Noninvasive referencing of intraocular tumors for external beam radiation therapy using optical coherence tomography: a proof of concept.

PURPOSE External beam radiation therapy is currently considered the most common treatment modality for intraocular tumors. Localization of the tumor and efficient compensation of tumor misalignment with respect to the radiation beam are crucial. According to the state of the art procedure, localization of the target volume is indirectly performed by the invasive surgical implantation of radiopaque clips or is limited to positioning the head using stereoscopic radiographies. This work represents a proof-of-concept for direct and noninvasive tumor referencing based on anterior eye topography acquired using optical coherence tomography (OCT). METHODS A prototype of a head-mounted device has been developed for automatic monitoring of tumor position and orientation in the isocentric reference frame for LINAC based treatment of intraocular tumors. Noninvasive tumor referencing is performed with six degrees of freedom based on anterior eye topography acquired using OCT and registration of a statistical eye model. The proposed prototype was tested based on enucleated pig eyes and registration accuracy was measured by comparison of the resulting transformation with tilt and torsion angles manually induced using a custom-made test bench. RESULTS Validation based on 12 enucleated pig eyes revealed an overall average registration error of 0.26 ± 0.08° in 87 ± 0.7 ms for tilting and 0.52 ± 0.03° in 94 ± 1.4 ms for torsion. Furthermore, dependency of sampling density on mean registration error was quantitatively assessed. CONCLUSIONS The tumor referencing method presented in combination with the statistical eye model introduced in the past has the potential to enable noninvasive treatment and may improve quality, efficacy, and flexibility of external beam radiotherapy of intraocular tumors.

A Bundle of Services Increased Ascertainment of Tuberculosis among HIV-Infected Individuals Enrolled in a HIV Cohort in Rural Sub-Saharan Africa.

OBJECTIVES To report on trends of tuberculosis ascertainment among HIV patients in a rural HIV cohort in Tanzania, and assessing the impact of a bundle of services implemented in December 2012, consisting of three components:(i)integration of HIV and tuberculosis services; (ii)GeneXpert for tuberculosis diagnosis; and (iii)electronic data collection. DESIGN Retrospective cohort study of patients enrolled in the Kilombero Ulanga Antiretroviral Cohort (KIULARCO), Tanzania.). METHODS HIV patients without prior history of tuberculosis enrolled in the KIULARCO cohort between 2005 and 2013 were included.Cox proportional hazard models were used to estimate rates and predictors of tuberculosis ascertainment. RESULTS Of 7114 HIV positive patients enrolled, 5123(72%) had no history of tuberculosis. Of these, 66% were female, median age was 38 years, median baseline CD4+ cell count was 243 cells/µl, and 43% had WHO clinical stage 3 or 4. During follow-up, 421 incident tuberculosis cases were notified with an estimated incidence of 3.6 per 100 person-years(p-y)[95% confidence interval(CI)3.26-3.97]. The incidence rate varied over time and increased significantly from 2.96 to 43.98 cases per 100 p-y after the introduction of the bundle of services in December 2012. Four independent predictors of tuberculosis ascertainment were identified:poor clinical condition at baseline (Hazard Ratio (HR) 3.89, 95% CI 2.87-5.28), WHO clinical stage 3 or 4 (HR 2.48, 95% CI 1.88-3.26), being antiretroviralnaïve (HR 2.97, 95% CI 2.25-3.94), and registration in 2013(HR 6.07, 95% CI 4.39-8.38). CONCLUSION The integration of tuberculosis and HIV services together with comprehensive electronic data collection and use of GeneXpert increased dramatically the ascertainment of tuberculosis in this rural African HIV cohort.

Malnutrition in the era of DRG

Malnutrition in hospital patients is of important medical and economic significance. The adverse consequences of malnutrition on quality of life and many more factors such as morbidity, mortality, tolerance of treatments and length of hospital stay are well documented in the medical literature. Nevertheless, the effects of malnutrition are still often underestimated and hence malnutrition is not recognised as a distinct diagnosis. Moreover, malnutrition is rarely documented in medical reports and often not adequately treated with adverse effects. The reason for this neglectfulness are diverse, e. g. inadequate training of doctors and nurses in clinical nutrition and lack of sensibilisation of the hospital staff for the problem of malnutrition. Therefore, a systematic screening for malnutrition is rarely undertaken in Swiss hospitals. The introduction of the Swiss-DRG system (DRG, diagnosis related groups) in January 2012 gave the chance to boost recording and to document malnutrition in a standardised way in the patient history, and to code precisely malnutrition as a distinct diagnosis. Moreover, this approach allowed to document the specific nutritional therapy. Here, we describe the way of documenting and coding malnutrition in the Swiss-DRG system and the medical and economic consequences of this procedure.

Brief Report: HIV Testing Among Pregnant Women Who Attend Antenatal Care in Malawi.

Malawi adopted the Option B+ strategy in 2011. Its success in reducing mother-to-child transmission depends on coverage and timing of HIV testing. We assessed HIV status ascertainment and its predictors during pregnancy. HIV status ascertainment was 82.3% (95% confidence interval: 80.2 to 85.9) in the pre-Option B+ period and 85.7% (95% confidence interval: 83.4 to 88.0) in the Option B+ period. Higher HIV ascertainment was independently associated with higher age, attending antenatal care more than once, and registration in 2010. The observed high variability of HIV ascertainment between sites (50.6%-97.7%) and over time suggests that HIV test kit shortages and insufficient numbers of staff posed major barriers to reducing mother-to-child transmission.

Investigating the potential of reported cattle mortality data in Switzerland for syndromic surveillance

Systems for the identification and registration of cattle have gradually been receiving attention for use in syndromic surveillance, a relatively recent approach for the early detection of infectious disease outbreaks. Real or near real-time monitoring of deaths or stillbirths reported to these systems offer an opportunity to detect temporal or spatial clusters of increased mortality that could be caused by an infectious disease epidemic. In Switzerland, such data are recorded in the "Tierverkehrsdatenbank" (TVD). To investigate the potential of the Swiss TVD for syndromic surveillance, 3 years of data (2009-2011) were assessed in terms of data quality, including timeliness of reporting and completeness of geographic data. Two time-series consisting of reported on-farm deaths and stillbirths were retrospectively analysed to define and quantify the temporal patterns that result from non-health related factors. Geographic data were almost always present in the TVD data; often at different spatial scales. On-farm deaths were reported to the database by farmers in a timely fashion; stillbirths were less timely. Timeliness and geographic coverage are two important features of disease surveillance systems, highlighting the suitability of the TVD for use in a syndromic surveillance system. Both time series exhibited different temporal patterns that were associated with non-health related factors. To avoid false positive signals, these patterns need to be removed from the data or accounted for in some way before applying aberration detection algorithms in real-time. Evaluating mortality data reported to systems for the identification and registration of cattle is of value for comparing national data systems and as a first step towards a European-wide early detection system for emerging and re-emerging cattle diseases.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

El ordenamiento territorial en zonas de montaña

El proyecto de investigación para el Ordenamiento Territorial del Valle de Lerma (Salta, Argentina), incluye tanto zonas de valle propiamente dicho como sectores altos (hasta la divisoria de cuencas – aproximadamente de 2000 msnm hacia E y 4500 msnm hacia O). Se plantea la necesidad de un diagnóstico socio-económico. El objetivo es una aproximación real al sistema, mediante la observación directa y la interacción con los pobladores locales. Interesa elaborar un modelo cognocitivo del escenario actual considerando las problemáticas y potencialidades asociadas a la calidad de vida, el uso del suelo y de los recursos naturales, las perspectivas de los pobladores locales y las tendencia de las actividades productivas. El fin último es llegar a elaborar propuestas que permitan la mejora de la calidad de vida y el desarrollo productivo, en un contexto de creatividad y respeto, si se pretende signar las bases para la “conservación" e impulso de estas áreas. La información secundaria disponible sobre las zonas altas es prácticamente inexistente, por lo cual se pretende efectuar salidas de campo a los sectores altos para la georeferenciación de recorridos, sitios de valor cultural y natural, accidentes geográficos, infraestructuras y comunidades dispersas, como así la observación y registro de problemáticas y potencialidades asociadas al uso de los recursos, visita a pobladores locales, entrevistas abiertas y participación en actividades cotidianas.

Terrain model of the Håkon Mosby Mud Volcano (10 m grid size)

The Håkon Mosby Mud Volcano is a natural laboratory to study geological, geochemical, and ecological processes related to deep-water mud volcanism. High resolution bathymetry of the Håkon Mosby Mud Volcano was recorded during RV Polarstern expedition ARK-XIX/3 utilizing the multibeam system Hydrosweep DS-2. Dense spacing of the survey lines and slow ship speed (5 knots) provided necessary point density to generate a regular 10 m grid. Generalization was applied to preserve and represent morphological structures appropriately. Contour lines were derived showing detailed topography at the centre of the Håkon Mosby Mud Volcano and generalized contours in the vicinity. We provide a brief introduction to the Håkon Mosby Mud Volcano area and describe in detail data recording and processing methods, as well as the morphology of the area. Accuracy assessment was made to evaluate the reliability of a 10 m resolution terrain model. Multibeam sidescan data were recorded along with depth measurements and show reflectivity variations from light grey values at the centre of the Håkon Mosby Mud Volcano to dark grey values (less reflective) at the surrounding moat.

Multi-microphone recordings (EigenMike32) inside a WFS system (Iosono) through Ambisonics techniques using Matlab

El audio multicanal ha avanzado a pasos agigantados en los últimos años, y no solo en las técnicas de reproducción, sino que en las de capitación también. Por eso en este proyecto se encuentran ambas cosas: un array microfónico, EigenMike32 de MH Acoustics, y un sistema de reproducción con tecnología Wave Field Synthesis, instalado Iosono en la Jade Höchscule Oldenburg. Para enlazar estos dos puntos de la cadena de audio se proponen dos tipos distintos de codificación: la reproducción de la toma horizontal del EigenMike32; y el 3er orden de Ambisonics (High Order Ambisonics, HOA), una técnica de codificación basada en Armónicos Esféricos mediante la cual se simula el campo acústico en vez de simular las distintas fuentes. Ambas se desarrollaron en el entorno Matlab y apoyadas por la colección de scripts de Isophonics llamada Spatial Audio Matlab Toolbox. Para probar éstas se llevaron a cabo una serie de test en los que se las comparó con las grabaciones realizadas a la vez con un Dummy Head, a la que se supone el método más aproximado a nuestro modo de escucha. Estas pruebas incluían otras grabaciones hechas con un Doble MS de Schoeps que se explican en el proyecto “Sally”. La forma de realizar éstas fue, una batería de 4 audios repetida 4 veces para cada una de las situaciones garbadas (una conversación, una clase, una calle y un comedor universitario). Los resultados fueron inesperados, ya que la codificación del tercer orden de HOA quedo por debajo de la valoración Buena, posiblemente debido a la introducción de material hecho para un array tridimensional dentro de uno de 2 dimensiones. Por el otro lado, la codificación que consistía en extraer los micrófonos del plano horizontal se mantuvo en el nivel de Buena en todas las situaciones. Se concluye que HOA debe seguir siendo probado con mayores conocimientos sobre Armónicos Esféricos; mientras que el otro codificador, mucho más sencillo, puede ser usado para situaciones sin mucha complejidad en cuanto a espacialidad. In the last years the multichannel audio has increased in leaps and bounds and not only in the playback techniques, but also in the recording ones. That is the reason of both things being in this project: a microphone array, EigenMike32 from MH Acoustics; and a playback system with Wave Field Synthesis technology, installed by Iosono in Jade Höchscule Oldenburg. To link these two points of the audio chain, 2 different kinds of codification are proposed: the reproduction of the EigenMike32´s horizontal take, and the Ambisonics´ third order (High Order Ambisonics, HOA), a codification technique based in Spherical Harmonics through which the acoustic field is simulated instead of the different sound sources. Both have been developed inside Matlab´s environment and supported by the Isophonics´ scripts collection called Spatial Audio Matlab Toolbox. To test these, a serial of tests were made in which they were compared with recordings made at the time by a Dummy Head, which is supposed to be the closest method to our hearing way. These tests included other recording and codifications made by a Double MS (DMS) from Schoeps which are explained in the project named “3D audio rendering through Ambisonics techniques: from multi-microphone recordings (DMS Schoeps) to a WFS system, through Matlab”. The way to perform the tests was, a collection made of 4 audios repeated 4 times for each recorded situation (a chat, a class, a street and college canteen or Mensa). The results were unexpected, because the HOA´s third order stood under the Well valuation, possibly caused by introducing material made for a tridimensional array inside one made only by 2 dimensions. On the other hand, the codification that consisted of extracting the horizontal plane microphones kept the Well valuation in all the situations. It is concluded that HOA should keep being tested with larger knowledge about Spherical Harmonics; while the other coder, quite simpler, can be used for situations without a lot of complexity with regards to spatiality.

Diseño, optimización y análisis de sistemas basados en técnicas láser, para el modelado geométrico, registro y documentación, aplicados a entidades de interés patrimonial.

El objetivo de la presente tesis doctoral es el desarrollo e implementación de un sistema para mejorar la metodología de extracción de la información geométrica necesaria asociada a los procesos de documentación de entidades de interés patrimonial, a partir de la información proporcionada por el empleo de sensores láser, tanto aéreos como terrestres. Para ello, inicialmente se realiza una presentación y justificación de los antecedentes y la problemática en el registro de información geométrica para el patrimonio, detallando todos aquellos sistemas de registro y análisis de la información geométrica utilizados en la actualidad. Este análisis permitirá realizar la comparación con los sistemas de registro basados en técnicas láser, aportando sugerencias de utilización para cada caso concreto. Posteriormente, se detallan los sistemas de registro basados en técnicas láser, comenzando por los sensores aerotransportados y concluyendo con el análisis pormenorizado de los sensores terrestres, tanto en su aplicación en modo estático como móvil. Se exponen las características técnicas y funcionamiento de cada uno de ellos, así como los ámbitos de aplicación y productos generados. Se analizan las fuentes de error que determinan la precisión que puede alcanzar el sistema. Tras la exposición de las características de los sistemas LiDAR, se detallan los procesos a realizar con los datos extraídos para poder generar la información necesaria para los diferentes tipos de objetos analizados. En esta exposición, se hace hincapié en los posibles riesgos que pueden ocurrir en algunas fases delicadas y se analizarán los diferentes algoritmos de filtrado y clasificación de los puntos, fundamentales en el procesamiento de la información LiDAR. Seguidamente, se propone una alternativa para optimizar los modelos de procesamiento existentes, basándose en el desarrollo de algoritmos nuevos y herramientas informáticas que mejoran el rendimiento en la gestión de la información LiDAR. En la implementación, se han tenido en cuenta características y necesidades particulares de la documentación de entidades de interés patrimonial, así como los diferentes ámbitos de utilización del LiDAR, tanto aéreo como terrestre. El resultado es un organigrama de las tareas a realizar desde la nube de puntos LiDAR hasta el cálculo de los modelos digitales del terreno y de superficies. Para llevar a cabo esta propuesta, se han desarrollado hasta 19 algoritmos diferentes que comprenden implementaciones para el modelado en 2.5D y 3D, visualización, edición, filtrado y clasificación de datos LiDAR, incorporación de información de sensores pasivos y cálculo de mapas derivados, tanto raster como vectoriales, como pueden ser mapas de curvas de nivel y ortofotos. Finalmente, para dar validez y consistencia a los desarrollos propuestos, se han realizado ensayos en diferentes escenarios posibles en un proceso de documentación del patrimonio y que abarcan desde proyectos con sensores aerotransportados, proyectos con sensores terrestres estáticos a media y corta distancia, así como un proyecto con un sensor terrestre móvil. Estos ensayos han permitido definir los diferentes parámetros necesarios para el adecuado funcionamiento de los algoritmos propuestos. Asimismo, se han realizado pruebas objetivas expuestas por la ISPRS para la evaluación y comparación del funcionamiento de algoritmos de clasificación LiDAR. Estas pruebas han permitido extraer datos de rendimiento y efectividad del algoritmo de clasificación presentado, permitiendo su comparación con otros algoritmos de prestigio existentes. Los resultados obtenidos han constatado el funcionamiento satisfactorio de la herramienta. Esta tesis está enmarcada dentro del proyecto Consolider-Ingenio 2010: “Programa de investigación en tecnologías para la valoración y conservación del patrimonio cultural” (ref. CSD2007-00058) realizado por el Consejo Superior de Investigaciones Científicas y la Universidad Politécnica de Madrid. ABSTRACT: The goal of this thesis is the design, development and implementation of a system to improve the extraction of useful geometric information in Heritage documentation processes. This system is based on information provided by laser sensors, both aerial and terrestrial. Firstly, a presentation of recording geometric information for Heritage processes is done. Then, a justification of the background and problems is done too. Here, current systems for recording and analyzing the geometric information are studied. This analysis will perform the comparison with the laser system techniques, providing suggestions of use for each specific case. Next, recording systems based on laser techniques are detailed. This study starts with airborne sensors and ends with terrestrial ones, both in static and mobile application. The technical characteristics and operation of each of them are described, as well as the areas of application and generated products. Error sources are also analyzed in order to know the precision this technology can achieve. Following the presentation of the LiDAR system characteristics, the processes to generate the required information for different types of scanned objects are described; the emphasis is on the potential risks that some steps can produce. Moreover different filtering and classification algorithms are analyzed, because of their main role in LiDAR processing. Then, an alternative to optimize existing processing models is proposed. It is based on the development of new algorithms and tools that improve the performance in LiDAR data management. In this implementation, characteristics and needs of the documentation of Heritage entities have been taken into account. Besides, different areas of use of LiDAR are considered, both air and terrestrial. The result is a flowchart of tasks from the LiDAR point cloud to the calculation of digital terrain models and digital surface models. Up to 19 different algorithms have been developed to implement this proposal. These algorithms include implementations for 2.5D and 3D modeling, viewing, editing, filtering and classification of LiDAR data, incorporating information from passive sensors and calculation of derived maps, both raster and vector, such as contour maps and orthophotos. Finally, in order to validate and give consistency to the proposed developments, tests in different cases have been executed. These tests have been selected to cover different possible scenarios in the Heritage documentation process. They include from projects with airborne sensors, static terrestrial sensors (medium and short distances) to mobile terrestrial sensor projects. These tests have helped to define the different parameters necessary for the appropriate functioning of the proposed algorithms. Furthermore, proposed tests from ISPRS have been tested. These tests have allowed evaluating the LiDAR classification algorithm performance and comparing it to others. Therefore, they have made feasible to obtain performance data and effectiveness of the developed classification algorithm. The results have confirmed the reliability of the tool. This investigation is framed within Consolider-Ingenio 2010 project titled “Programa de investigación en tecnologías para la valoración y conservación del patrimonio cultural” (ref. CSD2007-00058) by Consejo Superior de Investigaciones Científicas and Universidad Politécnica de Madrid.

Tecnología de registro y reproducción sonora para entornos de realidad virtual

Este proyecto de fin de carrera tiene como objetivo obtener una visión detallada de los sistemas y tecnologías de grabación y reproducción utilizadas para aplicaciones de audio 3D y entornos de realidad virtual, analizando las diferentes alternativas existentes, su funcionamiento, características, detalles técnicos y sus ámbitos de aplicación. Como punto de partida se estudiará la teoría psicoacústica y la localización de fuentes sonoras en el espacio, base para el estudio de los sistemas de audio 3D. Se estudiará tanto la espacialización sonora en un espacio real y la espacialización virtual (simulación mediante procesado de información de la localización de fuentes sonoras), en los que intervienen algunos fenómenos acústicos y psicoacústicos como ITD, o diferencia de tiempo que existe entre una señal acústica que llega a los pabellones auditivos, la ILD, o diferencia de intensidad o amplitud que hay entre la señal que llega a los pabellones auditivos y la localización espacial mediante otra serie de mecanismos biaurales. Tras una visión general de la teoría psicoacústica y la espacialización sonora, se analizarán con detalle los elementos de grabación y reproducción existentes para audio 3D. Concretamente, a lo largo del proyecto se profundizará en el funcionamiento del sistema estéreo, caracterizado por el posicionamiento sonoro mediante la utilización de dos canales; del sistema biaural, caracterizado por reconstruir campos sonoros mediante el uso de las HRTF; de los sistemas multicanal, detallando gran parte de las alternativas y configuraciones existentes; del sistema Ambiophonics, caracterizado por implementar filtros de cruce; del sistema Ambisonics, y sus diferentes formatos y técnicas de codificación y decodificación; y del sistema Wavefield Synthesis, caracterizado por recrear ambientes sonoros en grandes espacios. ABSTRACT This project aims to get a detailed view of recording and reproducing systems and technologies used to 3D audio applications and virtual reality environments, analyzing the different alternatives available, their functioning, features, technical details and their different scopes of applications. As a starting point, will be studied the psychoacoustic theory and the localization of sound sources in space, basis for the 3D audio study. Will be studied both the spacialization of sound sources in real space as virtual spatialization of sound sources (simulation by information processing of localization of sound sources), in which involves some acoustic and psychoacoustic phenomena like ITD (or the Interaural time difference), the ILD, (or the Interaural Level Difference) and spatial localization by another set of binaural mechanisms. After a general overview of the psychoacoustics theory and the sound spatialization, will be analyzed in detail existing methods of recording and reproducing for 3D audio. Specifically, during the project will analyze the characteristics of the stereo systems, characterized by sound positioning using two channels; the binaural systems, characterized by reconstructing sound fields by using the HRTF; the multichannel systems, detailing many of the existing alternatives and configurations; the Ambiophonics system, which is characterized by implementing crosstalk elimination techniques; the Ambiosonics system, and its various formats and encoding and decoding techniques; and the Wavefield Synthesis system, characterized by recreate soundscapes in large spaces.

Interfaz gráfica y fase de pruebas de software de vídeo forense (Sistema de codificación DV)

El presente proyecto fin de carrera, realizado por el ingeniero técnico en telecomunicaciones Pedro M. Matamala Lucas, es la fase final de desarrollo de un proyecto de mayor magnitud correspondiente al software de vídeo forense SAVID. El propósito del proyecto en su totalidad es la creación de una herramienta informática capacitada para realizar el análisis de ficheros de vídeo, codificados y comprimidos por el sistema DV –Digital Video-. El objetivo del análisis, es aportar información acerca de si la cinta magnética presenta indicios de haber sido manipulada con una edición posterior a su grabación original, además, de mostrar al usuario otros datos de interés como las especificaciones técnicas de la señal de vídeo y audio. Por lo tanto, se facilitará al usuario, analista de vídeo forense, información que le ayude a valorar la originalidad del contenido del soporte que es sujeto del análisis. El objetivo específico de esta fase final, es la creación de la interfaz de usuario del software, que informa tanto del código binario de los sectores significativos, como de su interpretación tras el análisis. También permitirá al usuario el reporte de los resultados, además de otras funcionalidades que le permitan la navegación por los sectores del código que han sido modificados como efecto colateral de la edición de la cinta magnética original. Otro objetivo importante del proyecto ha sido la investigación de metodologías y técnicas de desarrollo de software para su posterior implementación, buscando con esto, una mayor eficiencia en la gestión del tiempo y una mayor calidad de software con el fin de garantizar su evolución y sostenibilidad en el futuro. Se ha hecho hincapié en las metodologías ágiles que han ido ganando relevancia en el sector de las tecnologías de la información en las últimas décadas, sustituyendo a metodologías clásicas como el desarrollo en cascada. Su flexibilidad durante el ciclo de vida del software, permite obtener mejores resultados cuando las especificaciones no están del todo definidas, ajustándose de este modo a las condiciones del proyecto. Resumiendo las especificaciones técnicas del software, C++ es el lenguaje de programación orientado a objetos con el que se ha desarrollado, utilizándose la tecnología MFC -Microsoft Foundation Classes- para la implementación. Es un proyecto MFC de tipo cuadro de dialogo,creado, compilado y publicado, con la herramienta de desarrollo integrado Microsoft Visual Studio 2010. La arquitectura con la que se ha estructurado es la arquetípica de tres capas, compuesta por la interfaz de usuario, capa de negocio y capa de acceso a datos. Se ha visto necesario configurar el proyecto con compatibilidad con CLR –Common Languages Runtime- para poder implementar la funcionalidad de creación de reportes. Acompañando a la aplicación informática, se presenta la memoria del proyecto y sus anexos correspondientes a los documentos EDRF –Especificaciones Detalladas de Requisitos funcionales-, EIU –Especificaciones de Interfaz de Usuario , DT -Diseño Técnico- y Guía de Usuario. SUMMARY. This dissertation, carried out by the telecommunications engineer Pedro M. Matamala Lucas, is in its final stage and is part of a larger project for the software of forensic video called SAVID. The purpose of the entire project is the creation of a software tool capable of analyzing video files that are coded and compressed by the DV -Digital Video- System. The objective of the analysis is to provide information on whether the magnetic tape shows signs of having been tampered with after the editing of the original recording, and also to show the user other relevant data and technical specifications of the video signal and audio. Therefore the user, forensic video analyst, will have information to help assess the originality of the content of the media that is subject to analysis. The specific objective of this final phase is the creation of the user interface of the software that provides information about the binary code of the significant sectors and also its interpretation after analysis. It will also allow the user to report the results, and other features that will allow browsing through the sections of the code that have been modified as a secondary effect of the original magnetic tape being tampered. Another important objective of the project is the investigation of methodologies and software development techniques to be used in deployment, with the aim of greater efficiency in time management and enhanced software quality in order to ensure its development and maintenance in the future. Agile methodologies, which have become important in the field of information technology in recent decades, have been used during the execution of the project, replacing classical methodologies such as Waterfall Development. The flexibility, as the result of using by agile methodologies, during the software life cycle, produces better results when the specifications are not fully defined, thus conforming to the initial conditions of the project. Summarizing the software technical specifications, C + + the programming language – which is object oriented and has been developed using technology MFC- Microsoft Foundation Classes for implementation. It is a project type dialog box, created, compiled and released with the integrated development tool Microsoft Visual Studio 2010. The architecture is structured in three layers: the user interface, business layer and data access layer. It has been necessary to configure the project with the support CLR -Common Languages Runtime – in order to implement the reporting functionality. The software application is submitted with the project report and its annexes to the following documents: Functional Requirements Specifications - Detailed User Interface Specifications, Technical Design and User Guide.

El sistema de grabación y reproducción sonora ambiofónico

Este proyecto fin de carrera trata del sistema de grabación y reproducción sonora ambiofónico, destacar que este sistema y la tecnología que emplea es de dominio público. La ambiofonía se basa en un amalgama de investigaciones recientes y de los ya bien sabidos principios psicoacústicos y binaurales. Estos avances han expandido nuevas fronteras en lo concerniente a la grabación y reproducción de audio, así como de presentar al oyente un campo sonoro a la entrada de sus oídos lo más parecido posible al campo sonoro al que se expondría al oyente en el momento y lugar de la toma de sonido, es decir, reconstruye un campo sonora binaural. Este sistema ha podido desarrollarse, de una manera bastante satisfactoria, gracias a todos los estudios y textos anteriores en materia de psicoacústica y del mecanismo de escucha humano. Otro factor gracias al cual es posible y asequible, tanto el desarrollo como el disfrute de esta tecnología, es el hecho que en nuestros días es muy económico disponer de ordenadores lo suficientemente potentes y rápidos para realizar el procesado de señales que se requiere de una manera bastante rápida. Los desarrolladores de dicha tecnología han publicado diversos documentos y archivos descargables de la red con aplicaciones para la implementación de sistemas ambiofónicos de manera gratuita para uso privado. El sistema ambiofónico se basa en la combinación de factores psicoacústicos ignorados o subestimados y lo ya sabido sobre las propiedades acústicas de salas, tanto de salas en las que tienen lugar las ejecuciones musicales (auditorios, teatros, salas de conciertos...), como de salas de escucha (salones de domicilios, controles de estudios...). En la parte práctica del proyecto se van a realizar una serie de grabaciones musicales empleando tanto técnicas estereofónicas tradicionales como ambiofónicas de grabación con el fin de describir y comparar ambas técnicas microfónicas. También servirá para estudiar hasta que punto es favorable subjetivamente para el oyente el hecho de realizar la toma de sonido teniendo en cuenta las propiedades del sistema de reproducción ambiofónico. Esta comparación nos dará una idea de hasta donde se puede llegar, en cuanto a sensación de realidad para el oyente, al tener en cuenta durante el proceso de grabación efectos como la respuesta del pabellón auditivo del oyente, la cual es única, y que posteriormente la diafonía interaural va a ser cancelada mediante un procesado digital de señal. ABSTRACT. This final project is about the ambiophonic recording and playback system, note that this system and the technology it uses is of public domain. Ambiophonics is based on an amalgam of recent research and to the well known and binaural psychoacoustic principles. These advances have expanded new frontiers with regard to the audio recording and playback, as well as to present the listener a sound field at the entrance of their ears as close as possible to the sound field that would the listener be exposed to at the time and place of the mucial interpretation, so we can say that ambiophonics reconstructs a binaural sound field . This system has been developed, in a fairly satisfactory way, thanks to all the studies and previous texts on psychoacoustics and human listening mechanism. Another factor by which it is possible and affordable, both the development and the enjoyment of this technology, is the fact that in our days is inexpensive to usres to own computers that are powerful and fast enough to perform the signal processing that is required in a short time. The developers of this technology have published several documents and downloadable files on the network with applications for ambiophonics system implementation for free. Ambiophonics is based on a combination of factors ignored or underestimated psychoacousticly and what is already known about the acoustic properties of rooms, including rooms where musical performances take place (auditoriums, theaters, concert halls...), and listening rooms (concet halls, studios controls...). In the practical part of the project will be making a series of musical recordings using both traditional stereo recording techniques and recording techiniques compatible with ambiophonics in order to describe and compare both recording techniques. It will also examine to what extent is subjectively favorable for the listener the fact of considering the playback system properties of ambiophonics during the recording stage. This comparison will give us an idea of how far can we get, in terms of sense of reality to the listener, keeping in mind during the recording process the effects introduced by the response of the ear of the listener, which is unique, and that the subsequently interaural crosstalk will be canceled by a digital signal processing.

Simulation-based evaluation of susceptibility distortion correction methods in diffusion MRI for connectivity analysis

Connectivity analysis on diffusion MRI data of the whole-brain suffers from distortions caused by the standard echo-planar imaging acquisition strategies. These images show characteristic geometrical deformations and signal destruction that are an important drawback limiting the success of tractography algorithms. Several retrospective correction techniques are readily available. In this work, we use a digital phantom designed for the evaluation of connectivity pipelines. We subject the phantom to a “theoretically correct” and plausible deformation that resembles the artifact under investigation. We correct data back, with three standard methodologies (namely fieldmap-based, reversed encoding-based, and registration- based). Finally, we rank the methods based on their geometrical accuracy, the dropout compensation, and their impact on the resulting connectivity matrices.

Nuevos métodos y herramientas para la creación y utilización de recursos multimedia en la educación

La educación y los entornos educativos están en constante evolución. Tanto alumnos como educadores cambian de hábitos, de maneras de aprender, de gustos, de dispositivos que manejan y de aplicaciones que usan regularmente entre otras cosas. Todos estos cambios vienen acompañados y fomentados en gran medida por la evolución paralela que experimenta la tecnología, tanto software en los programas utilizados, como hardware en los dispositivos y capacidades de éstos. La educación debe también adaptarse a estos cambios, tanto personales como tecnológicos y sacar el mayor provecho de ellos. El uso de Sistemas de Gestión del Aprendizaje está muy extendido en todos los centros educativos. Estos sistemas poseen un gran número de características y funcionalidades que permiten desde la aplicación de un modelo didáctico totalmente tradicional en el que el profesor imparte un contenido y los alumnos lo reciben a uno totalmente innovador en el que ocurren procesos totalmente diferentes. Por otro lado, el potencial que ofrecen los recursos multimedia no ha sido completamente aprovechado en la educación y supone una gran oportunidad. Esta tesis doctoral propone un conjunto de métodos y herramientas para la creación y el uso de recursos multimedia en la educación. Para ello el desarrollo de esta tesis parte de la definición de un modelo didáctico social, colaborativo y centrado en el alumno que servirá de hilo conductor y que integrará los diferentes y métodos y herramientas estudiados y desarrollados. En un primer paso se identifican varias herramientas y métodos para el aula, tales son la grabación de clases, donde se crea y posteriormente se mejora un carrito portátil de grabación que da muy buen resultado, las herramientas de grabación de screencast y la videoconferencia. Estas herramientas además se integran en una plataforma colaborativa dando lugar a una arquitectura completa y escalable que permite la realización de dichas actividades y la interconexión sencilla con el Sistema de Gestión del Aprendizaje. A continuación y ya en un entorno totalmente online se desarrolla una nueva plataforma de e-learning llamada Virtual Science Hub (ViSH) que consta de cuatro funcionalidades principales, red social, videoconferencia, repositorio educativo y herramienta de autor. En esta plataforma se aplicaron técnicas de recomendación proactiva tanto de recursos educativos como de otros usuarios similares. Por último se validó el modelo educativo completo usando algunas de las herramientas identificadas y desarrolladas en dos escenarios diferentes con gran éxito. Finalmente, esta tesis discute las conclusiones obtenidas a lo largo de la extensa investigación llevada a cabo y que ha propiciado la consecución de una buena base teórica y práctica para la creación de herramientas y métodos para la generación y el uso de recursos multimedia en la educación. ABSTRACT Education and learning environments are constantly evolving. Students and educators change the things their habits, their ways of learning, the things they like or the devices and applications that they use regularly among other things. All these changes are accompanied and fostered by the parallel evolution that technology experiences, both in the software programs used as in the hardware and capabilities of these devices. Education must also adapt to these changes, both personal and technological and get the most out of them. Learning Management Systems are widely used in all educational centers. These systems have a large number of features and functionalities. They allow from the implementation of a traditional teaching model in which the teacher gives content and students receive it to one absolutely innovative teaching model where totally different processes occur. Furthermore, the potential of multimedia resources has not been fully exploited in education and can be a great opportunity. This thesis proposes a set of methods and tools for the creation and use of multimedia in education. The development of this thesis starts with the definition of a social, collaborative and learner-centered model, that serves as a common thread and that integrates different tools and methods studied and developed. In a first step, several tools and methods for the classroom are identified, such as recording, where a portable kit is created and then improved giving very good results, screencast recording and videoconferencing. These tools also are integrated into a collaborative platform resulting in a complete, scalable architecture that enables the execution of such activities and a simple interconnection with the Learning Management System. In an fully online environment a new e-learning platform called Virtual Science Hub (ViSH) is created. It consists of four main features that combine and complement each other, social network, videoconferencing, educational repository and authoring tool. In this platform proactive recommendation of both educational resources and similar users is applied. In a last step the entire educational model using some of the tools identified and developed is successfully validated in two different scenarios. Finally, this thesis discusses the findings obtained during the extensive research carried out and has led to the achievement of a good theoretical and practical basis for the development of tools and methods for the generation and use of multimedia in education.