PRISM: A Platform for Imaging in Precision Medicine

Advancing Precision Medicine: Algebraic Topology and Differential Geometry in Radiology and Computational Pathology

Precision medicine aims to provide personalized care based on individual patient characteristics, rather than guideline-directed therapies for groups of diseases or patient demographics. Images-both radiology- and pathology-derived-are a major source of information on presence, type, and status of disease. Exploring the mathematical relationship of pixels in medical imaging ("radiomics") and cellular-scale structures in digital pathology slides ("pathomics") offers powerful tools for extracting both qualitative and, increasingly, quantitative data. These analytical approaches, however, may be significantly enhanced by applying additional methods arising from fields of mathematics such as differential geometry and algebraic topology that remain underexplored in this context. Geometry's strength lies in its ability to provide precise local measurements, such as curvature, that can be crucial for identifying abnormalities at multiple spatial levels. These measurements can augment the quantitative features extracted in conventional radiomics, leading to more nuanced diagnostics. By contrast, topology serves as a robust shape descriptor, capturing essential features such as connected components and holes. The field of topological data analysis was initially founded to explore the shape of data, with functional network connectivity in the brain being a prominent example. Increasingly, its tools are now being used to explore organizational patterns of physical structures in medical images and digitized pathology slides. By leveraging tools from both differential geometry and algebraic topology, researchers and clinicians may be able to obtain a more comprehensive, multi-layered understanding of medical images and contribute to precision medicine's armamentarium.

Feasibility of regional center telehealth visits utilizing a rural research network in people with Parkinson's disease

Background

Impaired motor and cognitive function can make travel cumbersome for People with Parkinson's disease (PwPD). Over 50% of PwPD cared for at the University of Arkansas for Medical Sciences (UAMS) Movement Disorders Clinic reside over 30 miles from Little Rock. Improving access to clinical care for PwPD is needed.

Objective

To explore the feasibility of remote clinic-to-clinic telehealth research visits for evaluation of multi-modal function in PwPD.

Methods

PwPD residing within 30 miles of a UAMS Regional health center were enrolled and clinic-to-clinic telehealth visits were performed. Motor and non-motor disease assessments were administered and quantified. Results were compared to participants who performed at-home telehealth visits using the same protocols during the height of the COVID pandemic.

Results

Compared to the at-home telehealth visit group (n = 50), the participants from regional centers (n = 13) had similar age and disease duration, but greater disease severity with higher total Unified Parkinson's disease rating scale scores (Z = -2.218, p = 0.027) and lower Montreal Cognitive Assessment scores (Z = -3.350, p < 0.001). Regional center participants had lower incomes (Pearson's chi = 21.3, p < 0.001), higher costs to attend visits (Pearson's chi = 16.1, p = 0.003), and lived in more socioeconomically disadvantaged neighborhoods (Z = -3.120, p = 0.002). Prior research participation was lower in the regional center group (Pearson's chi = 4.5, p = 0.034) but both groups indicated interest in future research participation.

Conclusions

Regional center research visits in PwPD in medically underserved areas are feasible and could help improve access to care and research participation in these traditionally underrepresented populations.

Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach

Five new series of pyrrolo-fused heterocycles were designed through a scaffold hybridization strategy as analogs of the well-known microtubule inhibitor phenstatin. Compounds were synthesized using the 1,3-dipolar cycloaddition of cycloimmonium N-ylides to ethyl propiolate as a key step. Selected compounds were then evaluated for anticancer activity and ability to inhibit tubulin polymerization in vitro. Notably, pyrrolo[1,2-a]quinoline 10a was active on most tested cell lines, performing better than control phenstatin in several cases, most notably on renal cancer cell line A498 (GI₅₀ 27 nM), while inhibiting tubulin polymerization in vitro. In addition, this compound was predicted to have a promising ADMET profile. The molecular details of the interaction between compound 10a and tubulin were investigated through in silico docking experiments, followed by molecular dynamics simulations and configurational entropy calculations. Of note, we found that some of the initially predicted interactions from docking experiments were not stable during molecular dynamics simulations, but that configurational entropy loss was similar in all three cases. Our results suggest that for compound 10a, docking experiments alone are not sufficient for the adequate description of interaction details in terms of target binding, which makes subsequent scaffold optimization more difficult and ultimately hinders drug design. Taken together, these results could help shape novel potent antiproliferative compounds with pyrrolo-fused heterocyclic cores, especially from an in silico methodological perspective.

Bioisosteric replacement of 1H-1,2,3-triazole with 1H-tetrazole ring enhances anti-leukemic activity of (5-benzylthiazol-2-yl)benzamides

Previously, we discovered that N-(5-benzyl-1,3-thiazol-2-yl)-4-(5-methyl-1H-1,2,3-triazol-1-yl)benzamide possessed a remarkable cytotoxic effect on 28 cancer cell lines with IC₅₀ < 50 μM, including 9 cancer cell lines, where IC₅₀ was in the range of 2.02-4.70 μM. In the present study, we designed a novel N-(5-benzylthiazol-2-yl)amide compound 3d that was synthesized using the original bioisosteric replacement of 1H-1,2,3-triazole ring by the 1H-tetrazole ring. A significantly enhanced anticancer activity in vitro with an excellent anti-leukemic potency towards chronic myeloid leukemia cells of the K-562 line was demonstrated. Two compounds - 3d and 3l - were highly cytotoxic at nanomolar concentrations towards various tumor cells of the following lines: K-562, NCI-H460, HCT-15, KM12, SW-620, LOX IMVI, M14, UACC-62, CAKI-1, and T47D. As a highlight, the compound N-(5-(4-fluorobenzyl)thiazol-2-yl)-4-(1H-tetrazol-1-yl)benzamide 3d inhibited the growth of leukemia K-562 cells and melanoma UACC-62 cells with IС₅₀ of 56.4 and 56.9 nM (SRB test), respectively. The viability of leukemia K-562 and pseudo-normal HaCaT, NIH-3T3, and J774.2 cells was measured by the MTT assay. Together with SAR analysis, it allowed the selection of a lead compound 3d, which demonstrated the highest selectivity (SI = 101.0) towards treated leukemic cells. The compound 3d caused DNA damage (single-strand breaks detected by the alkaline comet assay) in the leukemic K-562 cells. The morphological study of the K-562 cells treated with compound 3d revealed changes consistent with apoptosis. Thus, the bioisosteric replacement in (5-benzylthiazol-2-yl)amide scaffold proved to be a perspective approach in the design of novel heterocyclic compounds with enhanced anticancer potential.

The informed consent form navigator: a tool for producing readable and compliant consent documents

Background/Objective

Informed consent forms (ICFs) and practices vary widely across institutions. This project expands on previous work at the University of Arkansas for Medical Sciences (UAMS) Center for Health Literacy to develop a plain language ICF template. Our interdisciplinary team of researchers, comprised of biomedical informaticists, health literacy experts, and stakeholders in the Institutional Review Board (IRB) process, has developed the ICF Navigator, a novel tool to facilitate the creation of plain language ICFs that comply with all relevant regulatory requirements.

Methods

Our team first developed requirements for the ICF Navigator tool. The tool was then implemented by a technical team of informaticists and software developers, in consultation with an informed consent legal expert. We developed and formalized a detailed knowledge map modeling regulatory requirements for ICFs, which drives workflows within the tool.

Results

The ICF Navigator is a web-based tool that guides researchers through creating an ICF as they answer questions about their project. The navigator uses those responses to produce a clear and compliant ICF, displaying a real-time preview of the final form as content is added. Versioning and edits can be tracked to facilitate collaborative revisions by the research team and communication with the IRB. The navigator helps guide the creation of study-specific language, ensures compliance with regulatory requirements, and ensures that the resulting ICF is easy to read and understand.

Conclusion

The ICF Navigator is an innovative, customizable, open-source software tool that helps researchers produce custom readable and compliant ICFs for research studies involving human subjects.

The PRISM semantic cohort builder: a novel tool to search and access clinical data in TCIA imaging collections

The cancer imaging archive (TICA) receives and manages an ever-increasing quantity of clinical (non-image) data containing valuable information about subjects in imaging collections. To harmonize and integrate these data, we have first cataloged the types of information occurring across public TCIA collections. We then produced mappings for these diverse instance data using ontology-based representation patterns and transformed the data into a knowledge graph in a semantic database. This repository combined the transformed instance data with relevant background knowledge from domain ontologies. The resulting repository of semantically integrated data is a rich source of information about subjects that can be queried across imaging collections. Building on this work we have implemented and deployed a REST API and a user-facing semantic cohort builder tool. This tool allows allow researchers and other users to search and identify groups of subject-level records based on non-image data that were not queryable prior to this work. The search results produced by this interface link to images, allowing users to quickly identify and view images matching the selection criteria, as well as allowing users to export the harmonized clinical data.

Radio-pathomic approaches in pediatric neuro-oncology: Opportunities and challenges

With medical software platforms moving to cloud environments with scalable storage and computing, the translation of predictive artificial intelligence (AI) models to aid in clinical decision-making and facilitate personalized medicine for cancer patients is becoming a reality. Medical imaging, namely radiologic and histologic images, has immense analytical potential in neuro-oncology, and models utilizing integrated radiomic and pathomic data may yield a synergistic effect and provide a new modality for precision medicine. At the same time, the ability to harness multi-modal data is met with challenges in aggregating data across medical departments and institutions, as well as significant complexity in modeling the phenotypic and genotypic heterogeneity of pediatric brain tumors. In this paper, we review recent pathomic and integrated pathomic, radiomic, and genomic studies with clinical applications. We discuss current challenges limiting translational research on pediatric brain tumors and outline technical and analytical solutions. Overall, we propose that to empower the potential residing in radio-pathomics, systemic changes in cross-discipline data management and end-to-end software platforms to handle multi-modal data sets are needed, in addition to embracing modern AI-powered approaches. These changes can improve the performance of predictive models, and ultimately the ability to advance brain cancer treatments and patient outcomes through the development of such models.

Feasibility of telemedicine research visits in people with Parkinson's disease residing in medically underserved areas

Introduction

Gait, balance, and cognitive impairment make travel cumbersome for People with Parkinson's disease (PwPD). About 75% of PwPD cared for at the University of Arkansas for Medical Sciences' Movement Disorders Clinic reside in medically underserved areas (MUAs). Validated remote evaluations could help improve their access to care. Our goal was to explore the feasibility of telemedicine research visits for the evaluation of multi-modal function in PwPD in a rural state.

Methods

In-home telemedicine research visits were performed in PwPD. Motor and non-motor disease features were evaluated and quantified by trained personnel, digital survey instruments for self-assessments, digital voice recordings, and scanned and digitized Archimedes spiral drawings. Participant's MUA residence was determined after evaluations were completed.

Results

Twenty of the fifty PwPD enrolled resided in MUAs. The groups were well matched for disease duration, modified motor UPDRS, and Montreal Cognitive assessment scores but MUA participants were younger. Ninety-two percent were satisfied with their visit, and 61% were more likely to participate in future telemedicine research. MUA participants traveled longer distances, with higher travel costs, lower income, and education level. While 50% of MUA participants reported self-reliance for in-person visits, 85% reported self-reliance for the telemedicine visit. We rated audio-video quality highly in approximately 60% of visits in both groups. There was good correlation with prior in-person research assessments in a subset of participants.

Conclusions

In-home research visits for PwPD in MUAs are feasible and could help improve access to care and research participation in these traditionally underrepresented populations.

Assessing the Need for Semantic Data Integration for Surgical Biobanks-A Knowledge Representation Perspective

To improve patient outcomes after trauma, the need to decrypt the post-traumatic immune response has been identified. One prerequisite to drive advancement in understanding that domain is the implementation of surgical biobanks. This paper focuses on the outcomes of patients with one of two diagnoses: post-traumatic arthritis and osteomyelitis. In creating surgical biobanks, currently, many obstacles must be overcome. Roadblocks exist around scoping of data that is to be collected, and the semantic integration of these data. In this paper, the generic component model and the Semantic Web technology stack are used to solve issues related to data integration. The results are twofold: (a) a scoping analysis of data and the ontologies required to harmonize and integrate it, and (b) resolution of common data integration issues in integrating data relevant to trauma surgery.

Medical-Blocks: A Platform for Exploration, Management, Analysis, and Sharing of Data in Biomedical Research

BACKGROUND

Biomedical research requires healthcare institutions to provide sensitive clinical data to leverage data science and artificial intelligence technologies. However, providing healthcare data to researchers simple and secure, proves to be challenging for healthcare institutions.

OBJECTIVE

We describe and introduce Medical-Blocks, a platform for data exploration, data management, data analysis, and data sharing in biomedical research.

METHODS

The specification requirements for Medical-Blocks included: i) Connection to data sources of healthcare institutions with an interface for data exploration, ii) management of data in an internal file storage system, iii) data analysis through visualization and classification of data, and iv) data sharing via a file hosting service for collaboration. Medical-Blocks should be simple to use via a web-based user interface and extensible with new functionalities by a modular design via microservices ("blocks"). The scalability of the platform should be ensured by containerization. Security and legal regulations were considered during the development.

RESULTS

Medical-Blocks is a web application that runs in the cloud or as a local instance at a healthcare institution. Local instances of Medical-Blocks access data sources such as electronic health records and picture archiving and communications system (PACS) at healthcare institutions. Researchers and clinicians can explore, manage, and analyze the available data through Medical-Blocks. The data analysis involves classification of data for metadata extraction and the formation of cohorts. In collaborations, metadata (e.g., number of patients per cohort) and/or the data itself can be shared through Medical-Blocks locally or via a cloud instance to other researchers and clinicians.

CONCLUSIONS

Medical-Blocks facilitates biomedical research by providing a centralized platform to interact with medical data in collaborative research projects. The access to and management of medical data is simplified. Data can be swiftly analyzed to form cohorts for research and be shared among researchers. The modularity of Medical-Blocks makes the platform feasible for biomedical research where heterogenous medical data is needed.

CLINICALTRIAL

Semantic Integration of Multi-Modal Data and Derived Neuroimaging Results Using the Platform for Imaging in Precision Medicine (PRISM) in the Arkansas Imaging Enterprise System (ARIES)

Neuroimaging is among the most active research domains for the creation and management of open-access data repositories. Notably lacking from most data repositories are integrated capabilities for semantic representation. The Arkansas Imaging Enterprise System (ARIES) is a research data management system which features integrated capabilities to support semantic representations of multi-modal data from disparate sources (imaging, behavioral, or cognitive assessments), across common image-processing stages (preprocessing steps, segmentation schemes, analytic pipelines), as well as derived results (publishable findings). These unique capabilities ensure greater reproducibility of scientific findings across large-scale research projects. The current investigation was conducted with three collaborating teams who are using ARIES in a project focusing on neurodegeneration. Datasets included magnetic resonance imaging (MRI) data as well as non-imaging data obtained from a variety of assessments designed to measure neurocognitive functions (performance scores on neuropsychological tests). We integrate and manage these data with semantic representations based on axiomatically rich biomedical ontologies. These instantiate a knowledge graph that combines the data from the study cohorts into a shared semantic representation that explicitly accounts for relations among the entities that the data are about. This knowledge graph is stored in a triple-store database that supports reasoning over and querying these integrated data. Semantic integration of the non-imaging data using background information encoded in biomedical domain ontologies has served as a key feature-engineering step, allowing us to combine disparate data and apply analyses to explore associations, for instance, between hippocampal volumes and measures of cognitive functions derived from various assessment instruments.

Advancing Research on Medical Image Perception by Strengthening Multidisciplinary Collaboration

Medical image interpretation is central to detecting, diagnosing, and staging cancer and many other disorders. At a time when medical imaging is being transformed by digital technologies and artificial intelligence, understanding the basic perceptual and cognitive processes underlying medical image interpretation is vital for increasing diagnosticians' accuracy and performance, improving patient outcomes, and reducing diagnostician burnout. Medical image perception remains substantially understudied. In September 2019, the National Cancer Institute convened a multidisciplinary panel of radiologists and pathologists together with researchers working in medical image perception and adjacent fields of cognition and perception for the "Cognition and Medical Image Perception Think Tank." The Think Tank's key objectives were to identify critical unsolved problems related to visual perception in pathology and radiology from the perspective of diagnosticians, discuss how these clinically relevant questions could be addressed through cognitive and perception research, identify barriers and solutions for transdisciplinary collaborations, define ways to elevate the profile of cognition and perception research within the medical image community, determine the greatest needs to advance medical image perception, and outline future goals and strategies to evaluate progress. The Think Tank emphasized diagnosticians' perspectives as the crucial starting point for medical image perception research, with diagnosticians describing their interpretation process and identifying perceptual and cognitive problems that arise. This article reports the deliberations of the Think Tank participants to address these objectives and highlight opportunities to expand research on medical image perception.

An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities

BACKGROUND

Population-based state cancer registries are an authoritative source for cancer statistics in the United States. They routinely collect a variety of data, including patient demographics, primary tumor site, stage at diagnosis, first course of treatment, and survival, on every cancer case that is reported across all U.S. states and territories. The goal of our project is to enrich NCI's Surveillance, Epidemiology, and End Results (SEER) registry data with high-quality population-based biospecimen data in the form of digital pathology, machine-learning-based classifications, and quantitative histopathology imaging feature sets (referred to here as Pathomics features).

MATERIALS AND METHODS

As part of the project, the underlying informatics infrastructure was designed, tested, and implemented through close collaboration with several participating SEER registries to ensure consistency with registry processes, computational scalability, and ability to support creation of population cohorts that span multiple sites. Utilizing computational imaging algorithms and methods to both generate indices and search for matches makes it possible to reduce inter- and intra-observer inconsistencies and to improve the objectivity with which large image repositories are interrogated.

RESULTS

Our team has created and continues to expand a well-curated repository of high-quality digitized pathology images corresponding to subjects whose data are routinely collected by the collaborating registries. Our team has systematically deployed and tested key, visual analytic methods to facilitate automated creation of population cohorts for epidemiological studies and tools to support visualization of feature clusters and evaluation of whole-slide images. As part of these efforts, we are developing and optimizing advanced search and matching algorithms to facilitate automated, content-based retrieval of digitized specimens based on their underlying image features and staining characteristics.

CONCLUSION

To meet the challenges of this project, we established the analytic pipelines, methods, and workflows to support the expansion and management of a growing repository of high-quality digitized pathology and information-rich, population cohorts containing objective imaging and clinical attributes to facilitate studies that seek to discriminate among different subtypes of disease, stratify patient populations, and perform comparisons of tumor characteristics within and across patient cohorts. We have also successfully developed a suite of tools based on a deep-learning method to perform quantitative characterizations of tumor regions, assess infiltrating lymphocyte distributions, and generate objective nuclear feature measurements. As part of these efforts, our team has implemented reliable methods that enable investigators to systematically search through large repositories to automatically retrieve digitized pathology specimens and correlated clinical data based on their computational signatures.

Joint Imaging Platform for Federated Clinical Data Analytics

PURPOSE

Image analysis is one of the most promising applications of artificial intelligence (AI) in health care, potentially improving prediction, diagnosis, and treatment of diseases. Although scientific advances in this area critically depend on the accessibility of large-volume and high-quality data, sharing data between institutions faces various ethical and legal constraints as well as organizational and technical obstacles.

METHODS

The Joint Imaging Platform (JIP) of the German Cancer Consortium (DKTK) addresses these issues by providing federated data analysis technology in a secure and compliant way. Using the JIP, medical image data remain in the originator institutions, but analysis and AI algorithms are shared and jointly used. Common standards and interfaces to local systems ensure permanent data sovereignty of participating institutions.

RESULTS

The JIP is established in the radiology and nuclear medicine departments of 10 university hospitals in Germany (DKTK partner sites). In multiple complementary use cases, we show that the platform fulfills all relevant requirements to serve as a foundation for multicenter medical imaging trials and research on large cohorts, including the harmonization and integration of data, interactive analysis, automatic analysis, federated machine learning, and extensibility and maintenance processes, which are elementary for the sustainability of such a platform.

CONCLUSION

The results demonstrate the feasibility of using the JIP as a federated data analytics platform in heterogeneous clinical information technology and software landscapes, solving an important bottleneck for the application of AI to large-scale clinical imaging data.

Artificial Intelligence and the Medical Physicist: Welcome to the Machine

Artificial intelligence (AI) is a branch of computer science dedicated to giving machines or computers the ability to perform human-like cognitive functions, such as learning, problem-solving, and decision making. Since it is showing superior performance than well-trained human beings in many areas, such as image classification, object detection, speech recognition, and decision-making, AI is expected to change profoundly every area of science, including healthcare and the clinical application of physics to healthcare, referred to as medical physics. As a result, the Italian Association of Medical Physics (AIFM) has created the “AI for Medical Physics” (AI4MP) group with the aims of coordinating the efforts, facilitating the communication, and sharing of the knowledge on AI of the medical physicists (MPs) in Italy. The purpose of this review is to summarize the main applications of AI in medical physics, describe the skills of the MPs in research and clinical applications of AI, and define the major challenges of AI in healthcare.