检索结果-内蒙古大学图书馆

Utility of gene-specific algorithms for predicting pathogenicity of uncertain gene variants

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2012年第2期19卷 207-211页

作者： Crockett, David K. Lyon, Elaine Williams, Marc S. Narus, Scott P. Facelli, Julio C. Mitchell, Joyce A. Univ Utah Sch Med Dept Biomed Informat Salt Lake City UT USA Univ Utah Sch Med Dept Pathol Salt Lake City UT USA Intermt Healthcare Clin Genet Inst Salt Lake City UT USA Univ Utah Ctr High Performance Comp Salt Lake City UT USA

The rapid advance of gene sequencing technologies has produced an unprecedented rate of discovery of genome variation in humans. A growing number of authoritative clinical repositories archive gene variants and disease phenotypes, yet there are currently many more gene variants that lack clear annotation or disease association. To date, there has been very limited coverage of gene-specific predictors in the literature. Here the evaluation is presented of "gene-specific" predictor models based on a naive Bayesian classifier for 20 gene-disease datasets, containing 3986 variants with clinically characterized patient conditions. The utility of gene-specific prediction is then compared with "all-gene" generalized prediction and also with existing popular predictors. Gene-specific computational prediction models derived from clinically curated gene variant disease datasets often outperform established generalized algorithms for novel and uncertain gene variants.

关键词： Amino acid properties gene variant classification machine learning phenotype prediction bioinformatics gene variants classification gene disease database developing/using computerized provider order entry designing usable (responsive) resources and systems methods for integration of information from disparate sources high-performance and large-scale computing distributed systems agents software engineering: architecture data exchange communication integration across care settings (inter- and intra-enterprise) system implementation and management issues languages computational methods statistical analysis of large datasets advanced algorithms identifying genome and protein structure and function detecting disease outbreaks and biological threats visualization of data and knowledge

来源：评论

学校读者我要写书评

暂无评论

Applying knowledge-anchored hypothesis discovery methods to advance clinical and translational research: the OAMiner project

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2012年第6期19卷 1110-1114页

作者： Payne, Philip R. O. Jackson, Rebecca D. Best, Thomas M. Borlawsky, Tara B. Lai, Albert M. James, Stephen Gurcan, Metin N. Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Ohio State Univ Dept Internal Med Columbus OH 43210 USA Ohio State Univ Dept Family Med Columbus OH 43210 USA

The conduct of clinical and translational research regularly involves the use of a variety of heterogeneous and large-scale data resources. Scalable methods for the integrative analysis of such resources, particularly when attempting to leverage computable domain knowledge in order to generate actionable hypotheses in a high-throughput manner, remain an open area of research. In this report, we describe both a generalizable design pattern for such integrative knowledge-anchored hypothesis discovery operations and our experience in applying that design pattern in the experimental context of a set of driving research questions related to the publicly available Osteoarthritis Initiative data repository. We believe that this 'test bed' project and the lessons learned during its execution are both generalizable and representative of common clinical and translational research paradigms.

关键词： Informatics computing methodologies knowledge bases research design phenotype biological markers visualization of data and knowledge translational research—application of biological knowledge to clinical care linking the genotype and phenotype methods for integration of information from disparate sources knowledge acquisition and knowledge management skeletal muscle cartilage osteoarthritis data modeling and integration knowledge representations data models imaging informatics image analysis CAD radiology pathology

来源：评论

学校读者我要写书评

暂无评论

Enabling distributed electronic research data collection for a rural Appalachian tobacco cessation study

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I140-I143页

作者： Borlawsky, Tara B. Lele, Omkar Jensen, Daniel Hood, Nancy E. Wewers, Mary Ellen Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Ohio State Univ Coll Publ Hlth Columbus OH 43210 USA

Tobacco use is increasingly prevalent among vulnerable populations, such as people living in rural Appalachian communities. Owing to limited access to a reliable internet service in such settings, there is no widespread adoption of electronic data capture tools for conducting community-based research. By integrating the REDCap data collection application with a custom synchronization tool, the authors have enabled a workflow in which field research staff located throughout the Ohio Appalachian region can electronically collect and share research data. In addition to allowing the study data to be exchanged in near-real-time among the geographically distributed study staff and centralized study coordinator, the system architecture also ensures that the data are stored securely on encrypted laptops in the field and centrally behind the Ohio State University Medical Center enterprise firewall. The authors believe that this approach can be easily applied to other analogous study designs and settings.

关键词： data collection community-based participatory research medical informatics software data modeling and integration machine learning predictive modeling statistical learning privacy technology visualization of data and knowledge knowledge representations methods for integration of information from disparate sources data models data exchange

来源：评论

学校读者我要写书评

暂无评论

Using the time and motion method to study clinical work processes and workflow: methodological inconsistencies and a call for standardized research

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第5期18卷 704-710页

作者： Zheng, Kai Guo, Michael H. Hanauer, David A. Univ Michigan Sch Publ Hlth Dept Hlth Management & Policy Ann Arbor MI 48109 USA Univ Michigan Sch Informat Ann Arbor MI 48109 USA Univ Florida Coll Med Gainesville FL USA Univ Michigan Dept Pediat Ann Arbor MI 48109 USA Univ Michigan Ctr Comprehens Canc Ann Arbor MI 48109 USA

Objective To identify ways for improving the consistency of design, conduct, and results reporting of time and motion (TEM) research in health informatics. Materials and methods We analyzed the commonalities and divergences of empirical studies published 1990-2010 that have applied the T&M approach to examine the impact of health IT implementation on clinical work processes and workflow. The analysis led to the development of a suggested 'checklist' intended to help future T&M research produce compatible and comparable results. We call this checklist STAMP (Suggested Time And Motion Procedures). Results STAMP outlines a minimum set of 29 data/information elements organized into eight key areas, plus three supplemental elements contained in an 'Ancillary data' area, that researchers may consider collecting and reporting in their future T&M endeavors. Discussion TEM is generally regarded as the most reliable approach for assessing the impact of health IT implementation on clinical work. However, there exist considerable inconsistencies in how previous TEN studies were conducted and/or how their results were reported, many of which do not seem necessary yet can have a significant impact on quality of research and generalisability of results. Therefore, we deem it is time to call for standards that can help improve the consistency of TEN research in health informatics. This study represents an initial attempt. Conclusion We developed a suggested checklist to improve the methodological and results reporting consistency of T&M research, so that meaningful insights can be derived from across-study synthesis and health informatics, as a field, will be able to accumulate knowledge from these studies.

关键词： Time and motion studies (F02.784.412.846.707) workflow (L01.906.893) health information technology (L01.700) medical informatics applications (L01.700.508) collaborative technologies personal health records and self-care systems developing/using clinical decision support (other than diagnostic) and guideline systems systems supporting patient-provider interaction human-computer interaction and human-centered computing improving healthcare workflow and process efficiency system implementation and management issues social/organizational study qualitative/ethnographic field study cognitive study (including experiments emphasizing verbal protocol analysis and usability) methods for integration of information from disparate sources information storage and retrieval (text and images) data exchange communication integration across care settings (inter- and intra-enterprise) visualization of data and knowledge developing/using computerized provider order entry

来源：评论

学校读者我要写书评

暂无评论

Handling anticipated exceptions in clinical care: investigating clinician use of 'exit strategies' in an electronic health records system

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第6期18卷 883-889页

作者： Zheng, Kai Hanauer, David A. Padman, Rema Johnson, Michael P. Hussain, Anwar A. Ye, Wen Zhou, Xiaomu Diamond, Herbert S. Univ Michigan Sch Informat Dept Hlth Management & Policy Sch Publ Hlth Ann Arbor MI 48109 USA Univ Michigan Dept Pediat Ann Arbor MI 48109 USA Carnegie Mellon Univ H John Heinz Coll 3 Pittsburgh PA 15213 USA Univ Massachusetts Dept Publ Policy & Publ Affairs John W McCormack Grad Sch Policy Studies Boston MA 02125 USA United Hlth Serv Hosp Johnson City NY USA Univ Michigan Sch Publ Hlth Dept Biostat Ann Arbor MI 48109 USA Rutgers State Univ Sch Commun & Informat New Brunswick NJ 08903 USA Univ Pittsburgh Sch Med Dept Med Div Rheumatol Pittsburgh PA USA

Unpredictable yet frequently occurring exception situations pervade clinical care. Handling them properly often requires aberrant actions temporarily departing from normal practice. In this study, the authors investigated several exception-handling procedures provided in an electronic health records system for facilitating clinical documentation, which the authors refer to as 'data entry exit strategies.' Through a longitudinal analysis of computer-recorded usage data, the authors found that (1) utilization of the exit strategies was not affected by postimplementation system maturity or patient visit volume, suggesting clinicians' needs to 'exit' unwanted situations are persistent;and (2) clinician type and gender are strong predictors of exit-strategy usage. Drilldown analyses further revealed that the exit strategies were judiciously used and enabled actions that would be otherwise difficult or impossible. However, many data entries recorded via them could have been 'properly' documented, yet were not, and a considerable proportion containing temporary or incomplete information was never subsequently amended. These findings may have significant implications for the design of safer and more user-friendly point-of-care information systems for healthcare.

关键词： Electronic health records (E05.318.308.940.968.625.500) workflow (L01.906.893) documentation (L01.453.245) exit strategy exception-handling collaborative technologies personal health records and self-care systems developing/using clinical decision support (other than diagnostic) and guideline systems systems supporting patient–provider interaction human–computer interaction and human-centered computing improving healthcare workflow and process efficiency system implementation and management issues social/organizational study qualitative/ethnographic field study cognitive study (including experiments emphasizing verbal protocol analysis and usability) methods for integration of information from disparate sources information storage and retrieval (text and images) data exchange communication and integration across care settings (inter- and intraenterprise) visualization of data and knowledge developing/using computerized provider order entry diamond

来源：评论

学校读者我要写书评

暂无评论

Factors influencing alert acceptance: a novel approach for predicting the success of clinical decision support

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第4期18卷 479-484页

作者： Seidling, Hanna M. Phansalkar, Shobha Seger, Diane L. Paterno, Marilyn D. Shaykevich, Shimon Haefeli, Walter E. Bates, David W. Brigham & Womens Hosp Div Gen Med & Primary Care Boston MA 02115 USA Harvard Univ Sch Med Boston MA USA Heidelberg Univ Dept Clin Pharmacol & Pharmacoepidemiol Heidelberg Germany Partners HealthCare Syst Wellesley MA USA

Background Clinical decision support systems can prevent knowledge-based prescription errors and improve patient outcomes. The clinical effectiveness of these systems, however, is substantially limited by poor user acceptance of presented warnings. To enhance alert acceptance it may be useful to quantify the impact of potential modulators of acceptance. Methods We built a logistic regression model to predict alert acceptance of drug drug interaction (DDI) alerts in three different settings. Ten variables from the clinical and human factors literature were evaluated as potential modulators of provider alert acceptance. ORs were calculated for the impact of knowledge quality, alert display, textual information, prioritization, setting, patient age, dose-dependent toxicity, alert frequency, alert level, and required acknowledgment on acceptance of the DDI alert. Results 50 788 DDI alerts were analyzed. Providers accepted only 1.4% of non-interruptive alerts. For interruptive alerts, user acceptance positively correlated with frequency of the alert (OR 1.30, 95% CI 1.23 to 1.38), quality of display (4.75, 3.87 to 5.84), and alert level (1.74, 1.63 to 1.86). Alert acceptance was higher in inpatients (2.63, 2.32 to 2.97) and for drugs with dose-dependent toxicity (1.13, 1.07 to 1.21). The textual information influenced the mode of reaction and providers were more likely to modify the prescription if the message contained detailed advice on how to manage the DDI. Conclusion We evaluated potential modulators of alert acceptance by assessing content and human factors issues, and quantified the impact of a number of specific factors which influence alert acceptance. This information may help improve clinical decision support systems design.

关键词： visualization of data and knowledge knowledge representations knowledge acquisition and knowledge management distributed systems agents software engineering: architecture developing and refining EHR data standards (including image standards) data models data exchange controlled terminologies and vocabularies communication integration across care settings (inter- and intra-enterprise) knowledge bases electronic decision support medication errors patient safety decision support

来源：评论

学校读者我要写书评

暂无评论

The Yale cTAKES extensions for document classification: architecture and application

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第5期18卷 614-620页

作者： Garla, Vijay Lo Re, Vincent, III Dorey-Stein, Zachariah Kidwai, Farah Scotch, Matthew Womack, Julie Justice, Amy Brandt, Cynthia Yale Univ Ctr Med Informat Interdept Program Computat Biol & Bioinformat New Haven CT 06520 USA Univ Penn Sch Med Ctr Clin Epidemiol & Biostat Philadelphia PA 19104 USA Connecticut VA Healthcare Syst West Haven CT USA Arizona State Univ Dept Biomed Informat Tempe AZ USA Yale Univ Sch Nursing New Haven CT 06520 USA Yale Univ Sch Med Gen Internal Med New Haven CT 06520 USA Yale Univ Ctr Med Informat Sch Med New Haven CT 06520 USA

Background Open-source clinical natural-language-processing (NLP) systems have lowered the barrier to the development of effective clinical document classification systems. Clinical natural-language-processing systems annotate the syntax and semantics of clinical text;however, feature extraction and representation for document classification pose technical challenges. Methods The authors developed extensions to the clinical Text Analysis and knowledge Extraction System (cTAKES) that simplify feature extraction, experimentation with various feature representations, and the development of both rule and machine-learning based document classifiers. The authors describe and evaluate their system, the Yale cTAKES Extensions (YTEX), on the classification of radiology reports that contain findings suggestive of hepatic decompensation. Results and discussion The F-1-Score of the system for the retrieval of abdominal radiology reports was 96%, and was 79%, 91%, and 95% for the presence of liver masses, ascites, and varices, respectively. The authors released YTEX as open source, available at http://***/p/ytex.

关键词： Hepatitis visualization of data and knowledge languages computational methods advanced algorithms natural-language processing distributed systems agents software engineering: architecture developing and refining EHR data standards (including image standards) data models data exchange communication integration across care settings (inter- and intra-enterprise) detecting disease outbreaks and biological threats translational research—application of biological knowledge to clinical care linking the genotype and phenotype natural-language processing delivering health information and knowledge to the public monitoring the health of populations

来源：评论

学校读者我要写书评

暂无评论

User perspectives on the usability of a regional health information exchange

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第5期18卷 711-716页

作者： Gadd, Cynthia S. Ho, Yun-Xian Cala, Cather Marie Blakemore, Dana Chen, Qingxia Frisse, Mark E. Johnson, Kevin B. Vanderbilt Univ Dept Biomed Informat Eskind Lib Nashville TN 37203 USA Vanderbilt Univ Dept Biostat Nashville TN 37203 USA

Objective We assessed the usability of a health information exchange (HIE) in a densely populated metropolitan region. This grant-funded HIE had been deployed rapidly to address the imminent needs of the patient population and the need to draw wider participation from regional entities. Design We conducted a cross-sectional survey of individuals given access to the HIE at participating organizations and examined some of the usability and usage factors related to the technology acceptance model. Measurements We probed user perceptions using the Questionnaire for User Interaction Satisfaction, an author-generated Trust scale, and user characteristic questions (eg, age, weekly system usage time). Results Overall, users viewed the system favorably (ratings for all usability items were greater than neutral (one-sample Wilcoxon test, p<0.0014, Bonferroni-corrected for 35 tests). System usage was regressed on usability, trust, and demographic and user characteristic factors. Three usability factors were positively predictive of system usage: overall reactions (p<0 0.01), learning (p<0.05), and system functionality (p<0.01). Although trust is an important component in collaborative relationships, we did not find that user trust of other participating healthcare entities was significantly predictive of usage. An analysis of respondents' comments revealed ways to improve the HIE. Conclusion We used a rapid deployment model to develop an HIE and found that perceptions of system usability were positive. We also found that system usage was predicted well by some aspects of usability. Results from this study suggest that a rapid development approach may serve as a viable model for developing usable HIEs serving communities with limited resources.

关键词： Information dissemination medical records system regional health planning usability usage biomedical informatics evaluation Qualitative/ethnographic field study Improving the education and skills training of health professionals System implementation and management issues Social/organizational study Collaborative technologies Methods for integration of information from disparate sources Demonstrating return on IT investment distributed systems agents Software engineering: architecture Supporting practice at a distance (telehealth) data exchange communication and integration across care settings (inter- and intra-enterprise) visualization of data and knowledge policy Legal historical ethical study methods clinical informatics biomedical informatics pediatrics e-prescribing human factors

来源：评论

学校读者我要写书评

暂无评论

Development and preliminary evidence for the validity of an instrument assessing implementation of human-factors principles in medication-related decision-support systems-I-MeDeSA

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I62-I72页

作者： Zachariah, Marianne Phansalkar, Shobha Seidling, Hanna M. Neri, Pamela M. Cresswell, Kathrin M. Duke, Jon Bloomrosen, Meryl Volk, Lynn A. Bates, David W. Partners Healthcare Syst CIRD Wellesley MA 02481 USA Brigham & Womens Hosp Div Gen Internal Med Boston MA 02115 USA Harvard Univ Sch Med Boston MA USA Univ Heidelberg Dept Clin Pharmacol & Pharmacoepidemiol Heidelberg Germany Univ Hosp Geneva Div Med Informat Sci Geneva Switzerland Univ Edinburgh Ctr Populat Hlth Sci eHlth Res Grp Edinburgh Midlothian Scotland Regenstrief Inst Hlth Care Indianapolis IN USA Amer Med Informat Assoc Bethesda MD USA

Background Medication-related decision support can reduce the frequency of preventable adverse drug events. However, the design of current medication alerts often results in alert fatigue and high over-ride rates, thus reducing any potential benefits. Methods The authors previously reviewed human-factors principles for relevance to medication-related decision support alerts. In this study, instrument items were developed for assessing the appropriate implementation of these human-factors principles in drug-drug interaction (DDI) alerts. User feedback regarding nine electronic medical records was considered during the development process. Content validity, construct validity through correlation analysis, and inter-rater reliability were assessed. Results The final version of the instrument included 26 items associated with nine human-factors principles. Content validation on three systems resulted in the addition of one principle (Corrective Actions) to the instrument and the elimination of eight items. Additionally, the wording of eight items was altered. Correlation analysis suggests a direct relationship between system age and performance of DDI alerts (p=0.0016). Inter-rater reliability indicated substantial agreement between raters (kappa=0.764). Conclusion The authors developed and gathered preliminary evidence for the validity of an instrument that measures the appropriate use of human-factors principles in the design and display of DDI alerts. Designers of DDI alerts may use the instrument to improve usability and increase user acceptance of medication alerts, and organizations selecting an electronic medical record may find the instrument helpful in meeting their clinicians' usability needs.

关键词： Human factors medication-related decision support clinical decision support medication alerts name visualization of data and knowledge designing usable (responsive) resources and systems developing/using clinical decision support (other than diagnostic) and guideline systems human–computer interaction and human-centered computing policy health IT innovation patient safety decision support data exchange

来源：评论

学校读者我要写书评

暂无评论

The TOKEn project: knowledge synthesis for in silico science

引用

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2011年第Sup1期18卷 I125-I131页

作者： Payne, Philip R. O. Borlawsky, Tara B. Lele, Omkar James, Stephen Greaves, Andrew W. Ohio State Univ Dept Biomed Informat Columbus OH 43210 USA Moores UCSD Canc Ctr CLL Res Consortium La Jolla CA USA

Objective The conduct of investigational studies that involve large-scale data sets presents significant challenges related to the discovery and testing of novel hypotheses capable of supporting in silico discovery science. The use of what are known as Conceptual knowledge Discovery in databases (CKDD) methods provides a potential means of scaling hypothesis discovery and testing approaches for large data sets. Such methods enable the high-throughput generation and evaluation of knowledge-anchored relationships between complexes of variables found in targeted data sets. Methods The authors have conducted a multipart model formulation and validation process, focusing on the development of a methodological and technical approach to using CKDD to support hypothesis discovery for in silico science. The model the authors have developed is known as the Translational Ontology-anchored knowledge Discovery Engine (TOKEn). This model utilizes a specific CKDD approach known as Constructive Induction to identify and prioritize potential hypotheses related to the meaningful semantic relationships between variables found in large-scale and heterogeneous biomedical data sets. Results The authors have verified and validated TOKEn in the context of a translational research data repository maintained by the NCI-funded Chronic Lymphocytic Leukemia Research Consortium. Such studies have shown that TOKEn is: (1) computationally tractable;and (2) able to generate valid and potentially useful hypotheses concerning relationships between phenotypic and biomolecular variables in that data collection. Conclusions The TOKEn model represents a potentially useful and systematic approach to knowledge synthesis for in silico discovery science in the context of large-scale and multidimensional research data sets.

关键词： Computing methodologies knowledge bases information theory research design phenotype biological markers visualization of data and knowledge translational research—application of biological knowledge to clinical care linking the genotype and phenotype methods for integration of information from disparate sources knowledge acquisition and knowledge management data modeling and integration knowledge representations data models methods for integration of information from disparate sources informatics

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：