Exploiting medical hierarchies for concept-based information retrieval

Search technologies are critical to enable clinical sta to rapidly and e ectively access patient information contained in free-text medical records. Medical search is challenging as terms in the query are often general but those in rel- evant documents are very speci c, leading to granularity mismatch. In this paper we propose to tackle granularity mismatch by exploiting subsumption relationships de ned in formal medical domain knowledge resources. In symbolic reasoning, a subsumption (or `is-a') relationship is a parent-child rela- tionship where one concept is a subset of another concept. Subsumed concepts are included in the retrieval function. In addition, we investigate a number of initial methods for combining weights of query concepts and those of subsumed concepts. Subsumption relationships were found to provide strong indication of relevant information; their inclusion in retrieval functions yields performance improvements. This result motivates the development of formal models of rela- tionships between medical concepts for retrieval purposes.

Active learning: A step towards automating medical concept extraction

Objective This paper presents an automatic active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort, and (2) the robustness of incremental active learning framework across different selection criteria and datasets is determined. Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional Random Fields as the supervised method, and least confidence and information density as two selection criteria for active learning framework were used. The effect of incremental learning vs. standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. Two clinical datasets were used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared to the Random sampling baseline, the saving is at least doubled. Discussion Incremental active learning guarantees robustness across all selection criteria and datasets. The reduction of annotation effort is always above random sampling and longest sequence baselines. Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models, while significantly reducing the burden of manual annotation.

Effective "on-boarding": transitioning from trainee to faculty.

Abstract The transition from trainee to junior faculty member can be both exciting and daunting. However, a paucity of medical literature exists to help guide new faculty in this transition. Therefore, we adapted work from the business management literature on what is referred to as "on-boarding"; effectively integrating and advancing one's position as a new employee. This article outlines strategies for cultivating one's own on-boarding as a junior faculty member at large academic medical centers. These strategies are extrapolated from management practices, culled from the medical literature on developing and retaining junior faculty, and, finally, borrowed from the hard-won knowledge of junior and senior faculty members. They advise new faculty to: (1) start early, (2) define your role--"managing yourself," (3) invest in/secure early wins, (4) manage your manager, (5) identify the "true (or hidden)" organizational culture, (6) reassess your own goals--"look in the rearview mirror and to the horizon," and (7) use your mentors effectively. These strategies provide a roadmap for new faculty members to transition as effectively as possible to their new jobs.

Interior medical school

Instructor in histology, probably Carl Huber, and students using the microscopes purchased by [Charles] Stowell. Histology was variously associated with pathology, physiology, and anatomy. (source: Not Just Any Medical School by Horace W. Davenport).

Choirboy haunted by painful memories

IT was in the magnificent Manchester Cathedral that Eli Ward's pure soprano attracted the attention of the new dean, the Reverend Robert Waddington. When Waddington called for volunteers to help him polish the gold leaf on the altar railings, several choirboys came forward. Among them was Eli, a working-class 11-year-old from a council estate, who loved singing in the choir and was happy to help...

Anglican Church fails to report abuse

Evidence has emerged that the Anglican Church in Britain failed to alert police about a senior member of the clergy who's alleged to have abused children in both the Britain and Australia. Anglican Priest Reverend Robert Waddington was principal of a school in North Queensland in 1960s. He went on to become the Dean of Manchester, but he died five years ago. Allegations of abuse reached the Anglican Church in England in the late 1990s - but no action was taken. The diocese of North Queensland has begun its own investigation but it seems crucial documents may have been lost.

Spirituality: Do teachers and students hold the same opinion?

Background:  Few studies have investigated potential differences between the opinions of educators and undergraduates regarding spirituality in patient care. Understanding these differences, could lead to better strategies for educational proposes. Purpose:  To compare the opinions of medical teachers (MTs) and medical students (MSs) regarding spirituality training in a Brazilian medical school. Methods:  A cross-sectional study was conducted. MTs and MSs filled out a questionnaire containing the Duke Religion Index, and questions regarding spirituality in clinical practice and at medical school. A comparison between early-curriculum MSs, late curriculum MSs and MTs was carried out. Chi-square (categorical) and Mann-Whitney (continuous/ordinal) tests were used. Results:  A total of 475 MSs and 44 MTs were evaluated. Results showed that MSs did not address spirituality as frequently as MTs (p<0.001), and that most participants did not feel prepared to address this issue, and believe that Brazilian medical schools are not giving all the required information in this field. Nevertheless, they believe MSs should be prepared to discuss these issues. Late-curriculum MSs believed that spirituality plays a more positive role in patient health (p=0.027), and were more prone to address this issue than early-curriculum MSs (p=0.023). Conclusion:  These findings revealed some of the challenges faced by spirituality medical training in Brazil, and differences between MTs and MSs regarding this issue. Further studies are needed to replicate these findings in other countries. © Blackwell Publishing Ltd 2013.

Interview with Julie Knobil

An oral interview with Juile (Hotchkiss) Knobil, research professor of physiology and then integrative biology at the Medical School, where she lectured on mammalian physiology and perinatal endocrinology.

Interview with Dianna Milewicz

An oral interview with Dianna Milewicz, M.D., Ph.D., Professor and Vice Chairman of the Department of Internal Medicine at The University of Texas Medical School at Houston and Director of the M.D./Ph.D. Program and co-Director of the Biomedical Engineering Center. Her research interests include the genetic basis of cardiovascular diseases, and understanding the effect of identified mutations on protein function. She has recently established a genetic core laboratory to provide molecular biology and genetic expertise to clinicians who want to initiate genetic studies on their patient populations.

Interview with Anna Steinberger

An oral interview with Dr. Anna Steinberger, who taught and conducted basic research in Reproductive Biology and served as Assistant Dean for Faculty Affairs at UT Medical School-Houston. Her research yielded over 250 scientific articles, books, and book chapters for which she received numerous awards and recognitions in the USA and abroad.

Instructor's Room, Animal Morphology

On verso: The man is Henry B. Ward

Morning sectional clinic

On verso: Exercise in obstetrics and gynecology in 1893. Prof. James Nelson Martin listening to the history read by a student.

A Demonstration in nervous diseases

On verso: Med School. Practical work pictures

Surgery and anatomy class

On verso: Homeopathic?