Active learning: A step towards automating medical concept extraction

Objective This paper presents an automatic active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort, and (2) the robustness of incremental active learning framework across different selection criteria and datasets is determined. Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional Random Fields as the supervised method, and least confidence and information density as two selection criteria for active learning framework were used. The effect of incremental learning vs. standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. Two clinical datasets were used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared to the Random sampling baseline, the saving is at least doubled. Discussion Incremental active learning guarantees robustness across all selection criteria and datasets. The reduction of annotation effort is always above random sampling and longest sequence baselines. Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models, while significantly reducing the burden of manual annotation.

Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Genetic correlation (rg) analysis determines how much of the correlation between two measures is due to common genetic influences. In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on white matter integrity, measured by fractional anisotropy (FA), at all points of the brain, yielding an NxN genetic correlation matrix rg(x,y) between FA values at all pairs of voxels in the brain. With hierarchical clustering, we identified brain regions with relatively homogeneous genetic determinants, to boost the power to identify causal single nucleotide polymorphisms (SNP). We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix. We identified a network of genes, with a scale-free topology, that influences white matter integrity over multiple brain regions.

Putting an "end" to the motor cortex representations of action words

Language processing is an example of implicit learning of multiple statistical cues that provide probabilistic information regarding word structure and use. Much of the current debate about language embodiment is devoted to how action words are represented in the brain, with motor cortex activity evoked by these words assumed to selectively reflect conceptual content and/or its simulation. We investigated whether motor cortex activity evoked by manual action words (e.g., caress) might reflect sensitivity to probabilistic orthographic-phonological cues to grammatical category embedded within individual words. We first review neuroimaging data demonstrating that nonwords evoke activity much more reliably than action words along the entire motor strip, encompassing regions proposed to be action category specific. Using fMRI, we found that disyllabic words denoting manual actions evoked increased motor cortex activity compared with non-body-part-related words (e.g., canyon), activity which overlaps that evoked by observing and executing hand movements. This result is typically interpreted in support of language embodiment. Crucially, we also found that disyllabic nonwords containing endings with probabilistic cues predictive of verb status (e.g., -eve) evoked increased activity compared with nonwords with endings predictive of noun status (e.g., -age) in the identical motor area. Thus, motor cortex responses to action words cannot be assumed to selectively reflect conceptual content and/or its simulation. Our results clearly demonstrate motor cortex activity reflects implicit processing of ortho-phonological statistical regularities that help to distinguish a word's grammatical class.

Action word meaning representations in cytoarchitectonically defined primary and premotor cortices

Recent models of language comprehension have assumed a tight coupling between the semantic representations of action words and cortical motor areas. We combined functional MRI with cytoarchitectonically defined probabilistic maps of left hemisphere primary and premotor cortices to analyse responses of functionally delineated execution- and observation-related regions during comprehension of action word meanings associated with specific effectors (e.g., punch, bite or stomp) and processing of items with various levels of lexical information (non body part-related meanings, nonwords, and visual character strings). The comprehension of effector specific action word meanings did not elicit preferential activity corresponding to the somatotopic organisation of effectors in either primary or premotor cortex. However, generic action word meanings did show increased BOLD signal responses compared to all other classes of lexical stimuli in the pre-SMA. As expected, the majority of the BOLD responses elicited by the lexical stimuli were in association cortex adjacent to the motor areas. We contrast our results with those of previous studies reporting significant effects for only 1 or 2 effectors outside cytoarchitectonically defined motor regions and discuss the importance of controlling for potentially confounding lexical variables such as imageability. We conclude that there is no strong evidence for a somatotopic organisation of action word meaning representations and argue the pre-SMA might have a role in maintaining abstract representations of action words as instructional cues.

One-step synthesis of high quality kesterite Cu2ZnSnS4nanocrystals: A hydrothermal approach

The present work demonstrates a systematic approach for the synthesis of pure kesterite-phase Cu2ZnSnS4 (CZTS) nanocrystals with a uniform size distribution by a one-step, thioglycolic acid (TGA)-assisted hydrothermal route. The formation mechanism and the role of TGA in the formation of CZTS compound were thoroughly studied. It has been found that TGA interacted with Cu2+ to form Cu+ at the initial reaction stage and controlled the crystal-growth of CZTS nanocrystals during the hydrothermal reaction. The consequence of the reduction of Cu2+ to Cu+ led to the formation Cu2−xS nuclei, which acted as the crystal framework for the formation of CZTS compound. CZTS was formed by the diffusion of Zn2+ and Sn4+ cations to the lattice of Cu2−xS during the hydrothermal reaction. The as-synthesized CZTS nanocrystals exhibited strong light absorption over the range of wavelength beyond 1000 nm. The band gap of the material was determined to be 1.51 eV, which is optimal for application in photoelectric energy conversion device.

The Step approach to Message Design and Testing (SatMDT): A conceptual framework to guide the development and evaluation of persuasive health messages

This paper provides an important and timely overview of a conceptual framework designed to assist with the development of message content, as well as the evaluation, of persuasive health messages. While an earlier version of this framework was presented in a prior publication by the authors in 2009, important refinements to the framework have seen it evolve in recent years, warranting the need for an updated review. This paper outlines the Step approach to Message Design and Testing (or SatMDT) in accordance with the theoretical evidence which underpins, as well as empirical evidence which demonstrates the relevance and feasibility, of each of the framework’s steps. The development and testing of the framework have thus far been based exclusively within the road safety advertising context; however, the view expressed herein is that the framework may have broader appeal and application to the health persuasion context.

The alchemy of junk: patent law and non-coding DNA

This article considers the recent international controversy over the patents held by a Melbourne firm, Genetic Technologies Limited (GTG), in respect of non-coding DNA and genomic mapping. It explores the ramifications of the GTG dispute in terms of licensing, litigation, and policy reform, and—as a result of this dispute—the perceived conflict between law and science. GTG has embarked upon an ambitious licensing program with twenty seven commercial licensees and five research licensees. Most significantly, GTG has obtained an exclusive licence from Myriad Genetics to use and exploit its medical diagnostics in Australia, New Zealand, and the Asia-Pacific region. In the US, GTG brought a legal action for patent infringement against the Applera Corporation and its subsidiaries. In response, Applera counterclaimed that the patents of GTG were invalid because they failed to comply with the requirements of US patent law, such as novelty, inventive step, and written specifications. In New Zealand, the Auckland District Health Board brought legal action in the High Court, seeking a declaration that the patents of GTG were invalid, and that, in any case, the Board has not infringed them. The New Zealand Ministry of Health and the Ministry of Economic Development have reported to Cabinet on the issues relating to the patenting of genetic material. Similarly, the Australian Law Reform Commission (ALRC) has also engaged in an inquiry into gene patents and human health; and the Advisory Council on Intellectual Property (ACIP) has considered whether there should be a new defence in respect of experimental use and research.

Mobilising School and Community Engagement to Implement Disability-Inclusive Education through Action Research: Fiji, Samoa, Solomon Islands and Vanuatu

This publication emanates from the four-country research project entitled “Strengthening capacity for disability-inclusive education development policy formulation, implementation and monitoring in the South Pacific region” funded by the Australian Development Research Award Scheme (ADRAS) and conducted jointly by the academic staff from the Queensland University of Technology and the University of the South Pacific.

Developing pictorial conceptual metaphors as a means of understanding and changing the Australian health system for Indigenous people

This paper describes the development of Pictorial Conceptual Metaphors, created out of a literature review on gendered Indigenous health and wellbeing that depicts the inherited effects of the ‘system’ past, present and future. The Pictorial Conceptual Metaphors are pictures that were created to tell the story of colonisation and its inherited and ongoing impacts on Indigenous people’s health and wellbeing. Aboriginal historical experiences, past, present and future are briefly overviewed in order to unpack and communicate to readers the significance and impact of these experiences on Aboriginal health, and ultimately, to bring about understanding to initiate change within the Australian health system. Systemic racism, embedded in the Australian health system, excludes and discriminates against Indigenous peoples through a lack of cultural consideration resulting in a cumulative and ongoing negative effect on Indigenous people’s health (Dudgeon et al. 2014; Fredericks 2008; Marmot 2011; Queensland Government 2012). Systemic action research identifies actions and processes in large systems such as health and education in order to bring about systemic change. Our intention to highlight the systemic changes needed in the Australian health system to improve Indigenous people’s health and wellbeing require us to understand the processes involved in bringing about systemic change. For this to occur, we needed to ‘see the system’ in order to identify the system dynamics in operation. The Pictorial Conceptual Metaphors are the first step in ‘seeing the system’; they illustrate the past and the present, and identify the preferred future for Indigenous health and wellbeing outcomes

Urban informatics beyond data: Media architecture, placemaking, and citizen action

Since 2006, we have been conducting urban informatics research that we define as “the study, design, and practice of urban experiences across different urban contexts that are created by new opportunities of real-time, ubiquitous technology and the augmentation that mediates the physical and digital layers of people networks and urban infrastructures” [1]. Various new research initiatives under the label “urban informatics” have been started since then by universities (e.g., NYU’s Center for Urban Science and Progress) and industry (e.g., Arup, McKinsey) worldwide. Yet, many of these new initiatives are limited to what Townsend calls, “data-driven approaches to urban improvement” [2]. One of the key challenges is that any quantity of aggregated data does not easily translate directly into quality insights to better understand cities. In this talk, I will raise questions about the purpose of urban informatics research beyond data, and show examples of media architecture, participatory city making, and citizen activism. I argue for (1) broadening the disciplinary foundations that urban science approaches draw on; (2) maintaining a hybrid perspective that considers both the bird’s eye view as well as the citizen’s view, and; (3) employing design research to not be limited to just understanding, but to bring about actionable knowledge that will drive change for good.

A rapid and efficient two-step gel electrophoresis method for the purification of major rye grass pollen allergens

Purified proteins are mandatory for molecular, immunological and cellular studies. However, purification of proteins from complex mixtures requires specialised chromatography methods (i.e., gel filtration, ion exchange, etc.) using fast protein liquid chromatography (FPLC) or high-performance liquid chromatography (HPLC) systems. Such systems are expensive and certain proteins require two or more different steps for sufficient purity and generally result in low recovery. The aim of this study was to develop a rapid, inexpensive and efficient gel-electrophoresis-based protein purification method using basic and readily available laboratory equipment. We have used crude rye grass pollen extract to purify the major allergens Lol p 1 and Lol p 5 as the model protein candidates. Total proteins were resolved on large primary gel and Coomassie Brilliant Blue (CBB)-stained Lol p 1/5 allergens were excised and purified on a secondary "mini"-gel. Purified proteins were extracted from unstained separating gels and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot analyses. Silver-stained SDS-PAGE gels resolved pure proteins (i.e., 875 μg of Lol p 1 recovered from a 8 mg crude starting material) while immunoblot analysis confirmed immunological reactivity of the purified proteins. Such a purification method is rapid, inexpensive, and efficient in generating proteins of sufficient purity for use in monoclonal antibody (mAb) production, protein sequencing and general molecular, immunological, and cellular studies.

Co-benefits of addressing climate change can motivate action around the world

Personal and political action on climate change is traditionally thought to be motivated by people accepting its reality and importance. However, convincing the public that climate change is real faces powerful ideological obstacles1, 2, 3, 4, and climate change is slipping in public importance in many countries5, 6. Here we investigate a different approach, identifying whether potential co-benefits of addressing climate change7 could motivate pro-environmental behaviour around the world for both those convinced and unconvinced that climate change is real. We describe an integrated framework for assessing beliefs about co-benefits8, distinguishing social conditions (for example, economic development, reduced pollution or disease) and community character (for example, benevolence, competence). Data from all inhabited continents (24 countries; 6,196 participants) showed that two co-benefit types, Development (economic and scientific advancement) and Benevolence (a more moral and caring community), motivated public, private and financial actions to address climate change to a similar degree as believing climate change is important. Critically, relationships were similar for both convinced and unconvinced participants, showing that co-benefits can motivate action across ideological divides. These relationships were also independent of perceived climate change importance, and could not be explained by political ideology, age, or gender. Communicating co-benefits could motivate action on climate change where traditional approaches have stalled.

Final report of Working Group 2: Traffic psychology [A COST Action TU1101 / HOPE collaboration]

BACKGROUND The workgroup of Traffic Psychology is concerned with the social, behavioral, and perceptual aspects that are associated with use and non-use of bicycle helmets, in their various forms and under various cycling conditions. OBJECTIVES The objectives of WG2 are to (1) share current knowledge among the people already working in the field, (2) suggest new ideas for research on and evaluation of the design of bicycle helmets, and (3) discuss options for funding of such research within the individual frameworks of the participants. Areas for research include 3.1. The patterns of use of helmets among different users: children, adults, and sports enthusiasts. 3.2. The use of helmets in different environments: rural roads, urban streets, and bike trails. 3.3. Concerns bicyclists have relative to their safety and convenience and the perceived impact of using helmets on comfort and convenience. 3.4. The benefit of helmets for enhancing visibility, and how variations in helmet design and colors affect daytime, nighttime, and dusktime visibility. 3.5. The role of helmets in the acceptance of city-wide pickup-and-drop-off bicycles. 3.6. The impact of helmets on visual search behaviour of bicyclists.

A comparative study of two design charrettes: Implications for codesign and participatory action research

The purpose of this paper is to explore how participatory prototyping, through the use of design charrettes, can advance participatory action research (PAR) approaches and contribute to codesign practices in organisational settings. This will be achieved through the comparison of two varying design charrette experiences from a PAR initiative to redesign spaces in the Auraria Library in Denver, Colorado. Each design charrette followed a three-stage sequence of information sharing, idea generation and prototyping, and prioritisation with each stage building upon the former, both in terms of design concepts and in building up elements of ‘making’. While both charrette structures were similar, leadership and execution varied considerably. Lessons learned from the two design charrette experiences are presented, including the value of participatory prototyping within PAR to support ‘research through design’ activities. In addition, it highlights the value of authentic design participation of ‘designing with’ rather than ‘designing for’ to encourage optimal design outcomes.