Algorithms for time series clustering applied to biomedical signals

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

Application of Discrete Fourier Inter-Coefficient Difference for Assessing Genetic Sequence Similarity

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.

Diseño y fabricación de dispositivos basados en cristal líquido polimérico

Esta tesis se centra en el estudio y desarrollo de dispositivos de aplicación basados en cristal líquido polimérico. Las propiedades de los cristales líquidos los hacen interesantes para su uso en el desarrollo de dispositivos de seguridad para autenticación de productos y marcas, y detección y prevención de falsificaciones. Asimismo, pueden ser muy útiles para fabricar dispositivos basados en CLs dispersos en polímero, los cuales tienen a su vez múltiples aplicaciones. La orientación de las moléculas de cristal líquido y la birrefringencia son las dos características principales que afectan a las propiedades de estos dispositivos. Un dispositivo de cristal líquido estándar consiste en un sándwich formado por dos sustratos de vidrio transparente, dotados con electrodo de ITO (Indium Tin Oxide) en su superficie interna, que confinan el cristal líquido en su interior. En la primera parte de esta tesis se describen las características más importantes que describen una célula de cristal líquido. Esta introducción básica en necesaria para la correcta comprensión de los capítulos posteriores en los que se detalla el desarrollo concreto de los dispositivos desarrollados en la investigación llevada a cabo. Por ejemplo, en el caso de los dispositivos de seguridad se han eliminado los sustratos de vidrio (en la última fase de su desarrollo) para conseguir dispositivos flexibles. En la segunda parte de la tesis se incluye la descripción completa de los dispositivos fabricados, así como de los protocolos de fabricación seguidos y diseñados específicamente para ello. También se detallan en esta parte los resultados obtenidos, así como las propiedades ópticas y electroópticas en cada caso, y el/los equipos de caracterización utilizados. Utilizando cristal líquido nemático y colorante dicroico, se han desarrollado dispositivos que contienen múltiples imágenes latentes en cada cara del mismo. Utilizando distintas técnicas de alineamiento se consigue crear cualquier tipo de motivo latente, ya sean símbolos sencillos, figuras, logotipos o incluso imágenes con escala de gris. Cuanto más complejo es el dispositivo, mayor es la dificultad para reproducirlo en una eventual falsificación. Para visualizar e identificar los motivos es necesario emplear luz polarizada, por ejemplo, con la ayuda de un sencillo polarizador lineal. Dependiendo de si el polarizador está colocado delante del dispositivo o detrás del él, se mostrarán las imágenes generadas en una u otra cara. Este efecto es posible gracias al colorante dicroico añadido al CL, a la orientación inducida sobre las moléculas, y a la estructura de twist utilizada en los dispositivos. En realidad, para ver el efecto de los dispositivos no es necesario el uso de un polarizador, basta con el reflejo de una superficie dielétrica (percialmente polarizado), o la luz emitida por la pantalla de dispositivos de consumo comunes como un televisor LCD, un monitor de ordenador o un “smartphone”. Por otro lado, utilizando una mezcla entre un CL nemático polimérico y un CL nemático no polimérico es posible fabricar dispositivos LCPC (Liquid Crystal Polymer Composite) con propiedades electroópticas muy interesantes, que funcionan a tensiones de conmutación bajas. El CL polimérico conforma una estructura de red en el interior del sándwich que mantiene confinado al CL nemático en pequeños microdominios. Se han fabricado dispositivos LCPC con conmutación inversa utilizando tanto alineamiento homogéneo como homeotrópico. Debido a que tanto la estructura de CL polimérico como el CL nemático que rellena los microdominios están orientados en una misma dirección de alineamiento preinducida, la luz dispersada por el dispositivo se encuentra polarizada. La dirección de polarización coincide con la dirección de alineamiento. La innovación aportada por esta investigación: un nuevo dispositivo LCPC inverso de respuesta ultrarápida y polarizada basado en la mezcla de dos CL nemáticos y, un dispositivo de seguridad y autenticación, patentado internacionalmente, basado en CL nemáticos dopados con colorante dicroico. Abstract This thesis is centered on the availability to use polymerizable liquid crystals to develop non-display application LC devices. Liquid crystal properties make them useful for the development of security devices in applications of authentication and detection of fakes, and also to achieve polymer dispersed LC devices to be used for different applications that will be studied here. Induced orientation of liquid crystal molecules and birefringence are the two main properties used in these devices. A standard liquid crystal device is a sandwich consisting of two parallel glass substrates carrying a thin transparent ITO (Indium‐Tin‐Oxide) electrode on their inner surfaces with the liquid crystal in the middle. The first part of this thesis will describe the most important parameters describing a liquid crystal cell. This basis is necessary for the understanding of later chapters where models of the liquid crystal devices will be discussed and developed. In the case of security devices the standard structure of an LC device has been modified by eliminating the glass substrates in order to achieve plastic and flexible devices. The second part of the thesis includes a detailed description of the devices achieved and the manufacturing protocols that have been developed ad-hoc. The optical and electrooptical properties and the characterization equipment are described here as well. Employing nematic liquid crystal and dichroic colorants, we have developed devices that show, with the aid of a polarizer, multiple images on each side of the device. By different alignment techniques it is possible to create any kind of symbols, drawings or motifs with a grayscale; the more complex the created device is, the more difficult is to fake it. To identify the motifs it is necessary to use polarized light. Depending on whether the polarizer is located in front of the LC cell or behind it, different motifs from one or the other substrate are shown. The effect arises from the dopant color dye added to the liquid crystal, the induced orientation and the twist structure. In practice, a grazing reflection on a dielectric surface is polarized enough to see the effect. Any LC flat panel display (LCD TV, computer, mobile phone) can obviously be used as backlight as well. On the other hand, by using a mixture of polymerizable and non-polymerizable nematics liquid crystals it is also possible to achieve LCPC (Liquid Crystal Polymer Composite) devices that show really interesting electrooptical characteristics using low switching voltages. Polymerizable LC creates a hollow structure inside the sandwich glass cell that keep nematics liquid crystal confined creating microdomains. Homogeneous and homeotropic alignments have been used to develop inverse switching mode LCPCs. Due to the double LC oriented structure, the outgoing scattered light from these devices is already polarized. The polarization axis coincides with LC molecules director, the alignment direction promoted. The novelties derived from the investigation presented here, new ultrafast inverse LCPC with polarized outgoing scattered light based on oriented nematic LC mixture, and an internationally patented security and authentication device based on nematics (doped with dichroic dye) oriented polymerizable LC.

Multiple sequence alignment correction using constraints

Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics

Cardiac motion estimation by joint alignment of tagged MRI sequences

Image registration has been proposed as an automatic method for recovering cardiac displacement fields from Tagged Magnetic Resonance Imaging (tMRI) sequences. Initially performed as a set of pairwise registrations, these techniques have evolved to the use of 3D+t deformation models, requiring metrics of joint image alignment (JA). However, only linear combinations of cost functions defined with respect to the first frame have been used. In this paper, we have applied k-Nearest Neighbors Graphs (kNNG) estimators of the -entropy (H ) to measure the joint similarity between frames, and to combine the information provided by different cardiac views in an unified metric. Experiments performed on six subjects showed a significantly higher accuracy (p < 0.05) with respect to a standard pairwise alignment (PA) approach in terms of mean positional error and variance with respect to manually placed landmarks. The developed method was used to study strains in patients with myocardial infarction, showing a consistency between strain, infarction location, and coronary occlusion. This paper also presentsan interesting clinical application of graph-based metric estimators, showing their value for solving practical problems found in medical imaging.

Extension schemes for the Alignment Model of English-Malayalam Statistical Machine Translator

In Statistical Machine Translation from English to Malayalam, an unseen English sentence is translated into its equivalent Malayalam sentence using statistical models. A parallel corpus of English-Malayalam is used in the training phase. Word to word alignments has to be set among the sentence pairs of the source and target language before subjecting them for training. This paper deals with certain techniques which can be adopted for improving the alignment model of SMT. Methods to incorporate the parts of speech information into the bilingual corpus has resulted in eliminating many of the insignificant alignments. Also identifying the name entities and cognates present in the sentence pairs has proved to be advantageous while setting up the alignments. Presence of Malayalam words with predictable translations has also contributed in reducing the insignificant alignments. Moreover, reduction of the unwanted alignments has brought in better training results. Experiments conducted on a sample corpus have generated reasonably good Malayalam translations and the results are verified with F measure, BLEU and WER evaluation metrics.

Techniques to Improve the word alignments in Statistical Machine Translation from English to Malayalam

In Statistical Machine Translation from English to Malayalam, an unseen English sentence is translated into its equivalent Malayalam translation using statistical models like translation model, language model and a decoder. A parallel corpus of English-Malayalam is used in the training phase. Word to word alignments has to be set up among the sentence pairs of the source and target language before subjecting them for training. This paper is deals with the techniques which can be adopted for improving the alignment model of SMT. Incorporating the parts of speech information into the bilingual corpus has eliminated many of the insignificant alignments. Also identifying the name entities and cognates present in the sentence pairs has proved to be advantageous while setting up the alignments. Moreover, reduction of the unwanted alignments has brought in better training results. Experiments conducted on a sample corpus have generated reasonably good Malayalam translations and the results are verified with F measure, BLEU and WER evaluation metrics

Assessing pragmatic interoperability for process alignment in collaborative working environment

This paper is an extension of our previous study on pragmatic interoperability assessment for process alignment. In this study, we conduct four case studies in industrial companies and hospitals in order to gather their viewpoints regarding the concerns when condensing process alignment in a collaborative working environment. Used techniques include interview, observation, and documentation. The collected results firstly are summarised into three layers based on our previous developed pragmatic assessment model, and then are transformed into the elements which constitutes the purposed method, and finally based on the summarised results we purpose a method for assessing pragmatic interoperability for process alignment in collaborative working environment. The method contains two parts: one gives all the elements of pragmatic interoperability that should be concerned when considering process alignment in collaborative working environment, and the other one is a supplementary method for dealing with technical concerns.

Alignment-based extraction of multiword expressions

Due to idiosyncrasies in their syntax, semantics or frequency, Multiword Expressions (MWEs) have received special attention from the NLP community, as the methods and techniques developed for the treatment of simplex words are not necessarily suitable for them. This is certainly the case for the automatic acquisition of MWEs from corpora. A lot of effort has been directed to the task of automatically identifying them, with considerable success. In this paper, we propose an approach for the identification of MWEs in a multilingual context, as a by-product of a word alignment process, that not only deals with the identification of possible MWE candidates, but also associates some multiword expressions with semantics. The results obtained indicate the feasibility and low costs in terms of tools and resources demanded by this approach, which could, for example, facilitate and speed up lexicographic work.

Techniques for measuring aerosol attenuation using the Central Laser Facility at the Pierre Auger Observatory

The Pierre Auger Observatory in Malargüe, Argentina, is designed to study the properties of ultra-high energy cosmic rays with energies above 1018 eV. It is a hybrid facility that employs a Fluorescence Detector to perform nearly calorimetric measurements of Extensive Air Shower energies. To obtain reliable calorimetric information from the FD, the atmospheric conditions at the observatory need to be continuously monitored during data acquisition. In particular, light attenuation due to aerosols is an important atmospheric correction. The aerosol concentration is highly variable, so that the aerosol attenuation needs to be evaluated hourly. We use light from the Central Laser Facility, located near the center of the observatory site, having an optical signature comparable to that of the highest energy showers detected by the FD. This paper presents two procedures developed to retrieve the aerosol attenuation of fluorescence light from CLF laser shots. Cross checks between the two methods demonstrate that results from both analyses are compatible, and that the uncertainties are well understood. The measurements of the aerosol attenuation provided by the two procedures are currently used at the Pierre Auger Observatory to reconstruct air shower data.

More accurate component alignment in navigated total knee arthroplasty has no clinical benefit at 5-year follow-up

Computer navigation in total knee arthroplasty is somewhat controversial. We have previously shown that femoral component positioning is more accurate with computed navigation than with conventional implantation techniques, but the clinical impact of this is unknown. We now report the 5-year outcome of our previously reported 2-year outcome study.

A Multiresolution Image Alignment Technique Based on Direct Methods for Pose Estimation of Aerial Vehicles

In this paper, we seek to expand the use of direct methods in real-time applications by proposing a vision-based strategy for pose estimation of aerial vehicles. The vast majority of approaches make use of features to estimate motion. Conversely, the strategy we propose is based on a MR (Multi-Resolution) implementation of an image registration technique (Inverse Compositional Image Alignment ICIA) using direct methods. An on-board camera in a downwards-looking configuration, and the assumption of planar scenes, are the bases of the algorithm. The motion between frames (rotation and translation) is recovered by decomposing the frame-to-frame homography obtained by the ICIA algorithm applied to a patch that covers around the 80% of the image. When the visual estimation is required (e.g. GPS drop-out), this motion is integrated with the previous known estimation of the vehicles' state, obtained from the on-board sensors (GPS/IMU), and the subsequent estimations are based only on the vision-based motion estimations. The proposed strategy is tested with real flight data in representative stages of a flight: cruise, landing, and take-off, being two of those stages considered critical: take-off and landing. The performance of the pose estimation strategy is analyzed by comparing it with the GPS/IMU estimations. Results show correlation between the visual estimation obtained with the MR-ICIA and the GPS/IMU data, that demonstrate that the visual estimation can be used to provide a good approximation of the vehicle's state when it is required (e.g. GPS drop-outs). In terms of performance, the proposed strategy is able to maintain an estimation of the vehicle's state for more than one minute, at real-time frame rates based, only on visual information.

Research on intermediate band solar cells and development of experimental techniques for their characterization under concentrated illumination

Abstract This work is a contribution to the research and development of the intermediate band solar cell (IBSC), a high efficiency photovoltaic concept that features the advantages of both low and high bandgap solar cells. The resemblance with a low bandgap solar cell comes from the fact that the IBSC hosts an electronic energy band -the intermediate band (IB)- within the semiconductor bandgap. This IB allows the collection of sub-bandgap energy photons by means of two-step photon absorption processes, from the valence band (VB) to the IB and from there to the conduction band (CB). The exploitation of these low energy photons implies a more efficient use of the solar spectrum. The resemblance of the IBSC with a high bandgap solar cell is related to the preservation of the voltage: the open-circuit voltage (VOC) of an IBSC is not limited by any of the sub-bandgaps (involving the IB), but only by the fundamental bandgap (defined from the VB to the CB). Nevertheless, the presence of the IB allows new paths for electronic recombination and the performance of the IBSC is degraded at 1 sun operation conditions. A theoretical argument is presented regarding the need for the use of concentrated illumination in order to circumvent the degradation of the voltage derived from the increase in the recombi¬nation. This theory is supported by the experimental verification carried out with our novel characterization technique consisting of the acquisition of photogenerated current (IL)-VOC pairs under low temperature and concentrated light. Besides, at this stage of the IBSC research, several new IB materials are being engineered and our novel character¬ization tool can be very useful to provide feedback on their capability to perform as real IBSCs, verifying or disregarding the fulfillment of the “voltage preservation” principle. An analytical model has also been developed to assess the potential of quantum-dot (QD)-IBSCs. It is based on the calculation of band alignment of III-V alloyed heterojunc-tions, the estimation of the confined energy levels in a QD and the calculation of the de¬tailed balance efficiency. Several potentially useful QD materials have been identified, such as InAs/AlxGa1-xAs, InAs/GaxIn1-xP, InAs1-yNy/AlAsxSb1-x or InAs1-zNz/Alx[GayIn1-y]1-xP. Finally, a model for the analysis of the series resistance of a concentrator solar cell has also been developed to design and fabricate IBSCs adapted to 1,000 suns. Resumen Este trabajo contribuye a la investigación y al desarrollo de la célula solar de banda intermedia (IBSC), un concepto fotovoltaico de alta eficiencia que auna las ventajas de una célula solar de bajo y de alto gap. La IBSC se parece a una célula solar de bajo gap (o banda prohibida) en que la IBSC alberga una banda de energía -la banda intermedia (IB)-en el seno de la banda prohibida. Esta IB permite colectar fotones de energía inferior a la banda prohibida por medio de procesos de absorción de fotones en dos pasos, de la banda de valencia (VB) a la IB y de allí a la banda de conducción (CB). El aprovechamiento de estos fotones de baja energía conlleva un empleo más eficiente del espectro solar. La semejanza antre la IBSC y una célula solar de alto gap está relacionada con la preservación del voltaje: la tensión de circuito abierto (Vbc) de una IBSC no está limitada por ninguna de las fracciones en las que la IB divide a la banda prohibida, sino que está únicamente limitada por el ancho de banda fundamental del semiconductor (definido entre VB y CB). No obstante, la presencia de la IB posibilita nuevos caminos de recombinación electrónica, lo cual degrada el rendimiento de la IBSC a 1 sol. Este trabajo argumenta de forma teórica la necesidad de emplear luz concentrada para evitar compensar el aumento de la recom¬binación de la IBSC y evitar la degradación del voltage. Lo anterior se ha verificado experimentalmente por medio de nuestra novedosa técnica de caracterización consistente en la adquisicin de pares de corriente fotogenerada (IL)-VOG en concentración y a baja temperatura. En esta etapa de la investigación, se están desarrollando nuevos materiales de IB y nuestra herramienta de caracterizacin está siendo empleada para realimentar el proceso de fabricación, comprobando si los materiales tienen capacidad para operar como verdaderas IBSCs por medio de la verificación del principio de preservación del voltaje. También se ha desarrollado un modelo analítico para evaluar el potencial de IBSCs de puntos cuánticos. Dicho modelo está basado en el cálculo del alineamiento de bandas de energía en heterouniones de aleaciones de materiales III-V, en la estimación de la energía de los niveles confinados en un QD y en el cálculo de la eficiencia de balance detallado. Este modelo ha permitido identificar varios materiales de QDs potencialmente útiles como InAs/AlxGai_xAs, InAs/GaxIni_xP, InAsi_yNy/AlAsxSbi_x ó InAsi_zNz/Alx[GayIni_y]i_xP. Finalmente, también se ha desarrollado un modelado teórico para el análisis de la resistencia serie de una célula solar de concentración. Gracias a dicho modelo se han diseñado y fabricado IBSCs adaptadas a 1.000 soles.

Methodology based on registration techniques for representing subjects and their deformations acquired from general purpose 3D sensors

In this thesis a methodology for representing 3D subjects and their deformations in adverse situations is studied. The study is focused in providing methods based on registration techniques to improve the data in situations where the sensor is working in the limit of its sensitivity. In order to do this, it is proposed two methods to overcome the problems which can difficult the process in these conditions. First a rigid registration based on model registration is presented, where the model of 3D planar markers is used. This model is estimated using a proposed method which improves its quality by taking into account prior knowledge of the marker. To study the deformations, it is proposed a framework to combine multiple spaces in a non-rigid registration technique. This proposal improves the quality of the alignment with a more robust matching process that makes use of all available input data. Moreover, this framework allows the registration of multiple spaces simultaneously providing a more general technique. Concretely, it is instantiated using colour and location in the matching process for 3D location registration.

A composite framework for the strategic alignment of information systems development

Information systems are corporate resources, therefore information systems development must be aligned with corporate strategy. This thesis proposes that effective strategic alignment of information systems requires information systems development, information systems planning and strategic management to be united. Literature in these areas is examined, breaching the academic boundaries which separate these areas, to contribute a synthesised approach to the strategic alignment of information systems development. Previous work in information systems planning has extended information systems development techniques, such as data modelling, into strategic planning activities, neglecting techniques of strategic management. Examination of strategic management in this thesis, identifies parallel trends in strategic management and information systems development; the premises of the learning school of strategic management are similar to those of soft systems approaches to information systems development. It is therefore proposed that strategic management can be supported by a soft systems approach. Strategic management tools and techniques frame individual views of a strategic situation; soft systems approaches can integrate these diverse views to explore the internal and external environments of an organisation. The information derived from strategic analysis justifies the need for an information system and provides a starting point for information systems development. This is demonstrated by a composite framework which enables each information system to be justified according to its direct contribution to corporate strategy. The proposed framework was developed through action research conducted in a number of organisations of varying types. This suggests that the framework can be widely used to support the strategic alignment of information systems development, thereby contributing to organisational success.