AEHRC & QUT at TREC 2011 Medical Track : a concept-based information retrieval approach

The Australian e-Health Research Centre and Queensland University of Technology recently participated in the TREC 2011 Medical Records Track. This paper reports on our methods, results and experience using a concept-based information retrieval approach. Our concept-based approach is intended to overcome specific challenges we identify in searching medical records. Queries and documents are transformed from their term-based originals into medical concepts as de ned by the SNOMED-CT ontology. Results show our concept-based approach performed above the median in all three performance metrics: bref (+12%), R-prec (+18%) and Prec@10 (+6%).

An evolving perspective on physical activity counselling by medical professionals

Background Physical inactivity is a modifiable risk factor for many chronic conditions and a leading cause of premature mortality. An increasing proportion of adults worldwide are not engaging in a level of physical activity sufficient to prevent or alleviate these adverse effects. Medical professionals have been identified as potentially powerful sources of influence for those who do not meet minimum physical activity guidelines. Health professionals are respected and expected sources of advice and they reach a large and relevant proportion of the population. Despite this potential, health professionals are not routinely practicing physical activity promotion. Discussion Medical professionals experience several known barriers to physical activity promotion including lack of time and lack of perceived efficacy in changing physical activity behaviour in patients. Furthermore, evidence for effective physical activity promotion by medical professionals is inconclusive. To address these problems, new approaches to physical activity promotion are being proposed. These include collaborating with community based physical activity behaviour change interventions, preparing patients for effective brief counselling during a consultation with the medical professional, and use of interactive behaviour change technology. Summary It is important that we recognise the latent risk of physical inactivity among patients presenting in clinical settings. Preparation for improving patient physical activity behaviours should commence before the consultation and may include physical activity screening. Medical professionals should also identify suitable community interventions to which they can refer physically inactive patients. Outsourcing the majority of a comprehensive physical activity intervention to community based interventions will reduce the required clinical consultation time for addressing the issue with each patient. Priorities for future research include investigating ways to promote successful referrals and subsequent engagement in comprehensive community support programs to increase physical activity levels of inactive patients. Additionally, future clinical trials of physical activity interventions should be evaluated in the context of a broader framework of outcomes to inform a systematic consideration of broad strengths and weaknesses regarding not only efficacy but cost-effectiveness and likelihood of successful translation of interventions to clinical contexts.

Langevin dynamics modeling of the water diffusion tensor in partially aligned collagen networks

In this work, a Langevin dynamics model of the diffusion of water in articular cartilage was developed. Numerical simulations of the translational dynamics of water molecules and their interaction with collagen fibers were used to study the quantitative relationship between the organization of the collagen fiber network and the diffusion tensor of water in model cartilage. Langevin dynamics was used to simulate water diffusion in both ordered and partially disordered cartilage models. In addition, an analytical approach was developed to estimate the diffusion tensor for a network comprising a given distribution of fiber orientations. The key findings are that (1) an approximately linear relationship was observed between collagen volume fraction and the fractional anisotropy of the diffusion tensor in fiber networks of a given degree of alignment, (2) for any given fiber volume fraction, fractional anisotropy follows a fiber alignment dependency similar to the square of the second Legendre polynomial of cos(θ), with the minimum anisotropy occurring at approximately the magic angle (θMA), and (3) a decrease in the principal eigenvalue and an increase in the transverse eigenvalues is observed as the fiber orientation angle θ progresses from 0◦ to 90◦. The corresponding diffusion ellipsoids are prolate for θ < θMA, spherical for θ ≈ θMA, and oblate for θ > θMA. Expansion of the model to include discrimination between the combined effects of alignment disorder and collagen fiber volume fraction on the diffusion tensor is discussed.

Infertility, medical advice and treatment with fertility hormones and/or in vitro fertilisation: a population perspective from the Australian Longitudinal Study on Women's Health

OBJECTIVE: To identify the factors associated with infertility, seeking advice and treatment with fertility hormones and/or in vitro fertilisation (IVF) among a general population of women. METHODS: Participants in the Australian Longitudinal Study on Women's Health aged 28-33 years in 2006 had completed up to four mailed surveys over 10 years (n=9,145). Parsimonious multivariate logistic regression was used to identify the socio-demographic, biological (including reproductive histories), and behavioural factors associated with infertility, advice and hormonal/IVF treatment. RESULTS: For women who had tried to conceive or had been pregnant (n=5,936), 17% reported infertility. Among women with infertility (n=1031), 72% (n=728) sought advice but only 50% (n=356) used hormonal/IVF treatment. Women had higher odds of infertility when: they had never been pregnant (OR=7.2, 95% CI 5.6-9.1) or had a history of miscarriage (OR range=1.5-4.0) than those who had given birth (and never had a miscarriage or termination). CONCLUSION: Only one-third of women with infertility used hormonal and/or IVF treatment. Women with PCOS or endometriosis were the most proactive in having sought advice and used hormonal/IVF treatment. IMPLICATIONS: Raised awareness of age-related declining fertility is important for partnered women aged approximately 30 years to encourage pregnancy during their prime reproductive years and reduce the risk of infertility.

Depression: an emotional obstacle to seeking medical advice for infertility

Objective: To investigate the mental and general health of infertile women who had not sought medical advice for their recognized infertility and were therefore not represented in clinical populations. Design: Longitudinal cohort study.Setting Population based.Patient(s) Participants in the Australian Longitudinal Study on Women's Health aged 28-33 years in 2006 who had ever tried to conceive or had been pregnant (n = 5,936).Intervention(s) None.Main Outcome Measure(s) Infertility, not seeking medical advice. Result(s): Compared with fertile women (n = 4,905), infertile women (n = 1,031) had higher odds of self-reported depression (odds ratio [OR] 1.20, 95% confidence interval [CI] 1.01-1.43), endometriosis (5.43, 4.01-7.36), polycystic ovary syndrome (9.52, 7.30-12.41), irregular periods (1.99, 1.68-2.36), type II diabetes (4.70, 1.79-12.37), or gestational diabetes (1.66, 1.12-2.46). Compared with infertile women who sought medical advice (n = 728), those who had not sought medical advice (n = 303) had higher odds of self-reported depression (1.67, 1.18-2.37), other mental health problems (3.14, 1.14-8.64), urinary tract infections (1.67, 1.12-2.49), heavy periods (1.63, 1.16-2.29), or a cancer diagnosis (11.33, 2.57-49.89). Infertile women who had or had not sought medical advice had similar odds of reporting an anxiety disorder or anxiety-related symptoms. Conclusion(s): Women with self-reported depression were unlikely to have sought medical advice for infertility. Depression and depressive symptoms may be barriers to seeking medical advice for infertility.

Agreement between self-reported use of in vitro fertilization or ovulation induction, and medical insurance claims in Australian women aged 28–36 years

STUDY QUESTION: What is the self-reported use of in vitro fertilization (IVF) and ovulation induction (OI) in comparison with insurance claims by Australian women aged 28–36 years? SUMMARY ANSWER: The self-reported use of IVF is quite likely to be valid; however, the use of OI is less well reported. WHAT IS KNOWN AND WHAT THIS PAPER ADDS: Population-based research often relies on the self-reported use of IVF and OI because access to medical records can be difficult and the data need to include sufficient personal identifying information for linkage to other data sources. There have been few attempts to explore the reliability of the self-reported use of IVF and OI using the linkage to medical insurance claims for either treatment. STUDY DESIGN: This prospective, population-based, longitudinal study included the cohort of women born during 1973–1978 and participating in the Australian Longitudinal Study on Women's Health (ALSWH) (n = 14247). From 1996 to 2009, participants were surveyed up to five times. PARTICIPANTS AND SETTING: Participants self-reported their use of IVF or OI in two mailed surveys when aged 28–33 and 31–36 years (n = 7280), respectively. This study links self-report survey responses and claims for treatment or medication from the universal national health insurance scheme (i.e. Medicare Australia). MAIN RESULTS AND THE ROLE OF CHANCE: Comparisons between self-reports and claims data were undertaken for all women consenting to the linkage (n = 3375). The self-reported use of IVF was compared with claims for OI for IVF (Kappa, K = 0.83), oocyte collection (K = 0.82), sperm preparation (K = 0.83), intracytoplasmic sperm injection (K = 0.40), fresh embryo transfers (K = 0.82), frozen embryo transfers (K = 0.64) and OI for IVF medication (K = 0.17). The self-reported use of OI was compared with ovulation monitoring (K = 0.52) and OI medication (K = 0.71). BIAS, CONFOUNDING AND OTHER REASONS FOR CAUTION: There is a possibility of selection bias due to the inclusion criteria for participants in this study: (1) completion of the last two surveys in a series of five and (2) consent to the linkage of their responses with Medicare data. GENERALIZABILITY TO OTHER POPULATIONS: The results are relevant to questionnaire-based research studies with infertile women in developed countries. STUDY FUNDING/COMPETING INTEREST(S): ALSWH is funded by the Australian Government Department of Health and Ageing. This research is funded by a National Health and Medical Research Council Centre of Research Excellence grant.

Sensors and imaging for wound healing : a review

Wound healing involves a complex series of biochemical events and has traditionally been managed with 'low tech' dressings and bandages. The concept that diagnostic and theranostic sensors can complement wound management is rapidly growing in popularity as there is tremendous potential to apply this technology to both acute and chronic wounds. Benefits in sensing the wound environment include reduction of hospitalization time, prevention of amputations and better understanding of the processes which impair healing. This review discusses the state-of-the-art in detection of markers associated with wound healing and infection, utilizing devices imbedded within dressings or as point-of-care techniques to allow for continual or rapid wound assessment and monitoring. Approaches include using biological or chemical sensors of wound exudates and volatiles to directly or indirectly detect bacteria, monitor pH, temperature, oxygen and enzymes. Spectroscopic and imaging techniques are also reviewed as advanced wound monitoring techniques. The review concludes with a discussion of the limitations of and future directions for this field.

Detection of right-to-left Atrial communication using agitated saline contrast imaging : experience with 1162 patients and recommendations for echocardiography

Background: Right-to-left shunting via a patent foramen ovale (PFO) has a recognized association with embolic events in younger patients. The use of agitated saline contrast imaging (ASCi) for detecting atrial shunting is well documented, however optimal technique is not well described. The purpose of this study is to assess the efficacy and safety of ASCi via TTE for assessment of right-to-left atrial communication in a large cohort of patients. Method: A retrospective review was undertaken of 1162 consecutive transthoracic (TTE) ASCi studies, of which 195 had also undergone clinically indicated transesophageal (TEE) echo. ASCi shunt results were compared with color flow imaging (CFI) and the role of provocative maneuvers (PM) assessed. Results: 403 TTE studies (35%) had paradoxical shunting seen during ASCi. Of these, 48% were positive with PM only. There was strong agreement between TTE ASCi and reported TEE findings (99% sensitivity, 85% specificity), with six false positive and two false negative results. In hindsight, the latter were likely due to suboptimal right atrial opacification, and the former due to transpulmonary shunting. TTE CFI was found to be insensitive (22%) for the detection of a PFO compared with TTE ASCi. Conclusions: TTE ASCi is minimally invasive and highly accurate for the detection of right-to-left atrial communication when PM are used. TTE CFI was found to be insensitive for PFO screening. It is recommended that TTE ASCi should be considered the initial diagnostic tool for the detection of PFO in clinical practice. A dedicated protocol should be followed to ensure adequate agitated saline contrast delivery and performance of provocative maneuvers.

Correction of step artefact associated with MRI scanning of long bones

3D models of long bones are being utilised for a number of fields including orthopaedic implant design. Accurate reconstruction of 3D models is of utmost importance to design accurate implants to allow achieving a good alignment between two bone fragments. Thus for this purpose, CT scanners are employed to acquire accurate bone data exposing an individual to a high amount of ionising radiation. Magnetic resonance imaging (MRI) has been shown to be a potential alternative to computed tomography (CT) for scanning of volunteers for 3D reconstruction of long bones, essentially avoiding the high radiation dose from CT. In MRI imaging of long bones, the artefacts due to random movements of the skeletal system create challenges for researchers as they generate inaccuracies in the 3D models generated by using data sets containing such artefacts. One of the defects that have been observed during an initial study is the lateral shift artefact occurring in the reconstructed 3D models. This artefact is believed to result from volunteers moving the leg during two successive scanning stages (the lower limb has to be scanned in at least five stages due to the limited scanning length of the scanner). As this artefact creates inaccuracies in the implants designed using these models, it needs to be corrected before the application of 3D models to implant design. Therefore, this study aimed to correct the lateral shift artefact using 3D modelling techniques. The femora of five ovine hind limbs were scanned with a 3T MRI scanner using a 3D vibe based protocol. The scanning was conducted in two halves, while maintaining a good overlap between them. A lateral shift was generated by moving the limb several millimetres between two scanning stages. The 3D models were reconstructed using a multi threshold segmentation method. The correction of the artefact was achieved by aligning the two halves using the robust iterative closest point (ICP) algorithm, with the help of the overlapping region between the two. The models with the corrected artefact were compared with the reference model generated by CT scanning of the same sample. The results indicate that the correction of the artefact was achieved with an average deviation of 0.32 ± 0.02 mm between the corrected model and the reference model. In comparison, the model obtained from a single MRI scan generated an average error of 0.25 ± 0.02 mm when compared with the reference model. An average deviation of 0.34 ± 0.04 mm was seen when the models generated after the table was moved were compared to the reference models; thus, the movement of the table is also a contributing factor to the motion artefacts.

Mastering medical terminology : Australia and New Zealand

Mastering Medical Terminology: Australia and New Zealand is medical terminology book of relevance to an audience in Australia and New Zealand. Australian terminology, perspectives, examples and spelling have been included and Australian pronunciation specified. The textbook is accompanied by a self-help workbook, an online workbook and a Smartphone app. Throughout Mastering Medical Terminology, review of medical terminology as it is used in clinical practice is highlighted. Features of the textbook, workbook and electronic product include: • Simple, non-technical explanations of medical terms • Workbook format with ample spaces to write answers • Explanations of clinical procedures, laboratory tests and abbreviations used in Australian clinical practice, as they apply to each body system and speciality area • Pronunciation of terms and spaces to write meanings of terms • Practical applications sections • Exercises that test understanding of terminology as students work through the text chapter by chapter • Review activities that pull together terminology to help students study • Comprehensive glossary and appendices for reference • Links to other useful references, such as websites and textbooks.

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.

Exploiting SNOMED CT concepts and relationships for clinical information retrieval : Australian e-Health Research Centre and Queensland University of Technology at the TREC 2012 Medical Track

The Australian e-Health Research Centre and Queensland University of Technology recently participated in the TREC 2012 Medical Records Track. This paper reports on our methods, results and experience using an approach that exploits the concept and inter-concept relationships defined in the SNOMED CT medical ontology. Our concept-based approach is intended to overcome specific challenges in searching medical records, namely vocabulary mismatch and granularity mismatch. Queries and documents are transformed from their term-based originals into medical concepts as defined by the SNOMED CT ontology, this is done to tackle vocabulary mismatch. In addition, we make use of the SNOMED CT parent-child `is-a' relationships between concepts to weight documents that contained concept subsumed by the query concepts; this is done to tackle the problem of granularity mismatch. Finally, we experiment with other SNOMED CT relationships besides the is-a relationship to weight concepts related to query concepts. Results show our concept-based approach performed significantly above the median in all four performance metrics. Further improvements are achieved by the incorporation of weighting subsumed concepts, overall leading to improvement above the median of 28% infAP, 10% infNDCG, 12% R-prec and 7% Prec@10. The incorporation of other relations besides is-a demonstrated mixed results, more research is required to determined which SNOMED CT relationships are best employed when weighting related concepts.

Semantic judgement of medical concepts : combining syntagmatic and paradigmatic information with the tensor encoding model

This paper outlines a novel approach for modelling semantic relationships within medical documents. Medical terminologies contain a rich source of semantic information critical to a number of techniques in medical informatics, including medical information retrieval. Recent research suggests that corpus-driven approaches are effective at automatically capturing semantic similarities between medical concepts, thus making them an attractive option for accessing semantic information. Most previous corpus-driven methods only considered syntagmatic associations. In this paper, we adapt a recent approach that explicitly models both syntagmatic and paradigmatic associations. We show that the implicit similarity between certain medical concepts can only be modelled using paradigmatic associations. In addition, the inclusion of both types of associations overcomes the sensitivity to the training corpus experienced by previous approaches, making our method both more effective and more robust. This finding may have implications for researchers in the area of medical information retrieval.

Encouraging, assisting and time to EAT : improved nutritional intake for older medical patients receiving Protected Mealtimes and/or additional nursing feeding assistance

Background & Aims: Inadequate feeding assistance and mealtime interruptions during hospitalisation may contribute to malnutrition and poor nutritional intake in older people. This study aimed to implement and compare three interventions designed to specifically address mealtime barriers and improve energy intakes of medical inpatients aged ≥65 years. Methods: Pre-post study compared three mealtime assistance interventions: PM: Protected Mealtimes with multidisciplinary education; AIN: additional assistant-in-nursing (AIN) with dedicated meal role; PM+AIN: combined intervention. Dietary intake of 254 patients (pre: n=115, post: n=141; mean age 80±8) was visually estimated on a single day in the first week of hospitalisation and compared with estimated energy requirements. Assistance activities were observed and recorded. Results: Mealtime assistance levels significantly increased in all interventions (p<0.01). Post-intervention participants were more likely to achieve adequate energy intake (OR=3.4, p=0.01), with no difference noted between interventions (p=0.29). Patients with cognitive impairment or feeding dependency appeared to gain substantial benefit from mealtime assistance interventions. Conclusions: Protected Mealtimes and additional AIN assistance (implemented alone or in combination) may produce modest improvements in nutritional intake. Targeted feeding assistance for certain patient groups holds promise; however, alternative strategies are required to address the complex problem of malnutrition in this population.