Six questions on the construction of ontologies in biomedicine

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today

Transmitter-side antennas correlation in SVD-assisted MIMO systems

MIMO techniques allow increasing wireless channel performance by decreasing the BER and increasing the channel throughput and in consequence are included in current mobile communication standards. MIMO techniques are based on benefiting the existence of multipath in wireless communications and the application of appropriate signal processing techniques. The singular value decomposition (SVD) is a popular signal processing technique which, based on the perfect channel state information (PCSI) knowledge at both the transmitter and receiver sides, removes inter-antenna interferences and improves channel performance. Nevertheless, the proximity of the multiple antennas at each front-end produces the so called antennas correlation effect due to the similarity of the various physical paths. In consequence, antennas correlation drops the MIMO channel performance. This investigation focuses on the analysis of a MIMO channel under transmitter-side antennas correlation conditions. First, antennas correlation is analyzed and characterized by the correlation coefficients. The analysis describes the relation between antennas correlation and the appearance of predominant layers which significantly affect the channel performance. Then, based on the SVD, pre- and post-processing is applied to remove inter-antenna interferences. Finally, bit- and power allocation strategies are applied to reach the best performance. The resulting BER reveals that antennas correlation effect diminishes the channel performance and that not necessarily all MIMO layers must be activated to obtain the best performance

Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support

In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with clinical data, to support clinical decision-making by: 1) analyzing clinically relevant knowledge contained in PGx knowledge resources; 2) evaluating the feasibility of a rule-based framework to support formal representation of clinically relevant knowledge contained in PGx knowledge resources; and, 3) evaluating the ability of an electronic medical record/electronic health record (EMR/EHR) to provide computable forms of clinical data needed for PGx clinical decision support. Findings suggest that the PharmGKB is a good source for PGx knowledge to supplement information contained in FDA approved drug labels. Furthermore, we found that with supporting knowledge (e.g. IF age <18 THEN patient is a child), sufficient clinical data exists in University of Washington’s EMR systems to support 50% of PGx knowledge contained in drug labels that could be expressed as rules

Application of a spring-dashpot system to clinical lung tumor motion data

A spring-dashpot system based on the Voigt model was developed to model the correlation between abdominal respiratory motion and tumor motion during lung radiotherapy. The model was applied to clinical data comprising 52 treatment beams from 10 patients, treated on the Mitsubishi Real-Time Radiation Therapy system, Sapporo, Japan. In Stage 1, model parameters were optimized for individual patients and beams to determine reference values and to investigate how well the model can describe the data. In Stage 2, for each patient the optimal parameters determined for a single beam were applied to data from other beams to investigate whether a beam-specific set of model parameters is sufficient to model tumor motion over a course of treatment. In Stage 1 the baseline root mean square (RMS) residual error for all individually-optimized beam data was 0.90 plus or minus 0.40 mm. In Stage 2, patient-specific model parameters based on a single beam were found to model the tumor position closely, even for irregular beam data, with a mean increase with respect to Stage 1 values in RMS error of 0.37 mm. On average the obtained model output for the tumor position was 95% of the time within an absolute bound of 2.0 mm and 2.6 mm in Stage 1 and 2, respectively. The model was capable of dealing with baseline, amplitude and frequency variations of the input data, as well as phase shifts between the input tumor and output abdominal signals. These results indicate that it may be feasible to collect patient-specific model parameters during or prior to the first treatment, and then retain these for the rest of the treatment period. The model has potential for clinical application during radiotherapy treatment of lung tumors

Underground Wireless Channel Bandwidth and Capacity

The UG channel bandwidth and capacity are vital parameters in wireless underground communication system design. In this chapter, a comprehensive analysis of the wireless underground channel capacity is presented. The impact of soil on return loss, bandwidth, and path loss is discussed. The results of underground multi-carrier modulation capacity are also outlined. Moreover, the single user capacity and multi-carrier capacity are also introduced with an in-depth treatment of soil texture, soil moisture, and distance effects on channel capacity. Finally, the chapter is concluded with a discussion of challenges and open research issues

Physicians' use of the 5As in counseling obese patients: is the quality of counseling associated with patients' motivation and intention to lose weight?

<p>Abstract</p> <p>Background</p> <p>Physicians are encouraged to counsel obese patients to lose weight, but studies measuring the quality of physicians' counseling are rare. We sought to describe the quality of physicians' obesity counseling and to determine associations between the quality of counseling and obese patients' motivation and intentions to lose weight, key predictors of behavior change.</p> <p>Methods</p> <p>We conducted post-visit surveys with obese patients to assess physician's use of 5As counseling techniques and the overall patient-centeredness of the physician.. Patients also reported on their motivation to lose weight and their intentions to eat healthier and exercise. One-way ANOVAs were used to describe mean differences in number of counseling practices across levels of self-rated intention and motivation. Logistic regression analyses were conducted to assess associations between number of 5As counseling practices used and patient intention and motivation.</p> <p>Results</p> <p>137 patients of 23 physicians were included in the analysis. While 85% of the patients were counseled about obesity, physicians used only a mean of 5.3 (SD = 4.6) of 18 possible 5As counseling practices. Patients with higher levels of motivation and intentions reported receiving more 5As counseling techniques than those with lower levels. Each additional counseling practice was associated with higher odds of being motivated to lose weight (OR 1.31, CI 1.11-1.55), intending to eat better (OR 1.23, CI 1.06-1.44), and intending to exercise regularly (OR 1.14, CI 1.00-1.31). Patient centeredness of the physician was also positively associated with intentions to eat better (OR 2.96, CI 1.03-8.47) and exercise (OR 26.07, CI 3.70-83.93).</p> <p>Conclusions</p> <p>Quality of physician counseling (as measured using the 5As counseling framework and patient-centeredness scales) was associated with motivation to lose weight and intentions to change behavior. Future studies should determine whether higher quality obesity counseling leads to improved behavioral and weight outcomes.</p

Physicians' attitudes about obesity and their associations with competency and specialty: A cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Physicians frequently report negative attitudes about obesity which is thought to affect patient care. However, little is known about how attitudes toward treating obese patients are formed. We conducted a cross-sectional survey of physicians in order to better characterize their attitudes and explore the relationships among attitudes, perceived competency in obesity care, including report of weight loss in patients, and other key physician, training, and practice characteristics.</p> <p>Methods</p> <p>We surveyed all 399 physicians from internal medicine, pediatrics, and psychiatry specialties at one institution regarding obesity care attitudes, competency, including physician report of percent of their patients who lose weight. We performed a factor analysis on the attitude items and used hierarchical regression analysis to explore the degree to which competency, reported weight loss, physician, training and practice characteristics explained the variance in each attitude factor.</p> <p>Results</p> <p>The overall response rate was 63%. More than 40% of physicians had a negative reaction towards obese patients, 56% felt qualified to treat obesity, and 46% felt successful in this realm. The factor analysis revealed 4 factors–<it>Physician Discomfort/Bias, Physician Success/Self Efficacy, Positive Outcome Expectancy</it>, and <it>Negative Outcome Expectancy</it>. Competency and reported percent of patients who lose weight were most strongly associated with the <it>Physician Success/Self Efficacy </it>attitude factor. Greater skill in patient assessment was associated with less <it>Physician Discomfort/Bias</it>. Training characteristics were associated with outcome expectancies with newer physicians reporting more positive treatment expectancies. Pediatric faculty was more positive and psychiatry faculty less negative in their treatment expectancies than internal medicine faculty.</p> <p>Conclusion</p> <p>Physician attitudes towards obesity are associated with competency, specialty, and years since postgraduate training. Further study is necessary to determine the direction of influence and to explore the impact of these attitudes on patient care.</p

Developing a Professional Studies Curriculum to Support Veterinary Professional Identity Formation

Professional studies teaching in medical and veterinary education is undergoing a period of change. Traditional approaches, aiming to teach students professional values and behaviors, are being enhanced by curricula designed to support students' professional identity formation. This development offers the potential for improving student engagement and graduates' mental well-being. The veterinary professional identity associated with emotional resilience and success in practice incorporates complexity in professional decision making and the importance of context on behaviors and actions. The veterinarian must make decisions that balance the sometimes conflicting needs of patient, clients, veterinarian, and practice; their subsequent actions are influenced by environmental challenges such as financial limitations, or stress and fatigue caused by a heavy workload. This article aims to describe how curricula can be designed to support the development of such an identity in students. We will review relevant literature from medical education and the veterinary profession to describe current best practices for supporting professional identity formation, and then present the application of these principles using the curriculum at the Royal Veterinary College (RVC) as a case study. Design of a “best practice” curriculum includes sequential development of complex thinking rather than notions of a single best solution to a problem. It requires managing a hidden curriculum that tends to reinforce a professional identity conceived solely on clinical diagnosis and treatment. It includes exposure to veterinary professionals with different sets of professional priorities, and those who work in different environments. It also includes the contextualization of taught content through reflection on workplace learning opportunities

How do family physicians communicate about cardiovascular risk? Frequencies and determinants of different communication formats

Background: Patients understand information about risk better if it is communicated in numerical or visual formats (e.g. graphs) compared to verbal qualifiers only. How frequently different communication formats are used in clinical primary care settings is unknown. Methods: We collected socioeconomic and patient understanding data using questionnaires and audio-recorded consultations about cardiovascular disease risk. The frequencies of the communication formats were calculated and multivariate regression analysis of associations between communication formats, patient and general practitioner characteristics, and patient subjective understanding was performed. Results: In 73% of 70 consultations, verbal qualifiers were used exclusively to communicate cardiovascular risk, compared to numerical (11%) and visual (16%) formats. Female GPs and female patient's gender were significantly associated with a higher use of verbal formats compared to visual formats (p = 0.001 and p = 0.039, respectively). Patient subjective understanding was significantly higher in visual counseling compared to verbal counseling (p = 0.001). Conclusions: Verbal qualifiers are the most often used communication format, though recommendations favor numerical and visual formats, with visual formats resulting in better understanding than others. Also, gender is associated with the choice of communication format. Barriers against numerical and visual communication formats among GPs and patients should be studied, including gender aspects. Adequate risk communication should be integrated into physicians' education

Proposed Standards for Medical Education Submissions to the Journal of General Internal Medicine

To help authors design rigorous studies and prepare clear and informative manuscripts, improve the transparency of editorial decisions, and raise the bar on educational scholarship, the Deputy Editors of the Journal of General Internal Medicine articulate standards for medical education submissions to the Journal. General standards include: (1) quality questions, (2) quality methods to match the questions, (3) insightful interpretation of findings, (4) transparent, unbiased reporting, and (5) attention to human subjects’ protection and ethical research conduct. Additional standards for specific study types are described. We hope these proposed standards will generate discussion that will foster their continued evolution