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1 Basics of Microbiology for Civil and Environmental Engineers |
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1 | (22) |
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1.1 References for the
Chapter |
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1 | (1) |
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1 | (1) |
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1.3 Groups of Microorganisms |
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2 | (1) |
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1.4 Cells of Microorganisms |
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2 | (1) |
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1.5 Microbial Populations and Communities |
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3 | (1) |
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1.6 Phenotypic Classifications and Identification of Microorganisms |
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3 | (1) |
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1.7 Phylogenetic (Genotyping) Classification and Identification of Prokaryotes |
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4 | (1) |
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1.8 Physiological Classification of Prokaryotes Using Periodic Table |
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5 | (1) |
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1.9 Three Types of Chemotrophic Energy Generation |
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6 | (1) |
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1.10 Three Sources of Origin of Prokaryotes |
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6 | (1) |
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1.11 Nine Physiological Groups of Chemotrophic Prokaryotes |
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7 | (1) |
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1.12 Additional Periodic Table of Phototrophic Prokaryotes |
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7 | (1) |
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1.13 Classification and Identification of Fungi |
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7 | (2) |
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1.14 Classification and Identification of Algae |
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9 | (1) |
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1.15 Classification and Identification of Protozoa |
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9 | (1) |
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1.16 Enzymes as the Catalysts of Biochemical Reactions |
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9 | (1) |
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1.17 Velocity of Biochemical Reaction |
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10 | (1) |
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1.18 Control of the Enzymatic Reaction Rate |
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11 | (1) |
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1.19 The Role of Enzyme Kinetics in Engineering |
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11 | (1) |
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1.20 Induction, Repression and Feed-Back Control of Enzymatic Activity |
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12 | (1) |
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1.21 The Types of Biogeochemical Reactions |
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12 | (1) |
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1.22 Biogeochemical Reactions that Can be Used for Production of Construction Materials and for Construction Processes in Situ |
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13 | (1) |
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13 | (3) |
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1.24 Biosafety in Construction Biotechnology |
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16 | (1) |
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1.25 Disinfection in Construction Biotechnology |
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17 | (1) |
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1.26 Theoretical Screening of Microorganisms for Construction Biotechnology |
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17 | (1) |
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1.27 Use of Anaerobic Fermenting Bacteria in Construction Biotechnology |
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18 | (1) |
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1.28 Use of Anaerobically Respiring (Anoxic) Bacteria in Construction Biotechnology |
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18 | (1) |
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1.29 Use of Facultative Anaerobic and Microaerophilic Bacteria in Construction Biotechnology |
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19 | (1) |
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1.30 Use of Aerobic Bacteria in Construction Biotechnology |
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20 | (1) |
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1.31 Use of Anaerobic Bacteria in Construction Biotechnology |
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21 | (1) |
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1.32 The Major Groups of Bacteria Suitable for Construction Biotechnology Processes |
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21 | (2) |
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2 Basics of Biotechnology for Civil and Environmental Engineers |
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23 | (18) |
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2.1 References for the
Chapter |
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23 | (1) |
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23 | (1) |
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2.2 Applicability of Construction Biotechnology |
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24 | (1) |
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2.3 Bioprocesses Used in Construction Biotechnology |
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24 | (1) |
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2.4 The Stages of Biotechnological Process |
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25 | (1) |
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2.5 Upstream Processes in Construction Biotechnology |
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26 | (1) |
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2.6 Upstream: Pretreatment of Raw Materials |
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26 | (1) |
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2.7 Upstream: Preparation of a Medium for Cultivation |
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26 | (1) |
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2.8 Upstream: Components of Medium |
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27 | (1) |
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2.9 Upstream: Isolation and Selection of Microbial Strain (Pure Culture) for Bioprocess |
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28 | (1) |
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2.10 Upstream: Acquiring of Microbial Strain from Collection |
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28 | (1) |
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2.11 Upstream: Selection of an Enrichment Culture |
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29 | (1) |
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2.12 Upstream: Selection of an Ecosystem |
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30 | (1) |
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2.13 Upstream: Construction of Genetically Engineered Microorganisms |
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30 | (1) |
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2.14 Upstream: Preparation of Inoculum |
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31 | (1) |
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2.15 Core Biotechnological Process: Batch Cultivation of Microorganisms in Bioreactor |
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32 | (1) |
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2.16 Core Biotechnological Process: Batch Cultivation of Introduced Microorganisms in Soil |
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33 | (2) |
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2.17 Core Biotechnological Process: Batch Cultivation of Indigenous Microorganisms in Soil |
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35 | (1) |
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2.18 Core Biotechnological Process: Continuous Cultivation of Microorganisms in Bioreactor |
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35 | (1) |
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2.19 Core Biotechnological Process: Continuous Cultivation of Microorganisms in Soil |
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36 | (2) |
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2.20 Downstream Processes |
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38 | (1) |
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2.21 Downstream: Separation and Concentration of Biomass |
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38 | (1) |
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2.22 Downstream: Aggregates of Cells |
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38 | (1) |
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2.23 Downstream: Separation and Concentration of Products |
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39 | (1) |
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2.24 Downstream: Drying, Mixing and Packing of Biotechnological Products |
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40 | (1) |
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3 Biotechnological Admixtures for Cement and Mortars |
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41 | (10) |
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3.1 The Types of Biopolymers |
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41 | (1) |
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3.2 Structural and Metabolically Active Biopolymers |
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41 | (1) |
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3.3 Historical Use of Biopolymers in Construction |
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42 | (1) |
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3.4 The Bioadmixtures for Cement |
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43 | (1) |
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3.5 Applications of Microbial Polysaccharides as Bioadmixtures |
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43 | (2) |
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3.6 Effect of Biopolymers on Cement Hydration |
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45 | (1) |
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3.7 Microbial Polysaccharides as Viscosity-Modifying Admixtures |
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45 | (1) |
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3.8 Pseudoplasticity of Microbial Polysaccharides |
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46 | (1) |
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3.9 Biotechnological Water and Permeability Reducers |
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46 | (1) |
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3.10 Industrial Biotechnology Wastes as Admixture |
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47 | (1) |
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3.11 Biotechnological Production of Polysaccharide Admixtures |
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47 | (2) |
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3.12 Low Cost Biotechnological Admixtures |
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49 | (1) |
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3.13 Biotechnological Production of Biopolymers on Biorefineries |
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50 | (1) |
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4 Construction Biotechnological Plastics |
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51 | (26) |
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4.1 Bio-Based and Biodegradable Plastics |
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51 | (1) |
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4.2 Biotechnologically Produced Biodegradable Bioplastics |
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52 | (1) |
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4.3 Biotechnological Production of Biodegradable Bioplastics for Construction |
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53 | (1) |
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4.4 Cost-Efficient Production of PHAs |
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54 | (1) |
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4.5 Crude PHAs Composite Material |
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55 | (1) |
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4.6 Biotechnological Production of Polylactic Acid |
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55 | (1) |
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4.7 Biorefinery as a Facility Producing Bioplastics for Construction Industry |
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56 | (3) |
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4.8 PHAs Production from Municipal Solid and Liquid Wastes |
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59 | (1) |
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4.9 Municipal Solid Wastes (MSW) as a Resource for Bioplastics Production |
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60 | (1) |
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4.10 Use of Non-carbohydrates for PHA Accumulation |
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61 | (1) |
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4.11 Acidogenic Fermentation as First Step of Bioplastic Production of PHAs |
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61 | (3) |
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4.12 Transformation of Volatile Fatty Acids to Bioplastic |
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64 | (2) |
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66 | (1) |
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4.14 Cost of Bioplastics Production |
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66 | (1) |
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4.15 Biodegradability of Biotechnologically Produced Bioplastics |
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67 | (1) |
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4.16 Environmental Impacts of Bioplastics |
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68 | (1) |
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4.17 Applicability of Crude PHAs |
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69 | (2) |
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4.18 The Applications of PHAs in Construction |
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71 | (1) |
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4.19 The Applications of PLA in Construction |
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72 | (1) |
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4.20 Advantages of Construction Biodegradable Bioplastics |
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73 | (1) |
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4.21 Composite and Blended Bioplastic Materials |
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73 | (4) |
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5 Biogeochemical Basis of Construction Bioprocesses |
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77 | (14) |
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5.1 The Functions of Microorganisms in Hydrosphere and Lithosphere |
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77 | (1) |
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5.2 The Biogeochemical Carbon Cycle |
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78 | (1) |
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5.3 Applications of the Biogeochemical Carbon Cycle in Construction Bioprocesses |
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79 | (1) |
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5.4 The Biogeochemical Nitrogen Cycle |
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80 | (1) |
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5.5 Applications of the Biogeochemical Nitrogen Cycle in Construction Bioprocesses |
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80 | (2) |
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5.6 The Biogeochemical Phosphorus Cycle |
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82 | (1) |
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5.7 The Biogeochemical Sulfur Cycle |
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82 | (1) |
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5.8 Applications of the Biogeochemical Sulfur Cycle in Construction Bioprocesses |
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83 | (1) |
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5.9 The Biogeochemical Iron Cycle |
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83 | (3) |
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5.10 Applications of the Biogeochemical Iron Cycle in Construction Bioprocesses |
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86 | (2) |
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5.11 The Biogeochemical Cycle of Calcium |
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88 | (1) |
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5.12 Applications of the Biogeochemical Cycle of Calcium in Construction Bioprocesses |
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88 | (1) |
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5.13 The Biogeochemical Cycle of Magnesium |
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89 | (1) |
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5.14 Applications of the Biogeochemical Cycle of Magnesium in Construction Bioprocesses |
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89 | (1) |
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5.15 The Biogeochemical Cycle of Silicon |
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90 | (1) |
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5.16 Applications of the Biogeochemical Cycle of Silicon in Construction Bioprocesses |
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90 | (1) |
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6 Biotechnological Improvement of Construction Ground and Construction Materials |
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91 | (18) |
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6.1 The Stages of Biotechnological Improvement of Ground |
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91 | (2) |
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6.2 The Types of Construction Biotechnological Processes |
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93 | (2) |
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6.3 Bioaggregation to Control Wind Soil Erosion and Dust Emission |
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95 | (1) |
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6.4 Dust Control Technologies |
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95 | (1) |
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6.5 Biotechnological Methods for Dust and Wind Erosion Control |
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96 | (1) |
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6.6 Biotechnological Control of Air-Born Movement of Sand Dust and Dust-Associated Chemical and Bacteriological Pollutants |
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97 | (1) |
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97 | (1) |
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6.8 Formation of Soil Crust by Filamentous and Photosynthetic Microorganisms |
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98 | (2) |
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6.9 Biocrusting Using Microbial Polysaccharides |
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100 | (1) |
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6.10 Biocrusting Using Calcium-Based Biocementation |
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100 | (1) |
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101 | (2) |
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6.12 Biocementation of Soil |
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103 | (1) |
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6.13 Biodesaturation of Water-Saturated Cohesionless Soil |
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103 | (1) |
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6.14 Bioencapsulation of Soft Soil |
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104 | (1) |
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6.15 Bioimmobilization of the Pollutants in Soil |
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105 | (1) |
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106 | (1) |
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6.17 Comparison of the Different Mechanisms of Ground Improvement |
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107 | (2) |
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7 Biocementation and Biocements |
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109 | (30) |
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7.1 Calcium-Based Microbial Cementation in Nature |
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109 | (1) |
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7.2 Calcium-Based Cementation in Macroorganisms |
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109 | (1) |
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7.3 Urease-Dependent, Calcium-Based Microbial Cementation (MICP) in Engineering |
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110 | (2) |
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112 | (1) |
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7.5 Use of Urease for MICP |
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112 | (1) |
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7.6 Bacteria Used in MICP |
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113 | (1) |
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7.7 Comparison of the Strains |
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113 | (2) |
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7.8 Selection of Enrichment Culture of UPB |
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115 | (1) |
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7.9 Pure or Enrichment Cultures Must Be Used? |
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115 | (1) |
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7.10 Biodiversity in Enrichment Culture |
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116 | (1) |
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7.11 Presence of the Potential Pathogens in Enrichment Culture of UPB |
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117 | (1) |
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7.12 Use of Enrichment Culture of Indigenous Microorganisms with Urease Activity In Situ |
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118 | (1) |
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7.13 Biosafety of MICP Using Pure Culture |
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119 | (1) |
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7.14 MICP Using Dead but Urease-Active Bacterial Cells |
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119 | (1) |
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7.15 Bioclogging of the Sand Using Dead but Urease-Active Cells of Yaniella sp. VS8 |
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120 | (2) |
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7.16 Biocementation by Injection, Percolation, and Spraying |
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122 | (1) |
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7.17 Types of Crystals Produced in MICP |
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123 | (1) |
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7.18 Effect of Chemical Factors on MICP |
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124 | (1) |
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7.19 Problems of MICP Applications |
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125 | (1) |
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7.20 Media for Production of Bacterial Biomass for Biocement |
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125 | (1) |
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7.21 Constitutive and Inducible Urease |
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126 | (1) |
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7.22 Activated Sludge of Municipal Wastewater Treatment Plants as Raw Material |
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127 | (3) |
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7.23 Dry Calcium-Based Biocement |
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130 | (1) |
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7.24 Unconfined Compressive (UC) Strength of Sand After MICP |
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131 | (1) |
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7.25 Engineering Applications of MICP |
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132 | (1) |
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7.26 Biocementation Based on Production of Carbonates by Aerobic Heterotrophic Bacteria |
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133 | (1) |
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7.27 Biocementation Based on Production of Carbonates by Anaerobic Heterotrophic Bacteria |
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134 | (1) |
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7.28 Effect of Magnesium Ions on MICP |
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135 | (2) |
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7.29 Calcium Phosphate Biocementation |
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137 | (1) |
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7.30 Self-healing of Concrete Using MICP |
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138 | (1) |
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8 Bioclogging and Biogrouts |
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139 | (40) |
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8.1 Microbial Processes of Bioclogging |
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139 | (1) |
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8.2 Parameters to Measure Bioclogging |
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139 | (3) |
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8.3 Bioclogging Using Production of Microbial Polysaccharides in Situ |
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142 | (1) |
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8.4 Microorganisms that Can Be Used for the Formation of Polysaccharides in Situ |
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142 | (1) |
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8.5 Slow Bioclogging with Microbial Exopolysaccharides Production in Situ |
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143 | (1) |
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8.6 Experimental Bioclogging of Sand with Pure Culture of Paracoccus Denitrificans DSMZ 413 |
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144 | (1) |
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8.7 Application of Enrichment Culture of Soil Microorganisms for Sand Bioclogging |
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145 | (2) |
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8.8 Use of Waste Organic Matter for Bioclogging |
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147 | (1) |
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8.9 Use of Industrially Produced Microbial Polysaccharides for Ground Improvement |
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147 | (1) |
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8.10 Laboratory Bioclogging Using MICP |
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148 | (1) |
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8.11 Effect of Precipitated Calcium Carbonate on Hydraulic Conductivity |
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149 | (1) |
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8.12 Applications of MICP Clogging |
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150 | (1) |
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8.13 Bioclogging in Oil and Gas Recovery |
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150 | (1) |
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8.14 Idea on Sequential Biogas Production and Biofixation of Its Bubbles in Sand |
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150 | (1) |
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8.15 Clogging Due to Biogas Production in Situ |
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151 | (1) |
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8.16 Instability of Biogas Bubbles in Sand |
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152 | (1) |
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8.17 Bacterial Strains Used for Biogas Production and Their Fixation in Sand |
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152 | (1) |
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8.18 Laboratory Examination: Biogas Production and Its Stabilization in 1 L Sand Columns |
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153 | (1) |
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8.19 Laboratory Examination of Simultaneous Denitrification and Biocementation |
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154 | (1) |
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8.20 Sequential Denitrification and Bioclogging in the Sand Columns |
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155 | (4) |
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8.21 Biosafe Bioclogging Using MICP |
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159 | (3) |
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8.22 Calcium Bicarbonate Bioclogging |
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162 | (2) |
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8.23 Effect of Partial MICP on Calcium Bicarbonate Decay |
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164 | (1) |
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8.24 Bioclogging of the Fissured Rocks with Calcium Bicarbonate Solution |
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164 | (2) |
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8.25 Delayed Calcium Bicarbonate Decay |
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166 | (2) |
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8.26 Microbially Mediated Precipitation of Iron Minerals |
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168 | (1) |
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8.27 Anaerobic Bioproduction of Dissolved Fe(II) |
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169 | (2) |
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8.28 Kinetics and Stoichiometry of Ferrous Bioproduction from Iron Ore |
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171 | (1) |
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8.29 Combined Application of Urease-Producing Bacteria and Iron-Reducing Bacteria for the Continuous Biogrouting of Porous Soil |
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172 | (2) |
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8.30 Bioclogging on the Geochemical Barriers |
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174 | (1) |
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8.31 Two Different Kinetics of Bioclogging |
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174 | (2) |
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8.32 Comparison of the Biogrouting Methods |
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176 | (1) |
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8.33 Development of the Biogrout |
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176 | (3) |
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9 Soil Surface Biotreatment |
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179 | (20) |
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9.1 Wind Erosion of Soil and Dust Emission |
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179 | (1) |
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9.2 Dust Control Technologies |
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179 | (1) |
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9.3 Biotechnological Methods for Dust and Wind Erosion Control |
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180 | (1) |
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9.4 Biotechnological Control of Air-Born Movement of Sand Dust and Dust-Associated Chemical and Bacteriological Pollutants |
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181 | (1) |
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9.5 Formation of Soil Crust by Filamentous and Photosynthetic Microorganisms |
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181 | (2) |
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9.6 Functions of the Soil Crust |
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183 | (1) |
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9.7 Functions of Microorganisms in Soil Crust |
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183 | (1) |
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9.8 The Role of Microbial Exopolysaccharides in Biocrusting |
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184 | (1) |
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9.9 Artificial Formation of Biocrust |
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185 | (1) |
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9.10 Formation of Thick Crust Using Calcium-Based Biocementation |
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186 | (2) |
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9.11 Formation of Crust to Diminish the Hydraulic Conductivity |
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188 | (3) |
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9.12 Formation of Crust to Diminish Soil Erosion and Dispersion of Soil Pollutants |
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191 | (1) |
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9.13 Biosafe Formation of Crust or Layer of Calcite |
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191 | (1) |
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9.14 Design of the Biocemented Layer of Sand |
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192 | (1) |
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9.15 Cost Comparison for Biosealing |
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193 | (1) |
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194 | (1) |
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9.17 Aerobic Bioaggregation and Biocementation of Soil Surface |
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195 | (4) |
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10 Biocoating of Surfaces |
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199 | (24) |
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10.1 Coating of Concrete Surface |
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199 | (1) |
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10.2 Biocoating of Concrete Surface |
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200 | (1) |
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10.3 The Biocoating Procedure |
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200 | (1) |
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10.4 Calcium Carbonate Layer on the Concrete Surface |
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201 | (2) |
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10.5 The Mechanism of Biocoating Using MICP |
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203 | (2) |
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10.6 Effect of Gravity on Adhesion of UPB Cells and Calcite Crystals |
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205 | (1) |
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10.7 Effect of Biocoating on Water Adsorption |
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206 | (1) |
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10.8 Freezing---Heating and Wetting-Drying Tests of the Coated Surfaces |
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207 | (1) |
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10.9 Corrosion-Protecting Carbonate Layer |
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208 | (1) |
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10.10 MICP on Granite Surface |
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209 | (1) |
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10.11 MICP Coating of the Surface of Different Materials |
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210 | (4) |
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10.12 Biotechnological Enhancement of Low-Crested Coastal Defense Structures |
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214 | (1) |
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10.13 Artificial Coral Reefs |
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214 | (1) |
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10.14 Biotechnological Construction of Artificial Coral Reefs |
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215 | (4) |
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10.15 Biocoating of Aquaculture Frames |
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219 | (1) |
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10.16 Biocoating (Biocapsulation) of Soft Clay Aggregates |
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219 | (2) |
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10.17 Other Biotechnologies of Biocoating |
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221 | (2) |
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11 Biorcmediation and Biodesaturation of Soil |
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223 | (12) |
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223 | (1) |
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11.2 Bioremediation of Soil |
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223 | (1) |
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11.3 Bioremediation Options |
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224 | (1) |
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11.4 Advantages and Disadvantages of Biogeotechnologies for Remediation |
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225 | (1) |
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11.5 Problems of Bioremediation |
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225 | (1) |
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11.6 In Situ, on-Site, and off-Site Bioremediation |
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226 | (1) |
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11.7 Microbiological Preparations for Bioremediation |
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226 | (1) |
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11.8 Biotechnological Control of Dispersion of Pollutants |
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227 | (2) |
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11.9 Leaching of the Pollutants from Sand |
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229 | (1) |
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11.10 Biomediated Immobilization of Sand-Associated Lead |
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230 | (1) |
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11.11 Potential Application of MICP Against Accidental Pollution |
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230 | (1) |
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11.12 Biomitigation of Soil Liquefaction Through Biogas Production in Situ |
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231 | (1) |
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11.13 Denitrification as a Source of Biogas Production in Situ |
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232 | (1) |
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11.14 Stability of Biogas Bubbles in Soil |
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233 | (1) |
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11.15 Biogas Production in Situ Decreased Primary Consolidation Settlement in Clayey Soils |
|
|
234 | (1) |
|
12 Optimization and Design of Construction Biotechnology Processes |
|
|
235 | (26) |
|
12.1 Urease Activity of MICP Agent |
|
|
235 | (1) |
|
|
|
236 | (1) |
|
12.3 Genetically Engineered Strains of UPB |
|
|
236 | (1) |
|
12.4 Media for Cultivation of Bioagent |
|
|
236 | (3) |
|
12.5 Optimum of Urease Activity for MICP |
|
|
239 | (1) |
|
12.6 Extra- and Intracellular Urease |
|
|
239 | (1) |
|
12.7 Influence of Calcium Concentration on MICP |
|
|
239 | (1) |
|
12.8 Calcium: Urea Molar Ratio for MICP |
|
|
240 | (1) |
|
12.9 Source of Calcium for MICP |
|
|
240 | (1) |
|
12.10 UPB Distribution and Immobilization |
|
|
241 | (1) |
|
12.11 Rate of MICP Per Cell During Bioclogging |
|
|
242 | (1) |
|
12.12 Effect of Temperature on MICP |
|
|
242 | (1) |
|
12.13 Formation of Nanocomposites |
|
|
242 | (1) |
|
12.14 Effect of Surfactants |
|
|
243 | (1) |
|
12.15 Design of Biocementation and Bioclogging Using MICP |
|
|
243 | (1) |
|
12.16 Parameters of Design |
|
|
244 | (1) |
|
12.17 Stoichiometry of Bioclogging and Biocementation |
|
|
244 | (1) |
|
12.18 Technological Calculations |
|
|
245 | (1) |
|
12.19 Optimization and Design of Biodesaturation |
|
|
246 | (1) |
|
12.20 Field and Pilot Tests of the Biotreatment of Sand and Porous Soil |
|
|
247 | (1) |
|
12.21 Tests of the Biotreatment of the Fractured Rocks |
|
|
248 | (2) |
|
12.22 MICP Bioclogging of the Mixture of the Rocks and Sand |
|
|
250 | (5) |
|
12.23 MICP Pilot Bioclogging of the Space Between Granite Sheets Using Dead but Urease-Active Bacterial Cells |
|
|
255 | (6) |
|
13 Biocorrosion, Biodeterioration, and Biofouling in Civil Engineering |
|
|
261 | (10) |
|
13.1 Microbial Biodeterioration of Construction Materials |
|
|
261 | (1) |
|
13.2 Deterioration of Cultural Heritage |
|
|
262 | (1) |
|
13.3 Microbial Biofouling |
|
|
262 | (1) |
|
13.4 Microbially Influenced Corrosion |
|
|
263 | (2) |
|
13.5 Microbial Formation of Acids |
|
|
265 | (1) |
|
13.6 Prevention of Microbially Influenced Corrosion, Biofouling and Biodeterioration |
|
|
265 | (1) |
|
|
|
266 | (1) |
|
|
|
266 | (1) |
|
13.9 Sources of Bioaerosols in the Buildings |
|
|
267 | (1) |
|
|
|
267 | (1) |
|
|
|
267 | (1) |
|
|
|
268 | (1) |
|
13.13 Fate of Bioaerosols |
|
|
268 | (1) |
|
13.14 Treatment of Odorous and Toxic Gases |
|
|
269 | (2) |
|
14 Advances and Future Developments of Construction Biotechnology |
|
|
271 | (8) |
|
14.1 Advances of Biotechnological Construction Materials |
|
|
271 | (1) |
|
14.2 Known Applications of Biocements and Biogrouts |
|
|
272 | (1) |
|
14.3 The Existing Problems of Biotechnological Ground Improvement and the Ways of Their Potential Solution |
|
|
273 | (1) |
|
14.4 New Potential Applications of Biotechnological Ground Improvement |
|
|
273 | (1) |
|
14.5 Future Products of Construction Biotechnology and Their Applications |
|
|
273 | (3) |
|
14.6 Eco-Efficient Biocement |
|
|
276 | (1) |
|
14.7 Calcium Carbonate Precipitation and CO2 Sequestration |
|
|
276 | (3) |
| References |
|
279 | |
