The Portuguese National Registry for Hemophilia: Developing of a Web-based Technological Solution

AbstractThe crucial role that patient records have in the management of the rare and chronic diseases greatly increases the need to create mechanisms to facilitate the identification and management of the patient's data. Hemophilia is an X-linked congenital bleeding disorder caused by a deficiency of coagulation factor that affects the population on a ratio of 1 case for 10,000 people born. Currently, there are several countries with technological platforms to support the National Patients’ Registries (NPR) of Hemophilia and other Congenital Coagulopathies (HoCC), due to its benefits in the management of the disease. This work presents the technological platform developed in a joint initiative between the University of Aveiro (UA) and the Portuguese Association of Congenital Coagulopathies (PACC), with the purpose of creating the first NPR with HoCC in Portugal. This web application is hosted in the data center of the University of Aveiro, and is being used by the clinicians of the different Hemophilia Treatment Centers (HTC) across the country

Methods and Applications for Summarising Free-Text Narratives in Electronic Health Records

As medical services move towards electronic health record (EHR) systems the breadth and depth of data stored at each patient encounter has increased. This growing wealth of data and investment in care systems has arguably put greater strain on services, as those at the forefront are pushed towards greater time spent in front of computers over their patients. To minimise the use of EHR systems clinicians often revert to using free-text data entry to circumvent the structured input fields. It has been estimated that approximately 80% of EHR data is within the free-text portion. Outside of their primary use, that is facilitating the direct care of the patient, secondary use of EHR data includes clinical research, clinical audits, service improvement research, population health analysis, disease and patient phenotyping, clinical trial recruitment to name but a few.This thesis presents a number of projects, previously published and original work in the development, assessment and application of summarisation methods for EHR free-text. Firstly, I introduce, define and motivate EHR free-text analysis and summarisation methods of open-domain text and how this compares to EHR free-text. I then introduce a subproblem in natural language processing (NLP) that is the recognition of named entities and linking of the entities to pre-existing clinical knowledge bases (NER+L). This leads to the first novel contribution the Medical Concept Annotation Toolkit (MedCAT) that provides a software library workflow for clinical NER+L problems. I frame the outputs of MedCAT as a form of summarisation by showing the tools contributing to published clinical research and the application of this to another clinical summarisation use-case ‘clinical coding’. I then consider methods for the textual summarisation of portions of clinical free-text. I show how redundancy in clinical text is empirically different to open-domain text discussing how this impacts text-to-text summarisation. I then compare methods to generate discharge summary sections from previous clinical notes using methods presented in prior chapters via a novel ‘guidance’ approach.I close the thesis by discussing my contributions in the context of state-of-the-art and how my work fits into the wider body of clinical NLP research. I briefly describe the challenges encountered throughout, offer my perspectives on the key enablers of clinical informatics research, and finally the potential future work that will go towards translating research impact to real-world benefits to healthcare systems, workers and patients alike

Clinical Natural Language Processing in languages other than English: opportunities and challenges

Background: Natural language processing applied to clinical text or aimed at a clinical outcome has been thriving in recent years. This paper offers the first broad overview of clinical Natural Language Processing (NLP) for languages other than English. Recent studies are summarized to offer insights and outline opportunities in this area. Main Body We envision three groups of intended readers: (1) NLP researchers leveraging experience gained in other languages, (2) NLP researchers faced with establishing clinical text processing in a language other than English, and (3) clinical informatics researchers and practitioners looking for resources in their languages in order to apply NLP techniques and tools to clinical practice and/or investigation. We review work in clinical NLP in languages other than English. We classify these studies into three groups: (i) studies describing the development of new NLP systems or components de novo, (ii) studies describing the adaptation of NLP architectures developed for English to another language, and (iii) studies focusing on a particular clinical application. Conclusion: We show the advantages and drawbacks of each method, and highlight the appropriate application context. Finally, we identify major challenges and opportunities that will affect the impact of NLP on clinical practice and public health studies in a context that encompasses English as well as other languages

PHOENI2X -- A European Cyber Resilience Framework With Artificial-Intelligence-Assisted Orchestration, Automation and Response Capabilities for Business Continuity and Recovery, Incident Response, and Information Exchange

As digital technologies become more pervasive in society and the economy, cybersecurity incidents become more frequent and impactful. According to the NIS and NIS2 Directives, EU Member States and their Operators of Essential Services must establish a minimum baseline set of cybersecurity capabilities and engage in cross-border coordination and cooperation. However, this is only a small step towards European cyber resilience. In this landscape, preparedness, shared situational awareness, and coordinated incident response are essential for effective cyber crisis management and resilience. Motivated by the above, this paper presents PHOENI2X, an EU-funded project aiming to design, develop, and deliver a Cyber Resilience Framework providing Artificial-Intelligence-assisted orchestration, automation and response capabilities for business continuity and recovery, incident response, and information exchange, tailored to the needs of Operators of Essential Services and the EU Member State authorities entrusted with cybersecurity

Electrohysterogram for ANN-Based Prediction of Imminent Labor in Women with Threatened Preterm Labor Undergoing Tocolytic Therapy

[EN] Threatened preterm labor (TPL) is the most common cause of hospitalization in the second half of pregnancy and entails high costs for health systems. Currently, no reliable labor proximity prediction techniques are available for clinical use. Regular checks by uterine electrohysterogram (EHG) for predicting preterm labor have been widely studied. The aim of the present study was to assess the feasibility of predicting labor with a 7- and 14-day time horizon in TPL women, who may be under tocolytic treatment, using EHG and/or obstetric data. Based on 140 EHG recordings, artificial neural networks were used to develop prediction models. Non-linear EHG parameters were found to be more reliable than linear for differentiating labor in under and over 7/14 days. Using EHG and obstetric data, the <7- and <14-day labor prediction models achieved an AUC in the test group of 87.1 +/- 4.3% and 76.2 +/- 5.8%, respectively. These results suggest that EHG can be reliable for predicting imminent labor in TPL women, regardless of the tocolytic therapy stage. This paves the way for the development of diagnostic tools to help obstetricians make better decisions on treatments, hospital stays and admitting TPL women, and can therefore reduce costs and improve maternal and fetal wellbeing.This work was supported by the Spanish Ministry of Economy and Competitiveness, the European Regional Development Fund (MCIU/AEI/FEDER, UE RTI2018-094449-A-I00-AR) and by the Generalitat Valenciana (AICO/2019/220).Mas-Cabo, J.; Prats-Boluda, G.; Garcia-Casado, J.; Alberola Rubio, J.; Monfort-Ortiz, R.; Martinez-Saez, C.; Perales, A.... (2020). Electrohysterogram for ANN-Based Prediction of Imminent Labor in Women with Threatened Preterm Labor Undergoing Tocolytic Therapy. 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I2ECR: Integrated and Intelligent Environment for Clinical Research

Clinical trials are designed to produce new knowledge about a certain disease, drug or treatment. During these studies, a huge amount of data is collected about participants, therapies, clinical procedures, outcomes, adverse events and so on. A multicenter, randomized, phase III clinical trial in Hematology enrolls up to hundreds of subjects and evaluates post-treatment outcomes on stratified sub- groups of subjects for a period of many years. Therefore, data collection in clinical trials is becoming complex, with huge amount of clinical and biological variables. Outside the medical field, data warehouses (DWs) are widely employed. A Data Ware-house is a “collection of integrated, subject-oriented databases designed to support the decision-making process”. To verify whether DWs might be useful for data quality and association analysis, a team of biomedical engineers, clinicians, biologists and statisticians developed the “I2ECR” project. I2ECR is an Integrated and Intelligent Environment for Clinical Research where clinical and omics data stand together for clinical use (reporting) and for generation of new clinical knowledge. I2ECR has been built from the “MCL0208” phase III, prospective, clinical trial, sponsored by the Fondazione Italiana Linfomi (FIL); this is actually a translational study, accounting for many clinical data, along with several clinical prognostic indexes (e.g. MIPI - Mantle International Prognostic Index), pathological information, treatment and outcome data, biological assessments of disease (MRD - Minimal Residue Disease), as well as many biological, ancillary studies, such as Mutational Analysis, Gene Expression Profiling (GEP) and Pharmacogenomics. In this trial forty-eight Italian medical centers were actively involved, for a total of 300 enrolled subjects. Therefore, I2ECR main objectives are: • to propose an integration project on clinical and molecular data quality concepts. The application of a clear row-data analysis as well as clinical trial monitoring strategies to implement a digital platform where clinical, biological and “omics” data are imported from different sources and well-integrated in a data- ware-house • to be a dynamic repository of data congruency quality rules. I2ECR allows to monitor, in a semi-automatic manner, the quality of data, in relation to the clinical data imported from eCRFs (electronic Case Report Forms) and from biologic and mutational datasets internally edited by local laboratories. Therefore, I2ECR will be able to detect missing data and mistakes derived from non-conventional data- entry activities by centers. • to provide to clinical stake-holders a platform from where they can easily design statistical and data mining analysis. The term Data Mining (DM) identifies a set of tools to searching for hidden patterns of interest in large and multivariate datasets. The applications of DM techniques in the medical field range from outcome prediction and patient classification to genomic medicine and molecular biology. I2ECR allows to clinical stake-holders to propose innovative methods of supervised and unsupervised feature extraction, data classification and statistical analysis on heterogeneous datasets associated to the MCL0208 clinical trial. Although MCL0208 study is the first example of data-population of I2ECR, the environment will be able to import data from clinical studies designed for other onco-hematologic diseases, too