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With the marked increases in electronic health record (EHR) use for providing clinical care, there have been parallel efforts to leverage EHR data for research. EHR repositories offer the promise of vast amounts of clinical data not easily captured with traditional research methods and facilitate clinical epidemiology and comparative effectiveness research, including analyses to identify patients at higher risk for complications or who are better candidates for treatment. These types of studies have been relatively slow to penetrate the field of infectious diseases, but the need for rapid turnaround during the COVID-19 global pandemic has accelerated the uptake. This review discusses the rationale for her network projects, opportunities and challenges that such networks present, and some prior studies within the field of infectious diseases.

With the advent of competency-based medical education, as well as Canadian efforts to include clinical informatics within undergraduate medical education, competency frameworks in the United States have not emphasized the skills associated with clinical informatics pertinent to the broader practice of medicine. By examining the competency frameworks with which undergraduate medical education in clinical informatics has been developed in Canada and the United States, we hypothesized that there is a gap: the lack of a unified competency set and frame for clinical informatics education across North America. We performed directional competency mapping between Canadian and American graduate clinical informatics competencies and general graduate medical education competencies. Directional competency mapping was performed between Canadian roles and American common program requirements using keyword matching at the subcompetency and enabling competency levels. In addition, for general graduate medical education competencies, the Physician Competency Reference Set developed for the Liaison Committee on Medical Education was used as a direct means of computing the ontological overlap between competency frameworks. Upon mapping Canadian roles to American competencies via both undergraduate and graduate medical education competency frameworks, the difference in focus between the 2 countries can be thematically described as a difference between the concepts of clinical and management reasoning. We suggest that the development or deployment of informatics competencies in undergraduate medical education should focus on 3 items: the teaching of diagnostic reasoning, such that the information tasks that comprise both clinical and management reasoning can be discussed; precision medical education, where informatics can provide for more fine-grained evaluation; and assessment methods to support traditional pedagogical efforts (both at the bedside and beyond). Assessment using cases or structured assessments (eg, Objective Structured Clinical Examinations) would help students draw parallels between clinical informatics and fundamental clinical subjects and would better emphasize the cognitive techniques taught through informatics.

Background Early introduction of peanut products to infants around 4- to 6- months of age may reduce peanut allergy incidence. However, clinician adherence to the National Institute of Allergy and Infectious Diseases’ 2017 Addendum Guidelines for the Prevention of Peanut Allergy (PPA), which recommend early peanut introduction based on risk levels, has been reportedly low. Documentation of clinician peanut introduction recommendations and peanut allergy risk in electronic health records (EHR) is variable and often in the form of unstructured data. Therefore, this study aims to develop and validate a Natural Language Processing (NLP) approach to identify and measure pediatric clinicians’ adherence to the PPA guidelines (peanut introduction recommendations and peanut allergy risk assessments, including eczema severity), as documented in EHR systems. Methods An NLP pipeline was developed to process clinical notes and patient instructions from EHRs in the Intervention to Reduce Early Peanut Allergy in Children (iREACH) trial. iREACH is a two-arm, cluster-randomized, controlled clinical trial that evaluates an intervention to enhance clinician adherence to the PPA guidelines. The database includes 4- and 6-month well-child care visits from 30 practices across three clinical networks in Illinois. The development of the NLP was organized into three main phases: exploratory (reviewed EHR notes to identify concepts for developing NLP algorithms), training (resulting in the first version of the NLP algorithm), and validation (based on gold standard datasets). Chart reviews were conducted to review the accuracy and reliability of the NLP model. The NLP pipeline assessed peanut introduction recommendations and severe eczema. Results NLP achieved high precision (0.98), recall (0.94) and overall performance F-measure (0.96) for identifying peanut introduction recommendations across the three networks. However, identifying severe eczema proved more challenging, with precision of 0.52, recall of 0.92, and overall performance F-measure of 0.67 across the three networks. Therefore, manual review was used to confirm the severe eczema results for the trial. Conclusions Considering the pragmatic study design, clinical notes were the only feasible source of data, yet documentation of severe eczema varied considerably across networks. Future refinement and validation of the severe eczema NLP pipeline are required. NLP is a valuable tool in assessing large EHR data sets in pragmatic, multi-site clinical trials. Trial registration This trial is registered on ClinicalTrials.gov (NCT04604431). Registered on October 14, 2020.

Objectives. We sought to estimate rates of sexually transmitted infections (STIs) among criminal offenders in the 1 year after arrest or release from incarceration. Methods. We performed a retrospective cohort study of risk of having a positive STI (chlamydia, gonorrhea, or syphilis) or incident-positive HIV test in the 1 year following arrest or incarceration in Marion County (Indianapolis), Indiana. Participants were 247 211 individuals with arrest or incarceration in jail, prison, or juvenile detention between 2003 and 2008. Results. Test positivity rates (per 100 000 and per year) were highest for chlamydia (2968) and gonorrhea (2305), and lower for syphilis (278) and HIV (61). Rates of positive STI and HIV were between 1.5 and 2.8 times higher in female than male participants and between 2.7 and 6.9 times higher for Blacks than Whites. Compared with nonoffenders, offenders had a relative risk of 3.9 for chlamydia, 6.6 for gonorrhea, 3.6 for syphilis, and 4.6 for HIV. Conclusions. The 1-year period following arrest or release from incarceration represents a high-impact opportunity to reduce STI and HIV infection rates at a population level.

Adverse drug events (ADEs) account for a significant mortality, morbidity, and cost burden. Pharmacogenetic testing has the potential to reduce ADEs and inefficacy. The objective of this INGENIOUS trial (NCT02297126) analysis was to determine whether conducting and reporting pharmacogenetic panel testing impacts ADE frequency. The trial was a pragmatic, randomized controlled clinical trial, adapted as a propensity matched analysis in individuals (N = 2612) receiving a new prescription for one or more of 26 pharmacogenetic-actionable drugs across a community safety-net and academic health system. The intervention was a pharmacogenetic testing panel for 26 drugs with dosage and selection recommendations returned to the health record. The primary outcome was occurrence of ADEs within 1 year, according to modified Common Terminology Criteria for Adverse Events (CTCAE). In the propensity-matched analysis, 16.1% of individuals experienced any ADE within 1-year. Serious ADEs (CTCAE level ≥ 3) occurred in 3.2% of individuals. When combining all 26 drugs, no significant difference was observed between the pharmacogenetic testing and control arms for any ADE (Odds ratio 0.96, 95% CI: 0.78–1.18), serious ADEs (OR: 0.91, 95% CI: 0.58–1.40), or mortality (OR: 0.60, 95% CI: 0.28–1.21). However, sub-group analyses revealed a reduction in serious ADEs and death in individuals who underwent pharmacogenotyping for aripiprazole and serotonin or serotonin-norepinephrine reuptake inhibitors (OR 0.34, 95% CI: 0.12–0.85). In conclusion, no change in overall ADEs was observed after pharmacogenetic testing. However, limitations incurred during INGENIOUS likely affected the results. Future studies may consider preemptive, rather than reactive, pharmacogenetic panel testing.

Background: Among physicians who perform endoscopic retrograde cholangiopancreatography (ERCP), the relationship between procedure volume and outcome is unknown. Objective: Quantify the ERCP volume-outcome relationship by measuring provider-specific failure rates, hospitalization rates, and other quality measures. Research Design: Retrospective cohort. Subjects: A total of 16,968 ERCPs performed by 130 physicians between 2001 and 2011, identified in the Indiana Network for Patient Care. Measures: Physicians were classified by their average annual Indiana Network for Patient Care volume and stratified into low (<25/y) and high (≥25/y). Outcomes included failed procedures, defined as repeat ERCP, percutaneous transhepatic cholangiography or surgical exploration of the bile duct ≤7 days after the index procedure, hospitalization rates, and 30-day mortality. Results: Among 15,514 index ERCPs, there were 1163 (7.5%) failures; the failure rate was higher among low (9.5%) compared with high volume (5.7%) providers (P<0.001). A second ERCP within 7 days (a subgroup of failure rate) occurred more frequently when the original ERCP was performed by a low-volume (4.1%) versus a high-volume physician (2.3%, P = 0.013). Patients were more frequently hospitalized within 24 hours when the ERCP was performed by a low-volume (28.3%) versus high-volume physician (14.8%, P = 0.002). Mortality within 30 days was similar (low = 1.9%, high = 1.9%). Among low-volume physicians and after adjusting, the odds of having a failed procedure decreased 3.3% (95% confidence interval, 1.6%-5.0%, P<0.001) with each additional ERCP performed per year. Conclusions: Lower provider volume is associated with higher failure rate for ERCP, and greater need for postprocedure hospitalization.

Background To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges. Methods We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies. We describe challenges and strategies in an implementation framework and typology to enable consistent definitions and cross-case comparisons. Strategies were linked to challenges based on expert review and shared themes. Results Three challenges were identified by all six projects, and strategies to address these challenges varied across the projects. One common challenge was to increase the relative priority of integrating genomics within the health system electronic health record (EHR). Four projects used data warehousing techniques to accomplish the integration. The second common challenge was to strengthen clinicians’ knowledge and beliefs about genomic medicine. To overcome this challenge, all projects developed educational materials and conducted meetings and outreach focused on genomic education for clinicians. The third challenge was engaging patients in the genomic medicine projects. Strategies to overcome this challenge included use of mass media to spread the word, actively involving patients in implementation (e.g., a patient advisory board), and preparing patients to be active participants in their healthcare decisions. Conclusions This is the first collaborative evaluation focusing on the description of genomic medicine innovations implemented in multiple real-world clinical settings. Findings suggest that strategies to facilitate integration of genomic data within existing EHRs and educate stakeholders about the value of genomic services are considered important for effective implementation. Future work could build on these findings to evaluate which strategies are optimal under what conditions. This information will be useful for guiding translation of discoveries to clinical care, which, in turn, can provide data to inform continual improvement of genomic innovations and their applications.

Background Children with JIA may experience difficulty with health related quality of life (HRQOL). The Patient Reported Outcomes Measurement Information System (PROMIS) a patient related outcome (PRO) measure, covers HRQOL domains that include physical function, mental health, and social interactions. During initial use, we found PROMIS identified children with symptoms of depression, sometimes before they shared those feelings with parents or members of the clinic team. We studied the use of PROMIS for this purpose, and to determine what demographic, clinical, and other characteristics might be related to higher depressive symptom scores. Methods From March 2014 – February 2017, at each visit, all JIA patients having met ILAR classification criteria seen by M.L.M. received the PROMIS Short Form 35 v.1.0, as part of routine care. T scores were calculated from raw scores for mobility, anxiety, depressive symptoms, fatigue, peer relationships, and pain interference domains. Data extracted by optical mark recognition software were merged with electronic medical record (EMR data), extracted by Extract/Transform/Load software, including joint counts, visit age, ANA, RF, and HLA-B27 status. Mixed effects models were used to identify significant associations of independent variables with depression T scores. Results Data from 148 patients were analyzed (114 females for 435 visits, 34 males for 118 visits; 13.8 ± 2.8 years): 70 persistent oligoarthritis, 9 extended oligoarthritis, 19 ERA, 21 polyarthritis (RF-), 5 polyarthritis (RF+), 11 undifferentiated arthritis, 3 psoriatic arthritis, 10 systemic arthritis). T scores showed wide ranges within individual JIA categories, with similar mean scores for all groups. Univariate linear mixed effects models showed significant relationships to depression T scores of gender and race (males and Asian patients with lower T scores, p  < .0001, p  = 0.091, respectively), joint count ( p  = 0.002), pain interference score ( p  = 0.0004), and Patient and Physician Global Assessment ( p  = 0.004, p  < .0001, respectively). No particular JIA category was associated with Depression T scores. HRQOL domains were interrelated (p < .0001), including patients reporting symptoms of depression tending also to report symptoms of anxiety. PROMIS identified 15 patients who did not otherwise report depressive symptoms, but needed referral for counseling; eight did not endorse depressive symptoms until the 2nd or 3rd visit. Only 3 patients had disease flare. Concerns besides arthritis such as parental conflict or school bullying were elicited in 7 patients during interviews with the social worker. All patients expressed being worried about their arthritis. Conclusion PROMIS is useful in screening JIA patients for symptoms of depression, particularly to identify patients who might not otherwise report these symptoms. The other PROMIS domain scores are related to reporting of symptoms of depression, as is Patient and Physician Global Assessment. Future studies will use PROMIS questionnaires incorporated into the EMR, permitting data entry by tablets and an online patient portal. This will make possible comparisons of HRQOL in children with JIA to those with other chronic rheumatic and non-rheumatic diseases.

Background Though social determinants are the primary drivers of health, few studies of people living with HIV focus on non-clinical correlates of insecure and/or fragmented connections with the care system. Our team uses linked clinical and multisector non‐clinical data to study how residential mobility and connection to social services influence the HIV care continuum. We engage a diverse group of individuals living with HIV and other invested community members to guide and inform this research. Our objective is to generate consultant-informed, research-based interventions that are relevant to the community, and to share our engagement approach and findings so that other researchers can do the same. Methods Our research team partnered with the Indiana Clinical and Translational Sciences Institute’s Research Jam to develop and implement a human-centered design research plan to engage individuals with experience relevant to our research. We recruited a panel of consultants composed of people living with HIV and/or clinicians and individuals from agencies that provide medical and non-medical services to people living with HIV in Marion County, Indiana. To date, we have used a variety of human-centered design tools and activities to engage individuals during six sessions, with results informing our future engagement and research activities. Results Since the inception of the project, 48 consultants have joined the panel. Thirty-five continue to be actively engaged and have participated in one or more of the six sessions conducted to date. Consultants have helped guide and prioritize analyses, aided in identification of data missing from our ecosystem, helped interpret results, provided feedback on future interventions, and co-presented with us at a local health equity conference. Conclusions We utilize community engagement to expand the scope of our research and find that the process provides value to both consultants and the research team. Human-centered design enhances this partnership by keeping it person-centered, developing empathy and trust between consultants and researchers, increasing consultant retention, and empowering consultants to collaborate meaningfully with the research team. The use of these methods is essential to conduct relevant, impactful, and sustainable research. We anticipate that these methods will be important for academic and public health researchers wishing to engage with and integrate the ideas of community consultants. Plain English Summary According to the U.S. Department of Health & Human Services, many people living with HIV do not get the care they need to stay healthy. They may face many problems that make it hard for them to access or afford medical services. They may also have barriers such as mental health or substance use disorders, unstable housing, or unreliable access to transportation. We want to understand how these factors influence the health of people living with HIV and find ways to help them overcome these barriers and improve their health. We use information from many sources, including records from health and social service agencies, to measure services received and health outcomes. We also work with a group of people living with HIV and/or who provide support or care to people living with HIV in our community. They help us understand what is important to them, what information we need, what the results mean, and what solutions we should try. To date, there are 48 people in this group. We have hosted six meetings where we shared and discussed our findings and asked for their input. We think that involving people living with HIV and those who seek to serve them is critical to our research. These individuals with lived experience relevant to our research have given us valuable feedback and suggestions that we can use to help guide our research, making it more relevant, useful, and impactful. It can also benefit the people who participate in the community-engaged process, with the consultants learning from each other and from us.

Recurrent hypoglycemia is understudied. This study evaluates recurrent hypoglycemia, fragmentation of care and mortality in a large urban center. The Chicago HealthLNK Data Repository (CHDR), a de-identified electronic health record data set from institutions across Chicago, identified 9741 patients with diabetes (DM) who had hypoglycemia (emergency department (ED) or inpatient admission (IA)) from 2006 to 2012. Recurrence was defined as more than one hypoglycemia encounter, and fragmentation of health care was defined as an ED visit or IA for hypoglycemia at >1 site. 187,644 patients were identified with DM; of 9741 patients with hypoglycemia, 2857 (29.3%) had recurrence. Patients with ≥4 hypoglycemic encounters (n = 1035) represented 10.6%, but accounted for 40.3% hypoglycemic encounters. Of 2857 patients with recurrence, 304 patients (10.6%) had fragmented care. In those with high hypoglycemic encounters (≥4), 22% (N = 226) had ≥10 encounters; race and insurance status differences were associated with number of hypoglycemic encounters. Having hypoglycemia was associated with increased mortality compared to no hypoglycemia (n = 2696, 27.7% vs n = 20,188, 11.4%; p < 0.00001 by chi-square). A small subset of patients with hypoglycemia accounted for a large subset of hypoglycemia encounters. Targeted interventions in this high-risk, high mortality group are needed. •Nearly 30% of those with emergency room visits or inpatient visits for hypoglycemia had recurrent events.•A minority of patients had ≥4 hypoglycemic encounters (10.6%) but accounted for 40.3% of all hypoglycemic encounters.•Race and insurance status differences were associated with number of hypoglycemic encounters•Hypoglycemia was associated with increased mortality in the short term (almost 30%).