abstract: The accurate and fast determination of carbon dioxide (CO2) levels is critical for many health and environmental applications. For example, the analysis of CO2 levels in exhaled breath allows for the evaluation of systemic metabolism, perfusion, and ventilation, and provides the doctors and patients with a non-invasive and simple method to predict the presence and severity of asthma, and Chronic Obstructive Pulmonary Disease (COPD). Similarly, the monitoring of CO2 levels in the atmosphere allows for assessment of indoor air quality (IAQ) as the indoor CO2 levels have been proved to be associated with increased prevalence of certain mucous membrane and respiratory sick building syndrome (SBS) symptoms. A pocket-sized CO2 analyzer has been developed for real-time analysis of breath CO2 and environmental CO2. This CO2 analyzer is designed to comprise two key components including a fluidic system for efficient gas sample delivery and a colorimetric detection unit integrated into the fluidic system. The CO2 levels in the gas samples are determined by a disposable colorimetric sensor chip. The sensor chip is a novel composite based sensor that has been optimized to provide fast and reversible response to CO2 over a wide concentration range, covering the needs of both environmental and health applications. The sensor is immune to the presence of various interfering gases in ambient or expired air. The performance of the sensor in real-time breath-by-breath analysis has also been validated by a commercial CO2 detector. Furthermore, a 3D model was created to simulate fluid dynamics of breath and chemical reactions for CO2 assessment to achieve overall understanding of the breath CO2 detection process and further optimization of the device. / Dissertation/Thesis / Ph.D. Chemical Engineering 2014

Pocket proteins (pRb, p107 and p130) are well studied in the role of regulating cell proliferation by controlling progression through the G1/S phase of the cell cycle. Increasing genetic and anatomical evidence suggests that these proteins also control early differentiation and even later stages of cell maturation including neural migration. However, the multifaceted functions of pocket proteins in the regulation of cell proliferation and cell death has complicated our interpretation of their role during development. As a result, the mechanisms through which pocket proteins regulate neuronal migration and neural maturation remain unknown. Using a pRb and p107 double knock out model, we show that a population of upper layer cortical neurons fails to pass through the intermediate zone into the cortical plate. Importantly, these neurons are born at the appropriate time and have exited the cell cycle. In addition, the role of pocket proteins in radial migration is independent cell death, since this migration defect cannot be rescued by eliminating ectopic cell death through Bax deletion. We also show a novel role of pRb and p107 in development of the dorsal midline and guidance of callosal axons. In the absence of pRb and p107, the structures of the commissural plate are highly disorganized and the callosal axons fail to cross the midline. We identify primary defects in axon extension and expression of multiple guidance cues, which can be observed prior to the disorganization of the midline axon guidance structures. Through the use of in vitro cortical explants and in utero electroporation, we identify defects in the rate of axon extension and directional guidance independent from the midline. In addition, protein levels of Netrin and Neuropilin-1 are decreased in the absence of pRb and p107, which could mediate the function of pocket proteins in guiding callosal axons. Indeed, we identify a previously undescribed population of Netrin expressing cells in the cingulate cortex of control embryos which is lost in the pRb/p107 deficient littermates. We propose that these cells play a significant role in callosal axon guidance during normal development. The results presented in this dissertation define multiple novel roles of pRb and p107 in the regulation of radial migration and axon guidance, independent from the role of these pocket proteins in cell death and proliferation.

Pocket Switched Networks (PSNs) offer a means of infrastructureless inter-human communication by utilising Delay and Disruption Tolerant Networking (DTN) technology. However, creating PSNs involves solving challenges which were not encountered in the Deep Space Internet for which DTN technology was originally intended.End-to-end communication over multiple hops in PSNs is a product of short range opportunistic wireless communication between personal mobile wireless devices carried by humans. Opportunistic data delivery in PSNs is far less predictable than in the Deep Space Internet because human movement patterns are harder to predict than the orbital motion of satellites. Furthermore, PSNs require some scheme for efficient neighbour discovery in order to save energy and because mobile devices in PSNs may be unaware of when their next encounter will take place.This thesis offers novel solutions for neighbour discovery and opportunistic data delivery in PSNs that make practical use of dynamic inter-human encounter patterns.The first contribution is a novel neighbour discovery algorithm for PSNs called PISTONS which relies on a new inter-probe time calculation (IPC) and the bursty encounter patterns of humans to set the time between neighbour discovery scans. The IPC equations and PISTONS also give participants the ability to easily specify their required level of connectivity and energy saving with a single variable.This thesis also contains novel distributed spatio-temporal clustering and opportunistic data delivery algorithms for PSNs which can be used to deliver data over multiple hops. The spatio-temporal clustering algorimths are also used to analyse the social networks and transient groups which are formed when humans interact.

[ES] El análisis de los fenómenos transitorios durante las operaciones de llenado en conducciones de agua ha sido estudiado de manera detallada comparado con las maniobras de vaciado. En este último se encontró que no existen modelos matemáticos capaces de predecir el fenómeno. Esta investigación inicia estudiando el fenómeno transitorio generado durante el vaciado en una tubería simple, como paso previo para entender el comportamiento de las variables hidráulicas y termodinámicas durante el vaciado de agua en conducciones presurizadas de perfil irregular. Los análisis son realizados considerando dos situaciones: (i) la situación No. 1 corresponde al caso donde no hay válvulas de aire instaladas o cuando éstas han fallado por problemas operacionales o de mantenimiento, que representa la condición más desfavorable con respecto a la depresión máxima alcanzada; y (ii) la situación No. 2 corresponde al caso en donde se han instalado válvulas de aire en los puntos más elevados de la conducción para dar fiabilidad mediante el aire introducido al sistema previniendo de esta manera la depresión máxima. En esta tesis doctoral se ha desarrollado un modelo matemático para predecir el comportamiento de las operaciones de vaciado. El modelo matemático es propuesto para las dos situaciones mencionadas anteriormente. La fase líquida (agua) es simulada con un modelo de columna rígida, en el cual se desprecia la elasticidad del agua y de la tubería debido a que la elasticidad del aire es mucho mayor que estas; y la interfaz aire-agua es modelada con un modelo de flujo pistón, el cual asume que la columna de agua es perpendicular a la dirección principal del flujo. La fase de aire es modelada usando tres ecuaciones: (a) un modelo politrópico basado en el comportamiento energético, que considera la expansión de las bolsas de aire; (b) la formulación de las válvulas de aire para cuantificar la magnitud del caudal de aire admitido; y (c) la ecuación de continuidad de la bolsa de aire. Un sistema ordinario de ecuaciones diferenciales es solucionado utilizando la herramienta de Simulink de Matlab. El modelo matemático es validado empleando bancos experimentales localizados en los laboratorios de hidráulica de la Universitat Politècnica de València (Valencia, España) y en el Instituto Superior Técnico de la Universidad de Lisboa (Lisboa, Portugal). Los resultados muestran que el modelo matemático predice adecuadamente los datos experimentales de las presiones de las bolsas de aire, las velocidades del agua y las longitudes de las columnas de agua. Finalmente, el modelo matemático es aplicado a un caso de estudio para mostrar su aplicabilidad a situaciones prácticas, con el fin de poder ser empleado por ingenieros para estudiar el fenómeno en conducciones reales y así tomar decisiones acerca de la planificación de esta operación. / [CAT] L'anàlisi dels fenòmens transitoris durant les operacions d'ompliment en conduccions d'aigua ha sigut estudiat de manera detallada comparat amb les maniobres de buidatge. En este últim es va trobar que no hi ha models matemàtics capaços de predir el fenomen. Esta investigació inicia estudiant el fenomen transitori generat durant el buidatge en una canonada simple, com a pas previ per a entendre el comportament de les variables hidràuliques i termodinàmiques durant el buidatge d'aigua en conduccions pressuritzades de perfil irregular. Les anàlisis són realitzats considerant dos situacions: (i) la situació No. 1 correspon al cas on no hi ha vàlvules d'aire instal·lades o quan estes han fallat per problemes operacionals o de manteniment, que representa la condició més desfavorable respecte a la depressió màxima aconseguida; i (ii) la situació No. 2 correspon al cas on s'han instal·lat vàlvules d'aire en els punts més elevats de la conducció per a donar fiabilitat per mitjà de l'aire introduït al sistema prevenint d'esta manera la depressió màxima. En esta tesi doctoral s'ha desenrotllat un model matemàtic per a predir el comportament de les operacions de buidatge. El model matemàtic és proposat per a les dos situacions mencionades anteriorment. La fase líquida (aigua) és simulada amb un model de columna rígida, en el qual es desprecia l'elasticitat de l'aigua i de la canonada pel fet que l'elasticitat de l'aire és molt major que estes; i la interfície aire-aigua és modelada amb un model de flux pistó, el qual assumix que la columna d'aigua és perpendicular a la direcció principal del flux. La fase d'aire és modelada usant tres equacions: (a) un model politròpic basat en el comportament energètic, que considera l'expansió de les bosses d'aire; (b) la formulació de les vàlvules d'aire per a quantificar la magnitud del cabal d'aire admés; i (c) l'equació de continuïtat de la bossa d'aire. Un sistema ordinari d'equacions diferencials és solucionat utilitzant la ferramenta de Simulink de Matlab. El model matemàtic és validat emprant bancs experimentals localitzats en els laboratoris d'hidràulica de la Universitat Politècnica de València (València, Espanya) i en l'Institut Superior Tècnic de la Universitat de Lisboa (Lisboa, Portugal). Els resultats mostren que el model matemàtic prediu adequadament les dades experimentals de les pressions de les bosses d'aire, les velocitats de l'aigua i les longituds de les columnes d'aigua. Finalment, el model matemàtic és aplicat a un cas d'estudi per a mostrar la seua aplicabilitat a situacions pràctiques, a fi de poder ser empleat per enginyers per a estudiar el fenomen en conduccions reals i així prendre decisions sobre la planificació d'esta operació. / [EN] The analysis of transient phenomena during water filling operations in pipelines of irregular profiles has been studied much more compared to emptying maneuvers. In the literature, there is a lack of knowledge about mathematical models of emptying operations. This research starts with the analysis of a transient phenomenon during emptying maneuvers in single pipelines, which is a previous stage to understand the emptying operation in pipelines of irregular profiles. Analysis are conducted under two typical situations: (i) one corresponding to either the situation where there are no air valves installed or when they have failed due to operational and maintenance problems which represents the worse condition due to causing the lowest troughs of subatmospheric pressure, and (ii) the other one corresponding to the situation where air valves have been installed at the highest point of hydraulic installations to give reliability by admitting air into the pipelines for preventing troughs of subatmospheric pressure. Particularly, this research developed a mathematical model to predict the behavior of the emptying operations. The mathematical model is proposed for the two aforementioned situations. The liquid phase (water) is simulated using a rigid water column model (RWCM), which neglects the pipe and water elasticity given that the elasticity of the entrapped air pockets is much higher than the one from the pipe and the water. The air-water interface is simulated with a piston flow model assuming that the water column is perpendicular with the main direction of the flow. Gas phase is modeled using three formulations: (a) a polytropic model based on its energetic behavior, which considers an expansion of air pockets; (b) an air valve characterization to quantify the magnitude of admitted air flow; and (c) a continuity equation of the air. An ordinary differential equations system is solved using the Simulink tool of Matlab. The proposed model has been validated using experimental facilities at the hydraulic laboratories of the Universitat Politècnica de València, Valencia, Spain, and the Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal. The results show how the mathematical model adequately predicts the experimental data, including the pressure oscillation patterns, the water velocities, and the lengths of the water columns. Finally, the mathematical model is applied to a case study to show a practical application, which can be used for engineers to study the phenomenon in real pipelines to make decisions about performing of the emptying operation. / Coronado Hernández, ÓE. (2019). Transient phenomena during the emptying process of water in pressurized pipelines [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/120024 / TESIS

A mixture-fraction-based thermodynamic equilibrium approach for modeling gas-phase combustion was adapted and used in FIRETEC, a wildfire computational fluid dynamics model. The motivation behind this work was the desire to incorporate the features of complex chemistry calculations from the thermodynamic equilibrium model into FIRETEC without significantly increasing the computational burden of the program. In order to implement the mixture-fraction-based thermodynamic equilibrium approach, a sub-grid pocket model was developed to simulate the local mixture fraction of sub-grid flame sheets. Numerical simulations of wildfires were performed using FIRETEC with the new sub-grid, mixture-fraction-based pocket model to model gas-phase combustion. The thermodynamic equilibrium model was used to calculate flame temperatures and combustion products, including CO2 and CO, for sub-grid, gas-phase combustion in FIRETEC simulations. Fire spread rates from simulations using the new sub-grid combustion model were 25-100% higher than fire spread rates from previous FIRETEC simulations, but the successes of modeling propagating fire lines and calculating detailed equilibrium combustion products from simulated sub-grid flame sheets demonstrated the feasibility of this new approach. Future work into the fine-tuning of pocket model parameters and modifying the conservation equation for energy in FIRETEC was recommended.

Le parasite Trypanosoma brucei est retrouvé en Afrique sub-Saharienne et est responsable de la maladie du sommeil chez l’homme et de la Nagana chez les animaux. Il cause de graves problèmes sanitaires et économiques car il affecte le bétail. La vaccination est impossible à cause de la variation antigénique. Les traitements actuels sont difficiles à mettre en place avec des effets secondaires importants. Il est donc urgent de trouver de nouvelles cibles thérapeutiques afin de développer de nouveaux médicaments. T. brucei possède un flagelle unique qui émerge de la cellule par une structure appelée la poche flagellaire (FP). Cette FP est une invagination de la membrane plasmique. Elle est nécessaire à la survie du parasite car c’est le seul site d’endo- et d’exocytose. Au cou de la FP on trouve le collier de la poche flagellaire (FPC) en forme d’anneau. Le FPC est composé de nombreuses protéines dont BILBO1 qui est nécessaire à la biogenèse de la FP et du FPC. De nombreux partenaires de BILBO1 ont été identifiés. Dans cette thèse, je caractérise deux d’entre eux : FPC5, une kinésine putative et FPC9, une synaptotagmine putative. J’ai pu montrer que FPC5 est localisée aux corps basaux mais aussi au FPC. Cette protéine n’est pas essentielle à la survie des parasites bien que des phénotypes de croissance et de ségrégation de la FP apparaissent après induction de l’ARNi. Nous ne sommes pas parvenus à prouver sa fonctionnalité, cependant j’ai pu montrer que son domaine moteur est capable de lier les microtubules. FPC9 est trouvée au niveau de la zone de transition du flagelle. L’ARNi contre cette protéine n’étant pas effectif, nous ne pouvons pas conclure quant à sa fonction dans la cellule. / Trypanosoma brucei is a parasite found in sub-Saharan Africa and is responsible for sleeping sickness in humans and Nagana in animals. It is the source of serious health and economic problems because it kills livestock. Vaccination is not possible because of antigenic variation and current treatments are difficult to implement or have toxic side effects. For these reasons it is urgent to find new therapeutic targets in order to develop effective treatments. T. brucei has a single copy flagellum that emerges from the cytoplasm through a unique structure called the Flagellar Pocket (FP). This pocket is an invagination of the pellicular membrane and because it is the sole site of endo- and exocytosis, it is essential for parasite survival. At the neck of the FP there is a cytoskeletal structure: the Flagellar Pocket Collar (FPC) that forms a “ring” around the flagellum. The FPC consists of numerous proteins, including the first to be identified - BILBO1, which is necessary for FP and FPC biogenesis. A number of potential BILBO1 partners were identified. In this thesis I characterize two of these proteins: FPC5, a putative kinesin and FPC9, a putative synaptotagmin. I show that FPC5 localizes mainly in the basal body area, but also at the FPC. This protein is not essential for parasite survival although reduced FP segregation and growth phenotypes appear after RNAi induction. We are not able to prove its functionality, however I could show its motor domain is able to bind microtubules. FPC9 is found in the transition zone of the flagellum. However RNAi knockdown against this protein was not efficient, so we are currently unable to define a function for this protein.

With the rapid development of technology for context awareness, pervasive computing is releasing people from their traditional desktops. Since mobile devices feature portability and are (nearly) always connected, people tend to carry them wherever they go. Hence, devices such as cellular phones and Pocket PCs are the most suitable platforms for developing context aware applications which users will utilize in their daily life. For these context aware systems, using this context information not only improves the user experience of ubiquitous computing, but also lets the system know who you are or what you have. More importantly, the device can know where you are and predict what you might like to do, thus simplifying many of the user’s interactions with devices and other people around them. This thesis project involves the design, implementation and evaluation of a context aware application, based upon a Pocket PC, that can remind the user of tasks when the user approaches the relevant location for this task. The application interacts with a context aware infrastructure by using the SIP for Instant Messaging and Presence Leveraging Extensions (SIMPLE) protocol, receives context information for the user described using XML. A number of new tags, based upon a new XML schema, have been introduced for this task. This context aware mechanism enables the user to receive any form of information updated by the context server. In this thesis, updates to this information are driven by changes in the user’s location. Additionally, by using the existing calendar application on the Pocket PC, the user can experience location based reminders without learning how to use a new user interface. / Med den snabba utvecklingen av kontextmedvetna teknologier befriar den genomträngande datoriseringen människor från deras traditionella datorer. Eftersom mobila apparater medför bärbarhet och är (nästan) alltid uppkopplade, tenderar människor att bära dem överallt. Följaktligen blir apparater som mobiltelefoner och Pocket-PC de mest passande plattformarna för utvecklandet avkontextmedvetna applikationer för daglig användning. För dessa kontextmedvetna system kommer inte bara användandet av kontexinformation förbättra användarens upplevelse av överallt förekommande datorisering, utan låter även systemet veta vem du är eller vad du har. ännu viktigare är att apparaten kan veta var du befinner dig samt förutsäga vad du skulle kunna vilja göra, och därigenom förenkla mycket av användarens interaktion med andra apparater och människor i omgivningen. Detta examensarbetsprojekt involverar designen, implementationen och evalueringen av en kontextmedvetet applikation, baserad på en Pocket-PC, som kan påminna användaren om uppgifter när användaren närmar sig det relevanta området för dessa uppgifter. Applikationen interagerar med en kontextmedveten infrastruktur genom användandet av protokollet “SIP for Instant Messaging and Presence Leveraging Extensions (SIMPLE)”, mottas kontextinformation för användaren beskriven i XML-format. Ett antal nya taggar, baserade på en ny XML-schema, har introducerats för denna uppgift. Denna kontextmedvetna mekanism gör det möjligt för användaren att ta emot alla typer av uppdaterad information från kontextservern. I denna avhandling uppdateras denna information genom att användaren förflyttar sig. Dessutom kan användaren, genom att använda den befintliga kalenderapplikationen i Pocket-PC:n, få lägesbaserade påminnelser skickade till sig utan att behöva lära sig använda ännu ett interface.

Human-computer interaction (HCI) is being revolutionized by computational design and artificial intelligence. As the diversity of user interfaces shifts from personal desktops to mobile and wearable devices, yesterday’s tools and interfaces are insufficient to meet the demands of tomorrow’s devices. This dissertation describes my research on leveraging different physical channels (e.g., vibration, light, capacitance) to enable novel interaction opportunities. We first introduce FontCode, an information embedding technique for text documents. Given a text document with specific fonts, our method can embed user-specified information (e.g., URLs, meta data, etc) in the text by perturbing the glyphs of text characters while preserving the text content. The embedded information can later be retrieved using a smartphone in real time. Then, we present Vidgets, a family of mechanical widgets, specifically push buttons and rotary knobs that augment mobile devices with tangible user interfaces. When these widgets are attached to a mobile device and a user interacts with them, the nonlinear mechanical response of the widgets shifts the device slightly and quickly. Subsequently, this subtle motion can be detected by the Inertial Measurement Units (IMUs), which is commonly installed on mobile devices. Next, we propose BackTrack, a trackpad placed on the back of a smartphone to track finegrained finger motions. Our system has a small form factor, with all the circuits encapsulated in a thin layer attached to a phone case. It can be used with any off-the-shelf smartphone, requiring no power supply or modification of the operating systems. BackTrack simply extends the finger tracking area of the front screen, without interrupting the use of the front screen. Lastly, we demonstrate MoiréBoard, a new camera tracking method that leverages a seemingly irrelevant visual phenomenon, the moiré effect. Based on a systematic analysis of the moiré effect under camera projection, MoiréBoard requires no power nor camera calibration. It can easily be made at a low cost (e.g., through 3D printing) and ready to use with any stock mobile device with a camera. Its tracking algorithm is computationally efficient and can run at a high frame rate. It is not only simple to implement, but also tracks devices at a high accuracy, comparable to the state-of-the-art commercial VR tracking systems.

This article provides an evaluation and overview of the Personal Digital Assistant (PDA) version of the evidence-based medicine database, InfoRetriever. Both the Pocket PC and Palm OS version are evaluated in this article. Topics covered are the access and installation of InfoRetriever for both PDA operating systems, the design and interface of InfoRetriever, the ease of access of the database contents, and its importance as a tool for point-of-care medicine.

Chloroperoxidase (CPO) is one of the most versatile heme enzyme isolated from the marine fungus, Caldariomyces fumago. Functionally, CPO can catalyze four types of reactions: peroxidation (peroxidase-like), dismutation (catalase-like), halogenation (halogenase-like), and peroxygenation (P450-like). Structurally, CPO has a distal and proximal pockets that can be best described as a hybrid of classical peroxidase and P450s. As a heme-thiolate protein, CPO contains the conserved proximal Pro28-Cys29-Pro30 stretch found in other members of the family. However, the structural and functional roles of these proline residues remain poorly understood. Site-directed mutagenesis was undertaken to generates three CPO mutants, P28A-, P30A-, P28A/P30A-CPO. The replacement of the rigid proline with a more flexible alanine residue, freed up the back bone amide for the formation of additional amide-sulfur hydrogen bond, allowing the investigation of the importance of these residues in CPO catalysis. The three CPO mutants displayed dramatic difference in ligand binding affinity and catalytic activities relative to WT-CPO. Any mutations on the proline resides within the proximal loop eliminated the halogenation and dismutation activities but enhanced the vii epoxidation and peroxidation activities by 4-14 fold. As the binding affinity for cyanide, the CPO mutants displayed significantly higher dissociation constant relative to WT-CPO. Our results revealed that Pro28 and Pro30 play important roles in maintaining the versatility of CPO. As a versatile enzyme, CPO has great application potential in pharmaceutical and chemical industry due to its ability to catalyze the formation of chiral epoxides. Phe103 and Phe186 located on the distal pocket have been proposed to guard the access of substrates to the ferryl oxygen of the heme center. The interactions of these two phenylalanine residues restricted the size of substrates and regulates CPO’s enantioselectivity. F186A- and F103A/F186A-CPO were generated and characterized where the rate of peroxidation and epoxidation were significantly enhanced at the expense of halogenation and dismutation activities. Our results demonstrated that Phe186 played a subtler role relative to Phe103 in terms of substrate specificity and product enantioselectivity of CPO.