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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
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
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
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
Opac: Controlla la disponibilità qui
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
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
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