ALBERT

Note: IntroductionSingle-particle motions -- Plasmas as fluids -- Waves in plasmas -- Diffusion and resistivity -- Equilibrium and stability -- Kinetic theory -- Nonlinear effects -- Special plasmas -- Plasma applications..

Note: Contents: The Theory of Externalities and Public Goods: The Lifework of Richard Cornes ; Efficiency in Contests Between Groups ; Multiple-Aggregate Games ; Strategic Coalition Formation in Global Public Good Provision ; Evolution of Consistent Conjectures in Semi-aggregative Representation of Games, with Applications to Public Good Games and Contests ; Mixed-Strategy Kant-Nash Equilibrium and Private Contributions to a Public Good ; Social Creation of Pro-social Preferences for Collective Action ; Community Size and Public Goods in Hume’s Treatise of Human Nature ; Decentralized Leadership ; Debt NeutralityWithout Altruism: Voluntary Contributions to Public Goods as ‘Operative Linkages’ ; Counterterrorism: A Public Goods Approach ; Linguistic Assimilation and Ethno-religious Conflict ; International Carbon Trade and National Taxes: Distributional Impacts of Double Regulation ; Thinking Local but Acting Global? The Interplay Between Local and Global Internalization of Externalities ; Showdown in Schönau: A Contest Case Study

Note: Contents Volume 1 Part I Natural Science Basics 1 Introduction into Physical Oceanography / Rebecca Hummels 2 Ecological Organization of the Sea / Birte Matthiessen, Franziska Julie Werner, and Matthias Paulsen 3 Marine Ecosystem Services / Markus Salomon and Henriette Dahms Part II Impacts of Sectoral Marine Activities 4 Impact of Fishing Activities on Marine Life / Gerd Kraus and Rabea Diekmann 5 Mariculture / Thomas A. Wilding, Kenneth D. Black, Steven Benjamins, and Iona Campbell 6 Shipping / Alan Simcock 7 Impacts of Coastal Developments on Ecosystems / Christian Winter 8 Offshore Oil and Gas Production and Transportation / Stanislav Patin 9 Exploitation of Offshore Wind Energy / Jens Lüdeke 10 Dredging for Navigation, for Environmental Cleanup, and for Sand/Aggregates / Craig Vogt, Eugene Peck, and Gregory Hartman 11 Environmental Risks of Deep-sea Mining / Philip P. E. Weaver, David S. M. Billett, and Cindy L. Van Dover 12 Dumped Chemical Weapons / Jacek Bełdowski 13 Marine Climate Engineering / David P. Keller Part III Impacts of Land-Based Activities 14 Agriculture / Oene Oenema, Qian Liu, and Jingmeng Wang 15 Land-Based Industries / Elisabeth Schmid 16 Land-Based Wastewater Management / Stephan Koester 17 Tourism / Alan Simcock Part IV Pollution from Diffuse Sources 18 Climate Change: Warming Impacts on Marine Biodiversity / Helmut Hillebrand, Thomas Brey, Julian Gutt, Wilhelm Hagen, Katja Metfies, Bettina Meyer, and Aleksandra Lewandowska 19 Ocean Acidification / Peter Thor and Sam Dupont 20 Pollution with Hazardous Substances / Katja Broeg and Norbert Theobald 21 Pollution with Radioactive Substances / Hartmut Nies 22 Eutrophication / Justus E. E. van Beusekom 23 Marine Litter / Stefanie Werner and Aleke Stöfen O’Brien 24 Input of Energy/Underwater Sound / Olaf Boebel, Elke Burkhardt, and Ilse van Opzeeland 25 Introduction of Non-indigenous Species / Ralph Kuhlenkamp and Britta Kind

Note: Contents Part I Setting the Scene The Anthropocene—What Does It Entail for Science? / Gesche Krause The Role of Knowledge Exchange in Earth System Science—The Earth System Knowledge Platform (ESKP) / Gesche Krause, Ute Münch, Jana Kandarr, Oliver Jorzik and Pia Klinghammer The AWI Approach at the Science-Stakeholder Interface / Gesche Krause, Klaus Grosfeld and Wolfgang Hiller Part II Dialogue Approaches of ESKP Contributions to AWI Knowledge Transfer Regional Awareness on Sea Level Rise Effects—What Do We Know About the South-Eastern North Sea Coast? / Nina Eschweiler, Tobias Dolch and Christian Buschbaum Climate Change and Biodiversity—Implications for the Local Fisheries Sector / Christina Hörterer, Maximilian Schupp, Andreas Benkens and Bela H. Buck Linking Biodiversity Research Communities / Sonja Knapp, Alexandra Kraberg, Stephan Frickenhaus, Stefan Klotz, Oliver Schweiger and Gesche Krause Engaging Forecast Users During the Year of Polar Prediction / Winfried Hoke, Kirstin Werner, Helge Goessling and Thomas Jung Governance of Resources for Arctic Sustainable Policy and Practice (GRASP)—Stakeholder Mapping / Sebastian Knecht, Andreas Herber and Kathrin Stephen Building Bridges at the Arctic Science-Policy Interface / Volker Rachold Part III Data-Products of ESKP Contributions to AWI Knowledge Transfer The Web Portal ‘meereisportal.de’ in Context of ESKP / Klaus Grosfeld, Renate Treffeisen, Jölund Asseng and Georg Heygster Knowledge Transfer by the Global Terrestrial Network for Permafrost (GTN-P) / Boris K. Biskaborn and Hugues Lantuit A Web-Based Information System for Macrobenthic Biodiversity in the German North Sea / Jan M. Holstein Tackling Marine Litter—LITTERBASE / Melanie Bergmann, Mine B. Tekman, Andreas Walter and Lars Gutow Part IV Modelling Approaches of ESKP Contributions to AWI Knowledge Transfer Arctic Sea Ice Change, Large-Scale Atmospheric Circulation Patterns and Extreme Climate and Weather in Europe / Ralf Jaiser and Dörthe Handorf Extending and Visualizing the TsunAWI Simulation Database of the Indonesia Tsunami Early Warning System (InaTEWS) / Antonia Immerz, Sven Harig and Natalja Rakowsky Streamflow Forecasting and Biodiversity / Monica Ionita, Madlene Pfeiffer and Stephan Frickenhaus Part V Pathways to Formalizing Knowledge Transfer Accompanying ESKP Projects—Development of a Process Assessment Strategy Within ESKP@AWI / Gesche Krause and Maximilian Felix Schupp Science and Society—The Time to Interact / Gesche Krause, Klaus Grosfeld and Annette Breckwoldt Erratum to: A Web-Based Information System for Macrobenthic Biodiversity in the German North Sea / Jan M. Holstein

Note: Contents 1 Introduction 1.1 Why Numerical Ecology? 1.2 Why R? 1.3 Readership and Structure of the Book 1.4 How to Use This Book 1.5 The Data Sets 1.5.1 The Doubs Fish Data 1.5.2 The Oribatid Mite Data 1.6 A Quick Reminder About Help Sources 1.7 Now It Is Time 2 Exploratory Data Analysis 2.1 Objectives 2.2 Data Exploration 2.2.1 Data Extraction 2.2.2 Species Data: First Contact 2.2.3 Species Data: A Closer Look 2.2.4 Ecological Data Transformation 2.2.5 Environmental Data 2.3 Conclusion 3 Association Measures and Matrices 3.1 Objectives 3.2 The Main Categories of Association Measures (Short Overview) 3.2.1 Q Mode and R Mode 3.2.2 Symmetrical or Asymmetrical Coefficients in Q Mode: The Double-Zero Problem 3.2.3 Association Measures for Qualitative or Quantitative Data 3.2.4 To Summarize 3.3 Q Mode: Computing Dissimilarity Matrices Among Objects 3.3.1 Q Mode: Quantitative Species Data 3.3.2 Q Mode: Binary (Presence-Absence) Species Data 3.3.3 Q Mode: Quantitative Data (Excluding Species Abundances) 3.3.4 Q Mode: Binary Data (Excluding Species Presence-Absence Data) 3.3.5 Q Mode: Mixed Types Including Categorical (Qualitative Multiclass) Variables 3.4 R Mode: Computing Dependence Matrices Among Variables 3.4.1 R Mode: Species Abundance Data 3.4.2 R Mode: Species Presence-Absence Data 3.4.3 R Mode: Quantitative and Ordinal Data (Other than Species Abundances) 3.4.4 R Mode: Binary Data (Other than Species Abundance Data) 3.5 Pre-transformations for Species Data 3.6 Conclusion 4 Cluster Analysis 4.1 Objectives 4.2 Clustering Overview 4.3 Hierarchical Clustering Based on Links 4.3.1 Single Linkage Agglomerative Clustering 4.3.2 Complete Linkage Agglomerative Clustering 4.4 Average Agglomerative Clustering 4.5 Ward's Minimum Variance Clustering 4.6 Flexible Clustering 4.7 Interpreting and Comparing Hierarchical Clustering Results 4.7.1 Introduction 4.7.2 Cophenetic Correlation 4.7.3 Looking for Inteipretable Clusters 4.8 Non-hierarchical Clustering 4.8.1 k-means Partitioning 4.8.2 Partitioning Around Medoids (PAM) 4.9 Comparison with Environmental Data 4.9.1 Comparing a Typology with External Data (ANOVA Approach) 4.9.2 Comparing Two Typologies (Contingency Table Approach) 4.10 Species Assemblages 4.10.1 Simple Statistics on Group Contents 4.10.2 Kendall's W Coefficient of Concordance 4.10.3 Species Assemblages in Presence-Absence Data 4.10.4 Species Co-occurrence Network 4.11 Indicator Species 4.11.1 Introduction 4.11.2 IndVal: Species Indicator Values 4.11.3 Correlation-Type Indices 4.12 Multivariate Regression Trees (MRT): Constrained Clustering 4.12.1 Introduction 4.12.2 Computation (Principle) 4.12.3 Application Using Packages mvpart and MVPARTwrap 4.12.4 Combining MRT and IndVal 4.13 MRT as a Monothetic Clustering Method 4.14 Sequential Clustering 4.15 A Very Different Approach: Fuzzy Clustering 4.15.1 Fuzzy c-means Using Package cluster's Function fanny () 4.15.2 Noise Clustering Using the vegclust () Function 4.16 Conclusion 5 Unconstrained Ordination 5.1 Objectives 5.2 Ordination Overview 5.2.1 Multidimensional Space 5.2.2 Ordination in Reduced Space 5.3 Principal Component Analysis (PCA) 5.3.1 Overview 5.3.2 PCA of the Environmental Variables of the Doubs River Data Using rda () 5.3.3 PCA on Transformed Species Data 5.3.4 Domain of Application of PCA 5.3.5 PCA Using Function PCA. newr () 5.3.6 Imputation of Missing Values in PCA 5.4 Correspondence Analysis (CA) 5.4.1 Introduction 5.4.2 CA Using Function cca () of Package vegan 5.4.3 CA Using Function CA. newr () 5.4.4 Arch Effect and Detrended Correspondence Analysis (DCA) 5.4.5 Multiple Correspondence Analysis (MCA) 5.5 Principal Coordinate Analysis (PCoA) 5.5.1 Introduction 5.5.2 Application of PCoA to the Doubs Data Set Using cmdscaleO and vegan 5.5.3 Application of PCoA to the Doubs Data Set Using pcoa () 5.6 Nonmetric Multidimensional Scaling (NMDS) 5.6.1 Introduction 5.6.2 Application to the Doubs Fish Data 5.6.3 PCoA or NMDS? 5.7 Hand-Written PCA Ordination Function 6 Canonical Ordination 6.1 Objectives 6.2 Canonical Ordination Overview 6.3 Redundancy Analysis (RDA) 6.3.1 Introduction 6.3.2 RDA of the Doubs River Data 6.3.3 Distance-Based Redundancy Analysis (db-RDA) 6.3.4 A Hand-Written RDA Function 6.4 Canonical Correspondence Analysis (CCA) 6.4.1 Introduction 6.4.2 CCA of the Doubs River Data 6.5 Linear Discriminant Analysis (LDA) 6.5.1 Introduction 6.5.2 Discriminant Analysis Using Ida () 6.6 Other Asymmetric Analyses 6.6.1 Principal Response Curves (PRC) 6.6.2 Co-correspondence Analysis (CoCA) 6.7 Symmetric Analysis of Two (or More) Data Sets 6.8 Canonical Correlation Analysis (CCorA) 6.8.1 Introduction 6.8.2 Canonical Correlation Analysis Using CCorA () 6.9 Co-inertia Analysis (CoIA) 6.9.1 Introduction 6.9.2 Co-inertia Analysis Using Function coinertia () of ade4 6.10 Multiple Factor Analysis (MFA) 6.10.1 Introduction 6.10.2 Multiple Factor Analysis Using FactoMineR 6.11 Relating Species Traits and Environment 6.11.1 The Fourth-Corner Method 6.11.2 RLQ Analysis 6.11.3 Application in R 6.12 Conclusion 7 Spatial Analysis of Ecological Data 7.1 Objectives 7.2 Spatial Structures and Spatial Analysis: A Short Overview 7.2.1 Introduction 7.2.2 Induced Spatial Dependence and Spatial Autocorrelation 7.2.3 Spatial Scale 7.2.4 Spatial Heterogeneity 7.2.5 Spatial Correlation or Autocorrelation Functions and Spatial Correlograms 7.2.6 Testing for the Presence of Spatial Correlation: Conditions 7.2.7 Modelling Spatial Structures 7.3 Multivariate Trend-Surface Analysis 7.3.1 Introduction 7.3.2 Trend-Surface Analysis in Practice 7.4 Eigenvector-Based Spatial Variables and Spatial Modelling 7.4.1 Introduction 7.4.2 Distance-Based Moran's Eigenvector Maps (dbMEM) and Principal Coordinates of Neighbour Matrices (PCNM) 7.4.3 MEM in a Wider Context: Weights Other than Geographic Distances 7.4.4 MEM with Positive or Negative Spatial Correlation: Which Ones should Be Used? 7.4.5 Asymmetric Eigenvector Maps (AEM): When Directionality Matters 7.5 Another Way to Look at Spatial Structures: Multiscale Ordination (MSO) 7.5.1 Principle 7.5.2 Application to the Mite Data - Exploratory Approach 7.5.3 Application to the Detrended Mite and Environmental Data 7.6 Space-Time Interaction Test in Multivariate ANOVA, Without Replicates 7.6.1 Introduction 7.6.2 Testing the Space-Time Interaction with the sti Functions 7.7 Conclusion 8 Community Diversity 8.1 Objectives 8.2 The Multiple Facets of Diversity 8.2.1 Introduction 8.2.2 Species Diversity Measured by a Single Number 8.2.3 Taxonomic Diversity Indices in Practice 8.3 When Space Matters: Alpha, Beta and Gamma Diversities 8.4 Beta Diversity 8.4.1 Beta Diversity Measured by a Single Number 8.4.2 Beta Diversity as the Variance of the Community Composition Table: SCBD and LCBD Indices 8.4.3 Partitioning Beta Diversity into Replacement, Richness Difference and Nestedness Components 8.5 Functional Diversity, Functional Composition and Phylogenetic Diversity of Communities 8.5.1 Alpha Functional Diversity 8.5.2 Beta Taxonomic, Phylogenetic and Functional Diversities 8.6 Conclusion Bibliography Index

Note: Contents I Plants as Unique Organisms; History and Tools of Plant Anatomy 1 The Nature of Plants 1.1 Plants Have Multiple Pigments with Multiple Functions 1.2 Plants Use Water, and the Properties of Water, in Unique Ways 1.3 Plants Use Anabolic Metabolism to Manufacture Every Molecule Needed for Growth and Produce Virtually No Waste 1.4 Cell Walls Are Nonliving Matrices Outside the Plant Cell Membrane that House and/or Perform a Variety of Functions 1.5 The Plant Life Cycle Alternates Between a Haploid Gametophyte Stage and a Diploid Sporophyte Stage 1.6 Meristematic Activity Continues Throughout the Life of a Plant 1.7 Fruits Disperse Seeds Through Space: Dormancy Disperses Seeds Through Time 1.8 Earth’s History Is Divided into Four Major Time Periods 1.8.1 The Precambrian: 4550 to 542 mya 1.8.2 The Paleozoic Era: 542 to 251 mya 1.8.3 The Mesozoic Era: 251–66 mya 1.8.4 The Cenozoic Era: 66 mya to Present 1.9 Life on Earth Has Experienced Five Mass Extinctions: A Sixth Is in Progress 1.10 Many Plants and Animals Have Coevolved 1.11 The Plant Body Consists of Four Organs 1.11.1 Roots 1.11.2 Stems 1.11.3 Leaves 1.11.4 Flowers and Fruit 1.12 Plant Organs Are Initially Made of Three Tissues 1.13 “Plant” Can Be Broadly Defined 1.14 Bryophytes Lack Vasculature and Produce Spores 1.15 Ferns and Fern Allies Are Seedless Tracheophytes 1.16 Gymnosperms Are Seed-Producing Tracheophytes that Lack Flowers and Fruit 1.17 Monocots and Eudicots Are the Two Largest Groups of Angiosperms 1.18 Understanding Plant Structure Requires a Sense of Scale 1.19 “Primary” and “Secondary” Are Important Concepts in Plant Anatomy 1.19.1 Primary Versus Secondary Growth and Meristems 1.19.2 Primary Versus Secondary Xylem and Phloem 1.19.3 Primary Versus Secondary Cell Walls 1.20 Chapter Review References and Additional Readings 2 Microscopy and Imaging 2.1 Robert Hooke, 1635–1703, Described a Cell as the Basic Unit of Life by Studying the Bark of the Cork Oak Tree, Quercus suber 2.2 Antoni Van Leeuwenhoek, 1632–1723, Was the First Scientist to Observe Microorganisms 2.3 Nehemiah Grew, 1641–1712, Was the Father of Plant Anatomy 2.4 Robert Brown, 1773–1858, Discovered the Nucleus of the Cell by Studying Orchid Petals 2.5 Katherine Esau, 1898–1997, Advanced the Field of Plant Anatomy with Her Influential Textbooks 2.6 Light Microscopy: The Most Useful Tool of the Plant Anatomist 2.7 The Compound Light Microscope Uses Multiple Lenses to Form and Capture Images 2.8 The Resolving Power of a Lens Places Limits on Resolution and Magnification 2.9 The Confocal Microscope Allows for Sharper Detail, Computer Control, and 3-D Imaging with a Modified Compound Microscope 2.10 Electron Microscopy Allows a View into the World of Cellular Ultrastructure 2.11 The Transmission Electron Microscope Reveals Internal Cellular Detail 2.12 The Scanning Electron Microscope Resolves Surface Detail 2.13 Different Microscopies Produce Different Images of the Same Specimen 2.14 Chapter Review References and Additional Readings II Cellular Plant Anatomy 3 Plant Cell Structure and Ultrastructure 3.1 Plant Cells Are Complex Structures 3.2 Plant Cells Synthesize an External Wall and Contain a Variety of Internal Compartments 3.3 Cells and Cell Organelles Are Typically Bound by Lipid Bilayer Membranes 3.4 Vacuoles Play a Role in Water and Ion Balance 3.5 Plastids Are a Diverse Family of Anabolic Organelles 3.5.1 Proplastid 3.5.2 Etioplast 3.5.3 Elaioplast 3.5.4 Amyloplast 3.5.5 Chromoplast 3.5.6 Gerontoplast 3.5.7 Chloroplast 3.5.8 Chloroplast Functions 3.5.9 The Dimorphic Chloroplasts of C 4 Photosynthesis 3.5.10 Guard Cell Chloroplasts 3.5.11 Sun Versus Shade Chloroplasts 3.6 All Plastids Are Developmentally Related 3.7 Mitochondria Synthesize ATP and Small Carbon Skeletons 3.8 Microbodies Are the Site of Specific Biochemical Pathways 3.9 The Endoplasmic Reticulum Synthesizes Proteins and Some Lipids 3.10 The Golgi Apparatus Processes and Packages Polysaccharides and Proteins for Secretion 3.11 The Nucleus Houses the Cell’s Genetic Material and Participates in Ribosome Synthesis 3.12 The Cytoskeleton Organizes the Cell and Helps Traffic Organelles 3.13 Chapter Review References and Additional Readings 4 Mitosis and Meristems 4.1 The Plant Cell Cycle Includes Interphase, Mitosis, and Cytokinesis 4.2 A Pre-prophase Microtubule Band Precedes Mitosis and Defines the Plane of Cell Division 4.3 Mitosis May Be Divided into Distinct, but Continuous, Stages 4.4 Cytokinesis Begins with Initiation of the Cell Plate and Grows by the Deposition of Callose 4.5 Microtubules Play a Critical Role in Mitosis and Cytokinesis 4.6 Apical Meristems Are the Sites of Primary Growth 4.7 The Shoot Apical Meristem Is the Site of Lateral Organ Initiation 4.8 Axillary Buds Arise De Novo in the Developing Leaf Axis 4.9 Tunica-Corpus Organization Describes Shoot Apical Meristem Growth in Many Eudicots 4.10 Gymnosperms Do Not Possess a Tunica-Corpus 4.11 The Root Apical Meristem Provides the Primary Growth of Roots 4.12 Lateral Roots Originate from Inside the Pericycle, Not from the Root Apical Meristem 4.13 Intercalary Meristems Contribute to Stem and Leaf Growth in Monocots 4.14 Many Lower Vascular Plants Have a Single Initial Cell in the Shoot and Root Apical Meristems 4.15 Lateral Meristems Are the Site of Secondary Growth in Eudicots 4.16 Chapter Review References and Additional Readings 5 Cell Walls 5.1 Transparent Plant Cell Walls Contain Cellulose and Are Synthesized to the Exterior of the Protoplast 5.2 Primary Cell Walls Are a Structural Matrix of Cellulose and Several Other Components 5.3 Plasmodesmata Connect Adjacent Cells Via Holes in the Primary Cell Wall 5.4 Secondary Cell Walls Are Rigid, Thick, and Lignified 5.5 Pits Are Holes in the Secondary Cell Wall 5.6 Transfer Cells Have Elaborated Primary Cell Walls for High Rates of Transport 5.7 Chapter Review References and Additional Readings 6 Parenchyma, Collenchyma, and Sclerenchyma 6.1 Parenchyma Cells Are the Most Common Plant Cell Type 6.2 Parenchyma Cells May Exhibit Totipotency 6.3 Collenchyma Cells Are Used for Support and Are the Least Common Cell Type 6.4 Birefringence Is a Common Phenomenon in Collenchyma Walls 6.5 Sclerenchyma Cells Provide Support, Protection, and Long-Distance Water Transport 6.6 Fibers Impart Support and Protection 6.7 Sclereids Are Reduced Sclerenchyma Cells That Occur Singly or in Clumps 6.8 Xylem Vessel Elements Are Water-Conducting Sclerenchyma 6.9 Chapter Review References and Additional Readings III Vascular Tissues 7 Xylem 7.1 Xylem Is a Complex Tissue Containing Multiple Cell Types, Each with a Specific Structure and Function 7.2 The Primary Functions of Xylem Are Water Conduction, Mineral Transport, and Support 7.3 Tracheids Are Imperforate Tracheary Elements and the Sole Water Conductors in Gymnosperms 7.4 Angiosperm Tracheids, Fiber Tracheids, and Libriform Fibers Represent a Continuum of Imperforate Tracheary Element Design and Function 7.5 Vessel Elements Are Perforate Cells and the Main Water Conductors in Angiosperms 7.6 Vessel Element Side Walls Are Patterned for Strength and Water Movement 7.7 Most Vessel Elements End in a Perforation Plate and Are Connected to Another Vessel Element 7.8 Xylem Parenchyma Are Living Cells Involved in Xylem Metabolism and Protection 7.9 Chapter Review References and Additional Readings 8 Phloem 8.1 Phloem Is a Complex Tissue Containing Multiple Cell Types, Each with a Specific Structure and Function 8.2 Phloem’s Main Function Is Photosynthate Translocation 8.3 Sieve Tube Elements Are Living Cells Responsible for Translocation 8.4 Companion Cells Support the Sieve Tube Element and Are Involved in Phloem Loading and Unloading in Angiosperms 8.5 Phloem Parenchyma Cells Are Involved in Radial Translocation, Xylem/Phloem Coordination, and Storage 8.6 Phloem Fibers Protect the Delicate Sieve Tubes 8.7 Secondary Phloem Typically Only Functions for One Growing Season 8.8 Gymnosperm Phloem Is Simpler Than An