A Guide to Virology for Engineers and Applied Scientists: Epidemiology, Emergency Management, and Optimization

Cover
Title Page
Copyright
Contents
Preface
About the Authors
Part I Introduction to Viruses
Chapter 1 Overview of Molecular Biology
1.1 Cell Basics
1.1.1 Cytoplasm
1.1.2 Ribosomes
1.1.3 Nucleus
1.2 Cell Replication
1.2.1 Nucleic Acids
1.2.2 DNA Replication
1.2.3 RNA Structure and Role
1.2.4 Protein Synthesis
1.3 Cellular Transport
1.3.1 Plasma Membrane
1.3.2 Cell Signaling
1.4 Immune Defense
1.4.1 Innate Immunity
1.4.2 Adaptive Immunity
1.4.2.1 Humoral Immunity
1.4.2.2 Cellular Immunity
1.5 Applications
1.6 Chapter Summary
1.7 Problems
References
Chapter 2 Basics of Virology
2.1 Viral Basics and Terminology
2.2 Viral Life Cycle
2.2.1 Attachment (Connection)
2.2.2 Penetration (Entry)
2.2.3 Uncoating
2.2.4 Replication
2.2.5 Assembly
2.2.6 Maturation and Release
2.3 Virus Structure and Classification
2.3.1 DNA Viruses
2.3.2 RNA Viruses
2.3.3 Reverse Transcription Viruses (Retroviruses)
2.4 Viruses in Context of the Tree of Life
2.5 Viral Genetics
2.5.1 Antigenic Shift
2.5.2 Antigenic Drift
2.5.3 Phenotypic Mixing
2.5.4 Complementation
2.6 Applications
2.7 Chapter Summary
2.8 Problems
References
Chapter 3 Pandemics, Epidemics, and Outbreaks
3.1 Human Viral Diseases
3.2 Ebola and Marburg Viruses
3.2.1 Symptoms
3.2.2 Diagnosis
3.2.3 Prevention and Treatment
3.3 Human Immunodeficiency Disease (HIV)
3.3.1 HIV Symptoms
3.3.1.1 Stage 1: Acute Infection
3.3.1.2 Stage 2: Chronic HIV Infection (Latent Phase)
3.3.1.3 Stage 3: Acquired Immunodeficiency Syndrome (AIDS)
3.3.2 Diagnosis
3.3.3 HIV Prevention and Treatment
3.4 Influenza
3.4.1 Influenza Symptoms
3.4.2 Influenza Diagnosis
3.4.3 Influenza Prevention and Treatment
3.4.4 Influenza Pandemics
3.5 Coronaviruses
3.5.1 Symptoms
3.5.1.1 Typical Acute Symptoms
3.5.1.2 Post‐COVID Conditions
3.5.1.3 COVID‐19 Multiorgan System Effects (MIS)
3.5.2 COVID‐19 Diagnosis
3.5.3 COVID‐19 Prevention and treatment
3.6 Current and Emerging Viral Threats
3.7 Applications
3.8 Chapter Summary
3.9 Problems
References
Chapter 4 Virus Prevention, Diagnosis, and Treatment
4.1 Vaccination Successes and Challenges
4.2 Current Vaccine Technology
4.2.1 Live‐attenuated vaccines
4.2.2 Inactivated vaccines
4.2.3 Recombinant Subunit Vaccines
4.2.4 Viral Vector Vaccines
4.2.5 Messenger RNA (mRNA) Vaccines
4.3 U.S.‐Approved Vaccines and Requirements
4.3.1 Commercially Available Viral Vaccines
4.3.2 Vaccination Requirements
4.4 Viral Testing and Diagnosis
4.4.1 Viral Testing
4.4.2 Antibody Testing
4.5 Antiviral Treatment Options
4.5.1 HIV
4.5.1.1 Nucleoside Reverse Transcriptase Inhibitors (NRTIs)
4.5.1.2 Non‐nucleoside Reverse Transcriptase Inhibitors (NNRTIs)
4.5.1.3 Protease Inhibitors (PIs)
4.5.1.4 Fusion Inhibitors (FIs)
4.5.1.5 Integrase Strand Transfer Inhibitors (INSTIs)
4.5.1.6 CCR5 Antagonists
4.5.1.7 Attachment Inhibitors
4.5.1.8 Post‐Attachment Inhibitors
4.5.1.9 Pharmacokinetic Enhancers
4.5.2 Influenza
4.5.3 Hepatitis C virus (HCV)
4.5.4 Other Treatment Options
4.6 Applications
4.7 Chapter Summary
4.8 Problems
References
Chapter 5 Safety Protocols and Personal Protection Equipment
5.1 Regulations and Oversight of Safety Protocols
5.2 Protective and Safety Systems
5.2.1 Personal Protective Devices and Practices
5.2.2 Antimicrobial Suppression And Eradication
5.3 Disinfection Categories and Procedures
5.4 Occupational Health and Safety Administration Hazmat Regulations
5.4.1 HAZMAT Level A Protection
5.4.2 HAZMAT Level B Protection
5.4.3 Level C Protection
5.4.4 Level D Protection
5.5 Bio Level Safety and Security
5.6 COVID‐Related Safety Precautions
5.6.1 Personal Protective Equipment
5.6.2 Transmission Control
5.7 Applications
5.8 Summary
5.9 Problems
References
Chapter 6 Epidemiology and Virus Transmission
6.1 Overview of Epidemiology
6.2 Government Agencies' Contributions to Public Health
6.2.1 The Role of the Centers for Disease Control and Prevention (CDC)
6.2.2 The World Health Organization (WHO): Successes and Challenges
6.3 Epidemiologic Study Design
6.3.1 Outbreak Case Example
6.3.2 Clinical Trials
6.4 Virus Transmission
6.4.1 Modes of Transmission
6.5 Applications
6.6 Chapter Summary
6.7 Problems
References
Part II Practical and Technical Considerations
Chapter 7 Engineering Principles and Fundamentals
7.1 History of Engineering
7.2 Problem Solving: The Engineering Approach
7.2.1 Problem‐Solving Methodology
7.2.2 Engineering and Scientific Sources
7.3 Units and Conversion Constants
7.3.1 The Metric System
7.3.2 The SI System
7.4 Dimensional Analysis
7.5 Process Variables
7.6 The Conservation Laws
7.7 Thermodynamics and Kinetics
7.8 Applications
7.9 Chapter Summary
7.10 Problems
References
Chapter 8 Legal and Regulatory Considerations
8.1 The Regulatory System
8.1.1 Laws, Regulations, Plans and policy: The Differences
8.1.2 Policies and Plans
8.2 The Role of Individual States
8.3 Key Government Agencies
8.3.1 Environmental Protection Agency (EPA)
8.3.2 Centers for Disease Control and Prevention (CDC)
8.3.3 Food and Drug Administration (FDA)
8.3.4 Occupational Health and Safety Administration (OSHA)
8.3.5 Legal Considerations during a Public Health Crisis
8.4 Public Health Emergency Declarations
8.5 Key Environmental Acts
8.6 The Clean Air Act
8.7 Regulation of Toxic Substances
8.7.1 Toxic Water Pollutants: Control and Classification
8.7.2 Drinking Water
8.7.3 Surface Water Treatment Rules (SWTR)
8.8 Regulations Governing Infectious Diseases
8.8.1 Vaccination Laws
8.8.2 State Healthcare Worker and Patient Vaccination Laws
8.8.3 State‐Mandated Childhood Vaccinations
8.9 Applications
8.10 Chapter Summary
8.11 Problems
References
Chapter 9 Emergency Planning and Response
9.1 The Importance of Emergency Planning and Response
9.2 Planning for Emergencies
9.2.1 Preparedness Training
9.3 Plan Implementation
9.3.1 Notification of Public and Regulatory Officials
9.4 EP&R for Epidemics and Pandemics
9.4.1 Federal Public Health and Medical Emergency Preparedness
9.4.2 Emergency Operations Center
9.4.3 Disease Containment
9.4.4 Public Notification of Pandemic Quarantines and Lockdowns
9.4.5 The National Strategy for Pandemic Influenza (NSPI)
9.5 EP&R for Industrial Accidents
9.5.1 Emergency Planning and Community Right‐to‐Know Act (EPCRA)
9.5.2 The Planning Committee
9.6 EP&R for Natural Disasters
9.7 Current and Future Trends
9.8 Applications
9.9 Chapter Summary
9.10 Problems
References
Chapter 10 Ethical Considerations within Virology
10.1 Core Ethics Principles
10.2 Important Tenets of Ethical Research
10.2.1 Conducting Research During a Health Crisis
10.2.2 Scientific Cooperation During a Health Crisis
10.2.3 Fair and Ethical Study Design and Implementation
10.3 Ethical Dilemmas in Public Health
10.3.1 Public Health Surveillance
10.3.2 Ethical Evaluation of Nonpharmaceutical Interventions
10.3.3 Ethical Consideration Involving Restrictions of Movement
10.4 Ethical Considerations Regarding Medical Interventions
10.4.1 Emergency Use Of Medical Interventions
10.5 Applications
10.6 Chapter Summary
10.7 Problems
References
Chapter 11 Health and Hazard Risk Assessment
11.1 Introduction to Risk Assessment
11.2 The Health Risk Assessment Process
11.3 Dose–Response Assessment
11.4 The Hazard Risk Assessment Process
11.5 Hazard Risk Versus Health Risk
11.5.1 Health Risk Assessment (HRA) Example
11.5.2 Hazard Risk Assessment (HRZA) Example
11.6 COVID‐19 Pandemic Hazard Risk
11.7 The Uncertainty Factor
11.8 Applications
11.9 Chapter Summary
11.10 Problems
References
Part III Engineering Considerations
Chapter 12 Introduction to Mathematical Methods
12.1 Differentiation
12.2 Integration
12.2.1 The Trapezoidal Rule
12.2.2 Simpson's Rule
12.3 Simultaneous Linear Algebraic Equations
12.3.1 Gauss–Jordan Reduction
12.3.2 Gauss Elimination
12.3.3 Gauss–Seidel Approach
12.4 Nonlinear Algebraic Equations
12.5 Ordinary Differential Equations
12.6 Partial Differential Equations
12.7 Applications
12.8 Chapter Summary
12.9 Problems
References
Chapter 13 Probability and Statistical Principles
13.1 Probability Definitions and Interpretations
13.2 Introduction to Probability Distributions
13.3 Discrete Probability Distributions
13.3.1 The Binomial Distribution
13.3.2 Multinomial Distribution
13.3.3 Hypergeometric Distribution
13.3.4 Poisson Distribution
13.4 Continuous Probability Distributions
13.4.1 Measures of Central Tendency and Scatter
13.4.2 The Normal Distribution
13.4.3 The Lognormal Distribution
13.4.4 The Exponential Distribution
13.4.5 The Weibull Distribution
13.5 Contemporary Statistics
13.5.1 Confidence Intervals for Means
13.5.2 Confidence Intervals for Proportions
13.5.3 Hypothesis Testing
13.5.4 Hypothesis Test for Means and Proportions
13.5.5 The F Distribution
13.5.6 Analysis of Variance (ANOVA)
13.5.7 Nonparametric Tests
13.6 Applications
13.7 Chapter Summary
13.8 Problems
References
Chapter 14 Linear Regression
14.1 Rectangular Coordinates
14.2 Logarithmic Coordinates
14.3 Methods of Plotting Data
14.4 Scatter Diagrams
14.5 Curve Fitting
14.6 Method of Least Squares
14.7 Applications
14.8 Chapter Summary
14.9 Problems
References
Chapter 15 Ventilation
15.1 Introduction to Industrial Ventilation Systems
15.2 Components of Ventilation Systems
15.3 Fans, Valves and Fittings, and Ductwork
15.3.1 Fans
15.3.2 Valves and Fittings
15.4 Selecting Ventilation Systems
15.5 Key Process Equations
15.5.1 Regarding Friction Losses
15.6 Ventilation Models
15.7 Model Limitations
15.8 Infection Control Implications
15.9 Applications
15.10 Chapter Summary
15.11 Problems
References
Chapter 16 Pandemic Health Data Modeling
16.1 COVID‐19: A Rude Awakening
16.2 Earlier Work
16.3 Planning for Pandemics
16.4 Generating Mathematical Models
16.5 Pandemic Health Data Models
16.6 In Review
16.7 Applications
16.8 Chapter Summary
16.9 Problems
References
Chapter 17 Optimization Procedures
17.1 The History of Optimization
17.2 The Scope of Optimization
17.3 Conventional Optimization Procedures
17.4 Analytical Fomulation of the Optimum
17.5 Contemporary Optimization: Concepts in Linear Programming
17.6 Applied Concepts in Linear Programming
17.7 Applications
17.8 Chapter Summary
17.9 Problems
References
Index
EULA