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Summary: Purpose: Over recent years, there has been a growing interest in extracting entities and relations from biomedical literature. There are a vast number of systems and approaches being proposed to extract biological relations, but none of them achieves satisfactory results. These methodologies are either parsing-based or pattern-based, which are not competent to handle the grammatical complexities of biomedical texts, or too complicated to be adapted. It is well known that appositive, coordinative propositions and such grammatical structures are extremely common in biomedical texts, particularly in full texts. However, these problems are still untouched for most of researchers. Methods: In this paper, we have proposed a new approach, which is hybrid with both shallow parsing and pattern matching, to extract relations between proteins from scientific papers of biomedical themes. In the method, appositive and coordinative structures are interpreted based on the shallow parsing analysis, with both syntactic and semantic constraints. Then long sentences are splitted into sub-ones, from which relations are extracted by a greedy pattern matching algorithm, along with automatically generated patterns. Results: Our approach is experimented to extract protein–protein interactions from full biomedical texts, and has achieved an average F-score of 80% on individual verbs, and 66% on all verbs. With the help of shallow parsing analysis, pattern matching is improved remarkably. Compared with the traditional pattern matching algorithm, our approach achieves about 7% improvement of both precision and F-score. In contrast to other systems, our approach achieves performance comparable to the best. A demo system has been available at http://spies.cs.tsinghua.edu.cn. [Copyright &y& Elsevier]

Summary: Clinical Practice Guidelines (CPGs) are being developed as a tool to promote best practice in medicine. However, the diffusion of paper guidelines has been shown to only have a limited impact. This is why computerization of CPGs has recently been suggested as a means to improve their dissemination as well as physicians’ compliance. The Guideline Elements Model (GEM) has been proposed to facilitate the encoding of CPGs and support the automatic processing of marked-up documents. In this paper, we explore the automatic generation of a rule base from a textual guideline using GEM. In this study, we propose an extension of the GEM model that introduces additional levels of structuring centered on decision variables. This allows a more efficient representation of the decision processes, which supports the automatic generation of decision rules from textual guidelines. The 1999 Canadian recommendations for the management of hypertension have been marked-up as a GEM-encoded instance of our extended DTD. We derived a rule base using an XML parser to extract the relevant elements to instantiate the IF and THEN clauses of decision rules. The rule base automatically generated compares favourably with the manual generation of decision rules in the ASTI project. This approach is an interesting case study in the computerization of CPGs, as it illustrates processing steps that are relevant to the various aspects of CPGs lifecycle, from production to consultation and use. [Copyright &y& Elsevier]

The medical procedures at the patient bedside are out of the scope of current HIS/RIS systems, which means that patient record and image data access during the medical visit or the execution, recording and confirmation of the medicine prescriptions, still do not enjoy computerized support. As a consequence, the necessary inclusion of new data to the patient record, still needs to be carried out through notations on paper and later typed, causes delays on the availability of this information (Mobile computing in a hospital: the Ward-In-Hand project. SAC 2000-ACM Symposium on Applied Computing, Marc¸o, 2000, Villa Olmo, Como, Italy). This paper presents a software technology where the medical and nursing staff will be equipped with a handheld computer connected by radio to a central server that provides access to the electronic patient records and that will actively inform about tasks pending distribution. The server acts as a database for multimodal electronic patient record information, storing patient data from computerized tomography (CT), ultrasonography (US), magnetic resonance (MRI) images and also medical findings, observations and prescriptions coded as DICOM Structured Reports (Digital Image and Communications in Medicine). The prototype described in this article implements a medical images and structured reports server that makes the search and recovery of data stored in the DICOM standard possible. [Copyright &y& Elsevier]

Background: Despite the growing interest in health data science education, it is not embedded in undergraduate medical curricula and little is known about best teaching practices. This paper presents a highly innovative course in a UK university that introduces undergraduate medical students to data science. It also discusses a study on student perspectives on the learning and teaching of health data science.Methods: The pedagogical design elements of the Data Science in Medicine course are discussed, along with its syllabus, assessment methodology and flipped classroom delivery. The course has been offered to approximately 630 students over three years. Student perspectives were investigated through three focus groups with the participation of 19 students across different study years in medicine. An experiment was conducted regarding instructor-led vs. video-based modalities of online programming labs, with the participation of 8 students.Results: The course has led to improved data competency among medical students and to a positive change in their opinions about data science. Motivating the course and showing relevance to clinical practice was one of the biggest challenges. Statistics was perceived by focus group participants as an essential data skill. Including data science in the medical curriculum was perceived as important by Year 1 students, while opinions varied between Year 4/5 participants. Video-based online labs were preferred over instructor-led online labs, and they were found to be more useful and enjoyable, without leading to any significant difference in academic performance.Conclusions: Teaching data science to undergraduate medicine students is highly desirable and feasible. We recommend including statistics in the curriculum and practical skill development through simple and clinically-relevant data science tasks, supported through video-based online labs. Further reporting on similar courses is needed, as well as larger-scale studies on student perspectives. [ABSTRACT FROM AUTHOR]

Abstract: Held on 21st to 23rd November 2009 in Hiroshima, the SiHIS working conference aimed at finding solutions to approach to an idealistic society where (1) the individual can trust information with full understanding and responsibility, (2) the individual can allow the use of information backed by sound legitimated environment, (3) information can play its role for better healthcare and the improvement of medicine. The purpose of this paper is to propose recommendations from this working conference. [ABSTRACT FROM AUTHOR]

Abstract: Introduction: E-prescribing is part of a new generation of electronic solutions for the medical industry that may have great potential for improving work flow and communication between medical practices and pharmacies. In the US, it has been introduced with minimal monitoring of errors and general usability. This paper examines refill functionality in e-prescribing software. Methods: A mixed method study including focus groups and surveys was conducted. Qualitative data were collected in on-site focus groups or individual interviews with clinicians and medical office staff at 64 physician office practices. Focus group participants described their experiences with the refill functionality of e-prescribing software, provided suggestions for improving it, and suggested improvements in office procedures and software functionality. Results: Overall, ∼50% reduction in time spent each day on refills was reported. Overall reports of refill functionality were positive; but clinicians and staff identified numerous difficulties and glitches associated managing prescription refills. These glitches diminished over time. Benefits included time saved as well as patient convenience. Potential for refilling without thought because of the ease of use was noted. Clinicians and staff appreciated the ability to track whether patients are filling and refilling prescriptions. Discussion: E-prescribing software for managing medication refills has not yet reached its full potential. To reduce work flow barriers and medication errors, software companies need to develop error reporting systems and response teams to deal effectively with problems experienced by users. Examining usability issues on both the medical office and pharmacy ends is required to identify the behavioral and cultural changes that accompany technological innovation and ease the transition to full use of e-prescribing software. [Copyright &y& Elsevier]

Summary: In the field of biomedicine, an overwhelming amount of experimental data has become available as a result of the high throughput of research in this domain. The amount of results reported has now grown beyond the limits of what can be managed by manual means. This makes it increasingly difficult for the researchers in this area to keep up with the latest developments. Information extraction (IE) in the biological domain aims to provide an effective automatic means to dynamically manage the information contained in archived journal articles and abstract collections and thus help researchers in their work. However, while considerable advances have been made in certain areas of IE, pinpointing and organizing factual information (such as experimental results) remains a challenge. In this paper we propose tackling this task by incorporating into IE information about rhetorical zones, i.e. classification of spans of text in terms of argumentation and intellectual attribution. As the first step towards this goal, we introduce a scheme for annotating biological texts for rhetorical zones and provide a qualitative and quantitative analysis of the data annotated according to this scheme. We also discuss our preliminary research on automatic zone analysis, and its incorporation into our IE framework. [Copyright &y& Elsevier]

Summary: In this paper, we present a biomedical name recognition system, called PowerBioNE. In order to deal with the special phenomena in the biomedical domain, various evidential features are proposed and integrated through a mutual information independence model (MIIM). In addition, a support vector machine (SVM) plus sigmoid is proposed to resolve the data sparseness problem in the MIIM. In this way, the data sparseness problem in MIIM-based biomedical name recognition can be resolved effectively and a biomedical name recognition system with better performance and better portability can be achieved. Finally, we present two post-processing modules to deal with the nested entity name and abbreviation phenomena in the biomedical domain to further improve the performance. Evaluation shows that our system achieves F-measures of 69.1 and 71.2 on the 23 classes of GENIA V1.1 and V3.0, respectively. In particular, our system achieves an F-measure of 77.8 on the “protein” class of GENIA V3.0. It also shows that our system outperforms the best-reported system on GENIA V1.1 and V3.0. [Copyright &y& Elsevier]

Summary: Privacy includes the right of individuals and organisations to determine for themselves when, how and to what extent information about them is communicated to others. The growing need of managing large amounts of both clinical and genetic data raises important legal and ethical challenges. This paper introduces some of the privacy-protection problems related to classical and genomic medicine, and highlights the relevance of trusted third parties and of privacy-enhancing techniques (PETs) in the context of data collection, e.g., for research. Practical approaches based on two pseudonymisation models, for both batch data collection and interactive data storage, are presented. The actual application of the described techniques today proves the possible benefits for medicine that innovative privacy-enhancing techniques can provide. Technical PET solutions can unlock valuable data sources, otherwise not available. [Copyright &y& Elsevier]

Summary: Objective:: The National Library of Medicine''s Unified Medical Language System (UMLS) is a rich source of knowledge in the biomedical domain. The UMLS is used for research and development across wide range of different applications. In this paper, we evaluated the coverage of UMLS as compared with medical terms extracted from Korean medical records and identified differences in concept representation between two terminology sets. Design and measurement:: We measured the concept coverage of the UMLS. For this study, we mapped the clinical terms extracted from the discharge records of Seoul National University Hospital (SNUH) to the UMLS. Results:: Thirty-five percent of the entry terms used in chief complaint of SNUH were conceptually matched with the UMLS ‘Sign or Symptom’ concepts. Fifty-eight percent of the terms were found to be matched with the UMLS ‘Disease or Syndrome’ concept rather than the ‘Sign or Symptom’ concept. The remaining 7% were not found in the UMLS concepts. We then analyzed some of different expression patterns used by the two term sets and addressed issues to be taken into consideration. Conclusion:: We found out that the UMLS was comparable with Korean medical records, since most of concepts of Korean medical records were covered with the UMLS concepts. [Copyright &y& Elsevier]

Objectives: Information technology (IT) is emerging in health care. A rigorous evaluation of this technology is recommended and of high importance for decision makers and users. However, many authors report problems during the evaluation of information technology in health care. In this paper, we discuss some of these problems, and propose possible solutions for these problems. Methods: Based on own experience and backed up by a literature review, some important problems during IT evaluation in health care together with their reasons, consequences and possible solutions are presented and structured. Results and conclusions: We define three main problem areas—the complexity of the evaluation object, the complexity of an evaluation project, and the motivation for evaluation. Many evaluation problems can be subsumed under those three problem areas. A broadly accepted framework for evaluation of IT in healthcare seems desirable to address those problems. Such a framework should help to formulate relevant questions, to find adequate methods and tools, and to apply them in a sensible way. [Copyright &y& Elsevier]

Physicians'' acceptance of telemedicine constitutes a prerequisite for its diffusion on a national scale. Based upon the Theory of Interpersonal Behavior, this study was aimed at assessing the predictors of physicians'' intention to use telemedicine in their clinical practice. All of the physicians involved in the RQTE, the extended provincial telemedicine network of Quebec (Canada) were mailed a questionnaire to identify the psychosocial determinants of their intention to adopt telemedicine. Confirmatory factor analysis (CFA) was performed to assess the measurement model and structural equation modelling (SEM) was applied to test the theoretical model. The adapted theoretical model explained 81% (P<0.001) of variance in physicians'' intention to use telehealth. The main predictors of intentions were a composite normative factor, comprising personal as well as social norms (β=1.08; P<0.001) and self identity (β=−0.33; P<0.001). Thus, physicians who perceived professional and social responsibilities regarding adoption of telehealth in their clinical practice had stronger intention to use this technology. However, it is likely that personal identity had a suppression effect in the regression equation, indicating that physicians'' intention to use telemedicine was better predicted if their self-perception as telemedicine users was considered. These results have several implications at the theoretical and practical levels that are discussed in this paper. [Copyright &y& Elsevier]