Range charts of stratigraphically important radiolarian species in sediments of ODP Leg 165 sites

The Paleogene sequences from three sites in the Caribbean were examined for radiolarians. In general, samples are highly lithified, requiring lengthy and repetitive cleaning procedures, and the assemblages are usually fragmented and/or partially dissolved. Both abundances and preservation of the assemblages vary considerably from site to site and within a single site; even within a single sample more than one degree of preservation was observed. It was possible, however, to construct at least partial stratigraphies for each of the three sites. Because the abundance of radiolarians is high even in extremely poorly preserved assemblages, we conclude that the differences in biogenic silica preservation are the result of postdepositional processes and not productivity. In both Sites 999 and 1001, near the Paleocene/Eocene boundary (Bekoma bidartensis Zone [RP7]), there is a short interval in which the abundance and preservation state of the radiolarians improves relative to overlying and underlying assemblages. In each case the intervals corresponds to the level, identified by calcareous microfossils, as representing changes in paleoceanographic conditions associated with the late Paleocene thermal maximum.

Granulometry and Bulk Geochemistry of Nearshore Sediments, Herschel Island, Yukon Territory, Canada

This dataset contains the results of granulometric and bulk geochemical analyses of Van Veen surface samples obtained by the Alfred Wegener Institute (AWI) in the course of the 2012 and 2013 summer field seasons. The sampling was performed along transects in depths generally <13 m, to a distance of about <5 km off Herschel Island. In 2012, 75 samples in Pauline Cove and in the vicinity of Simpson Point were obtained. Sample collection was expanded in 2013, on transects established the previous year, with additional locations in Tetris Bay and Workboat Passage. Samples consisted of approximately 100 g of the top 3-6 cm of sediment, and were frozen in the field and freeze dried at the AWI before undergoing analytical procedures. Sample locations were recorded with the onboard global positioning system (GPS) unit. Grain size distributions in our study were obtained using laser diffractometry at the AWI (Beckman Coulter LS200) on the <1 mm fraction of samples oxidized with 30% H2O2 until effervescence ceased to remove organics. Some samples were also sieved using a sieve stack with 1 phi intervals. GRADISTAT (Blott and Pye, 2001) was used to calculate graphical grain size statistics (Folk and Ward, 1957). Grain diameters were logarithmically transformed to phi values, calculated as phi=-log2d, where d is the grain diameter in millimeters (Blott and Pye, 2001; Krumbein, 1934). Freeze dried samples were ground and ground using an Elemetar Vario EL III carbon-nitrogen-sulphur analyzer at the AWI to measure total carbon (TC) and total nitrogen (TN). Tungsten oxide was added to the samples as a catalyst to the pyrolysis. Following this analysis, total organic carbon (TOC) was determined using an Elementar VarioMax. Stable carbon isotope ratios of 13C/12C of 118 samples were determined on a DELTAplusXL mass spectrometer (ThermoFisher Scientific, Bremen) at the German Research Centre for Geosciences (GFZ) in Potsdam, Germany . An additional analysis on 69 samples was carried out at the University of Hamburg with an isotope ratio mass spectrometer (Delta V, Thermo Scientific, Germany) coupled to an elemental analyzer (Flash 2000, Thermo Scientific, Germany). Prior to analysis, soil samples were treated with phosphoric acid (43%) to release inorganic carbon. Values are expressed relative to Vienna Peedee belemnite (VPDB) using external standards (USGS40, -26.4 per mil VPDB and IVA soil 33802153, -27.5 per mil VPDB).

A multimodal tablet-based interface for designing and reviewing 3D engineering models

The ability to view and interact with 3D models has been happening for a long time. However, vision-based 3D modeling has only seen limited success in applications, as it faces many technical challenges. Hand-held mobile devices have changed the way we interact with virtual reality environments. Their high mobility and technical features, such as inertial sensors, cameras and fast processors, are especially attractive for advancing the state of the art in virtual reality systems. Also, their ubiquity and fast Internet connection open a path to distributed and collaborative development. However, such path has not been fully explored in many domains. VR systems for real world engineering contexts are still difficult to use, especially when geographically dispersed engineering teams need to collaboratively visualize and review 3D CAD models. Another challenge is the ability to rendering these environments at the required interactive rates and with high fidelity. In this document it is presented a virtual reality system mobile for visualization, navigation and reviewing large scale 3D CAD models, held under the CEDAR (Collaborative Engineering Design and Review) project. It’s focused on interaction using different navigation modes. The system uses the mobile device's inertial sensors and camera to allow users to navigate through large scale models. IT professionals, architects, civil engineers and oil industry experts were involved in a qualitative assessment of the CEDAR system, in the form of direct user interaction with the prototypes and audio-recorded interviews about the prototypes. The lessons learned are valuable and are presented on this document. Subsequently it was prepared a quantitative study on the different navigation modes to analyze the best mode to use it in a given situation.

Conceptual framework for the design, implementation and validation of psychomotor skills’ assessment systems in minimally invasive surgery

Las técnicas de cirugía de mínima invasión (CMI) se están consolidando hoy en día como alternativa a la cirugía tradicional, debido a sus numerosos beneficios para los pacientes. Este cambio de paradigma implica que los cirujanos deben aprender una serie de habilidades distintas de aquellas requeridas en cirugía abierta. El entrenamiento y evaluación de estas habilidades se ha convertido en una de las mayores preocupaciones en los programas de formación de cirujanos, debido en gran parte a la presión de una sociedad que exige cirujanos bien preparados y una reducción en el número de errores médicos. Por tanto, se está prestando especial atención a la definición de nuevos programas que permitan el entrenamiento y la evaluación de las habilidades psicomotoras en entornos seguros antes de que los nuevos cirujanos puedan operar sobre pacientes reales. Para tal fin, hospitales y centros de formación están gradualmente incorporando instalaciones de entrenamiento donde los residentes puedan practicar y aprender sin riesgos. Es cada vez más común que estos laboratorios dispongan de simuladores virtuales o simuladores físicos capaces de registrar los movimientos del instrumental de cada residente. Estos simuladores ofrecen una gran variedad de tareas de entrenamiento y evaluación, así como la posibilidad de obtener información objetiva de los ejercicios. Los diferentes estudios de validación llevados a cabo dan muestra de su utilidad; pese a todo, los niveles de evidencia presentados son en muchas ocasiones insuficientes. Lo que es más importante, no existe un consenso claro a la hora de definir qué métricas son más útiles para caracterizar la pericia quirúrgica. El objetivo de esta tesis doctoral es diseñar y validar un marco de trabajo conceptual para la definición y validación de entornos para la evaluación de habilidades en CMI, en base a un modelo en tres fases: pedagógica (tareas y métricas a emplear), tecnológica (tecnologías de adquisición de métricas) y analítica (interpretación de la competencia en base a las métricas). Para tal fin, se describe la implementación práctica de un entorno basado en (1) un sistema de seguimiento de instrumental fundamentado en el análisis del vídeo laparoscópico; y (2) la determinación de la pericia en base a métricas de movimiento del instrumental. Para la fase pedagógica se diseñó e implementó un conjunto de tareas para la evaluación de habilidades psicomotoras básicas, así como una serie de métricas de movimiento. La validación de construcción llevada a cabo sobre ellas mostró buenos resultados para tiempo, camino recorrido, profundidad, velocidad media, aceleración media, economía de área y economía de volumen. Adicionalmente, los resultados obtenidos en la validación de apariencia fueron en general positivos en todos los grupos considerados (noveles, residentes, expertos). Para la fase tecnológica, se introdujo el EVA Tracking System, una solución para el seguimiento del instrumental quirúrgico basado en el análisis del vídeo endoscópico. La precisión del sistema se evaluó a 16,33ppRMS para el seguimiento 2D de la herramienta en la imagen; y a 13mmRMS para el seguimiento espacial de la misma. La validación de construcción con una de las tareas de evaluación mostró buenos resultados para tiempo, camino recorrido, profundidad, velocidad media, aceleración media, economía de área y economía de volumen. La validación concurrente con el TrEndo® Tracking System por su parte presentó valores altos de correlación para 8 de las 9 métricas analizadas. Finalmente, para la fase analítica se comparó el comportamiento de tres clasificadores supervisados a la hora de determinar automáticamente la pericia quirúrgica en base a la información de movimiento del instrumental, basados en aproximaciones lineales (análisis lineal discriminante, LDA), no lineales (máquinas de soporte vectorial, SVM) y difusas (sistemas adaptativos de inferencia neurodifusa, ANFIS). Los resultados muestran que en media SVM presenta un comportamiento ligeramente superior: 78,2% frente a los 71% y 71,7% obtenidos por ANFIS y LDA respectivamente. Sin embargo las diferencias estadísticas medidas entre los tres no fueron demostradas significativas. En general, esta tesis doctoral corrobora las hipótesis de investigación postuladas relativas a la definición de sistemas de evaluación de habilidades para cirugía de mínima invasión, a la utilidad del análisis de vídeo como fuente de información y a la importancia de la información de movimiento de instrumental a la hora de caracterizar la pericia quirúrgica. Basándose en estos cimientos, se han de abrir nuevos campos de investigación que contribuyan a la definición de programas de formación estructurados y objetivos, que puedan garantizar la acreditación de cirujanos sobradamente preparados y promocionen la seguridad del paciente en el quirófano. Abstract Minimally invasive surgery (MIS) techniques have become a standard in many surgical sub-specialties, due to their many benefits for patients. However, this shift in paradigm implies that surgeons must acquire a complete different set of skills than those normally attributed to open surgery. Training and assessment of these skills has become a major concern in surgical learning programmes, especially considering the social demand for better-prepared professionals and for the decrease of medical errors. Therefore, much effort is being put in the definition of structured MIS learning programmes, where practice with real patients in the operating room (OR) can be delayed until the resident can attest for a minimum level of psychomotor competence. To this end, skills’ laboratory settings are being introduced in hospitals and training centres where residents may practice and be assessed on their psychomotor skills. Technological advances in the field of tracking technologies and virtual reality (VR) have enabled the creation of new learning systems such as VR simulators or enhanced box trainers. These systems offer a wide range of tasks, as well as the capability of registering objective data on the trainees’ performance. Validation studies give proof of their usefulness; however, levels of evidence reported are in many cases low. More importantly, there is still no clear consensus on topics such as the optimal metrics that must be used to assess competence, the validity of VR simulation, the portability of tracking technologies into real surgeries (for advanced assessment) or the degree to which the skills measured and obtained in laboratory environments transfer to the OR. The purpose of this PhD is to design and validate a conceptual framework for the definition and validation of MIS assessment environments based on a three-pillared model defining three main stages: pedagogical (tasks and metrics to employ), technological (metric acquisition technologies) and analytical (interpretation of competence based on metrics). To this end, a practical implementation of the framework is presented, focused on (1) a video-based tracking system and (2) the determination of surgical competence based on the laparoscopic instruments’ motionrelated data. The pedagogical stage’s results led to the design and implementation of a set of basic tasks for MIS psychomotor skills’ assessment, as well as the definition of motion analysis parameters (MAPs) to measure performance on said tasks. Validation yielded good construct results for parameters such as time, path length, depth, average speed, average acceleration, economy of area and economy of volume. Additionally, face validation results showed positive acceptance on behalf of the experts, residents and novices. For the technological stage the EVA Tracking System is introduced. EVA provides a solution for tracking laparoscopic instruments from the analysis of the monoscopic video image. Accuracy tests for the system are presented, which yielded an average RMSE of 16.33pp for 2D tracking of the instrument on the image and of 13mm for 3D spatial tracking. A validation experiment was conducted using one of the tasks and the most relevant MAPs. Construct validation showed significant differences for time, path length, depth, average speed, average acceleration, economy of area and economy of volume; especially between novices and residents/experts. More importantly, concurrent validation with the TrEndo® Tracking System presented high correlation values (>0.7) for 8 of the 9 MAPs proposed. Finally, the analytical stage allowed comparing the performance of three different supervised classification strategies in the determination of surgical competence based on motion-related information. The three classifiers were based on linear (linear discriminant analysis, LDA), non-linear (support vector machines, SVM) and fuzzy (adaptive neuro fuzzy inference systems, ANFIS) approaches. Results for SVM show slightly better performance than the other two classifiers: on average, accuracy for LDA, SVM and ANFIS was of 71.7%, 78.2% and 71% respectively. However, when confronted, no statistical significance was found between any of the three. Overall, this PhD corroborates the investigated research hypotheses regarding the definition of MIS assessment systems, the use of endoscopic video analysis as the main source of information and the relevance of motion analysis in the determination of surgical competence. New research fields in the training and assessment of MIS surgeons can be proposed based on these foundations, in order to contribute to the definition of structured and objective learning programmes that guarantee the accreditation of well-prepared professionals and the promotion of patient safety in the OR.

Estructuras I: vigas de alma llena, resistencia y rigidez

Ejercicios de dimensionado y comprobación de vigas de alma llena.

Time-resolved evolution of coherent structures in turbulent channels

El objetivo de esta tesis es estudiar la dinámica de la capa logarítmica de flujos turbulentos de pared. En concreto, proponemos un nuevo modelo estructural utilizando diferentes tipos de estructuras coherentes: sweeps, eyecciones, grupos de vorticidad y streaks. La herramienta utilizada es la simulación numérica directa de canales turbulentos. Desde los primeros trabajos de Theodorsen (1952), las estructuras coherentes han jugado un papel fundamental para entender la organización y dinámica de los flujos turbulentos. A día de hoy, datos procedentes de simulaciones numéricas directas obtenidas en instantes no contiguos permiten estudiar las propiedades fundamentales de las estructuras coherentes tridimensionales desde un punto de vista estadístico. Sin embargo, la dinámica no puede ser entendida en detalle utilizando sólo instantes aislados en el tiempo, sino que es necesario seguir de forma continua las estructuras. Aunque existen algunos estudios sobre la evolución temporal de las estructuras más pequeñas a números de Reynolds moderados, por ejemplo Robinson (1991), todavía no se ha realizado un estudio completo a altos números de Reynolds y para todas las escalas presentes de la capa logarítmica. El objetivo de esta tesis es llevar a cabo dicho análisis. Los problemas más interesantes los encontramos en la región logarítmica, donde residen las cascadas de vorticidad, energía y momento. Existen varios modelos que intentan explicar la organización de los flujos turbulentos en dicha región. Uno de los más extendidos fue propuesto por Adrian et al. (2000) a través de observaciones experimentales y considerando como elemento fundamental paquetes de vórtices con forma de horquilla que actúan de forma cooperativa para generar rampas de bajo momento. Un modelo alternativo fué ideado por del Álamo & Jiménez (2006) utilizando datos numéricos. Basado también en grupos de vorticidad, planteaba un escenario mucho más desorganizado y con estructuras sin forma de horquilla. Aunque los dos modelos son cinemáticamente similares, no lo son desde el punto de vista dinámico, en concreto en lo que se refiere a la importancia que juega la pared en la creación y vida de las estructuras. Otro punto importante aún sin resolver se refiere al modelo de cascada turbulenta propuesto por Kolmogorov (1941b), y su relación con estructuras coherentes medibles en el flujo. Para dar respuesta a las preguntas anteriores, hemos desarrollado un nuevo método que permite seguir estructuras coherentes en el tiempo y lo hemos aplicado a simulaciones numéricas de canales turbulentos con números de Reynolds lo suficientemente altos como para tener un rango de escalas no trivial y con dominios computacionales lo suficientemente grandes como para representar de forma correcta la dinámica de la capa logarítmica. Nuestros esfuerzos se han desarrollado en cuatro pasos. En primer lugar, hemos realizado una campaña de simulaciones numéricas directas a diferentes números de Reynolds y tamaños de cajas para evaluar el efecto del dominio computacional en las estadísticas de primer orden y el espectro. A partir de los resultados obtenidos, hemos concluido que simulaciones con cajas de longitud 2vr y ancho vr veces la semi-altura del canal son lo suficientemente grandes para reproducir correctamente las interacciones entre estructuras coherentes de la capa logarítmica y el resto de escalas. Estas simulaciones son utilizadas como punto de partida en los siguientes análisis. En segundo lugar, las estructuras coherentes correspondientes a regiones con esfuerzos de Reynolds tangenciales intensos (Qs) en un canal turbulento han sido estudiadas extendiendo a tres dimensiones el análisis de cuadrantes, con especial énfasis en la capa logarítmica y la región exterior. Las estructuras coherentes han sido identificadas como regiones contiguas del espacio donde los esfuerzos de Reynolds tangenciales son más intensos que un cierto nivel. Los resultados muestran que los Qs separados de la pared están orientados de forma isótropa y su contribución neta al esfuerzo de Reynolds medio es nula. La mayor contribución la realiza una familia de estructuras de mayor tamaño y autosemejantes cuya parte inferior está muy cerca de la pared (ligada a la pared), con una geometría compleja y dimensión fractal « 2. Estas estructuras tienen una forma similar a una ‘esponja de placas’, en comparación con los grupos de vorticidad que tienen forma de ‘esponja de cuerdas’. Aunque el número de objetos decae al alejarnos de la pared, la fracción de esfuerzos de Reynolds que contienen es independiente de su altura, y gran parte reside en unas pocas estructuras que se extienden más allá del centro del canal, como en las grandes estructuras propuestas por otros autores. Las estructuras dominantes en la capa logarítmica son parejas de sweeps y eyecciones uno al lado del otro y con grupos de vorticidad asociados que comparten las dimensiones y esfuerzos con los remolinos ligados a la pared propuestos por Townsend. En tercer lugar, hemos estudiado la evolución temporal de Qs y grupos de vorticidad usando las simulaciones numéricas directas presentadas anteriormente hasta números de Reynolds ReT = 4200 (Reynolds de fricción). Las estructuras fueron identificadas siguiendo el proceso descrito en el párrafo anterior y después seguidas en el tiempo. A través de la interseción geométrica de estructuras pertenecientes a instantes de tiempo contiguos, hemos creado gratos de conexiones temporales entre todos los objetos y, a partir de ahí, definido ramas primarias y secundarias, de tal forma que cada rama representa la evolución temporal de una estructura coherente. Una vez que las evoluciones están adecuadamente organizadas, proporcionan toda la información necesaria para caracterizar la historia de las estructuras desde su nacimiento hasta su muerte. Los resultados muestran que las estructuras nacen a todas las distancias de la pared, pero con mayor probabilidad cerca de ella, donde la cortadura es más intensa. La mayoría mantienen tamaños pequeños y no viven mucho tiempo, sin embargo, existe una familia de estructuras que crecen lo suficiente como para ligarse a la pared y extenderse a lo largo de la capa logarítmica convirtiéndose en las estructuras observas anteriormente y descritas por Townsend. Estas estructuras son geométricamente autosemejantes con tiempos de vida proporcionales a su tamaño. La mayoría alcanzan tamaños por encima de la escala de Corrsin, y por ello, su dinámica está controlada por la cortadura media. Los resultados también muestran que las eyecciones se alejan de la pared con velocidad media uT (velocidad de fricción) y su base se liga a la pared muy rápidamente al inicio de sus vidas. Por el contrario, los sweeps se mueven hacia la pared con velocidad -uT y se ligan a ella más tarde. En ambos casos, los objetos permanecen ligados a la pared durante 2/3 de sus vidas. En la dirección de la corriente, las estructuras se desplazan a velocidades cercanas a la convección media del flujo y son deformadas por la cortadura. Finalmente, hemos interpretado la cascada turbulenta, no sólo como una forma conceptual de organizar el flujo, sino como un proceso físico en el cual las estructuras coherentes se unen y se rompen. El volumen de una estructura cambia de forma suave, cuando no se une ni rompe, o lo hace de forma repentina en caso contrario. Los procesos de unión y rotura pueden entenderse como una cascada directa (roturas) o inversa (uniones), siguiendo el concepto de cascada de remolinos ideado por Richardson (1920) y Obukhov (1941). El análisis de los datos muestra que las estructuras con tamaños menores a 30η (unidades de Kolmogorov) nunca se unen ni rompen, es decir, no experimentan el proceso de cascada. Por el contrario, aquellas mayores a 100η siempre se rompen o unen al menos una vez en su vida. En estos casos, el volumen total ganado y perdido es una fracción importante del volumen medio de la estructura implicada, con una tendencia ligeramente mayor a romperse (cascada directa) que a unirse (cascade inversa). La mayor parte de interacciones entre ramas se debe a roturas o uniones de fragmentos muy pequeños en la escala de Kolmogorov con estructuras más grandes, aunque el efecto de fragmentos de mayor tamaño no es despreciable. También hemos encontrado que las roturas tienen a ocurrir al final de la vida de la estructura y las uniones al principio. Aunque los resultados para la cascada directa e inversa no son idénticos, son muy simétricos, lo que sugiere un alto grado de reversibilidad en el proceso de cascada. ABSTRACT The purpose of the present thesis is to study the dynamics of the logarithmic layer of wall-bounded turbulent flows. Specifically, to propose a new structural model based on four different coherent structures: sweeps, ejections, clusters of vortices and velocity streaks. The tool used is the direct numerical simulation of time-resolved turbulent channels. Since the first work by Theodorsen (1952), coherent structures have played an important role in the understanding of turbulence organization and its dynamics. Nowadays, data from individual snapshots of direct numerical simulations allow to study the threedimensional statistical properties of those objects, but their dynamics can only be fully understood by tracking them in time. Although the temporal evolution has already been studied for small structures at moderate Reynolds numbers, e.g., Robinson (1991), a temporal analysis of three-dimensional structures spanning from the smallest to the largest scales across the logarithmic layer has yet to be performed and is the goal of the present thesis. The most interesting problems lie in the logarithmic region, which is the seat of cascades of vorticity, energy, and momentum. Different models involving coherent structures have been proposed to represent the organization of wall-bounded turbulent flows in the logarithmic layer. One of the most extended ones was conceived by Adrian et al. (2000) and built on packets of hairpins that grow from the wall and work cooperatively to gen- ´ erate low-momentum ramps. A different view was presented by del Alamo & Jim´enez (2006), who extracted coherent vortical structures from DNSs and proposed a less organized scenario. Although the two models are kinematically fairly similar, they have important dynamical differences, mostly regarding the relevance of the wall. Another open question is whether such a model can be used to explain the cascade process proposed by Kolmogorov (1941b) in terms of coherent structures. The challenge would be to identify coherent structures undergoing a turbulent cascade that can be quantified. To gain a better insight into the previous questions, we have developed a novel method to track coherent structures in time, and used it to characterize the temporal evolutions of eddies in turbulent channels with Reynolds numbers high enough to include a non-trivial range of length scales, and computational domains sufficiently long and wide to reproduce correctly the dynamics of the logarithmic layer. Our efforts have followed four steps. First, we have conducted a campaign of direct numerical simulations of turbulent channels at different Reynolds numbers and box sizes, and assessed the effect of the computational domain in the one-point statistics and spectra. From the results, we have concluded that computational domains with streamwise and spanwise sizes 2vr and vr times the half-height of the channel, respectively, are large enough to accurately capture the dynamical interactions between structures in the logarithmic layer and the rest of the scales. These simulations are used in the subsequent chapters. Second, the three-dimensional structures of intense tangential Reynolds stress in plane turbulent channels (Qs) have been studied by extending the classical quadrant analysis to three dimensions, with emphasis on the logarithmic and outer layers. The eddies are identified as connected regions of intense tangential Reynolds stress. Qs are then classified according to their streamwise and wall-normal fluctuating velocities as inward interactions, outward interactions, sweeps and ejections. It is found that wall-detached Qs are isotropically oriented background stress fluctuations, common to most turbulent flows, and do not contribute to the mean stress. Most of the stress is carried by a selfsimilar family of larger wall-attached Qs, increasingly complex away from the wall, with fractal dimensions « 2. They have shapes similar to ‘sponges of flakes’, while vortex clusters resemble ‘sponges of strings’. Although their number decays away from the wall, the fraction of the stress that they carry is independent of their heights, and a substantial part resides in a few objects extending beyond the centerline, reminiscent of the very large scale motions of several authors. The predominant logarithmic-layer structures are sideby- side pairs of sweeps and ejections, with an associated vortex cluster, and dimensions and stresses similar to Townsend’s conjectured wall-attached eddies. Third, the temporal evolution of Qs and vortex clusters are studied using time-resolved DNS data up to ReT = 4200 (friction Reynolds number). The eddies are identified following the procedure presented above, and then tracked in time. From the geometric intersection of structures in consecutive fields, we have built temporal connection graphs of all the objects, and defined main and secondary branches in a way that each branch represents the temporal evolution of one coherent structure. Once these evolutions are properly organized, they provide the necessary information to characterize eddies from birth to death. The results show that the eddies are born at all distances from the wall, although with higher probability near it, where the shear is strongest. Most of them stay small and do not last for long times. However, there is a family of eddies that become large enough to attach to the wall while they reach into the logarithmic layer, and become the wall-attached structures previously observed in instantaneous flow fields. They are geometrically self-similar, with sizes and lifetimes proportional to their distance from the wall. Most of them achieve lengths well above the Corrsin’ scale, and hence, their dynamics are controlled by the mean shear. Eddies associated with ejections move away from the wall with an average velocity uT (friction velocity), and their base attaches very fast at the beginning of their lives. Conversely, sweeps move towards the wall at -uT, and attach later. In both cases, they remain attached for 2/3 of their lives. In the streamwise direction, eddies are advected and deformed by the local mean velocity. Finally, we interpret the turbulent cascade not only as a way to conceptualize the flow, but as an actual physical process in which coherent structures merge and split. The volume of an eddy can change either smoothly, when they are not merging or splitting, or through sudden changes. The processes of merging and splitting can be thought of as a direct (when splitting) or an inverse (when merging) cascade, following the ideas envisioned by Richardson (1920) and Obukhov (1941). It is observed that there is a minimum length of 30η (Kolmogorov units) above which mergers and splits begin to be important. Moreover, all eddies above 100η split and merge at least once in their lives. In those cases, the total volume gained and lost is a substantial fraction of the average volume of the structure involved, with slightly more splits (direct cascade) than mergers. Most branch interactions are found to be the shedding or absorption of Kolmogorov-scale fragments by larger structures, but more balanced splits or mergers spanning a wide range of scales are also found to be important. The results show that splits are more probable at the end of the life of the eddy, while mergers take place at the beginning of the life. Although the results for the direct and the inverse cascades are not identical, they are found to be very symmetric, which suggests a high degree of reversibility of the cascade process.

In vivo analysis of the 3′ untranslated region of the hepatitis C virus after in vitro mutagenesis of an infectious cDNA clone

Large sections of the 3′ untranslated region (UTR) of hepatitis C virus (HCV) were deleted from an infectious cDNA clone, and the RNA transcripts from seven deletion mutants were tested sequentially for infectivity in a chimpanzee. Mutants lacking all or part of the 3′ terminal conserved region or the poly(U–UC) region were unable to infect the chimpanzee, indicating that both regions are critical for infectivity in vivo. However, the third region, the variable region, was able to tolerate a deletion that destroyed the two putative stem–loop structures within this region. Mutant VR-24 containing a deletion of the proximal 24 nt of the variable region of the 3′ UTR was viable in the chimpanzee and seemed to replicate as well as the undeleted parent virus. The chimpanzee became viremic 1 week after inoculation with mutant VR-24, and the HCV genome titer increased over time during the early acute infection. Therefore, the poly(U–UC) region and the conserved region, but not the variable region, of the 3′ UTR seem to be critical for in vivo infectivity of HCV.

Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction.

X-ray diffraction experiments revealed the structure of the N photointermediate of bacteriorhodopsin. Since the retinal Schiff base is reprotonated from Asp-96 during the M to N transition in the photocycle, and Asp-96 is reprotonated during the lifetime of the N intermediate, or immediately after, N is a key intermediate for understanding the light-driven proton pump. The N intermediate accumulates in large amounts during continuous illumination of the F171C mutant at pH 7 and 5 degrees Celsius. Small but significant changes of the structure were detected in the x-ray diffraction profile under these conditions. The changes were reversible and reproducible. The difference Fourier map indicates that the major change occurs near helix F. The observed diffraction changes between N and the original state were essentially identical to the diffraction changes reported for the M intermediate of the D96N mutant of bacteriorhodopsin. Thus, we find that the protein conformations of the M and N intermediates of the photocycle are essentially the same, in spite of the fact that in M the Schiff base is unprotonated and in N it is protonated. The observed structural change near helix F will increase access of the Schiff base and Asp-96 to the cytoplasmic surface and facilitate the proton transfer events that begin with the decay of the M state.

Evidence of Intracrystalline Mesostructured Porosity in Zeolites by Advanced Gas Sorption, Electron Tomography and Rotation Electron Diffraction

The small size of micropores (typically <1 nm) in zeolites causes slow diffusion of reactant and product molecules in and out of the pores and negatively impacts the product selectivity of zeolite based catalysts, for example, fluid catalytic cracking (FCC) catalysts. Size-tailored mesoporosity was introduced into commercial zeolite Y crystals by a simple surfactant-templating post-synthetic mesostructuring process. The resulting mesoporous zeolite Y showed significantly improved product selectivity in both laboratory testing and refinery trials. Advanced characterization techniques such as electron tomography, three-dimensional rotation electron diffraction, and high resolution gas adsorption coupled with hysteresis scanning and density functional theory, unambiguously revealed the intracystalline nature and connectivity of the introduced mesopores. They can be considered as molecular highways that help reactant and product molecules diffuse quickly to and away from the catalytically active sites within the zeolite crystals and, thus, shift the selectivity to favor the production of more of the valuable liquid fuels at reduced yields of coke and unconverted feed.

A função respiratória dos doentes adultos com fibrose quística, em repouso e no esforço

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Prevenção de proliferação vítreo-retiniana após cirurgia a descolamento de retina regmatogéneo primário

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014