Towards a smart cancer registry

Aims Pathology notification for a Cancer Registry is regarded as the most valid information for the confirmation of a diagnosis of cancer. In view of the importance of pathology data, an automatic medical text analysis system (Medtex) is being developed to perform electronic Cancer Registry data extraction and coding of important clinical information embedded within pathology reports. Methods The system automatically scans HL7 messages received from a Queensland pathology information system and analyses the reports for terms and concepts relevant to a cancer notification. A multitude of data items for cancer notification such as primary site, histological type, stage, and other synoptic data are classified by the system. The underlying extraction and classification technology is based on SNOMED CT1 2. The Queensland Cancer Registry business rules3 and International Classification of Diseases – Oncology – Version 34 have been incorporated. Results The cancer notification services show that the classification of notifiable reports can be achieved with sensitivities of 98% and specificities of 96%5, while the coding of cancer notification items such as basis of diagnosis, histological type and grade, primary site and laterality can be extracted with an overall accuracy of 80%6. In the case of lung cancer staging, the automated stages produced were accurate enough for the purposes of population level research and indicative staging prior to multi-disciplinary team meetings2 7. Medtex also allows for detailed tumour stream synoptic reporting8. Conclusions Medtex demonstrates how medical free-text processing could enable the automation of some Cancer Registry processes. Over 70% of Cancer Registry coding resources are devoted to information acquisition. The development of a clinical decision support system to unlock information from medical free-text could significantly reduce costs arising from duplicated processes and enable improved decision support, enhancing efficiency and timeliness of cancer information for Cancer Registries.

Creation of a new evaluation benchmark for information retrieval targeting patient information needs

Searching for health advice on the web is becoming increasingly common. Because of the great importance of this activity for patients and clinicians and the effect that incorrect information may have on health outcomes, it is critical to present relevant and valuable information to a searcher. Previous evaluation campaigns on health information retrieval (IR) have provided benchmarks that have been widely used to improve health IR and record these improvements. However, in general these benchmarks have targeted the specialised information needs of physicians and other healthcare workers. In this paper, we describe the development of a new collection for evaluation of effectiveness in IR seeking to satisfy the health information needs of patients. Our methodology features a novel way to create statements of patients’ information needs using realistic short queries associated with patient discharge summaries, which provide details of patient disorders. We adopt a scenario where the patient then creates a query to seek information relating to these disorders. Thus, discharge summaries provide us with a means to create contextually driven search statements, since they may include details on the stage of the disease, family history etc. The collection will be used for the first time as part of the ShARe/-CLEF 2013 eHealth Evaluation Lab, which focuses on natural language processing and IR for clinical care.

Combining word semantics within complex Hilbert space for information retrieval

Complex numbers are a fundamental aspect of the mathematical formalism of quantum physics. Quantum-like models developed outside physics often overlooked the role of complex numbers. Specifically, previous models in Information Retrieval (IR) ignored complex numbers. We argue that to advance the use of quantum models of IR, one has to lift the constraint of real-valued representations of the information space, and package more information within the representation by means of complex numbers. As a first attempt, we propose a complex-valued representation for IR, which explicitly uses complex valued Hilbert spaces, and thus where terms, documents and queries are represented as complex-valued vectors. The proposal consists of integrating distributional semantics evidence within the real component of a term vector; whereas, ontological information is encoded in the imaginary component. Our proposal has the merit of lifting the role of complex numbers from a computational byproduct of the model to the very mathematical texture that unifies different levels of semantic information. An empirical instantiation of our proposal is tested in the TREC Medical Record task of retrieving cohorts for clinical studies.

Overview of the ShARe/CLEF eHealth Evaluation Lab 2013

Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations,and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition.

Towards a visually enhanced medical search engine

This paper presents the prototype of an information retrieval system for medical records that utilises visualisation techniques, namely word clouds and timelines. The system simplifies and assists information seeking tasks within the medical domain. Access to patient medical information can be time consuming as it requires practitioners to review a large number of electronic medical records to find relevant information. Presenting a summary of the content of a medical document by means of a word cloud may permit information seekers to decide upon the relevance of a document to their information need in a simple and time effective manner. We extend this intuition, by mapping word clouds of electronic medical records onto a timeline, to provide temporal information to the user. This allows exploring word clouds in the context of a patient’s medical history. To enhance the presentation of word clouds, we also provide the means for calculating aggregations and differences between patient’s word clouds.

Automatic classification of free-text radiology reports to identify limb fractures using machine learning and the SNOMED CT ontology

Objective To develop and evaluate machine learning techniques that identify limb fractures and other abnormalities (e.g. dislocations) from radiology reports. Materials and Methods 99 free-text reports of limb radiology examinations were acquired from an Australian public hospital. Two clinicians were employed to identify fractures and abnormalities from the reports; a third senior clinician resolved disagreements. These assessors found that, of the 99 reports, 48 referred to fractures or abnormalities of limb structures. Automated methods were then used to extract features from these reports that could be useful for their automatic classification. The Naive Bayes classification algorithm and two implementations of the support vector machine algorithm were formally evaluated using cross-fold validation over the 99 reports. Result Results show that the Naive Bayes classifier accurately identifies fractures and other abnormalities from the radiology reports. These results were achieved when extracting stemmed token bigram and negation features, as well as using these features in combination with SNOMED CT concepts related to abnormalities and disorders. The latter feature has not been used in previous works that attempted classifying free-text radiology reports. Discussion Automated classification methods have proven effective at identifying fractures and other abnormalities from radiology reports (F-Measure up to 92.31%). Key to the success of these techniques are features such as stemmed token bigrams, negations, and SNOMED CT concepts associated with morphologic abnormalities and disorders. Conclusion This investigation shows early promising results and future work will further validate and strengthen the proposed approaches.

ShARe/CLEF eHealth Evaluation Lab 2013, Task 3: Information retrieval to address patients' questions when reading clinical reports

This paper presents the results of task 3 of the ShARe/CLEF eHealth Evaluation Lab 2013. This evaluation lab focuses on improving access to medical information on the web. The task objective was to investigate the effect of using additional information such as the discharge summaries and external resources such as medical ontologies on the IR effectiveness. The participants were allowed to submit up to seven runs, one mandatory run using no additional information or external resources, and three each using or not using discharge summaries.

Producing while consuming: Social interaction around photos shared within private group

User-generated content plays a pivotal role in the current social media. The main focus, however, has been on the explicitly generated user content such as photos, videos and status updates on different social networking sites. In this paper, we explore the potential of implicitly generated user content, based on users’ online consumption behaviors. It is technically feasible to record users’ consumption behaviors on mobile devices and share that with relevant people. Mobile devices with such capabilities could enrich social interactions around the consumed content, but it may also threaten users’ privacy. To understand the potentials of this design direction we created and evaluated a low-fidelity prototype intended for photo sharing within private groups. Our prototype incorporates two design concepts, namely, FingerPrint and MoodPhotos that leverage users’ consumption history and emotional responses. In this paper, we report user values and user acceptance of this prototype from three participatory design workshops.

Practices surrounding children's photos in homes

New parents cherish photos of their children. In their homes one can observe a varied set of arrangements of their young ones' photos. We studied eight families with young children to learn about their practices related to photos. We provide preliminary results from the field study and elaborate on three interesting themes that came out very strongly from our data: physical platforms; family dynamics and values; and creative uses of photos. These themes provide an insight into families' perceived values for photo curating, displaying and experiencing them over a longer period. We provide future directions for supporting practices surrounding children's photos.

Assessing exposure to polybrominated diphenyl ethers (PBDEs) for workers in the vicinity of a large recycling facility

Increased levels of polybrominated diphenyl ethers (PBDEs) can occur particularly in dust and soil surrounding facilities that recycle products containing PBDEs. This may be the source of increased exposure for nearby workers and residents. To investigate, we measured PBDE levels in soil, office dust and blood of workers at the closest workplace (i.e. within 100m) to a large automotive shredding and metal recycling facility in Brisbane, Australia. The workplace investigated in this study was independent of the automotive shredding facility and was one of approximately 50 businesses of varying types within a relatively large commercial/industrial area surrounding the recycling facility. Concentrations of PBDEs in soils were at least an order of magnitude greater than background levels in the area. Congener profiles were dominated by larger molecular weight congeners; in particular BDE-209. This reflected the profile in outdoor air samples previously collected at this site. Biomonitoring data from blood serum indicated no differential exposure for workers near the recycling facility compared to a reference group of office workers, also in Brisbane. Unlike air, indoor dust and soil sample profiles, serum samples from both worker groups were dominated by congeners BDE-47, BDE-153, BDE-99, BDE-100 and BDE-183 and was similar to the profile previously reported in the general Australian population. Estimated exposures for workers near the industrial point source suggested indoor workers had significantly higher exposure than outdoor workers due to their exposure to indoor dust rather than soil. However, no relationship was observed between blood PBDE levels and different roles and activity patterns of workers on-site. These comparisons of PBDE levels in serum provide additional insight into the inter-individual variability within Australia. Results also indicate congener patterns in the workplace environment did not match blood profiles of workers. This was attributed to the relatively high background exposures for the general Australian population via dietary intake and the home environment.

Short term variability in urinary bisphenol A in Australian children

Used frequently in food contact materials, bisphenol A (BPA) has been studied extensively in recent years, and ubiquitous exposure in the general population has been demonstrated worldwide. Characterising within- and between-individual variability of BPA concentrations is important for characterising exposure in biomonitoring studies, and this has been investigated previously in adults, but not in children. The aim of this study was to characterise the short-term variability of BPA in spot urine samples in young children. Children aged ≥2-<4 years (n = 25) were recruited from an existing cohort in Queensland Australia, and donated four spot urine samples each over a two day period. Samples were analysed for total BPA using isotope dilution online solid phase extraction-liquid chromatography-tandem mass spectrometry, and concentrations ranged from 0.53–74.5 ng/ml, with geometric mean and standard deviation of 2.70 ng/ml and 2.94 ng/ml, respectively. Sex and time of sample collection were not significant predictors of BPA concentration. The between-individual variability was approximately equal to the within-individual variability (ICC = 0.51), and this ICC is somewhat higher than previously reported literature values. This may be the result of physiological or behavioural differences between children and adults or of the relatively short exposure window assessed. Using a bootstrapping methodology, a single sample resulted in correct tertile classification approximately 70% of the time. This study suggests that single spot samples obtained from young children provide a reliable characterization of absolute and relative exposure over the short time window studied, but this may not hold true over longer timeframes.

The effectiveness of an intervention in reducing risk of dioxin exposure in Da Nang : changes in community knowledge, attitudes and prevention practices after 2.5 years

Introduction Environmental and biological samples taken around Da Nang Air Base have shown elevated levels of dioxin over many years [1-3]. A pre-intervention knowledge, attitudes and practices (KAP) survey (2009), a risk reduction program (2010) and a post intervention KAP survey (2011) were undertaken in four wards surrounding Danang Airbase. A follow-up evaluation was undertaken in 2013. Methods A KAP survey was implemented among 400 randomly selected food handlers. Eleven indepth interviews and four focus group discussions were also undertaken. Results The knowledge of respondents remained positive and/or improved at 2.5 years follow-up. There were no significant differences in attitudes toward preventing dioxin exposure across surveys; most respondents were positive in all three surveys. An increase in households (69.5%) undertaking measures to prevent exposure was observed, which was higher than in the pre-intervention survey (39.6%) and post- intervention survey (60.4%) (χ2 = 95.6; p < 0.001). The proportion of respondents practicing appropriate preventive measures was also significantly improved. Conclusions Despite most of the intervention program’s activities ceasing in 2010, the risk reduction program has resulted in positive outcomes over the longer-term, with many knowledge and attitude measures remaining stable or imporving. Some KAP indicators decreased, but these KAP indicators were still significantly higher than the pre-intervention levels.

Reply to the comments on “A study of the phosphate mineral kapundaite NaCa(Fe3+)4(PO4)4(OH)3·5(H2O) using SEM/EDX and vibrational spectroscopic methods” by Frost et al. (2014)

"The authors agree with the statements made by Mills and Christy on the study of kapundaite [1]. These authors are correct and have removed any confusion about the origin of the sample kapundaite. The authors (Frost et al.) confirm the sample of kapundaite studied in this work is from the Tom‘s quarry, Australia and can be considered a type material. The authors do not accept the statements by Mills and Christy on “type minerals”. The sample of kapundaite from the Australian source is from the collection of the Geology Department of the Federal University of Ouro Preto, Minas Gerais, Brazil with sample code SAC-111. At least if our mineral sample is not a co-type mineral, our sample is from the same origin as the type mineral. Samples..."--publisher website.

Why are there Different Age Related Trends for Different Chemicals?

Persistent organic pollutants (POPs) such as dioxins, PCBs, persistent organochlorine pesticides (OCPs) and polybrominated diphenyl ethers (PBDEs) as well as perfluorinated compounds (PFCs) and triclosan are ubiquitous in the human population. In Australia, we have pooled and subsequently analysed over 10 000 human serum samples for the determination of these chemicals by age group (0–0.5; 0.6–1; 1.1–1.5; 1.6–2; 2.1–2.5; 2.6–3; 3.1–3.5; 3.6–4; 4.1–6; 6.1–9; 9.1–12; 12.1–15; 16–30; 31–45; 46–60 and >60 years) and gender. The results of this analysis were then used to assess the trends of these different chemicals as a function of age, gender and to a lesser extent region. Our data demonstrate clear chemical specific age trends. In particular we demonstrate that for the traditional POPs there is an increase in body burden with age whereas the opposite is true for chemicals such as PBDEs. For PFCs we find chemical specific age trends that vary from compound to compound. For triclosan we show that no apparent age trend is observable. The results of the study and its implications to the collection and archiving of samples for retrospective analysis are discussed.