09815nam 2200601 450 99646640700331620230622193910.03-030-73351-3(CKB)5470000001298874(MiAaPQ)EBC6794567(Au-PeEL)EBL6794567(OCoLC)1281582862(PPN)258299126(EXLCZ)99547000000129887420220719d2021 uy 0engurcnu||||||||txtrdacontentcrdamediacrrdacarrierStatistical analysis of microbiome data /Somnath Datta and Subharup Guha, editorsCham, Switzerland :Springer,[2021]©20211 online resource (348 pages)Frontiers in probability and the statistical sciences3-030-73350-5 Intro -- Preface -- Acknowledgments -- Contents -- Part I Preprocessing and Bioinformatics Pipelines -- Denoising Methods for Inferring Microbiome Community Content and Abundance -- 1 Introduction -- 2 Common Algorithmic Denoising Strategies -- 3 Model-Based Denoising -- 3.1 Hierarchical Divisive Clustering -- 3.2 Finite Mixture Model -- 3.3 Denoising Long-Read Technology -- 4 Model Assessment -- 4.1 With Known Truth -- 4.1.1 Accuracy in ASV Identification -- 4.1.2 Accuracy in Read Assignments -- 4.2 With Unknown Truth -- 4.2.1 Assessment with UMIs -- 4.2.2 Clustering Stability -- 5 Conclusions -- References -- Statistical and Computational Methods for Analysis of Shotgun Metagenomics Sequencing Data -- 1 Introduction -- 2 Methods for Species Identification and Quantification of Microorganisms -- 3 Metagenome Assembly and Applications -- 3.1 de Bruijn Assembly of a Single Genome -- 3.2 Modification for Metagenome and Metagenome-Assembled Genomes -- 3.3 Compacted de Bruijn Graph -- 4 Estimation of Growth Rates for Metagenome-Assembled Genomes (MAGs) -- 5 Methods for Identifying Biosynthetic Gene Clusters -- 5.1 A Hidden Markov Model-Based Approach -- 5.2 A Deep Learning Approach -- 5.3 BGC Identification Based on Metagenomic Data -- 6 Future Directions -- References -- Bioinformatics Pre-Processing of Microbiome Data with An Application to Metagenomic Forensics -- 1 Introduction -- 2 Bioinformatics Pipeline -- 2.1 Microbiome Data -- 2.2 Quality Control -- 2.3 Taxonomic Profiling -- 2.3.1 MetaPhlAn2 -- 2.3.2 Kraken2 -- 2.3.3 Kaiju -- 2.4 Computing facilities -- 3 Methodology -- 3.1 Pre-Processing and Feature Selection -- 3.2 Exploration of Candidate Classifiers -- 3.3 The Ensemble Classifier -- 3.4 Class Imbalance -- 3.5 Performance Measures -- 3.6 Data Analysis -- 4 Results -- 5 Discussion -- 6 Data Acknowledgement -- 7 Code Availability.References -- Part II Exploratory Analyses of Microbial Communities -- Statistical Methods for Pairwise Comparison of Metagenomic Samples -- 1 Introduction -- 2 Microbial Community Comparison Methods Based on OTU Abundance Data -- 3 Microbial Community Comparison Measures Based on a Phylogenetic Tree -- 3.1 The Fst Statistic and Phylogenetic Test for Comparing Communities -- 3.2 UniFrac, W-UniFrac, VAW-UniFrac, and Generalized UniFrac for Comparing Microbial Communities -- 3.3 VAW-UniFrac for Comparing Communities -- 4 Alignment-Free Methods for the Comparison of Microbial Communities -- 5 A Tutorial on the Use of UniFrac Type and Alignment-Free Dissimilarity Measures for the Comparison of Metagenomic Samples -- 5.1 Analysis Steps for UniFrac, W-UniFrac, Generalized UniFrac, and VAW-UniFrac -- 5.2 Analysis Steps for the Comparison of Microbial Communities Based on Alignment-Free Methods -- 6 Discussion -- References -- Beta Diversity and Distance-Based Analysis of Microbiome Data -- 1 Introduction -- 2 Quantifying Dissimilarity: Common Beta Diversity Metrics -- 3 Ordination and Dimension Reduction -- 3.1 Principal Coordinates Analysis -- 3.2 Double Principal Coordinate Analysis -- 3.3 Biplots -- 3.4 Accounting for Compositionality -- 3.5 Model-Based Ordination Using Latent Variables -- 4 Distance-Based Hypothesis Testing -- 4.1 Permutation Tests -- 4.2 Kernel Machine Regression Tests -- 4.3 Sum of Powered Score Tests -- 4.4 Adaptive Tests -- 4.5 Comparison of Distance-Based Tests -- 5 Strengths, Weaknesses, and Future Directions -- References -- Part III Statistical Models and Inference -- Joint Models for Repeatedly Measured Compositional and Normally Distributed Outcomes -- 1 Introduction -- 2 Motivating Data -- 3 Statistical Models -- 3.1 The Multinomial Logistic Mixed Model (MLMM) -- 3.2 Dirichlet-Multinomial Mixed Model (DMMM).3.3 Goodness of Fit -- 4 Simulation Studies -- 4.1 Simulation Setting -- 4.2 Simulation Results -- 5 Data Analysis -- 6 Discussion -- 7 Software -- Appendix -- References -- Statistical Methods for Feature Identification in Microbiome Studies -- 1 Introduction -- 2 Differential Abundance Analysis -- 2.1 Compositional Methods -- 2.2 Count-Based Methods -- 2.3 Additional Notes -- 3 Mediation Analysis -- 4 Feature Identification Adjusting for Confounding -- 4.1 Covariate Adjustment -- 4.2 Model-Based Standardization -- 5 Summary -- References -- Statistical Methods for Analyzing Tree-Structured Microbiome Data -- 1 Introduction -- 2 Modeling Multivariate Count Data -- 2.1 Dirichlet-Multinomial Model -- 2.2 Dirichlet-Tree Multinomial Model -- 2.3 Implementation and Illustration -- 3 Estimating Microbial Compositions -- 3.1 Empirical Bayes Normalization -- 3.2 Phylogeny-Aware Normalization -- 3.3 Statistical Analysis of Compositional Data -- 3.4 Implementation and Illustration -- 4 Regression with Compositional Predictors -- 4.1 Constrained Lasso and Log-Ratio Lasso -- 4.2 Subcomposition Selection -- 4.3 Phylogeny-Aware Subcomposition Selection -- 4.4 Linear Regression and Variable Fusion -- 5 Additional References -- 6 Discussion -- References -- A Log-Linear Model for Inference on Bias in Microbiome Studies -- 1 Introduction -- 2 Methods -- 2.1 The Brooks' Data -- 2.2 Setup and Estimation -- 2.3 Inference -- 2.4 Testability of the Hypothesis -- 2.4.1 Example: Testable Hypotheses for Main Effects -- 2.4.2 Example: Testable Hypotheses for Interaction Effects -- 3 Simulations -- 3.1 Main Effect Simulation -- 3.2 Interaction Effect Simulation Based on the Brooks Data -- 4 Results -- 4.1 Simulation Results -- 4.2 Do Interactions Between Taxa Affect Bias in the Brooks' Data? -- 4.3 Plate and Sample Type Effects in the Brooks' Data -- 5 Discussion -- Appendix.References -- Part IV Bayesian Methods -- Dirichlet-Multinomial Regression Models with Bayesian Variable Selection for Microbiome Data -- 1 Introduction -- 2 Methods -- 2.1 Dirichlet-Multinomial Regression Models for Compositional Data -- 2.2 Variable Selection Priors -- 2.3 Network Priors -- 2.3.1 Unknown G -- 2.4 Dirichlet-Tree Multinomial Models -- 2.5 Posterior Inference -- 3 Simulated Data -- 3.1 Simulation Study for DM Regression Models -- 3.2 DM Sensitivity Analysis -- 3.3 Simulation Study for DTM Regression Models -- 3.4 DTM Sensitivity Analysis -- 4 Applications -- 4.1 Multi-omics Microbiome Study-Pregnancy Initiative (MOMS-PI) -- 4.2 Gut Microbiome Study -- 5 Conclusion -- References -- A Bayesian Approach to Restoring the Duality Between Principal Components of a Distance Matrix and Operational Taxonomic Units in Microbiome Analyses -- 1 Introduction -- 1.1 Motivating Datasets -- 1.2 Nonlinear or Stochastic Distances -- 1.3 Limitations of SVD-Based Approaches -- 2 A Bayesian Formulation -- 2.1 Posterior Density -- 3 Model Sum of Squares and Biplots -- 4 Posterior Inference -- 4.1 Gibbs Sampler -- 4.2 Dimension Reduction: Skinny Bayesian Technique -- 4.2.1 Subsetted Data Matrix -- 4.2.2 Lower Dimensional Parameters and Induced Posterior -- 4.2.3 Faster Inference Procedure -- 4.3 Model Parameter Estimates -- 5 Simulation Study -- 5.1 Generation Strategy -- 6 Data Analysis -- 6.1 Tobacco Data -- 6.2 Subway Data -- 7 Data Acknowledgement -- 8 Discussion -- Supplementary Materials -- Appendix -- Proof of Lemma 1 -- References -- Part V Special Topics -- Tree Variable Selection for Paired Case-Control Studies with Application to Microbiome Data -- 1 Introduction -- 2 Gini Index -- 2.1 Simulation Analysis -- 3 Multivariate Gini Index -- 3.1 Conditional Gini Index -- 4 Variable Importance -- 5 Analysis of Obesity Using Microbiome Data.6 Discussion -- Appendix -- References -- Networks for Compositional Data -- 1 Introduction -- 2 Methods -- 2.1 Learning Networks from Marginal Associations -- 2.1.1 ReBoot -- 2.1.2 SparCC -- 2.1.3 CCLasso -- 2.1.4 COAT -- 2.2 Learning Networks from Conditional Associations -- 2.2.1 SPIEC-EASI -- 2.2.2 gCoda -- 2.2.3 SPRING -- 3 Data-Generating Models -- 3.1 Null Models -- 3.2 Copula Models -- 3.3 Logistic-Normal Model -- 4 Results -- 4.1 Spurious (Partial) Correlations -- 4.2 Performance in Network Discovery -- 4.3 Case Studies in R -- 5 Future Directions -- References -- Index.Frontiers in probability and the statistical sciences.MicrobiologyStatistical methodsMicrobiologiathubEstadística matemàticathubMicroorganismesthubGenètica microbianathubLlibres electrònicsthubMicrobiologyStatistical methods.MicrobiologiaEstadística matemàticaMicroorganismesGenètica microbiana579Datta SomnathGuha SubharupMiAaPQMiAaPQMiAaPQBOOK996466407003316Statistical analysis of microbiome data2901910UNISA05259nam 22005055 450 99656557060331620231209095929.03-11-072539-810.1515/9783110725391(CKB)29270034000041(DE-B1597)571514(DE-B1597)9783110725391(EXLCZ)992927003400004120231209h20232023 fg gerur|||||||||||txtrdacontentcrdamediacrrdacarrierSchein und Anschein Dynamiken ästhetischer Praxis in der Vormoderne /hrsg. von Annette Gerok-Reiter, Volker Leppin, Martin Kovacs, Irmgard Männlein-RobertBerlin ;Boston : De Gruyter, [2023]20231 online resource (LI, 423 p.)Andere Ästhetik - Koordinaten ,2751-2665 ;39783110692709 Frontmatter -- Vorwort -- Dank -- Inhaltsverzeichnis -- Zur Einführung: Schein und Anschein - ein Problemaufriss -- I. Zugänge -- Die Ambiguität des Schein(en)s und ihr Erkenntnispotenzial: appear - seem - shine -- ... quae cum franguntur apparet argentum. Zum Verhältnis ästhetischer Praxis und Theorie -- Die scheinbar präsente Göttin. Evokationen göttlicher Präsenz in Bildwerken und Monumenten archaischer und klassischer Zeit -- II. Der Schein als (göttliches) Leuchten -- Bildtechnik(en) - Formate - Referenzräume. Vom Monumentalmosaik zu Mosaikikonen: Die Durchlässigkeit zum Heiligen und Kunstfertigkeit -- Symphonialis est anima. Die Evidenz der Stimme und das Erscheinen der Sympathie bei Hildegard von Bingen -- Vom Scheinen der Herrlichkeit Gottes. Offenbarung als Theopoiese im Fließenden Licht der Gottheit -- manic wunder wilde. Zur epistemischen Verunsicherung zwischen Schein und Sein im Partonopier Konrads von Würzburg -- III. Der Schein als Sichtbarmachen und Verbergen -- Lumineszenz und Erscheinung in Theokrits Idyll 2: Die Hexe Simaitha -- Sichtbarkeit und Verborgenheit Gottes im lateinischen Werk Meister Eckharts -- klebewort und übergulde. Evidenz und dissimulatio in Gottfrieds Tristan mit einem Seitenblick auf Dante -- Figurae Mortis. Visuelle Rhetorik und die Permeabilität des Todes in Juan de Valdés Leals Hieroglyphen für die Iglesia de la Caridad in Sevilla -- IV. Der Schein als Provokation und Bedrohung -- Trügerischer Anschein und Nachdenken im ekphrastischen Epigramm und in der hellenistischen Philosophie -- "Geplerr vor den Augen". Zur Ambiguität des Scheins in der publizistischen Auseinandersetzung von Johann Weyer und Jean Bodin über das crimen magiæ -- Illusion und Narration. Die Dämonie des Erzählens um 1600 -- Barocker Schein und dämonische Täuschung. Die Ambiguität der Illusion in Frankreich um 1600 -- Abbildungsnachweise -- RegisterDer Sonderforschungsbereich Andere Ästhetik untersucht, wie vormoderne Artefakte ihren ästhetischen Status reflektieren. Hieran anknüpfend, geht der vorliegende Band einem seit der Antike bis heute zentralen Themenfeld ästhetischer Diskussion nach: der Spannung von Schein und Anschein. Ausgangspunkt ist die Polyvalenz von Begriff wie Phänomen des Scheins, die im Wesentlichen drei Möglichkeiten eröffnet: Schein als Leuchten, Schein als Sichtbarwerden und In-Erscheinung-Treten sowie Schein als ,bloßer' Schein, als Täuschung. Der Band diskutiert den variantenreichen Umgang mit Phänomenen von Schein, Erscheinung und Anschein anhand ausgewählter Texte, Monumente und Bildwerke von der Antike bis in die Frühe Neuzeit. Die Beiträge aus unterschiedlichen Disziplinen verfolgen dabei insbesondere die Frage, unter welchen kulturhistorischen Voraussetzungen und in welchen konkreten Formen ästhetische Konfigurationen als erkenntnisfördernder und ,erhellender' Schein, wann als verstellender, ja täuschender Anschein wahrgenommen und bewertet werden.This interdisciplinary volume addresses the tension between illusion and appearance. The starting point is three differentiated forms of "Schein" in German: as a ray of light itself, as in "shine," or appearance as becoming visible or, finally, as an illusion - seeming to be so. The contributions analyze under which cultural-historical conditions and within which concrete forms aesthetic configurations are perceived and evaluated.LITERARY CRITICISM / European / GeneralbisacshAesthetics.appearance.art.illusion.LITERARY CRITICISM / European / General.Gerok-Reiter Annette, edthttp://id.loc.gov/vocabulary/relators/edtKovacs Martin, edthttp://id.loc.gov/vocabulary/relators/edtLeppin Volker, edthttp://id.loc.gov/vocabulary/relators/edtMännlein-Robert Irmgard, edthttp://id.loc.gov/vocabulary/relators/edtSonderforschungsbereich 1391 Andere Ästhetikfndhttp://id.loc.gov/vocabulary/relators/fndDE-B1597DE-B1597BOOK996565570603316Schein und Anschein3602694UNISA01923nam 2200445 450 991082351610332120230801235849.01-68325-362-0(CKB)3790000000535534(MiAaPQ)EBC5151611(Au-PeEL)EBL5151611(CaPaEBR)ebr11468682(OCoLC)1013822509(EXLCZ)99379000000053553420171215h20122012 uy 0engurcnu||||||||rdacontentrdamediardacarrier30 millennia of sculpture /Joseph Manca [and four others]New York :Parkstone International,2012.©20121 online resource (780 pages) color illustrations, photographsIncludes index.1-84484-817-5 " From its prehistoric origins to the conceptual modernity of the 20th century, sculpture has literally and figuratively moulded the art world. Offering an integral vision of the evolution of forms across civilisations and epochs, 30 Centuries of Sculpture presents the masterpieces of sculpture that, with their intriguing silhouettes, have shaped the current notion of beauty. Sculptures can reflect an era, an artist, or his public; this gallery in high relief presents, with its numerous references, detailed commentaries on works, and biographies of artists, an open door to history and art, and an ideal guide for both students and neophytes"--Provided by publisher.SculptureHistorySculptureHistory.730.9ART026000ARC000000bisacshManca Joseph1956-724886Manca JosephMiAaPQMiAaPQMiAaPQBOOK991082351610332130 millennia of sculpture3986282UNINA