Laboratory informatics capacity for effective antimicrobial resistance surveillance in resource-limited settings.

Antimicrobial resistance (AMR) is a major threat to human health globally. Surveillance is a key activity to determine AMR burden, impacts, and trends and to monitor effects of interventions. Surveillance systems require efficient capture and onward sharing of high-quality laboratory data. Substantial investment is being made to improve laboratory capacity, particularly in low-income and middle-income countries (LMICs) with high disease burdens. However, building capacity for effective laboratory data management remains an under-resourced area, which, unless addressed, will limit progress towards comprehensive AMR surveillance in LMICs. The lack of a fit-for-purpose and open-source laboratory information management system software is of particular concern. In this Personal View, we summarise the technical requirements for microbiology laboratory data management, provide a snapshot of laboratory data management in LMIC laboratories, and describe the key steps required to improve the situation. Without action to improve information technology infrastructure and data management systems in microbiology laboratories, the ongoing efforts to develop capacity for AMR surveillance in LMICs might not realise their full potential.

Intraocular Pressure Changes after Cataract Surgery in Patients with and without Glaucoma: An Informatics-Based Approach.

PURPOSE: To evaluate changes in intraocular pressure (IOP) after cataract surgery among patients with or without glaucoma using automated extraction of data from electronic health records (EHRs). DESIGN: Retrospective cohort study. PARTICIPANTS: Adults who underwent standalone cataract surgery at a single academic center from 2009-2018. METHODS: Patient information was identified from procedure and billing codes, demographic tables, medication orders, clinical notes, and eye examination fields in the EHR. A previously validated natural language processing pipeline was used to identify laterality of cataract surgery from operative notes and laterality of eye medications from medication orders. Cox proportional hazards modeling evaluated factors associated with the main outcome of sustained postoperative IOP reduction. MAIN OUTCOME MEASURES: Sustained post-cataract surgery IOP reduction, measured at 14 months or the last follow-up while using equal or fewer glaucoma medications compared with baseline and without additional glaucoma laser or surgery on the operative eye. RESULTS: The median follow-up for 7574 eyes of 4883 patients who underwent cataract surgery was 244 days. The mean preoperative IOP for all patients was 15.2 mmHg (standard deviation [SD], 3.4 mmHg), which decreased to 14.2 mmHg (SD, 3.0 mmHg) at 12 months after surgery. Patients with IOP of 21.0 mmHg or more showed mean postoperative IOP reduction ranging from -6.2 to -6.9 mmHg. Cataract surgery was more likely to yield sustained IOP reduction for patients with primary open-angle glaucoma (hazard ratio [HR], 1.19; 95% confidence interval, 1.05-1.36) or narrow angles or angle closure (HR, 1.21; 95% confidence interval, 1.08-1.34) compared with patients without glaucoma. Those with a higher baseline IOP were more likely to achieve postoperative IOP reduction (HR, 1.06 per 1-mmHg increase in baseline IOP; 95% confidence interval, 1.05-1.07). CONCLUSIONS: Our results suggest that patients with primary open-angle glaucoma or with narrow angles or chronic angle closure were more likely to achieve sustained IOP reduction after cataract surgery. Patients with higher baseline IOP had increasingly higher odds of achieving reduction in IOP. This evidence demonstrates the potential usefulness of a pipeline for automated extraction of ophthalmic surgical outcomes from EHR to answer key clinical questions on a large scale.

The Public Health Uniform National Data System (PHUND$): A Platform for Monitoring Fiscal Health and Sustainability of the Public Health System.

CONTEXT: Leaders of government agencies are responsible for stewardship over taxpayer investments. Stewardship strengthens agency performance that is critical to improving population health. Most industries, including health care, and public enterprises, such as education, have policies for uniform data reporting and financial systems for the application of theoretical analytical techniques to organizations and entire systems. However, this is not a mainstreamed practice in local and state government public health. PROGRAM: The Public Health Uniform National Data System (PHUND$) is a financial information system for local health departments that advances the application of uniform practices to close financial analytical gaps. A 10-year retrospective overview on the development, implementation, and utility of PHUND$ is provided and supported by documented program and agency improvements to validate the analytical features and demonstrate a best practice. RESULTS: Benefits found from utilizing PHUND$ included reducing financial risks, supporting requests for increased revenues, providing comparative analysis, isolating drivers of costs and deficits, increasing workforce financial management skills, enhancing decision-making processes, and fostering agency sustainability to support continuous improvements in quality and population health. The PHUND$ financial data definitions in the data dictionary provided the structure needed for standardized data collection and confirmed the feasibility of a standardized public health chart of accounts. CONCLUSION: PHUND$ analysis provided evidence on the relationship between financial and operational performance, as well as informing strategies for managing risks and improving quality. Such analysis is critical to identifying financial and operational problems and essential to mitigating financial crisis, avoiding disruption of services, and fostering agency sustainability. PHUND$ additionally serves as an instrument that can guide development of standards that measure for agency sound financial management systems.

A Progress Report on the State of Pharmacy Informatics Education in US Pharmacy Schools and Colleges.

Objective. To characterize informatics education opportunities in US colleges and schools of pharmacy curricula. Methods. Informatics curricular information online was catalogued via publicly available websites. Website content was searched via domain-specific keywords. Online course descriptions were reviewed. Website searches were also conducted for informatics-related opportunities. Results. Of 132 pharmacy curricula found online, 47 (36%) included an informatics course. Of those, 64% (n=30) were required while 47% (n=22) were elective courses. Additionally, 20% (n=26) provided informatics advanced and/or introductory pharmacy practice experiences, 20% (n=27) offered an informatics residency, and 17% (n=22) listed certificate and/or graduate degree programs in informatics. Conclusion. Over the past 10 years, little observable progress has been made in pharmacy school curricula in response to the increasing importance of informatics to the profession. Pharmacy programs can address this educational gap by internal (eg, course development) and external (eg, open source curriculum) solutions.

Applied Informatics Decision Support Tool for Mortality Predictions in Patients With Cancer.

PURPOSE: With rapidly evolving treatment options in cancer, the complexity in the clinical decision-making process for oncologists represents a growing challenge magnified by oncologists' disposition of intuition-based assessment of treatment risks and overall mortality. Given the unmet need for accurate prognostication with meaningful clinical rationale, we developed a highly interpretable prediction tool to identify patients with high mortality risk before the start of treatment regimens. METHODS: We obtained electronic health record data between 2004 and 2014 from a large national cancer center and extracted 401 predictors, including demographics, diagnosis, gene mutations, treatment history, comorbidities, resource utilization, vital signs, and laboratory test results. We built an actionable tool using novel developments in modern machine learning to predict 60-, 90- and 180-day mortality from the start of an anticancer regimen. The model was validated in unseen data against benchmark models. RESULTS: We identified 23,983 patients who initiated 46,646 anticancer treatment lines, with a median survival of 514 days. Our proposed prediction models achieved significantly higher estimation quality in unseen data (area under the curve, 0.83 to 0.86) compared with benchmark models. We identified key predictors of mortality, such as change in weight and albumin levels. The results are presented in an interactive and interpretable tool ( www.oncomortality.com ). CONCLUSION: Our fully transparent prediction model was able to distinguish with high precision between highest- and lowest-risk patients. Given the rich data available in electronic health records and advances in machine learning methods, this tool can have significant implications for value-based shared decision making at the point of care and personalized goals-of-care management to catalyze practice reforms.

*informatics: Identifying and Tracking Informatics Sub-Discipline Terms in the Literature.

OBJECTIVE: To identify the breadth of informatics sub-discipline terms used in the literature for enabling subsequent organization and searching by sub-discipline. METHODS: Titles in five literature sources were analyzed to extract terms for informatics sub-disciplines: 1) United States (U.S.) Library of Congress Online Catalog, 2) English Wikipedia, 3) U.S. National Library of Medicine (NLM) Catalog, 4) PubMed, and 5) PubMed Central. The extracted terms were combined and standardized with those in four vocabulary sources to create an integrated list: 1) Library of Congress Subject Headings (LCSH), 2) Medical Subject Headings (MeSH), 3) U.S. National Cancer Institute Thesaurus (NCIt), and 4) EMBRACE Data and Methods (EDAM). Searches for terms in titles from each literature source were conducted to obtain frequency counts and start years for characterizing established and potentially emerging sub-disciplines. RESULTS: Analysis of 6,949 titles from literature sources and 67 terms from vocabulary sources resulted in an integrated list of 382 terms for informatics sub-disciplines mapped to 292 preferred terms. In the last five decades, "bioinformatics", "medical informatics", "health informatics", "nursing informatics", and "biomedical informatics" were associated with the most literature. In the current decade, potentially emerging sub-disciplines include "disability informatics", "neonatal informatics", and "nanoinformatics" based on literature from the last five years. CONCLUSIONS: As the field of informatics continues to expand and advance, keeping up-to-date with historical and current trends will become increasingly challenging. The ability to track the accomplishments and evolution of a particular sub-discipline in the literature could be valuable for supporting informatics research, education, and training.

[Information as physical factor: problems of measurement, hygienic assessment and IT-automation].

The increasing flow of information, speeding up the progress of society, can impact the health that puts the task of its hygienic reglamentation. The physical aspects of information, parameters and units of quantities, aspects of measurement and evaluation with account of information quantity and quality as well as criteria of its permissible and optimal levels are considered. The results of measurements of quantity of text information produced per year on computer in 17 occupations of 10 economic sectors are presented. The principle of IT-automation of operator's work and of dynamic monitoring is proposed. On the basis of research performed the glossary of terms and guide on the problem with computer support are elaborated for the accumulation of experience and clarification of prospects.

Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods.

In ligand-based screening, retrosynthesis, and other chemoinformatics applications, one often seeks to search large databases of molecules in order to retrieve molecules that are similar to a given query. With the expanding size of molecular databases, the efficiency and scalability of data structures and algorithms for chemical searches are becoming increasingly important. Remarkably, both the chemoinformatics and information retrieval communities have converged on similar solutions whereby molecules or documents are represented by binary vectors, or fingerprints, indexing their substructures such as labeled paths for molecules and n-grams for text, with the same Jaccard-Tanimoto similarity measure. As a result, similarity search methods from one field can be adapted to the other. Here we adapt recent, state-of-the-art, inverted index methods from information retrieval to speed up similarity searches in chemoinformatics. Our results show a several-fold speed-up improvement over previous methods for both threshold searches and top-K searches. We also provide a mathematical analysis that allows one to predict the level of pruning achieved by the inverted index approach and validate the quality of these predictions through simulation experiments. All results can be replicated using data freely downloadable from http://cdb.ics.uci.edu/ .

Use of pharmacy informatics resources by clinical pharmacy services in acute care hospitals.

PURPOSE: The use of pharmacy informatics resources by clinical pharmacy services and the presence of a pharmacy informatics specialist in acute care hospitals were evaluated. METHODS: Two hundred randomly selected pharmacies in general medical and surgical hospitals in the United States with at least 100 acute care beds were surveyed via mail. Survey items gathered information regarding facility attributes, opinions about staff pharmacists' understanding of information technology, and departmental utilization of pharmacy informatics. RESULTS: Of the 200 surveys mailed, 114 (57%) were returned completed. When asked to rate their departments' use of pharmacy informatics, 82% indicated that pharmacy informatics use was good or fair, while 12% considered information use to be optimized. A majority of respondents (60%) indicated that a pharmacy informatics specialist was employed within the pharmacy, with 47% indicating that the specialist was a pharmacist. An overwhelming percentage of these pharmacists received informatics training on the job, and roughly half had specialty positions integrated into their pharmacist job description. No significant association existed between the use of pharmacy informatics and facility teaching status (teaching versus nonteaching), geographic location (urban versus rural), or use of computerized prescriber order entry. Employment of a pharmacy informatics specialist was significantly associated with the use of such informatics applications as database mining, renal-dosing-rules engines, antibiotic-pathogen matching-rules engines, and pharmacokinetic-monitoring rules engines. CONCLUSION: The use of clinical pharmacy informatics in patient care in acute care hospitals with at least 100 beds was significantly more likely when a pharmacy informatics specialist was present in the pharmacy. However, 4 in 10 hospital pharmacies did not employ a pharmacy informatics specialist.

ASHP national survey on informatics: assessment of the adoption and use of pharmacy informatics in U.S. hospitals--2007.

PURPOSE: Results of the 2007 ASHP national survey on informatics are presented. METHODS: All types and sizes of hospitals in the United States were included in the sample of 4112 pharmacy directors surveyed using an online data collection tool. The survey included over 300 data elements and was designed to assess the adoption and use of pharmacy informatics and technology within the medication-use process. RESULTS: In this national probability sample survey, the response rate was 25.9%. Hospitals appear to be moving toward an enterprise approach to information technology adoption and away from a best-of-breed approach. Although nearly half of hospitals have components of an electronic medical record (EMR), a complete digital hospital with a fully implemented EMR is far in the future, with only 5.9% of hospitals being fully digital (without paper records). An estimated 12.0% of hospitals use computerized prescriber-order-entry systems with decision support, 24.1% use bar-code medication administration, and 44.0% use intelligent infusion devices (smart pumps). Many of these technologies were not optimally configured, and significant advances must be made for hospitals to fully realize the benefits of these technologies. Hospitals have implemented many technologies in drug distribution, with 82.8% of hospitals having automated dispensing cabinets, 10.1% having robots, and 12.7% having carousel systems to manage inventory. Finally, most hospitals reported plans to adopt most of these technologies. CONCLUSION: This survey found that informatics and medication-use system technologies are widely present in all steps of the medication-use process. These technologies touch all health care professionals in the hospital and demonstrate the significant responsibility the pharmacy department holds for these technologies.

The role of the informatics framework in early lead discovery.

Recent developments in screening technologies and data analysis have been driven by promises that the numbers of new lead compounds will increase. Although many of these promises have become reality, the success of this strategy also depends on the information framework that ties the individual components together. In particular, high-content technologies represent a new force in challenging established informatics frameworks; largely because of their data volume, variety of assay parameters and increased scientific complexity. A successful informatics framework design can be regarded as crucial for new technologies, both in terms of scientific content and information, and process integration across large corporate networks.

Testicular cancer, occupation and exposure to chemical agents among Finnish men in 1971-1995.

OBJECTIVE: To find associations between testicular cancer, occupation and chemical exposure. METHODS: A cohort of all economically active Finnish men born between 1906 and 1945 was followed-up for 19.7 million person-years during 1971-1995. Incident cases of testicular cancer (n=387) were identified in a record linkage with the Finnish Cancer Registry. The Census occupations in 1970 were converted to chemical exposures with a job-exposure matrix (FINJEM). Cumulative exposure (CE) was calculated as the product of prevalence, level, and duration of the exposure. Standardised incidence ratio (SIR) was calculated for each of the 393 occupations, and for CE categories of the 43 chemical agents, using average male population as reference. Relative risks (RR) comparing various CE-categories with unexposed ones were defined for selected agents by Poisson regression analysis. RESULTS: Elevated SIRs were observed among railway traffic supervisors (5.8, 95% CI 1.6-14.7), programmers (4.3, 1.4-9.9), university teachers (4.1, 1.3-9.5) and electrical engineers (3.9, 1.1-10.1). A significant exposure-response trend (mainly contributed by seminoma) was observed for pesticides, textile dust, aliphatic and alicyclic hydrocarbons, and some other organic solvents. CONCLUSIONS: Risk of testicular cancer increased only in four occupations. Pesticides, textile dust, and some organic solvents may be related to an excess risk of seminoma.