This book seeks to work out which commitments are minimally sufficient to obtain an ontology of the natural world that matches all of today's well-established physical theories. We propose an ontology of the natural world that is defined only by two axioms: (1) There are distance relations that individuate simple objects, namely matter points. (2) The matter points are permanent, with the distances between them changing. Everything else comes in as a means to represent the change in the distance relations in a manner that is both as simple and as informative as possible. The book works this minimalist ontology out in philosophical as well as mathematical terms and shows how one can understand classical mechanics, quantum field theory and relativistic physics on the basis of this ontology. Along the way, we seek to achieve four subsidiary aims: (a) to make a case for a holistic individuation of the basic objects (ontic structural realism); (b) to work out a new version of Humeanism, dubbed Super-Humeanism, that does without natural properties; (c) to set out an ontology of quantum physics that is an alternative to quantum state realism and that avoids any ontological dualism of particles and fields; (d) to vindicate a relationalist ontology based on point objects also in the domain of relativistic physics.

This new edition continues to illustrate the power of biological data in knowledge discovery. It describes biological data types and representations with examples for creating a workflow in bioinformation discovery. The concepts in knowledge discovery from data are illustrated using line diagrams. The principles and concepts in knowledge discovery are used for the development of prediction models for simulations of biological reactions and events. Advanced topics in molecular evolution and cellular & molecular biology are addressed using bioinformation gleaned through discovery. Each chapter contains approximately 10 exercises for practice. This will help students to expand their problem solving skills in Bioinformation Discovery. In this new edition, there are three new chapters covering single nucleotide polymorphism, genes, proteins and disease, and protein functions driven by surface electrostatics.

This contributed volume comprises research articles and reviews on topics connected to the mathematical modeling of cellular systems. These contributions cover signaling pathways, stochastic effects, cell motility and mechanics, pattern formation processes, as well as multi-scale approaches. All authors attended the workshop on "Modeling Cellular Systems" which took place in Heidelberg in October 2014. The target audience primarily comprises researchers and experts in the field, but the book may also be beneficial for graduate students.

The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume I provides a panoramic view that illustrates the potential of such mathematical methods in systems and synthetic biology. Recent advances in systems and synthetic biology have clearly demonstrated the benefits of a rigorous and systematic approach rooted in the principles of systems and control theory - not only does it lead to exciting insights and discoveries but it also reduces the inordinately lengthy trial-and-error process of wet-lab experimentation, thereby facilitating significant savings in human and financial resources. In Volume I, some of the leading researchers in the field of systems and synthetic biology demonstrate how systems and control theoretic concepts and techniques can be useful, or should evolve to be useful, in order to understand how biological systems function. As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Applications: - Applications of Microbial Cell Sensors, by Mifumi Shimomura-Shimizu and Isao Karube - Whole-Cell Bioreporters for the Detection of Bioavailable Metals, by Anu Hynninen and Marko Virta - Bacteriophage-Based Pathogen Detection, by Steven Ripp - Cell-Based Genotoxicity Testing, by Georg Reifferscheid and Sebastian Buchinger - Cytotoxicity and Genotoxicity Reporter Systems Based on the Use of Mammalian Cells, by Christa Baumstark-Khan, Christine E. Hellweg, and Gunther Reitz - Live Cell Optical Sensing for High Throughput Applications, by Ye Fang - Cyanobacterial Bioreporters as Sensors of Nutrient Availability, by George S. Bullerjahn, Ramakrishna Boyanapalli, Mark J. Rozmarynowycz, and R. Michael L. McKay - Application of Microbial Bioreporters in Environmental Microbiology and Bioremediation, by E. E. Diplock, H. A. Alhadrami, and G. I. Paton

This research monograph utilizes exact and Monte Carlo permutation statistical methods to generate probability values and measures of effect size for a variety of measures of association. Association is broadly defined to include measures of correlation for two interval-level variables, measures of association for two nominal-level variables or two ordinal-level variables, and measures of agreement for two nominal-level or two ordinal-level variables. Additionally, measures of association for mixtures of the three levels of measurement are considered: nominal-ordinal, nominal-interval, and ordinal-interval measures. Numerous comparisons of permutation and classical statistical methods are presented. Unlike classical statistical methods, permutation statistical methods do not rely on theoretical distributions, avoid the usual assumptions of normality and homogeneity of variance, and depend only on the data at hand. This book takes a unique approach to explaining statistics by integrating a large variety of statistical methods, and establishing the rigor of a topic that to many may seem to be a nascent field. This topic is relatively new in that it took modern computing power to make permutation methods available to those working in mainstream research. Written for a statistically informed audience, it is particularly useful for teachers of statistics, practicing statisticians, applied statisticians, and quantitative graduate students in fields such as psychology, medical research, epidemiology, public health, and biology. It can also serve as a textbook in graduate courses in subjects like statistics, psychology, and biology.

This book contains a rich set of tools for nonparametric analyses, and the purpose of this text is to provide guidance to students and professional researchers on how R is used for nonparametric data analysis in the biological sciences: To introduce when nonparametric approaches to data analysis are appropriate To introduce the leading nonparametric tests commonly used in biostatistics and how R is used to generate appropriate statistics for each test To introduce common figures typically associated with nonparametric data analysis and how R is used to generate appropriate figures in support of each data set The book focuses on how R is used to distinguish between data that could be classified as nonparametric as opposed to data that could be classified as parametric, with both approaches to data classification covered extensively. Following an introductory lesson on nonparametric statistics for the biological sciences, the book is organized into eight self-contained lessons on various analyses and tests using R to broadly compare differences between data sets and statistical approach.

This BASS book Series publishes selected high-quality papers reflecting recent advances in the design and biostatistical analysis of biopharmaceutical experiments - particularly biopharmaceutical clinical trials. The papers were selected from invited presentations at the Biopharmaceutical Applied Statistics Symposium (BASS), which was founded by the first Editor in 1994 and has since become the premier international conference in biopharmaceutical statistics. The primary aims of the BASS are: 1) to raise funding to support graduate students in biostatistics programs, and 2) to provide an opportunity for professionals engaged in pharmaceutical drug research and development to share insights into solving the problems they encounter. The BASS book series is initially divided into three volumes addressing: 1) Design of Clinical Trials; 2) Biostatistical Analysis of Clinical Trials; and 3) Pharmaceutical Applications. This book is the second of the 3-volume book series. The topics covered include: Statistical Approaches to the Meta-analysis of Randomized Clinical Trials, Collaborative Targeted Maximum Likelihood Estimation to Assess Causal Effects in Observational Studies, Generalized Tests in Clinical Trials, Discrete Time-to-event and Score-based Methods with Application to Composite Endpoint for Assessing Evidence of Disease Activity-Free , Imputing Missing Data Using a Surrogate Biomarker: Analyzing the Incidence of Endometrial Hyperplasia, Selected Statistical Issues in Patient-reported Outcomes, Network Meta-analysis, Detecting Safety Signals Among Adverse Events in Clinical Trials, Applied Meta-analysis Using R, Treatment of Missing Data in Comparative Effectiveness Research, Causal Estimands: A Common Language for Missing Data, Bayesian Subgroup Analysis with Examples, Statistical Methods in Diagnostic Devices, A Question-Based Approach to the Analysis of Safety Data, Analysis of Two-stage Adaptive Seamless Trial Design, and Multiplicity Problems in Clinical Trials - A Regulatory Perspective.

This volume is based on the Workshop on Systems Biology of Tumor Dormancy meeting, held July 25th to July 28th, 2011. The first annual CCSB workshop brought together biologists, clinicians, mathematicians, and computer scientists to discuss various aspects of tumor dormancy and develop novel mathematical/computational models with the keynote speakers. Specific topics included the angiogenic switch, immune system interactions, cancer stem cells and signaling.

Since Darwin, Biology has been framed on the idea of evolution by natural selection, which has profoundly influenced the scientific and philosophical comprehension of biological phenomena and of our place in Nature. This book argues that contemporary biology should progress towards and revolve around an even more fundamental idea, that of autonomy. Biological autonomy describes living organisms as organised systems, which are able to self-produce and self-maintain as integrated entities, to establish their own goals and norms, and to promote the conditions of their existence through their interactions with the environment. Topics covered in this book include organisation and biological emergence, organisms, agency, levels of autonomy, cognition, and a look at the historical dimension of autonomy. The current development of scientific investigations on autonomous organisation calls for a theoretical and philosophical analysis. This can contribute to the elaboration of an original understanding of life - including human life - on Earth, opening new perspectives and enabling fecund interactions with other existing theories and approaches. This book takes up the challenge.

Food products are complex in nature which makes their analysis difficult. Different scientific disciplines such as biochemistry, microbiology, and nutrition, together with engineering concepts are involved in their characterization. However, imaging of food materials and data analysis has gained more importance due to innovations in the food industry, as well as the emergence of food nanotechnology. Image analysis protocols and techniques can be used in food structure analysis and process monitoring. Therefore, food structure imaging is crucial for various sections of the food chain starting from the raw material to the end product. This book provides information on imaging techniques such as electron microscopy, laser microscopy, x-ray tomography, raman and infrared imaging, together with data analysis protocols. It addresses the most recent advances in imaging technologies and data analysis of grains, liquid food systems (i.e. emulsions and gels), semi-solid and solid foams (i.e. bakery products, dough, expanded snacks), protein films, fruits and vegetable confectionery and nuts. This book also: Provides in-depth view of raw material characterization and process control Covers structure-functionality and structure-texture relationships Reviews applications to emerging areas of food science with an insight into future trends

Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Optical Methods of Measurement: Wholefield Techniques, Second Edition provides a comprehensive collection of wholefield optical measurement techniques for engineering applications. Along with the reorganization of contents, this edition includes a new chapter on optical interference, new material on nondiffracting and singular beams and their applications, and updated bibliography and additional reading sections. The book explores the propagation of laser beams, metrological applications of phase-singular beams, various detectors such as CCD and CMOS devices, and recording materials. It also covers interference, diffraction, and digital fringe pattern measurement techniques, with special emphasis on phase measurement interferometry and algorithms. The remainder of the book focuses on theory, experimental arrangements, and applications of wholefield techniques. The author discusses digital hologram interferometry, digital speckle photography, digital speckle pattern interferometry, Talbot interferometry, and holophotoelasticity. This updated book compiles the major wholefield methods of measurement in one volume. It provides a solid understanding of the techniques by describing the physics behind them. In addition, the examples given illustrate how the techniques solve measurement problems.

This edited monograph presents the collected interdisciplinary research results of the priority program "Information- and Communication Theory in Molecular Biology (InKoMBio, SPP 1395)", funded by the German Research Foundation DFG, 2010 until 2016. The topical spectrum is very broad and comprises, but is not limited to, aspects such as microRNA as part of cell communication, information flow in mammalian signal transduction pathway, cell-cell communication, semiotic structures in biological systems, as well as application of methods from information theory in protein interaction analysis. The target audience primarily comprises research experts in the field of biological signal processing, but the book is also beneficial for graduate students alike.

Scientists planning experiments in medical and behavioral research will find this handbook and dictionary an invaluable desk reference tool. Also recommended as a textbook for students of Experimental Design or accompanying courses in Statistics.
Principles of experimental design are introduced, techniques of experimental design are described, and advantages and disadvantages of often used designs are discussed. This two-part volume, a handbook of experimental design and a dictionary providing short explanations for many terms related to experimental design, contains information that will not quickly become outdated.

This book describes the methods of analysis and determination of oxidants and oxidative stress in biological systems. Reviews and protocols on select methods of analysis of ROS, RNS, oxygen, redox status, and oxidative stress in biological systems are described in detail. It is an essential resource for both novices and experts in the field of oxidant and oxidative stress biology.

Intelligence results from the interaction of the brain, body and environment. The question addressed in this book is, can we measure the contribution of the body and its' interaction with the environment? To answer this, we first present a comprehensive overview of the various ways in which a body reduces the amount of computation that the brain has to perform to solve a task. This chapter will broaden your understanding of how important inconspicuously appearing physical processes and physical properties of the body are with respect to our cognitive abilities. This form of contribution to intelligence is called Morphological Intelligence. The main contribution of this book to the field is a detailed discussion of how Morphological Intelligence can be measured from observations alone. The required mathematical framework is provided so that readers unfamiliar with information theory will be able to understand and apply the measures. Case studies from biomechanics and soft robotics illustrate how the presented quantifications can, for example, be used to measure the contribution of muscle physics to jumping and optimise the shape of a soft robotic hand. To summarise, this monograph presents various examples of how the physical properties of the body and the body's interaction with the environment contribute to intelligence. Furthermore, it treats theoretical and practical aspects of Morphological Intelligence and demonstrates the value in two case studies.

Volume II of this two-volume, interdisciplinary work is a unified presentation of a broad range of state-of-the-art topics in the rapidly growing field of mathematical modeling in the biological sciences. Highlighted throughout are mathematical and computational apporaches to examine central problems in the life sciences, ranging from the organization principles of individual cells to the dynamics of large populations. The chapters are thematically organized into the following main areas: epidemiology, evolution and ecology, immunology, neural systems and the brain, and innovative mathematical methods and education.

The work will be an excellent reference text for a broad audience of researchers, practitioners, and advanced students in this rapidly growing field at the intersection of applied mathematics, experimental biology and medicine, computational biology, biochemistry, computer science, and physics.

This book reviews the most significant advances in concepts, methods, and applications of quantum systems in a broad variety of problems in modern chemistry, physics, and biology. In particular, it discusses atomic, molecular, and solid structure, dynamics and spectroscopy, relativistic and correlation effects in quantum chemistry, topics of computational chemistry, physics and biology, as well as applications of theoretical chemistry and physics in advanced molecular and nano-materials and biochemical systems. The book contains peer-reviewed contributions written by leading experts in the fields and based on the presentations given at the Twenty-Fourth International Workshop on Quantum Systems in Chemistry, Physics, and Biology held in Odessa, Ukraine, in August 2019. This book is aimed at advanced graduate students, academics, and researchers, both in university and corporation laboratories, interested in state-of-the-art and novel trends in quantum chemistry, physics, biology, and their applications.

For many years, the authors have investigated the adaptive role of heat shock proteins (HSPs) in different animals, including the representatives of homothermic and poikilothermic organisms that inhabit regions with contrasting thermal conditions. This book will summarize the data accumulated in the course of these studies and describe the general molecular mechanisms underlying the adaptation of various organisms to aggressive environments. We also concentrate on different evolutionary trends characteristic for HSP systems in the course of adaptation to fluctuating environmental conditions. In addition, we describe the peculiarities in the regulatory regions of heat shock genes necessary for fine tuning of these systems providing the adaptation to adverse conditions. Special emphasis is given to the role of mobile elements in the evolution and functioning of various groups of HSP genes. The book combines the results of field studies and laboratory analysis of stress genes systems.

Sustainable and Circular Management of Resources and Waste Towards a Green Deal highlights the importance of resource recovery, phosphorus management, climate action, clean energy transition, and a circular economy. The world is facing significant challenges, including climate disruption, environmental changes, pollution, and population explosion. Sustainable management of finite natural resources within the carrying capacity of the bio-geo-hydrosphere is the crux of transforming the global economy for a sustainable future. Moreover, keeping raw materials in circulation as long as possible and minimizing the amount of waste generated has grown in significance as a part of transitioning to a circular economy (CE) model.

A New York Times bestselling writer explores what our unique sonic signature reveals about our species, our culture, and each one of us. Finally, a vital topic that has never had its own book gets its due. There's no shortage of books about public speaking or language or song. But until now, there has been no book about the miracle that underlies them all--the human voice itself. And there are few writers who could take on this surprisingly vast topic with more artistry and expertise than John Colapinto. Beginning with the novel--and compelling--argument that our ability to speak is what made us the planet's dominant species, he guides us from the voice's beginnings in lungfish millions of years ago to its culmination in the talent of Pavoratti, Martin Luther King Jr., and Beyonce--and each of us, every day. Along the way, he shows us why the voice is the most efficient, effective means of communication ever devised: it works in all directions, in all weathers, even in the dark, and it can be calibrated to reach one other person or thousands. He reveals why speech is the single most complex and intricate activity humans can perform. He travels up the Amazon to meet the Piraha, a reclusive tribe whose singular language, more musical than any other, can help us hear how melodic principles underpin every word we utter. He heads up to Harvard to see how professional voices are helped and healed, and he ventures out on the campaign trail to see how demagogues wield their voices as weapons. As far-reaching as this book is, much of the delight of reading it lies in how intimate it feels. Everything Colapinto tells us can be tested by our own lungs and mouths and ears and brains. He shows us that, for those who pay attention, the voice is an eloquent means of communicating not only what the speaker means, but also their mood, sexual preference, age, income, even psychological and physical illness. It overstates the case only slightly to say that anyone who talks, or sings, or listens will find a rich trove of thrills in This Is the Voice.

Exploring behaviour through bones has always been a fascinating topic to those that study human remains. Human bodies record and store vast amounts of information about the way we move, where we live, and our experiences of health and socioeconomic circumstances. We see it every day, and experience it, but when it comes to past populations, understanding behaviour is largely mediated by our ability to read it in bones. Behaviour in Our Bones: How Human Behaviour Influences Skeletal Morphology examines how human physical and cultural actions and interactions can be read through careful analyses of skeletal human remains. This book synthesises the latest research on reconstructing behaviour in the past. Each chapter is dedicated to a specific region of the human body, guiding the reader from head to toe and highlighting how evidence found on the skull, shoulder, thorax, spine, pelvis, and the upper and lower limbs has been used to infer patterns of activity and other behaviour. Chapter authors expertly summarise and critically discuss a range of methodological, theoretical, and interpretive approaches used to read skeletal remains and interpret a wide variety of behaviours, including tool use, locomotion, reproduction, health, pathology, and beyond.

This book is the third revised and updated English edition of the German textbook \Versuchsplanung und Modellwahl" by Helge Toutenburg which was based on more than 15 years experience of lectures on the course \- sign of Experiments" at the University of Munich and interactions with the statisticians from industries and other areas of applied sciences and en- neering. This is a type of resource/ reference book which contains statistical methods used by researchers in applied areas. Because of the diverse ex- ples combined with software demonstrations it is also useful as a textbook in more advanced courses, The applications of design of experiments have seen a signi?cant growth in the last few decades in di?erent areas like industries, pharmaceutical sciences, medical sciences, engineering sciences etc. The second edition of this book received appreciation from academicians, teachers, students and applied statisticians. As a consequence, Springer-Verlag invited Helge Toutenburg to revise it and he invited Shalabh for the third edition of the book. In our experience with students, statisticians from industries and - searchers from other ?elds of experimental sciences, we realized the importance of several topics in the design of experiments which will - crease the utility of this book. Moreover we experienced that these topics are mostly explained only theoretically in most of the available books.