Library Research Support in developing, testing and promoting an open cyberinfrastructure

QUT Library continues to rethink research support with eResearch as a primary driver. The support to the development of the Lens, an open global cyberinfrastructure, has been especially important in the light of technology transfer promotion, and partly in the response to researchers’ needs in following the innovation landscapes not only within the scientific but also patent literature. The Lens http://www.lens.org/lens/ project makes innovation more efficient, fair, transparent and inclusive. It is a joint effort between Cambia http://www.cambia.org.au and Queensland University of Technology (QUT). The Lens serves more than 84 million patent documents in the world as open, annotatable digital public goods that are integrated with scholarly and technical literature along with regulatory and business data. Users can link from search results to visualization and document clusters; from a patent document description to its full-text; from there, if applicable, the sequence data can also be found. Figure 1 shows a BLAST Alignment (DNA) using the Lens. A unique feature of the Lens is the ability to embed search and BLAST results into blogs and websites, and provide real-time updates to them. PatSeq Explorer http://www.lens.org/lens/bio/patseqexplorer allows users to navigate patent sequences that map onto the human genome and in the future, many other genomes. PatSeq Explorer offers three level views for the sequence information and links each group of sequences at the chromosomal level to their corresponding patent documents in the Lens. By integrating sequence and patent search and document clustering capabilities, users can now understand the big and small details on the true extent and scope of genetic sequence patents. QUT Library supported Cambia in developing, testing and promoting the Lens. This poster demonstrates QUT Library’s provision of best practice and holistic research support to a research group and how QUT Librarians have acquired new capabilities to meet the needs of the researchers beyond traditional research support practices.

ADMRG @ MediaEval 2013 Social Event Detection

This paper elaborates the approach used by the Applied Data Mining Research Group (ADMRG) for the Social Event Detection (SED) Tasks of the 2013 MediaEval Benchmark. We extended the constrained clustering algorithm to apply to the first semi-supervised clustering task, and we compared several classifiers with Latent Dirichlet Allocation as feature selector in the second event classification task. The proposed approach focuses on scalability and efficient memory allocation when applied to a high dimensional data with large clusters. Results of the first task show the effectiveness of the proposed method. Results from task 2 indicate that attention on the imbalance categories distributions is needed.

Timed Probabilistic Automaton : a bridge between Raven and Song Scope for automatic species recognition

Raven and Song Scope are two automated sound anal-ysis tools based on machine learning technique for en-vironmental monitoring. Many research works have been conducted upon them, however, no or rare explo-ration mentions about the performance and comparison between them. This paper investigates the comparisons from six aspects: theory, software interface, ease of use, detection targets, detection accuracy, and potential application. Through deep exploration one critical gap is identified that there is a lack of approach to detect both syllables and call structures, since Raven only aims to detect syllables while Song Scope targets call structures. Therefore, a Timed Probabilistic Automata (TPA) system is proposed which separates syllables first and clusters them into complex structures after.

Algorithm clustering for multi-algorithm processor design

An Application Specific Instruction-set Processor (ASIP) is a specialized processor tailored to run a particular application/s efficiently. However, when there are multiple candidate applications in the application’s domain it is difficult and time consuming to find optimum set of applications to be implemented. Existing ASIP design approaches perform this selection manually based on a designer’s knowledge. We help in cutting down the number of candidate applications by devising a classification method to cluster similar applications based on the special-purpose operations they share. This provides a significant reduction in the comparison overhead while resulting in customized ASIP instruction sets which can benefit a whole family of related applications. Our method gives users the ability to quantify the degree of similarity between the sets of shared operations to control the size of clusters. A case study involving twelve algorithms confirms that our approach can successfully cluster similar algorithms together based on the similarity of their component operations.

Global gene expression in skeletal muscle from well-trained strength and endurance athletes

PURPOSE: We used gene microarray analysis to compare the global expression profile of genes involved in adaptation to training in skeletal muscle from chronically strength-trained (ST), endurance-trained (ET), and untrained control subjects (Con). METHODS: Resting skeletal muscle samples were obtained from the vastus lateralis of 20 subjects (Con n = 7, ET n = 7, ST n = 6; trained [TR] groups >8 yr specific training). Total RNA was extracted from tissue for two color microarray analysis and quantative (Q)-PCR. Trained subjects were characterized by performance measures of peak oxygen uptake V?O 2peak) on a cycle ergometer and maximal concentric and eccentric leg strength on an isokinetic dynamometer. RESULTS: Two hundred and sixty-three genes were differentially expressed in trained subjects (ET + ST) compared with Con (P < 0.05), whereas 21 genes were different between ST and ET (P < 0.05). These results were validated by reverse transcriptase polymerase chain reaction for six differentially regulated genes (EIFSJ, LDHB, LMO4, MDH1, SLC16A7, and UTRN. Manual cluster analyses revealed significant regulation of genes involved in muscle structure and development in TR subjects compared with Con (P < 0.05) and expression correlated with measures of performance (P < 0.05). ET had increased whereas ST had decreased expression of gene clusters related to mitochondrial/oxidative capacity (P ?‰Currency sign 0.05). These mitochondrial gene clusters correlated with V?O2peak (P < 0.05). V?O2peak also correlated with expression of gene clusters that regulate fat and carbohydrate oxidation (P < 0.05). CONCLUSION: We demonstrate that chronic training subtly coregulates numerous genes from important functional groups that may be part of the long-term adaptive process to adapt to repeated training stimuli.

Formation of polyaniline/Pt nanoparticle composite films and their electrocatalytic properties

Polyaniline (PANI) thin films modified with platinum nanoparticles have been prepared by several methods, characterised and assessed in terms of electrocatalytic properties. These composite materials have been prepared by the in situ reduction of a platinum salt (K2PtCl4) by PANI, in a variety of solvents, resulting in the formation of platinum nanoparticles and clusters of different sizes. The further deposition of platinum clusters at spin cast thin films of PANI/Pt composites from a neutral aqueous solution of K2PtCl4 has also been demonstrated. Thin-film electrodes prepared from these materials have been investigated for their electrocatalytic activity by studying hydrazine oxidation and dichromate reduction. The properties of the composite materials have been determined using UV–visible spectroscopy, atomic force microscopy and transmission electron microscopy. The nature of the material formed is strongly dependent on the solvent used to dissolve PANI, the method of preparation of the PANI/Pt solution and the composition of the spin cast thin film before subsequent deposition of platinum from the aqueous solution of K2PtCl4.

Decoration of active sites to create bimetallic surfaces and its implication for electrochemical processes

The creation of electrocatalysts based on noble metals has received a significant amount of research interest due to their extensive use as fuel cell catalysts and electrochemical sensors. There have been many attempts to improve the activity of these metals through creating nanostructures, as well as post-synthesis treatments based on chemical, electrochemical, sonochemical and thermal approaches. In many instances these methods result in a material with active surface states, which can be considered to be adatoms or clusters of atoms on the surface that have a low lattice co-ordination number making them more prone to electrochemical oxidation at a wide range of potentials that are significantly less positive than those of their bulk metal counterparts. This phenomenon has been termed pre-monolayer oxidation and has been reported to occur on a range of metallic surfaces. In this work we present findings on the presence of active sites on Pd that has been: evaporated as a thin film; electrodeposited as nanostructures; as well as commercially available Pd nanoparticles supported on carbon. Significantly, advantage is taken of the low oxidation potential of these active sites whereby bimetallic surfaces are created by the spontaneous deposition of Ag from AgNO3 to generate Pd/Ag surfaces. Interestingly this approach does not increase the surface area of the original metal but has significant implications for its further use as an electrode material. It results in the inhibition or promotion of electrocatalytic activity which is highly dependent on the reaction of interest. As a general approach the decoration of active catalytic materials with less active metals for a particular reaction also opens up the possibility of investigating the role of the initially present active sites on the surface and identifying the degree to which they are responsible for electrocatalytic activity.

Exploiting the facile oxidation of evaporated gold films to drive electroless silver deposition for the creation of bimetallic Au/Ag surfaces

Gold is often considered as an inert material but it has been unequivocally demonstrated that it possesses unique electronic, optical, catalytic and electrocatalytic properties when in a nanostructured form.[1] For the latter the electrochemical behaviour of gold in aqueous media has been widely studied on a plethora of gold samples, including bulk polycrystalline and single-crystal electrodes, nanoparticles, evaporated films as well as electrodeposited nanostructures, particles and thin films.[1b, 2] It is now well-established that the electrochemical behaviour of gold is not as simple as an extended double-layer charging region followed by a monolayer oxide-formation/-removal process. In fact the so-called double-layer region of gold is significantly more complicated and has been investigated with a variety of electrochemical and surface science techniques. Burke and others[3] have demonstrated that significant processes due to the oxidation of low lattice stabilised atoms or clusters of atoms occur in this region at thermally and electrochemically treated electrodes which were confirmed later by Bond[4] to be Faradaic in nature via large-amplitude Fourier transformed ac voltammetric experiments. Supporting evidence for the oxidation of gold in the double-layer region was provided by Bard,[5] who used a surface interrogation mode of scanning electrochemical microscopy to quantify the extent of this process that forms incipient oxides on the surface. These were estimated to be as high as 20% of a monolayer. This correlated with contact electrode resistance measurements,[6] capacitance measurements[7] and also electroreflection techniques...

Structural characterization and vibrational spectroscopy of the arsenate mineral wendwilsonite

In this paper, we have investigated on the natural wendwilsonite mineral with the formulae Ca2(Mg,Co)(AsO4)2⋅2(H2O). Raman spectroscopy complimented with infrared spectroscopy has been used to determine the molecular structure of the wendwilsonite arsenate mineral. A comparison is made with the roselite mineral group with formula Ca2B(AsO4)2⋅2H2O (where B may be Co, Fe2+, Mg, Mn, Ni, Zn). The Raman spectra of the arsenate related to tetrahedral arsenate clusters with stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. The Raman arsenate (AsO4)3− stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. In the infrared spectra complexity exists of multiple to tetrahedral (AsO4)3− clusters with antisymmetric stretching vibrations observed indicating a reduction of the tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong Raman bands around 450 cm−1 are assigned to ν4 bending modes. Multiple bands in the 350–300 cm−1 region assigned to ν2 bending modes provide evidence of symmetry reduction of the arsenate anion. Three broad bands for wendwilsonite found at 3332, 3119 and 3001 cm−1 are assigned to OH stretching bands. By using a Libowitzky empirical equation, hydrogen bond distances of 2.65 and 2.75 Å are estimated. Vibrational spectra enable the molecular structure of the wendwilsonite mineral to be determined and whilst similarities exist in the spectral patterns with the roselite mineral group, sufficient differences exist to be able to determine the identification of the minerals.

Principle components analysis with covariance matrix on regional differences for mortality and percentages of cancers in Shandong province [山东省恶性肿瘤死亡率和构成比地区差异协方差矩阵主成分分析]

Objective To explore the characteristics of regional distribution of cancer deaths in Shandong Province with the principle components analysis. Methods The principle components analysis with co-variance matrix for age-adjusted mortality rates and percentages of 20 types of cancer in 22 counties （cities） were carried out using SAS Software. Results Over 90% of the total information could be reflected by the top 3 principle components and the first principle component alone represented more than half of the overall regional variances. The first component mainly reflected the area differences of esophageal cancer. The second component mainly reflected the area differences of lung cancer， stomach cancer and liver cancer. The value of the first principal component scores showed a clear trend that the west areas possessed higher values and the east the lower values. Based on the top two components，the 22 counties （cities） could be divided into several geographical clusters. Conclusion The overall difference of regional distribution of cancers in Shandong is dominated by several major cancers including esophageal cancer， lung cancer， stomach cancer and liver cancer. Among them，esophageal cancer makes the largest contribution. If the range of counties （cities） analyzed could be further widened， the characteristics of regional distribution of cancer mortality would be better examined. Abstract in Chinese 目的 利用主成分分析探讨山东省恶性肿瘤死亡的地区分布特征. 方法 利用SAS软件对山东省22个县市区2004～2006午的20种恶性肿瘤标化死亡率和构成比分别进行协方差矩阵主成分分析. 结果 前3个主成分就反映了总体差异90%以上的信息,其中仅第1主成分就提供了总体差异一半以上的信息.第1主成分主要反映了食管癌的地区差异,第2主成分主要反映肺癌的地区差异,兼顾胃癌和肝癌.各地区第1主成分得分呈现西高东低的趋势,根据第1和第2主成分可以将调查地区分为若干类别,表现为明显的地理聚集性. 结论 山东省各地区恶性肿瘤死亡的总体差异主要取决于少数高发肿瘤,包括食管癌、肺癌、胃癌、肝癌等,其中以食管癌地位最为突出.如能进一步扩大分析范围,可更好地查明恶性肿瘤死亡的地区特征.

Advance transit oriented development typology : case study in Brisbane, Australia

Internationally, transit oriented development (TOD) is characterised by moderate to high density development with diverse land use patterns and well connected street networks centred around high frequency transit stops (bus and rail). Although different TOD typologies have been developed in different contexts, they are based on subjective evaluation criteria derived from the context in which they are built and typically lack a validation measure. Arguably there exist sets of TOD characteristics that perform better in certain contexts, and being able to optimise TOD effectiveness would facilitate planning and supporting policy development. This research utilises data from census collection districts (CCDs) in Brisbane with different sets of TOD attributes measured across six objectively quantified built environmental indicators: net employment density, net residential density, land use diversity, intersection density, cul-de-sac density, and public transport accessibility. Using these measures, a Two Step Cluster Analysis was conducted to identify natural groupings of the CCDs with similar profiles, resulting in four unique TOD clusters: (a) residential TODs, (b) activity centre TODs, (c) potential TODs, and; (d) TOD non-suitability. The typologies are validated by estimating a multinomial logistic regression model in order to understand the mode choice behaviour of 10,013 individuals living in these areas. Results indicate that in comparison to people living in areas classified as residential TODs, people who reside in non-TOD clusters were significantly less likely to use public transport (PT) (1.4 times), and active transport (4 times) compared to the car. People living in areas classified as potential TODs were 1.3 times less likely to use PT, and 2.5 times less likely to use active transport compared to using the car. Only a little difference in mode choice behaviour was evident between people living in areas classified as residential TODs and activity centre TODs. The results suggest that: (a) two types of TODs may be suitable for classification and effect mode choice in Brisbane; (b) TOD typology should be developed based on their TOD profile and performance matrices; (c) both bus stop and train station based TODs are suitable for development in Brisbane.

Carbonic anhydrase IX expression, a novel surrogate marker of tumor hypoxia, is associated with a poor prognosis in non-small-cell lung cancer

Purpose To evaluate carbonic anhydrase (CA) IX as a surrogate marker of hypoxia and investigate the prognostic significance of different patterns of expression in non-small-cell lung cancer (NSCLC). Methods Standard immunohistochemical techniques were used to study CA IX expression in 175 resected NSCLC tumors. CA IX expression was determined by Western blotting in A549 cell lines grown under normoxic and hypoxic conditions. Measurements from microvessels to CA IX positivity were obtained. Results CA IX immunostaining was detected in 81.8% of patients. Membranous (m) (P = .005), cytoplasmic (c) (P = .018), and stromal (P < .001) CA IX expression correlated with the extent of tumor necrosis (TN). The mean distance from vascular endothelium to the start of tumor cell positivity was 90 μm, which equates to an oxygen pressure of 5.77 mmHg. The distance to blood vessels from individual tumor cells or tumor cell clusters was greater if they expressed mCA IX than if they did not (P < .001). Hypoxic exposure of A549 cells for 16 hours enhanced CAIX expression in the nuclear and cytosolic extracts. Perinuclear (p) CA IX (P = .035) was associated with a poor prognosis. In multivariate analysis, pCA IX (P = .004), stage (P = .001), platelet count (P = .011), sex (P = .027), and TN (P = .035) were independent poor prognostic factors. Conclusion These results add weight to the contention that mCA IX is a marker of tumor cell hypoxia. The absence of CA IX staining close to microvessels suggests that these vessels are functionally active. pCA IX expression is representative of an aggressive phenotype. © 2003 by American Society of Clinical Oncology.

A stepped-wedge cluster randomised controlled trial for evaluating rates of falls among inpatients in aged care rehabilitation units receiving tailored multimedia education in addition to usual care : a trial protocol

Introduction Falls are the most frequent adverse event reported in hospitals. Approximately 30% of in-hospital falls lead to an injury and up to 2% result in a fracture. A large randomised trial found that a trained health professional providing individualised falls prevention education to older inpatients reduced falls in a cognitively intact subgroup. This study aims to investigate whether this efficacious intervention can reduce falls and be clinically useful and cost-effective when delivered in the real-life clinical environment. Methods A stepped-wedge cluster randomised trial will be used across eight subacute units (clusters) which will be randomised to one of four dates to start the intervention. Usual care on these units includes patient's screening, assessment and implementation of individualised falls prevention strategies, ongoing staff training and environmental strategies. Patients with better levels of cognition (Mini-Mental State Examination >23/30) will receive the individualised education from a trained health professional in addition to usual care while patient's feedback received during education sessions will be provided to unit staff. Unit staff will receive training to assist in intervention delivery and to enhance uptake of strategies by patients. Falls data will be collected by two methods: case note audit by research assistants and the hospital falls reporting system. Cluster-level data including patient's admissions, length of stay and diagnosis will be collected from hospital systems. Data will be analysed allowing for correlation of outcomes (clustering) within units. An economic analysis will be undertaken which includes an incremental cost-effectiveness analysis. Ethics and dissemination The study was approved by The University of Notre Dame Australia Human Research Ethics Committee and local hospital ethics committees. Results The results will be disseminated through local site networks, and future funding and delivery of falls prevention programmes within WA Health will be informed. Results will also be disseminated through peer-reviewed publications and medical conferences.

Examining the impact of climate change on dengue transmission in the Asia-Pacific region

Dengue fever (DF) is a serious public health concern in many parts of the world. An increase in DF incidence has been observed globally over the past decades. Multiple factors including urbanisation, increased international travels and global climate change are thought to be responsible for increased DF. However, little research has been conducted in the Asia-Pacific region about the impact of these changes on dengue transmission. The overarching aim of this thesis is to explore the spatiotemporal pattern of DF transmission in the Asia-Pacific region and project the future risk of DF attributable to climate change. Annual data of DF outbreaks for sixteen countries in the Asia-Pacific region over the last fifty years were used in this study. The results show that the geographic range of DF in this region increased significantly over the study period. Thailand, Vietnam and Laos were identified as the highest risk areas and there was a southward expansion observed in the transmission pattern of DF which might have originated from Philippines or Thailand. Additionally, the detailed DF data were obtained and the space-time clustering of DF transmission was examined in Bangladesh. Monthly DF data were used for the entire country at the district level during 2000-2009. Dhaka district was identified as the most likely DF cluster in Bangladesh and several districts of the southern part of Bangladesh were identified as secondary clusters in the years 2000-2002. In order to examine the association between meteorological factors and DF transmission and to project the future risk of DF using different climate change scenarios, the climate-DF relationship was examined in Dhaka, Bangladesh. The results show that climate variability (particularly maximum temperature and relative humidity) was positively associated with DF transmission in Dhaka. The effects of climate variability were observed at a lag of four months which might help to potentially control and prevent DF outbreaks through effective vector management and community education. Based on the quantitative assessment of the climate-DF relationship, projected climate change will likely increase mosquito abundance and activity and DF in this area. Assuming a temperature increase of 3.3oC without any adaptation measures and significant changes in socio-economic conditions, the consequence will be devastating, with a projected annual increase of 16,030 cases in Dhaka, Bangladesh by the end of this century. Therefore, public health authorities need to be prepared for likely increase of DF transmission in this region. This study adds to the literature on the recent trends of DF and impacts of climate change on DF transmission. These findings may have significant public health implications for the control and prevention of DF, particularly in the Asia- Pacific region.

ADCS reaches adulthood : an analysis of the conference and its community over the last eighteen years

How influential is the Australian Document Computing Symposium (ADCS)? What do ADCS articles speak about and who cites them? Who is the ADCS community and how has it evolved? This paper considers eighteen years of ADCS, investigating both the conference and its community. A content analysis of the proceedings uncovers the diversity of topics covered in ADCS and how these have changed over the years. Citation analysis reveals the impact of the papers. The number of authors and where they originate from reveal who has contributed to the conference. Finally, we generate co-author networks which reveal the collaborations within the community. These networks show how clusters of researchers form, the effect geographic location has on collaboration, and how these have evolved over time.