Bioinformatik

The basic goal of the volume is to compile the most up to date research on the effect of ecotourism on Indonesia's primates. The tremendous diversity of primates in Indonesia, in conjunction with the conservation issues facing the primates of this region, have created a crisis whereby many of Indonesia's primates are threatened with extinction. Conservationists have developed the concept of "e;sustainable ecotourism"e; to fund conservation activities.  National parks agencies worldwide receive as much as 84% of their funding from ecotourism.  While ecotourism funds the majority of conservation activities, there have been very few studies that explore the effects of ecotourism on the habitat and species that they are designed to protect.  It is the burgeoning use of "e;ecotourism"e; throughout Indonesia that has created a need for this volume where the successes and pitfalls at various sites can be identified and compared. 

This book is a broad-based introduction to an increasingly important topic. The overview is easy because each chapter is structured uniformly: theory, methods, realization alternatives, methodical and practical advantages and disadvantages, and examples from industrial technology and medicine as well as research and development practice.Compared to the first edition ¿Biosignal Processing¿, the content of this book has been expanded by a sensor chapter (galvanic and capacitive sensors) and exemplary experimental data. Chapter 7: ¿Stochastic Processes¿ is also new with selected topics such as statistical analysis of time series, signal detection, and signal decomposition. Furthermore, various electronic measuring circuits and calculations have been adapted to the changed legal regulations and standards and some calculation errors have been corrected.The content is oriented to the sequence of the metrological and signal-analytical chain: neuron as a signal source¿sensor technology¿signal amplification and conditioning¿signal sampling and digitization¿methods of biosignal processing¿biostatistics and stochastic processes.The target groupsThe book is suitable for medical technology studies, research, and practice. You can inform yourself compactly across your professional boundaries about the neighbouring fields and topics at the interdisciplinary interface between medicine and technology.

This textbook provides an introduction to the mathematical models of population dynamics in mathematical biology. The focus of this book is on the biological meaning/translation of mathematical structures in mathematical models, rather than simply explaining mathematical details and literacies to analyze a model. In some recent usages of the mathematical model simply with computer numerical calculations, the model includes some inappropriate mathematical structure concerning the reasonability of modeling for the biological problem under investigation. For students and researchers who study or use mathematical models, it is important and helpful to understand what mathematical setup could be regarded as reasonable for the model with respect to the relation between the biological factors involved in the assumptions and the mathematical structure of the model.Topics covered in this book are; modeling with geometric progression, density effect in population dynamics, deriving continuous time models from discrete time models, basic modeling for birth-death stochastic processes, continuous time models, modeling interspecific reaction for the continuous time population dynamics model, competition and prey-predator dynamics, modeling for population dynamics with a heterogeneous structure of population, qualitative analysis on the discrete time dynamical system, necessary knowledge about fundamental mathematical theories to understand the dynamical nature of continuous time models. The book includes popular topics in ecology and mathematical biology, as well as classic theoretical topics.By understanding the biological meaning of modeling for simple models, readers will be able to derive a specific mathematical model for a biological problem by reasonable modeling. The contents of this book is made accessible for readers without strong Mathematical background.

This volume details state-of-the- art methods on computer-aided antibody design. Chapters guide readers through information on antibody sequences and structures,  modeling antibody structures and dynamics, prediction and optimization of biological and biophysical properties of antibodies, prediction of antibody-antigen interactions, and computer-aided antibody affinity maturation and beyond. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Authoritative and cutting-edge, Computer-Aided Antibody Design aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. Chapter 2 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book explores the most important processing steps of proteomics data analysis and presents practical guidelines, as well as software tools, that are both user-friendly and state-of-the-art in chemo- and biostatistics. Beginning with methods to control the false discovery rate (FDR), the volume continues with chapters devoted to software suites for constructing quantitation data tables, missing value related issues, differential analysis software, and more. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and implementation advice that leads to successful results. Authoritative and practical, Statistical Analysis of Proteomic Data: Methods and Tools serves as an ideal guide for proteomics researchers looking to extract the best of their data with state-of-the art tools while also deepening their understanding of data analysis.

This book presents cutting-edge research and developments in the field of biomedical engineering, with a special emphasis on results achieved in Vietnam and neighboring low- and middle-income countries. Covering both fundamental and applied research, and focusing on the theme of ¿Translational Healthcare Technology from Advanced to Low and Middle Income Countries in the Era of Covid and Digital Transformation¿, it reports on the design, fabrication, and application of low-cost and portable medical devices, biosensors, and microfluidic devices, on improved methods for biological data acquisition and analysis, on nanoparticles for biological applications, and on new achievements in biomechanics, tissue engineering, and regeneration. It describes the developments of molecular and cellular biology techniques, neuroengineering techniques, and statistical and computational methods, including artificial intelligence, for biomedical applications. It also discusses strategies to addresssome relevant issues in biomedical education and entrepreneurship. Gathering the proceedings of the 9th International Conference on The Development of Biomedical Engineering in Vietnam, BME 9, held on December 27-29, 2022, in Ho Chi Minh, Vietnam, the book offers important answers to current challenges in the field and a source of inspiration for scientists, engineers, and researchers with various backgrounds working in different research institutes, companies, and countries.

This book offers an accessible introduction to random walk and diffusion models at a level consistent with the typical background of students in the life sciences. In recent decades these models have become widely used in areas far beyond their traditional origins in physics, for example, in studies of animal behavior, ecology, sociology, sports science, population genetics, public health applications, and human decision making.  Developing the main formal concepts, the book provides detailed and intuitive step-by-step explanations, and moves smoothly from simple to more complex models. Finally, in the last chapter, some successful and original applications of random walk and diffusion models in the life and behavioral sciences are illustrated in detail. The treatment of basic techniques and models is consolidated and extended throughout by a set of carefully chosen exercises.  

This book covers recent trends and applications of nonlinear dynamics in various branches of society, science, and engineering. The selected peer-reviewed contributions were presented at the International Conference on Nonlinear Dynamics and Applications (ICNDA 2022) at Sikkim Manipal Institute of Technology (SMIT) and cover a broad swath of topics ranging from chaos theory and fractals to quantum systems and the dynamics of the COVID-19 pandemic. Organized by the SMIT Department of Mathematics, this international conference offers an interdisciplinary stage for scientists, researchers, and inventors to present and discuss the latest innovations and trends in all possible areas of nonlinear dynamics.

Boolean Satisfiability (SAT)is one of the famous problem present in the field of computer scienceand mathematical theory. Boolean Satisfiability can be defined as the problem of finding assignmentsto the variables such that, it satisfy the given a Boolean formula. Boolean Satisfiabilityproblems arise in many applications such as cryptology, hardware and software verification,reliability, artificial intelligence, decision under logic constraints, computational studies of Biologicalnetworks. Recent application of solving Boolean systems arises in Biological(Genetic Regulatory) Networks.The CNF Satisfiability(CNFSAT) Problem is one of the important case of of the SatisfiabilityProblem, where the Boolean formula is represented in the CNF form i.e.Conjunctive NormalForm (CNF).This means Boolean formula is a conjunction of clauses and each clause is a disjunctionof literals. A literal is a variable or its negation.CNF SAT has central importance incomputer science. SAT normally suits to the formulas if they are in Conjunctive NormalForm , as mentioned, should be a set of clauses.SAT is considered as NP-complete problem in its general form. Inspite of this reality,there are number of problems which can be successfully solved by SAT such as cryptanalysis,bioinformatics, hardware verification, etc. For recent past twenty years the effectiveness ofSAT algorithms has significantly increased. XOR-SAT is one special case of Boolean SAT where each equation is an exclusive OR(XOR) combination of variables. Such linear XOR systems naturally appear in problems suchas quadratic sieve method for prime factorization of numbers. Also in decoding of linearerror correction coding, linear XOR systems.In the specific case of cryptography, SAT solversbecame a very important tool to analyse and break encoding mechanisms. Within the case ofcryptanalytic application, many times SAT solvers have faced with issues that encode relativelylarge amount of XOR constraints.

This handbook in two volumes offers a heretofore unavailable compilation of detailed information on foraminifera of the Caspian-Black Sea-Mediterranean Corridors ("e;CORRIDORS"e;), including their taxonomy, ecology, and applications in the study of Quaternary stratigraphy, paleogeographic reconstruction, and environmental stress. This subject is significant in light of the ongoing debates regarding the Flood Hypotheses because foraminifera can provide more information about many of the disputed questions. Foraminifera are highly reliable paleoenvironmental indicators, ubiquitous in marine environments, and taxonomically diverse, which gives them the potential for a wide range of biological responses to varied environmental factors. Their tests are readily preserved and can record evidence of environmental change through time, thus providing historical baseline data even in the absence of background studies. This book presents taxonomic descriptions for about 500 species and subspecies from the Black Sea, Sea of Azov, Caspian Sea, Aral Sea, Sea of Marmara, and the Eastern Mediterranean. This catalogue is supplemented by ecological remarks, stratigraphic distributions, paleogeography, and environmental/paleoenvironmental applications, including responses to environmental stress, e.g., river discharge, pollution by different contaminants, etc. The book will be useful to specialists in Quaternary history of the "e;CORRIDORS"e; as well as those in environmental monitoring and risk assessment. This handbook offers detailed taxonomic descriptions of foraminifera from the Black Sea, Caspian Sea, Sea of Azov, Aral Sea (in Volume 1) and Eastern Mediterranean and Sea of Marmara (in Volume 2). 

This volume provides readers with a broad collection of theoretical, computational, and experimental methods to quantitatively study the properties of phase-separate biomolecular condensates in diverse systems. The chapters in this book cover topics such as theoretical and computational methods; methods for in vitro characterization of biomolecular condensates; and techniques that enable in-cell characterization of biomolecular condensates. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known pitfalls.Comprehensive and thorough, Phase-Separated Biomolecular Condensates: Methods and Protocols is a valuable resource that helps researchers learn and use established methods to study both biophysical properties and biological functions of biomolecular condensates. 

This volume provides protocols for computational, statistical, and machine learning methods that are mainly applied to the study of metabolic engineering, synthetic biology, and disease applications. These techniques support the latest progress in cross-disciplinary research that integrates the different scales of biological complexity. The topics covered in this book are geared toward researchers with a background in engineering, computational analytical, and modeling experience and cover a broad range of topics in computational and machine learning approaches. 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.Comprehensive and practical, Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology is a valuable resource for any researcher or scientist who wants to learn more about the latest computational methods and how they are applied toward the understanding and prediction of complex biology. 

Applied Multivariate Statistical Analysis in Medicine provides a multivariate conceptual framework that allows readers to understand the interconnectivity and interrelations among variables, which maintains the intrinsic precision of statistical theories. With a strong focus on the fundamental concepts of multivariate statistical analysis, the book also gives insight into the applications of multivariate distribution in biomedical fields. In 14 chapters, Applied Multivariate Statistical Analysis in Medicine covers the main topics of multivariate analysis methods widely used in health science research. The content is organized progressively from fundamental concepts to sophisticated methods. It begins with basic descriptive statistics in multivariate analysis and follows with parameter estimation, in addition to the hypothesis testing of a multivariate normal distribution, which has heavy applications in biomedical fields where the relationships among approximately normal variables are of great interest. Keeping mathematics to a minimum, considerable emphasis is placed on explanations and real-world applications of core principles to maintain a good balance between introducing theory and cultivating problem-solving skills. This book is a very valuable reference text for clinicians, medical researchers, and other researchers across medical and biomedical disciplines, all of whom confront increasingly complex statistical methods during the analysis and presentation of their results.

This 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).

This contributed volume investigates several mathematical techniques for the modeling and simulation of viral pandemics, with a special focus on COVID-19.  Modeling a pandemic requires an interdisciplinary approach with other fields such as epidemiology, virology, immunology, and biology in general.  Spatial dynamics and interactions are also important features to be considered, and a multiscale framework is needed at the level of individuals and the level of virus particles and the immune system.  Chapters in this volume address these items, as well as offer perspectives for the future.

"This concise book for scientists and students interested in bioinformatics and data science covers all aspects of predictive modeling for biomarker discovery based on high-dimensional data, as well as modern data science methods for identification of parsimonious and robust multivariate biomarkers for medical diagnosis and personalized medicine"--

This second edition volume expands on the previous edition with discussions of the latest advancements and methods used by scientists to study systems biology. The chapters in this book are organized into four parts. Part One looks at models in systems biology and parameters identification such as short peptide analysis, metastasis models, and metabolomics. Part Two covers computational methods in the study of organisms, and cancer non-linear dynamics. Part Three discusses critical transition states across Waddington¿s like landscapes such as understanding cell differentiation through single-cell approaches and modeling mammary organogenesis from biological first principles. Part Four talks about specific fields of investigation including inborn errors of metabolism, system biology approach in epithelial-mesenchymal transition, and an approach to understanding how COVID-19 spreads in the population. 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 comprehensive, Systems Biology, Second Edition is a valuable tool for any researcher looking to learn more about this important and developing field.

This book offers the reader a journey through the counterintuitive nature of Brownian motion under confinement. Diffusion is a universal phenomenon that controls a wide range of physical, chemical, and biological processes. The transport of spatially-constrained molecules and small particles is ubiquitous in nature and technology and plays an essential role in different processes. Understanding the physics of diffusion under conditions of confinement is essential for a number of biological phenomena and potential technological applications in micro- and nanofluidics, among others. Studies on diffusion under confinement are typically difficult to understand for young scientists and students because of the extensive background on diffusion processes, physics, and mathematics that is required. All of this information is provided in this book, which is essentially self-contained as a result of the authors¿ efforts to make it accessible to an audience of students from avariety of different backgrounds. The book also provides the necessary mathematical details so students can follow the technical process required to solve each problem. Readers will also find detailed explanations of the main results based on the last 30 years of research devoted to studying diffusion under confinement. The authors approach the physical problem from various angles and discuss the role of geometries and boundary conditions in diffusion. This textbook serves as a comprehensive and modern overview of Brownian motion under confinement and is intended for young scientists, graduate students, and advanced undergraduates in physics, physical chemistry, biology, chemistry, chemical engineering, biochemistry, bioengineering, and polymer and material sciences.

This book constitutes the refereed proceedings of the 21st International Conference on Computational Methods in Systems Biology, CMSB 2023, held in Luxembourg City, Luxembourg, during September 13¿15, 2023.The 14 full papers and 3 tool papers presented in this book were carefully reviewed and selected from 28 submissions. CMSB focuses on modeling, simulation, analysis, design and control of biological systems and covers the broad field of computational methods and tools in systems and synthetic biology and their applications.

This book reviews the advances in data gathering and processing in the biotech laboratory environment, and it sheds new lights on the various aspects that are necessary for the implementation of intelligent laboratory architecture and infrastructure. Smart technologies are increasingly dominating our everyday lives and have become an indispensable part of the industrial environment. The laboratory environment, which has long been rather conservative, has also set out to adapt smart technologies with regards to Industry 4.0 and the Internet of Things (IoT) for the laboratory. Due to the heterogeneity of the existing infrastructure and the often complex work processes, standardization is slow, e.g. to implement device interfaces or standardized driver protocols, which are urgently needed to generate standardized data streams that would be immanent for post-processing of data.Divided into 9 chapters, this book offers an authoritative overview of the diverse aspects in the generation and recording of uniform data sets in the laboratory, and in the processing of the data and enabling seamless processing towards machine learning and artificial intelligence. In the first part of the book, readers will find more about high throughout systems, automation, robotics, and the evolution of technology in the laboratory. The second part of the book is devoted to standardization in lab automation, in which readers will learn more about some regulatory aspects, the SiLA2 standards, the OPC LADS (Laboratory and Analytical Device Standard), and FAIR Data infrastructure

The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved.In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.

To date, processing of high-throughput Mass Spectrometry (MS) data is accomplished using serial algorithms. Developing new methods to process MS data is an active area of research but there is no single strategy that focuses on scalability of MS based methods.  Mass spectrometry is a diverse and versatile technology for high-throughput functional characterization of proteins, small molecules and metabolites in complex biological mixtures. In the recent years the technology has rapidly evolved and is now capable of generating increasingly large (multiple tera-bytes per experiment) and complex (multiple species/microbiome/high-dimensional) data sets. This rapid advance in MS instrumentation  must  be matched by equally fast and rapid evolution of scalable methods developed for analysis of these complex data sets. Ideally, the new methods should leverage the rich heterogeneous computational resources available in a ubiquitous fashion in the form of  multicore,  manycore,  CPU-GPU, CPU-FPGA, and IntelPhi architectures.  The absence of these high-performance computing algorithms now hinders scientific advancements for mass spectrometry research. In this book we illustrate the need for high-performance computing algorithms for MS based proteomics, and proteogenomics and showcase our progress in developing these high-performance algorithms.

This book presents contributions from the MICCAI 2022 Computational Biomechanics for Medicine Workshop. "Computational Biomechanics for Medicine - towards translation and better patient outcomes¿ comprises papers accepted for the MICCAI Computational Biomechanics for Medicine Workshop held in 2022 in Singapore. The content focuses on applications of computational biomechanics to computer-integrated medicine, which includes MICCAI topics of Medical Image Computing, Computer-Aided Modeling and Evaluation of Surgical Procedures, and Imaging, Analysis Methods for Image Guided Therapies, Computational Physiology, and Medical Robotics. Specific topics covered include medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book details state-of-the-art progress in the above fields to researchers, students, and professionals.