Review Paper: The Shape of Phylogenetic Treespace

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths

Testing for HFE-related haemochromatosis

HFE-haemochromatosis is a genetic disorder resulting from mutations of the HFE gene. It primarily affects people of Northern European descent. Clinical manifestations result from the progressive deposition of iron into various organs including the liver. An elevated serum ferritin concentration greater than 300 microgram/L and a transferrin saturation of greater than 45% will identify almost all patients with HFE-haemochromatosis. HFE genotyping confirms the diagnosis. In some patients, liver biopsy may still be necessary as the degree of hepatic fibrosis has prognostic implications

Walks on SPR Neighborhoods

A nearest-neighbor-interchange (NNI) walk is a sequence of unrooted phylogenetic trees, T_0, T_1, T_2,... where each consecutive pair of trees differ by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that visit all trees in an subtree-prune-and-regraft (SPR) neighborhood of a given tree. For any unrooted, binary tree, T, on n leaves, the shortest walk takes {\theta}(n^2) additional steps than the number of trees in the SPR neighborhood. This answers Bryant's Second Combinatorial Conjecture from the Phylogenetics Challenges List, the Isaac Newton Institute, 2011, and the Penny Ante Problem List, 2009

The Relationship of a Systemic Student Support Intervention to Academic Achievement in Urban Catholic Schools

Much of the achievement gap between rich and poor students can be attributed to out-of-school factors, yet few schools have a comprehensive, coordinated system for addressing students’ nonacademic needs. Within a group of Catholic schools located in one city, this study examines academic achievement on the Stanford Achievement Test battery in mathematics, reading, and language among 2nd through 8th grade students participating in such an intervention, and compares the results with those of similar nonparticipating students in nearby cities. Using hierarchical longitudinal growth modeling and adjusting for demographic characteristics, this study found that students in intervention schools outperformed the comparison group on average in 6th grade mathematics. Intervention students also experienced significantly higher rates of growth in achievement than the comparison group in all three subjects. The results suggest that systemic service provision models have the potential to help urban Catholic schools meet their mission of educating the whole child and serving the poorest families. Keywords Catholic education, longitudinal growth analysis, achievement gap Le lien entre une intervention systémique de soutien aux élèves et la réussite scolaire dans les écoles catholiques en milieu urbain. Une bonne partie de l\u27écart entre les résultats obtenus par les élèves riches et les pauvres peut être attribuée à des facteurs extérieurs à l\u27école, pourtant peu d\u27écoles disposent d\u27un système complet et coordonné pour résoudre les besoins extrascolaires des élèves. Cette étude, qui porte sur un groupe d\u27écoles catholiques situées dans une seule ville, examine la réussite scolaire sut la batterie de tests de réussite de Stanford en mathématiques, lecture et langage parmi des élèves de la 11eà la 3eparticipant à cette intervention et compare les résultats avec ceux d\u27élèves similaires, dans des villes voisines qui n\u27y participaient pas. À l\u27aide d\u27une modélisation longitudinale de croissance, avec un ajustement pour les caractéristiques démographiques, cette étude a trouvé que les élèves des écoles où avait lieu l\u27intervention avaient de meilleurs résultats en moyenne que le groupe de comparaison en mathématiques de classe de 6e. Les élèves bénéficiant de l\u27intervention ont aussi eu des taux de croissance plus élevés que le groupe de comparaison dans les trois matières. Ce résultat indique que des modèles de service systémique fourni aux élèves peuvent potentiellement aider les écoles catholiques urbaines à remplir leur mission d\u27éducation intégrale de l\u27enfant et rendre service aux familles pauvres. Mots-clés : éducation catholique, analyse longitudinale de croissance, écart de réussite Relación entre una intervención sistémica de apoyo al estudiante y los logros académicos en escuelas católicas urbanas La mayor parte de la brecha en los logros entre estudiantes ricos y pobres puede atribuirse a factores extraescolares, sin embargo, pocas escuelas disponen de un sistema comprensivo coordinado que aborde las necesidades no académicas de los estudiantes. Tomando un grupo de escuelas católicas ubicadas en una misma ciudad, este estudio examina los logros académicos en las pruebas de aptitud de Stanford (SAT) en matemáticas, lectura y lengua de estudiantes entre segundo y octavo curso que participan en tales intervenciones; y compara los resultados a los de estudiantes no participantes, con perfiles similares, en ciudades cercanas. Al emplear modelos de crecimiento longitudinal jerárquico y al ajustarlos a las características demográficas, el presente estudio encontró que los estudiantes de escuelas con intervención superaron la media de los resultados del grupo de comparación en 6º curso de matemáticas. Los estudiantes con intervención también experimentaron significativamente mayores tasas de crecimiento que los del grupo de comparación en las tres materias. Los resultados sugieren que los modelos que proveen servicios sistémicos disponen del potencial para ayudar a que las escuelas católicas urbanas cumplan su misión de educar al niño en su totalidad y de servir a las familias pobres. Palabras clave educación católica, análisis de crecimiento longitudinal, brecha de logro

The complexity of random ordered structures

"Vegeu el resum a l'inici del document del fitxer adjunt"

Data size sufficiency analyses of haplotype inference algortihms

We present experimental and theoretical analyses of data requirements for haplotype inference algorithms. Our experiments include a broad range of problem sizes under two standard models of tree distribution and were designed to yield statistically robust results despite the size of the sample space. Our results validate Gusfield's conjecture that a population size of n log n is required to give (with high probability) sufficient information to deduce the n haplotypes and their complete evolutionary history. The experimental results inspired our experimental finding with theoretical bounds on the population size. We also analyze the population size required to deduce some fixed fraction of the evolutionary history of a set of n haplotypes and establish linear bounds on the required sample size. These linear bounds are also shown theoretically

Simulation of Man in the Middle Attack On Smart Grid Testbed

Over the past decade, the frequency of cyber attacks against power grids has steadily increased, requiring researchers to find and patch vulnerabilities before they can be exploited. Our research introduces the prototype of a man-in-the-middle attack to be implemented on a microgrid emulator of a smart grid. We present a method of violating the integrity and authentication of packets that are using the IEEE Synchrophasor Protocol in a controlled environment, but this same approach could be used on any other protocol that lacks the proper overhead to ensure the integrity and authenticity of packets. In future research, we plan to implement and test the attack on the previously mentioned smart grid testbed in order to assess the attacks feasibility and tangible effects on Wide Area Monitoring and Control applications, as well as propose possible countermeasures. For this paper, we developed a working simulation of our intended attack using the software ModelSim 10.4. The attack will modify network packet data coming from a Schweitzer Engineering Labs (SEL) Phasor Measurement Unit (PMU) hardware sensor, which provides a stream of precise timing values associated with current and voltage values, as these measured values are en route to the Open Phasor Data Concentrator (OpenPDC) application running on a Windows server. Our simulation provides and validates all of the necessary code in order to program a Field Programmable Gate Array and execute our attack on the testbed in future research