Spatial Enablement to Support Environmental, Demographic, Socioeconomics, and Health Data Integration and Analysis for Big Cities: A Case Study With Asthma Hospitalizations in New York City

The percentage of the world's population living in urban areas is projected to increase in the next decades. Big cities are heterogeneous environments in which socioeconomic and environmental differences among the neighborhoods are often very pronounced. Each individual, during his/her life, is constantly subject to a mix of exposures that have an effect on their phenotype but are frequently difficult to identify, especially in an urban environment. Studying how the combination of environmental and socioeconomic factors which the population is exposed to influences pathological outcomes can help transforming public health from a reactive to a predictive system. Thanks to the application of state-of-the-art spatially enabled methods, patients can be stratified according to their characteristics and the geographical context they live in, optimizing healthcare processes and the reducing its costs. Some public health studies focusing specifically on urban areas have been conducted, but they usually consider a coarse spatial subdivision, as a consequence of scarce availability of well-integrated data regarding health and environmental exposure at a sufficient level of granularity to enable meaningful statistical analyses. In this paper, we present an application of highly fine-grained spatial resolution methods to New York City data. We investigated the link between asthma hospitalizations and a combination of air pollution and other environmental and socioeconomic factors. We first performed an explorative analysis using spatial clustering methods that shows that asthma is related to numerous factors whose level of influence varies considerably among neighborhoods. We then performed a Geographically Weighted Regression with different covariates and determined which environmental and socioeconomic factors can predict hospitalizations and how they vary throughout the city. These methods showed to be promising both for visualization and analysis of demographic and epidemiological urban dynamics, that can be used to organize targeted intervention and treatment policies to address the single citizens considering the factors he/she is exposed to. We found a link between asthma and several factors such as PM2.5, age, health insurance coverage, race, poverty, obesity, industrial areas, and recycling. This study has been conducted within the PULSE project, funded by the European Commission, briefly presented in this paper

Data Quality and Completeness in a Web Stroke Registry as the Basis for Data and Process Mining

Electronic health records often show missing values and errors jeopardizing their effective exploitation. We illustrate the re-engineering process needed to improve the data quality of a web-based, multicentric stroke registry by proposing a knowledge-based data entry support able to help users to homogeneously interpret data items, and to prevent and detect treacherous errors. The re-engineering also improves stroke units coordination and networking, through ancillary tools for monitoring patient enrollments, calculating stroke care indicators, analyzing compliance with clinical practice guidelines, and entering stroke units profiles. Finally we report on some statistics, such as calculation of indicators for assessing the quality of stroke care, data mining for knowledge discovery, and process mining for comparing different processes of care delivery. The most important results of the re-engineering are an improved user experience with data entry, and a definitely better data quality that guarantees the reliability of data analyses

Localising In-Domain Adaptation of Transformer-Based Biomedical Language Models

In the era of digital healthcare, the huge volumes of textual information generated every day in hospitals constitute an essential but underused asset that could be exploited with task-specific, fine-tuned biomedical language representation models, improving patient care and management. For such specialized domains, previous research has shown that fine-tuning models stemming from broad-coverage checkpoints can largely benefit additional training rounds over large-scale in-domain resources. However, these resources are often unreachable for less-resourced languages like Italian, preventing local medical institutions to employ in-domain adaptation. In order to reduce this gap, our work investigates two accessible approaches to derive biomedical language models in languages other than English, taking Italian as a concrete use-case: one based on neural machine translation of English resources, favoring quantity over quality; the other based on a high-grade, narrow-scoped corpus natively written in Italian, thus preferring quality over quantity. Our study shows that data quantity is a harder constraint than data quality for biomedical adaptation, but the concatenation of high-quality data can improve model performance even when dealing with relatively size-limited corpora. The models published from our investigations have the potential to unlock important research opportunities for Italian hospitals and academia. Finally, the set of lessons learned from the study constitutes valuable insights towards a solution to build biomedical language models that are generalizable to other less-resourced languages and different domain settings.Comment: 8 pages, 2 figures, 6 tables. Published in Journal of Biomedical Informatic

How Do Spinal Surgeons Perceive The Impact of Factors Used in Post-Surgical Complication Risk Scores?

When deciding about surgical treatment options, an important aspect of the decision-making process is the potential risk of complications. A risk assessment performed by a spinal surgeon is based on their knowledge of the best available evidence and on their own clinical experience. The objective of this work is to demonstrate the differences in the way spine surgeons perceive the importance of attributes used to calculate risk of post-operative and quantify the differences by building individual formal models of risk perceptions. We employ a preference-learning method - ROR-UTADIS - to build surgeon-specific additive value functions for risk of complications. Comparing these functions enables the identification and discussion of differences among personal perceptions of risk factors. Our results show there exist differences in surgeons\u27 perceived factors including primary diagnosis, type of surgery, patient\u27s age, body mass index, or presence of comorbidities

Development of a FHIR Layer on Top of the OMOP Common Data Model for the CAPABLE Project.

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Ideating Mobile Health Behavioral Support for Compliance to Therapy for Patients with Chronic Disease: A Case Study of Atrial Fibrillation Management

Poor patient compliance to therapy results in a worsening condition that often increases healthcare costs. In the MobiGuide project, we developed an evidence-based clinical decision-support system that delivered personalized reminders and recommendations to patients, helping to achieve higher therapy compliance. Yet compliance could still be improved and therefore building on the MobiGuide project experience, we designed a new component called the Motivational Patient Assistant (MPA) that is integrated within the MobiGuide architecture to further improve compliance. This component draws from psychological theories to provide behavioral support to improve patient engagement and thereby increasing patients\u27 compliance. Behavior modification interventions are delivered via mobile technology at patients\u27 home environments. Our approach was inspired by the IDEAS (Integrate, Design, Assess, and Share) framework for developing effective digital interventions to change health behavior; it goes beyond this approach by extending the Ideation phase\u27 concepts into concrete backend architectural components and graphical user-interface designs that implement behavioral interventions. We describe in detail our ideation approach and how it was applied to design the user interface of MPA for anticoagulation therapy for the atrial fibrillation patients. We report results of a preliminary evaluation involving patients and care providers that shows the potential usefulness of the MPA for improving compliance to anticoagulation therapy

A Health eLearning Ontology and Procedural Reasoning Approach for Developing Personalized Courses to Teach Patients about Their Medical Condition and Treatment

We propose a methodological framework to support the development of personalized courses that improve patients’ understanding of their condition and prescribed treatment. Inspired by Intelligent Tutoring Systems (ITSs), the framework uses an eLearning ontology to express domain and learner models and to create a course. We combine the ontology with a procedural reasoning approach and precompiled plans to operationalize a design across disease conditions. The resulting courses generated by the framework are personalized across four patient axes—condition and treatment, comprehension level, learning style based on the VARK (Visual, Aural, Read/write, Kinesthetic) presentation model, and the level of understanding of specific course content according to Bloom’s taxonomy. Customizing educational materials along these learning axes stimulates and sustains patients’ attention when learning about their conditions or treatment options. Our proposed framework creates a personalized course that prepares patients for their meetings with specialists and educates them about their prescribed treatment. We posit that the improvement in patients’ understanding of prescribed care will result in better outcomes and we validate that the constructs of our framework are appropriate for representing content and deriving personalized courses for two use cases: anticoagulation treatment of an atrial fibrillation patient and lower back pain management to treat a lumbar degenerative disc condition. We conduct a mostly qualitative study supported by a quantitative questionnaire to investigate the acceptability of the framework among the target patient population and medical practitioners

The Case Manager: Driving Medical Reasoning in a Distributed Environment for Home Patient Monitoring.

The CAPABLE project has been funded by the EU Horizon 2020 Programme over the years 2020-24 to support home care. A system is being designed and implemented supporting remote monitoring and virtual coaching for cancer patients. The system is based on a distributed modular architecture involving many components encapsulating various knowledge. The Case Manager has been designed as a separate component with the aim of coordinating the problem solving strategies. A first version of the Case Manager has been released and used by the components in a prototypical scenario shown at the first project review

Advancing Italian Biomedical Information Extraction with Large Language Models: Methodological Insights and Multicenter Practical Application

The introduction of computerized medical records in hospitals has reduced burdensome operations like manual writing and information fetching. However, the data contained in medical records are still far underutilized, primarily because extracting them from unstructured textual medical records takes time and effort. Information Extraction, a subfield of Natural Language Processing, can help clinical practitioners overcome this limitation, using automated text-mining pipelines. In this work, we created the first Italian neuropsychiatric Named Entity Recognition dataset, PsyNIT, and used it to develop a Large Language Model for this task. Moreover, we conducted several experiments with three external independent datasets to implement an effective multicenter model, with overall F1-score 84.77%, Precision 83.16%, Recall 86.44%. The lessons learned are: (i) the crucial role of a consistent annotation process and (ii) a fine-tuning strategy that combines classical methods with a "few-shot" approach. This allowed us to establish methodological guidelines that pave the way for future implementations in this field and allow Italian hospitals to tap into important research opportunities

A synthetic dataset of liver disorder patients

The data in this article include 10,000 synthetic patients with liver disorders, characterized by 70 different variables, including clinical features, and patient outcomes, such as hospital admission or surgery. Patient data are generated, simulating as close as possible real patient data, using a publicly available Bayesian network describing a casual model for liver disorders. By varying the network parameters, we also generated an additional set of 500 patients with characteristics that deviated from the initial patient population. We provide an overview of the synthetic data generation process and the associated scripts for generating the cohorts. This dataset can be useful for the machine learning models training and validation, especially under the effect of dataset shift between training and testing sets