Bioinformatics and Biomedical Engineering [[electronic resource] ] : 10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12–14, 2023, Proceedings, Part I / / edited by Ignacio Rojas, Olga Valenzuela, Fernando Rojas Ruiz, Luis Javier Herrera, Francisco Ortuño |
Autore | Rojas Ignacio |
Edizione | [1st ed. 2023.] |
Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
Descrizione fisica | 1 online resource (588 pages) |
Disciplina | 570.285 |
Altri autori (Persone) |
ValenzuelaOlga
Rojas RuizFernando HerreraLuis Javier OrtuñoFrancisco |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Bioinformatics
Computer networks Engineering—Data processing Biomedical engineering Computational and Systems Biology Computer Communication Networks Data Engineering Biomedical Engineering and Bioengineering |
ISBN | 3-031-34953-9 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
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. |
Record Nr. | UNISA-996538665103316 |
Rojas Ignacio | ||
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. di Salerno | ||
|
Bioinformatics and Biomedical Engineering [[electronic resource] ] : 10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12–14, 2023, Proceedings, Part II / / edited by Ignacio Rojas, Olga Valenzuela, Fernando Rojas Ruiz, Luis Javier Herrera, Francisco Ortuño |
Autore | Rojas Ignacio |
Edizione | [1st ed. 2023.] |
Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
Descrizione fisica | 1 online resource (520 pages) |
Disciplina | 570.285 |
Altri autori (Persone) |
ValenzuelaOlga
Rojas RuizFernando HerreraLuis Javier OrtuñoFrancisco |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Bioinformatics
Biomedical engineering Computer networks Engineering—Data processing Computational and Systems Biology Biomedical Engineering and Bioengineering Computer Communication Networks Data Engineering |
ISBN | 3-031-34960-1 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
Intro -- Preface -- Organization -- Contents - Part II -- Contents - Part I -- Feature Selection, Extraction, and Data Mining in Bioinformatics -- Agent Based Modeling of Fish Shoal Behavior -- 1 Introduction -- 2 Modeling -- 3 Methods -- 3.1 Multi agents Based Modeling and Simulation -- 4 Results and Discussion -- References -- Entropy Approach of Processing for Fish Acoustic Telemetry Data to Detect Atypical Behavior During Welfare Evaluation -- 1 Introduction -- 1.1 Biotelemetry -- 1.2 Fish Welfare -- 2 Dataset -- 3 Methods -- 4 Results -- 5 Conclusion -- References -- Determining HPV Status in Patients with Oropharyngeal Cancer from 3D CT Images Using Radiomics: Effect of Sampling Methods -- 1 Introduction -- 2 Material and Methods -- 2.1 Data Set -- 2.2 Image Pre-processing -- 2.3 Feature Extraction -- 2.4 Data Pre-processing and Resampling -- 2.5 Feature Selection -- 2.6 Model Training and Evaluation -- 3 Results -- 3.1 Data Pre-processing and Resampling -- 3.2 Feature Extraction -- 3.3 Feature Selection -- 3.4 Performance Evaluation -- 4 Discussion -- 5 Conclusion -- References -- MetaLLM: Residue-Wise Metal Ion Prediction Using Deep Transformer Model -- 1 Introduction -- 2 Methodology -- 2.1 MetaLLM: Residue-Wise Metal Ion Prediction -- 3 Experiments and Results -- 3.1 Experimental Details -- 3.2 Result Analysis -- 4 Conclusion -- References -- Genome-Phenome Analysis -- Prediction of Functional Effects of Protein Amino Acid Mutations -- 1 Introduction -- 2 Methods -- 2.1 nsSNV Datasets -- 2.2 Protein Mutation Prediction Methodology: The Holdout- nsSNV Algorithm -- 2.3 Consensus Holdout Training and Selection -- 2.4 Extreme Learning Machine -- 2.5 Random Forests -- 3 Results -- 4 Conclusions and Future Directions -- References -- Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach -- 1 Introduction.
2 Background -- 3 Methods -- 3.1 Reference -- 3.2 Dataset -- 3.3 Quality and Control -- 3.4 Pipeline -- 3.5 Workflow Management and Reproducibility -- 3.6 Benchmarking -- 3.7 Computational Resources -- 4 Results -- 4.1 Different Methods Performance -- 4.2 Computational Time -- 5 Discussion -- 6 Conclusion -- References -- Healthcare and Diseases -- Improving Fetal Health Monitoring: A Review of the Latest Developments and Future Directions -- 1 Introduction -- 2 Methods -- 2.1 Study Design -- 2.2 Search Strategy -- 2.3 Inclusion Criteria -- 2.4 Selection of Studies -- 2.5 Data Analysis -- 3 Result -- 4 Discussion -- 4.1 The Development of Monitoring Devices for Fetal Well-Being -- 4.2 Algorithm for More Accurate Maternal-Fetal FHR Filtering -- 4.3 Fetal Well-Being Indicators -- 4.4 Target Users -- 5 Conclusion -- References -- Deep Learning for Parkinson's Disease Severity Stage Prediction Using a New Dataset -- 1 Introduction -- 2 Related Work -- 3 Materials and Methods -- 3.1 Data Acquisition -- 3.2 Dataset Construction -- 3.3 Data Pre-processing -- 3.4 Proposed LSTM Model -- 4 Experiments -- 5 Conclusion -- References -- Improved Long-Term Forecasting of Emergency Department Arrivals with LSTM-Based Networks -- 1 Introduction -- 2 Materials and Methods -- 2.1 Data Acquisition -- 2.2 Exploration -- 2.3 Analysis Techniques -- 3 Results -- 4 Conclusion -- References -- High-Throughput Genomics: Bioinformatic Tools and Medical Applications -- Targeted Next Generation Sequencing of a Custom Capture Panel to Target Sequence 112 Cancer Related Genes in Breast Cancer Tumors ERBB2 Positive from Lleida (Spain) -- 1 Introduction -- 2 Methods -- 2.1 Breast Cancer Samples -- 2.2 Targeted Sequencing -- 2.3 Data Analysis -- 3 Results -- 3.1 Targeted Sequencing -- 3.2 Gene Signatures -- 4 Discussion -- References. An Accurate Algorithm for Identifying Mutually Exclusive Patterns on Multiple Sets of Genomic Mutations -- 1 Introduction -- 2 Method -- 2.1 Similarity and Mutual Exclusion Measure -- 2.2 Weighted Probability Search -- 2.3 Algorithm Steps -- 3 Discussion -- 3.1 ME Simulation Principle and Evaluation of Result -- 3.2 The Result and Analysis of ME Simulation Experiment -- 3.3 Ms Simulation Data -- 3.4 Real Datasets -- 4 Comparative Experiments and Results -- 5 Conclusion -- References -- A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases -- 1 Introduction -- 2 Related Work -- 3 Methods -- 3.1 Implementation -- 3.2 Relationship Between Data Sources -- 3.3 Semantic Structure -- 3.4 Data Readers -- 4 Results -- 5 Discussion -- 6 Conclusions -- References -- Unsupervised Investigation of Information Captured in Pathway Activity Score in scRNA-Seq Analysis -- 1 Introduction -- 2 Materials and Methods -- 2.1 Data Acquisition and Pre-processing -- 2.2 Tested Pathway Activity Transformation Algorithms -- 2.3 Algorithm's Evaluation -- 3 Results -- 3.1 Cell Type Separation -- 3.2 Clustering Accuracy -- 3.3 Biological Validation -- 4 Conclusions -- References -- Meta-analysis of Gene Activity (MAGA) Contributions and Correlation with Gene Expression, Through GAGAM -- 1 Introduction -- 2 Background -- 2.1 Single-Cell Sequencing Technologies -- 2.2 GAGAM -- 3 Meta-analysis -- 3.1 Peaks Information -- 3.2 Activity-Expression Correlation -- 3.3 Activity-Expression Coherence -- 3.4 Conclusions -- References -- Predicting Papillary Renal Cell Carcinoma Prognosis Using Integrative Analysis of Histopathological Images and Genomic Data -- 1 Introduction -- 2 Materials and Methods -- 2.1 Dataset Overview -- 2.2 Histopathological Image Processing -- 2.3 Gene Coexpression Analysis -- 2.4 Risk Categorization -- 2.5 Prognosis Prediction Model. 3 Results -- 3.1 Patient Characteristics -- 3.2 Prognosis-related Image Features and Co-expression Gene Module Selection -- 3.3 Enrichment Analysis of the Key Gene Modules -- 3.4 Construction and Evaluation of the Integrative Prognostic Model -- 4 Discussion and Conclusion -- References -- Image Visualization and Signal Analysis -- Medical X-ray Image Classification Method Based on Convolutional Neural Networks -- 1 Introduction -- 2 Image Classification Optimization -- 3 Segmentaion of X-ray Image -- 3.1 Conventional Diagnostics and Segmentation Data -- 3.2 Creating and Training a Segmenting Convolutional Network -- 4 Image Reduction and Neural Network Training -- 4.1 Generating of Segmented Images -- 4.2 Active Regions Computation -- 4.3 Analysis of the Segmented Image -- 4.4 Image Reduction -- 4.5 Training of a Classifying Convolutional Neural Network -- 5 Experimental Results and Discussion -- 6 Conclusion -- References -- Digital Breast Tomosynthesis Reconstruction Techniques in Healthcare Systems: A Review -- 1 Introduction -- 2 Tomosynthesis Technology for Breast Imaging -- 2.1 The Advantages of Tomosynthesis Compared to 2D Mammography -- 3 Methods of Reconstruction Phase -- 3.1 The Importance of the Reconstruction Phase in CAD Systems -- 3.2 Back-Projection Algorithms -- 3.3 Transform Algorithms -- 3.4 Algebraic Reconstruction Techniques -- 3.5 Statistical Reconstruction Techniques -- 4 Analysis and Discussions -- 5 Conclusion and Future Works -- References -- BCAnalyzer: A Semi-automated Tool for the Rapid Quantification of Cell Monolayer from Microscopic Images in Scratch Assay -- 1 Introduction -- 2 Materials and Methods -- 2.1 Sample Images Used for the Algorithm Demonstration -- 2.2 Image Set for a Systematic Algorithm Performance Validation -- 3 Software Implementation -- 4 Results and Discussion. 4.1 Prominent Examples of Cell Scratch Assay Analysis for Different Cell Lines -- 4.2 Systematic Algorithm Validation Using Previously Reported Reference Image Sets -- 5 Conclusion -- References -- Color Hippocampus Image Segmentation Using Quantum Inspired Firefly Algorithm and Merging of Channel-Wise Optimums -- 1 Introduction -- 2 Literature Survey -- 3 Proposed Method -- 4 Experimental Setup -- 5 Result and Analysis -- 6 Conclusion -- References -- Breast Cancer Histologic Grade Identification by Graph Neural Network Embeddings -- 1 Introduction -- 2 Related Works -- 3 Materials and Methods -- 3.1 The Used Datasets -- 3.2 Graph Neural Networks -- 3.3 Graph Construction -- 3.4 Experimental Setup -- 4 Results -- 5 Ablation Study -- 6 Conclusions -- References -- A Pilot Study of Neuroaesthetics Based on the Analysis of Electroencephalographic Connectivity Networks in the Visualization of Different Dance Choreography Styles -- 1 Introduction -- 2 Methods of Data Recording and Analysis -- 2.1 Experimental Paradigm -- 2.2 Processing and Analysis Methods -- 3 Results -- 4 Discussion -- 5 Conclusions -- References -- Machine Learning in Bioinformatics and Biomedicine -- Ethical Dilemmas, Mental Health, Artificial Intelligence, and LLM-Based Chatbots -- 1 Introduction -- 2 Methodology -- 3 Data Extraction and Analysis Procedure -- 4 Results -- 5 Ethical Analysis -- 6 Conclusions -- 7 LLM Chatbots, Quality of Care, Responsible Research, and Development in Mental Health -- 8 Access, Exclusion, and User Dependence on Chatbots -- 9 Responsibility and Human Supervision of Chatbots -- 10 Regulation and Chatbot Usage Policies -- 11 Limitations of the Present Review -- References -- Cyclical Learning Rates (CLR'S) for Improving Training Accuracies and Lowering Computational Cost -- 1 Introduction -- 2 Experimental Results and Analysis. 2.1 Data Collection, Preprocessing, Model Architecture, and Learning Rates. |
Record Nr. | UNISA-996538664803316 |
Rojas Ignacio | ||
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. di Salerno | ||
|
Bioinformatics and Biomedical Engineering : 10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12–14, 2023, Proceedings, Part I / / edited by Ignacio Rojas, Olga Valenzuela, Fernando Rojas Ruiz, Luis Javier Herrera, Francisco Ortuño |
Autore | Rojas Ignacio |
Edizione | [1st ed. 2023.] |
Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
Descrizione fisica | 1 online resource (588 pages) |
Disciplina |
570.285
610.28 |
Altri autori (Persone) |
ValenzuelaOlga
Rojas RuizFernando HerreraLuis Javier OrtuñoFrancisco |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Bioinformatics
Computer networks Engineering—Data processing Biomedical engineering Computational and Systems Biology Computer Communication Networks Data Engineering Biomedical Engineering and Bioengineering |
ISBN | 3-031-34953-9 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
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. |
Record Nr. | UNINA-9910734840903321 |
Rojas Ignacio | ||
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|
Bioinformatics and Biomedical Engineering : 10th International Work-Conference, IWBBIO 2023, Meloneras, Gran Canaria, Spain, July 12–14, 2023, Proceedings, Part II / / edited by Ignacio Rojas, Olga Valenzuela, Fernando Rojas Ruiz, Luis Javier Herrera, Francisco Ortuño |
Autore | Rojas Ignacio |
Edizione | [1st ed. 2023.] |
Pubbl/distr/stampa | Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 |
Descrizione fisica | 1 online resource (520 pages) |
Disciplina |
570.285
610.28 |
Altri autori (Persone) |
ValenzuelaOlga
Rojas RuizFernando HerreraLuis Javier OrtuñoFrancisco |
Collana | Lecture Notes in Bioinformatics |
Soggetto topico |
Bioinformatics
Biomedical engineering Computer networks Engineering—Data processing Computational and Systems Biology Biomedical Engineering and Bioengineering Computer Communication Networks Data Engineering |
ISBN | 3-031-34960-1 |
Formato | Materiale a stampa |
Livello bibliografico | Monografia |
Lingua di pubblicazione | eng |
Nota di contenuto |
Intro -- Preface -- Organization -- Contents - Part II -- Contents - Part I -- Feature Selection, Extraction, and Data Mining in Bioinformatics -- Agent Based Modeling of Fish Shoal Behavior -- 1 Introduction -- 2 Modeling -- 3 Methods -- 3.1 Multi agents Based Modeling and Simulation -- 4 Results and Discussion -- References -- Entropy Approach of Processing for Fish Acoustic Telemetry Data to Detect Atypical Behavior During Welfare Evaluation -- 1 Introduction -- 1.1 Biotelemetry -- 1.2 Fish Welfare -- 2 Dataset -- 3 Methods -- 4 Results -- 5 Conclusion -- References -- Determining HPV Status in Patients with Oropharyngeal Cancer from 3D CT Images Using Radiomics: Effect of Sampling Methods -- 1 Introduction -- 2 Material and Methods -- 2.1 Data Set -- 2.2 Image Pre-processing -- 2.3 Feature Extraction -- 2.4 Data Pre-processing and Resampling -- 2.5 Feature Selection -- 2.6 Model Training and Evaluation -- 3 Results -- 3.1 Data Pre-processing and Resampling -- 3.2 Feature Extraction -- 3.3 Feature Selection -- 3.4 Performance Evaluation -- 4 Discussion -- 5 Conclusion -- References -- MetaLLM: Residue-Wise Metal Ion Prediction Using Deep Transformer Model -- 1 Introduction -- 2 Methodology -- 2.1 MetaLLM: Residue-Wise Metal Ion Prediction -- 3 Experiments and Results -- 3.1 Experimental Details -- 3.2 Result Analysis -- 4 Conclusion -- References -- Genome-Phenome Analysis -- Prediction of Functional Effects of Protein Amino Acid Mutations -- 1 Introduction -- 2 Methods -- 2.1 nsSNV Datasets -- 2.2 Protein Mutation Prediction Methodology: The Holdout- nsSNV Algorithm -- 2.3 Consensus Holdout Training and Selection -- 2.4 Extreme Learning Machine -- 2.5 Random Forests -- 3 Results -- 4 Conclusions and Future Directions -- References -- Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach -- 1 Introduction.
2 Background -- 3 Methods -- 3.1 Reference -- 3.2 Dataset -- 3.3 Quality and Control -- 3.4 Pipeline -- 3.5 Workflow Management and Reproducibility -- 3.6 Benchmarking -- 3.7 Computational Resources -- 4 Results -- 4.1 Different Methods Performance -- 4.2 Computational Time -- 5 Discussion -- 6 Conclusion -- References -- Healthcare and Diseases -- Improving Fetal Health Monitoring: A Review of the Latest Developments and Future Directions -- 1 Introduction -- 2 Methods -- 2.1 Study Design -- 2.2 Search Strategy -- 2.3 Inclusion Criteria -- 2.4 Selection of Studies -- 2.5 Data Analysis -- 3 Result -- 4 Discussion -- 4.1 The Development of Monitoring Devices for Fetal Well-Being -- 4.2 Algorithm for More Accurate Maternal-Fetal FHR Filtering -- 4.3 Fetal Well-Being Indicators -- 4.4 Target Users -- 5 Conclusion -- References -- Deep Learning for Parkinson's Disease Severity Stage Prediction Using a New Dataset -- 1 Introduction -- 2 Related Work -- 3 Materials and Methods -- 3.1 Data Acquisition -- 3.2 Dataset Construction -- 3.3 Data Pre-processing -- 3.4 Proposed LSTM Model -- 4 Experiments -- 5 Conclusion -- References -- Improved Long-Term Forecasting of Emergency Department Arrivals with LSTM-Based Networks -- 1 Introduction -- 2 Materials and Methods -- 2.1 Data Acquisition -- 2.2 Exploration -- 2.3 Analysis Techniques -- 3 Results -- 4 Conclusion -- References -- High-Throughput Genomics: Bioinformatic Tools and Medical Applications -- Targeted Next Generation Sequencing of a Custom Capture Panel to Target Sequence 112 Cancer Related Genes in Breast Cancer Tumors ERBB2 Positive from Lleida (Spain) -- 1 Introduction -- 2 Methods -- 2.1 Breast Cancer Samples -- 2.2 Targeted Sequencing -- 2.3 Data Analysis -- 3 Results -- 3.1 Targeted Sequencing -- 3.2 Gene Signatures -- 4 Discussion -- References. An Accurate Algorithm for Identifying Mutually Exclusive Patterns on Multiple Sets of Genomic Mutations -- 1 Introduction -- 2 Method -- 2.1 Similarity and Mutual Exclusion Measure -- 2.2 Weighted Probability Search -- 2.3 Algorithm Steps -- 3 Discussion -- 3.1 ME Simulation Principle and Evaluation of Result -- 3.2 The Result and Analysis of ME Simulation Experiment -- 3.3 Ms Simulation Data -- 3.4 Real Datasets -- 4 Comparative Experiments and Results -- 5 Conclusion -- References -- A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases -- 1 Introduction -- 2 Related Work -- 3 Methods -- 3.1 Implementation -- 3.2 Relationship Between Data Sources -- 3.3 Semantic Structure -- 3.4 Data Readers -- 4 Results -- 5 Discussion -- 6 Conclusions -- References -- Unsupervised Investigation of Information Captured in Pathway Activity Score in scRNA-Seq Analysis -- 1 Introduction -- 2 Materials and Methods -- 2.1 Data Acquisition and Pre-processing -- 2.2 Tested Pathway Activity Transformation Algorithms -- 2.3 Algorithm's Evaluation -- 3 Results -- 3.1 Cell Type Separation -- 3.2 Clustering Accuracy -- 3.3 Biological Validation -- 4 Conclusions -- References -- Meta-analysis of Gene Activity (MAGA) Contributions and Correlation with Gene Expression, Through GAGAM -- 1 Introduction -- 2 Background -- 2.1 Single-Cell Sequencing Technologies -- 2.2 GAGAM -- 3 Meta-analysis -- 3.1 Peaks Information -- 3.2 Activity-Expression Correlation -- 3.3 Activity-Expression Coherence -- 3.4 Conclusions -- References -- Predicting Papillary Renal Cell Carcinoma Prognosis Using Integrative Analysis of Histopathological Images and Genomic Data -- 1 Introduction -- 2 Materials and Methods -- 2.1 Dataset Overview -- 2.2 Histopathological Image Processing -- 2.3 Gene Coexpression Analysis -- 2.4 Risk Categorization -- 2.5 Prognosis Prediction Model. 3 Results -- 3.1 Patient Characteristics -- 3.2 Prognosis-related Image Features and Co-expression Gene Module Selection -- 3.3 Enrichment Analysis of the Key Gene Modules -- 3.4 Construction and Evaluation of the Integrative Prognostic Model -- 4 Discussion and Conclusion -- References -- Image Visualization and Signal Analysis -- Medical X-ray Image Classification Method Based on Convolutional Neural Networks -- 1 Introduction -- 2 Image Classification Optimization -- 3 Segmentaion of X-ray Image -- 3.1 Conventional Diagnostics and Segmentation Data -- 3.2 Creating and Training a Segmenting Convolutional Network -- 4 Image Reduction and Neural Network Training -- 4.1 Generating of Segmented Images -- 4.2 Active Regions Computation -- 4.3 Analysis of the Segmented Image -- 4.4 Image Reduction -- 4.5 Training of a Classifying Convolutional Neural Network -- 5 Experimental Results and Discussion -- 6 Conclusion -- References -- Digital Breast Tomosynthesis Reconstruction Techniques in Healthcare Systems: A Review -- 1 Introduction -- 2 Tomosynthesis Technology for Breast Imaging -- 2.1 The Advantages of Tomosynthesis Compared to 2D Mammography -- 3 Methods of Reconstruction Phase -- 3.1 The Importance of the Reconstruction Phase in CAD Systems -- 3.2 Back-Projection Algorithms -- 3.3 Transform Algorithms -- 3.4 Algebraic Reconstruction Techniques -- 3.5 Statistical Reconstruction Techniques -- 4 Analysis and Discussions -- 5 Conclusion and Future Works -- References -- BCAnalyzer: A Semi-automated Tool for the Rapid Quantification of Cell Monolayer from Microscopic Images in Scratch Assay -- 1 Introduction -- 2 Materials and Methods -- 2.1 Sample Images Used for the Algorithm Demonstration -- 2.2 Image Set for a Systematic Algorithm Performance Validation -- 3 Software Implementation -- 4 Results and Discussion. 4.1 Prominent Examples of Cell Scratch Assay Analysis for Different Cell Lines -- 4.2 Systematic Algorithm Validation Using Previously Reported Reference Image Sets -- 5 Conclusion -- References -- Color Hippocampus Image Segmentation Using Quantum Inspired Firefly Algorithm and Merging of Channel-Wise Optimums -- 1 Introduction -- 2 Literature Survey -- 3 Proposed Method -- 4 Experimental Setup -- 5 Result and Analysis -- 6 Conclusion -- References -- Breast Cancer Histologic Grade Identification by Graph Neural Network Embeddings -- 1 Introduction -- 2 Related Works -- 3 Materials and Methods -- 3.1 The Used Datasets -- 3.2 Graph Neural Networks -- 3.3 Graph Construction -- 3.4 Experimental Setup -- 4 Results -- 5 Ablation Study -- 6 Conclusions -- References -- A Pilot Study of Neuroaesthetics Based on the Analysis of Electroencephalographic Connectivity Networks in the Visualization of Different Dance Choreography Styles -- 1 Introduction -- 2 Methods of Data Recording and Analysis -- 2.1 Experimental Paradigm -- 2.2 Processing and Analysis Methods -- 3 Results -- 4 Discussion -- 5 Conclusions -- References -- Machine Learning in Bioinformatics and Biomedicine -- Ethical Dilemmas, Mental Health, Artificial Intelligence, and LLM-Based Chatbots -- 1 Introduction -- 2 Methodology -- 3 Data Extraction and Analysis Procedure -- 4 Results -- 5 Ethical Analysis -- 6 Conclusions -- 7 LLM Chatbots, Quality of Care, Responsible Research, and Development in Mental Health -- 8 Access, Exclusion, and User Dependence on Chatbots -- 9 Responsibility and Human Supervision of Chatbots -- 10 Regulation and Chatbot Usage Policies -- 11 Limitations of the Present Review -- References -- Cyclical Learning Rates (CLR'S) for Improving Training Accuracies and Lowering Computational Cost -- 1 Introduction -- 2 Experimental Results and Analysis. 2.1 Data Collection, Preprocessing, Model Architecture, and Learning Rates. |
Record Nr. | UNINA-9910734849103321 |
Rojas Ignacio | ||
Cham : , : Springer Nature Switzerland : , : Imprint : Springer, , 2023 | ||
Materiale a stampa | ||
Lo trovi qui: Univ. Federico II | ||
|