Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

¿Esperando a los bárbaros? : la invención del (nos) otro (s) en la literatura de J. M. Coetzee

J. M. Coetzee es uno de los más importantes escritores sudafricanos. Ximena Picallo Visconti contextualiza al autor y sus obras en el marco de un cambio político cuyos basamentos fueron el postapartheid sudafricano y la desarticulación de un discurso dominante sedimentado durante mucho tiempo. En Sudáfrica, los procesos de identificación están plagados de intersticios y negociaciones (muchas veces dispares) en la búsqueda y construcción de significados (Picallo Visconti, 2007). La mirada de Coetzee nos impulsa como lectores a un proceso de deconstrucción y de cuestionamiento constante, superando las construcciones ancladas del eurocentrismo ejercidas por la práctica del colonialismo y por el sistema segregacionista del apartheid. Por ello, este trabajo indagará sobre la mirada del autor, intentando acercar algunas lógicas de su obra respecto de la invención de un "Otro". Se trabajará sobre la novela Esperando a los bárbaros, en la que otro y espacio se tensionan para poner al lector en una disyuntiva superadora, en la cual quizás nosotros (el imperio) seamos los que nos encontramos fuera del muro.

¿Esperando a los bárbaros? : la invención del (nos) otro (s) en la literatura de J. M. Coetzee

J. M. Coetzee es uno de los más importantes escritores sudafricanos. Ximena Picallo Visconti contextualiza al autor y sus obras en el marco de un cambio político cuyos basamentos fueron el postapartheid sudafricano y la desarticulación de un discurso dominante sedimentado durante mucho tiempo. En Sudáfrica, los procesos de identificación están plagados de intersticios y negociaciones (muchas veces dispares) en la búsqueda y construcción de significados (Picallo Visconti, 2007). La mirada de Coetzee nos impulsa como lectores a un proceso de deconstrucción y de cuestionamiento constante, superando las construcciones ancladas del eurocentrismo ejercidas por la práctica del colonialismo y por el sistema segregacionista del apartheid. Por ello, este trabajo indagará sobre la mirada del autor, intentando acercar algunas lógicas de su obra respecto de la invención de un "Otro". Se trabajará sobre la novela Esperando a los bárbaros, en la que otro y espacio se tensionan para poner al lector en una disyuntiva superadora, en la cual quizás nosotros (el imperio) seamos los que nos encontramos fuera del muro.

RDA and Linked Data: A New Way to Look at the Henson Collection

In 2005, the University of Maryland acquired over 70 digital videos spanning 35 years of Jim Henson’s groundbreaking work in television and film. To support in-house discovery and use, the collection was cataloged in detail using AACR2 and MARC21, and a web-based finding aid was also created. In the past year, I created an "r-ball" (a linked data set described using RDA) of these same resources. The presentation will compare and contrast these three ways of accessing the Jim Henson Works collection, with insights gleaned from providing resource discovery using RIMMF (RDA in Many Metadata Formats).

Paul Perny y el aprendizaje de la lengua china : estudio del Dictionnaire français-latin-chinois de la langue mandarine parlée como parte de una obra didáctica

This paper defends the idea that the Dictionnaire français-latin-chinois de la langue mandarine parlée (1869), written by French clergyman Paul Perny, represents a groundbreaking work within the French to Chinese multilingual lexicography based on its strong communicative stance. It outlines the relationship between Perny’s work and the sinological tradition initiated by the Jesuits in China, and further analyzes the dictionary’s organizational structure, including the nature of its lexical inventory. It is noteworthy that this dictionary features a large number of terms belonging to the Catholic religion, even though it is possible to identify a significant and systematic presence of vocabulary specific to pagan Chinese tradition. The Dictionnaire français-latin-chinois de la langue mandarine parlée also stands out for including the vocabulary of modern Chinese along with numerous expressions and terms related to Chinese culture which enable a closer understanding of the Chinese cultural universe.

Las vanguardias artísticas del siglo XX y su contribución teórica en la definición exhibicionista de la naturaleza del cine

A pesar de que las vanguardias artísticas de principios de siglo constituyen un grupo de movimientos heterogéneo coinciden en un ideal común: la ruptura del estatus del arte en la sociedad burguesa. El desplazamiento del sujeto del centro del proceso creador y la aparición de un nuevo sistema de representación basado en la perspectiva múltiple harán que el cine se sitúe en el punto de mira de distintas propuestas rupturistas como el cubismo, el futurismo o el dadaísmo. El objetivo del presente texto es destacar las aportaciones de los movimientos de vanguardia emergentes durante las primeras décadas del siglo XX en la fragua de conceptos teóricos capaces de dotar al cine de un estatus discursivo basado en la forma y la construcción al que denominaremos exhibicionista, que se opone al de su consideración como cine clásico supeditado a suceder a la literatura decimonónica en su misión narrativa

On making web accessibility more accessible: strategy and tools for social good

The world currently faces a paradox in terms of accessibility for people with disabilities. While digital technologies hold immense potential to improve their quality of life, the majority of web content still exhibits critical accessibility issues. This PhD thesis addresses this challenge by proposing two interconnected research branches. The first introduces a groundbreaking approach to improving web accessibility by rethinking how it is approached, making it more accessible itself. It involves the development of: 1. AX, a declarative framework of web components that enforces the generation of accessible markup by means of static analysis. 2. An innovative accessibility testing and evaluation methodology, which communicates test results by exploiting concepts that developers are already familiar with (visual rendering and mouse operability) to convey the accessibility of a page. This methodology is implemented through the SAHARIAN browser extension. 3. A11A, a categorized and structured collection of curated accessibility resources aimed at facilitating their intended audiences discover and use them. The second branch focuses on unleashing the full potential of digital technologies to improve accessibility in the physical world. The thesis proposes the SCAMP methodology to make scientific artifacts accessible to blind, visually impaired individuals, and the general public. It enhances the natural characteristics of objects, making them more accessible through interactive, multimodal, and multisensory experiences. Additionally, the prototype of \gls{a11yvt}, a system supporting accessible virtual tours, is presented. It provides blind and visually impaired individuals with features necessary to explore unfamiliar indoor environments, while maintaining universal design principles that makes it suitable for usage by the general public. The thesis extensively discusses the theoretical foundations, design, development, and unique characteristics of these innovative tools. Usability tests with the intended target audiences demonstrate the effectiveness of the proposed artifacts, suggesting their potential to significantly improve the current state of accessibility.

On the Democratization of AI: Bridging the Gap with AutoML

Riding the wave of recent groundbreaking achievements, artificial intelligence (AI) is currently the buzzword on everybody’s lips and, allowing algorithms to learn from historical data, Machine Learning (ML) emerged as its pinnacle. The multitude of algorithms, each with unique strengths and weaknesses, highlights the absence of a universal solution and poses a challenging optimization problem. In response, automated machine learning (AutoML) navigates vast search spaces within minimal time constraints. By lowering entry barriers, AutoML emerged as promising the democratization of AI, yet facing some challenges. In data-centric AI, the discipline of systematically engineering data used to build an AI system, the challenge of configuring data pipelines is rather simple. We devise a methodology for building effective data pre-processing pipelines in supervised learning as well as a data-centric AutoML solution for unsupervised learning. In human-centric AI, many current AutoML tools were not built around the user but rather around algorithmic ideas, raising ethical and social bias concerns. We contribute by deploying AutoML tools aiming at complementing, instead of replacing, human intelligence. In particular, we provide solutions for single-objective and multi-objective optimization and showcase the challenges and potential of novel interfaces featuring large language models. Finally, there are application areas that rely on numerical simulators, often related to earth observations, they tend to be particularly high-impact and address important challenges such as climate change and crop life cycles. We commit to coupling these physical simulators with (Auto)ML solutions towards a physics-aware AI. Specifically, in precision farming, we design a smart irrigation platform that: allows real-time monitoring of soil moisture, predicts future moisture values, and estimates water demand to schedule the irrigation.