Progress in plant biology relies on the quantification, analysis and mathematical modeling of data over different time and length scales. This book describes common mathematical and computational approaches as well as some carefully chosen case studies that demonstrate the use of these techniques to solve problems at the forefront of plant biology. Each chapter is written by an expert in field with the goal of conveying concepts whilst at the same time providing sufficient background and links to available software for readers to rapidly build their own models and run their own simulations. This book is aimed at postgraduate students and researchers working the field of plant systems biology and synthetic biology, but will also be a useful reference for anyone wanting to get into quantitative plant biology.

This book presents an exciting collection of contributions based on the workshop "Bringing Maths to Life" held October 27-29, 2014 in Naples, Italy. The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content useful as it addresses existing challenges in identifying the gaps between mathematical modeling and biological research. The shared solutions will aid and promote further collaboration between life sciences and mathematics.

This book provides a comprehensive overview of different biomedical data types, including both clinical and genomic data. Thorough explanations enable readers to explore key topics ranging from electrocardiograms to Big Data health mining and EEG analysis techniques. Each chapter offers a summary of the field and a sample analysis. Also covered are telehealth infrastructure, healthcare information association rules, methods for mass spectrometry imaging, environmental biodiversity, and the global nonlinear fitness function for protein structures. Diseases are addressed in chapters on functional annotation of lncRNAs in human disease, metabolomics characterization of human diseases, disease risk factors using SNP data and Bayesian methods, and imaging informatics for diagnostic imaging marker selection. With the exploding accumulation of Electronic Health Records (EHRs), there is an urgent need for computer-aided analysis of heterogeneous biomedical datasets. Biomedical data is notorious for its diversified scales, dimensions, and volumes, and requires interdisciplinary technologies for visual illustration and digital characterization. Various computer programs and servers have been developed for these purposes by both theoreticians and engineers. This book is an essential reference for investigating the tools available for analyzing heterogeneous biomedical data. It is designed for professionals, researchers, and practitioners in biomedical engineering, diagnostics, medical electronics, and related industries.

This book presents cutting-edge research on the use of physical and mathematical formalisms to model and quantitatively analyze biological phenomena ranging from microscopic to macroscopic systems. The systems discussed in this compilation cover protein folding pathways, gene regulation in prostate cancer, quorum sensing in bacteria to mathematical and physical descriptions to analyze anomalous diffusion in patchy environments and the physical mechanisms that drive active motion in large sets of particles, both fundamental descriptions that can be applied to different phenomena in biology. All chapters are written by well-known experts on their respective research fields with a vast amount of scientific discussion and references in order the interested reader can pursue a further reading. Given these features, we consider Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues as an excellent and up-to-date resource and reference for advanced undergraduate students, graduate students and junior researchers interested in the latest developments at the intersection of physics, mathematics, molecular biology, and computational sciences. Such research field, without hesitation, is one of the most interesting, challenging and active of this century and the next.

Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process. This book wants to address four main issues related to the building and validation of computational models of biomedical processes: 1. Modeling establishment under uncertainty 2. Model selection and parameter fitting 3. Sensitivity analysis and model adaptation 4. Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples. This book is intended for graduate students and researchers active in the field of computational modeling of biomedical processes who seek to acquaint themselves with the different ways in which to study the parameter space of their model as well as its overall behavior.

Many breakthroughs in experimental devices, advanced software, as well as analytical methods for systems biology development have helped shape the way we study DNA, RNA and proteins, on the genomic, transcriptional, translational and posttranslational level. This book highlights the comprehensive topics that encompass systems biology with enormous progress in the development of genome sequencing, proteomic and metabolomic methods in designing and understanding biological systems. Topics covered in this book include fundamentals of modelling networks, circuits and pathways, spatial and multi cellular systems, image-driven systems biology, evolution, noise and decision-making in single cells, systems biology of disease and immunology, and personalized medicine. Special attention is paid to epigenomics, in particular environmental conditions that impact genetic background. The breadth of exciting new data towards discovering fundamental principles and direct application of epigenetics in agriculture is also described. The chapter "Deciphering the Universe of RNA Structures and Trans RNA-RNA Interactions of Transcriptomes in vivo - from Experimental Protocols to Computational Analyses" is available open access under a CC BY 4.0 license via link.springer.com.

This book presents the key technology of electronic noses, and systematically describes how e-noses can be used to automatically analyse odours. Appealing to readers from the fields of artificial intelligence, computer science, electrical engineering, electronics, and instrumentation science, it addresses three main areas: First, readers will learn how to apply machine learning, pattern recognition and signal processing algorithms to real perception tasks. Second, they will be shown how to make their algorithms match their systems once the algorithms don't work because of the limitation of hardware resources. Third, readers will learn how to make schemes and solutions when the acquired data from their systems is not stable due to the fundamental issues affecting perceptron devices (e.g. sensors). In brief, the book presents and discusses the key technologies and new algorithmic challenges in electronic noses and artificial olfaction. The goal is to promote the industrial application of electronic nose technology in environmental detection, medical diagnosis, food quality control, explosive detection, etc. and to highlight the scientific advances in artificial olfaction and artificial intelligence. The book offers a good reference guide for newcomers to the topic of electronic noses, because it refers to the basic principles and algorithms. At the same time, it clearly presents the key challenges - such as long-term drift, signal uniqueness, and disturbance - and effective and efficient solutions, making it equally valuable for researchers engaged in the science and engineering of sensors, instruments, chemometrics, etc.

In this work we plan to revise the main techniques for enumeration algorithms and to show four examples of enumeration algorithms that can be applied to efficiently deal with some biological problems modelled by using biological networks: enumerating central and peripheral nodes of a network, enumerating stories, enumerating paths or cycles, and enumerating bubbles. Notice that the corresponding computational problems we define are of more general interest and our results hold in the case of arbitrary graphs. Enumerating all the most and less central vertices in a network according to their eccentricity is an example of an enumeration problem whose solutions are polynomial and can be listed in polynomial time, very often in linear or almost linear time in practice. Enumerating stories, i.e. all maximal directed acyclic subgraphs of a graph G whose sources and targets belong to a predefined subset of the vertices, is on the other hand an example of an enumeration problem with an exponential number of solutions, that can be solved by using a non trivial brute-force approach. Given a metabolic network, each individual story should explain how some interesting metabolites are derived from some others through a chain of reactions, by keeping all alternative pathways between sources and targets. Enumerating cycles or paths in an undirected graph, such as a protein-protein interaction undirected network, is an example of an enumeration problem in which all the solutions can be listed through an optimal algorithm, i.e. the time required to list all the solutions is dominated by the time to read the graph plus the time required to print all of them. By extending this result to directed graphs, it would be possible to deal more efficiently with feedback loops and signed paths analysis in signed or interaction directed graphs, such as gene regulatory networks. Finally, enumerating mouths or bubbles with a source s in a directed graph, that is enumerating all the two vertex-disjoint directed paths between the source s and all the possible targets, is an example of an enumeration problem in which all the solutions can be listed through a linear delay algorithm, meaning that the delay between any two consecutive solutions is linear, by turning the problem into a constrained cycle enumeration problem. Such patterns, in a de Bruijn graph representation of the reads obtained by sequencing, are related to polymorphisms in DNA- or RNA-seq data.

This book is the product of the 2nd World Conference on Environmental History, held in Guimaraes, Portugal, in 2014. It gathers works by authors from the five continents, addressing concerns raised by past events so as to provide information to help manage the present and the future. It reveals how our cultural background and examples of past territorial intervention can help to combat political and cultural limitations through the common language of environmental benefits without disguising harmful past human interventions. Considering that political ideologies such as socialism and capitalism, as well as religion, fail to offer global paradigms for common ground, an environmentally positive discourse instead of an ecological determinism might serve as an umbrella common language to overcome blocking factors, real or invented, and avoid repeating ecological loss. Therefore, agency, environmental speech and historical research are urgently needed in order to sustain environmental paradigms and overcome political, cultural an economic interests in the public arena. This book intertwines reflections on our bonds with landscapes, processes of natural and scientific transfer across the globe, the changing of ecosystems, the way in which scientific knowledge has historically both accelerated destruction and allowed a better distribution of vital resources or as it, in today's world, can offer alternatives that avoid harming those same vital natural resources: water, soil and air. In addition, it shows the relevance of cultural factors both in the taming of nature in favor of human comfort and in the role of the environment matters in the forging of cultural identities, which cannot be detached from technical intervention in the world. In short, the book firstly studies the past, approaching it as a data set of how the environment has shaped culture, secondly seeks to understand the present, and thirdly assesses future perspectives: what to keep, what to change, and what to dream anew, considering that conventional solutions have not sufficed to protect life on our planet.

Phelan's dynamic approach to teaching biology is the driving force behind What Is Life?-the most successful new non-majors biology textbook of the millennium. The rigorously updated new edition brings forward the features that made the book a classroom favourite (chapters anchored to intriguing questions about life, spectacular original illustrations, and innovative learning tools) with a more focused and flexible presentation and enhanced art. Available for the first time with Macmillan's new online learning tool, Achieve, What Is Life? teaches students to ask the questions they need to understand how biology plays out in their daily lives. The rigorously updated 5th edition brings forward the features that made the book a classroom favorite (chapters anchored to intriguing questions about life, spectacular original illustrations, innovative learning tools) with a more focused and flexible presentation, enhanced art, and full integration with Achieve, Macmillan's new online learning system. Achieve supports educators and students throughout the full range of instruction, including assets suitable for pre-class preparation, in-class active learning, and post-class study and assessment. The pairing of a powerful new platform with outstanding biology content provides an unrivaled learning experience.

The blood system is multi-scale, from the organism to the organs to cells to intracellular signaling pathways to macromolecule interactions. Blood consists of circulating cells, cellular fragments (platelets and microparticles), and plasma macromolecules. Blood cells and their fragments result from a highly-ordered process, hematopoiesis. Definitive hematopoiesis occurs in the bone marrow, where pluripotential stem cells give rise to multiple lineages of highly specialized cells. Highly-productive and continuously regenerative, hematopoiesis requires a microenvironment of mesenchymal cells and blood vessels. A Systems Biology Approach to Blood is divided into three main sections: basic components, physiological processes, and clinical applications. Using blood as a window, one can study health and disease through this unique tool box with reactive biological fluids that mirrors the prevailing hemodynamics of the vessel walls and the various blood cell types. Many blood diseases, rare and common can and have been exploited using systems biology approaches with successful results and therefore ideal models for systems medicine. More importantly, hematopoiesis offers one of the best studied systems with insight into stem cell biology, cellular interaction, development; linage programing and reprograming that are every day influenced by the most mature and understood regulatory networks.

This book is a treatise on cardiomyocytes, the most important cell for the contractile function of the heart. There has been significant progress in our understanding of the function-related structure, developmental processes and their determinants, mechanisms of cell cycle regulation, post-natal growth, energy metabolism, and reversible and irreversible response of cardiomyocytes to diverse forms of physiological stress and injury. There is also more clarity on the alterations in the biological mechanisms in cardiomyocytes that lead to pathological states and the changes in the cells that occur secondary to disease conditions. Thanks to these advances in knowledge, there have been great gains in attempts to identify disease biomarkers and therapeutic targets for better management of patients with heart diseases. Possibilities to induce regeneration or proliferation of cardiomyocytes and thus repair and or regenerate the damaged heart are also on the horizon.

This book examines discrete dynamical systems with memory-nonlinear systems that exist extensively in biological organisms and financial and economic organizations, and time-delay systems that can be discretized into the memorized, discrete dynamical systems. It book further discusses stability and bifurcations of time-delay dynamical systems that can be investigated through memorized dynamical systems as well as bifurcations of memorized nonlinear dynamical systems, discretization methods of time-delay systems, and periodic motions to chaos in nonlinear time-delay systems. The book helps readers find analytical solutions of MDS, change traditional perturbation analysis in time-delay systems, detect motion complexity and singularity in MDS; and determine stability, bifurcation, and chaos in any time-delay system.

Soybean Physiology and Genetics, Volume 102 presents comprehensive reviews on the latest development in soybean research, covering soybean genomics, physiology and genetics under biotic and abiotic stress, growth and development, nitrogen fixation and nutritional values, etc. Chapters in this new release cover Root Physiology and Morphology in Relationship to Stress Tolerance, Soybean Insects, Application of Genomic Studies in Soybean Breeding, Secondary metabolism in soybean, The roles of CLE peptides in nitrogen fixation in soybean, Seed morphology in soybean, Physiology and genetic regulations of oil and protein contents in soybean, Regulation of flowering and maturation in soybean, and much more. As soybeans are a key component in climate-smart agriculture because of their high nutritional value, large cultivation area, and nitrogen-fixing ability, this book fills a gap in information on this growing commodity.

This open access book relates to the III Annual Conference hosted by The Ministry of Education and Science of the Russian Federation in December 2016. This event has summarized, analyzed and discussed the interim results, academic outputs and scientific achievements of the Russian Federal Targeted Programme "Research and Development in Priority Areas of Development of the Russian Scientific and Technological Complex for 2014-2020." It contains 75 selected papers from 6 areas considered priority by the Federal Targeted Programme: computer science, ecology & environment sciences; energy and energy efficiency; lifesciences; nanoscience & nanotechnology and transport & communications. The chapters report the results of the 3-years research projects supported by the Programme and finalized in 2016.

In its first English-language edition, this book introduces the many-faceted interactions of animal populations with their habitats. From soil fauna, ants and termites to small and large herbivores, burrowing mammals and birds, the author presents a comprehensive analysis of animals and ecosystems that is as broad and varied as all nature. Chapter 2 addresses the functional role of animals in landscape ecosystems, emphasizing fluxes of energy and matter within and between ecosystems, and the effects of animals on qualitative and structural habitat change. Discussion includes chapters on the role of animal population density and the impacts of native herbivores on vegetation and habitats from the tropics to the polar regions. Cyclic mass outbreaks of species such as the larch bud moth in Switzerland, the mountain pine beetle and the African red-billed weaver bird are described and analyzed. Other chapters discuss Zoochory - the dispersal of seeds by ants, mammals and birds - and the influence of burrowing animals on soil development and geomorphology. Consideration extends to the impact of feral domestic animals. Chapter 5 focuses on problems resulting from introduction of alien animals and from re-introduction of animal species to their original habitats, discusses the effects on ecosystems of burrowing, digging and trampling by animals. The author also addresses keystone species such as kangaroo rats, termites and beavers. Chapter 6 addresses the role of animals in landscape management and nature conservation, with chapters on the impact of newcomer species such as animals introduced into Australia, New Zealand and Europe, and the consequences of reintroduction of species to original habitat. It also discusses the carrying capacity of natural habit, public attitudes toward conversation and more. The final section ponders the effects of climate on interactions between animals and their habitats.

MILS-13 provides an up-to-date review on the relationships between essential metals and human diseases, covering 13 metals and 3 metalloids: The bulk metals sodium, potassium, magnesium, and calcium, plus the trace elements manganese, iron, cobalt, copper, zinc, molybdenum, and selenium, all of which are essential for life. Also covered are chromium, vanadium, nickel, silicon, and arsenic, which have been proposed as being essential for humans in the 2nd half of the last century. However, if at all, they are needed only in ultra-trace amounts, and because of their prevalence in the environment, it has been difficult to prove whether or not they are required. In any case, all these elements are toxic in higher concentrations and therefore, transport and cellular concentrations of at least the essential ones, are tightly controlled; hence, their homeostasis and role for life, including deficiency or overload, and their links to illnesses, including cancer and neurological disorders, are thoroughly discussed. Indeed, it is an old wisdom that metals are indispensable for life. Therefore, Volume 13 provides in an authoritative and timely manner in 16 stimulating chapters, written by 29 internationally recognized experts from 7 nations, and supported by more than 2750 references, and over 20 tables and 80 illustrations, many in color, a most up-to-date view on the vibrant research area of the Interrelations between Essential Metal Ions and Human Diseases.

This highly informative and carefully presented book comprises select proceedings of Foundation for Molecular Modelling and Simulation (FOMMS 2018). The contents are written by invited speakers centered on the theme Innovation for Complex Systems. It showcases new developments and applications of computational quantum chemistry, statistical mechanics, molecular simulation and theory, and continuum and engineering process simulation. This volume will serve as a useful reference to researchers, academicians and practitioners alike.

Collates the most relevant and up to date information on renewable energy systems in a user friendly format for undergraduate and high school students Focused on power production technologies from renewable energy sources. An introduction to how sources of renewable energy work; their advantages and drawbacks. Timely text with the need for fast adoption of renewable energy technologies around the world. Diverse audience including students with some scientific background such as final year in high school wanting to know more about combatting climate change.

This volume guides readers through the field of systems medicine by defining the terminology, and describing how established computational methods form bioinformatics and systems biology can be taken forward to an integrative systems medicine approach. Chapters provide an outlook on the role that systems medicine may or should play in various medical fields, and describe different facets of the systems medicine approach in action. Ultimately it introduces tools, resources and methodologies from bioinformatics and systems biology, and how to apply these in a systems medicine project. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, and discuss experimental and computational approaches, methods, and tools that should be considered for a successful systems medicine project. Systems Medicine aims to motivate and provide guidance for collaborations across disciplines to tackle today's challenges related to human health and well-being.

This volume addresses recent and ongoing ethnobotanical studies in the Balkans. The book focuses on elaborating the relevance of such studies for future initiatives in this region, both in terms of sustainable and peaceful (trans-regional, trans-cultural) rural development. A multi-disciplinary viewpoint is utilized, with an incorporation of historical, ethnographic, linguistic, biological, nutritional and medical perspectives. The book is also authored by recognized scholars, who in the last decade have extensively researched the Balkan traditional knowledge systems as they pertain to perceptions of the natural world and especially plants. Ethnobotany and Biocultural Diversities in the Balkans is the first ethnobotany book on one of the most biologically and culturally diverse regions of the world and is a valuable resource for both scholars and students interested in the field of ethnobotany.

The book is a comprehensive introduction to the work of the Estonian-German biologist Jakob von Uexkull. After a first introductory chapter by Morten Tonnessen and a second chapter on Uexkull's life and philosophical background, it contains four chapters devoted to the analysis of his main works. They are followed by a vast eighth chapter which deals with the influence Uexkull had on other philosophers and scientists. Finally, the author discloses his conclusions, focused on the possibility of updating Uexkull's work. As far as the key issue is concerned, the Uexkullian Umwelt is the perceptive and operative world which surrounds animal species; it is a subjective species-specific construction which provides living organisms with great security and behaviour stability. The relationship that the animal carries out with its environment is a complex system of semiotic interactions: its behaviour is not a set of mechanical reactions, but a spontaneous attribution of meaning to the outside world.

This book integrates current advances in biology, economics of information and linguistics research through applications using agent-based modeling and social network analysis to develop scenarios of communication and language emergence in the social aspects of biological communications. The book presents a model of communication emergence that can be applied both to human and non-human living organism networks. The model is based on economic concepts and individual behavior fundamental for the study of trust and reputation networks in social science, particularly in economics; it is also based on the theory of the emergence of norms and historical path dependence that has been influential in institutional economics. Also included are mathematical models and code for agent-based models to explore various scenarios of language evolution, as well as a computer application that explores language and communication in biological versus social organisms, and the emergence of various meanings and grammars in human networks. Emergence of Communication in Socio-Biological Networks offers both a completely novel approach to communication emergence and language evolution and provides a path for the reader to explore various scenarios of language and communication that are not constrained to the human networks alone. By illustrating how computational social science and the complex systems approach can incorporate multiple disciplines and offer an integrated theory-model approach to the evolution of language, the book will be of interest to researchers working with computational linguistics, mathematical linguistics, and complex systems.

This book explains omics at the most basic level, including how this new concept can be properly utilized in molecular and systems biology research. Most reviews and books on this topic have mainly focused on the technicalities and complexity of each omics' platform, impeding readers to wholly understand its fundamentals and applications. This book tackles such gap and will be most beneficial to novice in this area, university students and even researchers. Basic workflow and practical guidance in each omics are also described, such that scientists can properly design their experimentation effectively. Furthermore, how each omics platform has been conducted in our institute (INBIOSIS) is also detailed, a comprehensive example on this topic to further enhance readers' understanding. The contributors of each chapter have utilized the platforms in various manner within their own research and beyond. The contributors have also been interactively integrated and combined these different omics approaches in their research, being able to systematically write each chapter with the conscious knowledge of other inter-relating topics of omics. The potential readers and audience of this book can come from undergraduate and postgraduate students who wish to extend their comprehension in the topics of molecular biology and big data analysis using omics platforms. Furthermore, researchers and scientists whom may have expertise in basic molecular biology can extend their experimentation using the omics technologies and workflow outlined in this book, benefiting their research in the long run.