Computational biology / bioinformatics Books

Book SynopsisThis book constitutes the proceedings of the 16th Brazilian Symposium on Bioinformatics on Advances in Bioinformatics and Computational Biology, BSB 2023, which took place in Curitiba, Brazil, in June 2023. The 11 full papers and 3 short papers presented in this volume were carefully reviewed and selected from 24 submissions. The papers focus on bioinformatics, computational biology, Biological Databases, Biological Networks, Cheminformatics, Evolutionary Genomics, Computational Proteomics, Systems Biology, Drug Design, Genomics, Machine Learning applications in Bioinformatics, Metagenomics, Molecular Docking and Modeling, Molecular Evolution and Phylogenetics, Protein Structure and Modeling, Proteomics, Transcriptomics, Single-Cell Analysis, Workflows in Bioinformatics. Table of ContentsBlock Interchange and Reversal Distance on Unbalanced Genomes.- circTIS: a weighted degree string kernel with support vector machine tool for translation initiation sites prediction in circRNA.- Evaluating the molecular-electronic structure and the antiviral effect of functionalized heparin on graphene oxide through ab initio computer simulations and molecular docking.- Make No Mistake! Why Do Tools Make Incorrect Long Non-Coding Rna Classification?.- Spectrum-Based Statistical Methods for Directed Graphs with Applications in Biological Data.- Feature Selection Investigation in Machine Learning Docking Scoring Functions.- Using natural language processing for context identification in COVID-19 literature.- A framework for inference and selection of cell signaling pathway dynamic models.- Intentional Semantics for Molecular Biology.- transcAnalysis: A Snakemake Pipeline for Differential Expression and Post-Transcriptional Modification Analysis.- Peptide-protein interface classification using convolutional neural networks.- A Power Law Semantic Similarity from Gene Ontology.- Gene Networks Inference by Reinforcement Learning Approach.- Exploring Identifiability in Hybrid Models of Cell Signaling Pathways.

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Book SynopsisThis book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary.Table of Contents1: Learning Through Programming 2: Downloading and Installing R 3: Basic Commands in R 4: Allele and Genotype Frequencies 5: Statistical Tests and Algorithms 6: Genetic Variation 7: Adaptation and Natural Selection 8: Population Differences 9: Pointing the Way to Additional Topics

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Book SynopsisTrade ReviewThe book is novel, easy to read and combines excellent cartoons with good personal vignettes and history. I spent many years mastering genetics and yet learned new and valuable things from this book. Take a look, you will not be disappointed. -- Robert Trivers, Rutgers University A unique, richly detailed, and fun biography of DNA grounded in deep historical and philosophical knowledge--Rosenfield, Ziff and Van Loon give us everything we need to know about biology's most important molecule. -- Oliver Sacks Right now, you may not know the difference between a prokaryote and a eukaryote, but read this richly detailed work and that could be your next cocktail party opener. Toronto Globe & Mail A clear summary of the DNA story with a lighthearted approach. CHOICE

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Book SynopsisNeuropathology of Transmissible Spongiform Encephalopathies (Prion Diseases).- Central Pathogenesis of Prion Diseases.- Hereditary Prion Protein Amyloidoses.- Mouse Behavioural Studies and What They Can Teach Us about Prion Diseases.- Electrophysiological Approaches to the Study of Prion Diseases.- Prion Protein, Prion Protein-Like Protein, and Neurodegeneration.- Oxidative Stress and Mitochondrial Dysfunction in Neurodegeneration of Transmissible Spongiform Encephalopathies (TSEs).- Mechanisms of Prion Toxicity and Their Relationship to Prion Infectivity.- A Stone Guest on the Brain: Death as a Prion.- Molecular Mechanisms Mediating Neuronal Cell Death in Experimental Models of Prion Diseases, in vitro.- Processing and Mis-Processing of the Prion Protein: Insights into the Pathogenesis of Familial Prion Disorders.- Signaling Pathways Controling Prion Neurotoxicity: Role of Endoplasmic Reticulum Stress-Mediated Apoptosis.- Cell Culture Models to Unravel Prion Protein Function and AberrTable of ContentsNeuropathology of transmissible spongiform encephalopathies (prion diseases).- Central pathogenesis of prion diseases.- Hereditory prion protein Amyloidoses.- Mouse behavioural studies and what they can teach us about prion diseases.- Electrophysiological approaches to the study of prion diseases.- Prion protein, prion protein-like protein, and neurodegeneration.- Oxidative stress and mitochondrial dysfunction in neurodegeneration of transmissible spongiform encephalopathies (TSEs).- Mechanisms of prion toxicity and their relationship to prion infectivity.- A stone guest on the brain: Death as a prion.- Molecular mechanisms mediating neuronal cell death in experimental models of prion diseases, in vitro.- Processing and mis-processing of the prion protein: Insights into the pathogenesis of familial prion disorders.- Signaling pathways controling prion protein neurotoxicity: Role of endoplasmic reticulum stress-mediated apoptosis.- Cell culture models to unravel prion protein function and aberrancies in TSE.- Insights into the cellular trafficking of prion proteins.- The molecular basis of prion protein-mediated neuronal damage.

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Book SynopsisGenomics research has made significant advances in recent years. In this book, a team of internationally-renowned researchers share the most up-to-date information in a field that has in recent years switched emphasis from gene identification to functional genomics and the characterization of genes and gene products. This volume approaches this complex subject with a broad perspective to supply the reader with a vital overview of genomics and its derivative fields, with a focus on pivotal issues such as data analysis. Expansive and current,this bookis a comprehensive research guide that describes both the key new techniques and more established methods. Every chapter discusses the merits and limitations of the various approaches and then provides selected tried-and-tested protocols, as well as a plethora of good practical advice for immediate use at the bench. Key features: Provides a broad introduction to current practices and techniques for lab-based research Trade Review Table of ContentsList of Contributors. Preface. 1 High-Resolution Analysis of Genomic Copy Number Changes (Mario Hermsen, Jordy Coffa, Bauke Ylstra, Gerrit Meijer, Hans Morreau, Ronald van Eijk, Jan Oosting and Tom van Wezel). 1.1 Introduction. 1.2 Methods and Approaches. 1.3 Troubleshooting. References. 2 Identification of Polymorphic Markers for Genetic Mapping (Daniel C. Koboldt and Raymond D. Miller). 2.1 Introduction. 2.2 Methods and Approaches. 2.3 Troubleshooting. References. 3 Genotyping and LOH Analysis on Archival Tissue Using SNP Arrays (Ronald van Eijk, Anneke Middeldorp, Esther H. Lips, Marjo van Puijenbroek, Hans Morreau, Jan Oosting and Tom van Wezel). 3.1 Introduction. 3.2 Methods and Approaches. 3.3 Troubleshooting. References. 4 Genetic Mapping of Complex Traits (Nancy L. Saccone). 4.1 Introduction. 4.2 Methods and Approaches. 4.3 Troubleshooting. References. 5 RNA Amplification Strategies: Toward Single-Cell Sensitivity (Natalie Stickle, Norman N. Iscove, Carl Virtanen, Mary Barbara, Carolyn Modi, Ari Baratz, Toni Di Berardino, Ellen Greenblatt, Ted Brown and Neil Winegarden). 5.1 Introduction. 5.2 Methods and Approaches. 5.3 Troubleshooting. References. 6 Real-Time Quantitative RT-PCR for mRNA Profiling (Stephen A. Bustin and Tania Nolan). 6.1 Introduction. 6.2 Methods and Approaches. 6.3 Troubleshooting. References. 7 Gene Expression in Mammalian Cells (Félix Recillas-Targa, Georgina Guerrero, Martín Escamilla-del-Arenal and Héctor Rincón-Arano). 7.1 Introduction. 7.2 Methods and Approaches. 7.3 Troubleshooting. Acknowledgments. References. 8 Using Yeast Two-Hybrid Methods to Investigate Large Numbers of Binary Protein Interactions (Panagoula Charalabous, Jonathan Woodsmith and Christopher M. Sanderson). 8.1 Introduction. 8.2 Methods and Approaches. 8.3 Troubleshooting. References. 9 Prediction of Protein Function (Hon Nian Chua). 9.1 Introduction. 9.2 Methods and Approaches. 9.3 Troubleshooting. References. 10 Elucidating Gene Function through Use of Genetically Engineered Mice (Mary P. Heyer, Cátia Feliciano, João Peca and Guoping Feng). 10.1 Introduction. 10.2 Methods and Approaches. 10.3 Troubleshooting. References. 11 Delivery Systems for Gene Transfer (Charlotte Lawson and Louise Collins). 11.1 Introduction. 11.2 Methods and Approaches. 11.3 Troubleshooting. References. 12 Gene Therapy Strategies: Constructing an AAV Trojan Horse (M. Ian Phillips, Edilamar M. de Oliveira, Leping Shen, Yao Liang Tang, and Keping Qian). 12.1 Introduction. 12.2 Methods and Approaches. 12.3 Troubleshooting. References. 13 An Introduction to Proteomics Technologies for the Genomics Scientist (David B. Friedman). 13.1 Introduction. 13.2 Methods and Approaches. 13.3 Troubleshooting. References. Index.

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Book SynopsisFully integrated and comprehensive in its coverage, Root Genomics and Soil Interactions examines the use of genome-based technologies to understand root development and adaptability to biotic and abiotic stresses and changes in the soil environment.Table of ContentsContributors ix Preface xv Chapter 1 Genomics of Root Development 3Boris Parizot and Tom Beeckman Introduction 3 Genomics of LRI 7 Rise of New Technologies to Understand Lateral Root Development 19 ComparativOmics, the Future 20 Acknowledgments 21 References 21 Chapter 2 The Complex Eukaryotic Transcriptome: Nonprotein-Coding RNAs and Root Development 29F. Ariel, A.B. Moreno, F. Bardou, and M. Crespi Genomic Approaches Reveal Novel Aspects of the Eukaryotic Transcriptome 29 The Role of RNA-Binding Proteins in npcRNA Metabolism and Activity 34 Nonprotein-Coding RNAs in Root Development 38 Future Perspectives 42 Acknowledgments 42 References 42 Chapter 3 Genomics of Auxin Action in Roots 49Elisabeth L. Williams and Ive De Smet Introduction 49 The Basis of Auxin Biology 49 Auxin Genomics in Root Development 55 Auxin and Root Hair Development 56 Auxin in Gravitropism 57 Auxin in LR Initiation 57 Conclusion 58 Acknowledgments 58 References 58 Chapter 4 Cell-Type Resolution Analysis of Root Development and Environmental Responses 63Jose R. Dinneny Introduction 63 Tools for Cell-Type Resolution Analysis 64 Analysis of Spatiotemporal Expression Patterns in the Arabidopsis Root 69 Analysis of Cell-Type-Specific Expression Patterns in the Rice Root 70 Cell-Type-Specific Analysis of Auxin 71 Cell-Type-Specific Analyses of Chromatin 71 Cell-Type-Specific Analyses of Responses to Environmental Change 72 Future Prospects 76 Acknowledgments 76 References 77 Chapter 5 Toward a Virtual Root: Interaction of Genomics and Modeling to Develop Predictive Biology Approaches 79Julien Lavenus, Leah Band, Alistair Middleton, Michael Wilson, Mikael Lucas, Laurent Laplaze, and Malcolm Bennett Assembling Root Gene Regulatory Pathways Using Genomics 79 Modeling Well-Characterized Small Root Gene Regulatory Networks 81 Building New Large-Scale Root Gene Regulatory Network 84 Multi-Scale Modeling Approaches to Study Root Growth and Development 88 Conclusions and Future Challenges 89 References 91 Chapter 6 Genomics of Root Hairs 93Hyung-Taeg Cho Genomics with Single Cells 93 Root Hair Development 94 High-Throughput Approaches for the Characterization of Root Hairs 95 Functions of Root Hair-Specific Genes 103 The Regulatory Pathway for Root Hair-Specific Genes 110 Perspective 111 Acknowledgments 111 References 112 Chapter 7 The Effects of Moisture Extremes on Plant Roots and Their Connections with Other Abiotic Stresses 117Laura M. Vaughn and Henry T. Nguyen Introduction 117 Low Water Availability—Drought 118 Excess Water—Soil Waterlogging, Flooding, and Submergence 128 Common Plant Root Responses to Abiotic Stressors 135 Continuing Challenges in Breeding for Plant Root Systems Tolerant to Abiotic Stress 137 Acknowledgments 138 References 138 Chapter 8 Legume Roots and Nitrogen-Fixing Symbiotic Interactions 145Philippe Laporte, Andreas Niebel, and Florian Frugier Genetic Dissection of the Legume Root System 145 Functional Genomic Analyses of Legume Nodules and Roots 155 Concluding Remarks 161 Acknowledgments 162 References 162 Chapter 9 What the Genomics of Arbuscular Mycorrhizal Symbiosis Teaches Us about Root Development 171Damien Formey, Cyril Jourda, Christophe Roux, and Pierre-Marc Delaux Forward and Reverse Genetics for Identifying Myc Mutants 172 Comparative Transcriptomics of AM Symbiosis: Toward Identification of Genes Involved in Root Development 175 Small RNAs in AM Symbiosis 181 Acknowledgments 183 References 183 Chapter 10 How Pathogens Affect Root Structure 189Michael Quentin, Tarek Hewezi, Isabelle Damiani, Pierre Abad, Thomas Baum, and Bruno Favery Introduction 189 Root Infection and Feeding Cell Ontogenesis 190 Genome-Wide Analysis of the Plant Response to Infection 192 The Plant Cytoskeleton Is Targeted by Root Pathogens 193 Root Pathogens Hijack Cell Cycle Regulators 194 Severe Cell Wall Remodeling Is Associated with Feeding Site Formation 195 Phytohormones Regulating Development and Defense May Control Feeding Site Formation 196 Role of miRNAs in Feeding Site Formation and Function 198 Nematode Effectors That Alter Root Cell Development during Parasitism 200 Conclusion 203 Acknowledgments 204 References 204 Chapter 11 Genomics of the Root—Actinorhizal Symbiosis 211Valerie Hocher, Nicole Alloisio, Laurent Laplaze, Didier Bogusz, and Philippe Normand Introduction 211 Actinorhizal Symbiosis 212 Development of Actinorhizal Nodules 214 Genomic Resources for Studying Actinorhizal Symbiosis 217 What Did We Learn from Actinorhizal Genomics? 220 Conclusion and Future Directions 222 Acknowledgments 222 References 223 Chapter 12 Plant Growth Promoting Rhizobacteria and Root Architecture 227Thais L.G. Carvalho, Paulo C.G. Ferreira, and Adriana S. Hemerly Introduction 227 Different Root Niches for PGPR Colonization 228 PGPR Recognition by Plants 229 Modulation of Root Growth and Architecture by PGPRs 232 Mechanisms of Plant Growth Promotion by PGPRs 234 Plant Genetic Programs Controlling Modulation of Root Growth and Architecture by PGPRs 240 Conclusions 241 Acknowledgments 242 References 242 Chapter 13 Translational Root Genomics for Crop Improvement 249Reyazul Rouf Mir, Mahendar Thudi, Siva K. Chamarthi, L. Krishnamurthy, Pooran M. Gaur, and Rajeev K. Varshney Introduction 249 Molecular Dissection of Root Trait 258 Molecular Breeding for Root Traits 259 Summary and Outlook 260 Acknowledgments 260 References 260 Index 265

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Book SynopsisThis book describes comprehensive step-by-step protocols for the delineation of genetic amplification and histological detection techniques. Each procedure has been tested and validated for its sensitivity, precision, and reproducibility, and the authors give advice on the design of primers for PCR applications and on optimizing these protocols for use with plant, insect, and prokaryotic cells.Table of ContentsOverview; Review of the PCR Technique; Preliminary Solution-Based Reactions; Preparation of Glass Slides and Tissues; In Situ PCR: DNA and RNA Targets; Special Applications of In Situ Amplification; Hybridization Reactions; Validation and Controls; Materials and Methods; Select Biography; Appendices; Index; About the Authors.

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Book SynopsisThe genetic revolution has provided incredibly valuable information about our DNA, information that can be used to benefit and inform - but also to judge, discriminate, and abuse. This book gives the background information critical to understanding how genetics is affecting our everyday lives.Trade Review"Goes a long way toward exploring these issues in a painstaking yet readable scholarly treatise... Throughout, they make a convincing case that we are not our genome alone." New England Journal Of Medicine "The book is anything but dry reporting... An enjoyable and stimulating read for specialists in the field and the curious public alike." Science (AAAS) "Readers will come away with a realistic and encouraging perspective on medical genetics, providing that neither fantastic optimism nor abject fear is necessary to make the true story of DNA exciting." Qtly Review Of Biology "Readers will come away with a realistic and encouraging perspective on medical genetics, proving that neither fantastic optimism nor abject fear is necessary to make the true story of DNA exciting." Qtly Review Of BiologyTable of ContentsForeword by Victor A. McKusick Acknowledgments 1. DNA Sequence Does Not Equal Destiny 2. What Is Genomics? 3. Genetic Determinism 4. The Evolution and Deconstruction of Human-Centered Biology 5. Race and Ethnicity: Your History Is Written in Your Genes 6. Gender as a Spectrum, Not a Dichotomy 7. Genome-Based Forensics 8. When Genes Belong to Groups and Not Individuals 9. Genes as Commodities: Ownership of Genes by Business Interests 10. Protection against Genetic Discrimination: The New Civil Right 11. Reproductive Technologies: On the Road to Designer Babies? 12. Reproductive Cloning: From Farm Animals to Pets to Humans? 13. Therapeutic Cloning and Regenerative Medicine 14. Gene Therapy: Can the Promise Be Fulfilled? 15. Large Population Assessments: The Foundation for Genomic Medicine 16. Hidden Destiny: Unbounded by Your DNA Bibliography Illustration Credits Index

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Book SynopsisIn situ hybridization is a technique that allows for the visualization of specific DNA and RNA sequences in individual cells, and is an especially important method for studying nucleic acids in heterogeneous cell populations. in situ Hybridization in Electron Microscopy reviews the three main methods developed for the ultrastructural visualization of genes: hybridization on ultrathin sections of tissue embedded in hydrophilic resin (post-embedding method) hybridization prior to embedding (pre-embedding) hybridization on ultrathin sections of frozen tissue (frozen tissue method). For each technique, the different stages are described in detail: the preparation of tissue, pretreatment, hybridization, and visualization of the hybridization products. The book combines theory and practice, starting with the basic principles, then breaking down the experimental process into successive steps illustrated by numerous diagrams, detailed protocols, and tables. This is aTable of ContentsGeneral Introduction. Abbreviations. Probes. Principles of Methodology. Sample Preparation. Post-Embedding Technique. Pre-Embedding Technique. Frozen Tissue Technique. Semithin Sections. Controls and Problems. Examples of Results. Appendices. Glossary. Index.

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Book SynopsisA Copernican revolution for the life sciences.—Medical TribuneUnlock the mysteries of biology, anthropology, and ancient civilizations in this thought-provoking read where science and spirituality intersect. Through Jeremy Narby′s travels and research in the Amazon, he discovered that shamans were able to use hallucinogens to tap into knowledge and insights that rival our discoveries using modern scientific methods, particularly with regards to DNA and molecular biology. Drawing on visionary experiences, indigenous knowledge, and pharmacology, Narby challenges conventional understanding, unraveling the connections between consciousness, serpent symbolism, and the origins of life itself. This enlightening book blends science, anthropology, and mysticism into a captivating narrative that will expand your mind.

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Book SynopsisThis volume details state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data. Chapters guide readers through fine-mapping and quantification of modifications, visual analytics, imputation methods, supervised analysis, and integrative approaches for single-cell data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Computational Epigenomics and Epitranscriptomics aims to provide an overview of epiomic protocols, making it easier for researchers to extract impactful biological insight from their data.Table of Contents1. DNA methylation data analysis using Msuite Xiaojian Liu, Pengxiang Yuan, and Kun Sun 2. Interactive DNA methylation arrays analysis with ShinyÉPICo Octavio Morante-Palacios 3. Predicting Chromatin Interactions from DNA Sequence using DeepC Ron Schwessinger 4. Integrating single-cell methylome and transcriptome data with MAPLE Yasin Uzun, Hao Wu, and Kai Tan 5. Quantitative comparison of multiple chromatin immunoprecipitation-sequencing (ChIP-seq) experiments with spikChIP Enrique Blanco, Cecilia Ballaré, Luciano Di Croce, and Sergi Aranda 6. A Guide To MethylationToActivity: A Deep-Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes In Individual Tumors Karissa Dieseldorff Jones, Daniel Putnam, Justin Williams, and Xiang Chen 7. DNA modification patterns filtering and analysis using DNAModAnnot Alexis Hardy, Sandra Duharcourt, and Matthieu Defrance 8. Methylome imputation by methylation patterns Ya-Ting Chang, Ming-Ren Yen, and Pao-Yang Chen 9. Sequoia: a framework for visual analysis of RNA modifications from direct RNA sequencing data Ratanond Koonchanok, Swapna Vidhur Daulatabad, Khairi Reda, and Sarath Chandra Janga 10. Predicting pseudouridine sites with Porpoise Xudong Guo, Fuyi Li, and Jiangning Song 11. Pseudouridine Identification and Functional Annotation with PIANO Jiahui Yao, Cuiyueyue Hao, Kunqi Chen, Jia Meng, and Bowen Song 12. Analyzing mRNA epigenetic sequencing data with TRESS Zhenxing Guo, Andrew M. Shafik, Peng Jin, Zhijin Wu, and Hao Wu 13. Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores Luca Cozzuto, Anna Delgado-Tejedor, Toni Hermoso Pulido, Eva Maria Novoa, and Julia Ponomarenko 14. Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq Florian Pichot, Virginie Marchand, Mark Helm, and Yuri Motorin 15. Analysis of RNA sequences and modifications using NASE Samuel Wein 16. Mapping of RNA modifications by direct Nanopore sequencing and JACUSA2 Amina Lemsara, Christoph Dieterich, and Isabel Naarmann-de Vries

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Book SynopsisA Step-by-Step Guide to Present and Future Uses of Microarray TechnologyMicroarray technology continues to evolve, taking on a variety of forms. From the spotting of cDNA and the in situ synthesis of oligonucleotide arrays now come microarrays comprising proteins, carbohydrates, drugs, tissues, and cells. With contributions from microarray experts in both academia and industry, Microarray Methods and Protocols is a turn-by-turn roadmap through the processes necessary to perform a successful microarray experiment.This easy to use book addresses the fundamental aspects of preparing and processing microarrays and bead arrays, labeling, and detection. It also includes a detailed How it Works section that discusses the underlying principles of a number of techniques. Troubleshooting guides offer additional advice for the successful performance of more than 100 protocols in 10 chapters that cover work iTrade ReviewThe book will be useful for researchers in protein chemistry and biochemistry, molecular biologists, and teachers and students of medical schools and universities specializing in microarray methods.--Doctor of Biological Sciences, G. Ya. Wiederschain. Biochemsitry - Moscow. 2010, VOL 75, No 9,1182Table of ContentsIntroduction to Microarray Technologies. Nucleic Acid Sample Preparation. Solid-Phase Substrates for Nucleic Acid Microarrays. Protein Sample Preparation for Microarrays. Solid-Phase Chemistries for Protein Microarrays. Protein Microarrays: The Link between Genomics and Proteomics. Bead Arrays: An Introduction to Multiplexed Bead-Based Assays for Proteins. Carbohydrate Arrays. Lectin Microarrays. Printing Methods. Appendix A: Microarray Reagent, Materials, and Equipment Sources. Appendix B: Image Analysis. Index.

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Book SynopsisScientists can use molecular profiling microarrays to compare healthy cells with their diseased counterparts and develop gene-specific treatments. Finding the best way to interpret original profiling data into accurate trends, however, continues to drive the development of normalization algorithms and software tools. Methods in Microarray Normalization compiles the most useful and novel techniques for the first time into a single, organized source. Experts in the field provide a diverse view of the mathematical processes that are important in normalizing data and avoiding inherent systematic biases. They also review useful software, including discussions on key algorithms, comparative data, and download locations. The book discusses the use of early normalization techniques for new profiling methods and includes strategies for assessing the utility of various normalization algorithms. It presents the latest microarray innovations from companies such as Agilent, Affymetrix,Trade Review"Methods in Microarray Normalization compiles the most useful and novel techniques for the first time into a single, organized source. Experts in the field provide a diverse view of the mathematical processes that are important in normalizing data and avoiding inherent systematic biases." – In Anticancer Research, July/August 2008, Vol. 28, No. 4ATable of ContentsA comprehensive analysis of the effect of microarray data preprocessing methods on differentially expressed transcript selection. Differentiation detection in microarray normalization. Preprocessing and normalization for affymetrix genechip expression microarrays. Spatial detrending and normalization methods for two-channel DNA and protein microarray data. A survey of cDNA microarray normalization and a comparison by k-NN classification. Technical variation in modeling the joint expression of several genes. Biological interpretation for microarray normalization selection. Methodology of functional analysis for omics data normalization. Exon array analysis for the detection of alternative splicing. Normalization of array CGH data. SNP array-based analysis for detection of chromosomal aberrations and copy number variations. Index.

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Book SynopsisA Step-by-Step Guide to Describing Biomolecular StructureComputational and Visualization Techniques for Structural Bioinformatics Using Chimera shows how to perform computations with Python scripts in the Chimera environment. It focuses on the three core areas needed to study structural bioinformatics: biochemistry, mathematics, and computation.Understand Important Concepts of Structural BioinformaticsThe book covers topics that deal primarily with protein structure and includes many exercises that are grounded in biological problems at the molecular level. The text encourages mathematical analysis by providing a firm foundation for computations. It analyzes numerous Python scripts for the Chimera environment, with the scripts and other material available on a supplementary website.Build Python Scripts to Extend the Capabilities of ChimeraThrough more than 60 exercises that involve the develTrade Review"This book supports an approach to bioinformatics that balances biological problems, mathematical modeling, and computational tools. It breaks down the mathematical complications into manageable parts and augments programming skills while developing biological insight."—L. Ridgway Scott, Louis Block Professor of Computer Science and Mathematics, Member of the Institute for Biophysical Design, Senior Fellow of the Computation Institute, University of Chicago"This book is a useful resource for experienced and newcomer Chimera users alike. It helps extend it programmatically, allowing users to perform any number of useful types of calculations that are often required in conjunction with visualization. From distances to graphs, any way you measure it, Prof. Burkowski’s book is a must have for Chimera users."—Rafael Najmanovich, PhD, Associate Professor, Université de Sherbrooke"Structural bioinformatics is a young science that lies at the crossroads of several synergizing disciplines, including biophysics, structural biology, mathematical modeling, and computational methods. In this context, the book by Forbes Burkowski constitutes a true landmark, enabling the practitioner to implement and exploit computational techniques to test the mathematical models and frame novel hypothesis. This engrossing book is directed at advanced undergraduates and professionals who seek to represent and explore novel structural concepts to describe biomolecular phenomena. Very useful practical applications of the computational techniques presented in the book are likely to emerge, especially in the fields of molecular engineering and structure-based drug design. Thus, I predict that the book will become mandatory for researchers interested in rational design in the pharmaceutical industry and materials science."—Ariel Fernandez, Ph.D., Former Hasselmann Professor of Bioengineering at Rice University and Pioneer of the Wrapping Technology in Drug Design"Students taught with Computational and Visualization Techniques for Structural Bioinformatics Using Chimera will gain not only a thorough understanding of the important concepts of structural bioinformatics, from the basics of protein structure through advanced topics such as molecular mechanics, but also the ability to perform their own analyses using the programming techniques and libraries offered by this book and its supporting materials. The exercises are engaging and vary from problems that can be solved in a few minutes to mini-projects that might require a week of effort. All concepts are clearly described and accompanied by helpful illustrations where needed. This text does an excellent job of turning students into investigators."—Eric Pettersen, UCSF Department of Pharmaceutical ChemistryTable of ContentsIntroduction: Macromolecules and Chimera. Accessing and Displaying Molecular Data with Chimera. Algorithms Dealing with Distance. Algorithms Dealing with Angles. Structure Overlap and Alignment. Potential Energy Functions. Rotamers and Side‑Chain Conformation. Residue Networks. Appendices. Index.

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Book SynopsisThis book presents the latest research on DNA damage, which due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome''s approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumour suppresser genes) can impede a cell''s ability to carry out its function and appreciably increase the likelihood of tumour formation. The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules'' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.

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Book SynopsisThis book introduces a discrete optimisation technique in four applications: classic Traveller Salesperson Problem (TSP), Multilocus Genetic Mapping, Multilocus Consensus Genetic Mapping, and Physical Mapping. Each of the four sections contains the problem formulation, description of the algorithm, and experimental results. The foregoing problems are solved on the basis of Guided Evolution Strategy (GES) algorithm. The algorithm was implemented in MultiPoint package (http://multiqtl.com). The developed analytical tools were applied in many genome mapping projects.

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Book SynopsisMicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Thousands of miRNAs have been identified in different organisms including viruses, insects, plants and animals. MiRNAs has emerged as key regulators of important biological processes. The differential expression of miRNAs in various human diseases has made them potential candidates for developing novel therapies and personalized medicines. This book is focused on microRNA let-7, the second miRNA discovered in the year 2000 and one of the most studied miRNA. This book discusses various aspects of miRNA let-7 starting from its discovery, biogenesis, transcriptional and posttranscriptional regulation to its crucial role in various fundamental cellular processes such as development, stem cell maintenance and differentiation, regulation of signalling pathways in cancer, drug resistance and therapeutic potential in different human diseases.

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Book SynopsisProline might be the most studied amino acid in nature. Many authors have reviewed its many functions in cell homoeostasis. Not only it is essential in primary metabolism, but it is also involved in cell defence response to a variety of stresses. This book presents topical research data in the study of pro-line functions, including role of pro-line in plant subject to salinity, pro-line cycle and its role in secondary metabolite accumulation, role of pro-line in catalysing the asymmetric reaction, studies of polyproline peptides, structural characteristics and transition mechanisms of proline-rich peptides, functions of proline in behaviour of neonatal chicks and tumour suppressor activities of proline oxidase.

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Book SynopsisFingerprints have provided a valuable method of personal identification in forensic science and criminal investigations for over 100 years. Fingerprints left at crime scenes generally are latent prints -- unintentional reproductions of the arrangement of ridges on the skin made by the transfer of materials (such as amino acids, proteins, polypeptides, and salts) to a surface. Palms and the soles of feet also have friction ridge skin that can leave latent prints. The examination of a latent print consists of a series of steps involving a comparison of the latent print to a known (or exemplar) print. Courts have accepted latent print evidence for the past century. However, several high-profile cases in the United States and abroad have highlighted the fact that human errors can occur, and litigation and expressions of concern over the evidentiary reliability of latent print examinations and other forensic identification procedures has increased in the last decade. This book discusses latent print examinations in detail, and provides methods to improving the practice through a systems approach.

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Book SynopsisEfficient computer programs have made it possible to elucidate and analyze large-scale genomic sequences. Fundamental tasks, such as the assembly of numerous whole-genome shotgun fragments, the alignment of complementary DNA sequences with a long genome, and the design of gene-specific primers or oligomers, require efficient algorithms and state-of-the-art implementation techniques. This textbook emphasizes basic software implementation techniques for processing large-scale genome sequences and provides executable sample programs.Table of ContentsSimple String Search Algorithms; Sorting; Lookup Tables; Suffix Arrays; Space-Efficient String Search; Approximate String Search Algorithms; Seeded Alignment; Highly-Specific Oligomer Design; Whole Genome Shotgun Sequencing.

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Book SynopsisThe DNA sequence that comprises the human genome--the genetic blueprint found in each of our cells--is undoubtedly the greatest code ever to be broken. Completed at the dawn of a new millennium, the feat electrified both the scientific community and the general public with its tantalizing promise of new and better treatments for countless diseases, including Alzheimer's, cancer, diabetes, and Parkinson's.Yet what is arguably the most important discovery of our time has also opened a Pandora's box of questions about who we are as humans and how the unique information stored in our genomes can and might be used, making it all the more important for everyone to understand the new science of genomics. In the CURIOSITY GUIDE TO THE HUMAN GENOME, Dr. John Quackenbush, a renowned scientist and professor, conducts a fascinating tour of the history and science behind the Human Genome Project and the technologies that are revolutionizing the practice of medicine today. With a clear and engaging narrative style, he demystifies the fundamental principles of genetics and molecular biology, including the astounding ways in which genes function, alone or together with other genes and the environment, to either sustain life or trigger disease.In addition, Dr. Quackenbush goes beyond medicine to examine how DNA-sequencing technology is changing how we think of ourselves as a species by providing new insights about our earliest ancestors and reconfirming our inextricable link to all life on earth.Finally, he explores the legal and ethical questions surrounding such controversial topics as stem cell research, prenatal testing, forensics, and cloning, making this volume of the Curiosity Guides series an indispensable resource for navigating our brave new genomic world.

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Book SynopsisMapping and, ultimately, deciphering the human genome is a major human and scientific adventure that involves thousands of researchers world-wide and considerable funds. Bertrand Jordan, an active scientist in this field, became also a privileged observer through a sabbatical year devoted to visiting nearly a hundred participating laboratories around the world. This placed him in an ideal position to see, discuss, record and analyse progress and difficulties in this endeavour. These observations are the basis for a regular feature, Chroniques Genomiques (Tales of the Genome) published in the French periodical médecine/sciences. This book is an integrated, expanded and updated version of the 1990-1993 chronicles. It provides a technically detailed but accessible account of the Genome World from the viewpoint of a practising scientist. It describes the strategies implemented in settings that range from small laboratories to semi-industrial installations such as Généthon, and the associated questions in terms of national policies, economic stakes and ethical issues.

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Book SynopsisThis essential book details intermediate-level statistical methods and frameworks for the clinician and medical researcher with an elementary grasp of health statistics and focuses on selecting the appropriate statistical method for many scenarios. Detailed evaluation of various methodologies familiarizes readers with the available techniques and equips them with the tools to select the best from a range of options. The inclusion of a hypothetical case study between a clinician and statistician charting the conception of the research idea through to results dissemination enables the reader to understand how to apply the concepts covered into their day-to-day clinical practice.Applied Statistical Considerations for Clinical Researchers focuses on how clinicians can approach statistical issues when confronted with a medical research problem by considering the data structure, how this relates to their study's aims and any potential knock-on effects relating to the evidence required to make correct clinical decisions. It covers the application of intermediate-level techniques in health statistics making it an ideal resource for the clinician seeking an up-to-date resource on the topic.Table of ContentsIntroduction.- Preliminaries.- Design.- Planning.- Data Acquisition.- Data Manipulation Analysis.- Inferencesty.- Dissemination.- A Case Study.- Conclusions.

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Book SynopsisThis open access book bridges common tools in medical imaging and neuroscience with the numerical solution of brain modelling PDEs. The connection between these areas is established through the use of two existing tools, FreeSurfer and FEniCS, and one novel tool, the SVM-Tk, developed for this book. The reader will learn the basics of magnetic resonance imaging and quickly proceed to generating their first FEniCS brain meshes from T1-weighted images. The book's presentation concludes with the reader solving a simplified PDE model of gadobutrol diffusion in the brain that incorporates diffusion tensor images, of various resolution, and complex, multi-domain, variable-resolution FEniCS meshes with detailed markings of anatomical brain regions. After completing this book, the reader will have a solid foundation for performing patient-specific finite element simulations of biomechanical models of the human brain.Trade Review“The book represents an excellent introduction and hands-on guide to this important and exciting field, for applied mathematicians and image processing practitioners … . It is, perhaps, most beneficial, to electrical and computer science majors who wish to rapidly immerse themselves in the field, in a manner that is mathematically correct and sound, yet also practical.” (Emil Saucan, zbMATH 1501.92001, 2023)Table of ContentsIntroduction.- Working with magnetic resonance images of the brain.- From T1 images to numerical simulation.- Introducing heterogeneities.- Introducing directionality with diffusion tensors.- Simulating anisotropic diffusion in heterogeneous brain regions.- Concluding remarks and outlook.- References.- Index.

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Book SynopsisMathematical Modeling for Epidemiology and Ecology provides readers with the mathematical tools needed to understand and use mathematical models and read advanced mathematical biology books. It presents mathematics in biological contexts, focusing on the central mathematical ideas and the biological implications, with detailed explanations. The author assumes no mathematics background beyond elementary differential calculus. An introductory chapter on basic principles of mathematical modeling is followed by chapters on empirical modeling and mechanistic modeling. These chapters contain a thorough treatment of key ideas and techniques that are often neglected in mathematics books, such as the Akaike Information Criterion. The second half of the book focuses on analysis of dynamical systems, emphasizing tools to simplify analysis, such as the Routh-Hurwitz conditions and asymptotic analysis. Courses can be focused on either half of the book or thematically chosen material from both halves, such as a course on mathematical epidemiology.The biological content is self-contained and includes many topics in epidemiology and ecology. Some of this material appears in case studies that focus on a single detailed example, and some is based on recent research by the author on vaccination modeling and scenarios from the COVID-19 pandemic.The problem sets feature linked problems where one biological setting appears in multi-step problems that are sorted into the appropriate section, allowing readers to gradually develop complete investigations of topics such as HIV immunology and harvesting of natural resources. Some problems use programs written by the author for Matlab or Octave; these combine with more traditional mathematical exercises to give students a full set of tools for model analysis. Each chapter contains additional case studies in the form of projects with detailed directions. New appendices contain mathematical details on optimization, numerical solution of differential equations, scaling, linearization, and sophisticated use of elementary algebra to simplify problems.Trade Review“This is a well-written book, highly suitable for applied math undergraduate students.” (Stephanie Abo, Chi-Chung Cheung, Ryth Dasgupta, Pritha Dutta, Shervin Hakimi, Amandeep Kaur, Anita T. Layton, Mehrshad Sadria, Melissa Stadt, Vasu Swaroop and Kaixin Zheng)Table of ContentsPart I Mathematical Modeling.- 1 Modeling in Biology.- 2 Empirical Modeling.- 3 Mechanistic Modeling. Part II Dynamical Systems.- 4 Dynamics of Single Populations.- 5 Discrete Linear Systems.- 6 Nonlinear Dynamical Systems.- Appendix A. Using Matlab and Octave.- Appendix B. Derivatives and Differentiation.- Appendix C. Nonlinear Optimization.- Appendix D. A Runge-Kutta Method for Numerical Solution of Differential Equations.- Appendix E. Scales and Dimensionless Parameters.- Appendix F. Approximating a Nonlinear System at an Equilibrium Point.- Appendix G. Best Practices in the Use of Algebra.- Hints and Answers to Selected Problems.- Index.

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Book SynopsisThis unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter so that these new methods can be readily applied in their own research. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.Table of ContentsChapter 1: Introduction to Linux and Unix(This chapter will introduce some important bioinformatics tools and basics of Linux/Unix system and basic operations with Linux/Unix.) 1.1. Bioinformatics tools and Linux/Unix1.2. Features of Linux/Unix1.3. Interact with Linux/Unix Chapter 2: Introduction to R, RStudio(This chapter will introduce the environment of microbiome data analysis: R, RStudio, and some important R functions and data manipulation skills. All these skills will provide a foundation of bioinformatic and biostatistical analyses of microbiome data.) 2.1. Introduction to R and RStudio2.1.1 Installing R, RStudio, and R Packages2.1.2 Set Working Directory in R2.1.3 Data Analysis through R Studio 2.1.4 Data Import and Export 2.1.5 Basic Data Manipulation2.1. 6 Simple Summary Statistics2.1.7 Other useful R functions2.2. Useful R Packages for Data Management Chapter 3: Bioinformatic Analysis of Next-Generation Sequencing(This chapter will cover next-generation sequencing (NGS) and bioinformatic analysis of NGS data, such as sequencing data quality check, trimming, gene annotation, sequencing alignment, and genome indexing.) 3.1. Introduction to Next-Generation Sequencing3.2. Bioinformatic Analysis of Next-Generation Sequencing3.2.1 Sequencing Data Quality Check3.2.2 Sequencing Data Trimming 3.2.3 Gene Annotation3.2.4 Sequencing Alignment3.2.5 Genome Indexing3.2.6 Remove PCR Duplicates3.3. Introduction to Genome Browsers3.3.1 IGV (Integrative Genome Brower)3.3.2 UCSC Chapter 4: Bioinformatic Analysis of Metagenomics(This chapter will cover bioinformatic analysis of NGS and metagenomics data step by step. The steps will focus on bioinformatic analysis of amplicon sequencing, such as generate OTUs, taxonomic annotation and create OUT table. ) 4.1 Definition of Metagenomics4.2 Amplicon Sequencing4.2.1 Preprocessing4.2.2 Generate OTUs4.2.3 Taxonomic Annotation4.2.4 Create OUT Table4.3 Bioinformatcs Tools for Amplicon Sequencing4.3.1 QIIME 24.3.2 mothur 4.3.3 Bioinformatic Analysis of 16S rRNA Sequence Data using QIIME 2 and mothur4.4 Bioinformatic Analysis of Shortgun Metagenomic Data 4.4.1 Processing of Samples, DNA and Library4.4.2 Quality Checking4.4.3 Assembly4.4.4 Binning4.4.5 Annotation4.4.5.1 Genome and Metagenome Functional Annotations4.4.5.2 Gene Prediction and Functional Annotation Chapter 5: Alpha Diversity(This chapter will introduce biostatistical analysis of alpha diversity of microbiome data. The contents will cover alpha diversity measures and calculations, exploration, statistical hypothesis testing, and power analysis.) 5.1 Introduction to Community Diversities5.1.1 Alpha Diversity5.1.2 Beta Diversity5.2 Alpha Diversity Measures and Calculations5.2.1 Chao 1 Richness Index5.2.2 Shannon-Wiener Diversity Index5.2.3 Simpson Diversity Index5.2.4 Pielou's Evenness Index5.3 Exploration of Alpha Diversity5.3.1 Richness5.3.2 Abundance Bar5.3.3 Heatmap5.3.4 Network 5.3.5 Phylogenetic Tree5.4 Statistical Hypothesis Testing of Alpha Diversity 5.4.1 Two-sample Welch's t-test 5.4.2 Wilcoxon Rank Sum Test 5.4.3 Chi-square Test 5.4.4 One-way ANOVA 5.5.5 Kruskal-Wallis Test 5.5 Multiple Comparisons and Multiple Testing 5.5.1 Pairwise Comparisons 5.5.2 E-value 5.5.3 FWER 5.5.4 FDR5.6. Power Analysis for Testing Differences in Diversity5.6.1 Using power.t.test()5.6.2 Using pwr.avova.test()5.6.3 Using power.prop.test() 5.6.4 Using pwr.chisq.test() 5.6.5 Using power.fisher.test() 5.6.6 Using power.exact.test() Chapter 6: Beta Diversity(This chapter will introduce biostatistical analysis of beta diversity of microbiome data. The contents will cover beta diversity measures and calculations, exploration, ordination, statistical hypothesis testing.) 6.1 Beta Diversity Measures and Calculations6.1.1 Jaccard Index6.1.2 Sørensen Index6.1.3 Bray–Curtis Index6.2 Exploration of Beta Diversity6.2.1 Clustering6.2.1.1 Single Linkage6.2.1.2 Complete Linkage6.2.1.3 Average Linkage 6.2.1.4 Ward’s Minimum Variance6.2.2 Ordination6.2.2.1 Principal Component Analysis (PCA)6.2.2.2 Principal Coordinate Analysis (PCoA) 6.2.2.3 Non-metric multidimensional scaling (NMDS)6.4 Statistical Hypothesis Testing of Beta Diversity 6.4.1 Permutational Multivariate Analysis of Variance (PERMANOVA) 6.4.1.1 Implement PERMANOVA using vegan Package 6.4.1.2 Implement Pairwise Permutational MANOVA using RVAideMemoire Package6.4.2 Analysis of Similarity (ANOSIM) 6.4.2.1 Implement ANOSIM using vegan Package 6.4.3 Compare Microbiome Communities 6.4.3.1 UniFrac, Weighted UniFrac and Generalized UniFrac Distance Metrics 6.4.3.2 Implement Comparison using GUniFrac Package Chapter 7: Differential Abundance Analysis(This chapter will cover two models for count-based differential abundance analysis of microbiome data: negative binomial (NB) models in edgeR and in DESeq2.) 7.1. Count-based Differential Abundance Analysis7.1.1 Biological and Technical Variations7.1.2 Poisson 7.1.3 Negative Binomial (NB)7.2 NB Model in edgeR7.2.1 Exploration of Differential Abundant Taxa7.2.1.1 PCoA7.2.1.2 Heatmap7.2.1.3 Volcano Plot7.2.2 Statistical Hypothesis Testing in edgeR7.2.2.1 The Wald Test7.2.2.2 The Generalized Linear model (GLM)7.3. NB Model in DESeq and DESeq27.3.1 Statistical Hypothesis Testing in DESeq2 7.3.2 Implement DESeq2 Chapter 8: Analyzing Zero-Inflated Microbiome Data(This chapter will introduce both classic and newly developed statistical models for analyzing zero-inflated count microbiome data and show how to use different tests to compare these models. ) 8.1 Zero-inflated Models8.1.1 ZIP Model8.1.2 ZINB Model8.2 Zero-Hurdle Models8.2.1 ZHP Model8.2.2 ZHNB Model8.3 Comparison of Zero-inflated and Zero-Hurdle Models8.3.1 Using Likelihood Ratio Test8.3.2 Using AIC8.3.3 Using BIC8.3.4 Using Vuong Test8.4 Zero-inflated Gaussian (ZIG)8.4.1 Statistical Hypothesis Testing 8.4.1.1 Non-parametric Permutation Test on t-statistics 8.4.1.2 Non-parametric Kruskal-Wallis Test8.4.2 Implement using metagenomeSeq package8.5 Marginalized two-part Beta Regression(MTPBR)8.5.1 Introduction to MTPBR8.4.2 Implement using NLMIXED Procedure8.6 Geometric Mean of Pairwise Ratios (GMPR)8.5.1 Introduction to GMPR8.4.2 Implement using GMPR Package Chapter 9: Compositional Analysis of Microbiome Data(This chapter will summarize the issues of compositional data analysis and introduce the newly developed statistical models and methods for compositional data analysis in microbiome research.) 9.1 Introduction to Compositional Data9.1.1 Aitchison Simplex9.1.2 Fundamental Principles9.1.3 A Family of Log-ratio Transformations 9.1.4 Relative Characteristics of Microbiome Abundance Data9.2 ANOVA-Like Differential Abundance Analysis for Compositional Data9.2.1 Exploratory Compositional Data Analysis9.2.1.1 Compositional Biplot9.2.1. 2 Compositional Scree Plot9.2.1. 3 Compositional Cluster Dendrogram 9.2.1. 4 Compositional Barplot 9.2.2 Using ALDEx2 Package9.3 Analysis of Composition of Microbiomes (ANCOM)9.3.1 Introduction to ANCOM 9.3.2 Implement using ANCOM Package9.4 Balances: a Relative Abundances Perspective for Microbiome Analysis9.4.1 Introduction to Balances9.4.2 Implementing Selection of Balances Using selbal Package Chapter 10: Longitudinal Data Analysis of Microbiome(This chapter will introduce several newly developed statistical models and methods for longitudinal data analysis of microbiome.) 10.1 Zero-inflated Beta Regression Model with Random Effects: ZIBR10.1.1 Statistical Hypothesis Testing of ZIBR10.1.2 Implement using ZIBR Package10.2 Differential Distribution Analysis of Microbiome Data10.1.1 A General Framework of Statistical Hypothesis Testing based on a ZINB10.1.2 Implement using MicrobiomeDDA package10.3 Negative Binomial Mixed Models (NBMMs)10.3.1 Introduction to NBMMs10.3.2 Implement using NBZIMMpackage Chapter 11: Meta-analysis of Microbiome Data (optional)(This chapter will summarize current approaches of meta-analysis of microbiome data and discuss the issues of current approaches. The zero-inflated Beta GAMLSS of meta-analysis of microbiome data will be introduced.) 11.1 Introduction to Meta-analysis in Microbiome Studies11.2 Zero-inflated Beta GAMLSS and Meta-analysis of Microbiome Relative Abundance11.3 Implement using metamicrobiomeR package

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Book SynopsisThe 5th World Congress on Genetics, Geriatrics and Neurodegenerative Diseases Research (GeNeDis 2022) focuses on the latest major challenges in scientific research, new drug targets, the development of novel biomarkers, new imaging techniques, novel protocols for early diagnosis of neurodegenerative diseases, and several other scientific advances, with the aim of better, safer, and healthier aging. This volume focuses on the sessions from the conference on Molecular Biology, Chemical Biology, and Cellular Biology.Table of Contents1-Stratification of patients with Chronic Obstructive Pulmonary Disease using Volatile Organic Compounds2-Evidence-based Leadership: A Study of its Application to General Hospital of the Public Health System through the Implementation Leadership Scale3-Greek nurses’ perception of hospital ethical climate. A cross-sectional study4-Investigating the main causes of conflicts and the managements strategies are used by healthcare professionals. The case of general hospital of Arta5-Incidence of deep vein thrombosis and its effect on health related quality of life among nurses of Greek public hospital. A multicenter study6-Factors affecting anxiety and depression in caregivers of hemodialysis patients7-Hand grip strength in patients on hemodialysis: An observational study8-The effect of spirituality on illness perceptions in patients undergoing hemodialysis.9-Validation of the STOP-Bang Questionnaire in Greek patients suffering from obstructive sleep apnea10-The role of Pythagorean Self-Awareness Intervention in obstructive sleep apnea. A randomized controlled trial11-Tissue characterization in Cardiology. Moving beyond function12-Psychiatric care in acute care units with locked doors: Nursing care providers’ perceptions and experiences13-Researching nursing students’ attitudes towards mental health practice: cultural adaptation and validation of the Greek version of the Acceptability of Locking the Door Questionnaire in acute psychiatric care14-Compliance of bronchial asthma patients' with the Mediterranean diet15-Nurses’ experiences of psychiatric care in acute care units with an open door policy16-Validation of the Greek Version of Hedonic, Eudaimonic and Extrinsic Motives for Activities (HEEMA) Instrument17-Event-Related Rumination Inventory: A Validation Process in the Greek Language18-The job rotation of nursing staff and its effects on nurse`s satisfaction and occupational engagement19-The burden on carers with multiple sclerosis20-Attitudes of the general population regarding patient information for a chronic and life-threatening disease. A cross-sectional study.21-Assessment of healthcare professionals’ knowledge and awareness on aspects related to ionizing radiation examinations in Athens, Greece22-Medication errors and their correlation with nurse's satisfaction. The case of the hospitals of Lasithi, Crete23-Health-Related Quality of Life and Living Costs of HIV-Infected Patients24-Evaluation of anxiety and depression in women undergoing mastectomy in Greece25-The effect of emotional intelligence on caring behaviors among psychiatric nurses in Greece26-Investigating nursing leadership in intensive care units of hospitals of Northern Greece and its relationship to the working environment27-Health-Related Quality of Life and Rehabilitation Costs of Patients with Amputated Limb28-Anxiety and depression in hemodialysis: Sex differences29-Patient knowledge, adherence to the therapeutic regimen, and quality of life in hemodialysis30-The burden of caregivers of patients after hip replacement and its impact on the cost of living of the family31-The effects of exercise in patients with Sarcopenia32-Fluid dynamics derived parameters in coronary vessels33-Level of knowledge about COPD among patients and caregivers34-Increased body mass index (BMI) and sunscreen use are associated with inadequate vitamin D status in Greek adults in winter.35-The effect of whole-body cryostimulation in healthy adults36-Exhaled Nitric Oxide (FeNO) in patients hospitalized for an exacerbation of bronchiectasis and/or COPD37-Formulation and Evaluation of Dermatological product containing Niacinamide38-Exhaled breath condensate and dyspnea in COPD39-The Effects of Pythagorean Self-Awareness Intervention on IrritableBowel Syndrome Patients: A Non-Randomized Controlled Trial40-Adults’ stress response to unexpected oral and arithmetic tasks insupine position41-Triangles and family engagement in drug and alcohol addictiontreatment42-Use of fortified bread for addressing vitamin D deficiency.

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Book SynopsisThis volume constitutes the proceedings of the 10th International Work-Conference on IWBBIO 2023, held in Meloneras, Gran Canaria, Spain, during July 12-14, 2022. The total of 79 papers presented in the proceedings, was carefully reviewed and selected from 209 submissions. The papers cove the latest ideas and realizations in the foundations, theory, models, and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine.

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Book SynopsisThis volume constitutes the proceedings of the 10th International Work-Conference on IWBBIO 2023, held in Meloneras, Gran Canaria, Spain, during July 12-14, 2022. The total of 79 papers presented in the proceedings, was carefully reviewed and selected from 209 submissions. The papers cove the latest ideas and realizations in the foundations, theory, models, and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine.

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Book SynopsisThis book constitutes the refereed conference proceedings of the 14th International Conference on Bio-inspired Information and Communications Technologies, held in Okinawa, Japan, during April 11-12, 2023. The 17 full papers were carefully reviewed and selected from 33 submissions. The papers focus on the latest research that leverages the understanding of key principles, processes, and mechanisms in biological systems for development of novel information and communications technologies (bio-inspired ICT). BICT 2023 will also highlight innovative research and technologies being developed for biomedicine that are inspired by ICT (ICT-inspired biomedicine).Table of ContentsElectromagnetic-induced Calcium signal with network coding for molecular communications.- Smart Farm Teaching Aids based on STEM concepts.- Reinforcement Learning for Multifocal Tumour Targeting.- Automatic Soil Testing Device for Agriculture.- A Novel Visualization Method of Vessel Network for tumour Targeting: A Vessel Matrix Approach.- Heterogeneous Group of Fish Response to Escape Reaction.- Modeling and Simulation of a Bio-inspired Nanorobotic Drug Delivery System.- Cooperative Relaying in Multi-Hop Mobile Molecular Communication via Diffusion.- Covid-19 Versus Monkeypox-2022: The Silent Struggle of Global Pandemics.- Monte Carlo Simulation of Arbitrium and the Probabilistic Behavior of Bacteriophages.- Instant Messaging Application for 5G Core Network.- Genetic Algorithm-based Fair Order Assignment Optimization of Food Delivery Platform.- Preliminary Considerations on Non-Invasive Home-Based Bone Fracture Healing Monitoring.- Features of Audio Frequency Content of Respiration to Distinguish Inhalation from Exhalation.- Management of the medical file in case of emergency.- A Novel Durable Fat Tissue Phantom for Microwave Based Medical Monitoring Applications.- ISI Mitigation with Molecular Degradation in Molecular Communication.- Signal Transmission Through Human Body Via Human Oxygen Saturation Detection.- Simple ISI-Avoiding and Rate-Increasing Modulation for Diffusion-base Molecular Communications.- Range Expansion in Neuro-spike Synaptic Communication: Error Performance Analysis.- [Extended Abstract] Collective Bio-nanomachine Rotation via Chemical and Physical Interactions: A Three- dimensional Model.- Wearable Vibration Device to Assist with Ambulation for the Visually Impaired.- Development of Capacitive Sensors to Detect and Quantify Fluids in the Adult Diaper.- Energy Cyber Attacks to Smart Healthcare Devices: A Testbed.- [Extended Abstract] Wet-laboratory Experiments and Computer Simulation of Interacting Cell Spheroids.- Ensembles of Heuristics and Computational Optimisation In Highly Flexible Manufacturing System.- A Intelligent Nanorobots Fish Swarm Strategy for Tumor Targetting.- [Extended abstract] Design and Implementation of A General-purpose Multicellular Molecular Communication Simulator.

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Book SynopsisThe mathematical models in this book are concerned with a variety of approaches to the manner in which the clinical radiologic treatment of human neoplasms can be improved. These improvements comprise ways of delivering radiation to the malignan­ cies so as to create considerable damage to tumor cells while sparing neighboring normal tissues. There is no unique way of dealing with these improvements. Accord­ ingly, in this book a number of different presentations are given. Each presentation has as its goal some aspect of the improvement, or optimization, of radiotherapy. This book is a collection of current ideas concerned with the optimization of human cancer radiotherapy. It is hoped that readers will build on this collection and develop superior approaches for the understanding of the ways to improve therapy. The author owes a special debt of thanks to Kathy Prindle who breezed through the typing of this book with considerable dexterity. TABLE OF CONTENTS Chapter GENERAL INTRODUCTION 1. 1 Introduction 1 1. 2 History of Cancer and its Treatment by Radiotherapy 8 1. 3 Some Mathematical Models of Tumor Growth 12 1. 4 Spatial Distribution of the Radiation Dose 20 Chapter 2 SURVIVAL CURVES FROM STATISTICAL MODELS 24 2. 1 Introduction 24 2. 2 The Target Model 26 2. 3 Single-hit-to-kill Model 27 2. 4 Multitarget, Single-hit Survival 29 2. 5 Multitarget, Multihit Survival 31 2. 6 Single-target, Multihit Survival 31 2.Table of Contents1 General Introduction.- 1.1 Introduction.- 1.2 History of Cancer and its Treatment by Radiotherapy.- 1.3 Some Mathematical Models of Tumor Growth.- 1.4 Spatial Distribution of the Radiation Dose.- 2 Survival Curves from Statistical Models.- 2.1 Introduction.- 2.2 The Target Model.- 2.3 Single-hit-to-kill Model.- 2.4 Multitarget, Single-hit Survival.- 2.5 Multitarget, Multihit Survival.- 2.6 Single-target, Multihit Survival.- 2.7 Properties of In Vitro Survival Curves.- 3 A Molecular Model of cell Survival.- 3.1 Introduction.- 3.2 The Molecular Model.- 3.3 Interpretations of the Molecular Model.- 4 Kinetic Models of Biological Radiation Response.- 4.1 Introduction.- 4.2 Basic Postulates in the Dienes Model.- 4.3 Low LET Kinetic Models with no Recovery.- 4.4 Further Discussion of the Models.- 4.5 Low LET Kinetic Models with Recovery.- 4.6 Low LET and High LET Kinetic Model with No Recovery.- 4.7 Other Kinetic Schemes: Sparsely-ionizing Radiation.- 4.8 Kinetic Schemes with Age-specific Compartments in the Cell Cycle.- 4.9 Thermal Potentiation of Cell Killing.- 5 Cell Survival after Successive Radiation Fractions.- 5.1 Introduction.- 5.2 Some Results in Connection with Instantaneous Cell Kill and Exponential Tumor Growth.- 5.3 Instantaneous Cell Kill Followed by Logistic Growth of Normal Tissue.- 5.4 Cohen’s Cell Population Kinetics Programs.- 5.5 A Model of Radiation Therapy with Resistant and Sensitive Cell Populations.- 5.6 Dose Fractionation and General Survival Curves.- 6 Optimization Models in Solid Tumor Radiotherapy.- 6.1 Introduction.- 6.2 Optimal Radiotherapy of Tumor Cells Based on Cumulative Radiation Effect and a Multitarget, Single-hit Survival Function.- 6.3 Optimal Radiotherapy of Tumor Cells Based on Cumulative Radiation Effect and an Exponential-quadratic Survival Expression.- 6.4 Fractionation Scheme with a Four Level Population Tumor Model.- 6.5 A Dynamic Programming Solution to the Problem of the Determination of Optimal Treatment Schedules.- 6.6 Optimal Treatment Schedules in Fractionated Radiation Therapy for Fischer’s Tumor Model.- 6.7 Optimal Radiation Schedules with Cell Cycle Analysis.- 7 Numerical Solution of Multistage Optimal Control Problems.- 7.1 Introduction.- 7.2 Continuous Time Optimal Control.- 7.3 Optimization of Multistage Systems.- 7.4 Multi-dimensional Optimization by Gradient Methods.- 7.5 Gradient Method with Penalty Function.- 7.6 A Numerical Scheme for a Nonlinear Problem.- 7.7 The Method of Conjugate Gradients.- 7.8 Discrete Dynamic Programming.- 8 Some Optimization Criteria in Radiotherapy.- 8.1 Introduction.- 8.2 Therapeutic Policy, Strategy and Tactics.- 8.3 Optimization and Clinical Trials.- 8.4 Score Functions and Age Response Functions.- 8.5 Comparison of Models Used in Optimization Procedures.- 8.6 The Complication Probability Factor.- 9 The Optimization of External Beam Radiation Therapy.- 9.1 Introduction.- 9.2 Some Approaches for Treatment Plans.- 9.3 Linear Programming.- 9.4 Linear Programming and Radiation Treatment Planning.- 9.5 Optimization of External Beam Radiation Therapy Using Nonlinear Programming.- 9.6 Quantitative Study of Relative Radiation Effects and Isoeffect Patterns.- 10 Reconstructive Tomography.- 10.1 Introduction.- 10.2 Reconstruction Algorithm.- 10.3 Numerical Approximations for the Attenuation Coefficient.- 10.4 Cross-sectional Absorption Density Reconstruction for Treatment Planning.- 10.5 Towards the Optimization of Dose Reduction in Computerized Tomography.- 10.6 Other Imaging Technologies.- Appendix 1.- Appendix 2.- Appendix 3.

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Book SynopsisThe Springer Handbook of Bio-/Neuro-Informatics is the first published book in one volume that explains together the basics and the state-of-the-art of two major science disciplines in their interaction and mutual relationship, namely: information sciences, bioinformatics and neuroinformatics. Bioinformatics is the area of science which is concerned with the information processes in biology and the development and applications of methods, tools and systems for storing and processing of biological information thus facilitating new knowledge discovery. Neuroinformatics is the area of science which is concerned with the information processes in biology and the development and applications of methods, tools and systems for storing and processing of biological information thus facilitating new knowledge discovery. The text contains 62 chapters organized in 12 parts, 6 of them covering topics from information science and bioinformatics, and 6 cover topics from information science and neuroinformatics. Each chapter consists of three main sections: introduction to the subject area, presentation of methods and advanced and future developments. The Springer Handbook of Bio-/Neuroinformatics can be used as both a textbook and as a reference for postgraduate study and advanced research in these areas. The target audience includes students, scientists, and practitioners from the areas of information, biological and neurosciences.With Forewords by Shun-ichi Amari of the Brain Science Institute, RIKEN, Saitama and Karlheinz Meier of the University of Heidelberg, Kirchhoff-Institute of Physics and Co-Director of the Human Brain Project.Trade ReviewFrom the book reviews:“This handbook is structured in 12 parts, covering a wide variety of notions associated with bio- and neuroinformatics … . The handbook is a valuable and timely resource, which can be used by undergraduates, postgraduates and established researchers. By presenting together a variety of (linked) approaches, it provides a fantastic source for bioinformaticians and neuroinformaticians alike.” (Irina Ioana Mohorianu, zbMATH, Vol. 1304, 2015)“This is the very best of the encyclopedias and comprehensive book’s about both Medical, Molecular, Genetic, and Neural Informatics currently available. … this is a good textbook for graduate students as a Primer on Neurophysiology and Molecular Medicine. Professionals in these areas will find this book very useful in their daily work … . book is very well referenced at the end of each chapter discussion. … I am pleased to recommend this book to new researchers in the field.” (Joseph J. Grenier, Amazon.com, November, 2014)Table of ContentsChap. 1 Understanding Nature - Symbiosis of Information Science, Bioinformatics and NeuroinformaticsPart A Understanding Information Processes in Biological Systems (Ed. Heike Sichtig)Chap. 2 Information Processing at the Cellular Level.- Chap. 3 Integrated Approaches for Understadning the Cell.- Chap. 4 Information Processing at the Genomics Level.- Chap. 5 Understanding Information Processes at the Proteomics Level.- Chap. 6 Pattern Formation and Animal Morphogenesis.- Chap. 7 Understanding Evolving Bacteria ColoniesPart B Molecular Biology, Genome and Proteome Informatics (Ed.: Chris Brown)Chap. 8 Exploring Interactions and Structural Organization of Genomes.- Chap. 9 Detecting microRNA Signatures Using Gene Expression Analysis.- Chap. 10 Bioinformatics Methods to Discover Cis-Regulatory Elements.- Chap. 11 Protein Modeling and Structural PredictionPart C Machine-Learning Methods (Eds: Irwin King, Kaizhu Huang, Heike Sichtig)Chap. 12 Machine Learning Methodology in Bioinformatics.- Chap. 13 Case-Based Reasoning for Biomedical Informatics and Medicine.- Chap. 14 Analysis of Multiple DNA Microarray Datasets.- Chap. 15 Fuzzy Logic and Rule-Based Methods in Bioinformatics.- Chap. 16 Phylogenetic Cladograms: Understanding and Learning from Biomedical Data.- Chap. 17 Understanding Protein Folding Modeling.- Chap. 18 Kernel Methods and Applications in BioinformaticsPart D Modeling Regulatory Networks: The Systems Biology Approach (Eds: Chris Brown, Heike Sichtig, Irwin King, Kaizhu Huang, Francesco Masulli)Chap. 19 Path Finding in Biological Networks.- Chap. 20 Inferring Transcription Networks from Data.- Chap. 21 Analysis of Transcriptional Regulation.- Chap. 22 Inferring Genetic Networks.- Chap. 23 Structural Pattern Discovery.- Chap. 24 Molecular Networks - Representation and Analysis.- Chap. 25 Whole-Exome Sequencing DataPart E Bioinformatics Databases and Ontologies (Ed.: Francesco Masulli)Chap. 26 Bioinformatics Databases.- Chap. 27 Ontologies for BioinformaticsPart F Bioinformatics in Medicine, Health and Ecology (Eds: Francesco Masulli, Danilo Mandic)Chap. 28 Statistical Signal Processing Models And Methods.- Chap. 29 Epigenetics.- Chap. 30 Control of Autoimmune Diseases.- Chap. 311 Nutrigenomics.- Chap. 32 Bioinformatics and Nanotechnologies: Nanomedicine.- Chap. 33 Information Modeling Technologies for Personalized Medicine.- Chap. 34 Health Informatics.- Chap. 35 Ecological Informatics Part G Understanding Information Processes in the Brain and the Nervous System (Ed.: Heike Sichtig)Chap. 36 Information Processing in Synapses.- Chap. 37 Spiking Neural Networks.- Chap. 38 Statistical Methods for fMRI Activation Detection.- Chap. 39 Neural Circuit Models and Neuropathological Oscillations.- Chap. 40 Understanding the Brain via fMRI ClassificationPart H Advanced Signal-Processing Methods for Brain Signal Analysis and Modeling (Ed.: Danilo Mandic)Chap. 41 Nonlinear Adaptive Filtering in Kernel Spaces.- Chap. 42 Analysis of Multiple Spike Trains.- Chap. 43 Adaptive Multiscale Time-Frequency AnalysisPart I Information Modeling of Perception, Sensation and Cognition (Eds: Lubica Benuskova, Heike Sichtig)Chap. 44 Modeling Vision with the Neocognitron.- Chap. 45 Information Processing in the Gustatory System.- Chap. 46 EEG Signal Processing for Brain Computer Interfaces.- Chap. 47 Spiking Neural Networks.- Chap. 48 Neurocomputational Models of Natural LanguagePart J Neuroinformatics Databases and Ontologies (Eds: Shiro Usui, Raphael Ritz)Chap. 49 Ontologies and Machine Learning Systems .- Chap. 50 Integration of Large-Scale NeuroinformaticsPart K Information Modeling for Brain Diseases (Eds: Lubica Benuskova, Francesco Masulli)Chap. 51 Alzheimer’s Disease.- Chap. 52 Integrating Data for Modeling Biological Complexity.- Chap. 53 A Machine Learning Pipeline .- Chap. 54 Modeling Gene-Dependent Dynamics of Cortex and Epilepsy.- Chap. 55 Information Methods for Predicting Stroke.- Chap. 56 Recognition of Rehabilitation ActionsPart L Nature Inspired Integrated Information Technologies(Eds: Lubica Benuskova, Danilo Mandic)Chap. 57 Brain-Like Robotics.- Chap. 58 Developmental Learning for User Activities.- Chap. 59 Quantum and Biocomputing - Common Notions and Targets.- Chap. 60 Brain-, Gene-, and Quantum-Inspired Computational Intelligence.- Chap. 61 The Brain and Creativity.- Chap. 62 The Allen Brain AtlasAcknowledgements.- About the Authors.- Subject Index

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Book SynopsisClustering is an important unsupervised classification technique where data points are grouped such that points that are similar in some sense belong to the same cluster. Cluster analysis is a complex problem as a variety of similarity and dissimilarity measures exist in the literature.This is the first book focused on clustering with a particular emphasis on symmetry-based measures of similarity and metaheuristic approaches. The aim is to find a suitable grouping of the input data set so that some criteria are optimized, and using this the authors frame the clustering problem as an optimization one where the objectives to be optimized may represent different characteristics such as compactness, symmetrical compactness, separation between clusters, or connectivity within a cluster. They explain the techniques in detail and outline many detailed applications in data mining, remote sensing and brain imaging, gene expression data analysis, and face detection.The book will be useful to graduate students and researchers in computer science, electrical engineering, system science, and information technology, both as a text and as a reference book. It will also be useful to researchers and practitioners in industry working on pattern recognition, data mining, soft computing, metaheuristics, bioinformatics, remote sensing, and brain imaging.Trade ReviewFrom the reviews:“The book focuses on emerging metaheuristic approaches to unsupervised classification, with an emphasis on a symmetry-based definition of similarity. … I found this book very appealing. I also thought of it as very valuable for my preoccupations towards the real-world application of unsupervised classification to medical imaging. I thus believe that, when reading this book, junior as well as experienced researchers will find many new challenging theoretical and practical ideas.” (Catalin Stoean, zbMATH, Vol. 1276, 2014)“The book views clustering as a (multiobjective) optimization problem and tackles it with metaheuristics algorithms. More interestingly, the authors of this book propose the exploitation of the concepts of point and line symmetry to define new distances to be used in clustering techniques. … researchers in the field will surely appreciate it as a good reference on the use of the symmetry notion in clustering.” (Nicola Di Mauro, Computing Reviews, July, 2013)Table of ContentsChap. 1 Introduction.- Chap. 2 Some Single- and Multiobjective Optimization Techniques.- Chap. 3 SimilarityMeasures.- Chap. 4 Clustering Algorithms.- Chap. 5 Point Symmetry Based Distance Measures and their Applications to Clustering.- Chap. 6 A Validity Index Based on Symmetry: Application to Satellite Image Segmentation.- Chap. 7 Symmetry Based Automatic Clustering.- Chap. 8 Some Line Symmetry Distance Based Clustering Techniques.- Chap. 9 Use of Multiobjective Optimization for Data Clustering.- References.- Index.

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Book SynopsisIn the present thesis we develop new strategies concerning the use of lanthanide cations as spectroscopic probes for the study of molecular structures in solution. A widespread interest for lanthanides is mainly centered in two large fields: organic synthesis and clinical practice. Systems containing lanthanides enjoy a very favorable situation, since these ions feature high coordination numbers, which assure rich binding chemistry, and at the same time they possess the right spectroscopic properties to monitor it. The present thesis develops the potentialities of electronic spectroscopy of lanthanide systems in solution. We point out and overcome the drawbacks which have mainly hampered this kind of study so far, namely: a sensivity problem, an instrumental problem and a calibration problem.

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Book SynopsisSensory experience can dynamically modify both the anatomy and function of the brain. In particular, neurons can modify their connections in response to enviromental stimuli. This process, generally referred to as “neuronal plasticity”, is the basis of learning and memory processes in the brain. Which are the bases of neuronal plasticity? That is, how can environmental factors and sensory experience modify the connections between neurons? Neurotrophic factors of the Nerve Growth Factor (NGF) family are known to finely regulate the development and maintenance of synaptic connections in the PNS. The results obtained by the group of Maffei firstly suggested the hypothesis that neurotrophic factors could play a key role in the plasticity of the mammalian visual system. The purpose of this thesis is to give a general overview about the recent advances in the field of neurotrophine-regulated plasticity of the mammalian visual system.

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Book SynopsisThis textbook covers all the essential elements of pharmacokinetics, from basics to applications. It describes authoritative equations and methods on pharmacokinetic evaluation procedures with their importance. Each chapter of the book is supplemented with numerous illustrations and figures for easy understanding of the subject. The book presents mathematical techniques, step- by-step descriptive equations, and applicable statistical analysis methods for the easy understanding of the topic. Further, it covers the preclinical applications and methods of pharmacokinetic aspects. The book also contains mathematical problems and questions related to pharmacokinetics for students. Special emphasis is on recent pharmacokinetic methods and their applications for managing clinical data and biostatistical approaches based on the current literature. This book is primarily meant for researchers and students from academic institutions and to R&D professionals.Table of ContentsChapter 1: Fundamentals of Pharmacokinetics.- Chapter 2: Drug absorption.- Chapter 3: The extent of drug absorption: bioavailability, clearance, bioequivalence, and protein-binding.- Chapter 4: Pharmacokinetic models and drug distribution.- Chapter 5: Drug metabolism .- Chapter 6: Drug elimination and nonlinear kinetics.- Chapter 7: Pharmacokinetic drug-drug interactions.- Chapter 8: Pharmacokinetic applications.- Chapter 9: Pharmacokinetic sample collection and processing.- Chapter 10: Important bio-analytical instrumental techniques in pharmacokinetics.- Chapter 11: Statistics in pharmacokinetics.- Chapter 12: Pharmacokinetic software and tools.- Chapter 13: Pharmacokinetic laboratory-based experiments.- Chapter 14: Pharmacokinetic numerical problems with solutions.- Chapter 15: Questions, and questions & answers for practice.

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Book SynopsisThis book presents the latest research findings on the laterality of fish and other animals. It describes all aspects of lateral asymmetry, including ecology, morphology, behaviour, dynamics of lefty and righty morphs, genetics and evolution, through field observations, experiments and modeling. Lateral asymmetry in scale-eating cichlids gives a simple and beautiful example of negative frequency-dependent selection and resulting oscillation of lefty and righty morph frequencies. Lateral dimorphism is found not only in scale-eaters but in all orders of fish, shrimps and cuttlefish. Lateral asymmetry interacts between species through "cross-predation." Contrary to fish, lateral asymmetry in snails acts as, in most cases, positive frequency-dependent selection and provides deep insights into speciation. Especially, snakes eating righty snails facilitate speciation of lefty snails.As a collaboration work of field ecologists and theoretical biologists, this book covers a variety of topics on lateral asymmetry, which are consistently related to predation. The topics include behavioral ecology, population dynamics, physiology, evolution, genetics, development, learning and neuroscience, statistics, with the subjects of fish, shrimp, prawn, and crayfish, crab, cuttlefish, and snake and snail. Chapters cover new research results such as cuttlefish laterality dynamics, interaction between laterality of snails and snakes, evolution of laterality genetic system, and statistical analysis of laterality oscillation. Readers will appreciate the simplicity and beauty of lateral asymmetry and its profound impact on ecology and evolution.Table of ContentsChapter 1. Laterality of Fish – Anti-symmetry in Fish Populations Maintained by the Interspecific Interaction.- Chapter 2. Universality of laterality among fish and invertebrates in aquatic communities.- Chapter 3.Predominance of Cross Predation or Parallel Predation in Fish.- Chapter 4.Behavioral laterality in the scale-eating cichlid fish: detailed movement, development, and neuronal mechanisms.- Chapter 5.Models of Lateral Asymmetry Dynamics:Realistic Oscillations by Time Delay andFrequency Dependence.- Chapter 6.Mathematical models of predators and prey with laterality.- Chapter 7.Statistical Analysis of Lateral Asymmetry:Detect Antisymmetry and Oscillation fromUnequal-Interval Binomial Data.- Chapter 8.Models of Genetic System of LateralAsymmetry: Population Dynamics DriveEvolution of Genetic System.- Chapter 9.Mechanisms Underlying Variations in the Dentition Asymmetry of Asian Snail-Eating Snakes.- Chapter 10.Single-gene speciation, balanced polymorphism, and antagonistic coevolution in left-right asymmetry of land snails.

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Book SynopsisPooling designs have been widely used in various aspects of DNA sequencing. In biological applications, the well-studied mathematical problem called “group testing” shifts its focus to nonadaptive algorithms while the focus of traditional group testing is on sequential algorithms. Biological applications also bring forth new models not previously considered, such as the error-tolerant model, the complex model, and the inhibitor model. This book is the first attempt to collect all the significant research on pooling designs in one convenient place.The coverage includes many real biological applications such as clone library screening, contig sequencing, exon boundary finding and protein-protein interaction detecting and introduces the mathematics behind it.Table of Contentsd-Disjunct Matrices and d-Separable Matrices; Geometric and Algebraic Designs; Random Designs; Subset-Containment Designs; Array and Transversal Designs; The Complex Model; The Inhibitor Model; Contig Sequencing; Gene Detection.

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