Science & Nature Books

Book SynopsisGuide to Foodborne Pathogens covers pathogens bacteria, viruses, and parasites that are most commonly responsible for foodborne illness.Table of ContentsContributors vii 1 Globalization and epidemiology of foodborne disease 1 Ewen C. D. Todd 2 Staphylococcus aureus 26 Reginald W. Bennett, Jennifer M. Hait and Sandra M. Tallent 3 Listeria monocytogenes 45 Catherine W. Donnelly and Francisco Diez-Gonzalez 4 Bacillus cereus 75 Toril Lindbäck and Per Einar Granum 5 Clostridium perfringens 82 Norma L. Heredia and Ronald G. Labbé 6 Clostridium botulinum 91 Barbara M. Lund and Michael W. Peck 7 Salmonella 112 Steven C. Ricke, Ok-Kyung Koo, Steven Foley and Rajesh Nayak 8 Shigella species 138 Keith A. Lampel 9 Vibrio vulnificus, Vibrio parahaemolyticus and Vibrio cholerae 148 Salina Parveen and Mark L. Tamplin 10 Yersinia enterocolitica 177 Saumya Bhaduri and James L. Smith 11 Campylobacter 188 Santos Garcia and Norma L. Heredia 12 Arcobacter and Helicobacter 197 Irene V. Wesley 13 Brucella 210 Axel Cloeckaert and Michel S. Zygmunt 14 Escherichia coli 222 Peter Feng 15 Cronobacter spp. (formerly Enterobacter sakazakii) 241 Qiongqiong Yan, Karen A. Power, Ben D. Tall and Séamus Fanning 16 Aflatoxins and Aspergillus flavus 257 Deepak Bhatnagar and Santos Garcia 17 Fusarium and fumonisins: Toxigenic Fusarium species in cereal grains and processed foods 273 Andreia Bianchini and Lloyd B. Bullerman 18 Other moulds and mycotoxins 284 Vicente Sanchis Almenar, Antonio J. Ramos girona and Sonia Marin Sillué 19 Foodborne protozoa 303 Ynes R. Ortega and Martin Kváè 20 Taenia solium, Taenia saginata and Taenia asiatica 317 Ana Flisser Steinbruch 21 Other foodborne helminthes 329 M. Guadalupe Ortega-Pierres, Gerardo Pérez-Ponce de León and Dante S. Zarlenga 22 Foodborne viruses 352 Anna M. Fabiszewski de Aceituno, Jennifer J. Rocks, Lee-Ann Jaykus and Juan S. Leon 23 Seafood toxins 377 James M. Hungerford 24 Prion diseases 399 Debbie McKenzie and Judd Aiken 25 Forthcoming new technologies for microbial detection 414 Arun K. Bhunia 26 Stress adaptation, survival and recovery of foodborne pathogens 422 Alissa M. Wesche and Elliot T. Ryser 27 Microbial biofilms and food safety 438 L. A. McLandsborough 28 Bacteriophage biocontrol 448 Lars Fieseler and Martin J. Loessner Index 457

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Book SynopsisThe first book to focus exclusively on the subject, Geodiversity, Second Edition describes the interrelationships between geodiversity and biodiversity, the value of geodiversity to society, as well as current threats to its existence. Illustrated with global case studies throughout, the book examines traditional approaches to protectinggeodiversity and the new management agenda now being implemented. The Second Edition of this successful textbook continues to build on the success of the first edition which is still the standard reference for the subject. Fully revised and updated throughout, the Second Edition now includes new material on geoparks, geotourism and implications of climate change for geoconservation. Reviews of previous edition: Murray Gray''s new book is the first widely available text to bring together and analyse some of these emerging ideas.The result is a book that should be in the library of every land manager and one that is lTrade Review“Let’s hope, for example, that those making decisions about the long-term response to recent flooding in the UK will have read this book and as a consequence work with, rather than against, geomorphological processes!.” (Geology Today, 1 September 2014) “Overall, ‘Geodiversity’ is a most valuable addi­tion to any geoscience library and I strongly recom­mend that people involved in geoconservation have a ready access to it. While the book provides us with a state-of-the-art (AD 2013), the fields of geodiversi­ty and geoconservation are highly dynamic and the perspectives for the future seem generally promis­ing. In this context, I hope that the strong assertion of the author that “there will not be a third edition” (p. viii) will not prove true and in some years from now we will enjoy an updated new edition of ‘Geodiversity’.” (Geologos, 1 June 2014) “It would be a fine basis for an advanced undergraduate or graduate level course and one that your students might actually read, the highest praise that I can give any textbook.” (Geological Journal, 1 June 2014) “The book can serve as an undergraduate/graduate-level textbook, but it will also have some appeal to professional geoscientist. Summing Up: Recommended. Upper-division undergraduates, graduate students, researchers/faculty, and professionals/practitioners.” (Choice, 1 July 2014)Table of ContentsPreface to Second Edition vii Preface to First Edition ix Part I What is Geodiversity? 1 1 Defining Geodiversity 3 2 Geodiversity: the Global Scale 15 3 Geodiversity: the Local Scale 29 Part II Values and Threats 73 4 Valuing Geodiversity in an ‘Ecosystem Services’ Context 75 5 Threats to Geodiversity 151 Part III Geoconservation: the ‘Protected Area’ Approach 193 6 International Geoconservation: an Introduction 195 7 World Heritage Sites 219 8 Global Geoparks 237 9 National Geoconservation 255 Part IV Geoconservation: the ‘Wider Landscape’ Approach 333 10 Geoconservation in the ‘Wider Landscape’ 335 11 Geoconservation and Land-use Planning 377 12 Geoconservation and Policy 393 Part V Putting It All Together 411 13 Geodiversity and Geoconservation: an Overview 413 14 Comparing and integrating geodiversity and biodiversity 429 15 A Future for Geodiversity? 449 References 455 Index 491

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Book SynopsisNonclinical Safety Assessment Nonclinical Safety Assessment A Guide to International Pharmaceutical Regulations Bringing a new drug to market is a costly time-consuming process. Increased regional and international regulation over the last twenty years, while necessary, has only served to amplify these costs. In response to this escalation, developmental strategies have shifted towards a more global approach. In order to create the most cost-effective and safe processes, it is critical for those bringing drugs to market to understand both the globally accepted regulations and the local variations. Nonclinical Safety Assessment: A Guide to International Pharmaceutical Regulations provides a practical description of nonclinical drug development regulations and requirements in the major market regions. It includes: ICH the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Trade Review“As a toxicologist with a quarter-century of experience in pharmaceutical drug development, I found the reading of this book thoroughly enjoyable and useful.” (British Toxicology Society Newsletter, 1 October 2013) Table of ContentsList of Contributors xvii Preface xix Part I International Regulations and Nonclinical Studies for Pharmaceuticals 1 1 Introduction 3 Kathy M. McGown and William J. Brock 1.1 The Global Pharmaceutical Market 6 1.2 Looking to the Future 9 1.3 Legal and Regulatory Considerations in Drug Development 10 1.4 The Drug Development Process – General Considerations 12 2 ICH: History and Nonclinical Guidances 17 Jan-Willem van der Laan and Kenneth L. Hastings 2.1 Introduction 17 2.2 Organization of the ICH 19 2.3 The ICH Process 20 2.4 Animal Welfare and Alternative Methods 22 2.5 ICH M3 23 2.6 New Initiatives and Topics 24 3 Food and Drug Administration: Nonclinical Program and Pharmaceutical Approval 27 William J. Brock and Kenneth L. Hastings 3.1 Legislative Authority of the FDA 27 3.2 Nonclinical Drug Development and the FDA 31 3.3 Nonclinical Testing: General Conditions and Considerations 34 3.4 Toxicity Testing: Small Molecules and Traditional Pharmaceuticals 34 3.5 Toxicity Testing of Pharmaceuticals – The General Approach 35 3.6 First-in-Human Dosing: Results from Nonclinical Studies 37 4 Nonclinical Pharmaceutical Development in MERCOSUR and Brazil 41 Cristiana Leslie Corr^ea, Giuliana Selmi, and Flavio Ailton Duque Zambrone 4.1 Introduction 41 4.2 MERCOSUR 41 4.3 Brazil 44 5 Nonclinical Safety Assessment: Canada 57 Jamie L. Doran and Mark T. Goldberg 5.1 Introduction 57 5.2 Organization of Health Canada 58 5.3 The Regulatory Framework for Drug Approval in Canada 60 5.4 Nonclinical Assessment in Canada 64 5.5 Clinical Trial Applications 70 5.6 Special Regulatory Considerations 74 6 European Pharmaceutical Regulation – Nonclinical Testing Requirements 79 Adam Woolley and Jan Willem van der Laan 6.1 Introduction 79 6.2.1 Overview 82 6.3 Nonclinical Testing in the Support of Clinical Trials 86 6.4 Overview 96 7 South Africa 99 Fariza Feraoun and Malik Feraoun 7.1 Introduction 99 7.2 Country Information 100 7.3 The Regulatory Aspects 101 7.4 The Nonclinical Safety Assessment 109 7.5 Conclusion 114 8 Asia Pacific: China 117 Lijie Fu and Qingli Wang 8.1 Introduction 117 8.2 History of Drug Administration 118 8.3 The Provisions for Drug Registration 122 8.4 The SFDA 123 8.5 The SFDA Affiliated Organizations 123 8.6 General Registration Procedures 125 8.7 Pharmaceutical Application 125 8.8 Import Drug Application 127 8.9 Testing Guidelines and Safety Evaluation 129 8.10 GLP Compliance in China 131 8.11 Animal Welfare Requirements 133 9 Pharmaceutical Regulations for Nonclinical Safety Assessment in Japan 135 Kazuichi Nakamura and Osamu Fueki 9.1 History of Regulation for Nonclinical Safety Assessment in Japan 135 9.2 Approval Application of New Drugs in Japan 136 9.3 Current Nonclinical Safety Guidelines Available in Japan 139 9.4 Current Trends of Conduct of Nonclinical Safety Evaluation in Japan 139 9.5 Safety Assessment of Unapproved Drugs 142 9.6 Necessity of 3Rs (Reduction/Refinement/Replacement) of Animal Studies 142 9.7 Attitude of Japanese Pharmaceutical Companies and the Regulatory Agency toward Nonclinical Safety Assessment 142 10 Indian Regulatory Process for Nonclinical Drug Development 145 K.S. Rao and S. Natesan 10.1 Introduction 145 10.2 Drug Development 146 10.3 Quality Systems 147 10.4 Nonclinical Drug Development – Key Regulatory Requirements 148 10.5 Nonclinical Safety Assessment – Key Approval Requirements 149 10.6 Data Required for Clinical Study Approval 151 10.7 Animal Toxicology 154 10.8 Animal Pharmacology 166 10.9 Safety Assessment Requirements: Indian Schedule Yand International Guidelines 168 10.10 Good Laboratory Practice Quality System in India 168 10.11 Safety Assessment Test Facilities in India 171 10.12 Investigational New Drug Application for Undertaking Clinical Trials 173 11 Asia Pacific: Australia 175 Douglas Francis 11.1 Introduction 175 11.2 Australian Therapeutic Goods Administration (TGA) 176 11.3 Clinical Trials in Australia 183 11.4 Nonclinical Data to Support the Conduct of Clinical Trials in Australia and Marketing Application to the TGA 188 Part II Toxicology Studies Supporting Clinical Development 197 12 Repeated-Dose Toxicity Studies in Nonclinical Drug Development 199 Shana Azri-Meehan and Louise Latriano 12.1 Introduction 199 12.2 General Considerations 200 12.3 Study Design Considerations 205 12.4 Study Observations and Assessments 211 13 Evaluation of Potential Carcinogenicity 219 James A. Popp and Matthew S. Bogdanffy 13.1 Introduction 219 13.2 Preparation for the Carcinogenicity Study 223 13.3 Elements of the Protocol/Study Plan 228 13.4 Study Performance 241 13.5 Alternative Models to Evaluate Potential Carcinogenicity in Lieu of a 2-Year Mouse Study 244 13.6 Special Consideration for Carcinogenicity Evaluation of Biotherapeutics 247 13.7 Regulatory Implications of a Study Identifying an Animal Carcinogenic Response 248 13.8 Interpreting the Relevance of Positive Results for Human Safety 249 13.9 Communicating the Results in the Product Label 251 14 Genetic Toxicology 255 Mark W. Powley 14.1 Background 255 14.2 Regulations Guiding Drug Development 256 14.3 Genotoxic Impurities 261 14.4 Regulatory Decision Making 263 15 Developmental and Reproductive Toxicology 265 Robert M. Parker and Raymond G. York 15.1 Introduction 265 15.2 Standard Reproduction and Developmental Toxicity Study Designs 266 15.3 Timing of Preclinical Developmental and Reproductive Toxicity Studies 273 15.4 Based on Disease Indication 275 15.5 Based on Pharmaceutical Characteristic 279 15.6 Other Reasons to Conduct Preclinical Reproductive and Developmental Toxicity Studies 291 15.7 Excipients 293 15.8 Conclusion 293 16 Juvenile Animal Toxicity Studies: Regulatory Expectations, Decision Strategies and Role in Paediatric Drug Development 297 Melissa S. Tassinari, Luc M. De Schaepdrijver, and Mark E. Hurtt 16.1 Introduction 297 16.2 Regulatory Environment 298 16.3 Relevance and Place in Drug Development 302 16.4 Strategies for Decision Making: When are Studies Needed and Appropriate? 304 16.5 Case Studies: Application of Data Review and Decision Making 307 16.6 Summary 309 17 Immunotoxicology 313 Leigh Ann Burns-Naas and Marc J. Pallardy 17.1 Introduction 313 17.2 Regulatory Expectations for the Immunotoxicology Evaluation of Pharmaceuticals 314 17.3 Special Considerations 335 17.4 Summary 342 References 342 18 Nonclinical Safety Assessment: Biotechnology-Derived Pharmaceuticals 347 Christopher E. Ellis, Melanie T. Hartsough, Martin D. Green, and Hanan Ghantous 18.1 Introduction 347 18.2 Unique Characteristics of Biopharmaceuticals 348 18.3 Species Selection 349 18.4 Immunogenicity 356 18.5 Biological Activity/Pharmacodynamics 358 18.6 Pharmacokinetics/Toxicokinetics 359 18.7 Nonclinical Safety Assessment 362 18.8 Tissue Cross-Reactivity (TCR) 371 18.9 Clinical Starting Dose Selection for Biopharmaceuticals 373 18.10 Comparability 375 19 International Safety Regulations for Vaccine Development 381 Robert V. House 19.1 Introduction 381 19.2 What "Toxicities" have been Attributed to Vaccination? 381 19.3 How Vaccines are (Slightly) Different from Other Biopharmaceuticals 383 19.4 Regulatory Framework for Assessing Safety of Vaccines 383 19.5 Parameters Monitored 387 19.6 Clinical Safety Assessment of Vaccines 389 19.7 Summary 390 20 Phototoxicity and Photocarcinogenicity 393 Robert E. Osterberg, Christopher P. Sambuco, and Paul Donald Forbes 20.1 History of Phototoxicity, Photocarcinogenicity and Photogenotoxicity Testing at the US Food and Drug Administration (FDA) 393 20.2 FDA Photosafety Testing Guidance 397 20.3 Status of In Vivo Testing for Photocarcinogenesis 417 20.4 Photocarcinogenesis Study Designs 418 20.5 Photo Co-Carcinogenesis 418 20.6 Future Testing Concepts, with Emphasis on Biomarkers 423 21 Degradants, Impurities, Excipients and Metabolites 431 Robert E. Osterberg and Mark W. Powley 21.1 Degradants, Impurities, and Excipients 431 21.2 Metabolites 442 References 446 Index 449

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Book SynopsisFor more information on this title, including student exercises, please visit, http://www.people.ex.ac.uk/DAColey/ Energy and Climate Change: Creating a Sustainable Future provides an up-to-date introduction to the subject examining the relationship between energy and our global environment. The book covers the fundamentals of the subject, discussing what energy is, why it is important, as well as the detrimental effect on the environment following our use of energy. Energy is placed at the front of a discussion of geo-systems, living systems, technological development and the global environment, enabling the reader to develop a deeper understanding of magnitudes. Learning is re-enforced, and the relevance of the topic broadened, through the use of several conceptual veins running through the book. One of these is an attempt to demonstrate how systems are related to each other through energy and energy flows. Examples being wind-power, and bio-mass which are reaTrade Review"At its modest price it must represent the bargain of the year." (Chromatographia, July 2010) "As a text book for GCSE level students, this title is worthy of 4 stars." (Enagri eMagazine, May 2010)Table of ContentsPreface. 1. Introduction. Part I: Energy: concepts, history and problems. 2. Energy. What is energy? Units. Power. Energy in various disguises. Energy quality and exergy. Student exercises. 3. The planet’s energy balance. The sun. The earth. Comparisons. Student exercises. 4. A history of humankind’s use of energy. Energy and society. Wealth, urbanization and conflict. Our current level of energy use. Student exercises. 5. Sustainability, climate change and the global environment. Sustainability. Climate change. Other concerns. Debating climate change and answering the sceptics. Student exercises. 6. Economics and the environment. Key concepts. Environmental economics. Student exercises. 7. Combustion, inescapable inefficiencies and the generation of electricity. Combustion. Calorific values. Inescapable inefficiencies. Heat pumps. Double Carnot efficiencies. The generation of electricity from heat. Student exercises. Part II – Unsustainable energy technologies. 8. Coal. History. Extraction. The combustion of coal. Technologies for use. Example applications. Global resource. Student exercises. 9. Oil. Extraction. The combustion of oil. Technologies for use. Example application: the motor car. Global resource. Student exercises. 10. Gas. Extraction. The combustion of gas. Technologies for use. Example application: the domestic boiler. Global resource. Student exercises. 11. Non-conventional hydrocarbons. Oil shale. Tar sands. Methane hydrate. Student exercises. 12. Nuclear power. Physical basis. Technologies for use. Environmental concerns. Waste. World resource. Example applications. Is nuclear power the solution to global warming? Student exercises. 13. Hydropower. History. Technologies for use. Example application: Itaipu hydroelectric station. Environmental impacts. Pumped storage. Global resource. Student exercises. 14. Transport and air quality. Present day problems. Air quality and health. Example application: air quality in Exeter, UK. Student exercises. 15. Figures and philosophy: an analysis of a nation’s energy supply. The economy. Production. Consumption. Oil and gas production. Prices. Fuel poverty. Carbon emissions. Sustainable energy in the UK: the current state of play. Student exercises. Part III – Climate change: predictions and policies. 16. Future world energy use and carbon emissions. The world's future use of energy. Student exercises. 17. The impact of a warmer world. Climate models. Natural variability and model reliability. Future climate change. Impacts. Costing the impact. Student exercises. 18. Politics in the greenhouse: contracting and converging. Climate negotiations. Another approach. Bringing it all together. Conclusion. Student exercises. Part IV – Sustainable energy technologies Current world sustainable energy provision. 19. Energy efficiency. Cogeneration. Reducing energy losses. Energy recovery. Energy efficiency in buildings. Student exercises. 20. Solar power. Passive solar heating. Heat pumps. Solar water heating. Low temperature solar water heating. Example application: solar water heating, Phoenix Federal Correction Institution, USA. High temperature solar power. Low temperature water-based thermal energy conversion. OECD resource. Student exercises. 21. Photovoltaics. History. Basic principles. Technologies for use. Electrical characteristics. Roof-top PV. Example application: Doxford Solar Office, UK. OECD resource. Student exercises. 22. Wind power. History. Technologies for use. The modern horizontal axis wind turbine. Environmental impacts. OECD resource. Example application: Harøy Island Wind Farm, Sandøy, Norway. Student exercises. 23. Wave power. Wave characteristics. Technologies for use. Example application: the Pelamis P-750 wave energy converter. Student exercises. 24. Tidal and small-scale hydropower. Tides. Small-scale hydropower. OECD resource. Student exercises. 25. Biomass. History. Basic principles. Technologies for use. Example application: anaerobic digester, Walford College Farm, UK. Global resource. OECD resource. Student exercises. 26. Geothermal. Background. History. Resource and technology. Technologies for use. Environmental problems. World resource. OECD resource. Example application: Hacchobaru geothermal power station, Kokonoe-machi, Japan. Student exercises. 27. Fast breeders and fusion. Fast breeder reactors. Fusion. Example application: JET Torus, Culham, UK. Student exercises. 28. Alternative transport futures and the hydrogen economy. Improving energy efficiency. Alternative transport fuels and engines. Hydrogen powered vehicles and the hydrogen economy. Fuel cells. Example application: the greening of natural gas. Student exercises. 29. Carbon sequestration and climate engineering. Capture technologies. Storage technologies. The reflection of solar radiation. Example application: Statoil, Sleipner West gas field, North Sea. Student exercises. 30. A sustainable, low carbon future? Methodology and assumptions. Results. Worldwide reductions. Conclusion. What can I do? Student exercises. References. Appendix 1: National energy data. Appendix 2: Answers to in-text problems. Appendix 3: Bibliography and suggested reading. Appendix 4: Useful data. Index.

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Book SynopsisPlant biomass is attracting increasing attention as a sustainable resource for large-scale production of renewable fuels and chemicals. However, in order to successfully compete with petroleum, it is vital that biomass conversion processes are designed to minimize costs and maximize yields.Table of ContentsList of Contributors xvii Foreword xxi Series Preface xxiii Preface xxv Acknowledgements xxvii 1 Introduction 1 Charles E. Wyman 1.1 Cellulosic Biomass: What and Why? 2 1.2 Aqueous Processing of Cellulosic Biomass into Organic Fuels and Chemicals 3 1.3 Attributes for Successful Pretreatment 5 1.4 Pretreatment Options 7 1.5 Possible Blind Spots in the Historic Pretreatment Paradigm 8 1.6 Other Distinguishing Features of Pretreatment Technologies 9 1.7 Book Approach 9 1.8 Overview of Book Chapters 10 Acknowledgements 10 References 11 2 Cellulosic Biofuels: Importance, Recalcitrance, and Pretreatment 17 Lee Lynd and Mark Laser 2.1 Our Place in History 17 2.2 The Need for Energy from Biomass 17 2.3 The Importance of Cellulosic Biomass 18 2.4 Potential Barriers 18 2.5 Biological and Thermochemical Approaches to the Recalcitrance Barrier 19 2.6 Pretreatment 20 Acknowledgements 21 References 21 3 Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion 23 Brian H. Davison, Jerry Parks, Mark F. Davis and Bryon S. Donohoe 3.1 Introduction 23 3.2 Biomass Diversity Leads to Variability in Cell-wall Structure and Composition 24 3.3 Processing Options for Accessing the Energy in the Lignocellulosic Matrix 26 3.4 Plant Tissue and Cell Types Respond Differently to Biomass Conversion 28 3.5 The Basics of Plant Cell-wall Structure 29 3.6 Cell-wall Surfaces and Multilamellar Architecture 30 3.7 Cell-wall Ultrastructure and Nanoporosity 31 3.8 Computer Simulation in Understanding Biomass Recalcitrance 32 3.8.1 What Can We Learn from Molecular Simulation? 32 3.8.2 Simulations of Lignin 33 3.8.3 Simulations of Cellulose 34 3.8.4 Simulation of Lignocellulosic Biomass 35 3.8.5 Outlook for Biomass Simulations 35 3.9 Summary 35 Acknowledgements 36 References 36 4 Biological Conversion of Plants to Fuels and Chemicals and the Effects of Inhibitors 39 Eduardo Ximenes, Youngmi Kim and Michael R. Ladisch 4.1 Introduction 39 4.2 Overview of Biological Conversion 40 4.3 Enzyme and Ethanol Fermentation Inhibitors Released during Pretreatment and/or Enzyme Hydrolysis 42 4.3.1 Enzyme Inhibitors Derived from Plant Cell-wall Constituents (Lignin, Soluble Phenolics, and Hemicellulose) 43 4.3.2 Effect of Furfurals and Acetic Acid as Inhibitors of Ethanol Fermentations 48 4.4 Hydrolysis of Pentose Sugar Oligomers Using Solid-acid Catalysts 50 4.4.1 Application of Solid-acid Catalysts for Hydrolysis of Sugar Oligomers Derived from Lignocelluloses 50 4.4.2 Factors Affecting Efficiency of Solid-acid-catalyzed Hydrolysis 51 4.5 Conclusions 56 Acknowledgements 57 References 57 5 Catalytic Strategies for Converting Lignocellulosic Carbohydrates to Fuels and Chemicals 61 Jesse Q. Bond, David Martin Alonso and James A. Dumesic 5.1 Introduction 61 5.2 Biomass Conversion Strategies 62 5.3 Criteria for Fuels and Chemicals 64 5.3.1 General Considerations in the Production of Fuels and Fuel Additives 64 5.3.2 Consideration for Specialty Chemicals 66 5.4 Primary Feedstocks and Platforms 66 5.4.1 Cellulose 66 5.4.2 Hemicellulose 67 5.5 Sugar Conversion and Key Intermediates 68 5.5.1 Sugar Oxidation 69 5.5.2 Sugar Reduction (Polyol Production) 70 5.5.3 Sugar Dehydration (Furan Production) 77 5.6 Conclusions 91 Acknowledgements 92 References 92 6 Fundamentals of Biomass Pretreatment at Low pH 103 Heather L. Trajano and Charles E. Wyman 6.1 Introduction 103 6.2 Effects of Low pH on Biomass Solids 104 6.2.1 Cellulose 104 6.2.2 Hemicellulose 105 6.2.3 Lignin 106 6.2.4 Ash 107 6.2.5 Ultrastructure 107 6.2.6 Summary of Effects of Low pH on Biomass Solids 108 6.3 Pretreatment in Support of Biological Conversion 108 6.3.1 Hydrolysis of Cellulose to Fermentable Glucose 108 6.3.2 Pretreatment for Improved Enzymatic Digestibility 109 6.3.3 Pretreatment for Improved Enzymatic Digestibility and Hemicellulose Sugar Recovery 110 6.4 Low-pH Hydrolysis of Cellulose and Hemicellulose 114 6.4.1 Furfural 114 6.4.2 Levulinic Acid 115 6.4.3 Drop-in Hydrocarbons 115 6.5 Models of Low-pH Biomass Reactions 116 6.5.1 Cellulose Hydrolysis 117 6.5.2 Hemicellulose Hydrolysis 118 6.5.3 Summary of Kinetic Models 120 6.6 Conclusions 122 Acknowledgements 123 References 123 7 Fundamentals of Aqueous Pretreatment of Biomass 129 Nathan S. Mosier 7.1 Introduction 129 7.2 Self-ionization of Water Catalyzes Plant Cell-wall Depolymerization 130 7.3 Products from the Hydrolysis of the Plant Cell Wall Contribute to Further Depolymerization 131 7.4 Mechanisms of Aqueous Pretreatment 131 7.4.1 Hemicellulose 131 7.4.2 Lignin 134 7.4.3 Cellulose 136 7.5 Impact of Aqueous Pretreatment on Cellulose Digestibility 137 7.6 Practical Applications of Liquid Hot Water Pretreatment 138 7.7 Conclusions 140 References 140 8 Fundamentals of Biomass Pretreatment at High pH 145 Rocıo Sierra Ramirez, Mark Holtzapple and Natalia Piamonte 8.1 Introduction 145 8.2 Chemical Effects of Alkaline Pretreatments on Biomass Composition 146 8.2.1 Non-oxidative Delignification 147 8.2.2 Non-oxidative Sugar Degradation 148 8.2.3 Oxidative Delignification 150 8.2.4 Oxidative Sugar Degradation 151 8.3 Ammonia Pretreatments 153 8.4 Sodium Hydroxide Pretreatments 155 8.5 Alkaline Wet Oxidation 155 8.6 Lime Pretreatment 158 8.7 Pretreatment Severity 161 8.8 Pretreatment Selectivity 161 8.9 Concluding Remarks 163 References 163 9 Primer on Ammonia Fiber Expansion Pretreatment 169 S.P.S. Chundawat, B. Bals, T. Campbell, L. Sousa, D. Gao, M. Jin, P. Eranki, R. Garlock, F. Teymouri, V. Balan and B.E. Dale 9.1 Historical Perspective of Ammonia-based Pretreatments 169 9.2 Overview of AFEX and its Physicochemical Impacts 170 9.3 Enzymatic and Microbial Activity on AFEX-treated Biomass 175 9.3.1 Impact of AFEX Pretreatment on Cellulase Binding to Biomass 175 9.3.2 Enzymatic Digestibility of AFEX-treated Biomass 176 9.3.3 Microbial Fermentability of AFEX-treated Biomass 178 9.4 Transgenic Plants and AFEX Pretreatment 183 9.5 Recent Research Developments on AFEX Strategies and Reactor Configurations 185 9.5.1 Non-extractive AFEX Systems 185 9.5.2 Extractive AFEX Systems 186 9.5.3 Fluidized Gaseous AFEX Systems 186 9.6 Perspectives on AFEX Commercialization 186 9.6.1 AFEX Pretreatment Commercialization in Cellulosic Biorefineries 186 9.6.2 Novel Value-added Products from AFEX-related Processes 190 9.6.3 AFEX-centric Regional Biomass Processing Depot 192 9.7 Environmental and Life-cycle Analyses for AFEX-centric Processes 193 9.8 Conclusions 194 Acknowledgements 195 References 195 10 Fundamentals of Biomass Pretreatment by Fractionation 201 Poulomi Sannigrahi and Arthur J. Ragauskas 10.1 Introduction 201 10.2 Organosolv Pretreatment 202 10.2.1 Organosolv Pulping 202 10.2.2 Overview of Organosolv Pretreatment 202 10.2.3 Solvents and Catalysts for Organosolv Pretreatment 203 10.2.4 Fractionation of Biomass during Organosolv Pretreatment 209 10.3 Nature of Organosolv Lignin and Chemistry of Organosolv Delignification 210 10.3.1 Composition and Structure of Organosolv Lignin 210 10.3.2 Mechanisms of Organosolv Delignification 213 10.3.3 Commercial Applications of Organosolv Lignin 214 10.4 Structural and Compositional Characteristics of Cellulose 214 10.5 Co-products of Biomass Fractionation by Organosolv Pretreatment 216 10.5.1 Hemicellulose 216 10.5.2 Furfural 217 10.5.3 Hydroxymethylfurfural (HMF) 218 10.5.4 Levulinic Acid 218 10.5.5 Acetic Acid 219 10.6 Conclusions and Recommendations 219 Acknowledgements 219 References 219 11 Ionic Liquid Pretreatment: Mechanism, Performance, and Challenges 223 Seema Singh and Blake A. Simmons 11.1 Introduction 223 11.2 Ionic Liquid Pretreatment: Mechanism 225 11.2.1 IL Polarity and Kamlet–Taft Parameters 226 11.2.2 Interactions between ILs and Cellulose 226 11.2.3 Interactions between ILs and Lignin 227 11.3 Ionic Liquid Biomass Pretreatment: Enzymatic Route 228 11.3.1 Grasses 228 11.3.2 Agricultural Residues 230 11.3.3 Woody Biomass 230 11.4 Ionic Liquid Pretreatment: Catalytic Route 231 11.4.1 Acid-catalyzed Hydrolysis 232 11.4.2 Metal-catalyzed Hydrolysis 232 11.5 Factors Impacting Scalability and Cost of Ionic Liquid Pretreatment 233 11.6 Concluding Remarks 234 Acknowledgements 234 References 234 12 Comparative Performance of Leading Pretreatment Technologies for Biological Conversion of Corn Stover, Poplar Wood, and Switchgrass to Sugars 239 Charles E. Wyman, Bruce E. Dale, Venkatesh Balan, Richard T. Elander, Mark T. Holtzapple, Rocıo Sierra Ramirez, Michael R. Ladisch, Nathan Mosier, Y.Y. Lee, Rajesh Gupta, Steven R. Thomas, Bonnie R. Hames, Ryan Warner and Rajeev Kumar 12.1 Introduction 240 12.2 Materials and Methods 242 12.2.1 Feedstocks 242 12.2.2 Enzymes 243 12.2.3 CAFI Pretreatments 243 12.2.4 Material Balances 244 12.2.5 Free Sugars and Extraction 244 12.3 Yields of Xylose and Glucose from Pretreatment and Enzymatic Hydrolysis 245 12.3.1 Yields from Corn Stover 245 12.3.2 Yields from Standard Poplar 247 12.3.3 Yields from Dacotah Switchgrass 248 12.4 Impact of Changes in Biomass Sources 249 12.5 Compositions of Solids Following CAFI Pretreatments 251 12.5.1 Composition of Pretreated Corn Stover Solids 252 12.5.2 Composition of Pretreated Switchgrass Solids 252 12.5.3 Composition of Pretreated Poplar Solids 253 12.5.4 Overall Trends in Composition of Pretreated Biomass Solids and Impact on Enzymatic Hydrolysis 253 12.6 Pretreatment Conditions to Maximize Total Glucose Plus Xylose Yields 254 12.7 Implications of the CAFI Results 255 12.8 Closing Thoughts 256 Acknowledgements 257 References 258 13 Effects of Enzyme Formulation and Loadings on Conversion of Biomass Pretreated by Leading Technologies 261 Rajesh Gupta and Y.Y. Lee 13.1 Introduction 261 13.2 Synergism among Cellulolytic Enzymes 262 13.3 Hemicellulose Structure and Hemicellulolytic Enzymes 263 13.4 Substrate Characteristics and Enzymatic Hydrolysis 264 13.5 Xylanase Supplementation for Different Pretreated Biomass and Effect of b-Xylosidase 265 13.6 Effect of b-Glucosidase Supplementation 269 13.7 Effect of Pectinase Addition 269 13.8 Effect of Feruloyl Esterase and Acetyl Xylan Esterase Addition 270 13.9 Effect of a-L-arabinofuranosidase and Mannanase Addition 270 13.10 Use of Lignin-degrading Enzymes (LDE) 271 13.11 Effect of Inactive Components on Biomass Hydrolysis 271 13.12 Adsorption and Accessibility of Enzyme with Different Cellulosic Substrates 271 13.13 Tuning Enzyme Formulations to the Feedstock 272 13.14 Summary 273 References 274 14 Physical and Chemical Features of Pretreated Biomass that Influence Macro-/Micro-accessibility and Biological Processing 281 Rajeev Kumar and Charles E. Wyman 14.1 Introduction 281 14.2 Definitions of Macro-/Micro-accessibility and Effectiveness 283 14.3 Features Influencing Macro-accessibility and their Impacts on Enzyme Effectiveness 284 14.3.1 Lignin 284 14.3.2 Hemicellulose 286 14.4 Features Influencing Micro-accessibility and their Impact on Enzymes Effectiveness 289 14.4.1 Cellulose Crystallinity (Structure) 289 14.4.2 Cellulose Chain Length/Reducing Ends 291 14.5 Concluding Remarks 293 Acknowledgements 296 References 296 15 Economics of Pretreatment for Biological Processing 311 Ling Tao, Andy Aden and Richard T. Elander 15.1 Introduction 311 15.2 Importance of Pretreatment 311 15.3 History of Pretreatment Economic Analysis 313 15.4 Methodologies for Economic Assessment 314 15.5 Overview of Pretreatment Technologies 315 15.5.1 Acidic Pretreatments 315 15.5.2 Alkaline Pretreatments 315 15.5.3 Solvent-based Pretreatments 316 15.6 Comparative Pretreatment Economics 316 15.6.1 Modeling Basis and Assumptions for Comparative CAFI Analysis 317 15.6.2 CAFI Project Comparative Data 320 15.6.3 Reactor Design and Costing Data 320 15.6.4 Comparison of Sugar and Ethanol Yields 324 15.6.5 Comparison of Pretreatment Capital Costs 325 15.6.6 Comparison of MESP 326 15.7 Impact of Key Variables on Pretreatment Economics 327 15.7.1 Yield 327 15.7.2 Conversion to Oligomers/Monomers (Shift of Burden between Enzymes and Pretreatment) 328 15.7.3 Biomass Loading/Concentration 328 15.7.4 Chemical Loading/Recovery/Metallurgy 329 15.7.5 Reaction Conditions: Pressure, Temperature, Residence Time 330 15.7.6 Reactor Orientation: Horizontal/Vertical 330 15.7.7 Batch versus Continuous Processing 330 15.8 Future Needs for Evaluation of Pretreatment Economics 331 15.9 Conclusions 332 Acknowledgements 332 References 332 16 Progress in the Summative Analysis of Biomass Feedstocks for Biofuels Production 335 F.A. Agblevor and J. Pereira 16.1 Introduction 335 16.2 Preparation of Biomass Feedstocks for Analysis 337 16.3 Determination of Non-structural Components of Biomass Feedstocks 338 16.3.1 Moisture Content of Biomass Feedstocks 338 16.3.2 Determination of Ash in Biomass 338 16.3.3 Protein Content of Biomass 338 16.3.4 Extractives Content of Biomass 339 16.4 Quantitative Determination of Lignin Content of Biomass 340 16.5 Quantitative Analysis of Sugars in Lignocellulosic Biomass 342 16.5.1 Holocellulose Content of Plant Cell Walls 342 16.5.2 Monoethanolamine Method for Cellulose Determination 343 16.6 Chemical Hydrolysis of Biomass Polysaccharides 343 16.6.1 Mineral Acid Hydrolysis 343 16.6.2 Trifluoroacetic Acid (TFA) 344 16.6.3 Methanolysis 344 16.7 Analysis of Monosaccharides 345 16.7.1 Colorimetric Analysis of Biomass Monosaccharides 345 16.7.2 Gas Chromatographic Sugar Analysis 345 16.8 Gas Chromatography-Mass Spectrometry (GC/MS) 347 16.9 High-performance Liquid Chromatographic Sugar Analysis 347 16.10 NMR Analysis of Biomass Sugars 349 16.11 Conclusions 349 References 349 17 High-throughput NIR Analysis of Biomass Pretreatment Streams 355 Bonnie R. Hames 17.1 Introduction 355 17.2 Rapid Analysis Essentials 356 17.2.1 Rapid Spectroscopic Techniques 357 17.2.2 Calibration and Validation Samples 358 17.2.3 Quality Calibration Data for Each Calibration Sample 359 17.2.4 Multivariate Analysis to Resolve Complex Sample Spectra 362 17.2.5 Validation of New Methods 364 17.2.6 Standard Reference Materials and Protocols for Ongoing QA/QC 364 17.3 Summary 366 References 367 18 Plant Biomass Characterization: Application of Solution- and Solid-state NMR Spectroscopy 369 Yunqiao Pu, Bassem Hallac and Arthur J. Ragauskas 18.1 Introduction 369 18.2 Plant Biomass Constituents 370 18.3 Solution-state NMR Characterization of Lignin 371 18.3.1 Lignin Sample Preparation 372 18.3.2 1 H NMR Spectroscopy 372 18.3.3 13 c NMR Spectroscopy 372 18.3.4 HSQC Correlation Spectroscopy 375 18.3.5 31 P NMR Spectroscopy 377 18.4 Solid-state NMR Characterization of Plant Cellulose 381 18.4.1 CP/MAS 13 C NMR Analysis of Cellulose 381 18.4.2 Cellulose Crystallinity 383 18.4.3 Cellulose Ultrastructure 385 18.5 Future Perspectives 387 Acknowledgements 387 References 387 19 Xylooligosaccharides Production, Quantification, and Characterization in Context of Lignocellulosic Biomass Pretreatment 391 Qing Qing, Hongjia Li, Rajeev Kumar and Charles E. Wyman 19.1 Introduction 391 19.1.1 Definition of Oligosaccharides 391 19.1.2 Types of Oligosaccharides Released during Lignocellulosic Biomass Pretreatment 392 19.1.3 The Importance of Measuring Xylooligosaccharides 392 19.2 Xylooligosaccharides Production 394 19.2.1 Thermochemical Production of XOs 394 19.2.2 Production of XOs by Enzymatic Hydrolysis 396 19.3 Xylooligosaccharides Separation and Purification 397 19.3.1 Solvent Extraction 397 19.3.2 Adsorption by Surface Active Materials 397 19.3.3 Chromatographic Separation Techniques 398 19.3.4 Membrane Separation 399 19.3.5 Centrifugal Partition Chromatography 401 19.4 Characterization and Quantification of Xylooligosaccharides 402 19.4.1 Measuring Xylooligosaccharides by Quantification of Reducing Ends 402 19.4.2 Characterizing Xylooligosaccharides Composition 402 19.4.3 Direct Characterization of Different DP Xylooligosaccharides 403 19.4.4 Determining Detailed Structures of Oligosaccharides by MS and NMR 408 19.5 Concluding Remarks 408 Acknowledgements 409 References 410 20 Experimental Pretreatment Systems from Laboratory to Pilot Scale 417 Richard T. Elander 20.1 Introduction 417 20.2 Laboratory-scale Pretreatment Equipment 421 20.2.1 Heating and Cooling Capability 421 20.2.2 Contacting of Biomass Particles with Water and/or Pretreatment Chemicals 421 20.2.3 Mass and Heat Transfer 422 20.2.4 Proper Materials of Construction 423 20.2.5 Instrumentation and Control Systems 424 20.2.6 Translating to Pilot-scale Pretreatment Systems 424 20.3 Pilot-scale Batch Pretreatment Equipment 424 20.4 Pilot-scale Continuous Pretreatment Equipment 427 20.4.1 Feedstock Handling and Size Reduction 427 20.4.2 Pretreatment Chemical and Water Addition 429 20.4.3 Pressurized Continuous Pretreatment Feeder Equipment 432 20.4.4 Pretreatment Reactor Throughput and Residence Time Control 436 20.4.5 Reactor Discharge Devices 438 20.4.6 Blow-down Vessel and Flash Vapor Recovery 438 20.5 Continuous Pilot-scale Pretreatment Reactor Systems 439 20.5.1 Historical Development of Pilot-scale Reactor Systems 439 20.5.2 NREL Gravity-flow Reactor Systems 441 20.6 Summary 445 Acknowledgements 446 References 447 21 Experimental Enzymatic Hydrolysis Systems 451 Todd Lloyd and Chaogang Liu 21.1 Introduction 451 21.2 Cellulases 452 21.2.1 Endoglucanase 452 21.2.2 Cellobiohydrolase 453 21.2.3 b-glucosidase 453 21.3 Hemicellulases 453 21.4 Kinetics of Enzymatic Hydrolysis 454 21.4.1 Empirical Models 455 21.4.2 Michaelis–Menten-based Models 455 21.4.3 Adsorption in Cellulose Hydrolysis Models 456 21.4.4 Rate Limitations and Decreasing Rates with Increasing Conversion 457 21.4.5 Summary of Enzyme Reaction Kinetics 459 21.5 Experimental Hydrolysis Systems 460 21.5.1 Laboratory Protocols 460 21.5.2 Considerations for Scale-up of Hydrolysis Processes 463 21.6 Conclusion 465 References 465 22 High-throughput Pretreatment and Hydrolysis Systems for Screening Biomass Species in Aqueous Pretreatment of Plant Biomass 471 Jaclyn DeMartini and Charles E. Wyman 22.1 Introduction: The Need for High-throughput Technologies 471 22.2 Previous High-throughput Systems and Application to Pretreatment and Enzymatic Hydrolysis 472 22.3 Current HTPH Systems 473 22.4 Key Steps in HTPH Systems 478 22.4.1 Material Preparation 478 22.4.2 Material Distribution 479 22.4.3 Pretreatment and Enzymatic Hydrolysis 480 22.4.4 Sample Analysis 481 22.5 HTPH Philosophy, Difficulties, and Limitations 482 22.6 Examples of Research Enabled by HTPH Systems 484 22.7 Future Applications 485 22.8 Conclusions and Recommendations 485 References 486 23 Laboratory Pretreatment Systems to Understand Biomass Deconstruction 489 Bin Yang and Melvin Tucker 23.1 Introduction 489 23.2 Laboratory-scale Batch Reactors 491 23.2.1 Sealed Glass Reactors 491 23.2.2 Tubular Reactors 492 23.2.3 Mixed Reactors 495 23.2.4 Zipperclave 496 23.2.5 Microwave Reactors 497 23.2.6 Steam Reactors 499 23.3 Laboratory-scale Continuous Pretreatment Reactors 501 23.4 Deconstruction of Biomass with Bench-Scale Pretreatment Systems 503 23.5 Heat and Mass Transfer 505 23.5.1 Mass Transfer 506 23.5.2 Direct and Indirect Heating 506 23.6 Biomass Handling and Comminuting 508 23.7 Construction Materials 508 23.7.1 Overall Considerations 508 23.7.2 Materials of Construction 509 23.8 Criteria of Reactor Selection and Applications 510 23.8.1 Effect of High/Low Solids Concentration on Reactor Choices 510 23.8.2 Role of Heat-up and Cool-down Rates in Laboratory Reactor Selection 510 23.8.3 Effect of Mixing and Catalyst Impregnation on Reactor Design 510 23.8.4 High Temperatures and Short Residence Times Result in High Yields 511 23.8.5 Pretreatment Severity: Tradeoffs of Time and Temperature 511 23.8.6 Minimizing Construction and Operating Costs 512 23.9 Summary 513 Acknowledgements 514 References 514 Index 523

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Book SynopsisEcohydraulics: An Integrated Approachprovides a research level text which highlights recent developments of this emerging and expanding field. With a focus on interdisciplinary research the text examines:- the evolution and scope of ecohydraulics interactions between hydraulics, hydrology, fluvial geomorphology and aquatic ecology the application of habitat modelling in ecohydraulic studies state of the art methodological developments and approaches detailed case studies including fish passage design and the management of environmental flow regimes research needs and the future of ecohydraulics research The contributions offer broad geographic coverage to encapsulate the wide range of approaches, case studies and methods used to conduct ecohydraulics research. The book considers a range of spatial and temporal scales of relevance and aquatic organisms ranging from algae and macrophytes to macroinvertebratTable of ContentsList of Contributors, xi 1 Ecohydraulics: An Introduction, 1 Ian Maddock, Atle Harby, Paul Kemp and Paul Wood 1.1 Introduction, 1 1.2 The emergence of ecohydraulics, 2 1.3 Scope and organisation of this book, 4 References, 4 Part I Methods and Approaches 2 Incorporating Hydrodynamics into Ecohydraulics: The Role of Turbulence in the Swimming Performance and Habitat Selection of Stream-Dwelling Fish, 9 Martin A. Wilkes, Ian Maddock, Fleur Visser and Michael C. Acreman 2.1 Introduction, 9 2.2 Turbulence: theory, structure and measurement, 11 2.3 The role of turbulence in the swimming performance and habitat selection of river-dwelling fish, 20 2.4 Conclusions, 24 Acknowledgements, 25 References, 25 3 Hydraulic Modelling Approaches for Ecohydraulic Studies: 3D, 2D, 1D and Non-Numerical Models, 31 Daniele Tonina and Klaus Jorde 3.1 Introduction, 31 3.2 Types of hydraulic modelling, 32 3.3 Elements of numerical hydrodynamic modelling, 33 3.4 3D modelling, 49 3.5 2D models, 55 3.6 1D models, 57 3.7 River floodplain interaction, 59 3.8 Non-numerical hydraulic modelling, 60 3.9 Case studies, 60 3.10 Conclusions, 64 Acknowledgements, 66 References, 66 4 The Habitat Modelling System CASiMiR: A Multivariate Fuzzy Approach and its Applications, 75 Markus Noack, Matthias Schneider and Silke Wieprecht 4.1 Introduction, 75 4.2 Theoretical basics of the habitat simulation tool CASiMiR, 76 4.3 Comparison of habitat modelling using the multivariate fuzzy approach and univariate preference functions, 80 4.4 Simulation of spawning habitats considering morphodynamic processes, 82 4.5 Habitat modelling on meso- to basin-scale, 85 4.6 Discussion and conclusions, 87 References, 89 5 Data-Driven Fuzzy Habitat Models: Impact of Performance Criteria and Opportunities for Ecohydraulics, 93 Ans Mouton, Bernard De Baets and Peter Goethals 5.1 Challenges for species distribution models, 93 5.2 Fuzzy modelling, 95 5.3 Case study, 100 References, 105 6 Applications of the MesoHABSIM Simulation Model, 109 Piotr Parasiewicz, Joseph N. Rogers, Paolo Vezza, Javier Gort´azar, Thomas Seager, Mark Pegg, Wies©©aw Wi´sniewolski and Claudio Comoglio 6.1 Introduction, 109 6.2 Model summary, 109 Acknowledgements, 123 References, 123 7 The Role of Geomorphology and Hydrology in Determining Spatial-Scale Units for Ecohydraulics, 125 Elisa Zavadil and Michael Stewardson 7.1 Introduction, 125 7.2 Continuum and dis-continuum views of stream networks, 126 7.3 Evolution of the geomorphic scale hierarchy, 127 7.4 Defining scale units, 131 7.5 Advancing the scale hierarchy: future research priorities, 139 References, 139 8 Developing Realistic Fish Passage Criteria: An Ecohydraulics Approach, 143 Andrew S. Vowles, Lynda R. Eakins, Adam T. Piper, James R. Kerr and Paul Kemp 8.1 Introduction, 143 8.2 Developing fish passage criteria, 144 8.3 Conclusions, 151 8.4 Future challenges, 152 References, 152 Part II Species–Habitat Interactions 9 Habitat Use and Selection by Brown Trout in Streams, 159 Jan Heggenes and Jens Wollebæk 9.1 Introduction, 159 9.2 Observation methods and bias, 160 9.3 Habitat, 161 9.4 Abiotic and biotic factors, 161 9.5 Key hydraulic factors, 163 9.6 Habitat selection, 163 9.7 Temporal variability: light and flows, 166 9.8 Energetic and biomass models, 168 9.9 The hyporheic zone, 169 9.10 Spatial and temporal complexity of redd microhabitat, 169 9.11 Summary and ways forward, 170 References, 170 10 Salmonid Habitats in Riverine Winter Conditions with Ice, 177 Ari Huusko, Teppo Vehanen and Morten Stickler 10.1 Introduction, 177 10.2 Ice processes in running waters, 178 10.3 Salmonids in winter ice conditions, 182 10.4 Summary and ways forward, 186 References, 188 11 Stream Habitat Associations of the Foothill Yellow-Legged Frog (Rana boylii): The Importance of Habitat Heterogeneity, 193 Sarah Yarnell 11.1 Introduction, 193 11.2 Methods for quantifying stream habitat, 194 11.3 Observed relationships between R. boylii and stream habitat, 198 11.4 Discussion, 204 References, 209 12 Testing the Relationship Between Surface Flow Types and Benthic Macroinvertebrates, 213 Graham Hill, Ian Maddock and Melanie Bickerton 12.1 Background, 213 12.2 Ecohydraulic relationships between habitat and biota, 213 12.3 Case study, 216 12.4 Discussion, 223 12.5 Wider implications, 226 12.6 Conclusion, 227 References, 227 13 The Impact of Altered Flow Regime on Periphyton, 229 Natas¢§a Smolar-Z¢§vanut and Aleksandra Krivograd Klemenc¢§ic¢§ 13.1 Introduction, 229 13.2 Modified flow regimes, 230 13.3 The impact of altered flow regime on periphyton, 231 13.4 Case studies from Slovenia, 236 13.5 Conclusions, 240 References, 240 14 Ecohydraulics and Aquatic Macrophytes: Assessing the Relationship in River Floodplains, 245 Georg A. Janauer, Udo Schmidt-Mumm and Walter Reckendorfer 14.1 Introduction, 245 14.2 Macrophytes, 246 14.3 Life forms of macrophytes in running waters, 248 14.4 Application of ecohydraulics for management: a case study on the Danube River and its floodplain, 249 14.5 Conclusion, 255 Acknowledgements, 255 Appendix 14.A: Abbreviations used in Figure 14.5, including full plant names and authorities, 255 References, 256 15 Multi-Scale Macrophyte Responses to Hydrodynamic Stress and Disturbances: Adaptive Strategies and Biodiversity Patterns, 261 Sara Puijalon and Gudrun Bornette 15.1 Introduction, 261 15.2 Individual and patch-scale response to hydrodynamic stress and disturbances, 262 15.3 Community responses to temporary peaks of flow and current velocity, 266 15.4 Macrophyte abundance, biodiversity and succession, 268 15.5 Conclusion, 269 References, 270 Part III Management Application Case Studies 16 Application of Real-Time Management for Environmental Flow Regimes, 277 Thomas B. Hardy and Thomas A. Shaw 16.1 Introduction, 277 16.2 Real-time management, 278 16.3 The setting, 278 16.4 The context and challenges with present water allocation strategies, 281 16.5 The issues concerning the implementation of environmental flow regimes, 282 16.6 Underlying science for environmental flows in the Klamath River, 283 16.7 The Water Resource Integrated Modelling System for The Klamath Basin Restoration Agreement, 285 16.8 The solution – real-time management, 285 16.9 Example RTM implementation, 287 16.10 RTM performance, 287 16.11 Discussion, 290 16.12 Conclusions, 290 Acknowledgements, 291 References, 291 17 Hydraulic Modelling of Floodplain Vegetation in Korea: Development and Applications, 293 Hyoseop Woo and Sung-Uk Choi 17.1 Introduction, 293 17.2 Modelling of vegetated flows, 294 17.3 Floodplain vegetation modelling: From white rivers to green rivers, 300 17.4 Conclusions, 306 References, 306 18 A Historical Perspective on Downstream Passage at Hydroelectric Plants in Swedish Rivers, 309 Olle Calles, Peter Rivinoja and Larry Greenberg 18.1 Introduction, 309 18.2 Historical review of downstream bypass problems in Sweden, 310 18.3 Rehabilitating downstream passage in Swedish Rivers today, 312 18.4 Concluding remarks, 319 References, 320 19 Rapid Flow Fluctuations and Impacts on Fish and the Aquatic Ecosystem, 323 Atle Harby and Markus Noack 19.1 Introduction, 323 19.2 Rapid flow fluctuations, 325 19.3 Methods to study rapid flow fluctuations and their impact, 325 19.4 Results, 326 19.5 Mitigation, 329 19.6 Discussion and future work, 331 Acknowledgements, 333 References, 334 20 Ecohydraulic Design of Riffle-Pool Relief and Morphological Unit Geometry in Support of Regulated Gravel-Bed River Rehabilitation, 337 Gregory B. Pasternack and Rocko A. Brown 20.1 Introduction, 337 20.2 Experimental design, 338 20.3 Results, 347 20.4 Discussion and conclusions, 351 Acknowledgements, 353 References, 353 21 Ecohydraulics for River Management: Can Mesoscale Lotic Macroinvertebrate Data Inform Macroscale Ecosystem Assessment?, 357 Jessica M. Orlofske, Wendy A. Monk and Donald J. Baird 21.1 Introduction, 357 21.2 Lotic macroinvertebrates in a management context, 358 21.3 Patterns in lotic macroinvertebrate response to hydraulic variables, 359 21.4 Linking ecohydraulics and lotic macroinvertebrate traits, 365 21.5 Trait variation among lotic macroinvertebrates in LIFE flow groups, 366 21.6 Upscaling from ecohydraulics to management, 370 21.7 Conclusions, 371 References, 371 22 Estuarine Wetland Ecohydraulics and Migratory Shorebird Habitat Restoration, 375 Jos´e F. Rodr´©¥guez and Alice Howe 22.1 Introduction, 375 22.2 Area E of Kooragang Island, 377 22.3 Ecohydraulic and ecogeomorphic characterisation, 378 22.4 Modifying vegetation distribution by hydraulic manipulation, 382 22.5 Discussion, 388 22.6 Conclusions and recommendations, 390 References, 392 23 Ecohydraulics at the Landscape Scale: Applying the Concept of Temporal Landscape Continuity in River Restoration Using Cyclic Floodplain Rejuvenation, 395 Gertjan W. Geerling, Harm Duel, Anthonie D. Buijse and Antonius J.M. Smits 23.1 Introduction, 395 23.2 The inspiration: landscape dynamics of meandering rivers, 397 23.3 The concept: temporal continuity and discontinuity of landscapes along regulated rivers, 399 23.4 Application: floodplain restoration in a heavily regulated river, 401 23.5 The strategy in regulated rivers: cyclic floodplain rejuvenation (CFR), 403 23.6 General conclusions, 405 References, 405 24 Embodying Interactions Between Riparian Vegetation and Fluvial Hydraulic Processes Within a Dynamic Floodplain Model: Concepts and Applications, 407 Gregory Egger, Emilio Politti, Virginia Gar´ofano-G´omez, Bernadette Blamauer, Teresa Ferreira, Rui Rivaes, Rohan Benjankar and Helmut Habersack 24.1 Introduction, 407 24.2 Physical habitat and its effects on floodplain vegetation, 408 24.3 Succession phases and their environmental context, 410 24.4 Response of floodplain vegetation to fluvial processes, 414 24.5 Linking fluvial processes and vegetation: the disturbance regime approach as the backbone for the dynamic model, 415 24.6 Model applications, 417 24.7 Conclusion, 423 Acknowledgements, 424 References, 424 Part IV Conclusion 25 Research Needs, Challenges and the Future of Ecohydraulics Research, 431 Ian Maddock, Atle Harby, Paul Kemp and Paul Wood 25.1 Introduction, 431 25.2 Research needs and future challenges, 432 References, 435 Index, 437

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