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.

Practical aspects of frequency-domain identification of dynamic models of marine structures from hydrodynamic data

The motion response of marine structures in waves can be studied using finite-dimensional linear-time-invariant approximating models. These models, obtained using system identification with data computed by hydrodynamic codes, find application in offshore training simulators, hardware-in-the-loop simulators for positioning control testing, and also in initial designs of wave-energy conversion devices. Different proposals have appeared in the literature to address the identification problem in both time and frequency domains, and recent work has highlighted the superiority of the frequency-domain methods. This paper summarises practical frequency-domain estimation algorithms that use constraints on model structure and parameters to refine the search of approximating parametric models. Practical issues associated with the identification are discussed, including the influence of radiation model accuracy in force-to-motion models, which are usually the ultimate modelling objective. The illustration examples in the paper are obtained using a freely available MATLAB toolbox developed by the authors, which implements the estimation algorithms described.

Hybrid frequency–time domain models for dynamic response analysis of marine structures

Time-domain models of marine structures based on frequency domain data are usually built upon the Cummins equation. This type of model is a vector integro-differential equation which involves convolution terms. These convolution terms are not convenient for analysis and design of motion control systems. In addition, these models are not efficient with respect to simulation time, and ease of implementation in standard simulation packages. For these reasons, different methods have been proposed in the literature as approximate alternative representations of the convolutions. Because the convolution is a linear operation, different approaches can be followed to obtain an approximately equivalent linear system in the form of either transfer function or state-space models. This process involves the use of system identification, and several options are available depending on how the identification problem is posed. This raises the question whether one method is better than the others. This paper therefore has three objectives. The first objective is to revisit some of the methods for replacing the convolutions, which have been reported in different areas of analysis of marine systems: hydrodynamics, wave energy conversion, and motion control systems. The second objective is to compare the different methods in terms of complexity and performance. For this purpose, a model for the response in the vertical plane of a modern containership is considered. The third objective is to describe the implementation of the resulting model in the standard simulation environment Matlab/Simulink.

Domain-specific application analysis for customized instruction identification

With the increasing importance of Application Domain Specific Processor (ADSP) design, a significant challenge is to identify special-purpose operations for implementation as a customized instruction. While many methodologies have been proposed for this purpose, they all work for a single algorithm chosen from the target application domain. Such algorithm-specific approaches are not suitable for designing instruction sets applicable to a whole family of related algorithms. For an entire range of related algorithms, this paper develops a methodology for identifying compound operations, as a basis for designing “domain-specific” Instruction Set Architectures (ISAs) that can efficiently run most of the algorithms in a given domain. Our methodology combines three different static analysis techniques to identify instruction sequences common to several related algorithms: identification of (non-branching) instruction sequences that occur commonly across the algorithms; identification of instruction sequences nested within iterative constructs that are thus executed frequently; and identification of commonly-occurring instruction sequences that span basic blocks. Choosing different combinations of these results enables us to design domain-specific special operations with different desired characteristics, such as performance or suitability as a library function. To demonstrate our approach, case studies are carried out for a family of thirteen string matching algorithms. Finally, the validity of our static analysis results is confirmed through independent dynamic analysis experiments and performance improvement measurements.

Exploring the impact of shared domain knowledge on strategic alignment in the Australian public sector

In this age of ever-increasing information technology (IT) driven environments, governments/or public sector organisations (PSOs) are expected to demonstrate the business value of the investment in IT and take advantage of the opportunities offered by technological advancements. Strategic alignment (SA) emerged as a mechanism to bridge the gap between business and IT missions, objectives, and plans in order to ensure value optimisation from investment in IT and enhance organisational performance. However, achieving and sustaining SA remains a challenge requiring even more agility nowadays to keep up with turbulent organisational environments. The shared domain knowledge (SDK) between the IT department and other diverse organisational groups is considered as one of the factors influencing the successful implementation of SA. However, SDK in PSOs has received relatively little empirical attention. This paper presents findings from a study which investigated the influence of SDK on SA within organisations in the Australian public sector. The developed research model examined the relationship of SDK between business and IT domains with SA using a survey of 56 public sector professionals and executives. A key research contribution is the empirical demonstration that increasing levels of SDK between IT and business groups leads to increased SA.

Knowledge work at the boundary : making a difference to educational disadvantage

This paper aims to contribute to the literature about boundary crossing and explicate how boundaries carry learning potential. We aim to do this by theorising the work of school-based researchers (SBRs) in a school–university partnership project aimed at addressing issues of educational disadvantage. We conceptualise the worlds of teaching and research as characterised by different types of knowledge work and ways of knowing, and by different interaction rituals and emotional investments for engaging with that knowledge. Yet we also contend that the practice boundary that separates also connects and intertwines, as people, objects and knowledge move back and forth across it and become transformed in the process. We suggest that the kind of transformative knowledge work discussed in this paper entails understanding the power and control relations involved in recontextualising knowledge as it moves across the research–practice gap. This process necessitates recognising and acknowledging the emotional investments, energies and interaction rituals attached to local, domain specific knowledge and ways of knowing. By discussing the work of school-based researchers we aim to show how processes of recontextualisation at the boundary between researcher and practitioner knowledge can hold the potential to make a difference to issues of seemingly entrenched educational disadvantage.

Observing privacy, modesty and hospitality in the home domain : three case studies of Muslim homes in Brisbane, Australia

A home embodies a sensorial space that is layered with personal memories and traces of history. The success of a home in providing a strong sense of place depends on various factors such as geographical location, climatic conditions, and occupants’ world-views and perceptions. This paper explores Muslims’ perceptions of privacy, modesty and hospitality within their homes through their lived experiences. This case study focuses on three Muslim families living in Australian designed homes within the same suburb of Brisbane, Australia. The study provides prefatory insight into the ways in which these families perform their daily activities and entertain their guests without jeopardizing their privacy needs. The study examines the significance of modesty in the design of Muslim homes as a means by which family members are able to achieve optimum privacy while simultaneously extending hospitality to guests inside and outside their homes. The findings of this study provide opportunities too, for expanding research into culturally adaptable housing systems to help meet the changing needs of Australian multicultural society.

A semi-alternating direction method for a 2-D fractional FitzHugh–Nagumo monodomain model on an approximate irregular domain

A FitzHugh-Nagumo monodomain model has been used to describe the propagation of the electrical potential in heterogeneous cardiac tissue. In this paper, we consider a two-dimensional fractional FitzHugh-Nagumo monodomain model on an irregular domain. The model consists of a coupled Riesz space fractional nonlinear reaction-diffusion model and an ordinary differential equation, describing the ionic fluxes as a function of the membrane potential. Secondly, we use a decoupling technique and focus on solving the Riesz space fractional nonlinear reaction-diffusion model. A novel spatially second-order accurate semi-implicit alternating direction method (SIADM) for this model on an approximate irregular domain is proposed. Thirdly, stability and convergence of the SIADM are proved. Finally, some numerical examples are given to support our theoretical analysis and these numerical techniques are employed to simulate a two-dimensional fractional Fitzhugh-Nagumo model on both an approximate circular and an approximate irregular domain.

Improving out-domain PLDA speaker verification using unsupervised inter-dataset variability compensation approach

Experimental studies have found that when the state-of-the-art probabilistic linear discriminant analysis (PLDA) speaker verification systems are trained using out-domain data, it significantly affects speaker verification performance due to the mismatch between development data and evaluation data. To overcome this problem we propose a novel unsupervised inter dataset variability (IDV) compensation approach to compensate the dataset mismatch. IDV-compensated PLDA system achieves over 10% relative improvement in EER values over out-domain PLDA system by effectively compensating the mismatch between in-domain and out-domain data.

A new public health context to understand male sex work

Background Researching male sex work offers insight into the sexual lives of men and women while developing a more realistic appreciation for the changing issues associated with male sex work. This type of research is important because it not only reflects a growing and diversifying consumer demand for male sex work, but also because it enables the construction of knowledge that is up-to-date with changing ideas around sex and sexualities. Discussion This paper discusses a range of issues emerging in the male sex industry. Notably, globalisation and technology have contributed to the normalisation of male sex work and reshaped the landscape in which the male sex industry operates. As part of this discussion, we review STI and HIV rates among male sex workers at a global level, which are widely disparate and geographically contextual, with rates of HIV among male sex workers ranging from 0% in some areas to 50% in others. The Internet has reshaped the way that male sex workers and clients connect and has been identified as a useful space for safer sex messages and research that seeks out hidden or commonly excluded populations. Future directions We argue for a public health context that recognises the emerging and changing nature of male sex work, which means programs and policies that are appropriate for this population group. Online communities relating to male sex work are important avenues for safer sexual messages and unique opportunities to reach often excluded sub-populations of both clients and male sex workers. The changing structure and organisation of male sex work alongside rapidly changing cultural, academic and medical discourses provide new insight but also new challenges to how we conceive the sexualities of men and male sex workers. Public health initiatives must reflect upon and incorporate this knowledge.

The tumour-promoting receptor tyrosine kinase, EphB4, regulates expression of Integrin-β8 in prostate cancer cells

Background The EphB4 receptor tyrosine kinase is overexpressed in many cancers including prostate cancer. The molecular mechanisms by which this ephrin receptor influences cancer progression are complex as there are tumor-promoting ligand-independent mechanisms in place as well as ligand-dependent tumor suppressive pathways. Methods We employed transient knockdown of EPHB4 in prostate cancer cells, coupled with gene microarray analysis, to identify genes that were regulated by EPHB4 and may represent linked tumor-promoting factors. We validated target genes using qRT-PCR and employed functional assays to determine their role in prostate cancer migration and invasion. Results We discovered that over 500 genes were deregulated upon EPHB4 siRNA knockdown, with integrin β8 (ITGB8) being the top hit (29-fold down-regulated compared to negative non-silencing siRNA). Gene ontology analysis found that the process of cell adhesion was highly deregulated and two other integrin genes, ITGA3 and ITGA10, were also differentially expressed. In parallel, we also discovered that over-expression of EPHB4 led to a concomitant increase in ITGB8 expression. In silico analysis of a prostate cancer progression microarray publically available in the Oncomine database showed that both EPHB4 and ITGB8 are highly expressed in prostatic intraepithelial neoplasia, the precursor to prostate cancer. Knockdown of ITGB8 in PC-3 and 22Rv1 prostate cancer cells in vitro resulted in significant reduction of cell migration and invasion. Conclusions These results reveal that EphB4 regulates integrin β8 expression and that integrin β8 plays a hitherto unrecognized role in the motility of prostate cancer cells and thus targeting integrin β8 may be a new treatment strategy for prostate cancer.

The development and refinement of the practice domain framework as a conceptual tool for understanding and guiding social care practice

This study identified the common factors that influence social care practice across disciplines (such as social work and psychology), practice fields, and geographical contexts and further developed the Practice Domain Framework as an empirically-based conceptual framework to assist practitioners in understanding practice complexities. The framework has application in critical reflection, professional supervision, interdisciplinary understanding, teamwork, management, teaching and research. A mixed-methods design was used to identify the components and structure of the refined framework. Eighteen influential factors were identified and organised into eight domains: the Societal, Structural, Organisational, Practice Field, Professional Practice, Accountable Practice, Community of Place, and Personal.

The chromosome 16q region associated with ankylosing spondylitis includes the candidate gene tumour necrosis factor receptor type 1-associated death domain (TRADD)

Objective: To replicate and refine the reported association of ankylosing spondylitis (AS) with two nonsynonymous single nucleotide polymorphisms (nsSNPs) on chromosome 16q22.1. Methods: Firstly, 730 independent UK patients with AS were genotyped for rs9939768 and rs6979 and allele frequencies were compared with 2879 previously typed historic disease controls. Secondly, the two data sets were combined in meta-analyses. Finally, 5 tagging SNPs, located between rs9939768 and rs6979, were analysed in 1604 cases and 1020 controls. Results: The association of rs6979 with AS was replicated, p=0.03, OR=1.14 (95% CI 1.01 to 1.28), and a trend for association with rs9939768 detected, p=0.06, OR=1.25 (95% CI 0.99 to 1.57). Meta-analyses revealed association of both SNPs with AS, p=0.0008, OR=1.31 (95% CI 1.12 to 1.54) and p=0.0009, OR=1.15 (95% CI 1.06 to 1.23) for rs9939768 and rs6979, respectively. New associations with rs9033 and rs868213 (p=0.00002, OR=1.23 (95% CI 1.12 to 1.36) and p=0.00002 OR=1.45 (95% CI 1.22 to 1.72), respectively, were identified. Conclusions: The region on chromosome 16 that has been replicated in the present work is interesting as the highly plausible candidate gene, tumour necrosis factor receptor type 1 (TNFR1)-associated death domain (TRADD), is located between rs9033 and rs868213. It will require additional work to identify the primary genetic association(s) with AS.

The return to work experiences of middle-aged Australian workers diagnosed with colorectal cancer: a matched cohort study

Background Few studies have been undertaken to understand the employment impact in patients with colorectal cancer and none in middle-aged individuals with cancer. This study described transitions in, and key factors influencing, work participation during the 12 months following a diagnosis of colorectal cancer. Methods We enrolled 239 adults during 2010 and 2011who were employed at the time of their colorectal cancer diagnosis and were prospectively followed over 12 months. They were compared to an age- and gender-matched general population group of 717 adults from the Household, Income and Labour Dynamics in Australia (HILDA) Survey. Data were collected using telephone and postal surveys. Primary outcomes included work participation at 12 months, changes in hours worked and time to work re-entry. Multivariable logistic and Cox proportional hazards models were undertaken. Results A significantly higher proportion of participants with colorectal cancer (27%) had stopped working at 12 months than participants from the comparison group (8%) (p < 0.001). Participants with cancer who returned to work took a median of 91 days off work (25–75 percentiles: 14–183 days). For participants with cancer, predictors of not working at 12 months included: being older, lower BMI and lower physical well-being. Factors related to delayed work re-entry included not being university-educated, working for an employer with more than 20 employees in a non-professional or managerial role, longer hospital stay, poorer perceived financial status and having or had chemotherapy. Conclusions In middle-adulthood, those working and diagnosed with colorectal cancer can expect to take around three months off work. Individuals treated with chemotherapy, without a university degree and from large employers could be targeted for specific assistance for a more timely work entry.

Exact solutions of coupled multispecies linear reaction–diffusion equations on a uniformly growing domain

Embryonic development involves diffusion and proliferation of cells, as well as diffusion and reaction of molecules, within growing tissues. Mathematical models of these processes often involve reaction–diffusion equations on growing domains that have been primarily studied using approximate numerical solutions. Recently, we have shown how to obtain an exact solution to a single, uncoupled, linear reaction–diffusion equation on a growing domain, 0 < x < L(t), where L(t) is the domain length. The present work is an extension of our previous study, and we illustrate how to solve a system of coupled reaction–diffusion equations on a growing domain. This system of equations can be used to study the spatial and temporal distributions of different generations of cells within a population that diffuses and proliferates within a growing tissue. The exact solution is obtained by applying an uncoupling transformation, and the uncoupled equations are solved separately before applying the inverse uncoupling transformation to give the coupled solution. We present several example calculations to illustrate different types of behaviour. The first example calculation corresponds to a situation where the initially–confined population diffuses sufficiently slowly that it is unable to reach the moving boundary at x = L(t). In contrast, the second example calculation corresponds to a situation where the initially–confined population is able to overcome the domain growth and reach the moving boundary at x = L(t). In its basic format, the uncoupling transformation at first appears to be restricted to deal only with the case where each generation of cells has a distinct proliferation rate. However, we also demonstrate how the uncoupling transformation can be used when each generation has the same proliferation rate by evaluating the exact solutions as an appropriate limit.