Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens.

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.

Strategies to evaluate the impact of rectal volume on prostate motion during three-dimensional conformal radiotherapy for prostate cancer

Abstract Objective: To evaluate the rectal volume influence on prostate motion during three-dimensional conformal radiotherapy (3D-CRT) for prostate cancer. Materials and Methods: Fifty-one patients with prostate cancer underwent a series of three computed tomography scans including an initial planning scan and two subsequent scans during 3D-CRT. The organs of interest were outlined. The prostate contour was compared with the initial CT images considering the anterior, posterior, superior, inferior and lateral edges of the organ. Variations in the anterior limits and volume of the rectum were assessed and correlated with prostate motion in the anteroposterior direction. Results: The maximum range of prostate motion was observed in the superoinferior direction, followed by the anteroposterior direction. A significant correlation was observed between prostate motion and rectal volume variation ( p = 0.037). A baseline rectal volume superior to 70 cm3 had a significant influence on the prostate motion in the anteroposterior direction ( p = 0.045). Conclusion: The present study showed a significant interfraction motion of the prostate during 3D-CRT with greatest variations in the superoinferior and anteroposterior directions, and that a large rectal volume influences the prostate motion with a cutoff value of 70 cm3. Therefore, the treatment of patients with a rectal volume > 70 cm3 should be re-planned with appropriate rectal preparation.

Power Consumption in Carbon Capture and Storage Systems (CCS) and Possibilities to Reduce Power Consumption with Variable Speed Drives

The aim of this master´s thesis is to study which processes increase the auxiliary power consumption in carbon capture and storage processes and if it is possible to reduce the auxiliary power consumption with variable speed drives. Also the cost of carbon capture and storage is studied. Data about auxiliary power consumption in carbon capture is gathered from various studies and estimates made by various research centres. Based on these studies a view is presented how the power auxiliary power consumption is divided between different processes in carbon capture processes. In a literary study, the operation of three basic carbon capture systems is described. Also different methods to transport carbon dioxide and carbon dioxide storage options are described in this section. At the end of the thesis processes that consume most of the auxiliary power are defined and possibilities to reduce the auxiliary power consumption are evaluated. Cost of carbon capture, transport and storage are also evaluated at this point and in the case that the carbon capture and storage systems are fully deployed. According to the results, it can be estimated what are the processes are where variable speed drives can be used and what kind of cost and power consumption reduction could be achieved. Results also show how large a project carbon capture and storage is if it is fully deployed.

Control of permanent magnet linear synchronous motor in motion control applications

The aim of the thesis is to study the principles of the permanent magnet linear synchronous motor (PMLSM) and to develop a simulator model of direct force controlled PMLSM. The basic motor model is described by the traditional two-axis equations. The end effects, cogging force and friction model are also included into the final motor model. Direct thrust force control of PMLSM is described and modelled. The full system model is proven by comparison with the data provided by the motor manufacturer.

Integration of Real-Time Simulator, Motion Platform and Haptics

This thesis describes the process of the integration of a real-time simulator environment with a motion platform and a haptic device as a part of the Kvalive project. Several programs running on two computers were made to control the different devices of the environment. User tests were made to obtain information of needed improvements to make the simulator more realistic. Also new ideas for improving the simulator and directions of further research were obtained with the help of this research.

Reconeixement de gestos de la mà amb el sensor Kinect

El reconeixement dels gestos de la mà (HGR, Hand Gesture Recognition) és actualment un camp important de recerca degut a la varietat de situacions en les quals és necessari comunicar-se mitjançant signes, com pot ser la comunicació entre persones que utilitzen la llengua de signes i les que no. En aquest projecte es presenta un mètode de reconeixement de gestos de la mà a temps real utilitzant el sensor Kinect per Microsoft Xbox, implementat en un entorn Linux (Ubuntu) amb llenguatge de programació Python i utilitzant la llibreria de visió artifical OpenCV per a processar les dades sobre un ordinador portàtil convencional. Gràcies a la capacitat del sensor Kinect de capturar dades de profunditat d’una escena es poden determinar les posicions i trajectòries dels objectes en 3 dimensions, el que implica poder realitzar una anàlisi complerta a temps real d’una imatge o d’una seqüencia d’imatges. El procediment de reconeixement que es planteja es basa en la segmentació de la imatge per poder treballar únicament amb la mà, en la detecció dels contorns, per després obtenir l’envolupant convexa i els defectes convexos, que finalment han de servir per determinar el nombre de dits i concloure en la interpretació del gest; el resultat final és la transcripció del seu significat en una finestra que serveix d’interfície amb l’interlocutor. L’aplicació permet reconèixer els números del 0 al 5, ja que s’analitza únicament una mà, alguns gestos populars i algunes de les lletres de l’alfabet dactilològic de la llengua de signes catalana. El projecte és doncs, la porta d’entrada al camp del reconeixement de gestos i la base d’un futur sistema de reconeixement de la llengua de signes capaç de transcriure tant els signes dinàmics com l’alfabet dactilològic.

Regime Switching Models for Electricity Time Series that Capture Fat Tailed Distributions

In the power market, electricity prices play an important role at the economic level. The behavior of a price trend usually known as a structural break may change over time in terms of its mean value, its volatility, or it may change for a period of time before reverting back to its original behavior or switching to another style of behavior, and the latter is typically termed a regime shift or regime switch. Our task in this thesis is to develop an electricity price time series model that captures fat tailed distributions which can explain this behavior and analyze it for better understanding. For NordPool data used, the obtained Markov Regime-Switching model operates on two regimes: regular and non-regular. Three criteria have been considered price difference criterion, capacity/flow difference criterion and spikes in Finland criterion. The suitability of GARCH modeling to simulate multi-regime modeling is also studied.

Print-capture PCR for detection of tomato begomoviruses from plants and whiteflies

Print-capture (PC) Polymerase chain reaction (PCR) was evaluated as a novel detection method of plant viruses. Tomato (Lycopersicon esculentum) plants infected with begomovirus (fam. Geminiviridae, gen. Begomovirus) and viruliferous whiteflies were used to study the efficiency of the method. Print-capturing steps were carried out using non-charged nylon membrane or filter paper as the solid support for DNA printings. Amplified DNA fragments of expected size were consistently obtained by PCR from infected plants grown in a greenhouse, after direct application of printed materials to the PCR mix. However, virus detection from a single whitefly and from field-grown tomato samples required a high temperature treatment of printed material prior to PCR amplification. Comparison of nylon membrane and filter paper as the solid support revealed the higher efficiency of the nylon membrane. The application of print-capture PCR reduces the chances of false-positive amplification by reducing manipulation steps during preparation of the target DNA. This method maintains all the advantages of PCR diagnosis, such as the high sensitivity and no requirement of radioactive reagents.

Model based study of a calcium oxide looping process for post-combustion carbon dioxide capture

Calcium oxide looping is a carbon dioxide sequestration technique that utilizes the partially reversible reaction between limestone and carbon dioxide in two interconnected fluidised beds, carbonator and calciner. Flue gases from a combustor are fed into the carbonator where calcium oxide reacts with carbon dioxide within the gases at a temperature of 650 ºC. Calcium oxide is transformed into calcium carbonate which is circulated into the regenerative calciner, where calcium carbonate is returned into calcium oxide and a stream of pure carbon dioxide at a higher temperature of 950 ºC. Calcium oxide looping has proved to have a low impact on the overall process efficiency and would be easily retrofitted into existing power plants. This master’s thesis is done in participation to an EU funded project CaOling as a part of the Lappeenranta University of Technology deliverable, reactor modelling and scale-up tools. Thesis concentrates in creating the first model frame and finding the physically relevant phenomena governing the process.

Centralized Motion Control of a Linear Tooth Belt Drive: Analysis of the Performance and Limitations

A centralized robust position control for an electrical driven tooth belt drive is designed in this doctoral thesis. Both a cascaded control structure and a PID based position controller are discussed. The performance and the limitations of the system are analyzed and design principles for the mechanical structure and the control design are given. These design principles are also suitable for most of the motion control applications, where mechanical resonance frequencies and control loop delays are present. One of the major challenges in the design of a controller for machinery applications is that the values of the parameters in the system model (parameter uncertainty) or the system model it self (non-parametric uncertainty) are seldom known accurately in advance. In this thesis a systematic analysis of the parameter uncertainty of the linear tooth beltdrive model is presented and the effect of the variation of a single parameter on the performance of the total system is shown. The total variation of the model parameters is taken into account in the control design phase using a Quantitative Feedback Theory (QFT). The thesis also introduces a new method to analyze reference feedforward controllers applying the QFT. The performance of the designed controllers is verified by experimentalmeasurements. The measurements confirm the control design principles that are given in this thesis.

Non-Markovian Dynamics and the Quantum-To-Classical Transition for Quantum Brownian Motion

In this Thesis I discuss the dynamics of the quantum Brownian motion model in harmonic potential. This paradigmatic model has an exact solution, making it possible to consider also analytically the non-Markovian dynamics. The issues covered in this Thesis are themed around decoherence. First, I consider decoherence as the mediator of quantum-to-classical transition. I examine five different definitions for nonclassicality of quantum states, and show how each definition gives qualitatively different times for the onset of classicality. In particular I have found that all characterizations of nonclassicality, apart from one based on the interference term in the Wigner function, result in a finite, rather than asymptotic, time for the emergence of classicality. Second, I examine the diverse effects which coupling to a non-Markovian, structured reservoir, has on our system. By comparing different types of Ohmic reservoirs, I derive some general conclusions on the role of the reservoir spectrum in both the short-time and the thermalization dynamics. Finally, I apply these results to two schemes for decoherence control. Both of the methods are based on the non-Markovian properties of the dynamics.

Modelling of calciner in post-combustion carbon capture process

Climate change has given an impetus to research and developed new technologies to reduce significantly carbon dioxide emissions in energy production in the developed countries. The major pollution source, fossil fuels, will be used as an energy source for many decades, which provides the demand for carbon capture and storage technologies. Over recent years many new technologies has been developed and one of the most promising is calcium-looping in post-combustion carbon capture process, which use carbonation-calcination cycle to capture carbon dioxide from the flue gas of a combustion process. First pilot plant for calcium-looping process has been built in Oviedo, Spain. In this study, a three-dimensional model has been created for the calciner, which is one of the two fluidized bed reactors needed for the process. The calciner is a regenerator where the captured carbon dioxide is removed from the calcium material and then collected after the reactor. Thesis concentrates in creating the calciner 3D-model frame with CFB3D-program and testing the model with two different example cases. Used input parameters and calciner geometry are Oviedo pilot plant design parameters. The calculation results give information about the process and show that pilot plant calciner should perform as planned. This Master’s Thesis is done in participation to EU FP7 project CaOling.

Comparison of Classical and Secondary Cytologic Criteria Relative to Hybrid Capture for Diagnosing Cervical-vaginal Infection by Human Papillomavirus

Objective To compare the diagnostic accuracy of the classic Meisels cytologic criteria and the Schneider secondary criteria relative to the hybrid capture method for diagnosing HPV infection. Methods This was a retrospective study performed at a public university hospital. A total of 41 patients with a cytologic diagnosis of HPV infection and 40 HPV-negative patients were selected for review of the cervical-vaginal smears seeking to classical and secondary criteria. A single pathologist reviewed the slides in search of the criteria. The classical and secondary cytologic criteria were compared with the hybrid capture for diagnosing HPV infection. Bartleti test was applied for the age analysis, and Fisher's exact test was used to compare proportions. The tests were considered significant when the probability of rejecting the null hypothesis was less than 5% (p < 0.05). Results The Meisels criteria were less sensitive (34.0%) than the secondary Schneider criteria (57.5%) when compared with the hybrid capture (p < 0.0001), although the specificity of the former criteria was non-significantly higher (91.2% and 67.7%, respectively). In cases of moderate or intense inflammation, the sensitivity and specificity of the Schneider criteria were decreased, 33.3% and 50.0% respectively (p = 0.0115). Conclusions Compared with hybrid capture for diagnosis of HPV infection, the sensitivity of the secondary Schneider criteria was higher than the classical Meisels criteria.Moderate or intense inflammation reduces the sensitivity and specificity of the secondary Schneider criteria for diagnosing HPV infection using the hybrid capture as the gold standard.