MONITORING ENZYME REACTIONS BY FAST ATOM BOMBARDMENT MASS SPECTROMETRY

The potential for the direct analysis of enzyme reactions by fast atom bombardment (FAB) mass spectrometry has been investigated. Conditions are presented for the maintenance of enzymatic activity under FAB conditions along with FAB mass spectrometric data showing that these conditions can be applied to solutions of enzyme and substrate to follow enzymatic reactions inside the mass spectrometer in real-time. In addition, enzyme kinetic behavior under FAB mass spectrometric conditions is characterized using trypsin and its assay substrate, TAME, as an enzyme-substrate reaction model. These results show that two monitoring methods can be utilized to follow reactions by FAB mass spectrometry. The advantages of each method are discussed and illustrated by obtaining kinetic parameters from the direct analysis of enzyme reactions with assay or peptide substrates. ^

THE NATURAL AND ORTHOGONAL INTERACTION (NOIA) MODELS FOR QUANTITATIVE TRAITS (QTs) AND COMPLEX DISEASES

My dissertation focuses on developing methods for gene-gene/environment interactions and imprinting effect detections for human complex diseases and quantitative traits. It includes three sections: (1) generalizing the Natural and Orthogonal interaction (NOIA) model for the coding technique originally developed for gene-gene (GxG) interaction and also to reduced models; (2) developing a novel statistical approach that allows for modeling gene-environment (GxE) interactions influencing disease risk, and (3) developing a statistical approach for modeling genetic variants displaying parent-of-origin effects (POEs), such as imprinting. In the past decade, genetic researchers have identified a large number of causal variants for human genetic diseases and traits by single-locus analysis, and interaction has now become a hot topic in the effort to search for the complex network between multiple genes or environmental exposures contributing to the outcome. Epistasis, also known as gene-gene interaction is the departure from additive genetic effects from several genes to a trait, which means that the same alleles of one gene could display different genetic effects under different genetic backgrounds. In this study, we propose to implement the NOIA model for association studies along with interaction for human complex traits and diseases. We compare the performance of the new statistical models we developed and the usual functional model by both simulation study and real data analysis. Both simulation and real data analysis revealed higher power of the NOIA GxG interaction model for detecting both main genetic effects and interaction effects. Through application on a melanoma dataset, we confirmed the previously identified significant regions for melanoma risk at 15q13.1, 16q24.3 and 9p21.3. We also identified potential interactions with these significant regions that contribute to melanoma risk. Based on the NOIA model, we developed a novel statistical approach that allows us to model effects from a genetic factor and binary environmental exposure that are jointly influencing disease risk. Both simulation and real data analyses revealed higher power of the NOIA model for detecting both main genetic effects and interaction effects for both quantitative and binary traits. We also found that estimates of the parameters from logistic regression for binary traits are no longer statistically uncorrelated under the alternative model when there is an association. Applying our novel approach to a lung cancer dataset, we confirmed four SNPs in 5p15 and 15q25 region to be significantly associated with lung cancer risk in Caucasians population: rs2736100, rs402710, rs16969968 and rs8034191. We also validated that rs16969968 and rs8034191 in 15q25 region are significantly interacting with smoking in Caucasian population. Our approach identified the potential interactions of SNP rs2256543 in 6p21 with smoking on contributing to lung cancer risk. Genetic imprinting is the most well-known cause for parent-of-origin effect (POE) whereby a gene is differentially expressed depending on the parental origin of the same alleles. Genetic imprinting affects several human disorders, including diabetes, breast cancer, alcoholism, and obesity. This phenomenon has been shown to be important for normal embryonic development in mammals. Traditional association approaches ignore this important genetic phenomenon. In this study, we propose a NOIA framework for a single locus association study that estimates both main allelic effects and POEs. We develop statistical (Stat-POE) and functional (Func-POE) models, and demonstrate conditions for orthogonality of the Stat-POE model. We conducted simulations for both quantitative and qualitative traits to evaluate the performance of the statistical and functional models with different levels of POEs. Our results showed that the newly proposed Stat-POE model, which ensures orthogonality of variance components if Hardy-Weinberg Equilibrium (HWE) or equal minor and major allele frequencies is satisfied, had greater power for detecting the main allelic additive effect than a Func-POE model, which codes according to allelic substitutions, for both quantitative and qualitative traits. The power for detecting the POE was the same for the Stat-POE and Func-POE models under HWE for quantitative traits.

Renal Cryoablation: Investigation of Periprocedural Visualization Tools and Treatment Response Quantification

Cryoablation for small renal tumors has demonstrated sufficient clinical efficacy over the past decade as a non-surgical nephron-sparing approach for treating renal masses for patients who are not surgical candidates. Minimally invasive percutaneous cryoablations have been performed with image guidance from CT, ultrasound, and MRI. During the MRI-guided cryoablation procedure, the interventional radiologist visually compares the iceball size on monitoring images with respect to the original tumor on separate planning images. The comparisons made during the monitoring step are time consuming, inefficient and sometimes lack the precision needed for decision making, requiring the radiologist to make further changes later in the procedure. This study sought to mitigate uncertainty in these visual comparisons by quantifying tissue response to cryoablation and providing visualization of the response during the procedure. Based on retrospective analysis of MR-guided cryoablation patient data, registration and segmentation algorithms were investigated and implemented for periprocedural visualization to deliver iceball position/size with respect to planning images registered within 3.3mm with at least 70% overlap and a quantitative logit model was developed to relate perfusion deficit in renal parenchyma visualized in verification images as a result of iceball size visualized in monitoring images. Through retrospective study of 20 patient cases, the relationship between likelihood of perfusion loss in renal parenchyma and distance within iceball was quantified and iteratively fit to a logit curve. Using the parameters from the logit fit, the margin for 95% perfusion loss likelihood was found to be 4.28 mm within the iceball. The observed margin corresponds well with the clinically accepted margin of 3-5mm within the iceball. In order to display the iceball position and perfusion loss likelihood to the radiologist, algorithms were implemented to create a fast segmentation and registration module which executed in under 2 minutes, within the clinically-relevant 3 minute monitoring period. Using 16 patient cases, the average Hausdorff distance was reduced from 10.1mm to 3.21 mm with average DSC increased from 46.6% to 82.6% before and after registration.

MorphCol 2004-2013. A collection of Fortran 77 programs for morphometry

This is a technical description in html format of simple fortran programs for Macintosh for the morphometric analysis of tests planktonic foraminifera under reflected light, with special focus on the Neogene group of Globorotalia menardii. The second part of this report gives information and performance tests about the development of AMOR (Automated Measurement system for the mORphometry of microfossils). AMOR is Windows based and helps to orientate and collect digital images of menardiform globorotalids. The above fortran programs may be useful to extract and analyze some morphometric parameters from images collected with AMOR. After unzipping the archive file please open the Start.html file using a common web browser like firefox. In case of any questions or problems, please contact Michael W. Knappertsbusch (mailto:michael.knappertsbusch@unibas.ch).

World distribution of land cover changes, model in NetCDF format

The role of Pre- and Protohistoric anthropogenic land cover changes needs to be quantified i) to establish a baseline for comparison with current human impact on the environment and ii) to separate it from naturally occurring changes in our environment. Results are presented from the simple, adaptation-driven, spatially explicit Global Land Use and technological Evolution Simulator (GLUES) for pre-Bronze age demographic, technological and economic change. Using scaling parameters from the History Database of the Global Environment as well as GLUES-simulated population density and subsistence style, the land requirement for growing crops is estimated. The intrusion of cropland into potentially forested areas is translated into carbon loss due to deforestation with the dynamic global vegetation model VECODE. The land demand in important Prehistoric growth areas - converted from mostly forested areas - led to large-scale regional (country size) deforestation of up to 11% of the potential forest. In total, 29 Gt carbon were lost from global forests between 10 000 BC and 2000 BC and were replaced by crops; this value is consistent with other estimates of Prehistoric deforestation. The generation of realistic (agri-)cultural development trajectories at a regional resolution is a major strength of GLUES. Most of the pre-Bronze age deforestation is simulated in a broad farming belt from Central Europe via India to China. Regional carbon loss is, e.g., 5 Gt in Europe and the Mediterranean, 6 Gt on the Indian subcontinent, 18 Gt in East and Southeast Asia, or 2.3 Gt in subsaharan Africa.

Seawater carbonate chemistry and swimming behaviors of the raphidophyte Heterosigma akashiwo in a laboratory experiment

We investigated the effects of pH on movement behaviors of the harmful algal bloom causing raphidophyte Heterosigma akashiwo. Motility parameters from >8000 swimming tracks of individual cells were quantified using 3D digital video analysis over a 6-h period in 3 pH treatments reflecting marine carbonate chemistry during the pre-industrial era, currently, and the year 2100. Movement behaviors were investigated in two different acclimation-to-target-pH conditions: instantaneous exposure and acclimation of cells for at least 11 generations. There was no negative impairment of cell motility when exposed to elevated PCO2 (i.e., low pH) conditions but there were significant behavioral responses. Irrespective of acclimation condition, lower pH significantly increased downward velocity and frequency of downward swimming cells (p < 0.001). Rapid exposure to lower pH resulted in 9% faster downward vertical velocity and up to 19% more cells swimming downwards (p < 0.001). Compared to pH-shock experiments, pre-acclimation of cells to target pH resulted in ~30% faster swimming speed and up to 46% faster downward velocities (all p < 0.001). The effect of year 2100 PCO2 levels on population diffusivity in pre-acclimated cultures was >2-fold greater than in pH-shock treatments (2.2 × 105 µm**2/s vs. 8.4 × 104 µm**2/s). Predictions from an advection-diffusion model, suggest that as PCO2 increased the fraction of the population aggregated at the surface declined, and moved deeper in the water column. Enhanced downward swimming of H. akashiwo at low pH suggests that these behavioral responses to elevated PCO2 could reduce the likelihood of dense surface slick formation of H. akashiwo through reductions in light exposure or growth independent surface aggregations. We hypothesize that the HAB alga's response to higher PCO2 may exploit the signaling function of high PCO2 as indicative of net heterotrophy in the system, thus indicative of high predation rates or depletion of nutrients.

The scenario of two-dimensional instabilities of the cylinder wake under EHD forcing: A linear stability analysis

We propose to study the stability properties of an air flow wake forced by a dielectric barrier discharge (DBD) actuator, which is a type of electrohydrodynamic (EHD) actuator. These actuators add momentum to the flow around a cylinder in regions close to the wall and, in our case, are symmetrically disposed near the boundary layer separation point. Since the forcing frequencies, typical of DBD, are much higher than the natural shedding frequency of the flow, we will be considering the forcing actuation as stationary. In the first part, the flow around a circular cylinder modified by EHD actuators will be experimentally studied by means of particle image velocimetry (PIV). In the second part, the EHD actuators have been numerically implemented as a boundary condition on the cylinder surface. Using this boundary condition, the computationally obtained base flow is then compared with the experimental one in order to relate the control parameters from both methodologies. After validating the obtained agreement, we study the Hopf bifurcation that appears once the flow starts the vortex shedding through experimental and computational approaches. For the base flow derived from experimentally obtained snapshots, we monitor the evolution of the velocity amplitude oscillations. As to the computationally obtained base flow, its stability is analyzed by solving a global eigenvalue problem obtained from the linearized Navier–Stokes equations. Finally, the critical parameters obtained from both approaches are compared.

Ensayos acelerados de fiabilidad de células solares de concentración

SUMMARY Concentration Photovoltaic Systems (CPV) have been proposed as an alternative to conventional systems. During the last years, there has been a boom of the CPV industry caused by the technological progress in all the elements of the system. and mainly caused by the use of multijunction solar cells based on III-V semiconductors, with efficiencies exceeding to 43%. III-V solar cells have been used with high reliability results in a great number of space missions without concentration. However, there are no previous results regarding their reliability in concentration terrestrial applications, where the working conditions are completely different. This lack of experience, together with the important industrial interest, has generated the need to evaluate the reliability of the cells. For this reason, nowadays there are several research centers around the undertaking this task. The evaluation of the reliability of this type of devices by means of accelerated tests is especially problematic when they work at medium or high concentration, because it is practically impossible to emulate real working conditions of the cell inside climatic chambers. In fact, as far as we know, the results that appear in this Thesis are the first estimating the Activation Energy of the failure mechanism involved, as well as the warranty of the III-V concentrator solar cells tested here. To evaluate the reliability of III-V very high concentrator solar cells by means of accelerated tests, a variety of activities, described in this Thesis have been carried out. The First Part of the memory presents the theoretical part of the Doctoral Thesis. After the Introduction, chapter 2 presents the state of the art in degradation and reliability of CPV systems and solar cells. Chapter 3 introduces some reliability definitions and the application of specific statistical functions to the evaluation of the reliability and parameters. From these functions, important parameters will be calculated to be used later in the experimental results of Thesis. The Second Part of the memory contains the experimental. Chapter 4 shows the types of accelerated tests and the main goals pursuit with them when carried out over CPV systems and solar cells. In order to evaluate quantitatively the reliability of the III-V concentrator solar cells used in these tests, some modifications have been introduced which discussion will be tackled here. Based on this analysis the working plan of the tests carried out in this Doctoral Thesis is presented. Chapter 5 presents a new methodology as well as the necessary instrumentation to carry out the tests described here. This new methodology takes into account the adaptation, improvement and novel techniques needed to test concentrator solar cells. The core of this memory is chapter 6, which presents the results of the characterization of the cells during the accelerated life tests and the analysis of the aforementioned results with the purpose of getting quantitative values of reliability in real working conditions. The acceleration factor of the accelerated life tests, under nominal working conditions has been calculated. Accordingly, the validity of the methodology as well as the calculations based on the reliability assessment, have also been demonstrated. Finally, quantitative values of degradation, reliability and warranty of the solar cells under field nominal working conditions have been calculated. With the development of this Doctoral Thesis the reliability of very high concentrator GaAs solar cells of small area has been evaluated. It is very interesting to generalize the procedures described up to this point to III-V multijunction solar cells of greater area. Therefore, chapter 7 develops this generalization and introduces also a useful thermal modeling by means of finite elements of the test cells’ circuits. In the last chapter, the summary of the results and the main contributions of this Thesis are outlined and future research activities are identified. RESUMEN Los Sistemas Fotovoltaicos de Concentración (SFC) han sido propuestos como una alternativa a los sistemas convencionales de generación de energía. Durante los últimos años ha habido un auge de los SFC debido a las mejoras tecnológicas en todos los elementos del sistema, y principalmente por el uso de células multiunión III-V que superan el 43% de rendimiento. Las células solares III-V han sido utilizadas con elevada fiabilidad en aplicaciones espaciales sin concentración, pero no existe experiencia de su fiabilidad en ambiente terrestre a altos niveles de concentración solar. Esta falta de experiencia junto al gran interés industrial ha generado la necesidad de evaluar la fiabilidad de las células, y actualmente hay un significativo número de centros de investigación trabajando en esta área. La evaluación de la fiabilidad de este tipo de dispositivos mediante ensayos acelerados es especialmente problemática cuando trabajan a media o alta concentración por la casi imposibilidad de emular las condiciones de trabajo reales de la célula dentro de cámaras climáticas. De hecho, que sepamos, en los resultados de esta Tesis se evalúa por primera vez la Energía de Activación del mecanismo de fallo de las células, así como la garantía en campo de las células de concentración III-V analizadas. Para evaluar la fiabilidad de células solares III-V de muy alta concentración mediante ensayos de vida acelerada se han realizado diversas actividades que han sido descritas en la memoria de la Tesis. En la Primera Parte de la memoria se presenta la parte teórica de la Tesis Doctoral. Tras la Introducción, en el capítulo 2 se muestra el estado del arte en degradación y fiabilidad de células y Sistemas Fotovoltaicos de Concentración. En el capítulo 3 se exponen de forma resumida las definiciones de fiabilidad y funciones estadísticas que se utilizan para la evaluación de la fiabilidad y sus parámetros, las cuales se emplearán posteriormente en los ensayos descritos en este Tesis. La Segunda Parte de la memoria es experimental. En el capítulo 4 se describen los tipos y objetivos de los ensayos acelerados actualmente aplicados a SFC y a las células, así como las modificaciones necesarias que permitan evaluar cuantitativamente la fiabilidad de las células solares de concentración III-V. En base a este análisis se presenta la planificación de los trabajos realizados en esta Tesis Doctoral. A partir de esta planificación y debido a la necesidad de adaptar, mejorar e innovar las técnicas de ensayos de vida acelerada para una adecuada aplicación a este tipo de dispositivos, en el capítulo 5 se muestra la metodología empleada y la instrumentación necesaria para realizar los ensayos de esta Tesis Doctoral. El núcleo de la memoria es el capítulo 6, en él se presentan los resultados de caracterización de las células durante los ensayos de vida acelerada y el análisis de dichos resultados con el objetivo de obtener valores cuantitativos de fiabilidad en condiciones reales de trabajo. Se calcula el Factor de Aceleración de los ensayos acelerados con respecto a las condiciones nominales de funcionamiento a partir de la Energía de Activación obtenida, y se demuestra la validez de la metodología y cálculos empleados, que son la base de la evaluación de la fiabilidad. Finalmente se calculan valores cuantitativos de degradación, fiabilidad y garantía de las células en condiciones nominales en campo durante toda la vida de la célula. Con el desarrollo de esta Tesis Doctoral se ha evaluado la fiabilidad de células III-V de área pequeña, pero es muy interesante generalizar los procedimientos aquí desarrollados para las células III-V comerciales de área grande. Por este motivo, en el capítulo 7 se analiza dicha generalización, incluyendo el modelado térmico mediante elementos finitos de los circuitos de ensayo de las células. En el último capítulo se realiza un resume del trabajo y las aportaciones realizadas, y se identifican las líneas de trabajo a emprender en el futuro.

Modelización de contactos termoelastohidrodinámicos

La mejora en la eficiencia energética y la reducción de la tasa de fallos en los contactos lubricados son aspectos que resultan de gran interés en numerosos sectores de la industria, y plantean en estos momentos nuevas dificultades operativas y retos para un futuro próximo. Los avances tecnológicos han incrementado las exigencias técnicas que se requieren a los aceites para cumplir su función al extender sus variables operativas a un mayor espectro de aplicaciones, tanto de condiciones de funcionamiento como a la gran variedad de nuevos materiales constitutivos de los engranajes en los que se tiene que utilizar. Por ello, actualmente se está incentivado el desarrollo de nuevos procedimientos que permitan comprender el comportamiento de este tipo de contactos lubricados, con el fin de lograr mejoras técnicas en su diseño y la correcta selección del aceite. En esta Tesis Doctoral se presenta una metodología de cálculo numérico que permite simular el comportamiento de contactos elastohidrodinámicos (EHD) puntuales, como puede ser el caso de un rodamiento. La resolución de este problema presenta diversas complejidades matemáticas y exige el desarrollo de un elaborado procedimiento de cálculo basado en técnicas multinivel. Para hacer del procedimiento una herramienta válida en un gran número de condiciones de funcionamiento y tipos de lubricantes, se ha tenido en cuenta en el cálculo la posible aparición de comportamientos no-Newtonianos del lubricante y fenómenos de generación y disipación de calor, provocados por el movimiento relativo del fluido y las superficies en contacto. Para la validación del procedimiento, se han contrastado los resultados numéricos obtenidos con nuestro método, con los resultados numéricos y experimentales publicados por otros autores y con valores experimentales propios medidos en un equipo de ensayo de contacto puntual tipo MTM. El desarrollo de este programa ha dotado a la División de Ingeniería de Máquinas de una herramienta que ha permitido, y sobre todo va permitir, evaluar la importancia de cada uno de los parámetros reológicos en los diferentes problemas que va a tener que abordar, evaluación que hasta el momento se realizaba con métodos aproximados que describen la fenomenología con mucha menos precisión. A la hora de emplear nuestro procedimiento numérico para simular situaciones reales, nos hemos encontrado con el obstáculo de que es muy complicado encontrar, en la bibliografía y bases de datos, los parámetros que caracterizan el comportamiento reológico del lubricante en las condiciones de presión, temperatura y grado de cizallamiento habituales en las que se trabaja en este tipo de contactos, y las pocas medidas que existen para estas condiciones de funcionamiento son poco fiables. Por ello como complemento al objetivo principal de esta Tesis hemos desarrollado una metodología para caracterizar los lubricantes en estas condiciones extremas. Dicha metodología está basada en la buena descripción que hace nuestro programa del coeficiente de fricción, lo que nos ha permitido obtener los parámetros reológicos del III lubricante a partir de las medidas experimentales del coeficiente de fricción generado en un equipo MTM lubricado con el lubricante que se desea caracterizar. Madrid, Octubre de 2012 IV Improving energy efficiency and reducing the failure rate in lubricated contacts are issues that are of great interest in many sectors of industry, and right now posed operational difficulties and new challenges for the near future. Technological advances have increased the technical demands required to oils to fulfil its role by extending its operational variables to a wider range of applications, both operating conditions and to the wide variety of new materials which constitute the gear in which must be used. For this reason, has being encouraged currently to develop new procedures to understand the behaviour of this type of lubricated contacts, in order to achieve improvements in design techniques and the correct oil selection. In this Thesis we present a numerical methodology to simulate the puntual elastohydrodynamic contact behaviour (EHD), such as a roller bearing. The resolution of this problem presents various mathematical complexities and requires the development of an elaborate calculation procedure based on multilevel techniques. To make the procedure a valid tool in a wide range of operating conditions and types of lubricants, has been taken into account in calculating the possible occurrence of non-Newtonian behaviour of the lubricant and phenomena of generation and dissipation of heat, caused by the fluid relative motion and contacting surfaces. For the validation of the method, we have compared the numerical results obtained with our method with numerical and experimental results published by other authors also with own experimental values measured on point-contact test equipment MTM. The development of this program has provided the Machines Engineering Division of a tool that has allowed, and especially will allow to evaluate the importance of each of the rheological parameters on the various problems that will have to be addressed, evaluation performed hitherto described methods that phenomenology approximated with much less accuracy. When using our numerical procedure to simulate real situations we have encountered the obstacle that is very difficult to find, in the literature and database, parameters characterizing the rheological behaviour of the lubricant in the usual conditions of pressure, temperature and shear rate in which you work in this type of contact, and the few measures that exist for these operating conditions are unreliable. Thus in addition to the main objective of this thesis, we have developed a methodology to characterize the lubricants in these extreme conditions. This methodology is based on the good description, which makes our program, of the coefficient of friction, that allowed us to obtain the lubricant rheological parameters from experimental measurements of the friction coefficient generated on lubricated MTM equipment with the lubricant to be characterized.