A synthetic data generation system for myalgic encephalomyelitis/chronic fatigue syndrome questionnaires

Artificial intelligence or machine-learning-based models have proven useful for better understanding various diseases in all areas of health science. Myalgic Encephalomyelitis or chronic fatigue syndrome (ME/CFS) lacks objective diagnostic tests. Some validated questionnaires are used for diagnosis and assessment of disease progression. The availability of a sufficiently large database of these questionnaires facilitates research into new models that can predict profiles that help to understand the etiology of the disease. A synthetic data generator provides the scientific community with databases that preserve the statistical properties of the original, free of legal restrictions, for use in research and education. The initial databases came from the Vall Hebron Hospital Specialized Unit in Barcelona, Spain. 2522 patients diagnosed with ME/CFS were analyzed. Their answers to questionnaires related to the symptoms of this complex disease were used as training datasets. They have been fed for deep learning algorithms that provide models with high accuracy [0.69–0.81]. The final model requires SF-36 responses and returns responses from HAD, SCL-90R, FIS8, FIS40, and PSQI questionnaires. A highly reliable and easy-to-use synthetic data generator is offered for research and educational use in this disease, for which there is currently no approved treatment

On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Unsupervised cluster analysis reveals distinct subtypes of ME/CFS patients based on peak oxygen consumption and SF-36 scores

PURPOSE: Myalgic encephalomyelitis, commonly referred to as chronic fatigue syndrome (ME/CFS), is a severe, disabling chronic disease and an objective assessment of prognosis is crucial to evaluate the efficacy of future drugs. Attempts are ongoing to find a biomarker to objectively assess the health status of (ME/CFS), patients. This study therefore aims to demonstrate that oxygen consumption is a biomarker of ME/CFS provides a method to classify patients diagnosed with ME/CFS based on their responses to the Short Form-36 (SF-36) questionnaire, which can predict oxygen consumption using cardiopulmonary exercise testing (CPET). METHODS: Two datasets were used in the study. The first contained SF-36 responses from 2,347 validated records of ME/CFS diagnosed participants, and an unsupervised machine learning model was developed to cluster the data. The second dataset was used as a validation set and included the cardiopulmonary exercise test (CPET) results of 239 participants diagnosed with ME/CFS. Participants from this dataset were grouped by peak oxygen consumption according to Weber's classification. The SF-36 questionnaire was correctly completed by only 92 patients, who were clustered using the machine learning model. Two categorical variables were then entered into a contingency table: the cluster with values {0,1} and Weber classification {A, B, C, D} were assigned. Finally, the Chi-square test of independence was used to assess the statistical significance of the relationship between the two parameters. FINDINGS: The results indicate that the Weber classification is directly linked to the score on the SF-36 questionnaire. Furthermore, the 36-response matrix in the machine learning model was shown to give more reliable results than the subscale matrix (p - value < 0.05) for classifying patients with ME/CFS. IMPLICATIONS: Low oxygen consumption on CPET can be considered a biomarker in patients with ME/CFS. Our analysis showed a close relationship between the cluster based on their SF-36 questionnaire score and the Weber classification, which was based on peak oxygen consumption during CPET. The dataset for the training model comprised raw responses from the SF-36 questionnaire, which is proven to better preserve the original information, thus improving the quality of the model

A synthetic data generation system for myalgic encephalomyelitis/chronic fatigue syndrome questionnaires

Computational models; Data acquisitionModelos computacionales; Adquisición de datosModels computacionals; Adquisició de dadesArtificial intelligence or machine-learning-based models have proven useful for better understanding various diseases in all areas of health science. Myalgic Encephalomyelitis or chronic fatigue syndrome (ME/CFS) lacks objective diagnostic tests. Some validated questionnaires are used for diagnosis and assessment of disease progression. The availability of a sufficiently large database of these questionnaires facilitates research into new models that can predict profiles that help to understand the etiology of the disease. A synthetic data generator provides the scientific community with databases that preserve the statistical properties of the original, free of legal restrictions, for use in research and education. The initial databases came from the Vall Hebron Hospital Specialized Unit in Barcelona, Spain. 2522 patients diagnosed with ME/CFS were analyzed. Their answers to questionnaires related to the symptoms of this complex disease were used as training datasets. They have been fed for deep learning algorithms that provide models with high accuracy [0.69–0.81]. The final model requires SF-36 responses and returns responses from HAD, SCL-90R, FIS8, FIS40, and PSQI questionnaires. A highly reliable and easy-to-use synthetic data generator is offered for research and educational use in this disease, for which there is currently no approved treatment

Patterns of inflammation, microstructural alterations, and sodium accumulation define multiple sclerosis subtypes after 15 years from onset

MRI; Machine learning; Multiple sclerosisRessonància magnètica; Aprenentatge automàtic; Esclerosi múltipleResonancia magnética; Aprendizaje automático; Esclerosis múltipleIntroduction: Conventional MRI is routinely used for the characterization of pathological changes in multiple sclerosis (MS), but due to its lack of specificity is unable to provide accurate prognoses, explain disease heterogeneity and reconcile the gap between observed clinical symptoms and radiological evidence. Quantitative MRI provides measures of physiological abnormalities, otherwise invisible to conventional MRI, that correlate with MS severity. Analyzing quantitative MRI measures through machine learning techniques has been shown to improve the understanding of the underlying disease by better delineating its alteration patterns. Methods: In this retrospective study, a cohort of healthy controls (HC) and MS patients with different subtypes, followed up 15 years from clinically isolated syndrome (CIS), was analyzed to produce a multi-modal set of quantitative MRI features encompassing relaxometry, microstructure, sodium ion concentration, and tissue volumetry. Random forest classifiers were used to train a model able to discriminate between HC, CIS, relapsing remitting (RR) and secondary progressive (SP) MS patients based on these features and, for each classification task, to identify the relative contribution of each MRI-derived tissue property to the classification task itself. Results and discussion: Average classification accuracy scores of 99 and 95% were obtained when discriminating HC and CIS vs. SP, respectively; 82 and 83% for HC and CIS vs. RR; 76% for RR vs. SP, and 79% for HC vs. CIS. Different patterns of alterations were observed for each classification task, offering key insights in the understanding of MS phenotypes pathophysiology: atrophy and relaxometry emerged particularly in the classification of HC and CIS vs. MS, relaxometry within lesions in RR vs. SP, sodium ion concentration in HC vs. CIS, and microstructural alterations were involved across all tasks.This project has received funding under the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No. 634541. FG received the support of a fellowship from “la Caixa” Foundation (ID 100010434). The fellowship code is “LCF/BQ/PR22/11920010”. FG has also received support from the Beatriu de Pinós (2020 BP 00117) programme, funded by the Secretary of Universities and Research (Government of Catalonia). BK, FP, and OC are supported by the National Institute of Health Research Biomedical Research Centre at UCL and UCLH. EPSRC grants EP/M020533/1 and EP/J020990/01, MRC MR/T046422/1 and MR/T046473/1, Wellcome Trust award 221915/Z/20/Z, and the NIHR UCLH BRC support DCA's work in this area. CGWK also receives funding from Horizon 2020 [Research and Innovation Action Grants Human Brain Project 945539 (SGA3)], BRC (#BRC704/CAP/CGW), MRC (#MR/S026088/1), and Ataxia UK

Unsupervised Cluster Analysis Reveals Distinct Subtypes of ME/CFS Patients Based on Peak Oxygen Consumption and SF-36 Scores

Biomarker; Cardiopulmonary exercise test; Chronic fatigue syndromeBiomarcador; Prova d'esforç cardiopulmonar; Síndrome de fatiga crònicaBiomarcador; Prueba de esfuerzo cardiopulmonar; Síndrome de fatiga crónicaPurpose Myalgic encephalomyelitis, commonly referred to as chronic fatigue syndrome (ME/CFS), is a severe, disabling chronic disease and an objective assessment of prognosis is crucial to evaluate the efficacy of future drugs. Attempts are ongoing to find a biomarker to objectively assess the health status of (ME/CFS), patients. This study therefore aims to demonstrate that oxygen consumption is a biomarker of ME/CFS provides a method to classify patients diagnosed with ME/CFS based on their responses to the Short Form-36 (SF-36) questionnaire, which can predict oxygen consumption using cardiopulmonary exercise testing (CPET). Methods Two datasets were used in the study. The first contained SF-36 responses from 2,347 validated records of ME/CFS diagnosed participants, and an unsupervised machine learning model was developed to cluster the data. The second dataset was used as a validation set and included the cardiopulmonary exercise test (CPET) results of 239 participants diagnosed with ME/CFS. Participants from this dataset were grouped by peak oxygen consumption according to Weber's classification. The SF-36 questionnaire was correctly completed by only 92 patients, who were clustered using the machine learning model. Two categorical variables were then entered into a contingency table: the cluster with values {0,1} and Weber classification {A, B, C, D} were assigned. Finally, the Chi-square test of independence was used to assess the statistical significance of the relationship between the two parameters. Findings The results indicate that the Weber classification is directly linked to the score on the SF-36 questionnaire. Furthermore, the 36-response matrix in the machine learning model was shown to give more reliable results than the subscale matrix (p − value < 0.05) for classifying patients with ME/CFS. Implications Low oxygen consumption on CPET can be considered a biomarker in patients with ME/CFS. Our analysis showed a close relationship between the cluster based on their SF-36 questionnaire score and the Weber classification, which was based on peak oxygen consumption during CPET. The dataset for the training model comprised raw responses from the SF-36 questionnaire, which is proven to better preserve the original information, thus improving the quality of the model

Comparison of Neurite Orientation Dispersion and Density Imaging and Two-Compartment Spherical Mean Technique Parameter Maps in Multiple Sclerosis

Microestructura; Esclerosi múltiple; Tècnica de mitjana esfèricaMicroestructura; Esclerosis múltiple; Técnica de la media esféricaMicrostructure; Multiple sclerosis; Spherical mean techniqueBackground: Neurite orientation dispersion and density imaging (NODDI) and the spherical mean technique (SMT) are diffusion MRI methods providing metrics with sensitivity to similar characteristics of white matter microstructure. There has been limited comparison of changes in NODDI and SMT parameters due to multiple sclerosis (MS) pathology in clinical settings. Purpose: To compare group-wise differences between healthy controls and MS patients in NODDI and SMT metrics, investigating associations with disability and correlations with diffusion tensor imaging (DTI) metrics. Methods: Sixty three relapsing-remitting MS patients were compared to 28 healthy controls. NODDI and SMT metrics corresponding to intracellular volume fraction (vin), orientation dispersion (ODI and ODE), diffusivity (D) (SMT only) and isotropic volume fraction (viso) (NODDI only) were calculated from diffusion MRI data, alongside DTI metrics (fractional anisotropy, FA; axial/mean/radial diffusivity, AD/MD/RD). Correlations between all pairs of MRI metrics were calculated in normal-appearing white matter (NAWM). Associations with expanded disability status scale (EDSS), controlling for age and gender, were evaluated. Patient-control differences were assessed voxel-by-voxel in MNI space controlling for age and gender at the 5% significance level, correcting for multiple comparisons. Spatial overlap of areas showing significant differences were compared using Dice coefficients. Results: NODDI and SMT show significant associations with EDSS (standardised beta coefficient −0.34 in NAWM and −0.37 in lesions for NODDI vin; 0.38 and −0.31 for SMT ODE and vin in lesions; p < 0.05). Significant correlations in NAWM are observed between DTI and NODDI/SMT metrics. NODDI vin and SMT vin strongly correlated (r = 0.72, p < 0.05), likewise NODDI ODI and SMT ODE (r = −0.80, p < 0.05). All DTI, NODDI and SMT metrics detect widespread differences between patients and controls in NAWM (12.57% and 11.90% of MNI brain mask for SMT and NODDI vin, Dice overlap of 0.42). Data Conclusion: SMT and NODDI detect significant differences in white matter microstructure between MS patients and controls, concurring on the direction of these changes, providing consistent descriptors of tissue microstructure that correlate with disability and show alterations beyond focal damage. Our study suggests that NODDI and SMT may play a role in monitoring MS in clinical trials and practice.This study has received funding under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 634541 (CDS-QuaMRI) and 666992. This study has also received support from the Engineering and Physical Sciences Research Council (EPSRC R006032/1, M020533/1, G007748, I027084, N018702), Spinal Research (UK), Wings for Life (Austria), Craig H. Neilsen Foundation (USA) for INSPIRED and UK Multiple Sclerosis Society (grants 892/08 and 77/2017). This study was supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre. FP was supported by a Guarantors of Brain post-doctoral non-clinical fellowship. AT was supported by an MRC grant (MR/S026088/1). EK was supported from the NIHR Great Ormond Street Hospital Biomedical Research Centre. FG was currently supported by the investigator-initiated PREdICT study at the Vall d'Hebron Institute of Oncology (Barcelona), funded by AstraZeneca and CRIS Cancer Foundation. AstraZeneca was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication

Utilización de una plataforma de e-learning en la docencia de bases de datos

Las bases de datos son una de las materias más importantes en las carreras de Informática. En este artículo presentamos el uso y las ventajas que ofrece la utilización de una plataforma de e-learning en el desarrollo de estas asignaturas, en el plan piloto de adaptación al EEES que se está llevando a cabo en las carreras de Ingeniería Técnica en Informática de Gestión (ITIG) y de Sistemas (ITIS) en la Universidad de Girona (UdG). La aportación más importante de esta herramienta es la corrección automática y on-line de los distintos tipos de ejercicios relacionados con la materia: diagramas entidad/relación, diseño de esquemas de bases de datos relacionales, normalización, etc., permitiendo al profesor conocer en todo momento el nivel de aprendizaje del alumno y detectar rápidamente posibles deficiencias. Con el uso de esta plataforma hemos logrado motivar al alumnado y mejorar los resultados académicos

Experiencia docente en diseño de bases de datos con la ayuda de herramientas de e-learning

Una de las competencias básicas en torno a la materia de bases de datos consiste en realizar el diseño conceptual y lógico de una base de datos relacional. En este artículo se presenta la experiencia realizada en el diseño de una base de datos con un número considerable de tablas y en relación a la organización y gestión de una empresa real. Para facilitar las tareas de corrección y evaluación a los profesores implicados se ha utilizado una plataforma de e-learning que corrige diagramas entidad/relación y los esquemas de bases de datos generados.Peer Reviewe