This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians.

MATRIX is Australia's international and residential mathematical research institute. It facilitates new collaborations and mathematical advances through intensive residential research programs, each 1-4 weeks in duration. This book is a scientific record of the eight programs held at MATRIX in 2018: - Non-Equilibrium Systems and Special Functions - Algebraic Geometry, Approximation and Optimisation - On the Frontiers of High Dimensional Computation - Month of Mathematical Biology - Dynamics, Foliations, and Geometry In Dimension 3 - Recent Trends on Nonlinear PDEs of Elliptic and Parabolic Type - Functional Data Analysis and Beyond - Geometric and Categorical Representation Theory The articles are grouped into peer-reviewed contributions and other contributions. The peer-reviewed articles present original results or reviews on a topic related to the MATRIX program; the remaining contributions are predominantly lecture notes or short articles based on talks or activities at MATRIX.

The convergence of biology and computer science was initially motivated by the need to organize and process a growing number of biological observations resulting from rapid advances in experimental techniques. Today, however, close collaboration between biologists, biochemists, medical researchers, and computer scientists has also generated remarkable benefits for the field of computer science. Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances presents new techniques that have resulted from the application of computer science methods to the organization and interpretation of biological data. The book covers three subject areas: bioinformatics, computational biology, and computational systems biology. It focuses on recent, systemic approaches in computer science and mathematics that have been used to model, simulate, and more generally, experiment with biological phenomena at any scale.

Robert Rosen was not only a biologist, he was also a brilliant mathematician whose extraordinary contributions to theoretical biology were tremendous. Founding, with this book, the area of Anticipatory Systems Theory is a remarkable outcome of his work in theoretical biology. This second edition of his book Anticipatory Systems, has been carefully revised and edited, and includes an Introduction by Judith Rosen. It has also been expanded with a set of Prolegomena by Dr. Mihai Nadin, who offers an historical survey of this fast growing field since the original work was published. There is also some exciting new work, in the form of an additional chapter on the Ontology of Anticipation, by Dr. John Kineman. An addendum-- with autobiographical reminiscences by Robert Rosen, himself, and a short story by Judith Rosen about her father-- adds a personal touch. This work, now available again, serves as the guiding foundations for the growing field of Anticipatory Systems and, indeed, any area of science that deals with living organisms in some way, including the study of Life and Mind. It will also be of interest to graduate students and researchers in the field of Systems Science.

The primary purpose of this textbook is to introduce the reader to a wide variety of elementary permutation statistical methods. Permutation methods are optimal for small data sets and non-random samples, and are free of distributional assumptions. The book follows the conventional structure of most introductory books on statistical methods, and features chapters on central tendency and variability, one-sample tests, two-sample tests, matched-pairs tests, one-way fully-randomized analysis of variance, one-way randomized-blocks analysis of variance, simple regression and correlation, and the analysis of contingency tables. In addition, it introduces and describes a comparatively new permutation-based, chance-corrected measure of effect size. Because permutation tests and measures are distribution-free, do not assume normality, and do not rely on squared deviations among sample values, they are currently being applied in a wide variety of disciplines. This book presents permutation alternatives to existing classical statistics, and is intended as a textbook for undergraduate statistics courses or graduate courses in the natural, social, and physical sciences, while assuming only an elementary grasp of statistics.

This book provides the latest information on bioplastics and biodegradable plastics. The initial chapters introduce readers to the various sources and substrates for the synthesis of bioplastics and biodegradable plastics, and explain their general structure, physio-chemical properties and classification. In turn, the book discusses innovative methods for the production of bioplastics at the industrial level and for the microbial production of bioplastics. It highlights the processes that are involved in the conversion of agro-industrial waste into bioplastics, while also summarizing the mechanisms of biodegradation in bioplastics. The book addresses a range of biotechnological applications of bioplastics such as in agriculture, food packaging and pharmaceutical industry, as well as biomedical applications.

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbruck Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry."

This treasure of popular science by the Russian biophysicist Mikhail V. Volkenstein is at last, more than twenty years after its appearance in Russian, available in English translation.

As its title Entropy and Information suggests, the book deals with the thermodynamical concept of entropy and its interpretation in terms of information theory. The author shows how entropy is not to be considered a mere shadow of the central physical concept of energy, but more appropriately as a leading player in all of the major natural processes: physical, chemical, biological, evolutionary, and even cultural.

The theory of entropy is thoroughly developed from its beginnings in the foundational work of Sadi Carnot and Clausius in the context of heat engines, including expositions of much of the necessary physics and mathematics, and illustrations from everyday life of the importance of entropy.

The author then turns to Boltzmann's epoch-making formula relating the entropy of a system directly to the degree of disorder of the system, and to statistical physics as created by Boltzmann and Maxwell---and here again the necessary elements of probability and statistics are expounded. It is shown, in particular, that the temperature of an object is essentially just a measure of the mean square speed of its molecules.

Fluctuations" in a system are introduced and used to explain why the sky is blue, and how, perhaps, the universe came to be so ordered. Whether statistical physics reduces ultimately to pure mechanics, as Laplace's demon" would have it, is also discussed.

The final three chapters concentrate on open systems, that is, systems which exchange energy or matter with their surroundings---first linear systems close to equilibrium, and then non-linear systems far from equilibrium. Here entropy, as it figures in the theory of such systems developed by Prigogine and others, affords explanations of the mechanism of division of cells, the process of aging in organisms, and periodic chemical reactions, among other phenomena.

Finally, information theory is developed---again from first principles---and the entropy of a system characterized as absence of information about the system. In the final chapter, perhaps the piece de resistance of the work, the author examines the thermodynamics of living organisms in the context of biological evolution. Here the value of biological information" is discussed, linked to the concepts of complexity and irreplaceability. The chapter culminates in a fascinating discussion of the significance of these concepts, all centered on entropy, for human culture, with many references to particular writers and artists.

The book is recommended reading for all interested in physics, information theory, chemistry, biology, as well as literature and art."

The book is organized so as to address in separate sections first the preparatory topics of medicine (clinical and epidemiological), science in general, and statistics (mathematical); then topics of epidemiological research proper; and, finally, topics of 'meta-epidemiological' clinical research. In those two main sections, a further grouping is based on the distraction between objects and methods of study. In this framework, the particular topics are addressed both descriptively and quasi-prescriptively, commonly with a number of explicatory annotations. This book is intended to serve as a handbook for whomever is, in whatever way, concerned with epidemiological or 'meta-epidemiological' clinical research. But besides this, it is also intended to serve as a textbook for students in introductory courses on 'epidemiological' research - to which end there is a suggested hierarchy of the concepts that might reasonably be covered.

Environmental variation plays an important role in many biological and ecological dynamical systems. This monograph focuses on the study of oscillation and the stability of delay models occurring in biology. The book presents recent research results on the qualitative behavior of mathematical models under different physical and environmental conditions, covering dynamics including the distribution and consumption of food. Researchers in the fields of mathematical modeling, mathematical biology, and population dynamics will be particularly interested in this material.

Histochemistry and cytochemistry are important fields for studying the inner workings of cells and tissues of the body. While visualization techniques have been in use for many years, new methods of detection developed recently help researchers and practitioners better understand cell activity. Histochemical and Cytochemical Methods of Visualization describes the essential techniques that can be used for histochemical investigations in both light and transmission electron microscopy. The book begins by discussing techniques in light microscopy. It reviews classical methods of visualization, histochemical and histoenzymatic methods, and methods used to visualize cell proliferation and apoptosis. Next, the book examines the cytochemical methods used in electron microscopy with traditional techniques, as well as more specialized methods. The final section provides an overview of image analysis and describes how image processing methods can be used to extract vital information. A 16-page insert supplies color illustrations to enhance the text. Techniques will continue to adapt to the latest technological innovations, allowing more and more precise quantification of images. These developments are essential to the biological as well as the medical sciences. This manual is a critical resource for novice and experienced researchers, technicians, and students who need to visualize what happens in the cell, the molecules expressed, the main enzymatic activities, and the repercussions of the molecular activities upon the structure of the cells in the body.

NOTE: Before purchasing, check with your instructor to ensure you select the correct ISBN. This ISBN is for the paperback PhysioEx Lab Manual and does NOT include access to the PhysioEx 10.0 website. The Lab Manual for PhysioEx (TM) 10.0 Laboratory Simulations in Physiology features 12 Exercises that contain 63 easy-to-use laboratory simulation activities to complement or replace wet labs, including those that are expensive or time-consuming to perform in class. PhysioEx allows students to repeat labs as often as they like, perform experiments without harming live animals, and conduct experiments that are difficult to perform in a wet lab environment because of time, cost, or safety concerns. 3 ways students can access the PhysioEx 10.0 website: By purchasing a Mastering A&P title that includes PhysioEx 10.0 -- the most common way students access the PhysioEx 10.0 website. By purchasing instant online access to PhysioEx 10.0 Premium Website (ISBN: 9780136447672 / 0136447678) at www.physioex.com. By purchasing the PhysioEx 10 Lab Manual package (ISBN: 9780136643746 / 0136643744) that includes an access code to the PhysioEx 10.0 website.

"Metallomics and the Cell" provides in an authoritative and timely manner in 16 stimulating chapters, written by 37 internationally recognized experts from 9 nations, and supported by more than 3000 references, several tables, and 110 illustrations, mostly in color, a most up-to-date view of the "metallomes" which, as defined in the "omics" world, describe the entire set of biomolecules that interact with or are affected by each metal ion. The most relevant tools for visualizing metal ions in the cell and the most suitable bioinformatic tools for browsing genomes to identify metal-binding proteins are also presented. Thus, MILS-12 is of relevance for structural and systems biology, inorganic biological chemistry, genetics, medicine, diagnostics, as well as teaching, etc.

This volume presents the latest developments in the highly active and rapidly growing field of diffusion MRI. The reader will find numerous contributions covering a broad range of topics, from the mathematical foundations of the diffusion process and signal generation, to new computational methods and estimation techniques for the in-vivo recovery of microstructural and connectivity features, as well as frontline applications in neuroscience research and clinical practice. These proceedings contain the papers presented at the 2017 MICCAI Workshop on Computational Diffusion MRI (CDMRI'17) held in Quebec, Canada on September 10, 2017, sharing new perspectives on the most recent research challenges for those currently working in the field, but also offering a valuable starting point for anyone interested in learning computational techniques in diffusion MRI. This book includes rigorous mathematical derivations, a large number of rich, full-colour visualisations and clinically relevant results. As such, it will be of interest to researchers and practitioners in the fields of computer science, MRI physics and applied mathematics.

Sustainable agriculture is a rapidly growing field aiming at producing food and energy in a sustainable way for humans and their children. Sustainable agriculture is a discipline that addresses current issues such as climate change, increasing food and fuel prices, poor-nation starvation, rich-nation obesity, water pollution, soil erosion, fertility loss, pest control, and biodiversity depletion. Novel solutions are proposed based on integrated knowledge from sciences as diverse as agronomy, soil science, molecular biology, chemistry, toxicology, ecology, economy, philosophy and social sciences. Because actual society issues are now intertwined, global, and fast-developing, sustainable agriculture will bring solutions to build a safer world. This book series gathers review articles that analyze current agricultural issues and knowledge, then propose alternative solutions. It will therefore help all scientists, decision-makers, professors, farmers and politicians who wish to build a safe agriculture, energy and food system for future generations.

Epidemiologic Methods: The Essentials is a concise, but thorough volume that provides a solid grounding in core methodologic issues. The book takes a streamlined approached on cohort studies, case-control studies, prevalence studies, randomized trials, demographic studies of morbidity and mortality, ecologic studies, screening, effect modification, bias and confounding. Organized according to study design, with each chapter building on those preceding it, the book provides detailed examples throughout, using data tables and graphs to reinforce methodologic points.

This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.

Howard Pattee is a physicist who for many years has taken his own path in studying the physics of symbols, which is now a foundation for biosemiotics. By extending von Neumann's logical requirements for self-replication, to the physical requirements of symbolic instruction at the molecular level, he concludes that a form of quantum measurement is necessary for life. He explains why all non-dynamic symbolic and informational controls act as special (allosteric) constraints on dynamical systems. Pattee also points out that symbols do not exist in isolation but in coordinated symbol systems we call languages. Such insights turn out to be necessary to situate biosemiotics as an objective scientific endeavor. By proposing a way to relate quiescent symbolic constraints to dynamics, Pattee's work builds a bridge between physical, biological, and psychological models that are based on dynamical systems theory. Pattee's work awakes new interest in cognitive scientists, where his recognition of the necessary separation-the epistemic cut-between the subject and object provides a basis for a complementary third way of relating the purely symbolic, computational models of cognition and the purely dynamic, non-representational models. This selection of Pattee's papers also addresses several other fields, including hierarchy theory, artificial life, self-organization, complexity theory, and the complementary epistemologies of the physical and biological sciences.

Long before the advent of the global economy, foreign goods were transported, traded, and exchanged through myriad means, over short and long distances. Archaeological tools for identifying foreign objects, such as provenance studies, stylistic analyses, and economic documentary sources reveal non-local materials in historic and prehistoric assemblages.

Trade and exchange represent more than mere production and consumption. Exchange of goods also led to an exchange of cultural and social experiences. Discoveries of the sources of alien objects surpass archaeological expectations of exchange and geographic distance, revealing important technological advances.

With thirteen case studies from around the world, this comprehensive work provides a fresh perspective on material culture studies. Evidence of ongoing negotiation between individuals, villages, and nations provides insight into the impact of trade on the micro-, meso-, and macro-level. Covering a wide array of time periods and areas, this work will be of interest to archaeologists, anthropologists, and anyone working in cultural studies.

Agriculture is the main occupation in India and about 75% of its population depends directly or indirectly on agriculture for their livelihood. It is the dominant sector that contributes 18% of the gross domestic product. Thus, agriculture is the foundation of the Indian economy. The maximum share of Indian exports is also from the agriculture sector. As the population of the country is increasing trem- dously, approximately at the rate of 19 million every year over the existing popu- tion of more than 1 billion (approximately 1. 18 billion), the food grain production must necessarily be increased. This can be done by increasing crop production to match the population growth rate of 2. 2% per annum, which is expected to stabilize at 1. 53 billion around 2050. There is no doubt that the Green Revolution in India during the late 1960s brought self-sufficiency in food grain production, mainly through the increase in rice and wheat crop yields - the two main crops of the country which play an important role from food security point of view. However, the excessive use of fertilizers and pesticides, and the neglect of organic manures for these crops, has resulted in the deterioration of physical, chemical and biological health of the ri- and wheat-growing soils. Owing to the deterioration of the health of these soils, the productivity of the rice-wheat cropping system has now either got reduced or in some places has become constant for the last decade.

Agriculture is the lifeblood of the majority of people in Africa. It is not just a provider of food, it is a way of life for rural people. Whilst subsistence farming is the most practiced form of agriculture, there are many parts of Africa where agriculture is highly developed and progressive. In many instances it is the very diversity of agricultural practices that raises complex problems and issues. These issues often manifest themselves in ways that create ethical dilemmas for farmers, policy-makers, academics, politicians and the general lay-person. In particular, the role of biotechnology in African agriculture has become a contentious issue. Some people hold the view that biotechnology will solve the food shortages experienced in many parts of Africa, however, there is an opposing viewpoint that Africa may become a dumping ground for technology that has not been acceptable in other parts of the world. The ethical issues in agriculture in Africa do not focus only on biotechnology. The role of nutrition in the persistence of HIV/AIDS is highly debated and sometimes controversial. Land-related issues also generate heated debates in communities and amongst policy-makers. The single core that runs through all of these and many other related issues is, what are ethically acceptable solutions to these problems? This book attempts, in simple, unambiguous terms, to discuss the most important issues in African agriculture that have an ethical thread.

This review emerged from several interdisciplinary meetings and schools gathering a group of astronomers, geologists, biologists, and chemists, attempting to share their specialized knowledge around a common question: how did life emerge on Earth? Their ultimate goal was to provide some kind of answer as a prerequisite to an even more demanding question: is life universal? The resulting state-of-the-art articles were written by twenty-five scientists telling a not-so linear story, but on the contrary, highlighting problems, gaps, and controversies. Needless to say, this approach yielded no definitive answers to both questions. However, by adopting a chronological approach to the question of the emergence of life on Earth, the only place where we know for sure that life exists; it was possible to break down this question into several sub-topics that can be addressed by the different disciplines.

The main chapters of this review present the formation and evolution of the solar system (3); the building of a habitable planet (4); prebiotic chemistry, biochemistry, and the emergence of life (5); the environmental context of the early Earth (6); and the ancient fossil record and early evolution (7). The concluding chapter (9) provides the highlights of the review and presents the different points of view about the universality of life. Two pedagogical chapters are included; one on chronometers (2), another in the form of a "frieze" (8) which summarizes in graphical form the present state of knowledge about the chronology of the emergence of life on Earth, before the Cambrian explosion.

Reviews of Environmental Contamination and Toxicology attempts to provide concise, critical reviews of timely advances, philosophy and significant areas of accomplished or needed endeavor in the total field of xenobiotics, in any segment of the environment, as well as toxicological implications.

The central theme of this book "Microbial BioEnergy: Hydrogen Production" is focused on the biological machinery that microorganisms use to produce hydrogen gas.The book summarizes the achievements over the past decade in the biochemistry, structural and molecular biology, genomics and applied aspects of microbial H2-production, including microbial fuel cells (MFC), by phototrophs such as purple sulfur and non-sulfur bacteria ("Thiocapsa" spp., "Rhodobacter "and "Rhodopseudomonas" spp.) microalgae ("Chlamydomonas")and cyanobacteria ("Anabaena spp.") along with anaerobes and thermophiles such as "Caldicellulosiruptor "and "Thermotoga." This is the first bookof this series entirely devoted to microbial bio-hydrogen production and is intended to be a precious source of information for PhD students, researchers and undergraduates from disciplines such as microbiology, biochemistry, biotechnology, photochemistry and chemical engineering, interested in basic and applied sciences."