Contributors ................................................. xiii
Preface ........................................................ xv
1 Microarray Data Analysis Using Machine Learning Methods ...... 1
1.1 Introduction ............................................ 1
1.2 Machine Learning Methods ................................ 3
1.2.1 Neural Networks .................................. 4
1.2.2 Support Vector Machines .......................... 7
1.2.3 Fuzzy Systems .................................... 7
1.2.4 Genetic Algorithms ............................... 9
1.2.5 Particle Swarm Optimization ...................... 9
1.2.6 Steps in Developing Machine Learning Models ..... 10
1.3 Microarray Technology .................................. 13
1.3.1 cDNA Microarray ................................. 13
1.3.2 High-Density Oligonucleotide Array .............. 15
1.4 Low-Level Analysis ..................................... 16
1.5 High-Level Analysis .................................... 18
1.5.1 Clustering ...................................... 18
1.5.2 Classification .................................. 20
1.5.3 Genetic Network Modeling ........................ 21
1.6 Summary ................................................ 26
References .................................................. 27
Glossary of Terms ........................................... 31
2 Biosystems Analysis and Optimization ........................ 33
2.1 Introduction ........................................... 33
2.1.1 Definitions ..................................... 33
2.2 System Representation .................................. 34
2.2.1 Block Diagram Representation .................... 34
2.2.2 Mathematical Representation ..................... 36
2.2.3 The Laplace Transform ........................... 38
2.2.4 Nonlinearities .................................. 44
2.3 System Analysis ........................................ 47
2.3.1 Response of the System to a Step Input .......... 47
2.3.2 Magnitude and Phase of a Transfer Function ...... 48
2.3.3 Bode Diagram of Transfer Functions .............. 51
2.4 System Identification .................................. 57
2.4.1 Excitation Experiments .......................... 59
2.4.2 Evaluating Experimental Data .................... 60
2.4.3 Estimating Nonlinearities ....................... 62
2.4.4 Parameter Estimation ............................ 64
2.5 Feedback Controller Design ............................. 67
2.5.1 Feedback Control Structure ...................... 67
2.5.2 Stability ....................................... 68
2.5.3 Loop-Shaping Controller Design .................. 69
2.5.4 Controller Design Example: Depth Control for
Slurry Injection ................................ 73
2.6 Nonlinear Optimization Example: Cruise Control on
a Combine Harvester .................................... 75
2.6.1 Motivation ...................................... 76
2.6.2 System Description .............................. 77
2.6.3 Control Objective ............................... 77
2.6.4 System Modeling ................................. 78
2.6.5 Nonlinear MPC ................................... 83
2.6.6 Experimental Setup .............................. 86
2.6.7 Results ......................................... 86
References .................................................. 88
3 Soil and Water Conservation ................................. 91
3.1 Introduction ........................................... 91
3.2 Hydrological Cycle ..................................... 92
3.3 Precipitation .......................................... 96
3.3.1 Rainfall Measurement ............................ 97
3.3.2 Mean Areal Rainfall Depth ....................... 98
3.4 Evaporation and Evapotranspiration ..................... 99
3.4.1 Some Relevant Concepts and Terminology ......... 100
3.4.2 Energy Balance Method for Estimating
Evaporation .................................... 101
3.4.3 Dalton's Law ................................... 102
3.4.4 Pan Evaporation ................................ 103
3.4.5 Evapotranspiration ............................. 103
3.5 Infiltration and Runoff ............................... 104
3.5.1 Infiltration ................................... 105
3.5.2 Runoff ......................................... 107
3.5.3 SCS Curve Number Method ........................ 108
3.5.4 Rational Method ................................ 109
3.6 Soil Erosion and Sediment Transport ................... 110
3.6.1 Mechanics of Soil Detachment and Deposition .... 110
3.6.2 Factors Affecting Soil Erosion and Sediment
Yield .......................................... 112
3.6.3 Types of Soil Erosion .......................... 113
3.6.4 Universal Soil Loss Equation ................... 114
3.7 Best Management Practices ............................. 117
3.7.1 Commonly Used BMPs ............................. 118
References ................................................. 123
4 Models for Heat Transfer in Heated Substrates .............. 125
4.1 Heat Transfer in Soils ................................ 125
4.1.1 The Soil Thermal Regime ........................ 125
4.1.2 Factors Affecting Soil Temperature ............. 126
4.2 Soil Thermal Properties ............................... 128
4.2.1 Specific Heat or Heat Capacity ................. 128
4.2.2 Effective Thermal Conductivity ................. 128
4.2.3 Effective Thermal Diffusivity .................. 130
4.2.4 Determination of Soil Thermal Properties ....... 130
4.3 Models for Predicting Soil Temperature ................ 139
4.3.1 Applications of the Models for Predicting
Soil Temperature ............................... 139
4.3.2 Methods Used to Build Models for Predicting
Soil Temperature ............................... 142
4.4 Greenhouse Substrate Heating .......................... 146
4.5 Models for Predicting Temperature in Heated
Substrates ............................................ 148
4.6 An Analysis of Electric Cable Heating Systems ......... 154
References ................................................. 160
5 Geographic Information System-Based Watershed Modeling
Systems .................................................... 169
5.1 Introduction .......................................... 169
5.2 Watershed Models ...................................... 170
5.2.1 Need for Watershed Models ...................... 170
5.2.2 Origin of Watershed Models ..................... 171
5.2.3 Characterization of Watershed Models ........... 171
5.2.4 Important Components of Watershed Models ....... 172
5.2.5 Examples of Commonly Used Watershed Models ..... 175
5.3 Geographic Information Systems (GIS) .................. 181
5.4 GIS and Watershed Models .............................. 182
5.4.1 Approaches for Interfacing GIS with
Watershed Models ............................... 184
5.4.2 Challenges with Interfacing .................... 185
5.4.3 Recent State-of-the Art GIS-Integrated
Watershed Modeling Systems ..................... 186
5.5 Future of GIS-based Watershed Modeling Systems ........ 190
References ................................................. 191
6 Design of Sustainable Water Management Systems ............. 195
6.1 Introduction .......................................... 195
6.2 Physical Properties of Soil ........................... 196
6.3 Water Management ...................................... 197
6.3.1 Plant Water Relations .......................... 197
6.3.2 Assessing Plant Water Needs .................... 198
6.4 Need for Irrigation ................................... 200
6.4.1 Meeting the Crop Water Demand .................. 200
6.4.2 Other Benefits of Irrigation ................... 201
6.5 Irrigation Systems .................................... 202
6.5.1 Introduction ................................... 202
6.5.2 Types of Irrigation Systems .................... 202
6.5.3 Irrigation Efficiency .......................... 202
6.5.4 Design of Irrigation Systems ................... 202
6.6 Drainage Systems ...................................... 207
6.6.1 Importance of Drainage ......................... 207
6.6.2 Methods for Dealing with Excess Water .......... 207
6.7 Salinity Control ...................................... 209
6.7.1 Introduction to Salinization ................... 210
6.7.2 Methods to Control Salinization ................ 210
6.7.3 Dealing with Water Quality Issues .............. 211
6.8 Summary ............................................... 211
References ................................................. 211
7 Biomass Pyrolysis and Bio-Oil Refineries ................... 213
7.1 Introduction .......................................... 213
7.2 Biomass Composition ................................... 215
7.2.1 Cellulose ...................................... 215
7.2.2 Hemicellulose .................................. 216
7.2.3 Lignin ......................................... 216
7.2.4 Extractives .................................... 217
7.2.5 Ash ............................................ 217
7.3 Overview of Biomass Pyrolysis Reactions ............... 217
7.3.1 Mechanism of Primary Reactions ................. 218
7.4 Single-Particle Models ................................ 220
7.5 Pyrolysis Technologies ................................ 222
7.5.1 Slow Pyrolysis ................................. 222
7.5.2 Fast Pyrolysis ................................. 223
7.6 Crude Bio-Oils ........................................ 226
7.6.1 Chemical Composition of Crude Bio-Oils ......... 226
7.6.2 Fuel Applications of Crude Bio-Oils ............ 231
7.6.3 Producing Chemicals from Bio-Oils .............. 234
7.6.4 Production of Transportation Fuels ............. 238
7.7 Bio-Oil Refineries .................................... 240
7.8 Summary and Conclusions ............................... 242
References ................................................. 242
8 Performance and Emissions of Biodiesel and Ethanol in
Engines .................................................... 253
8.1 Introduction .......................................... 253
8.1.1 Transesterification of Vegetable Oils .......... 256
8.1.2 Analyzing the Products ......................... 257
8.1.3 Property Measurement of Transesterified Oils ... 258
8.1.4 Measurement of Performance and Emission ........ 260
8.1.5 Comparing the Effect of Loads on Biodiesel
Performance .................................... 260
8.1.6 Comparison of the Effect of Load on
Biodiesel Emission ............................. 261
8.1.7 Exhaust Gas Temperature ........................ 265
8.2 Ethanol as an Alternative Fuel ........................ 266
8.2.1 Production of Ethanol .......................... 267
8.2.2 Effect of Brake Power on Brake Thermal
Efficiency ..................................... 271
8.2.3 Effect of Brake Power on Brake-Specific
Diesel Fuel Consumption ........................ 272
8.2.4 Effect of Brake Power on Diesel Substitutions
at Various Ethanol Fumigation Rates ............ 273
8.2.5 Effect of Brake Power on NOx Emission Levels
at Various Ethanol Fumigation Rates ............ 274
8.2.6 Effect of Brake Power on CO Emissions at
Various Ethanol Fumigation Rates ............... 275
8.2.7 Effect of Brake Power on Smoke Number at
Various Ethanol Fumigation Rates ............... 276
8.2.8 Effect of Brake Power on Exhaust Gas
Temperatures at Various Ethanol Fumigation
Rates .......................................... 277
References ................................................. 278
9 Bioseparation Processes .................................... 281
9.1 Introduction .......................................... 281
9.2 Different Stages of Bioseparation Process ............. 282
9.3 Unit Operations in Bioseparation ...................... 284
9.3.1 Disruption of Cells ............................ 284
9.3.2 Centrifugal Separation ......................... 288
9.3.3 Thickening ..................................... 290
9.3.4 Flocculation ................................... 291
9.3.5 Filtration ..................................... 292
9.3.6 Evaporation .................................... 296
9.3.7 Drying and Crystallization ..................... 297
9.3.8 Chromatographic Techniques ..................... 300
9.3.9 Membrane Technology ............................ 305
Further Reading ............................................ 308
10 Food Safety Management ..................................... 309
10.1 Introduction .......................................... 309
10.2 Zoonotic Foodborne Hazards ............................ 310
10.3 Food Safety Measures .................................. 311
10.3.1 World Trade .................................... 311
10.3.2 European Trade ................................. 312
10.3.3 Food Safety Targets ............................ 314
10.4 Risk Analysis ......................................... 315
10.4.1 Stages in Risk Assessment ...................... 318
10.4.2 Methodologies .................................. 319
10.5 Perspective ........................................... 320
10.6 Conclusions ........................................... 320
References ................................................. 321
11 Food Package Engineering ................................... 325
11.1 Introduction .......................................... 325
11.2 Packaging Materials ................................... 326
11.2.1 Packaging Polymers ............................. 326
11.2.2 Glass Packaging ................................ 332
11.2.3 Metal Packaging ................................ 334
11.2.4 Paper and Paper-Based Packaging ................ 337
11.3 Physical Properties of Packaging Materials ............ 338
11.3.1 Mechanical Properties .......................... 339
11.3.2 Thermal Properties ............................. 340
11.3.3 Optical Properties ............................. 341
11.3.4 Properties of Mass Transport ................... 342
11.4 Recent Advances in Packaging .......................... 344
References ................................................. 346
12 Evaluation of Transgenic Wood for Wood Productivity and
Quality .................................................... 347
12.1 Introduction .......................................... 347
12.2 Overview of Transgenic Woods .......................... 348
12.2.1 Transgenic Trees ............................... 348
12.2.2 Challenges for Evaluation and Safety ........... 350
12.3 Productivity and Quality of Transgenic Wood ........... 351
12.3.1 Growth Rate .................................... 351
12.3.2 Physical and Mechanical Properties ............. 352
12.3.3 Chemical Composition ........................... 355
12.3.4 Durability ..................................... 358
12.3.5 Advanced Analysis Tools ........................ 359
12.3.6 Impacts on Process and Utilization ............. 363
12.4 Conclusions ........................................... 364
References ................................................. 364
13 Extraction, Refining, and Stabilization of Edible Oils ..... 367
13.1 Introduction .......................................... 367
13.2 Determining Oil Content in Oil Seeds and Its
Extraction ............................................ 369
13.2.1 Extracting Oil from Seeds ..................... 370
13.3 Refining Edible Oil ................................... 374
13.4 Bleaching and Deodorization ........................... 375
13.5 Stability of Edible Oils and Antioxidants ............. 379
13.5.1 Mechanism of Antioxidants ...................... 380
13.5.2 Functions of Antioxidants ...................... 382
13.5.3 Different Types of Antioxidants ................ 383
13.6 Measuring Antioxidant Activities ...................... 385
References ................................................. 389
14 Phenolic Substances from Olives (Olea europeae) and
Related Olive Mill Products ................................ 391
14.1 Introduction .......................................... 391
14.2 Olives and Relative Olive Mill Products ............... 392
14.3 Nature of Olive Polyphenols ........................... 394
14.4 Antioxidant and Nutraceutical Properties .............. 398
14.5 Future Biotechnological Applications .................. 400
References ................................................. 401
Effect of Exogenous Bioregulators on the Mineral
15 Composition and Storability of Fruits ...................... 405
15.1 Introduction .......................................... 405
15.1.1 Auxins and the Mineral Status of Fruits ........ 406
15.1.2 Exogenous Use of Gibberellins .................. 408
15.1.3 Retardants Are Also Bioregulators .............. 409
15.1.4 Effect of Retardants on the Mineral
Composition of Fruits .......................... 410
15.1.5 Effect of Retardants on Calcium Uptake ......... 412
15.2 Fruit Quality ......................................... 413
15.3 Influence of Retardant and Auxin Treatment of Apple
Shoots and Fruits on Calcium Uptake and
Distribution .......................................... 423
15.4 The Effect of Fruitlet Thinning Using Bioregulators
on Mineral Content and Storage Quality of Fruits ...... 429
15.5 The Influence of Thinning and Treatment with Calcium
Chloride on the Quality of McIntosh Apples Treated
with SADH ............................................. 437
15.5.1 Apple Size ..................................... 439
15.5.2 Red Color of Apples ............................ 440
15.5.3 Ground Color of Skin ........................... 440
15.5.4 Apple Firmness ................................. 440
15.5.5 Physiological Disorders of Apples during
Storage ........................................ 440
15.5.6 Chemical Composition of Apples ................. 442
References ................................................. 442
16 Supercritical Fluid Extraction Applications for
Biosystems Engineering ..................................... 447
16.1 Introduction .......................................... 447
16.2 Supercritical Mass-Transfer Mechanisms ................ 450
16.3 Carbon Dioxide Explosion Processes .................... 451
16.4 Biological Systems Applications ....................... 453
16.4.1 Fungal Production of Extractable Oils .......... 454
16.4.2 Extracting Oil from Rice Bran .................. 460
16.5 Summary and Future Trends ............................. 463
References ................................................. 463
17 Agriculture Management ..................................... 469
17.1 Introduction .......................................... 469
17.2 Modern Agriculture Systems ............................ 470
17.2.1 Land-Use Planning and Irrigation Management .... 470
17.2.2 Preparing and Testing the Soil ................. 470
17.2.3 Seed Testing ................................... 480
17.2.4 Agricultural Mechanization ..................... 483
17.2.5 Manure and Vermicomposting ..................... 485
17.2.6 Biological Control ............................. 499
17.2.7 Harvesting ..................................... 501
References ................................................ 502
Index ......................................................... 505
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