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Bioinformatics and Computational Biology Solutions Using R and Bioconductor
Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R. This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including: Importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms / Curation and delivery of biological metadata for use in statistical modeling and interpretation. / Statistical analysis of high-throughput data, including machine learning and visualization,modeling and visualization of graphs and networks. This book is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.
Bioinformatics : Problem Solving Paradigms
This book highlights basic paradigms of problem analysis and algorithm design in the context of core bioinformatics problems. Mathematically demanding themes are put across to the reader by properly chosen representations with the aid of lots of illustrations.
Bioinformatics
In this textbook present mathematical models in bioinformatics and they describe the biological problems that inspire the computer science tools used to handle the enormous data sets involved. The first part of the book covers the mathematical and computational methods, while the practical applications are presented in the second part. The mathematical presentation is descriptive and avoids unnecessary formalism, and yet remains clear and precise. Emphasis is laid on motivation through biological problems and cross applications. Each of the four chapters in the first part is accompanied by exercises and problems to support an understanding of the techniques presented. Each of the six chapters of the second part is devoted to some specific application domain: sequence alignment, molecular phylogenetics and coalescence theory, genomics, proteomics, RNA, and DNA microarrays. Each chapter concludes with a problems and projects section, to deepen the reader's understanding and to allow for the design of derived methods. Many of the projects involve publicly available software and/or Web-based bioinformatics depositories. Finally, the book closes with a thorough bibliography, reaching from classic research results to very recent findings, providing many pointers for future research.Overall, this volume is ideally suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on its mathematical and computer science background.
Bioimage Data Analysis Workflows
This book provides students and researchers in the life sciences with essential practical information on how to quantitatively analyze data images. It refrains from focusing on theory, and instead uses practical examples and step-by step protocols to familiarize readers with the most commonly used image processing and analysis platforms such as ImageJ, MatLab and Python.
Biogeography, Time, and Place : Distributions, Barriers, and Islands
Biogeography considers the distribution of biological units over a wide range of scales. The units range from genotypes, populations and species to families and higher taxa. Processes can be local, such as the isolation on islands due to sea-level fluctuations, or large-scale tectonic processes that separates continents and creates oceans. In all processes time is an important factor and by combining data on recent patterns with paleontological data the understanding of the distribution of extant taxa can be improved. This volume focuses on speciation due to isolation in island-like settings, and the evolution of large-scale diversity as the result of origination, maintenance and extinction.
Biogeochemistry of Trace Elements in Arid Environments
Global warming has worsened the water resource crisis in many arid zones worldwide, from Africa to Asia, affecting millions of people and putting them at risk of hunger. Effective management of arid zone resources, including understanding the risks of toxic trace and heavy elements to humans, coupled with the need to produce more food to feed the world’s growing population, has thus become increasingly important. This very timely book, the only one of its kind on the market, fills the gap of our knowledge of trace elements in these regions. This book begins by introducing the nature and properties of arid zone soil, followed by an updated overview and comprehensive coverage of the major aspects of the trace elements and heavy metals of most concern in the world’s arid and semi-arid soils. These aspects include: - content and distribution - solution chemistry - solid-phase chemistry - selective sequential dissolution techniques - transfer fluxes - bioavailability - pollution and remediation In order to illustrate the themes, a comprehensive and focused case study on transfer fluxes of trace elements in Israeli arid soils is presented. Finally it closes with the global perspectives on anthropogenic interferences in the natural trace elements’ distribution.
Biogeochemical cycles in globalization and sustainable development
This valuable study of environmental subsystems functioning under various climatic and anthropogenic conditions provides a unique insight into the social context of global changes in biogeochemical cycles and demonstrates current understanding of globalization and sustainable development.
Biofuels, Solar and Wind as Renewable Energy Systems : Benefits and Risks
With shortages of fossil energy, especially oil and natural gas, and heavy biomass energy use occurring in both developed and developing countries, a major focus has developed worldwide on renewable energy systems. Renewable energy systems include wind power, biomass, photovoltaics, hydropower, solar thermal, thermal ponds, and biogas. Currently, a heavy focus is on biofuels made from crops, such as corn, sugarcane, and soybeans, for use as renewable energy sources. Wood and crop residues also are being used as fuel. Though it may seem beneficial to use renewable plant materials for biofuel, the use of crop residues and other biomass for biofuels raises many concerns about major environmental problems, including food shortages and serious destruction of vital soil resources.
Biofuels and sustainability : Holistic perspectives for policy-making
This open access book presents a comprehensive analysis of biofuel use strategies from an interdisciplinary perspective using sustainability science. This interdisciplinary perspective (social science-natural science) means that the strategies and policy options proposed will have significant impacts on the economy and society alike. Biofuels are expected to contribute to reducing greenhouse gas emissions, revitalizing economies in agricultural communities and alleviating poverty. However, despite these anticipated benefits, international organizations such as the FAO, OECD and UN have published reports expressing concerns that biofuel promotion may lead to deforestation, water pollution and water shortages. The impacts of biofuel use are extensive, cross-sectoral and complex, and as such, comprehensive analyses are required in order to assess the extent to which biofuels can contribute to sustainable societies.
Biofuels
In line with the current focus on a sustainable economy, bioethanol and other biofuels have received tremendous attention, making many headlines. Being produced in steadily growing volumes has made it necessary to consider production of biofuels from renewable raw materials that are not currently used. Therefore, the production of biofuels is at the gateway of moving from traditional raw materials to others such as lignocellulosic materials. However, sucha transfer requires new production processes that are economically feasible.This volume addresses and discusses the current status of biofuels, covering aspects from enabling technologies to different technology and processes options, as well as economical and policy perspectives.
Bioethics in Law
The idea for Bioethics in Law began more than a decade ago, while I was studying social science and law. I was parti- larly interested in the collaborations that comprised social s- ence in law. Economic and social data in the pioneering Brandeis brief had been used to defend an early 20th-century labor law; surveys of consumer confusion had helped resolve trademark - fringement cases; psychologists’ predictions of future violence had informed capital sentencing decisions. Additionally, Kenneth Clark’s “doll studies,” cited by the Supreme Court in Brown v. Board of Education, had helped change the course of American 1 history.
Bioethics and the Holocaust : A Comprehensive Study in How the Holocaust Continues to Shape the Ethics of Health, Medicine and Human Rights
This book offers a framework for understanding how the Holocaust has shaped and continues to shape medical ethics, health policy, and questions related to human rights around the world. The field of bioethics continues to face questions of social and medical controversy that have their roots in the lessons of the Holocaust, such as debates over beginning-of-life and medical genetics, end-of-life matters such as medical aid in dying, the development of ethical codes and regulations to guide human subject research, and human rights abuses in vulnerable populations. As the only example of medically sanctioned genocide in history, and one that used medicine and science to fundamentally undermine human dignity and the moral foundation of society, the Holocaust provides an invaluable framework for exploring current issues in bioethics and society today. This book, therefore, is of great value to all current and future ethicists, medical practitioners and policymakers – as well as laypeople.
Bioethics across the globe : Rebirthing bioethics
This book addresses a variety of issues relating to bioethics, in order to initiate cross-cultural dialogue. Beginning with the history, it introduces various views on bioethics, based on specific experiences from Japan. It describes how Japan has been confronted with Western bioethics and the ethical issues new to this modern age, and how it has found its foothold as it decides where it stands on these issues. In the last chapter, the author proposes discarding the overarching term ‘Global Bioethics’ in favor of the new term, ‘Bioethics Across the Globe (BAG)’, which carries a more universal connotation.
Bioengineering in cell and tissue research
This book reviews the latest technological developments of bioengineering approaches in cell and tissue research. It is meant to have life and spirit, and to become a pioneer in technology and sciences, especially the life science. The chapters are written by excellent scientists on advanced, frontier technology and address scientific questions that need considerable thinking in terms of engineering.
Bioelectricity : A Quantitative Approach
"The authors’ goal in producing this book was to provide an introductory text to electrophysiology, based on a quantitative approach. In attempting to achieve this goal, therefore, the authors have opened the book with a useful, and digestible, introduction to various aspects of the mathematics relevant to this field, including vectors, introduction to Laplace, Gauss’s theorem, and Green’s theorem. This book will be useful for students in medical physics and biomedical engineering wishing to enter the field of electrophysiological investigation. It will also be helpful for biologists and physiologists who wish to understand the mathematical treatment of the processes and signals at the center of the interesting interdisciplinary field.
Bioeconomy : Shaping the transition to a sustainable, biobased economy
This book defines the new field of "Bioeconomy" as the sustainable and innovative use of biomass and biological knowledge to provide food, feed, industrial products, bioenergy and ecological services. The chapters highlight the importance of bioeconomy-related concepts in public, scientific, and political discourse. Using an interdisciplinary approach, the authors outline the dimensions of the bioeconomy as a means of achieving sustainability.
Biodiversity-health-sustainability Nexus in socio-ecological production landscapes and seascapes (SEPLS)
It is a compilation of case studies that provide useful knowledge and lessons that derive from on-the-ground activities and contribute to policy recommendations, focusing on the interlinkages between biodiversity and multiple dimensions of health (e.g., physical, mental, and spiritual) in managing socio-ecological production landscapes and seascapes (SEPLS). This book provides insights on how SEPLS approaches can contribute to more sustainable management of natural resources, achieving global biodiversity and sustainable development goals, and good health for all. It is also expected to offer useful knowledge and information for an upcoming three-year thematic assessment of “the interlinkages among biodiversity, water, food, and health” (the so-called “nexus assessment”) by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). The book begins with an introductory chapter followed by eleven case study chapters demonstrating the nexus between biodiversity, health, and sustainable development, and then a synthesis chapter clarifying the relevance of the case study findings to policy and academic discussions. It will be of interest to scholars, policymakers, and professionals in the field related to sustainable development.
Biodiversity of angola : Science & conservation : A modern synthesis
The book identifies Angola as one of the most biologically diverse countries in Africa, but notes that its fauna, flora, habitats and the processes that drive the dynamics of its ecosystems.
Biodiversity in Enclosed Seas and Artificial Marine Habitats ; Proceedings of the 39th European Marine Biology Symposium, held in Genoa, Italy, 21-24 July 2004
The main themes of the Symposium were biodiversity in enclosed and semi-enclosed seas and artificial habitats, and the restoration of degraded systems. These themes are highly relevant today both from a basic scientific point of view and from an applied approach. The papers dealing with the first theme represent current research and concerns about marine biodiversity in enclosed seas and will have wide appeal to all those interested in understanding and preserving the biodiversity of the seas and in particular of the Mediterranean and Black Seas. The papers in the second theme represent a synthesis of up-to-date knowledge on artificial habitats and how they can contribute to protection of coastal marine ecosystems, to enhancement of species diversity and biological resources and to restoration of degraded marine environments.
Biodiversity Conservation and Phylogenetic Systematics : Preserving our evolutionary heritage in an extinction crisis
This book brings an updated state of the art of phylogenetic diversity in conservation biology. Nineteen chapters written by scientists from research institutions of fourteen countries demonstrate that approaches for preserving the evolutionary heritage are now very tuned into human impacts and sustainability issues. The questions, methods and applications around which it is organized show the importance of phylogenetic diversity in avoiding biodiversity losses in the present extinction crisis. They touch important points such as the way we value phylogenetic diversity, the importance of thinking at a much wider sample of the Tree of Life, the choice of adequate measures. In methods section, new solutions, such as dealing with abundances, sampling effort, or with information coming from conflicting phylogenetic trees are provided. Application section includes study cases of different groups of organi
