Orthology and paralogy distinguish whether a pair of genes originated by a speciation or a gene duplication event, whereas xenology refers to horizontal gene transfer. These concepts play a key role in phylogenomics and species tree inference is one of its prevalent tasks. Commonly, species tree inference is performed using sequence-based phylogenetic methods which heavily rely on the initial data sets to be solely composed of 1:1 orthologs. Such approaches are strongly restricted to a small set of genes that provide information about the species tree. In this work, it is shown that the restriction to 1:1 orthologs is not necessary to reconstruct a reliable hypothesis on the evolutionary history of species. Besides orthology, knowledge on all three major driving forces of gene evolution can be considered: speciation, gene duplication, and horizontal gene transfer. The corresponding concepts of orthology, paralogy, and xenology imply binary relations on pairs of genes. These relations, in turn, convey meaningful phylogenetic information and allow the inference of plausible phylogenetic species trees. To this end, it is shown that orthology, paralogy, and xenology have to fulfill certain mathematical properties. In particular, they have to be representable as a tree – the so-called gene tree. This work investigates the theoretical concepts of tree representable sets of binary relations to unfold the underlying mathematical structure. Various novel characterizations for those relations are given and the close connection between tree representable sets of binary relations and cographs, symbolic ultrametrics, and so-called unp 2-structures is revealed. Based on the novel characterizations, polynomial-time recognition algorithms for tree representable sets of relations are presented. In the case, a set of relations is tree representable, the corresponding tree representation can be found in polynomial time as well. Moreover, for the NP-complete problems of editing a given set of relations to its closest tree representable set, exact algorithms are developed by means of formulations as integer linear program. Finally, all algorithms have been implemented in the software ParaPhylo, a species tree inference method based on orthology and paralogy data. It is demonstrated on simulated data sets, as well as real-life data sets, that non-trivial phylogenies can indeed be reconstructed from tree-free orthology estimates alone.

Thesis advisor: Gabor J. Kalman / Mixtures of charged particles, where the components have different charge numbers (Z_A ), masses (m_A ) and densities (n_A ), with A = 1, 2 denoting the components, occur in Nature in a great variety. To be sure, even the simplest plasmas are necessarily multicomponent systems, consisting of negative and positive charges. This feature is, however, obscured within the centrally important and popular OCP (one component plasma) or jellium models, where the role of one of the components is reduced to providing a neutralizing background. When this background is inert, one is led to the Coulomb OCP model, while when the background is polarizable (such as an electron gas surrounding heavy particles), to a Yukawa OCP (YOCP), with a screened Yukawa potential replacing the Coulomb potential between the dynamically active particles. There are, however situations of physical importance, where the OCP description is inadequate and a genuine two component description of a plasma composed of two species is required. This Thesis focuses on the study of the dynamics of many-body systems consisting of two components of like charges (all the Z_A -s being of the same signature) in a neutralizing background. The methodology is based upon parallel attacks through theoretical analysis and Molecular Dynamics (MD) simulations, the latter yielding the capability of instant verification of the former. The investigation involves the study of the partial (i.e. species by species) structure functions S_AB (k, ω) and current-current correlation functions L_AB (k, ω). The Fluctuation–Dissipation Theorem (FDT) con- nects these quantities to the total and partial response functions χ_AB (k, ω) (matrices in species space), which are instrumental in the description of the collective mode excitations of the system. This analysis has revealed an entirely novel feature: both S_11 (k, ω) and S_22 (k, ω) exhibit very sharp and deep (several orders of magnitude) minima in the strongly coupled liquid phase at robust characteristic frequencies of the system, which are virtually coupling independent. The FDT then demands that these anti-resonances show up as well in the imaginary part of the partial density response function χ_AB (k, ω). Our theoretical analysis, based on the Quasi-Localized Charge Approximation (QLCA), has confirmed that this is indeed the case. These anti-resonant frequencies being related to the dissipative part of the response, require a physical description of the principal source of dissipation. This has been identified as the inter-species momentum transfer, governed by drag between the microscopic current fluctuations of the two species. The description of this effect was incorporatedv in the QLCA formalism, making it possible to derive a closed analytic representation of the fluctuation spectra in the frequency domain of interest and compare them with the results of the MD simulations. Other important novel concepts, such as the idea of coupling dependent effective mass, fast vs. slow sound, the mechanism of tran- sition from short-range to long-range interaction have been identified and analyzed. Furthermore, the investigation of the dynamics has led to the first comprehensive description of the mode structures of classical binary Coulomb and Yukawa mixtures at arbitrary coupling values, which has been a longstanding problem in statistical plasma physics. Focusing on the longitudinal excitations, we describe the transition from weak coupling (where one is acquainted with the RPA result yielding only the single plasmon mode in the Coulomb case or a single acoustic mode in the Yukawa case) to strong coupling, with a doublet of modes that arise from the complex rel- ative motion between the two components, as affected by the interaction with the background. / Thesis (PhD) — Boston College, 2019. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Physics.

El movimiento #NiUnaMenos en contra del femicidio iniciado en el 2015, las protestas de pañuelos verdes por la sanción de la ley de interrupción voluntaria del embarazo, así como las intervenciones del colectivo LGTBIQ en Argentina han hecho uso del lenguaje inclusivo no binario como una herramienta más en la lucha por la igualdad de derechos de la mujer y de otras minorías. Estos nuevos usos del lenguaje que desafían las normas y estructuras establecidas al intentar incluir identidades históricamente marginalizadas alterando la gramática de la lengua también se manifiestan en un corpus emergente de la literatura argentina contemporánea vinculado con dichos movimientos sociales.En este estudio situamos los usos y funciones de este lenguaje inclusivo en la literatura y en el corriente debate cultural que ha despertado tal gesto literario en la Argentina y, en particular, en el interrogante que plantea tal debate acerca del potencial del lenguaje inclusivo en la literatura para articular nuevas subjetividades más amplias y transformar las sensibilidades (Andruetto, 2019; Sarlo y Kalinowski, 2019). Para examinar este interrogante, en el presente estudio analizamos el uso del lenguaje inclusivo en relación con la articulación de nuevas subjetividades tras dicha ola de movimientos, protestas e intervenciones en un corpus de la literatura argentina contemporánea compuesto por dos poemas extraídos del compilado colectivo Martes Verde (2018) y la novela Vikinga Bonsái (2019) de Ana Ojeda. A partir de un análisis de las obras selectas desde teorías feministas provenientes tanto del contexto anglosajón (Irigaray, 1985, 1992; Butler, 2002) como de los feminismos latinoamericanos (Colanzi, 2019), así como  de la definición de subjetividad en las literaturas postautónomas (Ludmer, 2009, 2012), investigamos la configuración de una nueva subjetividad inclusiva no binaria que surge a través del uso literario del lenguaje inclusivo. En la primera parte del análisis nos concentramos en el poema “La pija de Hegel” del colectivo Máquina de Lavar publicado en Martes verde, donde examinamos cómo el uso inclusivo del lenguaje en paralelo a usos deconstructivos de la tradición filosófica occidental que excluyen a la mujer, construyen una subjetividad de la diferencia (Irigaray, 1985, 1992) respecto de la resignificación de la idea del sexo débil históricamente vinculada a la mujer. En la primera segunda parte del análisis, estudiamos el poema sin título de María Insúa también incluido en Martes verde, donde examinamos cómo el uso inclusivo del lenguaje en relación con una retórica del cuerpo en este poema problematiza la construcción del género en la repetición performativa de actos (Butler, 2002) y la marca que dicha reconstrucción imprime en los cuerpos femeninos. Finalmente abordamos la novela Vikinga Bonsái donde analizamos cómo el lenguaje inclusivo en esta novela plantea un colectivo inclusivo de sororidad cuya sensación de pertenencia e identificación entrelaza el colectivo femenino y LGTBIQ junto con otras identidades marginalizadas que se representan en la novela a partir de lenguajes rurales, locales, digitales e inventados y una polifonía de voces de diversos personajes cuya reunión en comunión potencia su diferencia (Irigaray, 1985, 1992), rompe los actos repetidos que construyen la identidad femenina (Butler, 2002) pero también producen un acto de desobediencia pública rompiendo normas como la familia, y proyectando una subjetividad que traspasa los límites del sujeto individual (Colanzi, 2019). Entre los resultados más sobresalientes, encontramos que, a pesar de las singularidades de cada texto y de los géneros a los que pertenecen (novela, poesía) en los textos literarios estudiados, el lenguaje inclusivo se relaciona predominantemente con escenarios urbanos. Sin embargo, el uso literario de este lenguaje construye una subjetividad más amplia que surge a partir de su interconexión con los movimientos sociales feministas contemporáneos, lo que nos permite proponer que las obras estudiadas acompañan la lucha por la igualdad de derechos sociales. / The #NiUnaMenos movement against femicide in 2015, the green scarf protests for the sanction of the pregnancy voluntary termination law as well as the interventions of the LGTBIQ collective in Argentina have made use of non-binary inclusive language as another tool in the fight for equal rights for women and other minorities. These new language uses that challenge established norms and structures by attempting to include historically marginalized identities by altering the grammar of the language are also manifested in an emerging corpus of contemporary Argentine literature linked to these social movements. In this study we situate the uses and functions of this inclusive language in literature in the current cultural debate in Argentina that has aroused such literary gesture and in the question raised by such debate about the potential of inclusive language in literature to articulate new, broader subjectivities, thus  transforming sensibilities (Andruetto, 2019; Sarlo & Kalinowski, 2019). To examine this question, in this study we analyze the use of inclusive language in relation to the articulation of new subjectivities after the mentioned wave of movements, protests and interventions in a corpus of contemporary Argentine literature composed of two poems included in the collective poetry book Martes Verde (2018) and the novel Vikinga Bonsái (2019) by Ana Ojeda. Based on an analysis of the selected literary works drawing on feminist theories both, from the Anglo-Saxon context (Irigaray, 1985, 1992; Butler, 2002) and Latin American feminisms (Colanzi, 2019) and the definition of subjectivity in post autonomous literatures (Ludmer, 2009, 2012), we investigate the configuration of a new inclusive non-binary subjectivity that arises through the literary use of inclusive language.  In the first part of the analysis, we focus on the poem "La pija de Hegel" by the Máquina de Lavar collective included in Martes verde, where we examine how the inclusive use of language in parallel to deconstructive uses of the philosophical tradition that excludes women, configures a subjectivity of difference (Irigaray, 1985, 1992,) regarding the resignification of the idea of the weaker sex historically linked to women. In the first second part of the analysis, we study the untitled poem by María Insúa also included in Martes verde, where we examine how the inclusive use of language in this poem in relation to a body rhetoric problematizes the construction of gender and the violence that construction imprints on female bodies. Finally, we address the novel Vikinga Bonsái where we analyze how inclusive language in this novel poses an inclusive group of sisterhood whose sense of belonging and identification that interweaves women and LGTBIQ collectives with other marginalized groups represented in the novel by rural, workers, digital and invented languages and a polyphony of voices of various characters whose interaction in communion enhances their difference (Irigaray, 1985, 1992), breaks the repeated acts that build female identity (Butler, 2002) but also produces an act of public disobedience, breaking norms such as the family, and projecting a subjectivity that transcends the limits of the individual subject (Colanzi, 2019). Among the most outstanding results, we found that, despite the singularities of each text and the genres to which they belong (novels, poetry) in the literary texts studied, inclusive language is predominantly related to urban settings. However, the literary use of this language builds a broader subjectivity that arises from its interconnections with the current feminist social movements, which allows us to propose that the works studied accompany the struggle for equal social rights.

One of the important tasks during software testing is the generation of appropriate test data. Various techniques have been proposed to automate this task. The techniques available, however, often have problems limiting their use. In the case of dynamic test data generation techniques, a frequent problem is that a large number of iterations might be necessary to obtain test data. This article proposes a novel technique for automated test data generation based on binary search. Binary search conducts searching tasks in logarithmic time, as long as its assumptions are fulfilled. This article shows that these assumptions can also be fulfilled in the case of path-oriented test data generation and presents a technique which can be used to generate test data covering certain paths in class methods.

In the epoch of advanced mHealth (mobile health) use in ophthalmology, there is a scientific call for regulating the validity and reliability of eye-related apps. For a positive health outcome that works towards enhancing mobile-application guided diagnosis in joint decision-making between eye specialists and individuals, the aging population should be provided with a reliable and valid tool for assessment of their eye status outside the physician office. This interdisciplinary study aims to determine through hypothesis testing validity and reliability of a limited set of five mHealth apps (mHAs ) and through binary logistic regression the prediction possibilities of investigated apps to exclude the four major eye diseases in the particular demographic population. The study showed that 189 aging adults (45- 86 years old) who did complete the mHAs’ tests were able to produce reliable results of selected eye function tests through four out of five mHAs measuring visual acuity, contrast sensitivity, red desaturation, visual field and Amsler grid in comparison with a “gold standard” - comprehensive eye examination. Also, part of the participants was surveyed for assessing the Quality of Experience on mobile apps. Understanding of current reliability of existing eye-related mHAs will lead to the creation of ideal mobile application’ self-assessment protocol predicting the timely need for clinical assessment and treatment of age-related macular degeneration, diabetic retinopathy, glaucoma and cataract. Detecting the level of eye function impairments by mHAs is cost-effective and can contribute to research methodology in eye diseases’ prediction by expanding the system of clear criteria specially created for mobile applications and provide returning significant value in preventive ophthalmology.

This study examines what support that exists in the Swedish upper secondary school curriculum and the English 7 syllabus for teaching postcolonial literature and the postcolonial literary concepts of binary pairs and Othering. This study also illustrates how Arvind Adiga’s The White Tiger (2008) could serve as an example of a postcolonial novel to exemplify said concepts in the EFL classroom. To answer these questions, a definition of the postcolonial genre as well as a definition of the concepts within postcolonial literary theory was formulated. With the theoretical framework in place, an analysis of the steering documents was conducted. The Swedish curriculum’s focus on the teaching of every human’s equal value and rights relate to the postcolonial genre, as the genre is dedicated to telling marginalised perspectives in the modern world. The syllabus states that teaching different genres of literature and the usage of different perspectives in the classroom should be a part of the English subject. This supports the teaching of postcolonial literature as it is a successor to Western classics as well as shift in perspective from the colonisers to the colonised. The teaching of the concepts of binary pairs and Othering were indicated to be potentially challenging to practically implement, as literary didactic literature stated the difficulties of adapting literary theory to an upper secondary school level. Teaching literary concepts was indicated to be achievable provided that teachers teach theory with clear guidance of what context to use it in and where not to use it. As for binary pairs and Othering within Adiga’s The White Tiger (2008), the examples focused on were the Indias of Light and Darkness, and how this binary pair Othered one another. As such, the results were found to indicate that there is support for teaching postcolonial literature as well as postcolonial concepts, and that Adiga’s novel would be an adequate text to use for exemplifying these in the classroom.

Classical Cepheids and eclipsing binary systems are powerful probes for measuring stellar fundamental parameters and constraining stellar astrophysics. A Cepheid in an eclipsing binary system is even more powerful, constraining stellar physics, the distance scale and the Cepheid mass discrepancy. However, these systems are rare, only three have been discovered. One of these, OGLE-LMC-CEP1812, presents a new mystery: where the Cepheid component appears to be younger than its red giant companion. In this work, we present stellar evolution models and show that the Cepheid is actually product of a stellar merger during main sequence evolution that causes the Cepheid to be a rejuvenated star. This result raises new questions into the evolution of Cepheids and their connections to smaller-mass anomalous Cepheids.

Syftet med denna uppsats var att jämföra två olika databashanteringssystem, MongoDB samt MariaDB, utifrån specifika krav från en uppdragsgivare gällande prestanda samt komplexitet. Då MariaDB är ett SQL-databashanteringssystem och MongoDB ett NoSQLdatabashanteringssystem som bygger på olika databasmodeller behandlas data på olika sätt, vilket ligger som grund till jämförelsen mellan de olika databashanteringssystemen. Uppsatsen fokuserar på att utifrån fyra olika tester, två prestandatestet och två tester som jämför komplexiteten, kunna jämföra databashanteringssystemen MariaDB och MongoDB. Dessa databashanteringssystem ställdes emot de angivna kraven från uppdragsgivaren för att se vilket av dem som är bäst lämpat. Två olika applikationer utvecklades med hjälp av C# och användes under testerna för att utföra testerna. Efter att testerna utförts rekommenderades MongoDB till uppdragsgivaren på grund av den prestandafördel som testerna visade på i långsiktig användning av systemet. Även komplexiteten för MongoDB visade sig vara mindre vilket stärker rekommendationen ytterligare.

The presence of a magnetic field is shown to affect the evolution and properties of stars. Hence, it is necessary to observe different types of stars to explore these effects. The detached eclipsing binary UV Piscium is the object of interest in this study, where a first step of analyzing its global magnetic field is done. The observational data was collected during 2016, at the 3.6-m Canada-France-Hawaii Telescope at Mauna Kea, Hawaii. The analysis of the magnetic field is based on the line-addition technique least-squares deconvolution (LDS) of the polarisation signatures, and the aim is to search for circular polarisation signals produced by the Zeeman effect. The result shows a strong circular polarisation signature for the primary star of the binary, which is a direct evidence for the presence of a magnetic field. In contrast to this, the secondary star only shows a weak signal of circular polarisation in one of the analysed observations and further analysis of its magnetic field is needed. The secondary goal of the project was to calculate the stellar masses of the binary. This is done by measuring the radial velocities of the two stars via the line profiles, and preforming an orbital fit. The results gave: M1= 1.0211 ± 0.0040 Msol and M2 = 0.7728 ± 0.0028 Msol.

In this thesis, we explore the idea of using binary visualization and image analysis to detect anomalous activity on an Industrial Internet of Things (IIoT) based network. The data is gathered into a pcap file and then fed into our encoder, which uses a space-filling curve to convert the 1-dimensional stream of data into pixels with a specific red, blue, and green gradient value.  The pixels create an image which is then given to an image analysis system based on a Convolutional Neural Network, which classifies if the traffic supplied is malicious or not. The results show that using a Binary and Multiclass classifier approach to the image analysis both work well reaching an accuracy of 100% and 94% respectively. While the binary classifier is more accurate both succeed at separating Malicious from Benign traffic. The choice of space-filling curves in our binary visualization ended up having little to no impact on overall classification accuracy.