Bioinformatics and Biomedical Engineering

Name: Bioinformatics and Biomedical Engineering | 10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12-14, 2023, Proceedings, Part I
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10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12-14, 2023, Proceedings, Part I

Ignacio Rojas Olga Valenzuela Fernando Rojas Ruiz Luis Javier Herrera Francisco Ortuño(Editor)

Springer (Publisher)

Published on 28. June 2023

XXIX, 576 pages

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978-3-031-34953-9 (ISBN)

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Content

Intro
Preface
Organization
Contents - Part I
Contents - Part II
Analysis of Molecular Dynamics Data in Proteomics
Recognition of Conformational States of a G Protein-Coupled Receptor from Molecular Dynamic Simulations Using Sampling Techniques
1 Introduction
2 Materials and Methods
2.1 Class Imbalance Correction Methods
2.2 Experimental Setup
2.3 Evaluation Metrics for Imbalanced Data Problems
3 Results and Discussion
3.1 Interpretation Results
4 Conclusions
References
Identification of InhA-Inhibitors Interaction Fingerprints that Affect Residence Time
1 Introduction
1.1 Ligand-Receptor Binding Kinetics
1.2 Computer Methods to Determine Binding Kinetic Parameters
1.3 Research Objective
2 Mycobacterium Enoyl Acyl Carrier Protein Reductase (InhA)
3 Methods
4 Results
4.1 Ligand Similarity
4.2 Drug-Like Ligand Properties that Affect Residence Time
5 Discussion and Conclusions
References
Bioinformatics
Validation of Height-for-Age and BMI-for-Age Z-scores Assessment Using Android-Based Mobile Apps
1 Introduction
2 Methods
2.1 Subjects
2.2 Anthropometric Measurements
2.3 Z-score Calculation
2.4 Statistical Analysis
3 Outcomes
4 Discussion
5 Conclusion
6 Limitations
References
An Algorithm for Pairwise DNA Sequences Alignment
1 Introduction
2 Related Work
3 An Algorithm for Pairwise DNA Sequences Alignment Based on the Proposed CAT Method
4 Experimental Results and Analysis
4.1 Implementation of the Proposed Method CAT for Sequences Alignment
4.2 Collision Analysis
4.3 Performance Analysis
5 Conclusion
References
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT
1 Introduction
2 Finding Maximal Blocks with Wildcards
3 The Algorithm
3.1 Positional BWT Extended to Wildcards
3.2 Building the Extended PBWT
3.3 Computing the Maximal Blocks
4 Experimental Results
5 Conclusions
References
GPU Cloud Architectures for Bioinformatic Applications
1 Introduction
2 GPU Usage in Bioinformatics
3 Processing Outsourcing
4 GPU Virtualisation in Cloud Architectures
5 Architecture Characteristics
6 Experiments
7 Conclusions
References
Biomarker Identification
Novel Gene Signature for Bladder Cancer Stage Identification
1 Introduction
2 Data Description
3 Metodology
3.1 Differential Expressed Genes Extraction and Visualization
3.2 Development of Classification Models
4 Results and Discussion
4.1 Gene Enrichment
5 Conclusions
References
Predicting Cancer Stage from Circulating microRNA: A Comparative Analysis of Machine Learning Algorithms
1 Introduction
2 Materials and Methods
2.1 Study Cohort
2.2 Algorithms
2.3 Evaluation Metrics
2.4 Experimental Design
2.5 Statistical Analysis
3 Results
4 Discussion
5 Conclusion
6 Ethical Statement
7 Appendix
References
Gait Asymmetry Evaluation Using FMCW Radar in Daily Life Environments
1 Introduction
2 Methodology
2.1 Gait Parameters Definition
2.2 FMCW Radar Signal Processing
2.3 Extraction of Radar-Based Gait Parameters
3 Experimental Setup and Equipment
4 Experimental Results
4.1 Raw Data Visualization
4.2 Gait Parameters Extraction Results
5 Conclusion and Further Work
References
Biomedical Computing
Whole Tumor Area Estimation in Incremental Brain MRI Using Dilation and Erosion-Based Binary Morphing
1 Introduction
2 Morphing Methods
3 Experiments
4 Results
5 Conclusions and Discussions
References
Three-Dimensional Representation and Visualization of High-Grade and Low-Grade Glioma by Nakagami Imaging
1 Introduction
2 Nakagami Imaging
3 Highlighting Experiments
3.1 High-Grade Glioma Experiment
3.2 Low-Grade Glioma Experiment
4 Results
5 Conclusions and Discussions
References
Speeding up Simulations for Radiotherapy Research by Means of Machine Learning
1 Introduction
2 Problem Description
2.1 PENELOPE Simulator
3 Methodology: Data Generation with PENELOPE and Modeling the Output by Means of Machine Learning Algorithms
3.1 Data Generation
3.2 Models Evaluated and Hyperparameter Tunning
3.3 Implementation Details and Model Deployment
4 Experiments and Results
4.1 Multi-Output Regression
4.2 Single Output Regression
5 Conclusions
References
A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph
1 Introduction
2 KG Construction from Bio-Medical Data Sources
3 RNA Molecules
4 RNA-Based Data Sources
5 A Meta-Graph Representing RNA-Centered Relationships
6 Concluding Remarks
References
Structural Analysis of RNA-Binding Protein EWSR1 Involved in Ewing's Sarcoma Through Domain Assembly and Conformational Molecular Dynamics Studies
1 Introduction
2 Computational Methodology
2.1 Retrieval of Human EWSR1 Sequence and Alignment
2.2 EWSR1 Conserved Sequence Analysis
2.3 Structure Prediction of Human EWSR1
2.4 Prediction of RNA Motifs Interacting with EWSR1
2.5 Molecular Docking
2.6 Molecular Dynamics (MD) Simulations
3 Results
3.1 Structural Analysis of Predicted EWSR1
3.2 Docking Energy Evaluation
3.3 Binding Pocket Conformational and Interaction Analysis
3.4 Root Mean Square Deviation Analysis
3.5 Radius of Gyration and Solvent Accessible Surface Area
4 Conclusion
References
Pharmacoinformatic Analysis of Drug Leads for Alzheimer's Disease from FDA-Approved Dataset Through Drug Repositioning Studies
1 Introduction
2 Computational Methodology
2.1 Retrieval of MADD Sequence and Protein Modelling
2.2 Structure Analysis of MADD Protein
2.3 Virtual Screening of Chemical Scaffolds
2.4 Active Binding Site of MADD Protein and Docking
2.5 Designing of Pharmacogenomics Networks
2.6 Molecular Dynamics (MD) Simulations
3 Results and Discussion
3.1 Predicted Model of MADD Protein
3.2 VADAR and Galaxy Refine Analysis
3.3 Binding Pocket Analysis of MADD Protein
3.4 Shape Based Screening and PyRx Docking
3.5 Pharmacogenomics Analysis
4 Molecular Docking Using Autodock
4.1 Docking Energy Analysis Against Death Domain of MADD
4.2 Binding Interaction Profile
5 Molecular Dynamic Simulations
5.1 Root Mean Square Deviation and Rg Analysis
6 Conclusions
References
Biomedical Engineering
Motion Control of a Robotic Lumbar Spine Model
1 Introduction
2 Related Work
3 Kinematics
4 Dynamic Model
5 PID Controller
6 Simulation and Results
7 Conclusions
References
Annotation-Free Identification of Potential Synteny Anchors
1 Background
2 Theory and Algorithmic Considerations
3 Results
3.1 Summary Statistics of Anchor Candidates
3.2 Evaluation of Anchor Candidates
3.3 Mapping of Anchors Candidates Across Genomes
3.4 Two Showcase Applications
3.5 Computational Effort
4 Discussion and Outlook
A Genomes Used in this Contribution
References
Analysing Dose Parameters of Radiation Therapy Treatment Planning and Estimation of Their Influence on Secondary Cancer Risks
1 Introduction
2 Materials and Methods
2.1 Patient Selection
2.2 Treatment Planning
3 Results and Discussion
4 Conclusion
References
A Platform for the Radiomic Analysis of Brain FDG PET Images: Detecting Alzheimer's Disease
1 Introduction
2 Methods
2.1 Participants and Data
2.2 PET Acquisition
2.3 ROI Extraction
2.4 Feature Extraction
2.5 Feature Selection
2.6 Classification and Tuning
2.7 Computational Hardware and Software
3 Results
4 Discussion
5 Conclusion
References
Biomedical Signal Analysis
Deep Learning for Automatic Electroencephalographic Signals Classification
1 Introduction
2 Methodology
2.1 Description of EEG Data
2.2 EEG Signal Preprocessing
2.3 Feature Extraction
2.4 Classification
3 Results and Discussions
3.1 Evaluation
4 Conclusions and Future Work
References
Evaluation of Homogeneity of Effervescent Tablets Containing Quercetin and Calcium Using X-ray Microtomography and Hyperspectral Analysis
1 Introduction
2 Materials and Methods
2.1 Tablets Selected for Analysis
2.2 Evaluation of the Tablets
2.3 Hyperspectral Imaging
2.4 X-ray Microtomography
2.5 Statistical Analysis
3 Results
3.1 Characteristics of the Tablets
3.2 The Analysis of Tablets' Homogeneity Using Hyperspectral Imaging
3.3 The Analysis of Inner Homogeneity Using X-ray Microtomography
4 Discussion
5 Conclusion
References
The Effect of Biofeedback on Learning the Wheelie Position on Manual Wheelchair
1 Introduction
2 Material and Methods
2.1 Subjects and Study Design
2.2 Materials
2.3 Methods
2.4 Statistical Analysis
3 Results
4 Discussion
5 Conclusion
References
Preliminary Study on the Identification of Diseases by Electrocardiography Sensors' Data
1 Introduction
2 Methods
2.1 Study Design and Participants
2.2 Feature Extraction
2.3 Data Classification
3 Results
4 Discussion and Conclusions
References
Computational Proteomics
Exploring Machine Learning Algorithms and Protein Language Models Strategies to Develop Enzyme Classification Systems
1 Introduction
2 Methods
2.1 Numerical Representation Strategies
2.2 Collecting and Processing Datasets
2.3 Developing Functional Classification Models
2.4 Implementation Strategies
3 Results and Discussions
3.1 Collecting and Processing Datasets
3.2 Protein Language Models Achieved Better Performances Than Amino Acid Encoding Strategies
3.3 Models Based on CNN Architectures Show Better Performance. But, They Tend to Overfit
4 Conclusions
References
A System Biology and Bioinformatics Approach to Determine the Molecular Signature, Core Ontologies, Functional Pathways, Drug Compounds in Between Stress and Type 2 Diabetes
1 Introduction
2 Proposed Mehtodology
2.1 Data Collection
2.2 Data Filtering and Finding of DEGs, and Identification of Concordant DEGs Between Stress and Type 2 Diabetes
2.3 Design of Protein-Protein Interaction Network and Analysis
2.4 Analysis of Hub Genes
2.5 Enrichment Analysis: Gene Ontology and Pathways
2.6 TF-Gene Interactions
2.7 Finding of Candidate Drug
3 Results
3.1 Findings of Differential Expressed Genes and Common DEGs Among Stress and Type 2 Diabetes
3.2 Analysis of Protein-Protein Interaction Network
3.3 Hub Gene Identification
3.4 According to the Common DEGs Analyze GO and Pathways
3.5 TF-Gene Interactions
3.6 Identification of Drug Compounds
4 Discussion
5 Conclusion
References
Recent Advances in Discovery of New Tyrosine Kinase Inhibitors Using Computational Methods
1 Introduction
2 Structure of SRC-Protein Kinase Domain
3 The Role of Computational Methods in Discovery of New Inhibitors of Src-Protein Kinase
4 Conclusion
References
The Coherent Multi-representation Problem with Applications in Structural Biology
1 Introduction
2 Coherent Multi-representation Problem
3 An Object-Oriented Implementation
4 A Simple Experiment
5 Conclusions
References
Computational Study of Conformational Changes in Intrinsically Disordered Regions During Protein-Protein Complex Formation
1 Introduction
2 Methods
2.1 Dataset Curation
2.2 IDRs in the Bound and Complex Proteins
2.3 Classification of IDRs
2.4 Interface Region and Hydrogen Bond Calculation
2.5 Secondary Structural Elements
2.6 Study of Conformational Changes
3 Results
3.1 The Dataset of Protein-Protein Complexes and Their Unbound Forms
3.2 Intrinsically Disordered Regions in Protein-Protein Complexes and Their Unbound Forms
3.3 Classification of IDRs in Unbound and Complex Proteins
3.4 Amino Acid Composition of IDRs
3.5 Distribution of IDRs After Complex Formation
3.6 Secondary Structural Elements
3.7 IDRs in Polar Interactions
3.8 Structural Superimposition of Unbound and Complex Proteins
4 Discussion
5 Conclusion
References
Computational Support for Clinical Decisions
Predicting and Detecting Coronary Heart Disease in Patients Using Machine Learning Method
1 Introduction
2 Methods
3 Summary
References
Systematic Comparison of Advanced Network Analysis and Visualization of Lipidomics Data
1 Introduction
2 Materials and Methods
2.1 Dataset
2.2 Methods
2.3 Undirected Approaches
2.4 Directed Approaches
3 Results
3.1 Undirected Analytical Methods for Network Visualization
3.2 Directed Analytical Methods for Network Visualization
4 Discussion
5 Conclusion
References
Comparison of Image Processing and Classification Methods for a Better Diet Decision-Making
1 Introduction
2 Related Work
3 Experimental Setup
3.1 Bag-of-Words Architecture
3.2 Deep Learning Architecture(s)
3.3 Baseline Survey
4 Comparison Study
4.1 Additional Results, CNN (16 Classes) vs. HVS
4.2 More (20) Epochs Impact on CNN Accuracy
4.3 Human, Resnet, Inception and Bag-of-Words
5 Conclusions
References
A Platform for the Study of Drug Interactions and Adverse Effects Prediction
1 Introduction
2 Related Work
3 Platform Description
4 User Controlled Data Manipulation
5 Automated Data Operations
6 Case Study - Dataset Creation and Results Analysis
7 Conclusions
8 Future Work
References
A Machine Learning Approach to Predict MRI Brain Abnormalities in Preterm Infants Using Clinical Data
1 Introduction
2 Dataset
2.1 Study Design and Participants
2.2 Data Curation and Pre-processing
3 Methodology and Experimental Settings
3.1 Methods
3.2 Evaluation Strategy
3.3 Dealing with Data Imbalance Issues
4 Results and Discussion
5 Conclusions and Future Work
References
Modelling of Anti-amyloid-Beta Therapy for Alzheimer's Disease*-12pt
1 Introduction
2 Model for AD
2.1 Anti-amyloid-Beta Treatments
2.2 Network Model for the Brain Connectome
3 Results and Discussions
3.1 Dynamics for the Homogeneous System
3.2 Solution for the Network Model
4 Conclusions
References
Using Digital Biomarkers for Objective Assessment of Perfusionists' Workload and Acute Stress During Cardiac Surgery
1 Introduction
2 Methods
2.1 Study Setting and Design
2.2 Population
2.3 Procedures
2.4 Measurements
3 Results
4 Discussion
5 Conclusion
References
Detecting Intra Ventricular Haemorrhage in Preterm Neonates Using LSTM Autoencoders
1 Introduction
2 Time Series Forecasting, LSTM and Autoencoders
3 Methodology
3.1 Data Collection and Preprocessing
3.2 Model Training and Testing
3.3 Validation Metrics
4 Results
5 Discussion
6 Conclusion
References
Measurement of Acute Pain in the Pediatric Emergency Department Through Automatic Detection of Behavioral Parameters: A Pilot Study
1 Introduction
2 Materials and Methods
2.1 Data Collection
2.2 Pain Scale Implementation
2.3 Face and Body Parameters Computation
3 Results and Discussion
4 Conclusion and Future Work
References
Clinical Text Classification in Cancer Real-World Data in Spanish
1 Introduction
2 Materials
3 Methods
3.1 Bag-of-Words and Machine Learning Supervised Methods
3.2 Word Embedding and Recurrent Neural Models
4 Experiments
5 Results
6 Conclusions
References
COVID-19 Advances in Bioinformatics and Biomedicine
Stochastic Model of Infection with the SARS-COV-2 Virus in a Small Group of Individuals Indoors
1 Introduction
2 Mathematical Modelling of SARS-CoV-2 Infection of Human Host Cells
2.1 Basic Equations of the Standard Model
2.2 Modified Model
2.3 Analysis of the Modified Model
2.4 Fluctuations in the Concentration of Virions in the Local Atmosphere
3 A Model of Chaotic Movement of a Group of People Indoors
3.1 Basic Equations
3.2 Numerical Simulation Results
4 Conclusion and Discussion
References
Training Strategies for Covid-19 Severity Classification
1 Introduction
2 Dataset Acquisition and Data Processing
2.1 Preprocessing/Filtering Stage
2.2 Heart Rate Variability Metrics
2.3 Summary Diagram
3 Machine Learning Strategies
3.1 First Stage
3.2 Second Stage - Grid Search
3.3 Third Stage - Test Dataset
4 Results
4.1 First Stage Results
4.2 Second Stage Results
4.3 Third Stage Results
5 Discussions and Conclusions
References
The Effectiveness of Quarantine in Viral and Bacterial Epidemics: New Evidence Provided by the Covid-19 Pandemic
1 Introduction
2 Literature Review
3 The SIRD Model of Infectious Diseases
4 Some Remarks About the COVID-19 Pandemic
5 Other Pandemics in History
6 Remarks
References
Physiological Polyphosphate: A New Molecular Paradigm in Biomedical and Biocomputational Applications for Human Therapy
1 Introduction
2 Methods
2.1 Preparation of Ca-polyP Nanoparticles and Coacervate
2.2 Fabrication of Compressed Collagen-Based Mats
2.3 Formulation of polyP-Containing Hydrogel
2.4 Cultivation of Bacteria
2.5 Treatment of Chronic Wounds
2.6 Preparation of polyP Dentifrice
2.7 Treatment of the Teeth
2.8 Analytical Procedures
2.9 In Silico Simulation
3 Results
3.1 polyP - Basic Studies: Nanoparticle and Coacervate Formation and Function
3.2 polyP - Application in Dentistry and Dental Care
3.3 polyP - Application in Wound Healing
3.4 polyP - Manufacturing and Safety
4 Discussion
5 Conclusion
References
Quantitative EEG Findings in Outpatients with Psychosomatic Manifestations After COVID-19
1 Introduction
2 Methods
3 Outcomes
4 Discussion
5 Conclusion
References
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Bioinformatics and Biomedical Engineering

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