Genomics in the Cloud

Genomics in the Cloud

Author: Geraldine A. Van der Auwera

Publisher: O'Reilly Media

Published: 2020-04-02

Total Pages: 496

ISBN-13: 1491975164

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Data in the genomics field is booming. In just a few years, organizations such as the National Institutes of Health (NIH) will host 50+ petabytes—or over 50 million gigabytes—of genomic data, and they’re turning to cloud infrastructure to make that data available to the research community. How do you adapt analysis tools and protocols to access and analyze that volume of data in the cloud? With this practical book, researchers will learn how to work with genomics algorithms using open source tools including the Genome Analysis Toolkit (GATK), Docker, WDL, and Terra. Geraldine Van der Auwera, longtime custodian of the GATK user community, and Brian O’Connor of the UC Santa Cruz Genomics Institute, guide you through the process. You’ll learn by working with real data and genomics algorithms from the field. This book covers: Essential genomics and computing technology background Basic cloud computing operations Getting started with GATK, plus three major GATK Best Practices pipelines Automating analysis with scripted workflows using WDL and Cromwell Scaling up workflow execution in the cloud, including parallelization and cost optimization Interactive analysis in the cloud using Jupyter notebooks Secure collaboration and computational reproducibility using Terra


Blood and Bone Marrow Pathology

Blood and Bone Marrow Pathology

Author: Anna Porwit

Publisher:

Published: 2011

Total Pages: 0

ISBN-13: 9780702031472

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Already a standard reference work in the field, the new edition of Blood and Bone Marrow Pathology incorporates the latest WHO classification schemes and the latest ancillary diagnostic techniques in immunohistochemistry and molecular biology in order to provide a comprehensive, well balanced and authoritative guide to the interpretation and diagnosis of neoplastic and non-neoplastic diseases of blood and bone marrow. The text is lavishly illustrated with high quality colour images that demonstrate the relevant pathological,features and immunohistochemical and molecular markers. The text features a well-organized approach that incorporates practical tips and clues to help avoid pitfalls and to ensure optimal diagnosis The book is lavishly illustrated with high quality color images that demonstrate the relevant pathological features and immunohistochemical and molecular markers. The text features a well-organized approach that incorporates practical tips and clues to help avoid pitfalls and to ensure optimal diagnosis. Chapters have been totally rewritten and new chapters have been added, especially on myeloid malignancies. The chapters on hematological malignancies have been written so that the reader can apply the latest WHO Classifications in their routine daily practice (especially the 2008 WHO Classification of Tumors of Hemopoietic and Lymphoid Tissues) All chapters have been revised to include new aspects of molecular biology and flow cytometry diagnostics. Many new schematic diagrams and color illustrations have been added to illustrate blood and bone marrow pathology. Access the full text online and download images via Expert Consult. Chapters have been totally rewritten and some new chapters have been added especially on myeloid malignancies, in line with the WHO 2008 Classification All chapters have been revised to include new aspects of molecular biology and updated concerning flow cytometry diagnostics Greater emphasis on practical diagnostic aspects for all disorders Brand new editorial and contributing author team. Full Online text through Expert Consult. Full downloadable Image Bank Already a standard reference work in the field, the new edition of Blood and Bone Marrow Pathology incorporates the latest WHO classification schemes and the latest ancillary diagnostic techniques in immunohistochemistry and molecular biology in order to provide a comprehensive, well balanced and authoritative guide to the interpretation and diagnosis of neoplastic and non-neoplastic diseases of blood and bone marrow. The text is lavishly illustrated with high quality colour images that demonstrate the relevant pathological,features and immunohistochemical and molecular markers. The text features a well-organized approach that incorporates practical tips and clues to help avoid pitfalls and to ensure optimal diagnosis


Natural Killer Cell Protocols

Natural Killer Cell Protocols

Author: Kerry S. Campbell

Publisher: Springer Science & Business Media

Published: 2008-02-03

Total Pages: 394

ISBN-13: 1592590446

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In Natural Killer Cell Protocols: Cellular and Molecular Methods, Kerry S. Campbell and Marco Colonna have assembled a comprehensive collection of readily reproducible methods designed to study natural killer (NK) cells from the broadest variety of viewpoints. These include not only classic techniques, but also new approaches to standard methods, newly evolved techniques that have become valuable for specific applications, and unique models for manipulating and studying NK cells. Among the advanced methods covered are those for in vitro transendothelial migration, in vivo detection of cells migrating into tumors, immunofluorescence staining of intracellular cytokines, and in vitro NK cell development. Valuable techniques for specific applications include vaccinia virus protein expression, soluble KIR-Fc fusions for HLA class I binding assays, calcium mobilization in cell conjugates, and identification of heterodimeric receptor complexes using cDNA library expression cloning. No less important are accounts of such classic methods as hybrid resistance, ADCC, viral defense, target cell cytotoxicity assays, cloning and culturing, tumor immunotherapy, and generation of HLA class I transfected target cells. Natural Killer Cell Protocols: Cellular and Molecular Methods offers immunologists, cancer researchers, virologists, and cell biologists today's most comprehensive collection of both established and cutting-edge techniques, methods that will contribute significantly to advancing our understanding of this fascinating and critically important class of cells.


Neuroimmune Diseases

Neuroimmune Diseases

Author: Hiroshi Mitoma

Publisher: Springer

Published: 2019-08-13

Total Pages: 822

ISBN-13: 3030195155

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A translational overview of neuroimmune diseases for neuroscientists and clinicians that clarifies the pathological mechanisms underlying neuroimmune diseases and builds a comprehensive bridge between the latest research findings and their clinical implications in daily practice. The material is presented in two steps. The first section comprises a review of the pathogenic actions of immune cells in brain diseases. Here the authors discuss the mechanisms through which immune cells disrupt the functions of nerve cells. The second section explores the ways in which the brain becomes dysfunctional due to impaired nerve cell function. Based on pathogenesis, diagnostic and therapeutic strategies are discussed for each clinical category. The book will be invaluable for use in clinical practice of neuroimmune diseases


Janeway's Immunobiology

Janeway's Immunobiology

Author: Kenneth Murphy

Publisher: Garland Science

Published: 2010-06-22

Total Pages:

ISBN-13: 9780815344575

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The Janeway's Immunobiology CD-ROM, Immunobiology Interactive, is included with each book, and can be purchased separately. It contains animations and videos with voiceover narration, as well as the figures from the text for presentation purposes.


Exercise Immunology

Exercise Immunology

Author: Michael Gleeson

Publisher: Routledge

Published: 2013-06-26

Total Pages: 581

ISBN-13: 113645585X

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Exercise immunology is an important, emerging sub-discipline within exercise physiology, concerned with the relationship between exercise, immune function and infection risk. This book offers a comprehensive, up-to-date and evidence-based introduction to exercise immunology, including the physiological and molecular mechanisms that determine immune function and the implications for health and performance in sport and everyday life. Written by a team of leading exercise physiologists, the book describes the characteristics of the immune system and how its components are organised to form an immune response. It explains the physiological basis of the relationship between stress, physical activity, immune function and infection risk, and identifies the ways in which exercise and nutrition interact with immune function in athletes and non-athletes. The book shows students how to evaluate the strengths and limitations of the evidence linking physical activity, immune system integrity and health, and explains why exercise is associated with anti-inflammatory effects that are potentially beneficial to long-term health. Every chapter includes useful features, such as clear summaries, definitions of key terms, discussions of seminal research studies and practical guidelines for athletes on ways to minimise infection risk, with additional learning resources available on a companion website. This is an essential textbook for any course on exercise immunology or advanced exercise physiology.


Multiparameter Flow Cytometry in the Diagnosis of Hematologic Malignancies

Multiparameter Flow Cytometry in the Diagnosis of Hematologic Malignancies

Author: Anna Porwit

Publisher: Cambridge University Press

Published: 2018-01-25

Total Pages: 248

ISBN-13: 1108548830

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Master implementation of the techniques of flow cytometry in diagnosing complex haematological diseases and malignancies in patients, worldwide. Featuring World Health Organization recommendations on pre-analytical steps, instrument settings and panel construction, this invaluable manual offers invaluable support for those researching, practising and analyzing the cause of hematological malignancies. Authored by leading experts, this book puts flow-cytometry into everyday context. With a focus on multicolour panels, the manual provides readers an experienced understanding of effective, implementation techniques. Practitioners of all levels are offered a background in a variety of diseases presented alongside the most current methodology. Wide-ranging and comprehensive; detailed images of healthy blood, bone marrow and lymph-nodes are illustrated throughout, allowing for effective diagnosis. Through engaging with differential diagnoses, the manual offers an understanding of similar symptoms and mimicking malignancies, avoiding inaccurate results. Featuring in-depth descriptions of chronic diseases; users can reach accurate diagnosis, first time.


Magnesium in the Central Nervous System

Magnesium in the Central Nervous System

Author: Robert Vink

Publisher: University of Adelaide Press

Published: 2011

Total Pages: 354

ISBN-13: 0987073052

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The brain is the most complex organ in our body. Indeed, it is perhaps the most complex structure we have ever encountered in nature. Both structurally and functionally, there are many peculiarities that differentiate the brain from all other organs. The brain is our connection to the world around us and by governing nervous system and higher function, any disturbance induces severe neurological and psychiatric disorders that can have a devastating effect on quality of life. Our understanding of the physiology and biochemistry of the brain has improved dramatically in the last two decades. In particular, the critical role of cations, including magnesium, has become evident, even if incompletely understood at a mechanistic level. The exact role and regulation of magnesium, in particular, remains elusive, largely because intracellular levels are so difficult to routinely quantify. Nonetheless, the importance of magnesium to normal central nervous system activity is self-evident given the complicated homeostatic mechanisms that maintain the concentration of this cation within strict limits essential for normal physiology and metabolism. There is also considerable accumulating evidence to suggest alterations to some brain functions in both normal and pathological conditions may be linked to alterations in local magnesium concentration. This book, containing chapters written by some of the foremost experts in the field of magnesium research, brings together the latest in experimental and clinical magnesium research as it relates to the central nervous system. It offers a complete and updated view of magnesiums involvement in central nervous system function and in so doing, brings together two main pillars of contemporary neuroscience research, namely providing an explanation for the molecular mechanisms involved in brain function, and emphasizing the connections between the molecular changes and behavior. It is the untiring efforts of those magnesium researchers who have dedicated their lives to unraveling the mysteries of magnesiums role in biological systems that has inspired the collation of this volume of work.


Immunophenotyping

Immunophenotyping

Author: J Philip McCoy Jr

Publisher: Humana

Published: 2019-09-29

Total Pages: 375

ISBN-13: 9781493996490

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This volume presents the latest collection of immunophenotypic techniques and applications used in research and clinical settings. Chapters in this book cover topics such as constructions of high dimensions fluorescence and mass cytometry panels; fluorescence barcoding; using dried or lyophilized reagents; and immunophenotypic examples of specific cell types. The book concludes with a discussion on the critical roles of quality control and immunophenotyping in the clinical environment. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Immunophenotyping: Methods and Protocols is a valuable resource for any researchers, clinician, or scientist interested in learning more about this evolving field.