Polyhedral geometry of Phylogenetic Rogue Taxa

It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we construct polyhedral cones computationally which give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.Comment: In this version, we add quartet distances and fix Table 4

Transcultural adaptation of the who oral health questionnaire and its validation in chilean children

Indexación: Scopus.Introduction: The last edition of the WHO "Oral Health Questionnaire for Children" was published in 2013. This is an only-English version, and as such it requires linguistic adaptation and validation to be applied in the Chilean population. Objectives: To translate and adapt the WHO Oral Health Questionnaire for Children to Spanish and validate it in a Chilean population. Methods: A translation and back translation of the original instrument from English to Spanish was carried out by four translators. The questionnaire was self-reported as a pilot test in ten individuals. A sample was subsequently selected for convenience taking into account the population distribution, resulting in a final sample of 103 individuals. The internal consistency was calculated with Cronbach's alpha, criterion validity with Pearson's correlation coefficient and construct validity with Exploratory Factor Analysis. Results: A conceptual and semantic equivalence of the instrument was obtained. Women and men accounted for 43.69% and 56.31% of the sample, respectively. Cronbach's alpha coefficient was 0.62, while criterion validity was slightly positive between the total dimensions and the DMFT (r=0.13, p-value= 0.20). The Exploratory Factor Analysis yielded a total of 11 factors that explain 70% of the variability in the data. Conclusions: The oral health questionnaire has been appropriately adapted to Spanish, having conceptual as well as semantic equivalence to the original version, being reliable and valid to be used in a population of 12-year-old Chilean children. © 2018, Universidad de Concepcion. All rights reserved.http://joralres.com/index.php/JOR/article/view/432/43

Plantinga-Vegter algorithm takes average polynomial time

We exhibit a condition-based analysis of the adaptive subdivision algorithm due to Plantinga and Vegter. The first complexity analysis of the PV Algorithm is due to Burr, Gao and Tsigaridas who proved a $O\big(2^{\tau d^{4}\log d}\big)$ worst-case cost bound for degree $d$ plane curves with maximum coefficient bit-size $\tau$. This exponential bound, it was observed, is in stark contrast with the good performance of the algorithm in practice. More in line with this performance, we show that, with respect to a broad family of measures, the expected time complexity of the PV Algorithm is bounded by $O(d^7)$ for real, degree $d$, plane curves. We also exhibit a smoothed analysis of the PV Algorithm that yields similar complexity estimates. To obtain these results we combine robust probabilistic techniques coming from geometric functional analysis with condition numbers and the continuous amortization paradigm introduced by Burr, Krahmer and Yap. We hope this will motivate a fruitful exchange of ideas between the different approaches to numerical computation.Comment: 8 pages, correction of typo

La constitucionalización del acceso a la información pública gubernamental en México

[Resumen] El presente trabajo muestra el camino recorrido en México para la consecución de la constitucionalización del derecho de acceso a la información pública gubernamental teniendo como punto de partida la doble faz del mismo, por un lado como facultad de la libertad de expresión y por otro como una obligación inherente a la actividad del estado de publicitarse. De igual manera el trabajo aborda todos aquellos aspectos que la reforma constitucional en México propuso como principios rectores del acceso a la información pública desde la obligación de publicidad hasta toda aquella información que aún y cuando no pudiera estar publicitada si debiera ser del conocimiento público.[Abstract] The herein document shows the overhauling in Mexico of the attainment of the constitutionalization of the governmental public information access law having as starting point its own double sight as authority of expression freedom and as an obligation inherent to the state to be published. In the same way, the document undertakes all those aspects proposed by the constitutional reform as governing principles of the access to public information starting with the publicity obligation and ending with all the information that should be of public knowledge

Genetic and Molecular Factors in Drug-Induced Liver Injury: A Review

The diagnosis of drug-induced liver injury (DILI) is challenging and based on complex diagnostic criteria. DILI falls into two main categories i) intrinsic 'dose-dependent' Type A reactions ii) 'idiosyncratic' or Type B reactions (which are usually not predictable). Idiosyncratic reactions can be immunoallergic (hypersensitivity), or metabolic, although overlap between categories can occur. The aim of this review is to summarise the general view of underlying mechanisms in DILI and to highlight individual risk factors for developing hepatotoxicity. Polymorphisms of bioactivation/ toxification pathways through CYP450 enzymes (Phase I), detoxification reactions (Phase II) and excretion/transport (Phase III) are explored together with immunological factors that might determine DILI. The importance of establishing a multidisciplinary and multi-centric network to promote the understanding and research in hepatotoxicity is underlined. Challenges such as genetic analyses for association studies and whole genome studies, pharmacogenetic testing and future approaches to study DILI are considered. Knowledge regarding these operational mechanisms could provide further insight for the prospective identification of susceptible patients at risk of developing drug-induced hepatotoxicity.

An Implicitization Challenge for Binary Factor Analysis

We use tropical geometry to compute the multidegree and Newton polytope of the hypersurface of a statistical model with two hidden and four observed binary random variables, solving an open question stated by Drton, Sturmfels and Sullivant in "Lectures on Algebraic Statistics" (Problem 7.7). The model is obtained from the undirected graphical model of the complete bipartite graph $K_{2,4}$ by marginalizing two of the six binary random variables. We present algorithms for computing the Newton polytope of its defining equation by parallel walks along the polytope and its normal fan. In this way we compute vertices of the polytope. Finally, we also compute and certify its facets by studying tangent cones of the polytope at the symmetry classes vertices. The Newton polytope has 17214912 vertices in 44938 symmetry classes and 70646 facets in 246 symmetry classes.Comment: 25 pages, 5 figures, presented at Mega 09 (Barcelona, Spain