Table of Contents

Cover image

Title page

Copyright

Contributors

Preface

Acknowledgments

Introduction

Chapter 1: Supervised Learning with the Artificial Neural Networks Algorithm for Modeling Immune Cell Differentiation

Abstract

Acknowledgments

1 Introduction

2 Related work

3 Modeling immune cell differentiation

4 Discussion

5 Conclusion

Chapter 2: Accelerating Techniques for Particle Filter Implementations on FPGA

Abstract

1 Introduction

2 PF and SLAM algorithms

3 Computational bottleneck identification and hardware/software partitioning

4 PF acceleration techniques

5 Hardware implementation

6 Hardware/software Architecture

7 Results and discussion

8 Conclusions

Chapter 3: Biological Study on Pulsatile Flow of Herschel-Bulkley Fluid in Tapered Blood Vessels

Abstract

1 Introduction

2 Formulation of the problem

3 Solution

4 Discussion

5 Conclusion

Chapter 4: Hierarchical k-Means: A Hybrid Clustering Algorithm and Its Application to Study Gene Expression in Lung Adenocarcinoma

Abstract

1 Introduction

2 Methods

3 Data set

4 Results and Discussion

5 Conclusions

Supplementary materials

Chapter 5: Molecular Classification of N-Aryloxazolidinone-5-carboxamides as Human Immunodeficiency Virus Protease Inhibitors

Abstract

Acknowledgments

1 Introduction

2 Computational method

3 Classification algorithm

4 Information entropy

5 The EC of entropy production

6 Learning procedure

7 Calculation results and discussion

8 Conclusions

Chapter 6: Review of Recent Protein-Protein Interaction Techniques

Abstract

1 Introduction

2 Technical challenges and open issues

3 Performance measures

4 Computational approaches

5 Conclusion

Chapter 7: Genetic Regulatory Networks: Focus on Attractors of Their Dynamics

Abstract

Acknowledgments

1 Introduction

2 Immunetworks

3 The iron control network

4 Morphogenetic networks

5 Biliary atresia control network

6 Conclusion and perspectives

Mathematical Annex

Chapter 8: Biomechanical Evaluation for Bone Allograft in Treating the Femoral Head Necrosis: Thorough Debridement or not?

Abstract

1 Introduction

2 Materials and methods

3 Results

4 Discussion

5 Conclusion

6 Disclaimer

Chapter 9: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?

Abstract

Acknowledgments

Graphical Abstract

1 Introduction

2 Computational methods

3 Results and discussion

4 Conclusions

Supplementary Material: Diels-Alderase Catalyzing the Cyclization Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?

1 Conformational analysis of macrocyclic lactone (4)

2 Modelling of a theozyme for the conversion of macrocyclic lactone (4) into tricyclic compound (5)

3 ELF bonding analysis of the conversion of macrocyclic lactone (4) into the tricyclic compound (5)

Chapter 10: CLAST: Clustering Biological Sequences

Abstract

Acknowledgments

1 Introduction

2 Methods

3 Evaluation and discussion

4 Conclusions

Chapter 11: Computational Platform for Integration and Analysis of MicroRNA Annotation

Abstract

1 Introduction

2 Material

3 MIRIA Database

4 MiRNA CFSim

5 Web Framework

6 Results

7 Conclusions

Chapter 12: Feature Selection and Analysis of Gene Expression Data Using Low-Dimensional Linear Programming

Abstract

Acknowledgments

1 Introduction

2 LP formulation of separability

3 Offline approach

4 Incremental approach

5 Gene selection

6 A new methodology for gene selection

7 Results and discussion

8 Conclusions

Chapter 13: The Big ORF Theory: Algorithmic, Computational, and Approximation Approaches to Open Reading Frames in Short- and Medium-Length dsDNA Sequences

Abstract

Acknowledgments

1 Introduction

2 Molecular genetic and bioinformatic considerations

3 Algorithmic and programming considerations

4 Analytical and random sampling solutions to L > 25 sequences: Triplet-based approximations

5 Alternative genetic codes

6 Implications for the evolution of ORF size

Chapter 14: Intentionally Linked Entities: A Detailed Look at a Database System for Health Care Informatics

Abstract

Acknowledgments

1 Introduction

2 Introducing ILE for Health Care Applications

3 ILE and epidemiological data modeling

4 Other nonrelational approaches to keeping medical records

5 Inside the ILE database system

6 An example of the Importance of an EHR implemented in ILE

7 Conclusions

Chapter 15: Region Growing in Nonpictorial Data for Organ-Specific Toxicity Prediction

Abstract

1 Introduction

2 Related works

3 Basic foundation

4 Methodology

5 Empirical results

6 Conclusions and future research

Chapter 16: Contribution of Noise Reduction Algorithms: Perception Versus Localization Simulation in the Case of Binaural Cochlear Implant (BCI) Coding

Abstract

Acknowledgments

1 Introduction

2 Materials and Methods

3 Results

4 Discussion

5 Conclusions

Chapter 17: Lowering the Fall Rate of the Elderly from Wheelchairs

Abstract

Acknowledgments

1 Introduction

2 Current solutions

3 A systems solution

4 The sparrow design

5 Assessment algorithm

6 Assessment decision algorithm

7 The future

8 Conclusion

Chapter 18: Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness

Abstract

Acknowledgments

1 Introduction

2 Participants

3 Apparatus and stimuli

4 Procedure

5 EEG recording

6 Experiment I

7 Experiment II

8 The grand average occipital and temporal electrical activity correlated with a contrast in access

9 Behavioral data

10 The grand average occipital and temporal electrical activity correlated with a contrast in phenomenology

11 The grand average occipital and temporal electrical activity co-occurring with unconsciousness

Chapter 19: Chaotic Dynamical States in the Izhikevich Neuron Model

Abstract

1 Introduction

2 Fundamental description

3 Chaotic properties of Izhikevich neuron model

4 Response efficiency in chaotic resonance

5 Conclusions

Chapter 20: Analogy, Mind, and Life

Abstract

Acknowledgements

1 Introduction

2 The artificial mind and cognitive science

3 Consciousness

4 The classic watchmaker analogy

5 The classic watchmaker analogy is fragile, remote and reductive

6 The analogy between life and information seems to suggest some type of reductionism

7 Conclusion

Chapter 21: Copy Number Networks to Guide Combinatorial Therapy of Cancer and Proliferative Disorders

Abstract

Acknowledgments

1 Introduction

2 A diminishing drug pipeline

3 Using genome data to replenish the pipeline by drug repositioning

4 The small-world properties of networks expedite combination therapies

5 Molecular networks can be used to guide drug combinations

6 Copy number alterations as a disease driver

7 Using correlated copy number alterations to construct survival networks

8 A pan-cancer CNA interaction network

9 Mapping genetic survival networks using correlated CNAs in radiation hybrid cells

10 A survival network for GBM at single-gene resolution

11 Using CNA networks to guide combination therapies

12 Targeting multiple drugs to single-disease genes in cancer

13 Targeting multiple drugs to a single-disease gene in autoimmunity

14 Targeting multiple genes in a single pathway for cancer

15 Targeting genes in parallel pathways converging on atherosclerosis

16 Using CNA networks to synergize drug combinations and minimize side effects

17 Disclaimer

Chapter 22: DNA Double-Strand Break–Based Nonmonotonic Logic

Abstract

1 Introduction

2 DNA DSBs

3 Logical model for system biology

4 Completing the signaling pathways by default abduction

5 Logic representation of a signaling pathway with the goal of reducing computational complexity

6 Algorithm and implementation

7 Results

8 Conclusions

Chapter 23: An Updated Covariance Model for Rapid Annotation of Noncoding RNA

Abstract

1 Introduction

2 Method

3 Test results

4 Conclusions

Chapter 24: SMIR: A Web Server to Predict Residues Involved in the Protein Folding Core

Abstract

Acknowledgments

1 Introduction

2 Methods

3 Results

4 Conclusion

Chapter 25: Predicting Extinction of Biological Systems with Competition

Abstract

Acknowledgments

1 Introduction

2 A Model of Competing Species

3 Density function of extinction time

4 Estimation of parameters

5 Numerical results

6 Summary

Chapter 26: Methodologies for the Diagnosis of the Main Behavioral Syndromes for Parkinson’s Disease with Bayesian Belief Networks

Abstract

1 Introduction

2 Diagnosis of FoG

3 Diagnosis of handwriting and speech

4 Toward a global methodology for PD

5 Conclusions and future work

Chapter 27: Practical Considerations in Virtual Screening and Molecular Docking

Abstract

1 Introduction

2 Receptor structure preparation

3 Accurately predicting the pose of solved crystal structures and differentiating decoys from actives

4 Side-chain flexibility and ensemble docking

5 Consensus docking

6 MM-GBSA

7 Incorporating pharmacophoric constraints within the virtual screen

8 Conclusion

Chapter 28: Knowledge Discovery in Proteomic Mass Spectrometry Data

Abstract

1 Introduction

2 Technical background

3 Computational workflow

4 Analysis tool

5 Conclusion

Chapter 29: A Comparative Analysis of Read Mapping and Indel Calling Pipelines for Next-Generation Sequencing Data

Abstract

1 Introduction

2 Mapping and calling software

3 Methods

4 Real data

5 Results and discussion

6 Conclusions

Chapter 30: Two-Stage Evolutionary Quantification of In Vivo MRS Metabolites

Abstract

Acknowledgments

1 Introduction

2 Proposed methodology

3 Experiment

4 Conclusions

Chapter 31: Keratoconus Disease and Three-Dimensional Simulation of the Cornea throughout the Process of Cross-Linking Treatment

Abstract

Acknowledgments

1 Introduction

2 Methodology

3 Conclusions and Recommendations

Chapter 32: Emerging Business Intelligence Framework for a Clinical Laboratory Through Big Data Analytics

Abstract

1 Introduction

2 Motivation

3 Material and methods

4 Use-cases

5 Case Study 1: Clinical laboratory test usage patterns visualization

6 Data source and methodology

7 Results and discussion

8 Limitations

9 Case Study 2: Provincial laboratory clinical test volume estimation

10 Data source and methodology

11 Results and discussion

12 Limitations

13 Conclusion and future work

Chapter 33: A Codon Frequency Obfuscation Heuristic for Raw Genomic Data Privacy

Abstract

1 Introduction

2 Background

3 Related work

4 Methodology

5 Experiment and results

6 Conclusion

Index

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