Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes ($Xiphophorus$: Poeciliidae), which is characterized by widespread hybridizations

MacroSight: A novel framework to analyze the shape and movement of interacting macrophages using MAtLABR †

This paper presents a novel software framework, called macrosight, which incorporates routines to detect, track, and analyze the shape and movement of objects, with special emphasis on macrophages. The key feature presented in macrosight consists of an algorithm to assess the changes of direction derived from cell-cell contact, where an interaction is assumed to occur. The main biological motivation is the determination of certain cell interactions influencing cell migration. Thus, the main objective of this work is to provide insights into the notion that interactions between cell structures cause a change in orientation. Macrosight analyzes the change of direction of cells before and after they come in contact with another cell. Interactions are determined when the cells overlap and form clumps of two or more cells. The framework integrates a segmentation technique capable of detecting overlapping cells and a tracking framework into a tool for the analysis of the trajectories of cells before and after they overlap. Preliminary results show promise into the analysis and the hypothesis proposed, and lays the groundwork for further developments. The extensive experimentation and data analysis show, with statistical significance, that under certain conditions, the movement changes before and after an interaction are different from movement in controlled cases

Comparison of Interactions Between Control and Mutant Macrophages

This paper presents a preliminary study on macrophages migration in Drosophila embryos, comparing two types of cells. The study is carried out by a framework called macrosight which analyses the movement and interaction of migrating macrophages. The framework incorporates a segmentation and tracking algorithm into analysing motion characteristics of cells after contact. In this particular study, the interactions between cells is characterised in the case of control embryos and Shot3 mutants, where the cells have been altered to suppress a specific protein, looking to understand what drives the movement. Statistical significance between control and mutant cells was found when comparing the direction of motion after contact in specific conditions. Such discoveries provide insights for future developments in combining biological experiments to computational analysis

Segmentation and Shape Analysis of Macrophages Using Anglegram Analysis

Cell migration is crucial in many processes of development and maintenance of multicellular organisms and it can also be related to disease, e.g., Cancer metastasis, when cells migrate to organs different to where they originate. A precise analysis of the cell shapes in biological studies could lead to insights about migration. However, in some cases, the interaction and overlap of cells can complicate the detection and interpretation of their shapes. This paper describes an algorithm to segment and analyse the shape of macrophages in fluorescent microscopy image sequences, and compares the segmentation of overlapping cells through different algorithms. A novel 2D matrix with multiscale angle variation, called the anglegram, based on the angles between points of the boundary of an object, is used for this purpose. The anglegram is used to find junctions of cells and applied in two different applications: (i) segmentation of overlapping cells and for non-overlapping cells; (ii) detection of the “corners” or pointy edges in the shapes. The functionalities of the anglegram were tested and validated with synthetic data and on fluorescently labelled macrophages observed on embryos of Drosophila melanogaster. The information that can be extracted from the anglegram shows a good promise for shape determination and analysis, whether this involves overlapping or non-overlapping objects

Bayesian species delimitation combining multiple genes and traits in a unified framework

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110547/1/evo12582.pd

Sparse Gaussian chain graphs with the spike-and-slab LASSO: Algorithms and asymptotics

The Gaussian chain graph model simultaneously parametrizes (i) the direct effects of $p$ predictors on $q$ correlated outcomes and (ii) the residual partial covariance between pair of outcomes. We introduce a new method for fitting sparse Gaussian chain graph models with spike-and-slab LASSO (SSL) priors. We develop an Expectation-Conditional Maximization algorithm to obtain sparse estimates of the $p \times q$ matrix of direct effects and the $q \times q$ residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior concentration rate for our model, buttressing our method's excellent empirical performance with strong theoretical guarantees. We use our method to reanalyze a dataset from a study of the effects of diet and residence type on the composition of the gut microbiome of elderly adults

Comparative Study of Contact Repulsion in Control and Mutant Macrophages Using a Novel Interaction Detection

In this paper, a novel method for interaction detection is presented to compare the contact dynamics of macrophages in the Drosophila embryo. The study is carried out by a framework called macrosight, which analyses the movement and interaction of migrating macrophages. The framework incorporates a segmentation and tracking algorithm into analysing the motion characteristics of cells after contact. In this particular study, the interactions between cells is characterised in the case of control embryos and Shot mutants, a candidate protein that is hypothesised to regulate contact dynamics between migrating cells. Statistical significance between control and mutant cells was found when comparing the direction of motion after contact in specific conditions. Such discoveries provide insights for future developments in combining biological experiments with computational analysis

Evaluación del índice de seguridad hospitalaria en el Hospital Regional de Sonsonate (ISSS), municipio de Sonsonate, departamento de Sonsonate

Con el tiempo, el uso de nuevas tecnologías ha tratado de reducir el impacto que un desastre natural tiene sobre la población y ciertamente se ha logrado, pero aún falta mucho ya que los impactos generados por un desastre natural siguen siendo significativamente grandes en todas las partes del mundo. Frente a los desastres naturales la necesidad de que existan hospitales seguros toma una gran importancia, puesto que son estos recintos a donde la población acude inmediatamente ocurrido el desastre; por lo que se debe garantizar un servicio adecuado de salud

Evaluación de cuatro dosis de poliacrilato de potasio en el desarrollo del cultivo de café (Coffea arabica L.) y en la conservación de humedad disponible para la planta en el suelo

La investigación se realizó de octubre de 2018 a abril de 2019, en el vivero de la Facultad de Ciencias Agronómicas de la Universidad de El Salvador, y en el laboratorio de química agrícola. La investigación consistió en evaluar cuatro dosis de Poliacrilato de Potasio en el desarrollo del cultivo de café (Coffea arabica L.) y en la conservación de humedad en el suelo disponible para las plantas. Durante el estudio se utilizaron plantas de café, a las cuales se les aplicó diferentes dosis de Poliacrilato de Potasio, para conocer el periodo de retención de humedad en el suelo, utilizando como indicador el registro de días a marchitez de las plantas y su desarrollo. Se tomaron datos como altura de la planta, número y largo de bandolas, volumen y longitud de la raíz principal, días a marchitez de la planta, análisis del suelo usado como sustrato; análisis químico de las raíces, del follaje y del Poliacrilato de Potasio. El estudio se realizó bajo el diseño de bloques al azar, se tuvieron cuatro bloques. El número de unidades experimentales por tratamiento fue de 4 plantas, teniendo un total de 64 plantas. Para el análisis de los datos se utilizó estadística descriptiva (gráficos y tablas) y la prueba de Tukey y se hizo uso del programa InfoStats. Se realizó el registro de días sin riego a las plantas de café obteniendo la mejor media el tratamiento tres con un promedio de 126.25 días, al realizar la prueba estadística de Tukey se obtuvo que los tratamientos en los cuales se utilizó el poliacrilato de potasio, el tratamiento tres, dos y uno (10 g, 7 g, y 5 g respectivamente), presentaron los mejores resultados (p>0.05). Se encontró un efecto significativo en las variables altura de la planta y volumen de raíz (p>0.05), en el cual el tratamiento tres presentó, los mejores resultados, presentado una ganancia de altura media de 23.5 cm y un volumen 14 cc. En ambas variables el tratamiento que obtuvo los menores resultados fue el tratamiento testigo, con una ganancia de altura promedio de 13.92 cm y un volumen de 8 cc. Los resultados de análisis de laboratorio no presentaron resultados significativos entre los tratamientos (P>0.05). Palabras claves: Poliacrilato de Potasio, café, Coffea arabica, agua, sequía, marchitez, hidroge