Hasil untuk "Analysis"

N. Marwan, M. Romano, M. Thiel et al.

Recurrence is a fundamental property of dynamical systems, which can be exploited to characterise the system’s behaviour in phase space.A powerful tool for their visualisation and analysis called recurrence plotwas introduced in the late 1980’s. This report is a comprehensive overview covering recurrence based methods and their applications with an emphasis on recent developments. After a brief outline of the theory of recurrences, the basic idea of the recurrence plot with its variations is presented. This includes the quantification of recurrence plots, like the recurrence quantification analysis, which is highly effective to detect, e. g., transitions in the dynamics of systems from time series. A main point is how to link recurrences to dynamical invariants and unstable periodic orbits. This and further evidence suggest that recurrences contain all relevant information about a system’s behaviour. As the respective phase spaces of two systems change due to coupling, recurrence plots allow studying and quantifying their interaction. This fact also provides us with a sensitive tool for the study of synchronisation of complex systems. In the last part of the report several applications of recurrence plots in economy, physiology, neuroscience, earth sciences, astrophysics and engineering are shown. The aim of this work is to provide the readers with the know how for the application of recurrence plot based methods in their own field of research. We therefore detail the analysis of data and indicate possible difficulties and pitfalls. © 2006 Elsevier B.V. All rights reserved. PACS: 05.45; 07.05.Kf; 07.05.Rm; 91.25.−r; 91.60.Pn

Jacquelin Perry, J. Burnfield

This text encompasses the work of Dr Jacquelin Perry in her years as a therapist and surgeon focusing on the human gait. The text is broken down into four sections: fundamentals; normal gait; pathological gait; and gait analysis systems. In addition to the descriptions of the gait functions, a representative group of clinical examples has been included to facilitate the interpretation of the identified gait deviations. The book includes detailed laboratory records with illustrations and photographs. Intended as a reference for health care professionals involved in musculoskeletal patient care, the text is suitable for incorporating into many athletic training programmes, university physical therapy programmes and gait workshops.

Edward Packel

Let Γ be a infinite countable group which acts naturally on (cid:3) p (Γ ) . We introduce a modification of mean dimension which is an obstruction for (cid:3) p (Γ ) and (cid:3) q (Γ ) to be Hölder conjugates. To cite this article: A. Gournay, C. R. Acad. Sci. Paris, Ser. I 347 (2009). © 2009 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved. Résumé Sur une modification Hölder covariante de la dimension moyenne. Soit Γ un groupe dénombrable infini qui agit naturel-lement sur (cid:3) p (Γ ) . Nous introduisons une obstruction, proche de la dimension moyenne, au fait que (cid:3) p (Γ ) et (cid:3) q (Γ ) soit Hölder conjugués. Pour citer cet article :A. Gournay, C. R. Acad. Sci. Paris, Ser. I 347 (2009). © 2009 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

K. Tamura, G. Stecher, Sudhir Kumar

Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.

Naveen Donthu, Satish Kumar, D. Mukherjee et al.

Edmund Taylor Whittaker, G. Watson

This classic work has been a unique resource for thousands of mathematicians, scientists and engineers since its first appearance in 1902. Never out of print, its continuing value lies in its thorough and exhaustive treatment of special functions of mathematical physics and the analysis of differential equations from which they emerge. The book also is of historical value as it was the first book in English to introduce the then modern methods of complex analysis. This fifth edition preserves the style and content of the original, but it has been supplemented with more recent results and references where appropriate. All the formulas have been checked and many corrections made. A complete bibliographical search has been conducted to present the references in modern form for ease of use. A new foreword by Professor S. J. Patterson sketches the circumstances of the book’s genesis and explains the reasons for its longevity. A welcome addition to any mathematician’s bookshelf, this will allow a whole new generation to experience the beauty contained in this text.

Y. Hao, S. Hao, E. Andersen-Nissen et al.

The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce ‘weighted-nearest neighbor’ analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 antibodies to construct a multimodal reference atlas of the circulating immune system. We demonstrate that integrative analysis substantially improves our ability to resolve cell states and validate the presence of previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets, and to interpret immune responses to vaccination and COVID-19. Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets, including paired measurements of RNA and chromatin state, and to look beyond the transcriptome towards a unified and multimodal definition of cellular identity. Availability Installation instructions, documentation, tutorials, and CITE-seq datasets are available at http://www.satijalab.org/seurat

Andrey D. Prjibelski, A. Korobeynikov, A. Lapidus

This chapter explores sequence analysis (SA), which conceives the social world as happening in processes, in series of events experienced by social entities. SA refers to a set of tools used to summarize, represent, and compare sequences — i.e. ordered lists of items. Job careers (succession of job positions) are typical examples of sequences. Various other topics have been studied through SA, such as steps in traditional English dances, country-level adoption of welfare policies over one century, or individual and family time-diaries. Andrew Abbott played a pioneering role in the diffusion of SA. With colleagues, Abbott introduced optimal matching analysis (OMA) in the social sciences, a tool to compare sequences borrowed from computer science and previously adapted to DNA sequences. Abbott’s work on SA was part of a wider methodological thinking on social processes. The chapter then looks at the most common type of sequences in social science: categorical time series — i.e. successions of states with a duration defined on a more or less refined chronological scale.

Suoqin Jin, C. Guerrero-Juarez, Lihua Zhang et al.

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues. Single-cell methods record molecule expressions of cells in a given tissue, but understanding interactions between cells remains challenging. Here the authors show by applying systems biology and machine learning approaches that they can infer and analyze cell-cell communication networks in an easily interpretable way.

Taiwen Li, Jingxin Fu, Zexian Zeng et al.

Abstract Tumor progression and the efficacy of immunotherapy are strongly influenced by the composition and abundance of immune cells in the tumor microenvironment. Due to the limitations of direct measurement methods, computational algorithms are often used to infer immune cell composition from bulk tumor transcriptome profiles. These estimated tumor immune infiltrate populations have been associated with genomic and transcriptomic changes in the tumors, providing insight into tumor–immune interactions. However, such investigations on large-scale public data remain challenging. To lower the barriers for the analysis of complex tumor–immune interactions, we significantly improved our previous web platform TIMER. Instead of just using one algorithm, TIMER2.0 (http://timer.cistrome.org/) provides more robust estimation of immune infiltration levels for The Cancer Genome Atlas (TCGA) or user-provided tumor profiles using six state-of-the-art algorithms. TIMER2.0 provides four modules for investigating the associations between immune infiltrates and genetic or clinical features, and four modules for exploring cancer-related associations in the TCGA cohorts. Each module can generate a functional heatmap table, enabling the user to easily identify significant associations in multiple cancer types simultaneously. Overall, the TIMER2.0 web server provides comprehensive analysis and visualization functions of tumor infiltrating immune cells.

Derrick E. Wood, Jennifer Lu, Ben Langmead

Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.

Yingyao Zhou, Bin Zhou, L. Pache et al.

A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era. With the increasing obtainability of multi-OMICs data comes the need for easy to use data analysis tools. Here, the authors introduce Metascape, a biologist-oriented portal that provides a gene list annotation, enrichment and interactome resource and enables integrated analysis of multi-OMICs datasets.

S. Balduzzi, G. Rücker, G. Schwarzer

Objective Meta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over the last three decades with mental health as a major research topic. It is then essential to well understand its methodology and interpret its results. In this publication, we describe how to perform a meta-analysis with the freely available statistical software environment R, using a working example taken from the field of mental health. Methods R package meta is used to conduct standard meta-analysis. Sensitivity analyses for missing binary outcome data and potential selection bias are conducted with R package metasens. All essential R commands are provided and clearly described to conduct and report analyses. Results The working example considers a binary outcome: we show how to conduct a fixed effect and random effects meta-analysis and subgroup analysis, produce a forest and funnel plot and to test and adjust for funnel plot asymmetry. All these steps work similar for other outcome types. Conclusions R represents a powerful and flexible tool to conduct meta-analyses. This publication gives a brief glimpse into the topic and provides directions to more advanced meta-analysis methods available in R.

P. Cunniff

Virginia Braun, Victoria Clarke

ABSTRACT Since initially writing on thematic analysis in 2006, the popularity of the method we outlined has exploded, the variety of TA approaches have expanded, and, not least, our thinking has developed and shifted. In this reflexive commentary, we look back at some of the unspoken assumptions that informed how we wrote our 2006 paper. We connect some of these un-identified assumptions, and developments in the method over the years, with some conceptual mismatches and confusions we see in published TA studies. In order to facilitate better TA practice, we reflect on how our thinking has evolved – and in some cases sedimented – since the publication of our 2006 paper, and clarify and revise some of the ways we phrased or conceptualised TA, and the elements of, and processes around, a method we now prefer to call reflexive TA.

S. Davis, Amanda Deliman, Breanya C. Hogue

This book investigates the alliance between deconstruction and feminism, highlighting some of the subversive strategies employed by both of these discursive modalities to undercut mainstream cultural cliches. Arguably, both types of discourse may be interpreted as synergistic effects of postmodernism, as they join forces to expose the construction of feminine/human nature, identity, and gender through discourses and other semiotic practices. Both lines of argument address some disquieting issues which present themselves as specifically postmodern, especially the cultural construction of nature, which is subjected to deconstructionist and ecocritical analysis. In examining the relation of latter-day feminisms (ecofeminism) to the postmodern project of deconstruction, this book addresses the question whether any kind of feminist discourse is possible, given the "death of the subject". Paradoxically, the very constituency through which any feminist discourse defines itself – i.e. woman or femininity – does seem to hold its position, in spite of its deconstructive "mise sous rature".

Sudhir Kumar, G. Stecher, Michael Li et al.

H. Hinterberger

Exploratory data analysis, or EDA for short, is a term coined by John W. Tukey for describing the act of looking at data to see what it seems to say. This article gives a description of some typical EDA procedures and discusses some of the principles of EDA. Copyright © 2009 John Wiley & Sons, Inc.

M. Aria, C. Cuccurullo

Virgilio Gómez-Rubio

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