John F. Hurdle

Sentiment Analysis of Suicide Notes: A Shared Task.

This paper reports on a shared task involving the assignment of emotions to suicide notes. Two features distinguished this task from previous shared tasks in the biomedical domain. One is that it resulted in the corpus of fully anonymized clinical text and annotated suicide notes. This resource is permanently available and will (we hope) facilitate future research. The other key feature of the task is that it required categorization with respect to a large set of labels. The number of participants was larger than in any previous biomedical challenge task. We describe the data production process and the evaluation measures, and give a preliminary analysis of the results. Many systems performed at levels approaching the inter-coder agreement, suggesting that human-like performance on this task is within the reach of currently available technologies.

Direct Text Entry in Electronic Progress Notes An Evaluation of Input Errors

OBJECTIVES It is not uncommon that the introduction of a new technology fixes old problems while introducing new ones. The Veterans Administration recently implemented a comprehensive electronic medical record system (CPRS) to support provider order entry. Progress notes are entered directly by clinicians, primarily through keyboard input. Due to concerns that there may be significant, invisible disruptions to information flow, this study was conducted to formally examine the incidence and characteristics of input errors in the electronic patient record. METHODS Sixty patient charts were randomly selected from all 2,301 inpatient admissions during a 5-month period. A panel of clinicians with informatics backgrounds developed the review criteria. After establishing inter-rater reliability, two raters independently reviewed 1,891 notes for copying, copying errors, inconsistent text, inappropriate object insertion and signature issues. RESULTS Overall, 60% of patients reviewed had one or more input-related errors averaging 7.8 errors per patient. About 20% of notes showed evidence of copying, with an average of 1.01 error per copied note. Copying another clinicians note and making changes had the highest risk of error. Templating resulted in large amounts of blank spaces. Overall, MDs make more errors than other clinicians even after controlling for the number of notes. CONCLUSIONS Moving towards a more progressive model for the electronic medical record, where actions are recorded only once, history and physical information is encoded for use later, and note generation is organized around problems, would greatly minimize the potential for error.

Developing a Taxonomy for Research in Adverse Drug Events: Potholes and Signposts

Computerized decision support and order entry shows great promise for reducing adverse drug events (ADEs). The evaluation of these solutions depends on a framework of definitions and classifications that is clear and practical. Unfortunately the literature does not always provide a clear path to defining and classifying adverse drug events. While not a systematic review, this paper uses examples from the literature to illustrate problems that investigators will confront as they develop a conceptual framework for their research. It also proposes a targeted taxonomy that can facilitate a clear and consistent approach to the research of ADEs and aid in the comparison to results of past and future studies. The taxonomy addresses the definition of ADE, types, seriousness, error, and causality.

Automated identification of adverse events related to central venous catheters

Methods for surveillance of adverse events (AEs) in clinical settings are limited by cost, technology, and appropriate data availability. In this study, two methods for semi-automated review of text records within the Veterans Administration database are utilized to identify AEs related to the placement of central venous catheters (CVCs): a Natural Language Processing program and a phrase-matching algorithm. A sample of manually reviewed records were then compared to the results of both methods to assess sensitivity and specificity. The phrase-matching algorithm was found to be a sensitive but relatively non-specific method, whereas a natural language processing system was significantly more specific but less sensitive. Positive predictive values for each method estimated the CVC-associated AE rate at this institution to be 6.4 and 6.2%, respectively. Using both methods together results in acceptable sensitivity and specificity (72.0 and 80.1%, respectively). All methods including manual chart review are limited by incomplete or inaccurate clinician documentation. A secondary finding was related to the completeness of administrative data (ICD-9 and CPT codes) used to identify intensive care unit patients in whom a CVC was placed. Administrative data identified less than 11% of patients who had a CVC placed. This suggests that other methods, including automated methods such as phrase matching, may be more sensitive than administrative data in identifying patients with devices. Considerable potential exists for the use of such methods for the identification of patients at risk, AE surveillance, and prevention of AEs through decision support technologies.

Effect of donors' intravenous drug use, cigarette smoking, and alcohol dependence on kidney transplant outcome.

Background. The shortage of organ donors for kidney transplants has made the expansion of the kidney donor pool a clinically significant issue. Previous studies suggest that kidneys from donors with a history of intravenous (IV) drug, cigarette, and/or alcohol use are considered to be a risky choice. However, these kidneys could potentially be used and expand the kidney supply pool if no evidence shows their association with adverse transplant outcomes. Methods. This study analyzed the United Network for Organ Sharing dataset from 1994 to 1999 using Kaplan-Meier survival analysis and Cox modeling. The effects on transplant outcome (graft and recipient survival) were examined with respect to the donors’ IV drug use, cigarette smoking, and alcohol dependency. Covariates including the recipient variables, the donor variables, and the transplant procedure variables were included in the Cox models. Results. The results show that the donors’ history of cigarette smoking is a statistically significant risk factor for both graft survival (hazard ratio = 1.05, P < 0.05) and recipient survival (1.06, P<0.05), whereas neither IV drug use nor alcohol dependency had significant adverse impact on graft or recipient survival. Conclusions. Assuming that adequate testing for potential infections is performed, there is no evidence to support avoiding the kidneys from donors with IV drug use or alcohol dependency in transplantation. Utilizing these kidneys would clearly expand the potential pool of donor organs.

Identifying clinical/translational research cohorts: ascertainment via querying an integrated multi-source database

BACKGROUND Ascertainment of potential subjects has been a longstanding problem in clinical research. Various methods have been proposed, including using data in electronic health records. However, these methods typically suffer from scaling effects-some methods work well for large cohorts; others work for small cohorts only. OBJECTIVE We propose a method that provides a simple identification of pre-research cohorts and relies on data available in most states in the USA: merged public health data sources. MATERIALS AND METHODS The Utah Population Database Limited query tool allows users to build complex queries that may span several types of health records, such as cancer registries, inpatient hospital discharges, and death certificates; in addition, these can be combined with family history information. The architectural approach incorporates several coding systems for medical information. It provides a front-end graphical user interface and enables researchers to build and run queries and view aggregate results. Multiple strategies have been incorporated to maintain confidentiality. RESULTS This tool was rapidly adopted; since its release, 241 users representing a wide range of disciplines from 17 institutions have signed the user agreement and used the query tool. Three examples are discussed: pregnancy complications co-occurring with cardiovascular disease; spondyloarthritis; and breast cancer. DISCUSSION AND CONCLUSIONS This query tool was designed to provide results as pre-research so that institutional review board approval would not be required. This architecture uses well-described technologies that should be within the reach of most institutions.

Interventions for disruptive behaviors. Use and success

Health care providers deal with disruptions from geriatric patients routinely. Despite the negative impact on provider efficiency, provider-patient relations, and patient well-being, there have been no systematic clinical studies of the impact of disruptive behaviors on geriatric inpatient care. This article presents a taxonomy for these behaviors, applying them to a study of disruptive behaviors and concomitant nursing interventions on a geriatric evaluation and management (GEM) unit. The sample, consisting of 23 nursing staff (16 RNs, 4 LPNs, and 3 nurse aides), was followed over 8 weeks (five shifts per week, distributed randomly over day, evening, and night shifts). An experienced pair of RN observers logged all disruptive behaviors and the associated interventions employed by the nursing providers. The taxonomy was validated on 97 disruptive events (113 disruptive behaviors) initiated by 87 patients. The major findings of the study were: (a) disruptive behaviors are common on a GEM unit; (b) behaviors that disrupt care are recognized only 50% of the time by nursing staff; (c) interventions, when used singly, were found successful 45% of the time; (d) multiple simultaneous interventions may be more successful than single interventions but were used in only 16% of cases; and (e) selection of interventions may be associated with staff education level.

Nurse's role in tracking adverse drug events: the impact of provider order entry.

Adverse drug events (ADE), or injuries caused by drug therapy, are a frequent and serious problem in hospitalized patients. Monitoring, preventing, and treating ADEs is an important patient safety function. Nurses play a significant role in this function, because their data is a unique and important indicator of ADEs and because they are the final point of medication administration. New provider order entry systems with electronic medical records have been viewed as an effective innovation and solution to high rates of ADEs. These systems increase legibility of drug orders, provide decision support, and increase access to the medical record. However, they may not interface with nursing processes effectively. This study reports the experience of a team conducting an ADE surveillance study in a Veterans Health Administration setting where extensive computerized innovations are in place. Lessons learned regarding the integration of nursing work processes with the computerized setting are described. Three areas of concern are highlighted: decreased access to nursing narratives, lack of decision support for medication administration, and failure to code nursing data. Each of these is discussed in terms of relevance to patient safety and the design of information systems.

Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information.

OBJECTIVE This paper examines the development and evaluation of an automatic summarization system in the domain of molecular genetics. The system is a potential component of an advanced biomedical information management application called Semantic MEDLINE and could assist librarians in developing secondary databases of genetic information extracted from the primary literature. METHODS An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease. The summarization system was evaluated on the task of identifying data describing genes associated with bladder cancer in MEDLINE citations. A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard. Recall, precision, and F-measure were calculated. RESULTS The system achieved recall of 46%, and precision of 88% (F-measure=0.61) by taking Gene References into Function (GeneRIFs) into account. CONCLUSION The new summarization schema for genetic etiology has potential as a component in Semantic MEDLINE to support the work of data curators.

AMIA's code of professional and ethical conduct

AMIA, as other professional societies, has a long-standing interest in promoting a strong ethical framework for its membership. This white paper presents the latest AMIA Code of Professional and Ethical Conduct. It was approved in November of 2011 by the AMIA Board of Directors. This document constitutes a revision of, and update to, the first code, approved and published in J Am Med Inform Assoc 1 in 2007. In an effort to keep pace with the fields vitality, the code presented here is intended to be a dynamic document, and will continue to evolve as AMIA and the field itself evolve. AMIA will publish on its web site this version of the code as part of a process that seeks ongoing response from, and involvement by, AMIA members. The code is meant to be practical and easily understood, so it is compact and uses general language. Unlike the ethics codes of some professional societies, the AMIA code is not intended to be prescriptive or legislative; it is aspirational, and as such, provides the broad strokes of a set of important ethical principles especially pertinent to the field of biomedical and health informatics. The code is organized around the common roles of AMIA members and the constituents they serve—including patients, students, and others—and with whom they interact. The AMIA Board and the AMIA Ethics Committee encourage members to offer suggestions for improvements and other changes. In this way, the code will continue to progress and best serve AMIA and the larger informatics community. Codes of ethics for professionals present special challenges in conception and execution. The goal of this code is to lay out the core values of this profession in a way that inspires AMIA members to acknowledge and embrace these values. While the crafting of the code involved many …