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Bioinformatics and Biomedical Engineering - Francisco Ortuno


Year 2015

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e-Health Informed Foreign Patient and Physician Communication: The Perspective of Informed Consent1 Introduction2 Theoretical Framework: Media Mediated Communication3 e-Health Communication System3.1 Patient Module3.2 Physician Module4 Research MethodStudy 1 Patient-Physician Communication Experiences SharingStudy 2 Patient-Physician Communication System Design5 Results and DiscussionReferencesAppendixEmpirical Analysis of the Effect of eHealth on Medical Expenditures of Patients with Chronic Diseases1 Introduction2 eHealth of Nishi-Aizu Town2.1 Background of eHealth2.2 Implementation of e-Health3 Date and Methodology3.1 Sample Selection3.2 Characteristics of Data3.3 Methodology4 Results of Estimation4.1 Result of Estimation (1): All Diseases Individual Characteristics4.2 Results of Estimation (2): Individual Chronic Diseases5 Conclusion5.1 Success Factors of e-Health5.2 Economic Foundation of e-HealthReferencesImpact of Health Apps in Health and Computer Science Publications. A Systematic Review from 2010 to 20141 Introduction2 Methods3 Results and Discussion4 ConclusionsReferencesReviewed ArticlesAutomated Extraction of Food Intake Indicators from Continuous Meal Weight Measurements1 Introduction2 Methods2.1 Rule-Based Algorithm (RB)2.2 Greedy Quadratic Fitting (GQF)2.3 Rule Based with Quadratic Fitting (RBQF)3 Experimental Setup and Indicators4 Experimental Results5 ConclusionsReferencesSystem Development Ontology to Discover Lifestyle Patterns Associated with NCD1 Introduction2 Related Work3 Methodology4 Study Case4.1 Macrolevel Ontology Design4.2 Individual Ontology Design4.3 Ontologies Integration and Evaluation5 ConclusionsReferencesUSSD Technology a Low Cost Asset in Complementing Public Health Workers' Work Processes1 Introduction2 USSD Technology and eHealth Projects in Zimbabwe2.1 Mobile Money Transactions and mHealth Using USSD Technology3 Method4 Discussion5 ConclusionsReferencesEnergy Efficiency Study of Representative Microcontrollers for Wearable Electronics1 Introduction2 State of Art2.1 Human Body Applications2.2 State of Art of Energy Harvesting on Human Bodies3 Benchmarks on the Microcontrollers3.1 Benchmarks Overview3.2 Application of Benchmarks on the Microcontrollers3.3 Hardware Test Setup4 Performance Analysis5 ConclusionReferencesAnalysis of Inter-rater Reliability of the Mammography Assessment after Image Processing1 Introduction2 Materials and Methods2.1 Collection of Mammography Images2.2 Evaluation of Images by Radiologists2.3 Data Transformation2.4 Observer Consistency3 Results4 Discussion5 ConclusionReferencesA LOD-Based Service for Extracting Linked Open Emergency Healthcare Data1 Introduction2 Methods2.1 LOD Standards2.2 The LOD-Based Service2.3 Security Issues3 Results4 ConclusionReferencesDevelopment of an Auditory Cueing System to Assist Gait in Patients with Parkinson's Disease1 Introduction2 Background3 Methods3.1 Participants3.2 System Setup3.3 Procedures3.4 Analysis4 Results4.1 Non-Cued vs. Cued Walking Tests4.2 Free Walking Results4.3 Questionnaires5 Discussion6 ConclusionReferencesLinear Accelerator Bunkers: Shielding Verification1 Introduction2 Data and Methodology2.1 Case I: Cobalt System to Linear Accelerator Conversion2.2 Case II: Two Rooms with Irregular Walls of 1 m Thickness2.3 Case III: Two Rooms Design Upgrading from Low Energy to High Energy Devices3 Discussion and ConclusionReferencesNew IT Tools and Methods Improving Lifestyle of Young People1 Introduction2 Materials and Methods2.1 The Design Architecture2.2 The System Architecture3 ConclusionsReferencesXTENS A JSON-Based Digital Repository for Biomedical Data Management1 Background2 Results2.1 The Repository2.2 SEEG Use Case3 Discussion4 ConclusionsReferencesAn Innovative Platform for Person-Centric Health and Wellness Support1 Introduction2 Requirements of a Person-Centric Digital Health and Wellness Framework3 Mining Minds Platform3.1 Data Curation Layer3.2 Information Curation Layer3.3 Service Curation Layer3.4 Supporting Layer4 Business Model and Service Scenario5 ConclusionsReferencesAn Ontology for Dynamic Sensor Selection in Wearable Activity Recognition1 Introduction2 Related Work3 Motivation for the Use of Ontologies for Sensor Selection4 The Sensor Selection for Real-World Wearable Activity Recognition Ontology4.1 SS4RWWAR Upper Ontology4.2 SS4RWWAR Human Body Ontology5 ConclusionsReferencesProposal for Interoperability Standards Applications in the Health Sector1 Introduction2 Research Methodology3 HL74 Research Results4.1 General Architecture of the HCEU System4.2 HCEU Services4.3 CDA Services4.4 XDS Services4.5 PIX Services5 ConclusionsReferencesAn Event-Driven Architecture for Biomedical Data Integration and Interoperability1 Introduction2 Methods2.1 Background2.2 Architecture2.3 Workflow3 Discussion4 ConclusionsReferencesLocal Search for Multiobjective Multiple Sequence Alignment1 Introduction2 Multiple Sequence Alignment3 Multiobjective Multiple Sequence Alignment4 Pareto Local Search5 Experimental Analysis6 Conclusions and Further WorkReferencesAlignment Free Frequency Based Distance Measures for Promoter Sequence Comparison1 Introduction2 Method2.1 Generation of PSMM2.2 Frequency Distribution Analysis Methods2.2.1 Frequency Distribution Based Approach2.2.2 Frequency Variant 12.2.3 Frequency Variant 22.2.4 Cumulative Frequency Distribution3 Experimental Analysis3.1 Description of the Datasets3.2 Results and Discussion4 ConclusionReferencesEnergy-Efficient Architecture for DP Local Sequence Alignment: Exploiting ILP and DLP*1 Introduction2 Dynamic Programming Algorithms2.1 Smith-Waterman2.2 HMM Viterbi2.3 Parallelism Exploitation3 Proposed Architecture3.1 Architectural Units3.2 Instruction Set3.3 Interface4 Prototyping4.1 Scalability5 Evaluation5.1 Reference State-of-the-Art Architectures5.2 Algorithm Implementations5.3 Smith-Waterman Evaluation5.4 Viterbi Evaluation6 ConclusionReferencesHierarchical Assembly of Pools1 Introduction2 Methods2.1 Pool Pre-processing2.2 Overlap Detection2.3 A Merging Strategy3 Results4 Conclusions and Future WorkReferencesSimpLiSMS: A Simple, Lightweight and Fast Approach for Structured Motifs Searching*1 Introduction2 Preliminaries3 Methods4 SimpLiSMS Algorithm outline5 Handling Degenerate Strings6 Results7 ConclusionReferencesSuccesses and Pitfalls in Scoring Molecular Interactions1 Introduction2 Methods2.1 Interaction Model2.2 Ligand Pose Analysis2.3 Enrichment Analysis3 Results and DiscussionReferencesThe Use of Random Forest to Predict Binding Affinity in Docking1 Introduction2 Random Forest (RF) Scoring Functions3 Experimental Setup3.1 The PDBbind v2007 Benchmark3.2 The 2013 Blind Benchmark3.3 Performance Measures4 Results and Discussion4.1 Comparing the Performance of Scoring Functions4.2 Comparing RF-Score-3 with Vina4.3 Performance Improvement with Training Set Size 4.4 RF for Virtual Screening4.5 Conclusions and Future ProspectsReferencesStrong Inhomogeneity in Triplet Distribution Alongside a Genome1 Introduction2 Distribution to the Nearest Neighbour2.1 The Longest Bridges3 Results4 Discussion5 ConclusionReferencesPredicting Sub-cellular Location of Proteins Based on Hierarchical Clustering and Hidden Markov Models1 Introduction2 Background3 Experimental Set-Up3.1 Database4 Results and Discussion5 Conclusions and Future WorkReferencesRisk Quantification of Multigenic Conditions for SNP Array Based Direct-to-Consumer Genomic Services1 Introduction2 Methodology2.1 Importing Data and Associating SNPs with GWAS2.2 Filtering SNP-Trait Associations2.3 Asymptotic Bayes Factor Calculation2.4 Redundancy Check3 Results3.1 Filtering the SNPs for Multigenic Risk Assessment3.2 Asymptotic Bayes Factor3.3 Removing Redundant SNP/Trait Association Based on the ABF4 DiscussionReferencesComputational Inference in Systems Biology1 Introduction2 Methodology3 Alternative Methods for Comparison4 Data5 Simulation6 Results7 DiscussionReferencesA Price We Pay for Inexact Dimensionality Reduction1 Introduction2 LDA, a Case When Sample Size Exceeds Dimensionality3 LDA, a Case When Dimensionality Exceeds Sample Size4 Simulation Experiments5 ConclusionsReferencesAn Ensemble of Cooperative Parallel Metaheuristics for Gene Selection in Cancer Classification1 Introduction2 Proposed Approach ECPM-FS2.1 General Framework of the Proposed Approach2.2 Generation Step2.3 Consensus Step3 Experiments and Discussions3.1 Experimental Setting3.2 Results and Discussions4 Conclusion and Future WorkReferencesDEgenes Hunter A Self-customised Gene Expression Analysis Workflow for Non-model1 Introduction2 Methods2.1 Data Import2.2 Experimental Data2.3 Normalisation and Data Filtering2.4 R Packages and DEG Analyses3 Results3.1 Workflow Details3.2 Performance Testing3.3 PDF Report4 DiscussionReferencesBioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes1 Introduction2 Materials and Methods2.1 Prediction Algorithms2.2 Gold Standard Dataset2.3 Full-LengtherNext Transcriptome Analysis and Annotation2.4 Preparation of de novo Transcriptome Samples3 Results and Discussion3.1 Software Comparison Using Known Coding Sequences3.2 Software Comparison Using de novo Transcriptomes3.3 Validation of FLN Sure and Putative Quality Assessment3.4 Detection of Species-Specific TranscriptsReferencesEvaluation of Combined Genome Assemblies: A Case Study with Fungal Genomes1 Introduction2 Method2.1 Data2.2 Assemblies2.3 Metrics3 Results4 Discussion and ConclusionsAuthors' ContributionsReferencesUsing Multivariate Analysis and Bioinformatic Tools to Elucidate the Functions of a Cyanobacterial Global Regulator from RNA-Seq Data Obtained in Different Genetic and Environmental Backgrounds1 Introduction2 Methods3 Results and Discussion3.1 Marker Allele Φ(C.S3-pipX ) Affects Expression of Multiple Genes in S. elongatus3.2 Insights into PipX Functions at Different Regulons Informed by Clustering of Gene Expression Patterns3.3 Development of the Perl-Based Program MultiGS and Searches for Regulatory MotifsReferencesHvDBase : A Web Resource on Hydra VulgarisTranscriptome1 Introduction2 Material and Methods2.1 HvDBase Annotation2.2 HvDBase Pipeline2.3 Database Technology3 Results3.1 Database Content3.2 A Case Study4 ConclusionReferencesNucleotide Sequence Alignment and Compression via Shortest Unique Substring*1 IntroductionThe Idea and Our ContributionOrganization of the Paper2 Shortest Unique Substring Identifiers of the Genome3 SUS Analysis of the Human Reference Genome4 SUS Dictionary MatchingThe Preprocessing PhaseThe Searching Phase5 Results6 Conclusions and Future WorksReferencesModeling of the Urothelium with an Agent Based Approach1 Introduction2 Methods2.1 Biological Processes2.2 Fitness Function3 Results4 Discussion5 ConclusionReferencesSystematic Comparison of Machine Learning Methods for Identification of miRNA Species1. Introduction2. Methods2.1 Human miRNA Expression Data Sets2.2 Machine Leaning Methods3 Results3.1 Selection of the Human miRNA Expression Data Sets3.2 Empirical Prediction Ability of the Machine Learning Methods3.3 Selected Candidate Disease-Related miRNAs4 DiscussionReferencesNumerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues1 Background2 Methodology3 Results3.1 Most Informative Eigenvalues3.2 Graph Spectra Behavior of Evolving Networks3.3 Spectra Signatures4 ConclusionsReferencesMixture Model Based Efficient Method for Magnetic Resonance Spectra Quantification1 Introduction2 Methods2.1 Data2.2 Data Pre-processing2.3 Gaussian Mixture Model2.4 Metabolite Quantification2.5 EM Algorithm Implementation2.6 Hardware3 Results3.1 Simulated Data3.2 Phantom Dataset4 Discussion5 ConclusionsReferencesNoise and Baseline Filtration in Mass Spectrometry1 Introduction2 ApproachReferencesBioWes – From Design of Experiment, through Protocol to Repository, Control, Standardization and Back-Tracking1 Introduction2 Protocol Generator3 Local Database4 Sharing and ManagementReferencesMeasurement in Biological Systems from the Self-organisation Point of View1 Introduction2 Technical Limits of the Information Content of the Measurement3 Phenomenological Variables and Measurement in Chemistry4 Properties of the Model of a Biological Experimental System5 Measurement in Biological Systems6 ConclusionsReferencesFRAP & FLIP: Two Sides of the Same Coin?1 Introduction2 Preliminaries2.1 FRAP & FLIP Images Acquisition and Their Biological Interpretation2.2 FRAP & FLIP Data Structure and (Pre)Processing2.3 Reaction-Diffusion System as Initial Boundary Value Problem3 Model Parameter Estimation and Sensitivity Analysis3.1 Parameter Estimation Based on Spatio-temporal Data3.2 Sensitivity Analysis and Confidence Intervals3.3 Theoretical Results on Data Space Selection and DOE4 Concluding RemarksReferencesMicroRNA Target Prediction Based Upon Metastable RNA Secondary Structures1 Introduction2 Methods2.1 Metastable Secondary Structures2.2 Identification of Putative Nucleation Sites2.3 [Binding Region, miRNA]-Duplex Structure Prediction2.4 Integration of Target Site Accessibility2.5 miRNA-Target Score Derived from a Single Binding Site2.6 MicroRNA Target Prediction Scores2.7 Metastable Conformations Sets3 Results3.1 Test Dataset3.2 Energy Scores3.3 Comparison to other Computational Methods4 ConclusionReferencesInference of Circadian Regulatory Pathways Based on Delay Differential Equations1 Introduction1.1 Biological Background/Motivation1.2 Network Inference2 Methods2.1 Reaction Graph2.2 The Dynamical Model2.3 The Observation Model2.4 Adaptive Gradient Matching2.5 Gaussian Process Modelling2.6 Statistical Model2.7 Sampling2.8 Model Selection Using Deviance Information Criterion3 Results3.1 Mouse Liver Model3.2 Model Selection Experiment3.3 Parameter Estimation4 ConclusionReferencesSimplifying Tele-rehabilitation Devices for Their Practical Use in Non-clinical Environments*1 Introduction2 Wearable Tele-Rehabilitation System Components3 System Requirements3.1 Monitoring Subsystem3.2 Interaction Between System and User3.3 Handling of Errors and Unforeseen Conditions4 Proposed System4.1 Sensor Nodes4.2 The Application Running on the Mobile Device4.3 The Complete System Usage5 ConclusionsReferencesNon-intrusive Patient Monitoring for Supporting General Practitioners in Following Diseases Evolution1 Introduction2 Reference Methodology3 Considered Motor Tests3.1 Gait Speed3.2 Sit-to-Stand3.3 Technology for Index Extraction4 Scenarios4.1 Single Patient Scenario4.2 Associations Scenario5 ConclusionsReferencesInteractive Business Models for Telerehabilitation after Total Knee Replacement: Preliminary Results from Tuscany1 Introduction2 Methods2.1 Key Activities2.2 Customer/Patient Segments2.3 Key Resources3 Results3.1 Designing Phase: Models for Telerehabilitation3.2 Development Phase: Insights from Decision Makers in Tuscany4 DiscussionReferencesOntological Personal Healthcare Using Medical Standards1 Introduction2 Background3 Personal Mobile Healthcare System (PMHS)4 Personalized Disease Tracking Framework (PDTF)4.1 Vital Sign Analysis4.2 Categories of Patterns5 ConclusionFuture WorkReferencesApplications of High Performance Computing in Bioinformatics, Computational Biology1 Introduction2 HPC Architectures2.1 GPU Computing3 Applications3.1 Virtual Screening3.2 Parallel Processing of Microarray Data3.3 Big Data Analytics and Network Models in Biomedical Informatics4 Conclusions and OutlookReferencesComputing Biological Model Parameters by Parallel Statistical Model Checking*1 Introduction2 Background2.1 Parametric Dynamical Systems2.2 Biological Admissibility3 Computation of Admissible Parameters3.1 Algorithm Outline3.2 Parameter Probability Space3.3 Algorithm Correctness4 Experimental Results4.1 Experimental Setting4.2 Experimental Results5 ConclusionsReferencesMobile Access to On-line Analytic Bioinformatics Tools1 Introduction2 Background2.1 Considerations for Mobile Interfaces2.2 Repositories of Bioinformatics Services: Browsing, Discovering and Invocation2.3 Additional Functionality3 System and Methods3.1 The Proposed Architecture3.2 Implementation3.3 User Interface3.3.1 Browsing the Catalogue3.3.2 Discovering Services3.3.3 Invocation3.3.4 File System4 ResultsDiving into the mORCA application5 Discussion and ConclusionsReferencesisDNA: A Tool for Real-Time Visualization of Plasmid DNA Monte-Carlo Simulations in 3D1 Introduction2 Related Work2.1 DNA Assembly Methods: Predictive versus Adaptive2.2 Deformation Methods for pDNA Simulations3 Real-Time Adaptive DNA Assembly4 Plasmid DNA Monte-Carlo Simulation Method4.1 Monte-Carlo Method4.2 Deformation Algorithm5 The Software5.1 The GUI5.2 The API5.3 Features and Future Work6 ConclusionsReferencesTransport Properties of RNA Nanotubes Using Molecular Dynamics Simulation1 Introduction2 Computational Details3 Results and Discussion4 Conclusions and OutlookReferencesMolecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach1 Introduction2 Method3 Results and Discussion4 ConclusionReferencesPredicting Atherosclerotic Plaque Location in an Iliac Bifurcation Using a Hybrid CFD/Biomechanical Approach1 Introduction2 Methods2.1 Geometry2.2 Computational Fluid Dynamics2.3 Atherogenesis3 Results4 Discussion5 ConclusionsReferencesIdentification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments1 Introduction2 Experimental Suite2.1 Network Creation and Manipulation2.2 Gateway Node Identification2.3 High Performance Computing Environment2.4 Parallel Implementation3 Results3.1 Model Organism – S. cerevisiae Gateway Nodes3.2 Known Dataset – GSE5078 Gateway Nodes3.3 Scalability4 DiscussionReferencesEnhancing the Parallelization of Non-bonded Interactions Kernel for Virtual Screening1 Introduction2 The Lennard-Jones Potential on the Graphics Processing Units2.1 The Roadmap for the Optimization2.2 Our Departure GPU Design2.3 Improving Memory Usage and Throughput3 Experimental Results4 Conclusions and OutlookReferencesPrediction of Functional Types of Ligands for G Protein-Coupled Receptors with Dynamically Discriminable States Embedded in Low Dimension1 Introduction2 Adenosine Receptor3 Markov Model Analysis4 Conformations in Different StatesReferencesImproving Activity Prediction of Adenosine A2B Receptor Antagonists by Nonlinear Models1 Introduction2 Material and Methods2.1 MaterialData setMolecular Descriptors2.2 MethodsSample Interval SelectionClassification and Estimation the Range of Each Ligand Activity3 Results3.1 Interval Selection3.2 Classification and Estimation the Range of Each Ligand Activity4 Discussion5 ConclusionsReferencesSupport Vector Machine Prediction of Drug Solubility on GPUs1 Introduction2 Methodology2.1 GPU Architecture and CUDA Overview2.2 Support Vector Machines2.3 Ligand Databases and Molecular Properties3 Experimentation SVM3.1 Sequential version of SVM (CPU)3.2 Parallel Version of SVM (GPU)4 Experimentation5 Conclusions and Future WorkReferencesDIA-DB: A Web-Accessible Database for the Prediction of Diabetes Drugs1 Introduction2 DIA-DB Architecture3 Diabetes Database Model4 Virtual Screening4.1 Ligand Similarity Based Virtual Screening4.2 Structure Based Virtual Screening: Docking5 Use Cases6 Conclusion and OutlookReferencesMolecular Docking and Biological Evaluation of Functionalized benzo[h]quinolones as Colon Cancer Agents1 Introduction2 Material Methods2.1 Chemical Synthesis2.1.1 General Experimental Procedures2.2 Biology2.2.1 Reagents and Consumables2.2.2 MTT Assay2.3 Molecular Docking Study3 Result and Discussion3.1 Biological Evaluation Study3.1.1 Cytotoxicity3.1.2 Molecular Modeling and Analysis of the Docked Results3.1.3 Pharmacokinetic Parameters Compliance4 ConclusionReferencesPredicting Cross-Reactivity from Computational Studies for Pre-evaluation of Specific Hepatic Glycogen Phosphorylase Inhibitors-insilico Screening of Drugs for Evaluating Specificity1 Introduction2 Materials and Methods2.1 Data Set2.2 Sequence Analysis2.3 Homology Modelling2.4 Computation Details2.5 Molecular Docking3 Results and Discussion3.1 Sequence Analysis and Homology Modeling3.2 Molecular Docking Studies4 ConclusionReferencesExternalising Moods and Psychological States to Smooth Pet-robot/Child Interaction through Bluetooth Communication1 Introduction1.1 Therapeutic Robots1.2 Robot Autonomy1.3 Technical Framework2 The Proposed Solution2.1 Hardware2.2 Interface3 Development of the Solution3.1 Connection via Terminal3.2 Bluetooth Assembly3.3 Power Troubles3.4 Android App4 Results and Discussion5 ConclusionsReferencesPatient Lifecycle Management: An Approach for Clinical Processes1 Introduction2 About PLM3 Patient Oriented Clinical Processes4 Conclusions and Future WorkReferencesAdvertising Liking Recognition Technique Applied to Neuromarketing by Using Low-Cost EEG Headset1 Introduction2 Related Works3 Dataset4 Advertising Recognition Method5 Future Works6 ConclusionsReferencesHeart Rate Variability Indicating Stress Visualized by Correlations Plots1 Introduction2 State of the Art3 System Architecture4 Stress Detection Method5 Application of System and Results Obtained6 Conclusions and Future WorkReferencesEmotions and Diabetes1 Introduction2 Stress, Illness and Diabetes3 Addition of Sensors4 Discussion5 ConclusionReferencese-Health Informed Foreign Patient and Physician Communication: The Perspective of Informed Consent1 Introduction2 Theoretical Framework: Media Mediated Communication3 e-Health Communication System3.1 Patient Module3.2 Physician Module4 Research MethodStudy 1 Patient-Physician Communication Experiences SharingStudy 2 Patient-Physician Communication System Design5 Results and DiscussionReferencesAppendixEmpirical Analysis of the Effect of eHealth on Medical Expenditures of Patients with Chronic Diseases1 Introduction2 eHealth of Nishi-Aizu Town2.1 Background of eHealth2.2 Implementation of e-Health3 Date and Methodology3.1 Sample Selection3.2 Characteristics of Data3.3 Methodology4 Results of Estimation4.1 Result of Estimation (1): All Diseases Individual Characteristics4.2 Results of Estimation (2): Individual Chronic Diseases5 Conclusion5.1 Success Factors of e-Health5.2 Economic Foundation of e-HealthReferencesImpact of Health Apps in Health and Computer Science Publications. A Systematic Review from 2010 to 20141 Introduction2 Methods3 Results and Discussion4 ConclusionsReferencesReviewed ArticlesAutomated Extraction of Food Intake Indicators from Continuous Meal Weight Measurements1 Introduction2 Methods2.1 Rule-Based Algorithm (RB)2.2 Greedy Quadratic Fitting (GQF)2.3 Rule Based with Quadratic Fitting (RBQF)3 Experimental Setup and Indicators4 Experimental Results5 ConclusionsReferencesSystem Development Ontology to Discover Lifestyle Patterns Associated with NCD1 Introduction2 Related Work3 Methodology4 Study Case4.1 Macrolevel Ontology Design4.2 Individual Ontology Design4.3 Ontologies Integration and Evaluation5 ConclusionsReferencesUSSD Technology a Low Cost Asset in Complementing Public Health Workers' Work Processes1 Introduction2 USSD Technology and eHealth Projects in Zimbabwe2.1 Mobile Money Transactions and mHealth Using USSD Technology3 Method4 Discussion5 ConclusionsReferencesEnergy Efficiency Study of Representative Microcontrollers for Wearable Electronics1 Introduction2 State of Art2.1 Human Body Applications2.2 State of Art of Energy Harvesting on Human Bodies3 Benchmarks on the Microcontrollers3.1 Benchmarks Overview3.2 Application of Benchmarks on the Microcontrollers3.3 Hardware Test Setup4 Performance Analysis5 ConclusionReferencesAnalysis of Inter-rater Reliability of the Mammography Assessment after Image Processing1 Introduction2 Materials and Methods2.1 Collection of Mammography Images2.2 Evaluation of Images by Radiologists2.3 Data Transformation2.4 Observer Consistency3 Results4 Discussion5 ConclusionReferencesA LOD-Based Service for Extracting Linked Open Emergency Healthcare Data1 Introduction2 Methods2.1 LOD Standards2.2 The LOD-Based Service2.3 Security Issues3 Results4 ConclusionReferencesDevelopment of an Auditory Cueing System to Assist Gait in Patients with Parkinson's Disease1 Introduction2 Background3 Methods3.1 Participants3.2 System Setup3.3 Procedures3.4 Analysis4 Results4.1 Non-Cued vs. Cued Walking Tests4.2 Free Walking Results4.3 Questionnaires5 Discussion6 ConclusionReferencesLinear Accelerator Bunkers: Shielding Verification1 Introduction2 Data and Methodology2.1 Case I: Cobalt System to Linear Accelerator Conversion2.2 Case II: Two Rooms with Irregular Walls of 1 m Thickness2.3 Case III: Two Rooms Design Upgrading from Low Energy to High Energy Devices3 Discussion and ConclusionReferencesNew IT Tools and Methods Improving Lifestyle of Young People1 Introduction2 Materials and Methods2.1 The Design Architecture2.2 The System Architecture3 ConclusionsReferencesXTENS A JSON-Based Digital Repository for Biomedical Data Management1 Background2 Results2.1 The Repository2.2 SEEG Use Case3 Discussion4 ConclusionsReferencesAn Innovative Platform for Person-Centric Health and Wellness Support1 Introduction2 Requirements of a Person-Centric Digital Health and Wellness Framework3 Mining Minds Platform3.1 Data Curation Layer3.2 Information Curation Layer3.3 Service Curation Layer3.4 Supporting Layer4 Business Model and Service Scenario5 ConclusionsReferencesAn Ontology for Dynamic Sensor Selection in Wearable Activity Recognition1 Introduction2 Related Work3 Motivation for the Use of Ontologies for Sensor Selection4 The Sensor Selection for Real-World Wearable Activity Recognition Ontology4.1 SS4RWWAR Upper Ontology4.2 SS4RWWAR Human Body Ontology5 ConclusionsReferencesProposal for Interoperability Standards Applications in the Health Sector1 Introduction2 Research Methodology3 HL74 Research Results4.1 General Architecture of the HCEU System4.2 HCEU Services4.3 CDA Services4.4 XDS Services4.5 PIX Services5 ConclusionsReferencesAn Event-Driven Architecture for Biomedical Data Integration and Interoperability1 Introduction2 Methods2.1 Background2.2 Architecture2.3 Workflow3 Discussion4 ConclusionsReferencesLocal Search for Multiobjective Multiple Sequence Alignment1 Introduction2 Multiple Sequence Alignment3 Multiobjective Multiple Sequence Alignment4 Pareto Local Search5 Experimental Analysis6 Conclusions and Further WorkReferencesAlignment Free Frequency Based Distance Measures for Promoter Sequence Comparison1 Introduction2 Method2.1 Generation of PSMM2.2 Frequency Distribution Analysis Methods2.2.1 Frequency Distribution Based Approach2.2.2 Frequency Variant 12.2.3 Frequency Variant 22.2.4 Cumulative Frequency Distribution3 Experimental Analysis3.1 Description of the Datasets3.2 Results and Discussion4 ConclusionReferencesEnergy-Efficient Architecture for DP Local Sequence Alignment: Exploiting ILP and DLP*1 Introduction2 Dynamic Programming Algorithms2.1 Smith-Waterman2.2 HMM Viterbi2.3 Parallelism Exploitation3 Proposed Architecture3.1 Architectural Units3.2 Instruction Set3.3 Interface4 Prototyping4.1 Scalability5 Evaluation5.1 Reference State-of-the-Art Architectures5.2 Algorithm Implementations5.3 Smith-Waterman Evaluation5.4 Viterbi Evaluation6 ConclusionReferencesHierarchical Assembly of Pools1 Introduction2 Methods2.1 Pool Pre-processing2.2 Overlap Detection2.3 A Merging Strategy3 Results4 Conclusions and Future WorkReferencesSimpLiSMS: A Simple, Lightweight and Fast Approach for Structured Motifs Searching*1 Introduction2 Preliminaries3 Methods4 SimpLiSMS Algorithm outline5 Handling Degenerate Strings6 Results7 ConclusionReferencesSuccesses and Pitfalls in Scoring Molecular Interactions1 Introduction2 Methods2.1 Interaction Model2.2 Ligand Pose Analysis2.3 Enrichment Analysis3 Results and DiscussionReferencesThe Use of Random Forest to Predict Binding Affinity in Docking1 Introduction2 Random Forest (RF) Scoring Functions3 Experimental Setup3.1 The PDBbind v2007 Benchmark3.2 The 2013 Blind Benchmark3.3 Performance Measures4 Results and Discussion4.1 Comparing the Performance of Scoring Functions4.2 Comparing RF-Score-3 with Vina4.3 Performance Improvement with Training Set Size 4.4 RF for Virtual Screening4.5 Conclusions and Future ProspectsReferencesStrong Inhomogeneity in Triplet Distribution Alongside a Genome1 Introduction2 Distribution to the Nearest Neighbour2.1 The Longest Bridges3 Results4 Discussion5 ConclusionReferencesPredicting Sub-cellular Location of Proteins Based on Hierarchical Clustering and Hidden Markov Models1 Introduction2 Background3 Experimental Set-Up3.1 Database4 Results and Discussion5 Conclusions and Future WorkReferencesRisk Quantification of Multigenic Conditions for SNP Array Based Direct-to-Consumer Genomic Services1 Introduction2 Methodology2.1 Importing Data and Associating SNPs with GWAS2.2 Filtering SNP-Trait Associations2.3 Asymptotic Bayes Factor Calculation2.4 Redundancy Check3 Results3.1 Filtering the SNPs for Multigenic Risk Assessment3.2 Asymptotic Bayes Factor3.3 Removing Redundant SNP/Trait Association Based on the ABF4 DiscussionReferencesComputational Inference in Systems Biology1 Introduction2 Methodology3 Alternative Methods for Comparison4 Data5 Simulation6 Results7 DiscussionReferencesA Price We Pay for Inexact Dimensionality Reduction1 Introduction2 LDA, a Case When Sample Size Exceeds Dimensionality3 LDA, a Case When Dimensionality Exceeds Sample Size4 Simulation Experiments5 ConclusionsReferencesAn Ensemble of Cooperative Parallel Metaheuristics for Gene Selection in Cancer Classification1 Introduction2 Proposed Approach ECPM-FS2.1 General Framework of the Proposed Approach2.2 Generation Step2.3 Consensus Step3 Experiments and Discussions3.1 Experimental Setting3.2 Results and Discussions4 Conclusion and Future WorkReferencesDEgenes Hunter A Self-customised Gene Expression Analysis Workflow for Non-model1 Introduction2 Methods2.1 Data Import2.2 Experimental Data2.3 Normalisation and Data Filtering2.4 R Packages and DEG Analyses3 Results3.1 Workflow Details3.2 Performance Testing3.3 PDF Report4 DiscussionReferencesBioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes1 Introduction2 Materials and Methods2.1 Prediction Algorithms2.2 Gold Standard Dataset2.3 Full-LengtherNext Transcriptome Analysis and Annotation2.4 Preparation of de novo Transcriptome Samples3 Results and Discussion3.1 Software Comparison Using Known Coding Sequences3.2 Software Comparison Using de novo Transcriptomes3.3 Validation of FLN Sure and Putative Quality Assessment3.4 Detection of Species-Specific TranscriptsReferencesEvaluation of Combined Genome Assemblies: A Case Study with Fungal Genomes1 Introduction2 Method2.1 Data2.2 Assemblies2.3 Metrics3 Results4 Discussion and ConclusionsAuthors' ContributionsReferencesUsing Multivariate Analysis and Bioinformatic Tools to Elucidate the Functions of a Cyanobacterial Global Regulator from RNA-Seq Data Obtained in Different Genetic and Environmental Backgrounds1 Introduction2 Methods3 Results and Discussion3.1 Marker Allele Φ(C.S3-pipX ) Affects Expression of Multiple Genes in S. elongatus3.2 Insights into PipX Functions at Different Regulons Informed by Clustering of Gene Expression Patterns3.3 Development of the Perl-Based Program MultiGS and Searches for Regulatory MotifsReferencesHvDBase : A Web Resource on Hydra VulgarisTranscriptome1 Introduction2 Material and Methods2.1 HvDBase Annotation2.2 HvDBase Pipeline2.3 Database Technology3 Results3.1 Database Content3.2 A Case Study4 ConclusionReferencesNucleotide Sequence Alignment and Compression via Shortest Unique Substring*1 IntroductionThe Idea and Our ContributionOrganization of the Paper2 Shortest Unique Substring Identifiers of the Genome3 SUS Analysis of the Human Reference Genome4 SUS Dictionary MatchingThe Preprocessing PhaseThe Searching Phase5 Results6 Conclusions and Future WorksReferencesModeling of the Urothelium with an Agent Based Approach1 Introduction2 Methods2.1 Biological Processes2.2 Fitness Function3 Results4 Discussion5 ConclusionReferencesSystematic Comparison of Machine Learning Methods for Identification of miRNA Species1. Introduction2. Methods2.1 Human miRNA Expression Data Sets2.2 Machine Leaning Methods3 Results3.1 Selection of the Human miRNA Expression Data Sets3.2 Empirical Prediction Ability of the Machine Learning Methods3.3 Selected Candidate Disease-Related miRNAs4 DiscussionReferencesNumerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues1 Background2 Methodology3 Results3.1 Most Informative Eigenvalues3.2 Graph Spectra Behavior of Evolving Networks3.3 Spectra Signatures4 ConclusionsReferencesMixture Model Based Efficient Method for Magnetic Resonance Spectra Quantification1 Introduction2 Methods2.1 Data2.2 Data Pre-processing2.3 Gaussian Mixture Model2.4 Metabolite Quantification2.5 EM Algorithm Implementation2.6 Hardware3 Results3.1 Simulated Data3.2 Phantom Dataset4 Discussion5 ConclusionsReferencesNoise and Baseline Filtration in Mass Spectrometry1 Introduction2 ApproachReferencesBioWes – From Design of Experiment, through Protocol to Repository, Control, Standardization and Back-Tracking1 Introduction2 Protocol Generator3 Local Database4 Sharing and ManagementReferencesMeasurement in Biological Systems from the Self-organisation Point of View1 Introduction2 Technical Limits of the Information Content of the Measurement3 Phenomenological Variables and Measurement in Chemistry4 Properties of the Model of a Biological Experimental System5 Measurement in Biological Systems6 ConclusionsReferencesFRAP & FLIP: Two Sides of the Same Coin?1 Introduction2 Preliminaries2.1 FRAP & FLIP Images Acquisition and Their Biological Interpretation2.2 FRAP & FLIP Data Structure and (Pre)Processing2.3 Reaction-Diffusion System as Initial Boundary Value Problem3 Model Parameter Estimation and Sensitivity Analysis3.1 Parameter Estimation Based on Spatio-temporal Data3.2 Sensitivity Analysis and Confidence Intervals3.3 Theoretical Results on Data Space Selection and DOE4 Concluding RemarksReferencesMicroRNA Target Prediction Based Upon Metastable RNA Secondary Structures1 Introduction2 Methods2.1 Metastable Secondary Structures2.2 Identification of Putative Nucleation Sites2.3 [Binding Region, miRNA]-Duplex Structure Prediction2.4 Integration of Target Site Accessibility2.5 miRNA-Target Score Derived from a Single Binding Site2.6 MicroRNA Target Prediction Scores2.7 Metastable Conformations Sets3 Results3.1 Test Dataset3.2 Energy Scores3.3 Comparison to other Computational Methods4 ConclusionReferencesInference of Circadian Regulatory Pathways Based on Delay Differential Equations1 Introduction1.1 Biological Background/Motivation1.2 Network Inference2 Methods2.1 Reaction Graph2.2 The Dynamical Model2.3 The Observation Model2.4 Adaptive Gradient Matching2.5 Gaussian Process Modelling2.6 Statistical Model2.7 Sampling2.8 Model Selection Using Deviance Information Criterion3 Results3.1 Mouse Liver Model3.2 Model Selection Experiment3.3 Parameter Estimation4 ConclusionReferencesSimplifying Tele-rehabilitation Devices for Their Practical Use in Non-clinical Environments*1 Introduction2 Wearable Tele-Rehabilitation System Components3 System Requirements3.1 Monitoring Subsystem3.2 Interaction Between System and User3.3 Handling of Errors and Unforeseen Conditions4 Proposed System4.1 Sensor Nodes4.2 The Application Running on the Mobile Device4.3 The Complete System Usage5 ConclusionsReferencesNon-intrusive Patient Monitoring for Supporting General Practitioners in Following Diseases Evolution1 Introduction2 Reference Methodology3 Considered Motor Tests3.1 Gait Speed3.2 Sit-to-Stand3.3 Technology for Index Extraction4 Scenarios4.1 Single Patient Scenario4.2 Associations Scenario5 ConclusionsReferencesInteractive Business Models for Telerehabilitation after Total Knee Replacement: Preliminary Results from Tuscany1 Introduction2 Methods2.1 Key Activities2.2 Customer/Patient Segments2.3 Key Resources3 Results3.1 Designing Phase: Models for Telerehabilitation3.2 Development Phase: Insights from Decision Makers in Tuscany4 DiscussionReferencesOntological Personal Healthcare Using Medical Standards1 Introduction2 Background3 Personal Mobile Healthcare System (PMHS)4 Personalized Disease Tracking Framework (PDTF)4.1 Vital Sign Analysis4.2 Categories of Patterns5 ConclusionFuture WorkReferencesApplications of High Performance Computing in Bioinformatics, Computational Biology1 Introduction2 HPC Architectures2.1 GPU Computing3 Applications3.1 Virtual Screening3.2 Parallel Processing of Microarray Data3.3 Big Data Analytics and Network Models in Biomedical Informatics4 Conclusions and OutlookReferencesComputing Biological Model Parameters by Parallel Statistical Model Checking*1 Introduction2 Background2.1 Parametric Dynamical Systems2.2 Biological Admissibility3 Computation of Admissible Parameters3.1 Algorithm Outline3.2 Parameter Probability Space3.3 Algorithm Correctness4 Experimental Results4.1 Experimental Setting4.2 Experimental Results5 ConclusionsReferencesMobile Access to On-line Analytic Bioinformatics Tools1 Introduction2 Background2.1 Considerations for Mobile Interfaces2.2 Repositories of Bioinformatics Services: Browsing, Discovering and Invocation2.3 Additional Functionality3 System and Methods3.1 The Proposed Architecture3.2 Implementation3.3 User Interface3.3.1 Browsing the Catalogue3.3.2 Discovering Services3.3.3 Invocation3.3.4 File System4 ResultsDiving into the mORCA application5 Discussion and ConclusionsReferencesisDNA: A Tool for Real-Time Visualization of Plasmid DNA Monte-Carlo Simulations in 3D1 Introduction2 Related Work2.1 DNA Assembly Methods: Predictive versus Adaptive2.2 Deformation Methods for pDNA Simulations3 Real-Time Adaptive DNA Assembly4 Plasmid DNA Monte-Carlo Simulation Method4.1 Monte-Carlo Method4.2 Deformation Algorithm5 The Software5.1 The GUI5.2 The API5.3 Features and Future Work6 ConclusionsReferencesTransport Properties of RNA Nanotubes Using Molecular Dynamics Simulation1 Introduction2 Computational Details3 Results and Discussion4 Conclusions and OutlookReferencesMolecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach1 Introduction2 Method3 Results and Discussion4 ConclusionReferencesPredicting Atherosclerotic Plaque Location in an Iliac Bifurcation Using a Hybrid CFD/Biomechanical Approach1 Introduction2 Methods2.1 Geometry2.2 Computational Fluid Dynamics2.3 Atherogenesis3 Results4 Discussion5 ConclusionsReferencesIdentification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments1 Introduction2 Experimental Suite2.1 Network Creation and Manipulation2.2 Gateway Node Identification2.3 High Performance Computing Environment2.4 Parallel Implementation3 Results3.1 Model Organism – S. cerevisiae Gateway Nodes3.2 Known Dataset – GSE5078 Gateway Nodes3.3 Scalability4 DiscussionReferencesEnhancing the Parallelization of Non-bonded Interactions Kernel for Virtual Screening1 Introduction2 The Lennard-Jones Potential on the Graphics Processing Units2.1 The Roadmap for the Optimization2.2 Our Departure GPU Design2.3 Improving Memory Usage and Throughput3 Experimental Results4 Conclusions and OutlookReferencesPrediction of Functional Types of Ligands for G Protein-Coupled Receptors with Dynamically Discriminable States Embedded in Low Dimension1 Introduction2 Adenosine Receptor3 Markov Model Analysis4 Conformations in Different StatesReferencesImproving Activity Prediction of Adenosine A2B Receptor Antagonists by Nonlinear Models1 Introduction2 Material and Methods2.1 MaterialData setMolecular Descriptors2.2 MethodsSample Interval SelectionClassification and Estimation the Range of Each Ligand Activity3 Results3.1 Interval Selection3.2 Classification and Estimation the Range of Each Ligand Activity4 Discussion5 ConclusionsReferencesSupport Vector Machine Prediction of Drug Solubility on GPUs1 Introduction2 Methodology2.1 GPU Architecture and CUDA Overview2.2 Support Vector Machines2.3 Ligand Databases and Molecular Properties3 Experimentation SVM3.1 Sequential version of SVM (CPU)3.2 Parallel Version of SVM (GPU)4 Experimentation5 Conclusions and Future WorkReferencesDIA-DB: A Web-Accessible Database for the Prediction of Diabetes Drugs1 Introduction2 DIA-DB Architecture3 Diabetes Database Model4 Virtual Screening4.1 Ligand Similarity Based Virtual Screening4.2 Structure Based Virtual Screening: Docking5 Use Cases6 Conclusion and OutlookReferencesMolecular Docking and Biological Evaluation of Functionalized benzo[h]quinolones as Colon Cancer Agents1 Introduction2 Material Methods2.1 Chemical Synthesis2.1.1 General Experimental Procedures2.2 Biology2.2.1 Reagents and Consumables2.2.2 MTT Assay2.3 Molecular Docking Study3 Result and Discussion3.1 Biological Evaluation Study3.1.1 Cytotoxicity3.1.2 Molecular Modeling and Analysis of the Docked Results3.1.3 Pharmacokinetic Parameters Compliance4 ConclusionReferencesPredicting Cross-Reactivity from Computational Studies for Pre-evaluation of Specific Hepatic Glycogen Phosphorylase Inhibitors-insilico Screening of Drugs for Evaluating Specificity1 Introduction2 Materials and Methods2.1 Data Set2.2 Sequence Analysis2.3 Homology Modelling2.4 Computation Details2.5 Molecular Docking3 Results and Discussion3.1 Sequence Analysis and Homology Modeling3.2 Molecular Docking Studies4 ConclusionReferencesExternalising Moods and Psychological States to Smooth Pet-robot/Child Interaction through Bluetooth Communication1 Introduction1.1 Therapeutic Robots1.2 Robot Autonomy1.3 Technical Framework2 The Proposed Solution2.1 Hardware2.2 Interface3 Development of the Solution3.1 Connection via Terminal3.2 Bluetooth Assembly3.3 Power Troubles3.4 Android App4 Results and Discussion5 ConclusionsReferencesPatient Lifecycle Management: An Approach for Clinical Processes1 Introduction2 About PLM3 Patient Oriented Clinical Processes4 Conclusions and Future WorkReferencesAdvertising Liking Recognition Technique Applied to Neuromarketing by Using Low-Cost EEG Headset1 Introduction2 Related Works3 Dataset4 Advertising Recognition Method5 Future Works6 ConclusionsReferencesHeart Rate Variability Indicating Stress Visualized by Correlations Plots1 Introduction2 State of the Art3 System Architecture4 Stress Detection Method5 Application of System and Results Obtained6 Conclusions and Future WorkReferencesEmotions and Diabetes1 Introduction2 Stress, Illness and Diabetes3 Addition of Sensors4 Discussion5 ConclusionReferences
 
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