| Acknowledgments |
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xi | |
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3 | (10) |
| PART I: BACKGROUND |
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13 | (9) |
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14 | (1) |
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Specific Immunity: Antigens and Epitopes |
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15 | (1) |
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16 | (3) |
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19 | (1) |
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20 | (2) |
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Benefits of Antigenic Variation |
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22 | (11) |
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Extend Length of Infection |
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23 | (1) |
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Infect Hosts with Prior Exposure |
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24 | (2) |
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Infect Hosts with Genetically Variable Resistance |
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26 | (1) |
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Vary Attachment Characters |
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26 | (2) |
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28 | (1) |
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Problems for Future Research |
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29 | (4) |
| PART II: MOLECULAR PROCESSES |
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Specificity and Cross-Reactivity |
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33 | (24) |
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Antigens and Antibody Epitopes |
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35 | (1) |
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36 | (2) |
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Antibody Affinity Maturation |
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38 | (1) |
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Natural Antibodies---Low-Affinity Binding to Diverse Antigens |
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39 | (1) |
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Affinity versus Specificity |
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40 | (2) |
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Cross-Reaction of Polyclonal Antibodies to Divergent Antigens |
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42 | (2) |
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44 | (8) |
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52 | (2) |
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Problems for Future Research |
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54 | (3) |
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57 | (16) |
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Mutation and Hypermutation |
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58 | (3) |
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Stochastic Switching between Archival Copies |
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61 | (5) |
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New Variants by Intragenomic Recombination |
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66 | (1) |
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67 | (1) |
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Problems for Future Research |
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68 | (5) |
| PART III: INDIVIDUAL INTERACTIONS |
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Immunodominance within Hosts |
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73 | (20) |
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74 | (5) |
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79 | (8) |
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Sequence of Exposure to Antigens: Original Antigenic Sin |
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87 | (2) |
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Problems for Future Research |
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89 | (4) |
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Parasite Escape within Hosts |
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93 | (18) |
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Natural Selection of Antigenic Variants |
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94 | (3) |
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Pathogen Manipulation of Host Immune Dynamics |
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97 | (1) |
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Sequence of Variants in Active Switching from Archives |
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98 | (4) |
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Ecological Coexistence of Variants within a Host |
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102 | (4) |
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Problems for Future Research |
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106 | (5) |
| PART IV: POPULATION CONSEQUENCES |
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Genetic Variability of Hosts |
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111 | (13) |
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Polymorphisms in Specificity |
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112 | (3) |
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Polymorphisms in Immune Regulation |
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115 | (6) |
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Problems for Future Research |
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121 | (3) |
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Immunological Variability of Hosts |
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124 | (24) |
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125 | (4) |
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129 | (3) |
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Immunodominance of Memory |
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132 | (3) |
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Cross-Reactivity and Interference |
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135 | (1) |
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Distribution of Immune Profiles among Hosts |
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136 | (8) |
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Problems for Future Research |
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144 | (4) |
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Genetic Structure of Parasite Populations |
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148 | (27) |
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Kinds of Genetic Structure |
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149 | (2) |
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151 | (2) |
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Genome-wide Linkage Disequilibrium |
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153 | (11) |
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Antigenic Linkage Disequilibrium |
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164 | (2) |
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Population Structure: Hosts as Islands |
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166 | (2) |
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Problems for Future Research |
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168 | (7) |
| PART V: STUDYING EVOLUTION |
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Classifications by Antigenicity and Phylogeny |
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175 | (13) |
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Immunological Measures of Antigenicity |
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176 | (2) |
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178 | (1) |
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Hypothetical Relations between Immunology and Phylogeny |
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179 | (2) |
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Immunology Matches Phylogeny over Long Genetic Distances |
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181 | (1) |
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Immunology-Phylogeny Mismatch with Radiations into New Hosts |
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181 | (2) |
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Short-Term Phylogenetic Diversification Driven by Immunological Selection |
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183 | (1) |
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Discordant Patterns of Phylogeny and Antigenicity Created by Within-Host Immune Pressure |
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183 | (3) |
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Problems for Future Research |
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186 | (2) |
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Experimental Evolution: Foot-and-Mouth Disease Virus |
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188 | (17) |
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Overview of Antigenicity and Structure |
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189 | (3) |
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192 | (4) |
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196 | (4) |
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Fitness Consequences of Substitutions |
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200 | (2) |
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Problems for Future Research |
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202 | (3) |
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Experimental Evolution: Influenza |
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205 | (25) |
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Overview of Antigenicity and Structure |
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206 | (8) |
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214 | (2) |
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216 | (2) |
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Fitness Consequences of Substitutions |
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218 | (6) |
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Experimental Evolution of Other Pathogens |
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224 | (3) |
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Problems for Future Research |
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227 | (3) |
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Experimental Evolution: CTL Escape |
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230 | (16) |
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Cleavage and Transport of Peptides |
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231 | (1) |
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232 | (5) |
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237 | (2) |
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Functional Consequences of Escape |
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239 | (1) |
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240 | (3) |
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Problems for Future Research |
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243 | (3) |
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Measuring Selection with Population Samples |
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246 | (19) |
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Kinds of Natural Selection |
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247 | (2) |
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Positive Selection to Avoid Host Recognition |
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249 | (2) |
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Phylogenetic Analysis of Nucleotide Substitutions |
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251 | (4) |
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255 | (5) |
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Problems for Future Research |
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260 | (5) |
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Recap of Some Interesting Problems |
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265 | (4) |
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Population-Level Explanation for Low Molecular Variability |
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265 | (1) |
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Molecular-Level Explanation for Population Dynamics |
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266 | (1) |
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Binding Kinetics and the Dynamics of Immunodominance |
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266 | (1) |
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Diversity and Regulation of Archival Repertoires |
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267 | (1) |
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268 | (1) |
| References |
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269 | (44) |
| Author Index |
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313 | (24) |
| Subject Index |
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337 | |