Enriching information extraction pipelines in clinical decision support systems

Programa Oficial de Doutoramento en Tecnoloxías da Información e as Comunicacións. 5032V01[Resumo] Os estudos sanitarios de múltiples centros son importantes para aumentar a repercusión dos resultados da investigación médica debido ao número de suxeitos que poden participar neles. Para simplificar a execución destes estudos, o proceso de intercambio de datos debería ser sinxelo, por exemplo, mediante o uso de bases de datos interoperables. Con todo, a consecución desta interoperabilidade segue sendo un tema de investigación en curso, sobre todo debido aos problemas de gobernanza e privacidade dos datos. Na primeira fase deste traballo, propoñemos varias metodoloxías para optimizar os procesos de estandarización das bases de datos sanitarias. Este traballo centrouse na estandarización de fontes de datos heteroxéneas nun esquema de datos estándar, concretamente o OMOP CDM, que foi desenvolvido e promovido pola comunidade OHDSI. Validamos a nosa proposta utilizando conxuntos de datos de pacientes con enfermidade de Alzheimer procedentes de distintas institucións. Na seguinte etapa, co obxectivo de enriquecer a información almacenada nas bases de datos de OMOP CDM, investigamos solucións para extraer conceptos clínicos de narrativas non estruturadas, utilizando técnicas de recuperación de información e de procesamento da linguaxe natural. A validación realizouse a través de conxuntos de datos proporcionados en desafíos científicos, concretamente no National NLP Clinical Challenges(n2c2). Na etapa final, propuxémonos simplificar a execución de protocolos de estudos provenientes de múltiples centros, propoñendo solucións novas para perfilar, publicar e facilitar o descubrimento de bases de datos. Algunhas das solucións desenvolvidas están a utilizarse actualmente en tres proxectos europeos destinados a crear redes federadas de bases de datos de saúde en toda Europa.[Resumen] Los estudios sanitarios de múltiples centros son importantes para aumentar la repercusión de los resultados de la investigación médica debido al número de sujetos que pueden participar en ellos. Para simplificar la ejecución de estos estudios, el proceso de intercambio de datos debería ser sencillo, por ejemplo, mediante el uso de bases de datos interoperables. Sin embargo, la consecución de esta interoperabilidad sigue siendo un tema de investigación en curso, sobre todo debido a los problemas de gobernanza y privacidad de los datos. En la primera fase de este trabajo, proponemos varias metodologías para optimizar los procesos de estandarización de las bases de datos sanitarias. Este trabajo se centró en la estandarización de fuentes de datos heterogéneas en un esquema de datos estándar, concretamente el OMOP CDM, que ha sido desarrollado y promovido por la comunidad OHDSI. Validamos nuestra propuesta utilizando conjuntos de datos de pacientes con enfermedad de Alzheimer procedentes de distintas instituciones. En la siguiente etapa, con el objetivo de enriquecer la información almacenada en las bases de datos de OMOP CDM, hemos investigado soluciones para extraer conceptos clínicos de narrativas no estructuradas, utilizando técnicas de recuperación de información y de procesamiento del lenguaje natural. La validación se realizó a través de conjuntos de datos proporcionados en desafíos científicos, concretamente en el National NLP Clinical Challenges (n2c2). En la etapa final, nos propusimos simplificar la ejecución de protocolos de estudios provenientes de múltiples centros, proponiendo soluciones novedosas para perfilar, publicar y facilitar el descubrimiento de bases de datos. Algunas de las soluciones desarrolladas se están utilizando actualmente en tres proyectos europeos destinados a crear redes federadas de bases de datos de salud en toda Europa.[Abstract] Multicentre health studies are important to increase the impact of medical research findings due to the number of subjects that they are able to engage. To simplify the execution of these studies, the data-sharing process should be effortless, for instance, through the use of interoperable databases. However, achieving this interoperability is still an ongoing research topic, namely due to data governance and privacy issues. In the first stage of this work, we propose several methodologies to optimise the harmonisation pipelines of health databases. This work was focused on harmonising heterogeneous data sources into a standard data schema, namely the OMOP CDM which has been developed and promoted by the OHDSI community. We validated our proposal using data sets of Alzheimer’s disease patients from distinct institutions. In the following stage, aiming to enrich the information stored in OMOP CDM databases, we have investigated solutions to extract clinical concepts from unstructured narratives, using information retrieval and natural language processing techniques. The validation was performed through datasets provided in scientific challenges, namely in the National NLP Clinical Challenges (n2c2). In the final stage, we aimed to simplify the protocol execution of multicentre studies, by proposing novel solutions for profiling, publishing and facilitating the discovery of databases. Some of the developed solutions are currently being used in three European projects aiming to create federated networks of health databases across Europe

Studies to inform the development and practical roll-out of a digital adherence intervention, Video-Observed Therapy (VOT)

BACKGROUND: Prior to the COVID-19 pandemic, globally, tuberculosis (TB) was the leading cause of death from a single infectious agent. It is an important example of a curable condition which has well-documented treatment adherence challenges. WHO recommends the use of video-observed therapy (VOT) as a flexible alternative to DOT (Directly Observed Treatment). There is limited evidence of VOT’s acceptability and how it may enable patients to engage with their treatment to elicit optimal adherence outcomes. This PhD thesis aims to improve understanding of patient groups who may benefit most from VOT. METHODS: Drawing upon a narrative literature review, this PhD thesis includes: a) a study to identify factors that predict non-completion of TB treatment through a retrospective cohort analysis of cases with TB notified to the Enhanced TB Surveillance System in England, Wales and Northern Ireland between 2010 and 2017; b) a study comparing VOT to in-person DOT to examine the factors which affect the levels of engagement with DOT and VOT and whether these affect the level of treatment observation achieved in DOT and VOT groups through a secondary analysis of the UK DOT/VOT trial dataset using descriptive analysis and logistic regression; c) a qualitative study exploring the lived experiences and perspectives of DOT and VOT users in two settings, the UK and Republic of Moldova using semi-structured interviews with 16 UK DOT/VOT trial participants and 22 Moldovan DOT/VOT trial participants. Themes were mapped onto the Capability Opportunity Motivation Behaviour (COM-B) model, Theoretical Domains Framework (TDF) and Behaviour Change Wheel (BCW) to identify how the VOT and DOT functions, strategies and its policy categories elicit treatment adherence outcomes to support decision-making on commissioning of DOT and VOT interventions. RESULTS: Recent migration to the UK (0 -1 years from entry to the UK to TB notification), multidrug resistance, increasing social complexity and a previous TB diagnosis were significantly associated with non-completion of TB treatment. Higher levels of initial engagement with VOT (90% initially engaged) rather than DOT (49% initially engaged) were observed amongst all patient groups. Amongst those who initially engaged with either DOT or VOT, patients with TB on VOT had improved TB treatment adherence compared those on DOT. Women were less likely to adhere and those with a history of being lost to follow-up were also less likely to adhere. The COM-B model and TDF provided explanatory frameworks highlighting how VOT acted on key behaviour change domains and utilised key strategies to facilitate adherence behaviour change. VOT facilitated patient-provider interactions served as a prompt/reminder to address forgetfulness through regular personalised messages from VOT observers, building rapport and habit-forming practices. VOT was a flexible, time- and cost-saving alternative to DOT and supported patients with split dosing or negotiated timing of dosing to manage side effects and pill burden. VOT also served as an incentive through the provision of a smartphone and data plan, free domestic calls, text messages and internet access linking patients to providers, banking and social support services. In turn these ‘capability and ‘opportunity’ components of the model enhanced ‘motivation’ by supporting patients to re-gain autonomy, self-responsibility and establish regular dosing. There were mixed views on privacy with participants expressing concerns on how video clips would be used, shared and may compromise confidentiality and increase stigma. The Behaviour Change Wheel identified seven key functions (‘active ingredients’) of VOT: Enablement (increasing means/reducing barriers to increase capability), Education (increasing knowledge or understanding), Persuasion (using communication to induce positive or negative feelings or stimulate action), Training (imparting skills), Incentivisation (creating expectation of reward), Restriction (using rules to reduce opportunity to engage in target behaviour) and Environmental restructuring (changing the physical or social context). While participants on DOT felt cared for, they had doubts about their personal necessity for treatment, found DOT invasive and stigmatising, time-consuming and costly. At a health system level, DOT was resource-intensive and batch collections of medicines made it difficult to prove fidelity. CONCLUSION: VOT promotes engagement and adherence to TB treatment in all groups at risk of non-adherence, which suggest it is a more acceptable approach to TB treatment observation compared to DOT. VOT can be universally applied to all patient groups in need of adherence support, including inclusion health groups (those with a current or history of homelessness, imprisonment, drug misuse and current alcohol misuse, vulnerable migrant groups (asylum seekers and refugees), in low TB incidence settings. DOT is an acceptable intervention to some groups with multiple needs (participants who were aged over 55, had a prison history, a history of homelessness (more than 5 years ago) and those with current alcohol problems). The evidence from this research could be used to develop a personalised decision support tool to support clinicians to offer VOT to groups based on risk of poor adherence and quantitative and qualitative assessment of acceptability and engagement. Use of the e-Health Implementation Toolkit (e-HIT) supports the national and practical roll-out of VOT to all patient groups in need of adherence support, including those with social complexity. In the era of COVID-19 and acceleration of the use of digital innovations, monitoring the roll-out of VOT should also involve engagement with patients on privacy and confidentiality issues. Engagement with the TB workforce is needed to examine staff attitudes to support learning on what adaptations could be made to VOT and to inform their needs and health system readiness, strengthen health protection and global health security. Further engagement with healthcare professionals to secure their buy-in, address their concerns and to minimise “technology fatigue” is needed. VOT has shown that it improves treatment adherence and while trials are yet to provide convincing evidence to data that it enhances final outcomes, the technology itself does have the potential to reduce treatment-related costs at a patient and health service level. In 2020 WHO proposed VOT as one of the options to support adherence in its target product profiles for TB preventative treatment. Further real-world programmatic evidence on how VOT works and health system cost-effectiveness should continue to be conducted under different conditions of care, including in different geographical settings, patient sub-groups and at different stages of treatment. FUNDING: UCL discretionary funds, Royal Society of Tropical Medicine and Hygiene and UCL Public Policy small grant award

What health care for undocumented migrants in Belgium?

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Proceedings of the 2012 Workshop on Ambient Intelligence Infrastructures (WAmIi)

This is a technical report including the papers presented at the Workshop on Ambient Intelligence Infrastructures (WAmIi) that took place in conjunction with the International Joint Conference on Ambient Intelligence (AmI) in Pisa, Italy on November 13, 2012. The motivation for organizing the workshop was the wish to learn from past experience on Ambient Intelligence systems, and in particular, on the lessons learned on the system architecture of such systems. A significant number of European projects and other research have been performed, often with the goal of developing AmI technology to showcase AmI scenarios. We believe that for AmI to become further successfully accepted the system architecture is essential

Proceedings of the 2012 Workshop on Ambient Intelligence Infrastructures (WAmIi)

This is a technical report including the papers presented at the Workshop on Ambient Intelligence Infrastructures (WAmIi) that took place in conjunction with the International Joint Conference on Ambient Intelligence (AmI) in Pisa, Italy on November 13, 2012. The motivation for organizing the workshop was the wish to learn from past experience on Ambient Intelligence systems, and in particular, on the lessons learned on the system architecture of such systems. A significant number of European projects and other research have been performed, often with the goal of developing AmI technology to showcase AmI scenarios. We believe that for AmI to become further successfully accepted the system architecture is essential

Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque

Carotid intima media thickness (cIMT) and plaque determined by ultrasonography are established measures of subclinical atherosclerosis that each predicts future cardiovascular disease events. We conducted a meta-analysis of genome-wide association data in 31,211 participants of European ancestry from nine large studies in the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. We then sought additional evidence to support our findings among 11,273 individuals using data from seven additional studies. In the combined meta-analysis, we identified three genomic regions associated with common carotid intima media thickness and two different regions associated with the presence of carotid plaque (P < 5 × 10 -8). The associated SNPs mapped in or near genes related to cellular signaling, lipid metabolism and blood pressure homeostasis, and two of the regions were associated with coronary artery disease (P < 0.006) in the Coronary Artery Disease Genome-Wide Replication and Meta-Analysis (CARDIoGRAM) consortium. Our findings may provide new insight into pathways leading to subclinical atherosclerosis and subsequent cardiovascular events

Japan's silver market: creating a new industry under uncertainty

It has often been asked whether today´s Japan will be able to move into new and promising industries, or whether it is locked into an innovation system with an inherent inability to give birth to new industries. One argument reasons that the thick institutional complementarities among labour, innovation, and finance among its enterprises and the public sector favour industrial development in sectors of intermediate uncertainty, while it is difficult to move into areas of major uncertainty. In this paper, we present the case of the silver industry or, somewhat more prosaically, the 60+ or even 50+ industry, for which most would agree that Japan has indeed become a lead market and lead producer on the global market. For an institutional economist, the case of the silver industry is particularly interesting, because Japan´s success is based on the cooperation of existing actors, the enterprise and public sector in particular, which helped overcome the information uncertainties and asymmetries involved in the new market by relying on several established mechanisms developed well before. In that sense, Japan´s silver industry presents a case of of what we propose to call successful institutional path activation with the effect of an innovative market creation, instead of the problematic lockin effects that are usually associated with the term path dependence

Addressing geographical variation in the progression of non-communicable diseases in Peru: the CRONICAS cohort study protocol

Background The rise in non-communicable diseases in developing countries has gained increased attention. Given that around 80% of deaths related to non-communicable diseases occur in low- and middle-income countries, there is a need for local knowledge to address such problems. Longitudinal studies can provide valuable information about disease burden of non-communicable diseases in Latin America to inform both public health and clinical settings. Methods The CRONICAS cohort is a longitudinal study performed in three Peruvian settings that differ by degree of urbanisation, level of outdoor and indoor pollution and altitude. The author sought to enrol an age- and sex-stratified random sample of 1000 participants at each site. Study procedures include questionnaires on socio-demographics and well-known risk factors for cardiopulmonary disease, blood draw, anthropometry and body composition, blood pressure and spirometry before and after bronchodilators. All participants will be visited at baseline, at 20 and 40 months. A random sample of 100 households at each site will be assessed for 24 h particulate matter concentration. Primary outcomes include prevalence of risk factors for cardiopulmonary diseases, changes in blood pressure and blood glucose over time and decline in lung function. Discussion There is an urgent need to characterise the prevalence and burden of non-communicable diseases in low- and middle-income countries. Peru is a middle-income country currently undergoing a rapid epidemiological transition. This longitudinal study will provide valuable information on cardiopulmonary outcomes in three different settings and will provide a platform to address potential interventions that are locally relevant or applicable to other similar settings in Latin America