This manual offers a stand-alone reading companion, unique in simplifying the practical components of Bioinformatics in a unique and user-friendly manner. It covers the practical component of syllabi used at most leading universities and discusses the most extensively used tools and methodologies in Bioinformatics. Research in the biological sciences has made tremendous strides in recent years due in part to the increased automation in data generation. At the same time, storing, managing and interpreting huge volumes of data has become one of the most challenging tasks for scientists. These two aspects have ultimately necessitated the application of computers, giving rise to a highly interdisciplinary discipline-Bioinformatics. Despite the richness of bioinformatics resources and methods, the exposure of life sciences undergraduates and postgraduates to bioinformatics is extremely limited. Though the internet offers various tools for free, and provides guides for using them, it fails to help users interpret the processed data. Moreover, most sites fail to update their help pages to accommodate software upgrades. Though the market is flooded with books discussing the theoretical concepts in Bioinformatics, a manual of this kind is rarely found. The content developed to meet the needs of readers from diverse background and to incorporate the syllabi of undergraduate and postgraduate courses at various universities.

From the groundbreaking partnership of Macmillan Learning and Scientific American comes this one-of-a-kind introduction to the science of biology and its impact on the way we live. Available for the first time with Macmillan's new online learning tool, Achieve, Biology for a Changing World explores the core ideas of biology through chapters written and illustrated in the style of a Scientific American article. Chapters don't just feature compelling stories of real people-each chapter is a newsworthy story that serves as a context for covering the standard curriculum for the non-majors biology course. Achieve is Macmillan's new online learning platform that 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.

This unique textbook/reference presents unified coverage of bioinformatics topics relating to both biological sequences and biological networks, providing an in-depth analysis of cutting-edge distributed algorithms, as well as of relevant sequential algorithms. In addition to introducing the latest algorithms in this area, more than fifteen new distributed algorithms are also proposed. Topics and features: reviews a range of open challenges in biological sequences and networks; describes in detail both sequential and parallel/distributed algorithms for each problem; suggests approaches for distributed algorithms as possible extensions to sequential algorithms, when the distributed algorithms for the topic are scarce; proposes a number of new distributed algorithms in each chapter, to serve as potential starting points for further research; concludes each chapter with self-test exercises, a summary of the key points, a comparison of the algorithms described, and a literature review.

The book is based on lectures presented on the International Summer School on Biophysics held in Croatia in September 2009. The advantage of the School is that it provides advanced training in very broad scope of areas related to biophysics contrary to other similar schools or workshops that are centered mainly on one topic or technique. In this volume, tenth in the row, the papers in the field of biophysics are presented. The topics are biological phenomena from single protein to macromolecular aggregations structure by using variant physical methods (NMR, EPR, FTIR, Mass Spectrometry, etc.). The interrelationship of supramolecular structures and their functions is enlightened by applications of principals of these physical methods in the biophysical and molecular biology context.

Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician's fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual's susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain-machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.

The book deals with various clinical aspects of cytochrome P450 2E1 (CYP2E1), which is a potent source for oxidative stress. Oxidative stress is critical for pathogenesis of diseases and CYP2E1 is a major contributor for oxidative stress. Several clinical disorders are associated with changes in regulation of CYP2E1 and the consequent abnormalities, which include alcoholic liver disease, alcoholic pancreatitis, carcinogenesis, non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, obesity, hepatitis C virus infection, reproductive organ toxicity, hepatocellular and cholestatic liver cirrhosis, inhibition of bone repair, cross- tolerance in smokers and people treated with nicotine, disorders of the central nervous system, changes in metabolism of protoxicants in the circulatory system and susceptibility to human papillomavirus infection. Hence, CYP2E1 emerges as a new and potent player in aggravating injury and furthering disease complications.

r ed Algae in Genome Age book most people reading this book have childhood memories about being enthralled at the beach with those rare and mysterious living forms we knew as seaweeds. We were fascinated at that time by their range of red hues and textures, and most of all, their exotic beauty. t o a scientist, red algae represent much more than apparent features. t heir complex forms have attracted morphologists for centuries; their intricate life cycles have brought more than one surprise to plant biologists familiar only with ferns and fowering plants; their unusual tastes have been appreciated for mill- nia, and their valuable chemical constituents have been exploited for nearly as long, most recently by biotech companies; their diversity in marine, freshwater, and t- restrial environments has offered centuries of engaging entertainment for botanists eager to arrange them in orderly classifcation systems; still, the red algae continue to teach us how many more challenges need to be overcome in order to understand their biodiversity, biological functions, and evolutionary histories.

This book compiles and presents new developments in statistical causal inference. The accompanying data and computer programs are publicly available so readers may replicate the model development and data analysis presented in each chapter. In this way, methodology is taught so that readers may implement it directly. The book brings together experts engaged in causal inference research to present and discuss recent issues in causal inference methodological development. This is also a timely look at causal inference applied to scenarios that range from clinical trials to mediation and public health research more broadly. In an academic setting, this book will serve as a reference and guide to a course in causal inference at the graduate level (Master's or Doctorate). It is particularly relevant for students pursuing degrees in statistics, biostatistics, and computational biology. Researchers and data analysts in public health and biomedical research will also find this book to be an important reference.

VLSI 2010 Annual Symposium will present extended versions of the best papers presented in ISVLSI 2010 conference. The areas covered by the papers will include among others: Emerging Trends in VLSI, Nanoelectronics, Molecular, Biological and Quantum Computing. MEMS, VLSI Circuits and Systems, Field-programmable and Reconfigurable Systems, System Level Design, System-on-a-Chip Design, Application-Specific Low Power, VLSI System Design, System Issues in Complexity, Low Power, Heat Dissipation, Power Awareness in VLSI Design, Test and Verification, Mixed-Signal Design and Analysis, Electrical/Packaging Co-Design, Physical Design, Intellectual property creating and sharing.

The aim of this manual is to provide a comprehensive guide to the methods involved in collecting, preparing and screening plants for bioactive properties for manipulating key ruminal fermentation pathways and against gastrointestinal pathogens. The manual will better equip the reader with methodological approaches to initiate screening programmes to test for bioactivity in native plants and find natural alternatives to chemicals for manipulating ruminal fermentation and gut health. The manual provides isotopic and non-isotopic techniques to efficiently screen plants or plant parts for a range of potential bioactives for livestock production. Each chapter has been contributed by experts in the field and methods have been presented in a format that is easily reproducible in the laboratory. It is hoped that this manual will be of great value to students, researchers and those involved in developing efficient and environmentally friendly livestock production systems."

This book addresses in detail multifaceted approaches to boosting nutrient use efficiency (NUE) that are modified by plant interactions with environmental variables and combine physiological, microbial, biotechnological and agronomic aspects. Conveying an in-depth understanding of the topic will spark the development of new cultivars and strains to induce NUE, coupled with best management practices that will immensely benefit agricultural systems, safeguarding their soil, water, and air quality. Written by recognized experts in the field, the book is intended to provide students, scientists and policymakers with essential insights into holistic approaches to NUE, as well as an overview of some successful case studies. In the present understanding of agriculture, NUE represents a question of process optimization in response to the increasing fragility of our natural resources base and threats to food grain security across the globe. Further improving nutrient use efficiency is a prerequisite to reducing production costs, expanding crop acreage into non-competitive marginal lands with low nutrient resources, and preventing environmental contamination. The nutrients most commonly limiting plant growth are N, P, K, S and micronutrients like Fe, Zn, B and Mo. NUE depends on the ability to efficiently take up the nutrient from the soil, but also on transport, storage, mobilization, usage within the plant and the environment. A number of approaches can help us to understand NUE as a whole. One involves adopting best crop management practices that take into account root-induced rhizosphere processes, which play a pivotal role in controlling nutrient dynamics in the soil-plant-atmosphere continuum. New technologies, from basic tools like leaf color charts to sophisticated sensor-based systems and laser land leveling, can reduce the dependency on laboratory assistance and manual labor. Another approach concerns the development of crop plants through genetic manipulations that allow them to take up and assimilate nutrients more efficiently, as well as identifying processes of plant responses to nutrient deficiency stress and exploring natural genetic variation. Though only recently introduced, the ability of microbial inoculants to induce NUE is gaining in importance, as the loss, immobilization, release and availability of nutrients are mediated by soil microbial processes.

The contributed volume puts emphasis on a superior role of water in (bio)systems exposed to a mechanical stimulus. It is well known that water plays an extraordinary role in our life. It feeds mammalian or other organism after distributing over its whole volume to support certain physiological and locomotive (friction-adhesion) processes to mention but two of them, both of extreme relevance. Water content, not only in the mammalian organism but also in other biosystems such as whether those of soil which is equipped with microbiome or the ones pertinent to plants, having their own natural network of water vessels, is always subjected to a force field.The decisive force field applied to the biosystems makes them biomechanically agitated irrespective of whether they are subjected to external or internal force-field conditions. It ought to be noted that the decisive mechanical factor shows up in a close relation with the space-and-time scale in which it is causing certain specific phenomena to occur.The scale problem, emphasizing the range of action of gravitational force, thus the millimeter or bigger force vs. distance scale, is supposed to enter the so-called macroscale approach to water transportation through soil or plants' roots system. It is merely related to a percolation problem, which assumes to properly inspect the random network architecture assigned to the biosystems invoked. The capillarity conditions turn out to be of prior importance, and the porous-medium effect has to be treated, and solved in a fairly approximate way.The deeper the scale is penetrated by a force-exerting and hydrated agent the more non-gravitational force fields manifest. This can be envisaged in terms of the corresponding thermodynamic (non-Newtonian) forces, and the phenomena of interest are mostly attributed to suitable changes of the osmotic pressure. In low Reynolds number conditions, thus in the (sub)micrometer distance-scale zone, they are related with the corresponding viscosity changes of the aqueous, e.g. cytoplasmatic solutions, of semi-diluted and concentrated (but also electrolytic) characteristics. For example, they can be observed in articulating systems of mammals, in their skin, and to some extent, in other living beings, such as lizards, geckos or even insects. Through their articulating devices an external mechanical stimulus is transmitted from macro- to nanoscale, wherein the corresponding osmotic-pressure conditions apply. The content of the proposed work can be distributed twofold. First, the biomechanical mammalian-type (or, similar) systems with extraordinary relevance of water for their functioning will be presented, also including a presentation of water itself as a key physicochemical system/medium. Second, the suitably chosen related systems, mainly of soil and plant addressing provenience, will be examined thoroughly. As a common denominator of all of them, it is proposed to look at their hydrophobic and/or (de)hydration effects, and how do they impact on their basic mechanical (and related, such as chemo-mechanical or piezoelectric, etc.) properties. An additional tacit assumption employed throughout the monograph concerns statistical scalability of the presented biosystems which is equivalent to take for granted a certain similarity between local and global system's properties, mostly those of mechanical nature. The presented work's chapters also focus on biodiversity and ecological aspects in the world of animals and plants, and the related systems. The chapters' contents underscore the bioinspiration as the key landmark of the proposed monograph.

Does nature have intrinsic value? Should we be doing more to save wilderness and ocean ecosystems? What are our duties to future generations of humans? Do animals have rights? This revised edition of "Life Science Ethics" introduces these questions using narrative case studies on genetically modified foods, use of animals in research, nanotechnology, and global climate change, and then explores them in detail using essays written by nationally-recognized experts in the ethics field.

Part I introduces ethics, the relationship of religion to ethics, how we assess ethical arguments, and a method ethicists use to reason about ethical theories. Part II demonstrates the relevance of ethical reasoning to the environment, land, farms, food, biotechnology, genetically modified foods, animals in agriculture and research, climate change, and nanotechnology. Part III presents case studies for the topics found in Part II.

Presents a unique study of Integrative Problem-Solving (IPS). The consideration of 'Decadence' is essential in the scientific study of environmental and other problems and their rigorous solution, because the broad context within which the problems emerge can affect their solution. Stochastic reasoning underlines the conceptual and methodological framework of IPS, and its formulation has a mathematical life of its own that accounts for the multidisciplinarity of real world problems, the multisourced uncertainties characterizing their solution, and the different thinking modes of the people involved. Only by interpolating between the full range of disciplines (including stochastic mathematics, physical science, neuropsychology, philosophy, and sociology) and the associated thinking modes can scientists arrive at a satisfactory account of problem-solving, and be able to distinguish between a technically complete problem-solution, and a solution that has social impact.

Peter Hunter Computational physiology for the cardiovascular system is entering a new and exciting phase of clinical application. Biophysically based models of the human heart and circulation, based on patient-specific anatomy but also informed by po- lation atlases and incorporating a great deal of mechanistic understanding at the cell, tissue, and organ levels, offer the prospect of evidence-based diagnosis and treatment of cardiovascular disease. The clinical value of patient-specific modeling is well illustrated in application areas where model-based interpretation of clinical images allows a more precise analysis of disease processes than can otherwise be achieved. For example, Chap. 6 in this volume, by Speelman et al. , deals with the very difficult problem of trying to predict whether and when an abdominal aortic aneurysm might burst. This requires automated segmentation of the vascular geometry from magnetic re- nance images and finite element analysis of wall stress using large deformation elasticity theory applied to the geometric model created from the segmentation. The time-varying normal and shear stress acting on the arterial wall is estimated from the arterial pressure and flow distributions. Thrombus formation is identified as a potentially important contributor to changed material properties of the arterial wall. Understanding how the wall adapts and remodels its material properties in the face of changes in both the stress loading and blood constituents associated with infl- matory processes (IL6, CRP, MMPs, etc.

In its extensively revised and updated Second Edition, this book provides a solid foundation for readers interested in clinical research. Discussion encompasses genetic, pharmacoepidemiologic and implementation research.

All chapters have been updated with new information and many new tables have been added to elucidate key points. The book now offers discussion on how to handle missing data when analyzing results, and coverage of Adaptive Designs and Effectiveness Designs and new sections on Comparative Effectiveness Research and Pragmatic Trials. Chapter 6 includes new material on Phase 0 Trials, expanded coverage of Futility Trials, a discussion of Medical Device approval, Off Label Drug use and the role of the FDA in regulating advertising. Additional new information includes the role of pill color and shape in association with the placebo effect and an examination of issues surrounding minority recruitment. The final chapter offers a new section on manuscript preparation along with a discussion of various guidelines being adopted by journals: CONSORT, STROBE, PRISMA, MOOSE and others; and coverage of Conflicts of Interest, Authorship, Coercive Citation, and Disclosures in Industry-Related Associations.

Building on the strengths of its predecessor in its comprehensive approach and authoritative advice, the new edition offers more of what has made this book a popular, trusted resource for students and working researchers alike.

Integrated bioinformatics solutions have become increasingly valuable in past years, as technological advances have allowed researchers to consider the potential of omics for clinical diagnosis, prognosis, and therapeutic purposes, and as the costs of such techniques have begun to lessen. In Bioinformatics Methods in Clinical Research, experts examine the latest developments impacting clinical omics, and describe in great detail the algorithms that are currently used in publicly available software tools. Chapters discuss statistics, algorithms, automated methods of data retrieval, and experimental consideration in genomics, transcriptomics, proteomics, and metabolomics. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, provides practical examples illustrating methods, results, and conclusions from data mining strategies wherever possible, and includes a Notes section which shares tips on troubleshooting and avoiding known pitfalls.

Informative and ground-breaking, Bioinformatics Methods in Clinical Research establishes a much-needed bridge between theory and practice, making it an indispensable resource for bioinformatics researchers."

In Silico Chemistry and Biology: Current and Future Prospects provides a compact overview on recent advances in this highly dynamic branch of chemistry. Various methods of protein modelling and computer-assisted drug design are presented, including fragment- and ligand-based approaches. Many successful practical applications of these techniques are demonstrated. The authors also look to the future and describe the main challenges of the field.

Our lives and well being intimately depend on the exploitation of the plant genetic resources available to our breeding programs. Therefore, more extensive exploration and effective exploitation of plant genetic resources are essential prerequisites for the release of improved cultivars. Accordingly, the remarkable progress in genomics approaches and more recently in sequencing and bioinformatics offers unprecedented opportunities for mining germplasm collections, mapping and cloning loci of interest, identifying novel alleles and deploying them for breeding purposes. This book collects 48 highly interdisciplinary articles describing how genomics improves our capacity to characterize and harness natural and artificially induced variation in order to boost crop productivity and provide consumers with high-quality food. This book will be an invaluable reference for all those interested in managing, mining and harnessing the genetic richness of plant genetic resources.

The 21st ESACT conference was held in the beautiful surroundings of the CityWest Hotel resort in Dublin, Ireland. For the first time in ESACT history the number of participants exceeded 900: a sign of the ever increasing importance of this area. The conference commenced on Sunday June 5th with two sets of parallel workshops on the subjects listed below. An additional workshop was held on Monday lunchtime of the conferenceProcess Analytical Technology (PAT), Quality by Design (QbD) and other recent regulatory developments.

2. Innovative media products for the 21st century biopharmaceutical industry.

3. The impact of high titre media feed-streams on monoclonal antibody purification.

4. Advances in genomics and proteomics.

5. Stem Cell Technology: new developments and clinical applications.

Symbiotic Fungi Principles and Practice presents current protocols for the study of symbiotic fungi and their interactions with plant roots, such as techniques for analyzing nutrient transfer, ecological restoration, microbial communication, and mycorrhizal bioassays, AM inoculum procedures and mushroom technology.

The protocols offer practical solutions for researchers and students involved in the study of symbiotic microorganisms. The volume will be of great use for basic research, biotechnological applications, and the development of commercial products."

The idea of creation and creativity is among the most powerful and pervasive of metaphors bequeathed to the modern world by the scriptures of Judaism, Christianity and Islam. Twelve specialists here explore the original sources and contemporary manifestations of the theme in both high and low culture, from the Book of Genesis to James Joyce's Ulysses, Children of Gebalawi by the Egyptian novelist Naguib Mahfouz, and the Polish poetry of Wislawa Szymborska, and to popular films, such as Bruce Almighty and Animatrix, and animation films for children. Even current debates on genetics and ecology and the public exhibition of plastinated human bodies invoke these same themes, and make this volume a topical contribution to cultural studies today. Jonneke Bekkenkamp, Why on Earth? Creation and Creativity in the Vocabularies of Patricia de Martelaere, Wislawa Szymborska and Julia Cameron Athalya Brenner, Recreating the Biblical Creation for Western Children: Provisional Reflections on Some Case Studies Wim Drees, Vocabularies of Creation and Creativity in Debates on Genetics and Ecology Jan Willem van Henten, Playing God in the Movies: Bruce Almighty and the Preposterous History of Genesis 1:26-27 Alistair Hunter, Creation out of (almost) Nothing or Does God Wear Genes? Alison Jasper, Mysteries under Your Skin David Jasper, 'Down through all Christian minstrelsy': Genesis, James Joyce and Contemporary Vocabularies of Creation Louise Joy Lawrence, Tracing Tricksters: Creation and Creativity in John's Gospel Richard van Leeuwen, Creation and Revelation in Naguib Mahfouz's Novel Children of Gebelawi Lloyd Ridgeon, Is the God of Islam an Evil Creator? Caroline Vander Stichele and Todd Penner, Terminatrix: Visualizing the End of Creation in Animatrix

Fifty years ago, a new approach to reaction kinetics began to emerge: one based on mathematical models of reaction kinetics, or formal reaction kinetics. Since then, there has been a rapid and accelerated development in both deterministic and stochastic kinetics, primarily because mathematicians studying differential equations and algebraic geometry have taken an interest in the nonlinear differential equations of kinetics, which are relatively simple, yet capable of depicting complex behavior such as oscillation, chaos, and pattern formation. The development of stochastic models was triggered by the fact that novel methods made it possible to measure molecules individually. Now it is high time to make the results of the last half-century available to a larger audience: students of chemistry, chemical engineering and biochemistry, not to mention applied mathematics. Based on recent papers, this book presents the most important concepts and results, together with a wealth of solved exercises. The book is accompanied by the authors' Mathematica package, ReactionKinetics, which helps both students and scholars in their everyday work, and which can be downloaded from http://extras.springer.com/ and also from the authors' websites. Further, the large set of unsolved problems provided may serve as a springboard for individual research.

These proceedings from the 37th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (MaxEnt 2017), held in Sao Carlos, Brazil, aim to expand the available research on Bayesian methods and promote their application in the scientific community. They gather research from scholars in many different fields who use inductive statistics methods and focus on the foundations of the Bayesian paradigm, their comparison to objectivistic or frequentist statistics counterparts, and their appropriate applications. Interest in the foundations of inductive statistics has been growing with the increasing availability of Bayesian methodological alternatives, and scientists now face much more difficult choices in finding the optimal methods to apply to their problems. By carefully examining and discussing the relevant foundations, the scientific community can avoid applying Bayesian methods on a merely ad hoc basis. For over 35 years, the MaxEnt workshops have explored the use of Bayesian and Maximum Entropy methods in scientific and engineering application contexts. The workshops welcome contributions on all aspects of probabilistic inference, including novel techniques and applications, and work that sheds new light on the foundations of inference. Areas of application in these workshops include astronomy and astrophysics, chemistry, communications theory, cosmology, climate studies, earth science, fluid mechanics, genetics, geophysics, machine learning, materials science, medical imaging, nanoscience, source separation, thermodynamics (equilibrium and non-equilibrium), particle physics, plasma physics, quantum mechanics, robotics, and the social sciences. Bayesian computational techniques such as Markov chain Monte Carlo sampling are also regular topics, as are approximate inferential methods. Foundational issues involving probability theory and information theory, as well as novel applications of inference to illuminate the foundations of physical theories, are also of keen interest.