Graph-based concept weighting for medical information retrieval

This paper presents a graph-based method to weight medical concepts in documents for the purposes of information retrieval. Medical concepts are extracted from free-text documents using a state-of-the-art technique that maps n-grams to concepts from the SNOMED CT medical ontology. In our graph-based concept representation, concepts are vertices in a graph built from a document, edges represent associations between concepts. This representation naturally captures dependencies between concepts, an important requirement for interpreting medical text, and a feature lacking in bag-of-words representations. We apply existing graph-based term weighting methods to weight medical concepts. Using concepts rather than terms addresses vocabulary mismatch as well as encapsulates terms belonging to a single medical entity into a single concept. In addition, we further extend previous graph-based approaches by injecting domain knowledge that estimates the importance of a concept within the global medical domain. Retrieval experiments on the TREC Medical Records collection show our method outperforms both term and concept baselines. More generally, this work provides a means of integrating background knowledge contained in medical ontologies into data-driven information retrieval approaches.

Natural history of trees

Courtney Pedersen and Charles Robb's A Natural History of Trees was a installation mounted at Blindside ARI in Melbourne's CBD in 2012. The work took the form of a pine-panelled room containing a pair of life-sized tree trunks composed entirely of stacks of cut paper discs. A faux bois stool reinforced the sense of artificiality. Claustrophic and precarious, the installation was simultaneously a response to the complexity of our relationship with nature and place, and an evocation of the precarious quality of the collaborative process. The exhibition was accompanied by a catalogue with an essay by writer/curator, Jane O'Neill.

Words and Silences : The journal of the International Oral History Association

Words and Silences is the official on-line journal of the International Oral History Association. It is an internationally peer reviewed, high quality forum for oral historians from a wide range of disciplines and a means for the professional community to share projects and current trends of oral history from around the world. We are extremely pleased to release the first online issue of Word &Silences. This e-journal is the result of long standing discussion and debate about the best way to publish a quality bilingual oral history journal (including a blind peer reviewed section) as a viable solution to mounting difficulties associated with publishing in print. We have discovered that an online version is also not without its challenges and requires tremendous labor intensive dedication. We strongly encourage members to assist us with small review process tasks in the future, so that we can ensure the sustainability of an annual W&S publication for our members and beyond.

Risk factors for moderate and severe microbial keratitis in daily wear contact lens users

Objective: To establish risk factors for moderate and severe microbial keratitis among daily contact lens (CL) wearers in Australia. Design: A prospective, 12-month, population-based, case-control study. Participants: New cases of moderate and severe microbial keratitis in daily wear CL users presenting in Australia over a 12-month period were identified through surveillance of all ophthalmic practitioners. Case detection was augmented by record audits at major ophthalmic centers. Controls were users of daily wear CLs in the community identified using a national telephone survey. Testing: Cases and controls were interviewed by telephone to determine subject demographics and CL wear history. Multiple binary logistic regression was used to determine independent risk factors and univariate population attributable risk percentage (PAR%) was estimated for each risk factor.; Main Outcome Measures: Independent risk factors, relative risk (with 95% confidence intervals [CIs]), and PAR%. Results: There were 90 eligible moderate and severe cases related to daily wear of CLs reported during the study period. We identified 1090 community controls using daily wear CLs. Independent risk factors for moderate and severe keratitis while adjusting for age, gender, and lens material type included poor storage case hygiene 6.4× (95% CI, 1.9-21.8; PAR, 49%), infrequent storage case replacement 5.4× (95% CI, 1.5-18.9; PAR, 27%), solution type 7.2× (95% CI, 2.3-22.5; PAR, 35%), occasional overnight lens use (<1 night per week) 6.5× (95% CI, 1.3-31.7; PAR, 23%), high socioeconomic status 4.1× (95% CI, 1.2-14.4; PAR, 31%), and smoking 3.7× (95% CI, 1.1-12.8; PAR, 31%). Conclusions: Moderate and severe microbial keratitis associated with daily use of CLs was independently associated with factors likely to cause contamination of CL storage cases (frequency of storage case replacement, hygiene, and solution type). Other factors included occasional overnight use of CLs, smoking, and socioeconomic class. Disease load may be considerably reduced by attention to modifiable risk factors related to CL storage case practice.

Disaster strikes, then what? Using evaluation in narrative driven (oral history & digital storytelling) community-based projects

In 2011 Queensland suffered both floods and cyclones, leaving residents without homes and their communities in ruins (2011). This paper presents how researchers from QUT, who are also members of the Oral History Association of Australia (OHAA) Queensland’s chapter, are using oral history, photographs, videography and digital storytelling to help heal and empower rural communities around the state and how evaluation has become a key element of our research. QUT researchers ran storytelling workshops in the capital city of Brisbane i early 2011, after the city suffered sever flooding. Cyclone Yasi then struck the town of Cardwell (in February 2011) destroying their historical museum and recording equipment. We delivered an 'emergency workshop', offering participants hands on use of the equipment, ethical and interviewing theory, so that the community could start to build a new collection. We included oral history workshops as well as sessions on how best to use a video camera, digital camera and creative writing sessions, so the community would also know how to make 'products' or exhibition pieces out of the interviews they were recording. We returned six months later to conduct follow-up workshops and the material produced by and with the community had been amazing. More funding has now been secured to replicate audio/visual/writing workshops in other remote rural Queensland communities including Townsville, Mackay and Cunnamulla and Toowoomba in 2012, highlighting the need for a multi media approach, to leverage the most out of OH interviews as a mechanism to restore and promote community resilience and pride.

A prospective window into medical device-related pressure ulcers in intensive care

Objective: To determine the prevalence, severity, location, etiology, treatment, and healing of medical device-related pressure ulcers in intensive care patients for up to 7 days. Design: Prospective repeated measures study. Setting and participants: Patients in 6 intensive care units of 2 major medical centers, one each in Australia and the United States, were screened 1 day per month for 6 months. Those with device-related ulcers were followed daily up to 7 days. Outcome measures: Device-related ulcer prevalence, pain, infection, treatment, healing. Results: 15/483 patients had device-related ulcers and 9/15 with 11 ulcers were followed beyond screening. Their mean age was 60.5 years, most were men, over-weight, and at increased pressure ulcer risk. Endotracheal and nasogastric tubes were the cause of most device-related ulcers. Repositioning was the most frequent treatment. 4/11 ulcers healed within the 7 day observation period. Conclusion: Device-related ulcer prevalence was 3.1%, similar to that reported in the limited literature available, indicating an ongoing problem. Systematic assessment and repositioning of devices are the mainstays of care. We recommend continued prevalence determination and that nurses remain vigilant to prevent device-related ulcers, especially in patients with nasogastric and endotracheal tubes.

Michel Foucault : the unconscious of history and culture

Michel Foucault: The unconscious of history and culture The French thinker, Michel Foucault (1926–84), is noted for his extensive and controversial forays into the historical disciplines. When his work first began to circulate in the 1950s and 1960s, historians did not quite know what to make of it and philosophers resented the appearance of what they saw as the importation of the tedium of concrete events into the pure untainted realm of ideas. If these responses to his work remain alive and well decades after Foucault's death, the uptake of his work has become far more complex. To restrict ourselves to the discipline of history here: if one very visible and vocal camp of historians remains deeply ambivalent about his work, this merely disguises the fact that a far larger contingent of historians of all kinds – not just those located in history departments – use his ideas quite unremarkably ...

The largest eruptions in Earth's history

Large igneous provinces (LIPs) host the most frequently recurring, largest volume basaltic & silicic eruptions on Earth. The largest volume (>1000 km^3 DRE) and magnitude (>M8) eruptions produce areally extensive (10^4-10^5 km^2) basaltic flow fields and sills, and silicic ignimbrites that are the main LIP building blocks. Basaltic and silicic eruptions have comparable magnitudes, but silicic ignimbrite volumes may be significantly underestimated due to unrecognized and correlated, but voluminous co-ignimbrite ash deposits. Magma composition is no barrier to individual eruption volume. Despite similar magnitudes, flood basaltic and silicic eruptions are very different in eruption mechanism, duration, intensity, vent configuration, and emplacement style. Flood basalts are dominantly effusive Hawaiian-Strombolian, with magma discharge rates of ~10^7-10^8 kg s^-1, and produce dominantly compound pahoehoe flow fields over eruption durations most likely >10 yrs. Most silicic eruptions are moderately to highly explosive, producing cocurrent pyroclastic fountains (rarely Plinian) and suggested to be of short-duration (hours to days) and high intensity (~10^11 kg s^-1). Eruption frequencies are elevated for largemagnitude eruptions of both magma types during LIP formation. In basalt-dominated provinces, large magnitude (>M8) eruptions have much shorter recurrence intervals (10^3-10^4 years) than similar magnitude silicic eruptions (~10^5 years). The huge volumes of magma erupted rapidly in LIPs raises several unresolved issues in terms of locus of magma generation and storage (if any) in the crust prior to eruption, the paths and rates of ascent from magma reservoirs to the surface, and relative aerosol contributions to the stratosphere from the flood basaltic and rhyolitic eruptions.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

The decline in activities of daily living at discharge (DADLD) index : stratifying patients at lower and higher risk

Background: Decreased ability to perform Activities of Daily Living (ADLs) during hospitalisation has negative consequences for patients and health service delivery. Objective: To develop an Index to stratify patients at lower and higher risk of a significant decline in ability to perform ADLs at discharge. Design: Prospective two cohort study comprising a derivation (n=389; mean age 82.3 years; SD� 7.1) and a validation cohort (n=153; mean age 81.5 years; SD� 6.1). Patients and setting: General medical patients aged = 70 years admitted to three university-affiliated acute care hospitals in Brisbane, Australia. Measurement and main results: The short ADL Scale was used to identify a significant decline in ability to perform ADLs from premorbid to discharge. In the derivation cohort, 77 patients (19.8%) experienced a significant decline. Four significant factors were identified for patients independent at baseline: 'requiring moderate assistance to being totally dependent on others with bathing'; 'difficulty understanding others (frequently or all the time)'; 'requiring moderate assistance to being totally dependent on others with performing housework'; a 'history of experiencing at least one fall in the previous 90 days prior to hospital admission' in addition to 'independent at baseline', which was protective against decline at discharge. 'Difficulty understanding others (frequently or all the time)' and 'requiring moderate assistance to being totally dependent on others with performing housework' were also predictors for patients dependent in ADLs at baseline. Sensitivity, specificity, Positive Predictive Value (PPV), and Negative Predictive Value (NPV) of the DADLD dichotomised risk scores were: 83.1% (95% CI 72.8; 90.7); 60.5% (95% CI 54.8; 65.9); 34.2% (95% CI 27.5; 41.5); 93.5% (95% CI 89.2; 96.5). In the validation cohort, 47 patients (30.7%) experienced a significant decline. Sensitivity, specificity, PPV and NPV of the DADLD were: 78.7% (95% CI 64.3; 89.3); 69.8% (95% CI 60.1, 78.3); 53.6% (95% CI 41.2; 65.7); 88.1% (95% CI 79.2; 94.1). Conclusions: The DADLD Index is a useful tool for identifying patients at higher risk of decline in ability to perform ADLs at discharge.

An evaluation of corpus-driven measures of medical concept similarity for information retrieval

Measures of semantic similarity between medical concepts are central to a number of techniques in medical informatics, including query expansion in medical information retrieval. Previous work has mainly considered thesaurus-based path measures of semantic similarity and has not compared different corpus-driven approaches in depth. We evaluate the effectiveness of eight common corpus-driven measures in capturing semantic relatedness and compare these against human judged concept pairs assessed by medical professionals. Our results show that certain corpus-driven measures correlate strongly (approx 0.8) with human judgements. An important finding is that performance was significantly affected by the choice of corpus used in priming the measure, i.e., used as evidence from which corpus-driven similarities are drawn. This paper provides guidelines for the implementation of semantic similarity measures for medical informatics and concludes with implications for medical information retrieval.

Malaria antibody persistence correlates with duration of exposure

Background and Objectives  In Australia, the risk of transfusion-transmitted malaria is managed through the identification of ‘at-risk’ donors, antibody screening enzyme-linked immunoassay (EIA) and, if reactive, exclusion from fresh blood component manufacture. Donor management depends on the duration of exposure in malarious regions (>6 months: ‘Resident’, <6 months: ‘Visitor’) or a history of malaria diagnosis. We analysed antibody testing and demographic data to investigate antibody persistence dynamics. To assess the yield from retesting 3 years after an initial EIA reactive result, we estimated the proportion of donors who would become non-reactive over this period. Materials and Methods  Test results and demographic data from donors who were malaria EIA reactive were analysed. Time since possible exposure was estimated and antibody survival modelled. Results  Among seroreverters, the time since last possible exposure was significantly shorter in ‘Visitors’ than in ‘Residents’. The antibody survival modelling predicted 20% of previously EIA reactive ‘Visitors’, but only 2% of ‘Residents’ would become non-reactive within 3 years of their first reactive EIA. Conclusion  Antibody persistence in donors correlates with exposure category, with semi-immune ‘Residents’ maintaining detectable antibodies significantly longer than non-immune ‘Visitors’.