meteorológica. En su lugar, podría compartirse una descripción de la trayectoria independiente de las condiciones meteorológicas, de manera que la trayectoria real se pudiese calcular a partir de dicha descripción. Esta descripción de la trayectoria debería ser fácil de procesar usando un programa de ordenador —ya que parte del proceso de toma de decisiones estará automatizado—, pero también fácil de entender para un operador humano —que será el que supervise el proceso y tome las decisiones oportunas—. Esta tesis presenta una serie de lenguajes formales que pueden usarse para este propósito. Estos lenguajes proporcionan los medios para describir trayectorias de aviones durante todas las fases de vuelo, desde la maniobra de push-back (remolcado hasta la calle de rodaje), hasta la llegada a la terminal del aeropuerto de destino. También permiten describir trayectorias tanto de aeronaves tripuladas como no tripuladas, incluyendo aviones de ala fija y cuadricópteros. Algunos de estos lenguajes están estrechamente relacionados entre sí, y organizados en una jerarquía. Uno de los lenguajes fundamentales de esta jerarquía, llamado aircraft intent description language (AIDL), ya había sido desarrollado con anterioridad a esta tesis. Este lenguaje fue derivado de las ecuaciones del movimiento de los aviones de ala fija, y puede utilizarse para describir sin ambigüedad trayectorias de este tipo de aeronaves. Una variante de este lenguaje, denominada quadrotor AIDL (QR-AIDL), ha sido desarrollada en esta tesis para permitir describir trayectorias de cuadricópteros con el mismo nivel de detalle. Seguidamente, otro lenguaje, denominado intent composite description language (ICDL), se apoya en los dos lenguajes anteriores, ofreciendo más flexibilidad para describir algunas partes de la trayectoria y dejar otras sin especificar. El ICDL se usa para proporcionar descripciones genéricas de maniobras comunes, que después se particularizan y combinan para formar descripciones complejas de un vuelo. Otro lenguaje puede construirse a partir del ICDL, denominado flight intent description language (FIDL). El FIDL especifica requisitos de alto nivel sobre las trayectorias —incluyendo restricciones y objetivos—, pero puede utilizar características del ICDL para proporcionar niveles de detalle arbitrarios en las distintas partes de un vuelo. Tanto el ICDL como el FIDL han sido desarrollados en colaboración con Boeing Research & Technology Europe (BR&TE). También se ha desarrollado un lenguaje para definir misiones en las que interactúan varias aeronaves, el mission intent description language (MIDL). Este lenguaje se basa en el FIDL y mantiene todo su poder expresivo, a la vez que proporciona nuevas semánticas para describir tareas, restricciones y objetivos relacionados con la misión. En ATM, los movimientos de un avión en la superficie de aeropuerto también tienen que ser monitorizados y gestionados. Otro lenguaje formal ha sido diseñado con este propósito, llamado surface movement description language (SMDL). Este lenguaje no pertenece a la jerarquía de lenguajes descrita en el párrafo anterior, y se basa en las clearances (autorizaciones del controlador) utilizadas durante las operaciones en superficie de aeropuerto. También proporciona medios para expresar incertidumbre y posibilidad de cambios en las distintas partes de la trayectoria. Finalmente, esta tesis explora las aplicaciones de estos lenguajes a la predicción de trayectorias y a la planificación de misiones. El concepto de trajectory language processing engine (TLPE) se usa en ambas aplicaciones. Un TLPE es una función de ATM cuya principal entrada y salida se expresan en cualquiera de los lenguajes incluidos en la jerarquía descrita en esta tesis. El proceso de predicción de trayectorias puede definirse como una combinación de TLPEs, cada uno de los cuales realiza una pequeña sub-tarea. Se le ha dado especial importancia a uno de estos TLPEs, que se encarga de generar el perfil horizontal, vertical y de configuración de la trayectoria. En particular, esta tesis presenta un método novedoso para la generación del perfil vertical. El proceso de planificar una misión también se puede ver como un TLPE donde la entrada se expresa en MIDL y la salida consiste en cierto número de trayectorias —una por cada aeronave disponible— descritas utilizando FIDL. Se ha formulado este problema utilizando programación entera mixta. Además, dado que encontrar caminos óptimos entre distintos puntos es un problema fundamental en la planificación de misiones, también se propone un algoritmo de búsqueda de caminos. Este algoritmo permite calcular rápidamente caminos cuasi-óptimos que esquivan todos los obstáculos en un entorno urbano. Los diferentes lenguajes formales definidos en esta tesis pueden utilizarse como una especificación estándar para la difusión de información entre distintos actores de la gestión del tráfico aéreo. En conjunto, estos lenguajes permiten describir trayectorias con el nivel de detalle necesario en cada aplicación, y se pueden utilizar para aumentar el nivel de automatización explotando esta información utilizando sistemas de soporte a la toma de decisiones. La aplicación de estos lenguajes a algunas funciones básicas de estos sistemas, como la predicción de trayectorias, han sido analizadas. ABSTRACT Future air traffic management (ATM) will require a paradigm shift from today’s mainly tactical ATM to trajectory-based operations (TBOs). An increase in the level of automation will also relieve humans —air traffic control officers (ATCOs), flight crew, etc.— from many of the tasks they perform today. Humans will still be central in this future ATM, as decision-makers and managers. These two improvements (TBOs and increased automation) are expected to provide the increase in ATM performance that will allow coping with the expected increase in air transport demand. Under TBOs, trajectories are negotiated between the airspace user (an airline, pilot, or operator) and the air navigation service provider (ANSP) using a collaborative decision making (CDM) process. A suitable method for sharing aircraft trajectories is necessary for this negotiation. Sharing a whole trajectory would require a high amount of bandwidth, and the shared trajectory might become invalid if the weather forecast changed. Instead, a description of the trajectory, decoupled from the weather conditions, could be shared, so that the actual trajectory could be computed from this trajectory description. This trajectory description should be easy to process using a computing program —as some of the CDM processes will be automated— but also easy to understand for a human operator —who will be supervising the process and making decisions. This thesis presents a series of formal languages that can be used for this purpose. These languages provide the means to describe aircraft trajectories during all phases of flight, from push back to arrival at the gate. They can also describe trajectories of both manned and unmanned aircraft, including fixedwing and some rotary-wing aircraft (quadrotors). Some of these languages are tightly interrelated and organized in a language hierarchy. One of the key languages in this hierarchy, the aircraft intent description language (AIDL), had already been developed prior to this thesis. This language was derived from the equations of motion of fixed-wing aircraft, and can provide an unambiguous description of fixed-wing aircraft trajectories. A variant of this language, the quadrotor AIDL (QR-AIDL), is developed in this thesis to allow describing a quadrotor aircraft trajectory with the same level of detail. Then, the intent composite description language (ICDL) is built on top of these two languages, providing more flexibility to describe some parts of the trajectory while leaving others unspecified. The ICDL is used to provide generic descriptions of common aircraft manoeuvres, which can be particularized and combined to form complex descriptions of flight. Another language is built on top of the ICDL, the flight intent description language (FIDL). The FIDL specifies high-level requirements on trajectories —including constraints and objectives—, but can use features of the ICDL to provide arbitrary levels of detail in different parts of the flight. The ICDL and FIDL have been developed in collaboration with Boeing Research & Technology Europe (BR&TE). Also, the mission intent description language (MIDL) has been developed to allow describing missions involving multiple aircraft. This language is based on the FIDL and keeps all its expressive power, while it also provides new semantics for describing mission tasks, mission objectives, and constraints involving several aircraft. In ATM, the movement of aircraft while on the airport surface also has to be monitored and managed. Another formal language has been designed for this purpose, denoted surface movement description language (SMDL). This language does not belong to the language hierarchy described above, and it is based on the clearances used in airport surface operations. Means to express uncertainty and mutability of different parts of the trajectory are also provided. Finally, the applications of these languages to trajectory prediction and mission planning are explored in this thesis. The concept of trajectory language processing engine (TLPE) is used in these two applications. A TLPE is an ATM function whose main input and output are expressed in any of the languages in the hierarchy described in this thesis. A modular trajectory predictor is defined as a combination of multiple TLPEs, each of them performing a small subtask. Special attention is given to the TLPE that builds the horizontal, vertical, and configuration profiles of the trajectory. In particular, a novel method for the generation of the vertical profile is presented. The process of planning a mission can also be seen as a TLPE, where the main input is expressed in the MIDL and the output consists of a number of trajectory descriptions —one for each aircraft available in the mission— expressed in the FIDL. A mixed integer linear programming (MILP) formulation for the problem of assigning mission tasks to the available aircraft is provided. In addition, since finding optimal paths between locations is a key problem to mission planning, a novel path finding algorithm is presented. This algorithm can compute near-shortest paths avoiding all obstacles in an urban environment in very short times. The several formal languages described in this thesis can serve as a standard specification to share trajectory information among different actors in ATM. In combination, these languages can describe trajectories with the necessary level of detail for any application, and can be used to increase automation by exploiting this information using decision support tools (DSTs). Their applications to some basic functions of DSTs, such as trajectory prediction, have been analized.

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: Comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the δ- and ɛ-tautomers of the distal His-64. Vibrational population relaxation times of 335 ± 115 ps for the δ-tautomer and 640 ± 185 ps for the ɛ-tautomer were estimated by using the Landau–Teller model. Normal mode analysis was used to identify those protein residues that act as the primary “doorway” modes in the vibrational relaxation of the oscillator. Although the CO relaxation rates in both the ɛ- and δ-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the δ-tautomer with the distal His playing an important role in the energy relaxation mechanism. Time-resolved mid-IR absorbance measurements were performed on photolyzed carbonmonoxy hemoglobin (Hb13CO). From these measurements, a T1 time of 600 ± 150 ps was determined. The simulation and experimental estimates are compared and discussed.

Comparison of Reading Development Across Socioeconomic Status in the United States

It is well known that higher parental socioeconomic status (SES) predicts better child reading outcomes, but little work has been done to unpack this finding. The main overall question addressed by this project was whether cognitive models of the two main reading outcomes, single word reading (SWR) and reading comprehension (RC), performed similarly across levels of parental SES. The current study predicted a differential relation between parental SES and both predictors and outcomes because of the known large relation between parental SES and child oral language development. Three questions examined the mediating effects of cognitive predictors on the relation between parental SES and reading outcomes, the moderating effects of SES on the developmental trajectories of reading outcomes, and the strength of the relationship between SES and the two reading outcomes. Participants were part of two large and comprehensive datasets: the cross-sectional Colorado Learning Disability Research Center (CLDRC; n=1554) sample, and the International Longitudinal Twin Study (ILTS; n=463 twin pairs) sample. In terms of cognitive predictors, the relation between SES and SWR was disproportionately mediated by two language skills, vocabulary (VOC) and phonological awareness (PA). For the RC models, both SWR and oral listening comprehension (OLC) did not disproportionally mediate the relation between RC and SES; however, full mediation was not exhibited. With regard to the trajectory of reading outcomes, SES moderated the starting values of SWR and RC, and the slopes of SWR development. When performance on the control measures of early reading skills (e.g., print knowledge, vocabulary, and decoding skills) was included the models, the moderating effects of SES were completely accounted for by these measures. In terms of outcomes, SES had a stronger relation to RC than to SWR, especially at later ages. These findings have implications for interventions aimed at improving reading outcomes in children from lower SES families.

A Novel Prediction Method for Early Recognition of Global Human Behaviour in Image Sequences

Human behaviour recognition has been, and still remains, a challenging problem that involves different areas of computational intelligence. The automated understanding of people activities from video sequences is an open research topic in which the computer vision and pattern recognition areas have made big efforts. In this paper, the problem is studied from a prediction point of view. We propose a novel method able to early detect behaviour using a small portion of the input, in addition to the capabilities of it to predict behaviour from new inputs. Specifically, we propose a predictive method based on a simple representation of trajectories of a person in the scene which allows a high level understanding of the global human behaviour. The representation of the trajectory is used as a descriptor of the activity of the individual. The descriptors are used as a cue of a classification stage for pattern recognition purposes. Classifiers are trained using the trajectory representation of the complete sequence. However, partial sequences are processed to evaluate the early prediction capabilities having a specific observation time of the scene. The experiments have been carried out using the three different dataset of the CAVIAR database taken into account the behaviour of an individual. Additionally, different classic classifiers have been used for experimentation in order to evaluate the robustness of the proposal. Results confirm the high accuracy of the proposal on the early recognition of people behaviours.

Narratives and counter-narratives on "marriage of convenience" : conjugality and (il)legality in portuguese migration policies and in couples’ experiences

Tese de doutoramento, Sociologia (Sociologia da Família, Juventude e das Relações do Género), Universidade de Lisboa, Instituto de Ciências Sociais, 2016

Aggressive incidents inside a Montreal barroom involving patrons, barmaids and bouncers : a micro level examination of routine activity theory

Objectives: This article further examines the phenomenon of aggression inside barrooms by relying on the “bouncer-ethnographer” methodology. The objective is to investigate variations in aggression through time and space according to the role and routine of the target in a Montreal barroom. Thus, it provides an examination of routine activity theory at the micro level: the barroom. Methods: For a period of 258 nights of observation in a Canadian barroom, bouncers completed reports on each intervention and provided specific information regarding what happened, when and where within the venue. In addition, the bouncer-ethnographer compiled field observations and interviews with bar personnel in order to identify aggression hotspots and “rush hours” for three types of actors within barrooms: (a) bouncers, (b) barmaids and (c) patrons. Findings: Three different patterns emerged for shifting hotspots of aggression depending on the target. As the night progresses, aggressive incidents between patrons, towards barmaids and towards bouncers have specific hotspots and rush hours influenced by the specific routine of the target inside the barroom. Implications: The current findings enrich those of previous work by pointing to the relevance of not only examining the environmental characteristics of the barroom, but also the role of the target of aggression. Crime opportunities follow routine activities, even within a specific location on a micro level. Routine activity theory is thus relevant in this context, because as actors in differing roles follow differing routines, as do their patterns of victimization.

Enriching plant diversity in grasslands by large-scale experimental sward disturbance and seed addition along gradients of land-use intensity

Aims The relationship between biodiversity and ecosystem functioning is among the most active areas of ecological research. Furthermore, enhancing the diversity of degraded ecosystems is a major goal in applied restoration ecology. In grasslands, many species may be locally absent due to dispersal or microsite limitation and may therefore profit from mechanical disturbance of the resident vegetation. We established a seed addition and disturbance experiment across several grassland sites of different land use to test whether plant diversity can be increased in these grasslands. Additionally, the experiment will allow us testing the consequences of increased plant diversity for ecosystem processes and for the diversity of other taxa in real-world ecosystems. Here we present details of the experimental design and report results from the first vegetation survey one year after disturbance and seed addition. Moreover, we tested whether the effects of seed addition and disturbance varied among grassland depending on their land use or pre-disturbance plant diversity. Methods A full-factorial experiment was installed in 73 grasslands in three regions across Germany. Grasslands were under regular agricultural use, but varied in the type and the intensity of management, thereby representing the range of management typical for large parts of Central Europe. The disturbance treatment consisted of disturbing the top 10 cm of the sward using a rotavator or rotary harrow. Seed addition consisted of sowing a high-diversity seed mixture of regional plant species. These species were all regionally present, but often locally absent, depending on the resident vegetation composition and richness of each grassland. Important findings One year after sward disturbance it had significantly increased cover of bare soil, seedling species richness and numbers of seedlings. Seed addition had increased plant species richness, but only in combination with sward disturbance. The increase in species richness, when both seed addition and disturbance was applied, was higher at high land-use intensity and low resident diversity. Thus, we show that at least the early recruitment of many species is possible also at high land-use intensity, indicating the potential to restore and enhance biodiversity of species-poor agricultural grasslands. Our newly established experiment provides a unique platform for broad-scale research on the land-use dependence of future trajectories of vegetation diversity and composition and their effects on ecosystem functioning.

Prevalence of mixed neuropathologies in autopsied older adults and associations with clinical disease progression

Thesis (Ph.D.)--University of Washington, 2016-06

State Social Safety Net Programs and the Great Recession: The First Line of Defense and the Last Resort for the Economically Disadvantaged

Thesis (Ph.D.)--University of Washington, 2016-06

The Long and Winding Road: Heterogeneity in the Form and Timing of Postsecondary Education

Thesis (Ph.D.)--University of Washington, 2016-06

Disabilities, justice and the new eugenics of gene therapy

Eugenics is a difficult matter for discussion because, even as a term, it has fallen into disrepute. Yet a eugenic mindset pervades the discourses of reproduction and genetics in the West. I utilise the futures scenario of gene therapy to explore conceptually how the intersecting trajectories of science and religion make a new eugenics possible. The problematic of an inherent elitism within these sources, combined with a quest for power, leads me to renew the call for an adequate moral space within which to explore the requirements of social justice.

Identifying and predicting adolescent smokers' developmental trajectories

Very few studies have defined trajectories of smoking. In the present study, we modeled growth in adolescent smoking and empirically identified prototypical trajectories. We conceptualized escalation of smoking as a growth process and modeled rates of change and heterogeneity of these patterns using latent growth mixture modeling. The analysis identified six trajectories with low ambiguity about group membership (early rapid escalators, late rapid escalators, late moderate escalators, late slow escalators-smokers, stable puffers, and late slow escalators-puffers). A trajectory of quitters was not identified. We also examined predictors of the smoking trajectories. The predictors were assessed across the adolescent years and included variables related to smoking and other substance use, as well as a range of variables related to sociodemographic factors and mental health. Observed change in the pattern of predictors across age has implications for the mechanism of effect of these variables in relation to smoking trajectories, including predictors that differentiated among daily smokers, variables that may determine the trajectory (e.g., friends smoking), and variables that may result from the trajectory (e.g., marijuana use, less attachment to friends).

Tractable molecular theory of transport of Lennard-Jones fluids in nanopores

We present here a tractable theory of transport of simple fluids in cylindrical nanopores, which is applicable over a wide range of densities and pore sizes. In the Henry law low-density region the theory considers the trajectories of molecules oscillating between diffuse wall collisions, while at higher densities beyond this region the contribution from viscous flow becomes significant and is included through our recent approach utilizing a local average density model. The model is validated by means of equilibrium as well nonequilibrium molecular dynamics simulations of supercritical methane transport in cylindrical silica pores over a wide range of temperature, density, and pore size. The model for the Henry law region is exact and found to yield an excellent match with simulations at all conditions, including the single-file region of very small pore size where it is shown to provide the density-independent collective transport coefficient. It is also shown that in the absence of dispersive interactions the model reduces to the classical Knudsen result, but in the presence of such interactions the latter model drastically overpredicts the transport coefficient. For larger micropores beyond the single-file region the transport coefficient is reduced at high density because of intermolecular interactions and hindrance to particle crossings leading to a large decrease in surface slip that is not well represented by the model. However, for mesopores the transport coefficient increases monotonically with density, over the range studied, and is very well predicted by the theory, though at very high density the contribution from surface slip is slightly overpredicted. It is also seen that the concept of activated diffusion, commonly associated with diffusion in small pores, is fundamentally invalid for smooth pores, and the apparent activation energy is not simply related to the minimum pore potential or the adsorption energy as generally assumed. (C) 2004 American Institute of Physics.

Pumice rafting and faunal dispersion during 2001-2002 in the Southwest Pacific: record of a dacitic submarine explosive eruption from Tonga

A new influx of sea-rafted pumice reached the eastern coast of Australia in October 2002, approximately 1 year after a felsic, shallow-marine explosive eruption at a previously unknown volcano (0403-091) along the Tofua volcanic arc (Tonga). The eruption produced floating pumice rafts that first became stranded in Fiji in November 2001, approximately I month after the eruption. Strandings of sea-rafted pumice along shorelines have been the only record of products from this submarine explosive eruption at the remote, submerged volcano. Computed drift trajectories of the sea-rafted pumice using numerical models of southwest Pacific surface wind fields and ocean currents indicate two cyclonic systems disturbed the drift of pumice to eastern Australia, as well as the importance of the combined wave and direct wind effect on pumice trajectory. Pumice became stranded along at least two-thirds (>2000 km) of the coastline of eastern Australia, being deposited on beaches during a sustained period of fresh onshore winds. Typical amounts of pumice initially stranded on beaches were 500-4000 individual clasts per in, and a minimum volume estimate of pumice that arrived to eastern Australia is 1.25 x 10(5) m(3). Pumice was beached below maximum tidal/storm surge levels and was quickly reworked back into the ocean, such that the concentration of beached pumice rapidly dissipated within weeks of the initial stranding, and little record of this stranding event now exists. Most stranded pumice clasts ranged in size from 2 to 5 cm in diameter; the largest measured clasts were 10 cm in Australia and 20 cm in Fiji. The pumice has a low phenocryst content (3500 km) and period of pumice floatation (greater than or equal to1 year), confirm the importance of sea-rafted pumice as a long-distance dispersal mechanism for marine organisms including marine pests and harmful invasive species. Billions of individual rafting pumice clasts can be generated in a single small-volume eruption, such as observed here, and the geological implications for the transport of sessile taxa over large distances are significant. An avenue for future research is to examine whether speciation events and volcanicity are linked; the periodic development of globalism for some taxa (e.g., corals, gastropods, bryozoa) may correlate in time and/or space with voluminous silicic igneous events capable of producing >10(6) km(3) of silicic pumice-rich pyroclastic material and emplaced into ocean basins. (C) 2004 Elsevier B.V. All rights reserved.