Browsing by Author "Jones, Josette F."
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Item Acceptance of use of personal health record: factors affecting physicians' perspective(2011-10-19) Agrawal, Ekta; Jones, Josette F.; Weiner, Michael; Simmermaker, JenniferAcceptance of PHR by physicians is fundamental as they play important role towards the promotion of PHR adoption by providing the access to the data to be maintained in PHR and also, using the information within the PHR for decision making. Therefore it is important to measure physicians' perspective on usefulness of PHR, and also the value and trust they have in PHR usage. Review of previous researches identifies the lack of availability of a valid survey instrument that can be used to measure physicians' perception on all different aspects of PHR use and acceptance. Using the integrated literature review methodology and Unified Theory of Acceptance and Use of Technology (UTAUT) as a guiding framework, this study was aimed to identify the factors that can be used in the development of comprehensive evaluation instrument to understand physicians' acceptance of PHR. Total 15 articles were selected for literature review and using the content analysis method, 189 undifferentiated data units were extracted from those articles. These data units were then categorized into the four core constructs of UTAUT. ―Other categorization system was also created for the data units that could not be classified into one of the UTAUT core constructs. Among four core UTAUT constructs, Performance Expectancy is found to be the most influential factor in physicians' acceptance of PHR, followed by ―Other factors, Facilitating Condition and Social Influence. Effort expectancy was found to be the least influential. The identified specific factors within each domain can be used to develop a valid survey instrument to measure physicians' perception on PHR.Item ACLRO: An Ontology for the Best Practice in ACLR Rehabilitation(2020-10) Phalakornkule, Kanitha; Jones, Josette F.; Boukai, Ben; Liu, Xiaowen; Purkayatha, Saptarshi; Duncan, William D.With the rise of big data and the demands for leveraging artificial intelligence (AI), healthcare requires more knowledge sharing that offers machine-readable semantic formalization. Even though some applications allow shared data interoperability, they still lack formal machine-readable semantics in ICD9/10 and LOINC. With ontology, the further ability to represent the shared conceptualizations is possible, similar to SNOMED-CT. Nevertheless, SNOMED-CT mainly focuses on electronic health record (EHR) documenting and evidence-based practice. Moreover, due to its independence on data quality, the ontology enhances advanced AI technologies, such as machine learning (ML), by providing a reusable knowledge framework. Developing a machine-readable and sharable semantic knowledge model incorporating external evidence and individual practice’s values will create a new revolution for best practice medicine. The purpose of this research is to implement a sharable ontology for the best practice in healthcare, with anterior cruciate ligament reconstruction (ACLR) as a case study. The ontology represents knowledge derived from both evidence-based practice (EBP) and practice-based evidence (PBE). First, the study presents how the domain-specific knowledge model is built using a combination of Toronto Virtual Enterprise (TOVE) and a bottom-up approach. Then, I propose a top-down approach using Open Biological and Biomedical Ontology (OBO) Foundry ontologies that adheres to the Basic Formal Ontology (BFO)’s framework. In this step, the EBP, PBE, and statistic ontologies are developed independently. Next, the study integrates these individual ontologies into the final ACLR Ontology (ACLRO) as a more meaningful model that endorses the reusability and the ease of the model-expansion process since the classes can grow independently from one another. Finally, the study employs a use case and DL queries for model validation. The study's innovation is to present the ontology implementation for best-practice medicine and demonstrate how it can be applied to a real-world setup with semantic information. The ACLRO simultaneously emphasizes knowledge representation in health-intervention, statistics, research design, and external research evidence, while constructing the classes of data-driven and patient-focus processes that allow knowledge sharing explicit of technology. Additionally, the model synthesizes multiple related ontologies, which leads to the successful application of best-practice medicine.Item Advanced natural language processing and temporal mining for clinical discovery(2015-08-17) Mehrabi, Saeed; Jones, Josette F.; Palakal, Mathew J.; Chien, Stanley Yung-Ping; Liu, Xiaowen; Schmidt, C. MaxThere has been vast and growing amount of healthcare data especially with the rapid adoption of electronic health records (EHRs) as a result of the HITECH act of 2009. It is estimated that around 80% of the clinical information resides in the unstructured narrative of an EHR. Recently, natural language processing (NLP) techniques have offered opportunities to extract information from unstructured clinical texts needed for various clinical applications. A popular method for enabling secondary uses of EHRs is information or concept extraction, a subtask of NLP that seeks to locate and classify elements within text based on the context. Extraction of clinical concepts without considering the context has many complications, including inaccurate diagnosis of patients and contamination of study cohorts. Identifying the negation status and whether a clinical concept belongs to patients or his family members are two of the challenges faced in context detection. A negation algorithm called Dependency Parser Negation (DEEPEN) has been developed in this research study by taking into account the dependency relationship between negation words and concepts within a sentence using the Stanford Dependency Parser. The study results demonstrate that DEEPEN, can reduce the number of incorrect negation assignment for patients with positive findings, and therefore improve the identification of patients with the target clinical findings in EHRs. Additionally, an NLP system consisting of section segmentation and relation discovery was developed to identify patients' family history. To assess the generalizability of the negation and family history algorithm, data from a different clinical institution was used in both algorithm evaluations.Item Advancing Toxicology-Based Cancer Risk Assessment with Informatics(2010-05-03T19:38:33Z) Bercu, Joel P.; Mahoui, Malika; Romero, Pedro R.; Stevens, James L.; Jones, Josette F.; Palakal, Mathew J.Since exposure to carcinogens can occur in the environment from various point sources, cancer risk assessment attempts to define and limit potential exposure such that the risk of developing cancer is negligible. While cancer risk assessment is widely used with certain methodologies well accepted in the scientific literature and regulatory guidances, there are still gaps which increase uncertainties when assessing risk including: (1) mixtures of genotoxins, (2) genotoxic metabolites, and (3) nongenotoxic carcinogens. An in silico model was developed to predict the cancer risk of a genotoxin which improved methodology for a single compound and mixtures. Monte Carlo simulations performed with a carcinogenicity potency database to estimate the overall carcinogenic risk of a mixture of genotoxic compounds showed that structural similarity would not likely increase the overall cancer risk. A cancer risk model was developed for genotoxic metabolites using excretion material in both animals and humans to determine the probability not exceeding a 1 in 100,000 excess cancer risk. Two model nongenotoxic compounds (fenofibrate and methapyraline) were tested in short-term microarray studies to develop a framework for cancer risk assessment. It was determined that a threshold for potential key events could be derived using benchmark dose analysis in combination with well developed ontologies (Kegg/GO), which were at or below measured tumorigenic and precursor events. In conclusion, informatics was effective in advancing toxicology-based cancer risk assessment using databases and predictive techniques which fill critical gaps in its methodology.Item Ambulatory Computerized Provider Order Entry and PDA-Based Clinical Decision Support Systems: An Investigation of their Patient Safety Effectiveness via an Integrative and Systematic ReviewTaffel, Jared Ross; Jones, Josette F.Substantial research has been done on inpatient provider order entry systems with varying degrees of clinical decision support. Such studies have examined how these technologies impact patient safety as well as the quality and cost of care. However, given that most medical care and prescriptions are administered in an ambulatory setting, the dearth of research on ACPOE systems is quite astonishing. This knowledge gap demonstrates the need for an integrative and systematic literature review that attempts to assess the research done on computerized patient safety interventions in ambulatory care. This review’s findings provided adequate evidence that ACPOE systems are effective interventions for reducing medication errors. Other evidence further indicated that, in terms of functional capabilities, commercial ACPOE and e-prescribing systems may be catching up with their homegrown counterparts. PDA-based CDSSs were depicted as useful tools for raising adherence to guidelines and inducing safer prescribing. These findings suggest that ACPOE And PDA-based CDS systems show promise for improving safety and healthcare quality in ambulatory settings. ACPOE specifically, tended to have more advanced CDS attributes but, nonetheless, showed more negative results compared to the e-prescribing systems. Close scrutiny should therefore be given to the elements of decision support that ambulatory physicians find most useful.Item AZEBRA (Almost Zero Error Basepair-based Record Alert): A genomic clinical decision support system(2017) Kulanthaivel, Anand; Kshirsagar, Madhura M.; Alarifi, Mohammad; Oki, Mark N.; Jones, Josette F.The idea of the United States's Precision Medicine Initiative (PMI) was to allow providers (and patients) to leverage large amounts of information (including patient genomic data) in order to create actionable knowledge that increases patient well-being. To this end, we propose a system called AZEBRA; the acronym stands for Almost Zero Error Basepair-based Record Alerts. Zebra, in addition to being a well-known wild animal, is a common medical slang term for the clinician's fallacy of mistakenly corning to a rare and sometimes dire diagnosis (the rare zebra diagnosis) due to having missed more common causes of patient symptoms (the common horse diagnosis); conversely, patients with rare conditions would be better thought of as zebras and not horses. AZEBRA is intended to leverage the principles of genetically-enhanced precision medicine in order to alert clinicians to the presence of patients with five (four rare, one common) genetic pathologies that are ordinarily sources of unnecessary morbidity and mortality in clinical settings.Item A big data augmented analytics platform to operationalize efficiencies at community clinics(2016-04-15) Kunjan, Kislaya; Jones, Josette F.; Toscos, Tammy; Wu, Huanmei; Holden, RichardCommunity Health Centers (CHCs) play a pivotal role in delivery of primary healthcare to the underserved, yet have not benefited from a modern data analytics platform that can support clinical, operational and financial decision making across the continuum of care. This research is based on a systems redesign collaborative of seven CHC organizations spread across Indiana to improve efficiency and access to care. Three research questions (RQs) formed the basis of this research, each of which seeks to address known knowledge gaps in the literature and identify areas for future research in health informatics. The first RQ seeks to understand the information needs to support operations at CHCs and implement an information architecture to support those needs. The second RQ leverages the implemented data infrastructure to evaluate how advanced analytics can guide open access scheduling – a specific use case of this research. Finally, the third RQ seeks to understand how the data can be visualized to support decision making among varying roles in CHCs. Based on the unique work and information flow needs uncovered at these CHCs, an end to-end analytics solution was designed, developed and validated within the framework of a rapid learning health system. The solution comprised of a novel heterogeneous longitudinal clinic data warehouse augmented with big data technologies and dashboard visualizations to inform CHCs regarding operational priorities and to support engagement in the systems redesign initiative. Application of predictive analytics on the health center data guided the implementation of open access scheduling and up to a 15% reduction in the missed appointment rates. Performance measures of importance to specific job profiles within the CHCs were uncovered. This was followed by a user-centered design of an online interactive dashboard to support rapid assessments of care delivery. The impact of the dashboard was assessed over time and formally validated through a usability study involving cognitive task analysis and a system usability scale questionnaire. Wider scale implementation of the data aggregation and analytics platform through regional health information networks could better support a range of health system redesign initiatives in order to address the national ‘triple aim’ of healthcare.Item Consolidation of CDA-based documents from multiple sources : a modular approach(2016-09) Hosseini Asanjan, Seyed Masoud; Jones, Josette F.; Dixon, Brian E.; Vreeman, Daniel J.; Faiola, Anthony; Wu, HuanmeiPhysicians receive multiple CCDs for a single patient encompassing various encounters and medical history recorded in different information systems. It is cumbersome for providers to explore different pages of CCDs to find specific data which can be duplicated or even conflicted. This study describes the steps towards a system that integrates multiple CCDs into one consolidated document for viewing or processing patient-level data. Also, the impact of the system on healthcare providers’ perceived workload is evaluated. A modular system is developed to consolidate and de-duplicate CDA-based documents. The system is engineered to be scalable, extensible and open source. The system’s performance and output has evaluated first based on synthesized data and later based on real-world CCDs obtained from INPC database. The accuracy of the consolidation system along with the gaps in identification of the duplications were assessed. Finally, the impact of the system on healthcare providers’ workload is evaluated using NASA TLX tool. All of the synthesized CCDs were successfully consolidated, and no data were lost. The de-duplication accuracy was 100% based on synthesized data and the processing time for each document was 1.12 seconds. For real-world CCDs, our system de-duplicated 99.1% of the problems, 87.0% of allergies, and 91.7% of medications. Although the accuracy of the system is still very promising, however, there is a minor inaccuracy. Due to system improvements, the processing time for each document is reduced to average 0.38 seconds for each CCD. The result of NASA TLX evaluation shows that the system significantly decreases healthcare providers’ perceived workload. Also, it is observed that information reconciliation reduces the medical errors. The time for review of medical documents review time is significantly reduced after CCD consolidation. Given increasing adoption and use of Health Information Exchange (HIE) to share data and information across the care continuum, duplication of information is inevitable. A novel system designed to support automated consolidation and de-duplication of information across clinical documents as they are exchanged shows promise. Future work is needed to expand the capabilities of the system and further test it using heterogeneous vocabularies across multiple HIE scenarios.Item Dietary intake and urinary excretion of phytoestrogens in relation to cancer and cardiovascular disease(2014) Reger, Michael Kent; Zollinger, Terrell; Jones, Josette F.; Liu, Ziyue; Zhang, JianjunPhytoestrogens that abound in soy products, legumes, and chickpeas can induce biologic responses in animals and humans due to structural similarity to 17β-estradiol. Although experimental studies suggest that phytoestrogen intake may alter the risk of cancer and cardiovascular disease, few epidemiologic studies have investigated this research question. This dissertation investigated the associations of intake of total and individual phytoestrogens and their urinary biomarkers with these chronic conditions using data previously collected from two US national cohort studies (NHANES and PLCO). Utilizing NHANES data with urinary phytoestrogen concentrations and follow-up mortality, Cox proportional hazards regression (HR; 95% CI) were performed to evaluate the association between total cancer, cardiovascular disease, and all-cause mortality and urinary phytoestrogens. After adjustment for confounders, it was found that higher concentrations of lignans were associated with a reduced risk of death from cardiovascular disease (0.48; 0.24-0.97), whereas higher concentrations of isoflavones (2.14; 1.03-4.47) and daidzein (2.05; 1.02-4.11) were associated with an increased risk. A reduction in all-cause mortality was observed for elevated concentrations of lignans (0.65; 0.43-0.96) and enterolactone (0.65; 0.44-0.97). Utilizing PLCO data and dietary phytoestrogens, Cox proportional hazards regression examined the associations between dietary phytoestrogens and the risk of prostate cancer incidence. After adjustment for confounders, a positive association was found between dietary intake of isoflavones (1.58; 1.11-2.24), genistein (1.42; 1.02-1.98), daidzein (1.62; 1.13-2.32), and glycitein (1.53; 1.09-2.15) and the risk of advanced prostate cancer. Conversely, an inverse association existed between dietary intake of genistein and the risk of non-advanced prostate cancer (0.88; 0.78-0.99) and total prostate cancer (0.90; 0.81-1.00). C-reactive protein (CRP) concentration levels rise in response to inflammation and higher levels are a risk factor for some cancers and cardiovascular disease reported in epidemiologic studies. Logistic regression performed on NHANES data evaluated the association between CRP and urinary phytoestrogen concentrations. Higher concentrations of total and individual phytoestrogens were associated with lower concentrations of CRP. In summary, dietary intake of some phytoestrogens significantly modulates prostate cancer risk and cardiovascular disease mortality. It is possible that these associations may be in part mediated through the influence of phytoestrogen intake on circulating levels of C-reactive protein.Item Dietary intake of isoflavones and coumestrol and the risk of prostate cancer in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial(Wiley, 2018-02) Reger, Michael K.; Zollinger, Terrell W.; Liu, Ziyue; Jones, Josette F.; Zhang, Jianjun; Epidemiology, School of Public HealthExperimental studies have revealed that phytoestrogens may modulate the risk of certain sites of cancer due to their structural similarity to 17β‐estradiol. The present study investigates whether intake of these compounds may influence prostate cancer risk in human populations. During a median follow up of 11.5 years, 2,598 cases of prostate cancer (including 287 advanced cases) have been identified among 27,004 men in the intervention arm of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Dietary intake of phytoestrogens (excluding lignans) was assessed with a food frequency questionnaire. Cox proportional hazards regression analysis was performed to estimate hazard ratios (HRs) and 95% confidence intervals (CI) for dietary isoflavones and coumestrol in relation to prostate cancer risk. After adjustment for confounders, an increased risk of advanced prostate cancer [HR (95% CI) for quintile (Q) 5 vs. Q1] was found for the dietary intake of total isoflavones [1.91 (1.25–2.92)], genistein [1.51 (1.02–2.22), daidzein [1.80 (1.18–2.75) and glycitein [1.67 (1.15–2.43)] (p‐trend for all associations ≤0.05). For example, HR (95% CI) for comparing the Q2, Q3, Q4 and Q5 with Q1 of daidzein intake was 1.45 (0.93–2.25), 1.65 (1.07–2.54), 1.73 (1.13–2.66) and 1.80 (1.18–2.75), respectively (p‐trend: 0.013). No statistically significant associations were observed between the intake of total isoflavones and individual phytoestrogens and non‐advanced and total prostate cancer after adjustment for confounders. This study revealed that dietary intake of isoflavones was associated with an elevated risk of advanced prostate cancer.