Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for translational research and are often found only in free text clinical notes. A key required step for IE is the manual annotation of clinical corpora and the creation of a reference standard for (1) training and validation tasks and (2) to focus and clarify NLP system requirements. These tasks are time consuming, expensive, and require considerable effort on the part of human reviewers.</p> <p>Methods</p> <p>Using a set of clinical documents from the VA EMR for a particular use case of interest we identify specific challenges and present several opportunities for annotation tasks. We demonstrate specific methods using an open source annotation tool, a customized annotation schema, and a corpus of clinical documents for patients known to have a diagnosis of Inflammatory Bowel Disease (IBD). We report clinician annotator agreement at the document, concept, and concept attribute level. We estimate concept yield in terms of annotated concepts within specific note sections and document types.</p> <p>Results</p> <p>Annotator agreement at the document level for documents that contained concepts of interest for IBD using estimated Kappa statistic (95% CI) was very high at 0.87 (0.82, 0.93). At the concept level, F-measure ranged from 0.61 to 0.83. However, agreement varied greatly at the specific concept attribute level. For this particular use case (IBD), clinical documents producing the highest concept yield per document included GI clinic notes and primary care notes. Within the various types of notes, the highest concept yield was in sections representing patient assessment and history of presenting illness. Ancillary service documents and family history and plan note sections produced the lowest concept yield.</p> <p>Conclusion</p> <p>Challenges include defining and building appropriate annotation schemas, adequately training clinician annotators, and determining the appropriate level of information to be annotated. Opportunities include narrowing the focus of information extraction to use case specific note types and sections, especially in cases where NLP systems will be used to extract information from large repositories of electronic clinical note documents.</p

Instant availability of patient records, but diminished availability of patient information: A multi-method study of GP's use of electronic patient records

<p>Abstract</p> <p>Background</p> <p>In spite of succesful adoption of electronic patient records (EPR) by Norwegian GPs, what constitutes the actual benefits and effects of the use of EPRs in the perspective of the GPs and patients has not been fully characterized. We wanted to study primary care physicians' use of electronic patient record (EPR) systems in terms of use of different EPR functions and the time spent on using the records, as well as the potential effects of EPR systems on the clinician-patient relationship.</p> <p>Methods</p> <p>A combined qualitative and quantitative study that uses data collected from focus groups, observations of primary care encounters and a questionnaire survey of a random sample of general practitioners to describe their use of EPR in primary care.</p> <p>Results</p> <p>The overall availability of individual patient records had improved, but the availability of the information within each EPR was not satisfactory. GPs' use of EPRs were efficient and comprehensive, but have resulted in transfer of administrative work from secretaries to physicians. We found no indications of disturbance of the clinician-patient relationship by use of computers in this study.</p> <p>Conclusion</p> <p>Although GPs are generally satisfied with their EPRs systems, there are still unmet needs and functionality to be covered. It is urgent to find methods that can make a better representation of information in large patient records as well as prevent EPRs from contributing to increased administrative workload of physicians.</p

A randomised controlled trial testing a web-based, computer-tailored self-management intervention for people with or at risk for chronic obstructive pulmonary disease: a study protocol

Contains fulltext : 125231.pdf (publisher's version ) (Open Access)BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a major cause of morbidity and mortality. Effective self-management support interventions are needed to improve the health and functional status of people with COPD or at risk for COPD. Computer-tailored technology could be an effective way to provide this support. METHODS/DESIGN: This paper presents the protocol of a randomised controlled trial testing the effectiveness of a web-based, computer-tailored self-management intervention to change health behaviours of people with or at risk for COPD. An intervention group will be compared to a usual care control group, in which the intervention group will receive a web-based, computer-tailored self-management intervention. Participants will be recruited from an online panel and through general practices. Outcomes will be measured at baseline and at 6 months. The primary outcomes will be smoking behaviour, measuring the 7-day point prevalence abstinence and physical activity, measured in minutes. Secondary outcomes will include dyspnoea score, quality of life, stages of change, intention to change behaviour and alternative smoking behaviour measures, including current smoking behaviour, 24-hour point prevalence abstinence, prolonged abstinence, continued abstinence and number of quit attempts. DISCUSSION: To the best of our knowledge, this will be the first randomised controlled trial to test the effectiveness of a web-based, computer-tailored self-management intervention for people with or at risk for COPD. The results will be important to explore the possible benefits of computer-tailored interventions for the self-management of people with or at risk for COPD and potentially other chronic health conditions. DUTCH TRIAL REGISTER: NTR3421

Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina).

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations

Impact of Educational Level on Study Attrition and Evaluation of Web-Based Computer-Tailored Interventions: Results From Seven Randomized Controlled Trials

Background: Web-based computer-tailored interventions have shown to be effective in improving health behavior; however, high dropout attrition is a major issue in these interventions. Objective: The aim of this study is to assess whether people with a lower educational level drop out from studies more frequently compared to people with a higher educational level and to what extent this depends on evaluation of these interventions. Methods: Data from 7 randomized controlled trials of Web-based computer-tailored interventions were used to investigate dropout rates among participants with different educational levels. To be able to compare higher and lower educated participants, intervention evaluation was assessed by pooling data from these studies. Logistic regression analysis was used to assess whether intervention evaluation predicted dropout at follow-up measurements. Results: In 3 studies, we found a higher study dropout attrition rate among participants with a lower educational level, whereas in 2 studies we found that middle educated participants had a higher dropout attrition rate compared to highly educated participants. In 4 studies, no such significant difference was found. Three of 7 studies showed that participants with a lower or middle educational level evaluated the interventions significantly better than highly educated participants ("Alcohol-Everything within the Limit": F-2,F-376=5.97, P=.003; "My Healthy Behavior": F-2,F-359=5.52, P=.004; "Master Your Breath": F-2,F-317=3.17, P=.04). One study found lower intervention evaluation by lower educated participants compared to participants with a middle educational level ("Weight in Balance": F-2,F-37=3.17, P=.05). Low evaluation of the interventions was not a significant predictor of dropout at a later follow-up measurement in any of the studies. Conclusions: Dropout attrition rates were higher among participants with a lower or middle educational level compared with highly educated participants. Although lower educated participants evaluated the interventions better in approximately half of the studies, evaluation did not predict dropout attrition. Further research is needed to find other explanations for high dropout rates among lower educated participants

Akt phosphorylation of zyxin mediates its interaction with acinus-S and prevents acinus-triggered chromatin condensation

Zyxin, a focal adhesion molecule, contains LIM domains and shuttles between the cytoplasm and the nucleus. Nuclear zyxin promotes cardiomyocyte survival, which is mediated by nuclear-activated Akt. However, the molecular mechanism of how zyxin antagonizes apoptosis remains elusive. Here, we report that zyxin binds to acinus-S, a nuclear speckle protein inducing apoptotic chromatin condensation after cleavage by caspases, and prevents its apoptotic action, which is regulated by Akt. Akt binds and phosphorylates zyxin on serine 142, leading to its association with acinus. Interestingly, 14-3-3γ, but not ζ isoform selectively, triggers zyxin nuclear translocation, which is Akt phosphorylation dependent. Zyxin is also a substrate of caspases, but Akt phosphorylation is unable to prevent its apoptotic cleavage. Expression of zyxin S142D, a phosphorylation mimetic mutant, diminishes acinus proteolytic cleavage and chromatin condensation; by contrast, wild-type zyxin or unphosphorylated S142A mutant fails. Thus, Akt regulates zyxin/acinus complex formation in the nucleus, contributing to suppression of apoptosis.Link_to_subscribed_fulltex