Evaluation of an Artificial Intelligence web-based software to detect and classify dental structures and treatments in panoramic radiographs.

OBJECTIVES: To evaluate the diagnostic reliability of a web-based Artificial Intelligence program on the detection and classification of dental structures and treatments present on panoramic radiographs. METHODS: A total of 300 orthopantomographies (OPG) were randomly selected for this study. First, the images were visually evaluated by two calibrated operators with radiodiagnosis experience that, after consensus, established the "ground truth". Operators' findings on the radiographs were collected and classified as follows: metal restorations (MR), resin-based restorations (RR), endodontic treatment (ET), Crowns (C) and Implants (I). The orthopantomographies were then anonymously uploaded and automatically analyzed by the web-based software (Denti.Ai). Results were then stored, and a statistical analysis was performed by comparing them with the ground truth in terms of Sensitivity (S), Specificity (E), Positive Predictive Value (PPV) Negative Predictive Value (NPV) and its later representation in the area under (AUC) the Receiver Operating Characteristic (ROC) Curve. RESULTS: Diagnostic metrics obtained for each study variable were as follows: (MR) S=85.48%, E=87.50%, PPV=82.8%, NPV=42.51%, AUC=0.869; (PR) S=41.11%, E=93.30%, PPV=90.24%, NPV=87.50%, AUC=0.672; (ET) S=91.9%, E=100%, PPV=100%, NPV=94.62%, AUC=0.960; (C) S=89.53%, E=95.79%, PPV=89.53%, NPV=95.79%, AUC=0.927; (I) S, E, PPV, NPV=100%, AUC=1.000. CONCLUSIONS: Findings suggest that the web-based Artificial intelligence software provides a good performance on the detection of implants, crowns, metal fillings and endodontic treatments, not being so accurate on the classification of dental structures or resin-based restorations. CLINICAL SIGNIFICANCE: General diagnostic and treatment decisions using orthopantomographies can be improved by using web-based artificial intelligence tools, avoiding subjectivity and lapses from the clinician.

A deep learning approach using synthetic images for segmenting and estimating 3D orientation of nanoparticles in EM images.

BACKGROUND AND OBJECTIVE: Nanoparticles present properties that can be applied to a wide range of fields such as biomedicine, electronics or optics. The type of properties depends on several characteristics, being some of them related with the particle structure. A proper characterization of nanoparticles is crucial since it could affect their applications. To characterize a particle shape and size, the nanotechnologists employ Electron Microscopy (EM) to obtain images of nanoparticles and perform measures over them. This task could be tedious, repetitive and slow, we present a Deep Learning method based on Convolutional Neural Networks (CNNs) to detect, segment, infer orientations and reconstruct microscope images of nanoparticles. Since machine learning algorithms depend on annotated data and there is a lack of annotated datasets of nanoparticles, our work makes use of artificial datasets of images resembling real nanoparticles photographs. METHODS: Our work is divided into three tasks. Firstly, a method to create annotated datasets of artificial images resembling Scanning Electron Microscope (SEM). Secondly, two models of convolutional neural networks are trained using the artificial datasets previously generated, the first one is in charge of the detection and segmentation of the nanoparticles while the second one will infer the nanoparticle orientation. Finally, the 3D reconstruction module will recreate in a 3D scene the set of detected particles. RESULTS: We have tested our method with five different shapes of basic nanoparticles: spheres, cubes, ellipsoids, hexagonal discs and octahedrons. An analysis of the reconstructions was conducted by manually comparing each of them with the real images. The results obtained have been promising, the particles are segmented and reconstructed accordingly to their shapes and orientations. CONCLUSIONS: We have developed a method for nanoparticle detection and segmentation in microscope images. Moreover, we can also infer an approximation of the 3D orientation of the particles and, in conjunction with the detections, create a 3D reconstruction of the photographs. The novelty of our approximation lies in the dataset used. Instead of using annotated images, we have created the datasets simulating the microscope images by using basic geometrical objects that imitate real nanoparticles.

Enhancing vessel visibility in fundus images to aid the diagnosis of retinopathy of prematurity.

Retinopathy of prematurity is a disease that can affect premature or in similar conditions babies. For diagnosing of retinopathy of prematurity, the infant is examined as soon as possible. Due to the nature of the examination, the images obtained are poor in quality. This article presents an automated method for processing fundus images to improve the visibility of the vascular network. The method includes several processing tasks whose parameters are predicted using an artificial neural network. A set of 88 clinical images were used in this work. The performance of our proposal is efficient, and the average processing time was 42 ms. The method was assessed using both the contrast improvement index and expert opinions. The contrast improvement index average was 2; this means the processed image successfully improved its contrast. Three pediatric ophthalmologists validated the proposed method and agreed that the visual enhancement can help observe clearly the retinal vessels.

genoDraw: A Web Tool for Developing Pedigree Diagrams Using the Standardized Human Pedigree Nomenclature Integrated with Biomedical Vocabularies.

The integration of genetic information in current clinical routine has raised a need for tools to exploit family genetic knowledge. On the clinical side, an application for managing and visualizing pedigree diagrams could provide genetics specialists with an integrated environment with potential positive impact on their current practice. This article presents a web tool (genoDraw) that provides clinical practitioners with the ability to create, maintain and visualize patients' and their families' information in the form of pedigree diagrams. genoDraw implements a graph-based three-step process for generating diagrams according to a de facto standard in the area and clinical terminologies. It also complies with five characteristics identified as indispensable for the next-generation of pedigree drawing software: comprehensiveness, data-drivenness, automation, interactivity and compatibility with biomedical vocabularies. The platform was implemented and tested, confirming its potential interest to clinical routine.

Measuring Relevant Information in Health Social Network Conversations and Clinical Diagnosis Cases.

The Internet and social media is an enormous source of information. Health social networks and online collaborative environments enable users to create shared content that afterwards can be discussed. The aim of this paper is to present a novel methodology designed for quantifying relevant information provided by different participants in clinical online discussions. The main goal of the methodology is to facilitate the comparison of participant interactions in clinical conversations. A set of key indicators for different aspects of clinical conversations and specific clinical contributions within a discussion have been defined. Particularly, three new indicators have been proposed to make use of biomedical knowledge extraction based on standard terminologies and ontologies. These indicators allow measuring the relevance of information of each participant of the clinical conversation. Proposed indicators have been applied to one discussion extracted from PatientsLikeMe, as well as to two real clinical cases from the Sanar collaborative discussion system. Results obtained from indicators in the tested cases have been compared with clinical expert opinions to check indicators validity. The methodology has been successfully used for describing participant interactions in real clinical cases belonging to a collaborative clinical case discussion tool and from a conversation from a health social network. This work can be applied to assess collaborative diagnoses, discussions among patients, and the participation of students in clinical case discussions. It permits moderators and educators to obtain a quantitatively measure of the contribution of each participant.

Querying clinical data in HL7 RIM based relational model with morph-RDB.

BACKGROUND: Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshness. RESULTS: In this paper we present a solution that uses an ontology based on the HL7 v3 Reference Information Model and a set of R2RML mappings that relate this ontology to an underlying relational database implementation, and where morph-RDB is used to expose a virtual, non-materialized SPARQL endpoint over the data. CONCLUSIONS: By applying a set of optimization techniques on the SPARQL-to-SQL query translation algorithm, we can now issue SPARQL queries to the underlying relational data with generally acceptable performance.

A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer.

INTRODUCTION: The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. METHODS: This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations. RESULTS: The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models. CONCLUSIONS: The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies.

Enhancing Collaborative Case Diagnoses Through Unified Medical Language System-Based Disambiguation: A Case Study of the Zika Virus.

BACKGROUND: During clinical case diagnoses, especially in low-resourced areas, the use of vocabularies within Unified Medical Language System (UMLS) can strengthen discussions between health professionals and, in certain cases, eliminate the need, enabling faster treatment. INTRODUCTION: This article presents the benefits of using UMLS as a collaborative discussion tool and verifies its impact. MATERIALS AND METHODS: The Sanar system has been improved by UMLS when using text retrieval to extract relevant medical concepts from cases investigated by the user and to provide contextualized searches of related articles. An experiment was conducted, focused on team engagement and discussion of a Zika virus case using Sanar, both with and without UMLS contextualization. RESULTS: The use of the tool was measured, and it was determined that the discussion in the group with UMLS support was more complete based on better information and inclusion of more variables. Clinicians involved responded to a questionnaire evaluating the relevance of functions. DISCUSSION: From the questionnaire showed that most of the group supported UMLS as important in complex diagnostics; the use of knowledge extraction before discussion is relevant to align knowledge of participants with more variables, such as the Zika virus, and to minimize the need for interaction in widely discussed cases. CONCLUSIONS: Based on the results obtained with the questionnaire, the use of UMLS provides acceleration in the diagnostic process that precedes interaction with other health professionals through clinical discussion tools. For future work, a mobile version will support offline navigation for locations with limited Internet access.

Cohort Selection and Management Application Leveraging Standards-based Semantic Interoperability and a Groovy DSL.

This paper describes a new Cohort Selection application implemented to support streamlining the definition phase of multi-centric clinical research in oncology. Our approach aims at both ease of use and precision in defining the selection filters expressing the characteristics of the desired population. The application leverages our standards-based Semantic Interoperability Solution and a Groovy DSL to provide high expressiveness in the definition of filters and flexibility in their composition into complex selection graphs including splits and merges. Widely-adopted ontologies such as SNOMED-CT are used to represent the semantics of the data and to express concepts in the application filters, facilitating data sharing and collaboration on joint research questions in large communities of clinical users. The application supports patient data exploration and efficient collaboration in multi-site, heterogeneous and distributed data environments.

Enabling semantic interoperability in multi-centric clinical trials on breast cancer.

BACKGROUND AND OBJECTIVES: Post-genomic clinical trials require the participation of multiple institutions, and collecting data from several hospitals, laboratories and research facilities. This paper presents a standard-based solution to provide a uniform access endpoint to patient data involved in current clinical research. METHODS: The proposed approach exploits well-established standards such as HL7 v3 or SPARQL and medical vocabularies such as SNOMED CT, LOINC and HGNC. A novel mechanism to exploit semantic normalization among HL7-based data models and biomedical ontologies has been created by using Semantic Web technologies. RESULTS: Different types of queries have been used for testing the semantic interoperability solution described in this paper. The execution times obtained in the tests enable the development of end user tools within a framework that requires efficient retrieval of integrated data. CONCLUSIONS: The proposed approach has been successfully tested by applications within the INTEGRATE and EURECA EU projects. These applications have been deployed and tested for: (i) patient screening, (ii) trial recruitment, and (iii) retrospective analysis; exploiting semantically interoperable access to clinical patient data from heterogeneous data sources.

Semantic Normalization and Query Abstraction Based on SNOMED-CT and HL7: Supporting Multicentric Clinical Trials.

Advances in the use of omic data and other biomarkers are increasing the number of variables in clinical research. Additional data have stratified the population of patients and require that current studies be performed among multiple institutions. Semantic interoperability and standardized data representation are a crucial task in the management of modern clinical trials. In the past few years, different efforts have focused on integrating biomedical information. Due to the complexity of this domain and the specific requirements of clinical research, the majority of data integration tasks are still performed manually. This paper presents a semantic normalization process and a query abstraction mechanism to facilitate data integration and retrieval. A process based on well-established standards from the biomedical domain and the latest semantic web technologies has been developed. Methods proposed in this paper have been tested within the EURECA EU research project, where clinical scenarios require the extraction of semantic knowledge from biomedical vocabularies. The aim of this paper is to provide a novel method to abstract from the data model and query syntax. The proposed approach has been compared with other initiatives in the field by storing the same dataset with each of those solutions. Results show an extended functionality and query capabilities at the cost of slightly worse performance in query execution. Implementations in real settings have shown that following this approach, usable interfaces can be developed to exploit clinical trial data outcomes.

Supporting patient screening to identify suitable clinical trials.

To support the efficient execution of post-genomic multi-centric clinical trials in breast cancer we propose a solution that streamlines the assessment of the eligibility of patients for available trials. The assessment of the eligibility of a patient for a trial requires evaluating whether each eligibility criterion is satisfied and is often a time consuming and manual task. The main focus in the literature has been on proposing different methods for modelling and formalizing the eligibility criteria. However the current adoption of these approaches in clinical care is limited. Less effort has been dedicated to the automatic matching of criteria to the patient data managed in clinical care. We address both aspects and propose a scalable, efficient and pragmatic patient screening solution enabling automatic evaluation of eligibility of patients for a relevant set of trials. This covers the flexible formalization of criteria and of other relevant trial metadata and the efficient management of these representations.

A data model based on semantically enhanced HL7 RIM for sharing patient data of breast cancer clinical trials.

Breast cancer clinical trial researchers have to handle heterogeneous data coming from different data sources, overloading biomedical researchers when they need to query data for retrospective analysis. This paper presents the Common Data Model (CDM) proposed within the INTEGRATE EU project to homogenize data coming from different clinical partners. This CDM is based on the Reference Information Model (RIM) from the Health Level 7 (HL7) version 3. Semantic capabilities through an SPARQL endpoint were also required to ensure the sustainability of the platform. For the SPARQL endpoint implementation, a comparison has been carried out between a Relational SQL database + D2R and a RDF database. The results show that the first option can store all clinical data received from institutions participating in the project with a better performance. It has been also evaluated by the EU Commission within a patient recruitment demonstrator.

Analyzing SNOMED CT and HL7 terminology binding for semantic interoperability on post-genomic clinical trials.

Current post-genomic clinical trials in cancer involve the collaboration of several institutions. Multi-centric retrospective analysis requires advanced methods to ensure semantic interoperability. In this scenario, the objective of the EU funded INTEGRATE project, is to provide an infrastructure to share knowledge and data in post-genomic breast cancer clinical trials. This paper presents the process carried out in this project, to bind domain terminologies in the area, such as SNOMED CT, with the HL7 v3 Reference Information Model (RIM). The proposed terminology binding follow the HL7 recommendations, but should also consider important issues such as overlapping concepts and domain terminology coverage. Although there are limitations due to the large heterogeneity of the data in the area, the proposed process has been successfully applied within the context of the INTEGRATE project. An improvement in semantic interoperability of patient data from modern breast cancer clinical trials, aims to enhance the clinical practice in oncology.