Contributors |
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xix | |
Preface |
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xxvii | |
Acknowledgments |
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xxxiii | |
Introduction |
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xxxv | |
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Chapter 1 Supervised Learning with the Artificial Neural Networks Algorithm for Modeling Immune Cell Differentiation |
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1 | (18) |
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1 | (4) |
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1.A Immune Cell Differentiation and Modeling |
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1 | (2) |
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1.B MSM and Model Reduction |
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3 | (1) |
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1.C ANN Algorithm and its Applications |
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4 | (1) |
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5 | (4) |
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3 Modeling Immune Cell Differentiation |
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9 | (5) |
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3.3 T Cell Differentiation Process as a use Case |
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9 | (1) |
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3.3 Data for Training and Testing Models |
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9 | (1) |
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9 | (2) |
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3.3 Comparative Analysis with the LR Model and SVM |
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11 | (2) |
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3.3 Capability of ANN Model to Analyze Data with Noise |
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13 | (1) |
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14 | (1) |
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15 | (4) |
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15 | (1) |
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16 | (3) |
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Chapter 2 Accelerating Techniques for Particle Filter Implementations on FPGA |
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19 | (20) |
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19 | (2) |
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21 | (4) |
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21 | (2) |
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2.2 Application of PF to SLAM |
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23 | (2) |
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3 Computational Bottleneck Identification and Hardware/software Partitioning |
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25 | (1) |
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4 PF Acceleration Techniques |
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26 | (4) |
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4.4 CORDIC Acceleration Technique |
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26 | (2) |
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4.4 Ziggurat Acceleration Technique |
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28 | (2) |
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5 Hardware Implementation |
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30 | (1) |
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6 Hardware/Software Architecture |
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31 | (3) |
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34 | (1) |
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35 | (4) |
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35 | (4) |
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Chapter 3 Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels |
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39 | (12) |
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39 | (2) |
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2 Formulation of the Problem |
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41 | (2) |
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43 | (2) |
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45 | (3) |
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48 | (3) |
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49 | (2) |
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Chapter 4 Hierarchical k-Means: A Hybrid Clustering Algorithm and its Application to Study Gene Expression in Lung Adenocarcinoma |
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51 | (18) |
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51 | (2) |
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53 | (4) |
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57 | (1) |
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57 | (7) |
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64 | (5) |
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65 | (2) |
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67 | (2) |
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Chapter 5 Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors |
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69 | (30) |
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69 | (2) |
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71 | (1) |
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3 Classification Algorithm |
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71 | (2) |
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73 | (1) |
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5 The EC of Entropy Production |
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74 | (1) |
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74 | (1) |
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7 Calculation Results and Discussion |
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75 | (18) |
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93 | (6) |
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94 | (1) |
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94 | (5) |
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Chapter 6 Review of Recent Protein-Protein Interaction Techniques |
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99 | (24) |
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99 | (1) |
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2 Technical Challenges and Open Issues |
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100 | (1) |
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101 | (1) |
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4 Computational Approaches |
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102 | (13) |
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4.4 Sequence-based Approaches |
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103 | (7) |
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4.4 Structure-based Approaches |
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110 | (5) |
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115 | (8) |
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116 | (7) |
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Chapter 7 Genetic Regulatory Networks: Focus on Attractors Of Their Dynamics |
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123 | (32) |
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123 | (1) |
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124 | (3) |
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2.2 The Immunetwork Responsible of the Toll-Like Receptor (TLR) expression |
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124 | (1) |
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2.2 The Links with the microRNAs |
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124 | (1) |
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2.2 The Adaptive Immunetworks |
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125 | (2) |
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3 The Iron Control Network |
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127 | (3) |
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130 | (3) |
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5 Biliary Atresia Control Network |
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133 | (4) |
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6 Conclusion and Perspectives |
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137 | (18) |
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138 | (1) |
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138 | (2) |
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140 | (2) |
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A3 Tangent and Intersecting Circuits |
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142 | (3) |
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A4 State-dependent Updating Schedule |
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145 | (1) |
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A5 The Circular Hamming Distance |
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146 | (1) |
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A6 The ArchetypaL Sequence AL |
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147 | (2) |
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149 | (1) |
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149 | (6) |
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Chapter 8 Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or Not? |
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155 | (14) |
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155 | (1) |
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156 | (3) |
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156 | (1) |
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2.2 Generation of Intact Finite Element Models |
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156 | (3) |
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159 | (5) |
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159 | (1) |
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3.3 Stress of the Anterolateral Column |
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160 | (1) |
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3.3 Peak Stress of the Residual Necrotic Bone |
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161 | (1) |
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162 | (2) |
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164 | (1) |
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165 | (1) |
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165 | (4) |
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165 | (1) |
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165 | (4) |
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Chapter 9 Diels-Alderase Catalyzing the Cyclization Step In the Biosynthesis of Spinosyn A: Reality or Fantasy? |
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169 | (34) |
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170 | (4) |
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174 | (1) |
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174 | (5) |
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179 | (4) |
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181 | (1) |
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181 | (2) |
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Supplementary Material: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy? |
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183 | (1) |
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1 Conformational Analysis of Macrocyclic Lactone (4) |
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183 | (1) |
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2 Modelling of a Theozyme for the Conversion of Macrocyclic Lactone (4) into Tricyclic Compound (5) |
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184 | (2) |
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3 ELF Bonding Analysis of the Conversion of Macrocyclic Lactone (4) Into the Tricyclic Compound (5) |
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186 | (17) |
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201 | (2) |
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Chapter 10 CLAST: Clustering Biological Sequences |
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203 | (18) |
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203 | (2) |
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204 | (1) |
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205 | (6) |
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205 | (1) |
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206 | (4) |
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210 | (1) |
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3 Evaluation and Discussion |
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211 | (8) |
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219 | (2) |
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220 | (1) |
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220 | (1) |
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Chapter 11 Computational Platform for Integration and Analysis of MicroRNA Annotation |
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221 | (14) |
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221 | (2) |
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223 | (2) |
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225 | (1) |
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226 | (1) |
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227 | (1) |
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227 | (4) |
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231 | (4) |
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232 | (3) |
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Chapter 12 Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming |
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235 | (30) |
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235 | (2) |
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2 LP Formulation of Separability |
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237 | (2) |
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239 | (1) |
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240 | (7) |
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4.4 Incremental Approach---2D |
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241 | (2) |
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4.4 Incremental Approach---3D |
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243 | (1) |
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4.4 Linear Programming Formulation of Unger and Chor's Incremental Algorithm |
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244 | (3) |
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247 | (1) |
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247 | (1) |
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6 A New Methodology for Gene Selection |
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248 | (1) |
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248 | (1) |
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249 | (1) |
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249 | (13) |
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262 | (3) |
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263 | (1) |
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263 | (2) |
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Chapter 13 The Big ORF Theory: Algorithmic, Computational, and Approximation Approaches to Open Reading Frames in Short- and Medium-Length dsDNA Sequences |
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265 | (10) |
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265 | (1) |
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2 Molecular Genetic and Bioinformatic Considerations |
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266 | (1) |
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2.2 Molecular Genetics of DNA →RNA →Protein |
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266 | (1) |
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2.2 Bioinformatic Data-mining |
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267 | (1) |
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3 Algorithmic and Programming Considerations |
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267 | (2) |
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4 Analytical and Random Sampling Solutions to L>25 Sequences: Triplet-based Approximations |
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269 | (2) |
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5 Alternative Genetic Codes |
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271 | (1) |
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6 Implications for the Evolution of ORF Size |
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272 | (3) |
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273 | (1) |
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273 | (2) |
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Chapter 14 Intentionally Linked Entities: A Detailed Look At a Database System for Health Care Informatics |
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275 | (20) |
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275 | (3) |
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2 Introducing ILE for Health Care Applications |
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278 | (3) |
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3 ILE and Epidemiological Data Modeling |
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281 | (2) |
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4 Other Nonrelational Approaches to Keeping Medical Records |
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283 | (3) |
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5 Inside the ILE Database System |
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286 | (6) |
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6 An Example of the Importance of An EHR Implemented in ILE |
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292 | (1) |
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292 | (3) |
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293 | (1) |
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293 | (2) |
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Chapter 15 Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction |
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295 | (12) |
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295 | (1) |
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296 | (1) |
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296 | (2) |
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298 | (4) |
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298 | (3) |
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4.4 A Region-based-Prediction Methodology |
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301 | (1) |
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302 | (2) |
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6 Conclusions and Future Research |
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304 | (3) |
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305 | (2) |
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Chapter 16 Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding |
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307 | (18) |
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307 | (2) |
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309 | (7) |
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309 | (4) |
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2.2 Phoneme Recognition Session |
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313 | (2) |
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315 | (1) |
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316 | (1) |
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316 | (1) |
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316 | (1) |
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317 | (1) |
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317 | (5) |
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4.4 Source Localization (PCL) |
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317 | (3) |
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320 | (1) |
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321 | (1) |
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4.4 Simulation with Normal Hearing Listeners |
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321 | (1) |
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322 | (3) |
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322 | (1) |
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323 | (2) |
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Chapter 17 Lowering the Fall Rate of the Elderly From Wheelchairs |
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325 | (10) |
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325 | (1) |
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1.1 The Fundamental Problem |
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325 | (1) |
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326 | (1) |
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326 | (2) |
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328 | (1) |
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329 | (2) |
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331 | (1) |
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6 Assessment Decision Algorithm |
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331 | (1) |
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332 | (1) |
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333 | (2) |
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333 | (1) |
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333 | (2) |
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Chapter 18 Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness |
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335 | (20) |
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335 | (1) |
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335 | (1) |
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335 | (1) |
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336 | (1) |
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337 | (1) |
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337 | (1) |
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338 | (2) |
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8 The Grand Average Occipital and Temporal Electrical Activity Correlated with a Contrast in Access |
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340 | (2) |
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340 | (2) |
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342 | (2) |
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10 The Grand Average Occipital and Temporal Electrical Activity Correlated with a Contrast in Phenomenology |
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344 | (6) |
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11 The Grand Average Occipital and Temporal Electrical Activity Co-occurring with Unconsciousness |
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350 | (5) |
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354 | (1) |
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354 | (1) |
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Chapter 19 Chaotic Dynamical States in the Izhikevich Neuron Model |
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355 | (22) |
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355 | (1) |
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2 Fundamental Description |
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356 | (5) |
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356 | (2) |
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2.2 Izhikevich Neuron Model |
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358 | (3) |
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3 Chaotic Properties of Izhikevich Neuron Model |
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361 | (5) |
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361 | (1) |
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3.3 Chaotic Behaviors in Izhikevich Neuron Model |
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362 | (4) |
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4 Response Efficiency in Chaotic Resonance |
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366 | (6) |
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4.4 Extended Izhikevich Neuron Model with a Periodic Signal |
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367 | (1) |
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4.4 Dependence on Parameter d |
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368 | (3) |
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4.4 Dependence on Signal Strength A |
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371 | (1) |
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372 | (5) |
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373 | (4) |
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Chapter 20 Analogy, Mind, and Life |
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377 | (12) |
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377 | (1) |
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2 The Artificial Mind and Cognitive Science |
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377 | (1) |
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378 | (4) |
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4 The Classic Watchmaker Analogy |
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382 | (1) |
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5 The Classic Watchmaker Analogy Is Fragile, Remote and Reductive |
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383 | (1) |
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6 The Analogy Between Life and Information Seems to Suggest Some Type of Reductionism |
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384 | (1) |
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385 | (4) |
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387 | (1) |
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387 | (2) |
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Chapter 21 Copy Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative Disorders |
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389 | (20) |
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389 | (1) |
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2 A Diminishing Drug Pipeline |
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389 | (1) |
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3 Using Genome Data to Replenish the Pipeline by Drug Repositioning |
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390 | (1) |
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4 The Small-world Properties of Networks Expedite Combination Therapies |
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390 | (1) |
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5 Molecular Networks can be Used to Guide Drug Combinations |
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391 | (1) |
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6 Copy Number Alterations as a Disease Driver |
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391 | (1) |
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7 Using Correlated Copy Number Alterations to Construct Survival Networks |
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392 | (1) |
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8 A Pan-cancer CNA Interaction Network |
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392 | (1) |
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9 Mapping Genetic Survival Networks Using Correlated CNAs in Radiation Hybrid Cells |
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393 | (1) |
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10 A Survival Network for GBM At Single-gene Resolution |
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393 | (1) |
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11 Using CNA Networks to Guide Combination Therapies |
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394 | (1) |
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12 Targeting Multiple Drugs to Single-disease Genes in Cancer |
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395 | (3) |
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13 Targeting Multiple Drugs to a Single-disease Gene in Autoimmunity |
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398 | (1) |
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14 Targeting Multiple Genes in a Single Pathway for Cancer |
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399 | (1) |
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15 Targeting Genes in Parallel Pathways Converging on Atherosclerosis |
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400 | (1) |
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16 Using CNA Networks to Synergize Drug Combinations and Minimize Side Effects |
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401 | (1) |
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401 | (8) |
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401 | (1) |
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401 | (8) |
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Chapter 22 DNA Double-Strand Break--Based Nonmonotonic Logic |
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409 | (20) |
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409 | (1) |
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410 | (2) |
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3 Logical Model for System Biology |
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412 | (5) |
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3.3 Declarative Representation of Signaling Pathway |
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412 | (1) |
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413 | (1) |
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3.3 Causality and Classical Inference |
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414 | (1) |
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3.3 Causality and Nonmonotonic Logics |
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415 | (1) |
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415 | (1) |
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3.3 Extensions and Choice of Extensions |
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416 | (1) |
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4 Completing the Signaling Pathways by Default Abduction |
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417 | (1) |
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5 Logic Representation of a Signaling Pathway with the Goal of Reducing Computational Complexity |
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418 | (4) |
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5.5 Clauses and Horn Clauses |
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419 | (1) |
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420 | (1) |
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5.5 Hard Rules and Default Rules |
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421 | (1) |
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5.5 Cell Signaling Pathway Representation |
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421 | (1) |
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6 Algorithm and Implementation |
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422 | (1) |
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423 | (2) |
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425 | (4) |
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426 | (3) |
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Chapter 23 An Updated Covariance Model for Rapid Annotation of Noncoding RNA |
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429 | (8) |
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429 | (1) |
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430 | (2) |
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430 | (1) |
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430 | (1) |
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2.2 Sequence-structure Alignment |
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431 | (1) |
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2.2 Computing the Length Restrictions |
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431 | (1) |
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432 | (1) |
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433 | (4) |
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434 | (3) |
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Chapter 24 SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core |
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437 | (18) |
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437 | (2) |
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439 | (2) |
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441 | (10) |
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441 | (1) |
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442 | (1) |
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443 | (2) |
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3.3 Use Case and Discussion |
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445 | (6) |
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451 | (4) |
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452 | (1) |
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452 | (3) |
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Chapter 25 Predicting Extinction of Biological Systems with Competition |
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455 | (12) |
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455 | (2) |
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2 A Model of Competing Species |
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457 | (1) |
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3 Density Function of Extinction Time |
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458 | (2) |
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4 Estimation of Parameters |
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460 | (1) |
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461 | (3) |
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464 | (3) |
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464 | (1) |
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464 | (3) |
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Chapter 26 Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson's Disease with Bayesian Belief Networks |
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467 | (20) |
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467 | (1) |
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468 | (7) |
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2.2 Data Acquisition and Preparation |
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469 | (3) |
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2.2 Causality and Methodology |
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472 | (1) |
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473 | (1) |
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2.2 Results and Discussion |
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474 | (1) |
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3 Diagnosis of Handwriting and Speech |
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475 | (3) |
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3.3 Experimental Protocol |
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476 | (1) |
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476 | (2) |
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4 Toward a Global Methodology for PD |
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478 | (3) |
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4.4 Handwriting and Speech Link |
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478 | (1) |
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4.4 Results and Discussion |
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479 | (2) |
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5 Conclusions and Future Work |
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481 | (6) |
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482 | (5) |
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Chapter 27 Practical Considerations in Virtual Screening and Molecular Docking |
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487 | (16) |
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487 | (1) |
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2 Receptor Structure Preparation |
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488 | (3) |
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488 | (2) |
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2.2 Selecting Important Active Site Water Molecules |
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490 | (1) |
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3 Accurately Predicting the Pose of Solved Crystal Structures and Differentiating Decoys From Actives |
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491 | (1) |
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4 Side-chain Flexibility and Ensemble Docking |
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492 | (1) |
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493 | (1) |
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494 | (2) |
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7 Incorporating Pharmacophoric Constraints Within the Virtual Screen |
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496 | (1) |
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496 | (7) |
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497 | (6) |
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Chapter 28 Knowledge Discovery in Proteomic Mass Spectrometry Data |
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503 | (18) |
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503 | (1) |
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504 | (1) |
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505 | (8) |
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505 | (7) |
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3.3 Identification of Biomarker Candidates |
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512 | (1) |
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513 | (4) |
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513 | (3) |
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4.4 KD3 Functional Object |
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516 | (1) |
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516 | (1) |
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517 | (4) |
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517 | (4) |
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Chapter 29 A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data |
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521 | (16) |
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521 | (1) |
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2 Mapping and Calling Software |
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522 | (2) |
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522 | (1) |
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522 | (1) |
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2.2 Smith-Waterman Algorithm |
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523 | (1) |
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2.2 Dindel Indel Calling Model |
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524 | (1) |
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524 | (3) |
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524 | (2) |
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526 | (1) |
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527 | (1) |
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527 | (1) |
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528 | (6) |
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5.5 Analysis of F1-score and Coverage on Simulated Data |
|
|
528 | (1) |
|
5.5 Precision and Recall on Simulated Data with Smaller and Longer Indels |
|
|
529 | (2) |
|
5.5 Effect of Read Length on Simulated Data |
|
|
531 | (1) |
|
5.5 Accuracy of Sanger Real Data |
|
|
531 | (1) |
|
5.5 Run-time Performance on Sanger Data |
|
|
531 | (1) |
|
5.5 Accuracy of 1000 Genomes Real Data |
|
|
531 | (3) |
|
|
534 | (3) |
|
|
534 | (3) |
|
Chapter 30 Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites |
|
|
537 | (24) |
|
|
537 | (1) |
|
|
538 | (8) |
|
2.2 Methodology Description |
|
|
539 | (1) |
|
2.2 Stage 1: MRS Signal Preprocessing |
|
|
539 | (6) |
|
2.2 Stage 2: GA Quantification |
|
|
545 | (1) |
|
|
546 | (12) |
|
3.3 Scenario 1: Complete Prior Knowledge |
|
|
549 | (1) |
|
3.3 Scenario 2: Limited Prior Knowledge |
|
|
550 | (8) |
|
|
558 | (3) |
|
|
559 | (1) |
|
|
559 | (2) |
|
Chapter 31 Keratoconus Disease and Three-Dimensional Simulation of the Cornea Throughout the Process of Cross-Linking Treatment |
|
|
561 | (16) |
|
|
561 | (3) |
|
|
564 | (7) |
|
|
564 | (1) |
|
|
564 | (7) |
|
3 Conclusions and Recommendations |
|
|
571 | (6) |
|
|
574 | (1) |
|
|
574 | (3) |
|
Chapter 32 Emerging Business Intelligence Framework for a Clinical Laboratory Through Big Data Analytics |
|
|
577 | (26) |
|
|
577 | (1) |
|
|
578 | (1) |
|
|
579 | (5) |
|
|
579 | (1) |
|
|
579 | (1) |
|
3.3 The Hadoop Distributed File System |
|
|
580 | (1) |
|
3.3 The Emerging Framework |
|
|
580 | (2) |
|
3.3 Laboratory Management System Components |
|
|
582 | (1) |
|
3.3 Lab Management Application Interface |
|
|
583 | (1) |
|
3.3 Administration Services |
|
|
583 | (1) |
|
3.3 Test Procedure Services |
|
|
583 | (1) |
|
3.3 Operational Management Services |
|
|
583 | (1) |
|
3.3 Service Infrastructure-Hadoop Platform and Hadoop Enabled Automated Laboratory Transformation Hub (HEALTH) Cluster |
|
|
583 | (1) |
|
3.3 Data Warehouse Management Service |
|
|
583 | (1) |
|
3.3 Ubuntu Juju as a Service Orchestration and Bundling |
|
|
584 | (1) |
|
3.3 Typical Framework Usage Scenario in a Clinical Laboratory Setting |
|
|
584 | (1) |
|
|
584 | (1) |
|
5 Case Study 1: Clinical Laboratory Test Usage Patterns Visualization |
|
|
585 | (1) |
|
6 Data Source and Methodology |
|
|
585 | (2) |
|
|
587 | (1) |
|
|
588 | (1) |
|
9 Case Study 2: Provincial Laboratory Clinical Test Volume Estimation |
|
|
589 | (1) |
|
10 Data Source and Methodology |
|
|
589 | (5) |
|
|
589 | (1) |
|
|
590 | (2) |
|
|
592 | (1) |
|
10.10 ARIMA Model Selection |
|
|
592 | (2) |
|
10.10 Performance Comparison and Model Selection |
|
|
594 | (1) |
|
11 Results and Discussion |
|
|
594 | (4) |
|
|
598 | (1) |
|
13 Conclusion and Future Work |
|
|
598 | (5) |
|
|
599 | (4) |
|
Chapter 33 A Codon Frequency Obfuscation Heuristic for Raw Genomic Data Privacy |
|
|
603 | (18) |
|
|
603 | (1) |
|
|
603 | (1) |
|
|
604 | (2) |
|
|
606 | (4) |
|
|
610 | (6) |
|
|
616 | (5) |
|
|
618 | (3) |
Index |
|
621 | |