Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Propagation of DEM Varying Accuracy into Terrain-Based Analysis.

Análisis de precisión en modelos digitales de elevación globales. ABSTRACT: Terrain-Based Analysis results in derived products from an input DEM and these products are needed to perform various analyses. To efficiently use these products in decision-making, their accuracies must be estimated systematically. This paper proposes a procedure to assess the accuracy of these derived products, by calculating the accuracy of the slope dataset and its significance, taking as an input the accuracy of the DEM. Based on the output of previously published research on modeling the relative accuracy of a DEM, specifically ASTER and SRTM DEMs with Lebanon coverage as the area of study, analysis have showed that ASTER has a low significance in the majority of the area where only 2% of the modeled terrain has 50% or more significance. On the other hand, SRTM showed a better significance, where 37% of the modeled terrain has 50% or more significance. Statistical analysis deduced that the accuracy of the slope dataset, calculated on a cell-by-cell basis, is highly correlated to the accuracy of the input DEM. However, this correlation becomes lower between the slope accuracy and the slope significance, whereas it becomes much higher between the modeled slope and the slope significance.

Subjective QoE Analysis of HTTP Adaptive Streaming Applications

Actualmente la optimization de la calidad de experiencia (Quality of Experience- QoE) de HTTP Adaptive Streaming (HAS) de video recibe una atención creciente. Este incremento de interés proviene fundamentalmente de las carencias de las soluciones actuales HAS, que, al no ser QoE-driven, no incluyen la percepción de la calidad de los usuarios finales como una parte integral de la lógica de adaptación. Por lo tanto, la obtención de información de referencia fiable en QoE en HAS presenta retos importantes, ya que las metodologías de evaluación subjetiva de la calidad de vídeo propuestas en las normas actuales no son adecuadas para tratar con la variación temporal de la calidad que es consustancial de HAS. Esta tesis investiga la influencia de la adaptación dinámica en la calidad de la transmisión de vídeo considerando métodos de evaluación subjetiva. Tras un estudio exhaustivo del estado del arte en la evaluación subjetiva de QoE en HAS, se han resaltado los retos asociados y las líneas de investigación abiertas. Como resultado, se han seleccionado dos líneas principales de investigación: el análisis del impacto en la QoE de los parámetros de las técnicas de adaptación y la investigación de las metodologías de prueba subjetiva adecuada para evaluación de QoE en HAS. Se han llevado a cabo un conjunto de experimentos de laboratorio para investigar las cuestiones planteadas mediante la utilización de diferentes metodologáas para pruebas subjetivas. El análisis estadístico muestra que no son robustas todas las suposiciones y reivindicaciones de las referencias analizadas, en particular en lo que respecta al impacto en la QoE de la frecuencia de las variaciones de calidad, de las adaptaciones suaves o abruptas y de las oscilaciones de calidad. Por otra parte, nuestros resultados confirman la influencia de otros parámetros, como la longitud de los segmentos de vídeo y la amplitud de las oscilaciones de calidad. Los resultados también muestran que tomar en consideración las características objetivas de los contenidos puede ser beneficioso para la mejora de la QoE en HAS. Además, todos los resultados han sido validados mediante extensos análisis experimentales que han incluido estudio tanto en otros laboratorios como en crowdsourcing Por último, sobre los aspectos metodológicos de las pruebas subjetivas de QoE, se ha realizado la comparación entre los resultados experimentales obtenidos a partir de un método estandarizado basado en estímulos cortos (ACR) y un método semi continuo (desarrollado para la evaluación de secuencias prolongadas de vídeo). A pesar de algunas diferencias, el resultado de los análisis estadísticos no muestra ningún efecto significativo de la metodología de prueba. Asimismo, aunque se percibe la influencia de la presencia de audio en la evaluación de degradaciones del vídeo, no se han encontrado efectos estadísticamente significativos de dicha presencia. A partir de la ausencia de influencia del método de prueba y de la presencia de audio, se ha realizado un análisis adicional sobre el impacto de realizar comparaciones estadísticas múltiples en niveles estadísticos de importancia que aumentan la probabilidad de los errores de tipo-I (falsos positivos). Nuestros resultados muestran que, para obtener un efectos sólido en el análisis estadístico de los resultados subjetivos, es necesario aumentar el número de sujetos de las pruebas claramente por encima de los tamaños de muestras propuestos por las normas y recomendaciones actuales. ABSTRACT Optimizing the Quality of Experience (QoE) of HTTP adaptive video streaming (HAS) is receiving increasing attention nowadays. The growth of interest is mainly caused by the fact that current HAS solutions are not QoE-driven, i.e. end-user quality perception is not integral part of the adaptation logic. However, obtaining the necessary reliable ground truths on HAS QoE faces substantial challenges, since the subjective video quality assessment methodologies as proposed by current standards are not well-suited for dealing with the time-varying quality properties that are characteristic for HAS. This thesis investigates the influence of dynamic quality adaptation on the QoE of streaming video by means of subjective evaluation approaches. Based on a comprehensive survey of related work on subjective HAS QoE assessment, the related challenges and open research questions are highlighted and discussed. As a result, two main research directions are selected for further investigation: analysis of the QoE impact of different technical adaptation parameters, and investigation of testing methodologies suitable for HAS QoE evaluation. In order to investigate related research issues and questions, a set of laboratory experiments have been conducted using different subjective testing methodologies. Our statistical analysis demonstrates that not all assumptions and claims reported in the literature are robust, particularly as regards the QoE impact of switching frequency, smooth vs. abrupt switching, and quality oscillation. On the other hand, our results confirm the influence of some other parameters such as chunk length and switching amplitude on perceived quality. We also show that taking the objective characteristics of the content into account can be beneficial to improve the adaptation viewing experience. In addition, all aforementioned findings are validated by means of an extensive cross-experimental analysis that involves external laboratory and crowdsourcing studies. Finally, to address the methodological aspects of subjective QoE testing, a comparison between the experimental results obtained from a (short stimuli-based) ACR standardized method and a semi-continuous method (developed for assessment of long video sequences) has been performed. In spite of observation of some differences, the result of statistical analysis does not show any significant effect of testing methodology. Similarly, although the influence of audio presence on evaluation of video-related degradations is perceived, no statistically significant effect of audio presence could be found. Motivating by this finding (no effect of testing method and audio presence), a subsequent analysis has been performed investigating the impact of performing multiple statistical comparisons on statistical levels of significance which increase the likelihood of Type-I errors (false positives). Our results show that in order to obtain a strong effect from the statistical analysis of the subjective results, it is necessary to increase the number of test subjects well beyond the sample sizes proposed by current quality assessment standards and recommendations.

Analysis of the relation between the sequence and secondary and three-dimensional structures of immunoglobulin molecules.

Methods of structural and statistical analysis of the relation between the sequence and secondary and three-dimensional structures are developed. About 5000 secondary structures of immunoglobulin molecules from the Kabat data base were predicted. Two statistical analyses of amino acids reveal 47 universal positions in strands and loops. Eight universally conservative positions out of the 47 are singled out because they contain the same amino acid in > 90% of all chains. The remaining 39 positions, which we term universally alternative positions, were divided into five groups: hydrophobic, charged and polar, aromatic, hydrophilic, and Gly-Ala, corresponding to the residues that occupied them in almost all chains. The analysis of residue-residue contacts shows that the 47 universal positions can be distinguished by the number and types of contacts. The calculations of contact maps in the 29 antibody structures revealed that residues in 24 of these 47 positions have contacts only with residues of antiparallel beta-strands in the same beta-sheet and residues in the remaining 23 positions always have far-away contacts with residues from other beta-sheets as well. In addition, residues in 6 of the 47 universal positions are also involved in interactions with residues of the other variable or constant domains.

Serve analysis of professional players in beach volleyball

This study has been developed for the European Beach Volleyball Championship in 2005. The video-recorded analysis was held using Sportcode Pro v.8.5.2 software. The aim of study was to determine the types of serve used, depending on the time of the set in which they occur. Quantitative analysis with a sample of 10 players that make up 5 teams with a total of four meetings with a total of 327 serves analyzed. The serves were classified depending on the period which they occurred, the period being 1 (items 1 to 7), period 2 (from point 8 to 14) and period 3 (point 15 to 21). he statistical analysis was conducted using the statistical software SPSS 19, Chi-square test established significant differences between the different types of serve for period 1 and 2 (p<0.05), but no significant differences were established in the period 3 to floating serve and power jump (p>0.05). The results showed a decrease of using a serve with jump power at period 1 (89.7%) compared to the period 3 (27.3%), while the floating and floating serve jump respectively increase at period 1 (6.3% -4%) in the period 3 (23.4% -49.4%).

Analysis of the Kondo effect in ferromagnetic atomic-sized contacts

Atomic contacts made of ferromagnetic metals present zero-bias anomalies in the differential conductance due to the Kondo effect. These systems provide a unique opportunity to perform a statistical analysis of the Kondo parameters in nanostructures since a large number of contacts can be easily fabricated using break-junction techniques. The details of the atomic structure differ from one contact to another so a large number of different configurations can be statistically analyzed. Here we present such a statistical analysis of the Kondo effect in atomic contacts made from the ferromagnetic transition metals Ni, Co, and Fe. Our analysis shows clear differences between materials that can be understood by fundamental theoretical considerations. This combination of experiments and theory allows us to extract information about the origin and nature of the Kondo effect in these systems and to explore the influence of geometry and valence in the Kondo screening of atomic-sized nanostructures.

Analysis of physical and physiological requirements in soccer trainings in young soccer players (under -10 years)

The aim of this study is to analyse the physical and physiological factors in soccer training at different categories of training. The participants were 30 soccer players of 8-aside soccer in the under 10’s age group (9.93±0.25 years) who participated in the under 10 Provincial Tournament in Alicante. During training, the variables of covered distance, heart rate, speed (average and maximum values) as well as the methodology used and position were registered. After the statistical analysis and its related discussion, it was concluded that the players do not show differences in the covered total distance in relation to the category. Notwithstanding, there are differences with regards to speed and heart rate, which are caused by the greater physical development of the players in comparison to the under10’s age group category. Regarding the methodology employed, it is worth stressing that the coaches used, to a greater extend, the global method, followed by the mixed method.

The orchestration of modes and EFL audio-visual comprehension: A multimodal discourse analysis of vodcasts

This thesis explores the role of multimodality in language learners’ comprehension, and more specifically, the effects on students’ audio-visual comprehension when different orchestrations of modes appear in the visualization of vodcasts. Firstly, I describe the state of the art of its three main areas of concern, namely the evolution of meaning-making, Information and Communication Technology (ICT), and audio-visual comprehension. One of the most important contributions in the theoretical overview is the suggested integrative model of audio-visual comprehension, which attempts to explain how students process information received from different inputs. Secondly, I present a study based on the following research questions: ‘Which modes are orchestrated throughout the vodcasts?’, ‘Are there any multimodal ensembles that are more beneficial for students’ audio-visual comprehension?’, and ‘What are the students’ attitudes towards audio-visual (e.g., vodcasts) compared to traditional audio (e.g., audio tracks) comprehension activities?’. Along with these research questions, I have formulated two hypotheses: Audio-visual comprehension improves when there is a greater number of orchestrated modes, and students have a more positive attitude towards vodcasts than traditional audios when carrying out comprehension activities. The study includes a multimodal discourse analysis, audio-visual comprehension tests, and students’ questionnaires. The multimodal discourse analysis of two British Council’s language learning vodcasts, entitled English is GREAT and Camden Fashion, using ELAN as the multimodal annotation tool, shows that there are a variety of multimodal ensembles of two, three and four modes. The audio-visual comprehension tests were given to 40 Spanish students, learning English as a foreign language, after the visualization of vodcasts. These comprehension tests contain questions related to specific orchestrations of modes appearing in the vodcasts. The statistical analysis of the test results, using repeated-measures ANOVA, reveal that students obtain better audio-visual comprehension results when the multimodal ensembles are constituted by a greater number of orchestrated modes. Finally, the data compiled from the questionnaires, conclude that students have a more positive attitude towards vodcasts in comparison to traditional audio listenings. Results from the audio-visual comprehension tests and questionnaires prove the two hypotheses of this study.

Does immediate loading affect clinical and patient-centered outcomes of mandibular 2-unsplinted-implant overdenture? : a 2-year within-case analysis

Objective To provide 2-year clinical- and patient-oriented data with regard to mandibular overdenture assisted by 2 immediately loaded unsplinted implants. Material and methods In this pre-post design, Phase-I clinical trial, 18 edentate individuals (62.4 ± 7.7 years) received a new set of complete denture. Then, following standard procedures, 3 threaded implants (OsseoSpeed TX™, Dentsply Implants, Mölndal, Sweden) were placed in the mandible in each patient, and locator abutments (Zest Anchors LLC, Escondido, U.S.A.) were inserted on the right and left side implants. The midline implant served as a control for within-patient comparison. The immediate loading was conducted within 24 h of surgery. Data were collected at baseline (T0), 12 (T1) and 24 (T2) months after immediate loading. The clinical outcomes included implant survival rate, crestal bone level changes and implant stability. These criteria were assessed through clinical and radiographic examinations as well as resonance frequency analysis. Patient-centered outcomes included patient satisfaction and oral health-related quality of life measured using validated questionnaires. Brunner-Langer approach was used for statistical analysis. Results Implant survival rate for immediate loaded implants was 91.7% at 2-year follow-up. None of the unloaded implants failed. There was no statistically significant difference at baseline and follow-ups with regard to clinical outcomes between loaded and unloaded implants. Patient satisfaction and quality of life improved (p < 0.0001) from baseline to 2-year follow-up. Conclusion Immediate loading protocol did not negatively affect clinical outcomes, satisfaction and quality of life of patients wearing 2-unsplinted-implant mandibular overdenture for 2 years. This conclusion requires confirmation by randomized control trials. Clinical significance statement Mandibular overdenture assisted by two immediately-loaded unsplinted implants is successful treatment based on 2-year clinical and patient-based outcomes.

Does immediate loading affect clinical and patient-centered outcomes of mandibular 2-unsplinted-implant overdenture? : a 2-year within-case analysis

Objective To provide 2-year clinical- and patient-oriented data with regard to mandibular overdenture assisted by 2 immediately loaded unsplinted implants. Material and methods In this pre-post design, Phase-I clinical trial, 18 edentate individuals (62.4 ± 7.7 years) received a new set of complete denture. Then, following standard procedures, 3 threaded implants (OsseoSpeed TX™, Dentsply Implants, Mölndal, Sweden) were placed in the mandible in each patient, and locator abutments (Zest Anchors LLC, Escondido, U.S.A.) were inserted on the right and left side implants. The midline implant served as a control for within-patient comparison. The immediate loading was conducted within 24 h of surgery. Data were collected at baseline (T0), 12 (T1) and 24 (T2) months after immediate loading. The clinical outcomes included implant survival rate, crestal bone level changes and implant stability. These criteria were assessed through clinical and radiographic examinations as well as resonance frequency analysis. Patient-centered outcomes included patient satisfaction and oral health-related quality of life measured using validated questionnaires. Brunner-Langer approach was used for statistical analysis. Results Implant survival rate for immediate loaded implants was 91.7% at 2-year follow-up. None of the unloaded implants failed. There was no statistically significant difference at baseline and follow-ups with regard to clinical outcomes between loaded and unloaded implants. Patient satisfaction and quality of life improved (p < 0.0001) from baseline to 2-year follow-up. Conclusion Immediate loading protocol did not negatively affect clinical outcomes, satisfaction and quality of life of patients wearing 2-unsplinted-implant mandibular overdenture for 2 years. This conclusion requires confirmation by randomized control trials. Clinical significance statement Mandibular overdenture assisted by two immediately-loaded unsplinted implants is successful treatment based on 2-year clinical and patient-based outcomes.

Statistical models of accidents on interchange ramps and speed-change lanes.

Federal Highway Administration, Office of Safety and Traffic Operations, Washington, D.C.

Accident trend monitoring and exploratory analysis. Final report.

National Highway Traffic Safety Administration, National Center for Statistics and Analysis, Washington, D.C.

Statistical views of transportation safety.

Mode of access: Internet.

Data analysis /

"In any comprehensive research project, there are essentially five steps. First, one starts with a literature review with regard to a particular research question. Second, one seeks to develop a theory. Third, the research question is finalized, frequently in the form of a hypothesis to be tested. Fourth, data are collected. Fifth, the subject matter of this paper, the data are analyzed in order to come to a resolution of the research question. There are two general approaches to analyzing research data. If the data were gathered concerning a 'research question,' a description of the data may be sufficient. However, if the data were gathered to accept or reject a formal hypothesis, statistical analysis is usually in order. This paper briefly surveys the principal data analysis methodologies that are available."