The use of scientific computing tools is currently customary for solving problems at several complexity levels in Applied Sciences. The great need for reliable software in the scientific community ...conveys a continuous stimulus to develop new and better performing numerical methods that are able to grasp the particular features of the problem at hand. This has been the case for many different settings of numerical analysis, and this Special Issue aims at covering some important developments in various areas of application.
A practical introduction to epidemiology, biostatistics, and research methodology for the whole health care community This comprehensive text, which has been extensively revised with new material and ...additional topics, utilizes a practical slant to introduce health professionals and students to epidemiology, biostatistics, and research methodology. It draws examples from a wide range of topics, covering all of the main contemporary health research methods, including survival analysis, Cox regression, and systematic reviews and meta-analysis—the explanation of which go beyond introductory concepts. This second edition of Quantitative Methods for Health Research: A Practical Interactive Guide to Epidemiology and Statistics also helps develop critical skills that will prepare students to move on to more advanced and specialized methods. A clear distinction is made between knowledge and concepts that all students should ensure they understand, and those that can be pursued further by those who wish to do so. Self-assessment exercises throughout the text help students explore and reflect on their understanding. A program of practical exercises in SPSS (using a prepared data set) helps to consolidate the theory and develop skills and confidence in data handling, analysis, and interpretation. Highlights of the book include: * Combining epidemiology and bio-statistics to demonstrate the relevance and strength of statistical methods * Emphasis on the interpretation of statistics using examples from a variety of public health and health care situations to stress relevance and application * Use of concepts related to examples of published research to show the application of methods and balance between ideals and the realities of research in practice * Integration of practical data analysis exercises to develop skills and confidence * Supplementation by a student companion website which provides guidance on data handling in SPSS and study data sets as referred to in the text Quantitative Methods for Health Research, Second Edition is a practical learning resource for students, practitioners and researchers in public health, health care and related disciplines, providing both a course book and a useful introductory reference.
This book is the first in the market to treat single- and multi-period risk measures (risk functionals) in a thorough, comprehensive manner. It combines the treatment of properties of the risk ...measures with the related aspects of decision making under risk.
Abstract Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can ...be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
Abstract Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to ...pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterize their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterize the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete “trait” independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.
Abstract Most algorithms that are used to predict the effects of variants rely on evolutionary conservation. However, a majority of such techniques compute evolutionary conservation by solely using ...the alignment of multiple sequences while overlooking the evolutionary context of substitution events. We had introduced PHACT, a scoring-based pathogenicity predictor for missense mutations that can leverage phylogenetic trees, in our previous study. By building on this foundation, we now propose PHACTboost, a gradient boosting tree–based classifier that combines PHACT scores with information from multiple sequence alignments, phylogenetic trees, and ancestral reconstruction. By learning from data, PHACTboost outperforms PHACT. Furthermore, the results of comprehensive experiments on carefully constructed sets of variants demonstrated that PHACTboost can outperform 40 prevalent pathogenicity predictors reported in the dbNSFP, including conventional tools, metapredictors, and deep learning–based approaches as well as more recent tools such as AlphaMissense, EVE, and CPT-1. The superiority of PHACTboost over these methods was particularly evident in case of hard variants for which different pathogenicity predictors offered conflicting results. We provide predictions of 215 million amino acid alterations over 20,191 proteins. PHACTboost is available at https://github.com/CompGenomeLab/PHACTboost. PHACTboost can improve our understanding of genetic diseases and facilitate more accurate diagnoses.
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