An ensemble method for predicting subnuclear localizations from primary protein structures

Background Predicting protein subnuclear localization is a challenging problem. Some previous works based on non-sequence information including Gene Ontology annotations and kernel fusion have respective limitations. The aim of this work is twofold: one is to propose a novel individual feature extraction method; another is to develop an ensemble method to improve prediction performance using comprehensive information represented in the form of high dimensional feature vector obtained by 11 feature extraction methods. Methodology/Principal Findings A novel two-stage multiclass support vector machine is proposed to predict protein subnuclear localizations. It only considers those feature extraction methods based on amino acid classifications and physicochemical properties. In order to speed up our system, an automatic search method for the kernel parameter is used. The prediction performance of our method is evaluated on four datasets: Lei dataset, multi-localization dataset, SNL9 dataset and a new independent dataset. The overall accuracy of prediction for 6 localizations on Lei dataset is 75.2% and that for 9 localizations on SNL9 dataset is 72.1% in the leave-one-out cross validation, 71.7% for the multi-localization dataset and 69.8% for the new independent dataset, respectively. Comparisons with those existing methods show that our method performs better for both single-localization and multi-localization proteins and achieves more balanced sensitivities and specificities on large-size and small-size subcellular localizations. The overall accuracy improvements are 4.0% and 4.7% for single-localization proteins and 6.5% for multi-localization proteins. The reliability and stability of our classification model are further confirmed by permutation analysis. Conclusions It can be concluded that our method is effective and valuable for predicting protein subnuclear localizations. A web server has been designed to implement the proposed method. It is freely available at http://bioinformatics.awowshop.com/snlpr​ed_page.php.

Transnational field experience : making the familiar strange

This study explores the impact of field experience in Australian primary classrooms on the developing professional identities of Malaysian pre-service teachers. This group of 24 Malaysian students are undertaking their Bachelor of Education in Teaching English as a Foreign Language (BEd TESL) at an Australian university, as part of a transnational twinning program. The globalisation of education has seen an increase in such transnational school experiences for pre-service teachers, with the aim of extending professional experience and intercultural competence by engaging in communities of practice beyond the local (Tsui 2005, Luke 2004). Despite overseas governments, such as Malaysia, having sponsored multimillion dollar twinning programs for their pre-service teachers, there is a lack of research regarding the outcomes of transnational professional practice within such programs. This study adopts a qualitative approach focusing on participants’ narratives as revealed in their reflective writing and through semi-structured interviews. Adopting a Bakhtinian framework, this research uses the concept of ‘voice’ to explore how pre-service teachers negotiate their identities as EFL teachers in response to their lived professional experiences (Bakhtin 1981, 1986). Encountering different cultural and educational practices in their transnational field experiences can lead pre-service teachers to question taken-for-granted practices that they have grown up with. This has been described as a process of making the familiar strange, and can lead to a shift in professional understandings. This study investigates how such questioning occurs and how the transnational field experience is perceived by the participants as contributing to their developing professional identities.

Load-unloading response of intact and artificially degraded articular cartilage correlated with near infrared (NIR) absorption spectra

The conventional mechanical properties of articular cartilage, such as compressive stiffness, have been demonstrated to be limited in their capacity to distinguish intact (visually normal) from degraded cartilage samples. In this paper, we explore the correlation between a new mechanical parameter, namely the reswelling of articular cartilage following unloading from a given compressive load, and the near infrared (NIR) spectrum. The capacity to distinguish mechanically intact from proteoglycan-depleted tissue relative to the "reswelling" characteristic was first established, and the result was subsequently correlated with the NIR spectral data of the respective tissue samples. To achieve this, normal intact and enzymatically degraded samples were subjected to both NIR probing and mechanical compression based on a load-unload-reswelling protocol. The parameter δ(r), characteristic of the osmotic "reswelling" of the matrix after unloading to a constant small load in the order of the osmotic pressure of cartilage, was obtained for the different sample types. Multivariate statistics was employed to determine the degree of correlation between δ(r) and the NIR absorption spectrum of relevant specimens using Partial Least Squared (PLS) regression. The results show a strong relationship (R(2)=95.89%, p<0.0001) between the spectral data and δ(r). This correlation of δ(r) with NIR spectral data suggests the potential for determining the reswelling characteristics non-destructively. It was also observed that δ(r) values bear a significant relationship with the cartilage matrix integrity, indicated by its proteoglycan content, and can therefore differentiate between normal and artificially degraded proteoglycan-depleted cartilage samples. It is therefore argued that the reswelling of cartilage, which is both biochemical (osmotic) and mechanical (hydrostatic pressure) in origin, could be a strong candidate for characterizing the tissue, especially in regions surrounding focal cartilage defects in joints.

Low temperature response of nanostructured tungsten oxide thin films toward hydrogen and ethanol

Semiconducting metal oxide based gas sensors usually operate in the temperature range 200–500 °C. In this paper, we present a new WO3 thin film based gas sensor for H2 and C2H5OH, operating at 150 °C. Nanostructured WO3 thin films were synthesized by thermal evaporation method. The properties of the as-deposited films were modified by annealing in air at 300 °C and 400 °C. Various analytical techniques such as AFM, TEM, XPS, XRD and Raman spectroscopy have been employed to characterize their properties. A clear indication from TEM and XRD analysis is that the as-deposited WO3 films are highly amorphous and no improvement is observed in the crystallinity of the films after annealing at 300 °C. Annealing at 400 °C significantly improved the crystalline properties of the films with the formation of about 5 nm grains. The films annealed at 300 °C show no response to C2H5OH (ethanol) and a little response to H2, with maximum response obtained at 280 °C. The films annealed at 400 °C show a very good response to H2 and a moderate response to C2H5OH (ethanol) at 150 °C. XPS analysis revealed that annealing of the WO3 thin films at 400 °C produces a significant change in stoichiometry, increasing the number of oxygen vacancies in the film, which is highly beneficial for gas sensing. Our results demonstrate that gas sensors with significant performance at low operating temperatures can be obtained by annealing the WO3 films at 400 °C and optimizing the crystallinity and nanostructure of the as-deposited films.

Hybrid graphene and graphitic carbon nitride nanocomposite : gap opening, electron–hole puddle, interfacial charge transfer, and enhanced visible light response

Opening up a band gap and finding a suitable substrate material are two big challenges for building graphene-based nanodevices. Using state-of-the-art hybrid density functional theory incorporating long range dispersion corrections, we investigate the interface between optically active graphitic carbon nitride (g-C3N4) and electronically active graphene. We find an inhomogeneous planar substrate (g-C3N4) promotes electronrich and hole-rich regions, i.e., forming a well-defined electron−hole puddle, on the supported graphene layer. The composite displays significant charge transfer from graphene to the g-C3N4 substrate, which alters the electronic properties of both components. In particular, the strong electronic coupling at the graphene/g-C3N4 interface opens a 70 meV gap in g-C3N4-supported graphene, a feature that can potentially allow overcoming the graphene’s band gap hurdle in constructing field effect transistors. Additionally, the 2-D planar structure of g-C3N4 is free of dangling bonds, providing an ideal substrate for graphene to sit on. Furthermore, when compared to a pure g-C3N4 monolayer, the hybrid graphene/g-C3N4 complex displays an enhanced optical absorption in the visible region, a promising feature for novel photovoltaic and photocatalytic applications.

Hybrid graphene/titania nanocomposite : interface charge transfer, hole doping, and sensitization for visible light response

We demonstrated for the first time by large-scale ab initio calculations that a graphene/titania interface in the ground electronic state forms a charge-transfer complex due to the large difference of work functions between graphene and titania, leading to substantial hole doping in graphene. Interestingly, electrons in the upper valence band can be directly excited from graphene to the conduction band, that is, the 3d orbitals of titania, under visible light irradiation. This should yield well-separated electron−hole pairs, with potentially high photocatalytic or photovoltaic performance in hybrid graphene and titania nanocomposites. Experimental wavelength-dependent photocurrent generation of the graphene/titania photoanode demonstrated noticeable visible light response and evidently verified our ab initio prediction.

Comparing child product safety concerns with injury incidents : does the evidence support the response?

Background Efficient effective child product safety (PS) responses require data on hazards, injury severity and injury probability. PS responses in Australia largely rely on reports from manufacturers/retailers, other jurisdictions/regulators, or consumers. The extent to which reactive responses reflect actual child injury priorities is unknown. Aims/Objectives/Purpose This research compared PS issues for children identified using data compiled from PS regulatory data and data compiled from health data sources in Queensland, Australia. Methods PS regulatory documents describing issues affecting children in Queensland in 2008–2009 were compiled and analysed to identify frequent products and hazards. Three health data sources (ED, injury surveillance and hospital data) were analysed to identify frequent products and hazards. Results/Outcomes Projectile toys/squeeze toys were the priority products for PS regulators with these toys having the potential to release small parts presenting choking hazards. However, across all health datasets, falls were the most common mechanism of injury, and several of the products identified were not subject to a PS system response. While some incidents may not require a response, a manual review of injury description text identified child poisonings and burns as common mechanisms of injuries in the health data where there was substantial documentation of product-involvement, yet only 10% of PS system responses focused on these two mechanisms combined. Significance/contribution to the field Regulatory data focused on products that fail compliance checks with ‘potential’ to cause harm, and health data identified actual harm, resulting in different prioritisation of products/mechanisms. Work is needed to better integrate health data into PS responses in Australia.

An evaluation of the Australian Capital Territory Sexual Assault Reform Program (SARP): Final Report

In 2005 the Australian Capital Territory (ACT) Office of the Director of Public Prosecutions (DPP) and the Australian Federal Police (AFP) produced a report, Responding to sexual assault: The challenge of change (DPP & AFP 2005), which made 105 recommendations for reforming the way sexual offence cases are handled by the ACT’s criminal justice system. The Sexual Assault Reform Program (SARP) is one key initiative developed in response to these recommendations. Managed by the ACT Justice and Community Safety Directorate (JACS), SARP’s main objective is to improve aspects of the criminal justice system relating to: processes and support for victims of sexual offences as they progress through the system; attrition in sexual offence matters in the criminal justice system; and coordination and collaboration among the agencies involved. In November 2007 the ACT Attorney-General announced $4 million of funding for several SARP reforms. This funding provided for additional victim support staff; a dedicated additional police officer, prosecutor and legal policy officer; and an upgrade of equipment for the Supreme Court and Magistrates Court, including improvements in technology to assist witnesses in giving evidence, and the establishment of an off-site facility to allow witnesses to give evidence from a location outside of the court. In addition, the reform agenda included a number of legislative amendments that changed how evidence can be given by victims of sexual and family violence offences, children and other vulnerable witnesses. The primary objectives of these legislative changes are to provide an unintimidating, safe environment for vulnerable witnesses (including sexual offence complainants) to give evidence and to obtain prompt statements from witnesses to improve the quality of evidence captured (DPP 2009: 13). The current evaluation The funding for SARP reforms also provided for a preliminary evaluation of the reforms; this report outlines findings from the evaluation. The evaluation sought to address whether the program has met its key objectives: better support for victims, lower attrition rates and improved coordination and collaboration among agencies involved in administering SARP. The evaluation was conducted in two stages and involved a mixed-methods approach. During stage 1 key indicators for the evaluation were developed with stakeholders. During stage 2 quantitative data were collected by stakeholders and provided to the AIC for analysis. Qualitative interviews were also conducted with service delivery providers, and with a small number (n=5) of victim/survivors of sexual offences whose cases had recently been resolved in the ACT criminal justice system. The current evaluation is preliminary in nature. As the SARP reforms will take time to become entrenched within the ACT’s criminal justice system, some of the impacts of the reforms may not yet be evident. Nonetheless, this evaluation provides an insight into how well the SARP reforms have been implemented to date, as well as key areas that could be addressed in the future. Key findings from the preliminary evaluation are outlined briefly below.

Genetic variability and antimicrobial resistance of Ureaplasma parvum in response to maternal erythromycin treatment : a study in pregnant sheep

Background: Ureaplasmas are the most frequently isolated microorganisms from the amniotic fluid (AF) of pregnant women and can cause chronic infections that are difficult to eradicate with standard macrolide treatment. We tested the effects of erythromycin treatment on phenotypic and genotypic markers of ureaplasmal antimicrobial resistance in sheep. Method: At 50 days of gestation (d, term=145d) 12 pregnant ewes received intra-amniotic injections of U. parvum serovar 3 (erythromycin-sensitive, 2x104 colony-forming-units). At 100d ewes received: erythromycin treatment (500 mg, q3h for 4 days, IM, n=6) or no treatment (n=6). Fetuses were delivered surgically (125d) and AF and chorioamnion were collected for: culture, minimum inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC) testing; 23S rRNA sequencing; and detection of macrolide-lincosamide-streptogramin resistance (MLSr) genes. Results: MICs of erythromycin, azithromycin and roxithromycin against AF isolates were low (range = 0.06 mg/L to 1.0 mg/L); however, chorioamnion isolates demonstrated increased resistance to roxithromycin (0.13 – 5.33 mg/L). 62.5% of chorioamnion ureaplasmas formed biofilms in vitro and mutations (125 nucleotides, 29.6%) were found in the 23S rRNA gene (domain V) of chorioamnion (but not AF) ureaplasmas. MLSr genes (ermB, msrC and msrD) were detected in 100% of chorioamnion isolates and only msrD was detected in AF isolates (40%). Conclusions: 23S rRNA mutations and MLSr genes occurred independently of erythromycin treatment, suggesting that the anatomical site of infection and microenvironment may exert selective pressures on ureaplasmas that cause genetic changes and alter antimicrobial sensitivity profiles. These results have serious implications for treatment of in utero infections.

Rod and cone pathway signaling and interaction under mesopic illumination

This study investigates the time-course and post-receptoral pathway signaling of photoreceptor interactions when the rod (R) and three cone (L, M, S) photoreceptor classes contribute to mesopic vision. A four-primary photostimulator independently controls photoreceptor activity in human observers. The first experiment defines the temporal adaptation response of receptoral (L-, S-cone, rod) and post-receptoral (LMS, LMSR,+L-M) signaling and interactions. Here we show that nonopponent cone-cone interactions (L-cone, LMS, LMSR) have monophasic temporal response patterns whereas opponent signals (+L-M, S-cone) show biphasic response patterns with slower recovery. By comparison, rod-cone interactions with nonopponent signals have faster adaptation responses and reduced sensitivity loss whereas opponent rod-cone interactions are small or absent. Additionally, the rod-rod interaction differs from these interaction types and acts to increase rod sensitivity due to temporal summation but with a slower time course. The second experiment shows that the temporal profile of the rod signal alters the relative rod contributions to the three primary post-receptoral pathways. We demonstrate that rod signals generate luminance (þLþM) signals mediated via the MC pathway with all rod temporal profiles and chromatic signals (L/LþM, S/LþM) in both the PC and KC pathways with durations .75 ms. Thus, we propose that the change in relative weighting of rod signals within the post-receptoral pathways contributes to the sensitivity and temporal response of rod and cone pathway signaling and interactions.

Discussion: Response of a plastic pipe buried in expansive clay

Response to discussion on Gallage CPK, Chan D and Kodilara J (2012) Response of a plastic pipe buried in expansive clay. Proceedings of ICE, Geotechnical Engineering, Vol 164, February 2012, Issue GE1, pages 45-57.

Fluid Infrastructure : A response to a natural flood disaster in Brisbane

Fluid Infrastructure: Landscape Architecture Exhibition: This exhibition showcases the work of 4th Year undergraduate landscape architecture students in response to the 2011 Queensland floods through five installations: Systima Fluid Flux Flex Fluid Connectivity The Floods Verge Fluid Evolution The focus of these installations is the post-flood conditions of Brisbane’s riverside public infrastructure, within a scenario of flood as a normalised event. It recognises that within this scenario, parts of this city cannot be described as definitively ‘land’ or ‘water,’ but are best described as ‘fluid terrains’(Mathur, A. and Da Cunha, D. 2006). The landscape design propositions within the five installations include public transport diversification (RiverRats) schemes, greenspace elevations, ephemeral gardens and evolving landscapes, creative interpretation and warning devices and systems. These propositions do not resist fluid conditions, but work with them to propose a more resilient urban river landscape than Brisbane currently has. This QUT exhibition was developed as part of the 2011 Flood of Ideas Project (http://www.floodofideas.org.au) in partnership with Healthy Waterways (Water by Design), State Library of Queensland (The Edge), Brisbane City Council, Australian Institute of Architects, University of Queensland, Green Cross Australia, Stormwater Industry Association.

Evaluation of primary epidermal lamellar density in the forefeet of near-term fetal Australian feral and domesticated horses

Objective: To investigate the density of the primary epidermal lamellae (PEL) around the solar circumference of the forefeet of near-term fetal feral and nonferal (ie, domesticated) horses. Sample: Left forefeet from near-term Australian feral (n = 14) and domesticated (4) horse fetuses. Procedures: Near-term feral horse fetuses were obtained from culled mares within 10 minutes of death; fetuses that had died in utero 2 weeks prior to anticipated birth date and were delivered from live Thoroughbred mares were also obtained. Following disarticulation at the carpus, the left forefoot of each fetus was frozen during dissection and data collection. In a standard section of each hoof, the stratum internum PEL density was calculated at the midline center (12 o'clock) and the medial and lateral break-over points (11 and 1 o'clock), toe quarters (10 and 2 o'clock), and quarters (4 and 6 o'clock). Values for matching lateral and medial zones were averaged and expressed as 1 density. Density differences at the 4 locations between the feral and domesticated horse feet were assessed by use of imaging software analysis. Results: In fetal domesticated horse feet, PEL density did not differ among the 4 locations. In fetal feral horse feet, PEL density differed significantly among locations, with a pattern of gradual reduction from the dorsal to the palmar aspect of the foot. The PEL density distribution differed significantly between fetal domesticated and feral horse feet. Conclusions and Clinical Relevance: Results indicated that PEL density distribution differs between fetal feral and domesticated horse feet, suggestive of an adaptation of feral horses to environment challenges.

Binocular rivalry and visuospatial ability in individuals with schizophrenia

Visual abnormalities, both at the sensory input and the higher interpretive levels, have been associated with many of the symptoms of schizophrenia. Individuals with schizophrenia typically experience distortions of sensory perception, resulting in perceptual hallucinations and delusions that are related to the observed visual deficits. Disorganised speech, thinking and behaviour are commonly experienced by sufferers of the disorder, and have also been attributed to perceptual disturbances associated with anomalies in visual processing. Compounding these issues are marked deficits in cognitive functioning that are observed in approximately 80% of those with schizophrenia. Cognitive impairments associated with schizophrenia include: difficulty with concentration and memory (i.e. working, visual and verbal), an impaired ability to process complex information, response inhibition and deficits in speed of processing, visual and verbal learning. Deficits in sustained attention or vigilance, poor executive functioning such as poor reasoning, problem solving, and social cognition, are all influenced by impaired visual processing. These symptoms impact on the internal perceptual world of those with schizophrenia, and hamper their ability to navigate their external environment. Visual processing abnormalities in schizophrenia are likely to worsen personal, social and occupational functioning. Binocular rivalry provides a unique opportunity to investigate the processes involved in visual awareness and visual perception. Binocular rivalry is the alternation of perceptual images that occurs when conflicting visual stimuli are presented to each eye in the same retinal location. The observer perceives the opposing images in an alternating fashion, despite the sensory input to each eye remaining constant. Binocular rivalry tasks have been developed to investigate specific parts of the visual system. The research presented in this Thesis provides an explorative investigation into binocular rivalry in schizophrenia, using the method of Pettigrew and Miller (1998) and comparing individuals with schizophrenia to healthy controls. This method allows manipulations to the spatial and temporal frequency, luminance contrast and chromaticity of the visual stimuli. Manipulations to the rival stimuli affect the rate of binocular rivalry alternations and the time spent perceiving each image (dominance duration). Binocular rivalry rate and dominance durations provide useful measures to investigate aspects of visual neural processing that lead to the perceptual disturbances and cognitive dysfunction attributed to schizophrenia. However, despite this promise the binocular rivalry phenomenon has not been extensively explored in schizophrenia to date. Following a review of the literature, the research in this Thesis examined individual variation in binocular rivalry. The initial study (Chapter 2) explored the effect of systematically altering the properties of the stimuli (i.e. spatial and temporal frequency, luminance contrast and chromaticity) on binocular rivalry rate and dominance durations in healthy individuals (n=20). The findings showed that altering the stimuli with respect to temporal frequency and luminance contrast significantly affected rate. This is significant as processing of temporal frequency and luminance contrast have consistently been demonstrated to be abnormal in schizophrenia. The current research then explored binocular rivalry in schizophrenia. The primary research question was, "Are binocular rivalry rates and dominance durations recorded in participants with schizophrenia different to those of the controls?" In this second study binocular rivalry data that were collected using low- and highstrength binocular rivalry were compared to alternations recorded during a monocular rivalry task, the Necker Cube task to replicate and advance the work of Miller et al., (2003). Participants with schizophrenia (n=20) recorded fewer alternations (i.e. slower alternation rates) than control participants (n=20) on both binocular rivalry tasks, however no difference was observed between the groups on the Necker cube task. Magnocellular and parvocellular visual pathways, thought to be abnormal in schizophrenia, were also investigated in binocular rivalry. The binocular rivalry stimuli used in this third study (Chapter 4) were altered to bias the task for one of these two pathways. Participants with schizophrenia recorded slower binocular rivalry rates than controls in both binocular rivalry tasks. Using a ‘within subject design’, binocular rivalry data were compared to data collected from a backwardmasking task widely accepted to bias both these pathways. Based on these data, a model of binocular rivalry, based on the magnocellular and parvocellular pathways that contribute to the dorsal and ventral visual streams, was developed. Binocular rivalry rates were compared with performance on the Benton’s Judgment of Line Orientation task, in individuals with schizophrenia compared to healthy controls (Chapter 5). The Benton’s Judgment of Line Orientation task is widely accepted to be processed within the right cerebral hemisphere, making it an appropriate task to investigate the role of the cerebral hemispheres in binocular rivalry, and to investigate the inter-hemispheric switching hypothesis of binocular rivalry proposed by Pettigrew and Miller (1998, 2003). The data were suggestive of intra-hemispheric rather than an inter-hemispheric visual processing in binocular rivalry. Neurotransmitter involvement in binocular rivalry, backward masking and Judgment of Line Orientation in schizophrenia were investigated using a genetic indicator of dopamine receptor distribution and functioning; the presence of the Taq1 allele of the dopamine D2 receptor (DRD2) receptor gene. This final study (Chapter 6) explored whether the presence of the Taq1 allele of the DRD2 receptor gene, and thus, by inference the distribution of dopamine receptors and dopamine function, accounted for the large individual variation in binocular rivalry. The presence of the Taq1 allele was associated with slower binocular rivalry rates or poorer performance in the backward masking and Judgment of Line Orientation tasks seen in the group with schizophrenia. This Thesis has contributed to what is known about binocular rivalry in schizophrenia. Consistently slower binocular rivalry rates were observed in participants with schizophrenia, indicating abnormally-slow visual processing in this group. These data support previous studies reporting visual processing abnormalities in schizophrenia and suggest that a slow binocular rivalry rate is not a feature specific to bipolar disorder, but may be a feature of disorders with psychotic features generally. The contributions of the magnocellular or dorsal pathways and parvocellular or ventral pathways to binocular rivalry, and therefore to perceptual awareness, were investigated. The data presented supported the view that the magnocellular system initiates perceptual awareness of an image and the parvocellular system maintains the perception of the image, making it available to higher level processing occurring within the cortical hemispheres. Abnormal magnocellular and parvocellular processing may both contribute to perceptual disturbances that ultimately contribute to the cognitive dysfunction associated with schizophrenia. An alternative model of binocular rivalry based on these observations was proposed.

Alteration of the foetal skin's response to Lipopolysaccharide (LPS) following Ureplasma Parvum exposure

Early preterm birth (<32 weeks) is associated with in utero infection and inflammation. We used an ovine model of in utero infection to ask if exposure to Ureaplasma serovar 3 (UP) modulated the response of the fetal skin to LPS.