Quantum cognition: A new theoretical approach to psychology

What type of probability theory best describes the way humans make judgments under uncertainty and decisions under conflict? Although rational models of cognition have become prominent and have achieved much success, they adhere to the laws of classical probability theory despite the fact that human reasoning does not always conform to these laws. For this reason we have seen the recent emergence of models based on an alternative probabilistic framework drawn from quantum theory. These quantum models show promise in addressing cognitive phenomena that have proven recalcitrant to modeling by means of classical probability theory. This review compares and contrasts probabilistic models based on Bayesian or classical versus quantum principles, and highlights the advantages and disadvantages of each approach.

Adolescent self-reported physical activity and autonomy: A case for constrained and structured environments?

The provision of autonomy supportive environments that promote physical activity engagement have become popular in contemporary youth settings. However, questions remain about whether adolescent perceptions of their autonomy have implications for physical activity. The purpose of this investigation was to examine the association between adolescents’ self-reported physical activity and their perceived autonomy. Participants (n = 384 adolescents) aged between 12 and 15 years were recruited from six secondary schools in metropolitan Brisbane, Australia. Self-reported measures of physical activity and autonomy were obtained. Logistic regression with inverse probability weights were used to examine the association between autonomy and the odds of meeting youth physical activity guidelines. Autonomy (OR 0.61, 95% CI 0.49-0.76) and gender (OR 0.62, 95% CI 0.46-0.83) were negatively associated with meeting physical activity guidelines. However, the model explained only a small amount of the variation in whether youth in this sample met physical activity guidelines (R2 = 0.023). For every 1 unit decrease in autonomy (on an index from 1 to 5), participants were 1.64 times more likely to meet physical activity guidelines. The findings, which are at odds with several previous studies, suggest that interventions designed to facilitate youth physical activity should limit opportunities for youth to make independent decisions about their engagement. However, the small amount of variation explained by the predictors in the model is a caveat, and should be considered prior to applying such suggestions in practical settings. Future research should continue to examine a larger age range, longitudinal observational or intervention studies to examine assertions of causality, as well as objective measurement of physical activity.

The ENIGMA Consortium: Large-scale collaborative analyses of neuroimaging and genetic data

The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.

Associations between individual socioeconomic position, neighbourhood disadvantage, and transport mode: Baseline results from the HABITAT multilevel study

Background Understanding how different socioeconomic indicators are associated with transport modes provide insight into which interventions might contribute to reducing socioeconomic inequalities in health. The purpose of this study was to examine associations between neighbourhood-level socioeconomic disadvantage, individual-level socioeconomic position (SEP) and usual transport mode. Methods This investigation included 11,036 residents from 200 neighbourhoods in Brisbane, Australia. Respondents self-reported their usual transport mode (car or motorbike, public transport, walking or cycling). Indicators for individual-level SEP were education, occupation, and household income; and neighbourhood disadvantage was measured using a census-derived index. Data were analysed using multilevel multinomial logistic regression. High SEP respondents and residents of the most advantaged neighbourhoods who used a private motor vehicle as their usual form of transport was the reference category. Results Compared with driving a motor vehicle, the odds of using public transport were higher for white collar employees (OR1.68, 95%CrI 1.41-2.01), members of lower income households (OR 1.71 95%CrI 1.25-2.30), and residents of more disadvantaged neighbourhoods (OR 1.93, 95%CrI 1.46-2.54); and lower for respondents with a certificate-level education (OR 0.60, 95%CrI 0.49-0.74) and blue collar workers (OR 0.63, 95%CrI 0.50-0.81). The odds of walking for transport were higher for the least educated (OR 1.58, 95%CrI 1.18-2.11), those not in the labour force (OR 1.94, 95%CrI 1.38-2.72), members of lower income households (OR 2.10, 95%CrI 1.23-3.64), and residents of more disadvantaged neighbourhoods (OR 2.73, 95%CrI 1.46-5.24). The odds of cycling were lower among less educated groups (OR 0.31, 95% CrI 0.19-0.48). Conclusion The relationships between socioeconomic characteristics and transport modes are complex, and provide challenges for those attempting to encourage active forms of transportation. Further work is required exploring the individual- and neighbourhood-level mechanisms behind transport mode choice, and what factors might influence individuals from different socioeconomic backgrounds to change to more active transport modes.

Comparison of silicate-substituted calcium phosphate (Actifuse®) with rhBMP-2 (Infuse®) in posterolateral instrumented lumbar fusion

Study Design This was a randomised controlled trial in patients with degenerative disc disease (DDD) who underwent instrumented posterolateral lumbar fusion (PLF) surgery. Objective The aim of this study was to assess the efficacy of the bone grafting substitute, silicate-substituted calcium phosphate (SiCaP) compared with bone morphogenetic protein (rhBMP-2) and to evaluate clinical outcomes over a period of two years. Methods Patients undergoing PLF surgery for DDD at a single centre were recruited and randomised to one of two groups; SiCaP (n=9) or rhBMP-2 (n=10). One patient withdrew prior to randomisation and another from the rhBMP-2 group after randomisation. The radiological and clinical outcomes were examined and compared. Fusion was assessed at 12 months with computed tomography (CT) and plain radiographs. Clinical outcomes were evaluated by recording measures of pain, quality of life, disability and neurological status from six weeks to two years postoperatively. Results In the SiCaP and rhBMP-2 groups, fusion was observed in 9/9 and 8/9 patients respectively. Pain and disability scores were reduced and quality of life increased in both groups. Leg pain, disability and satisfaction scores were similar between the groups at each postoperative time point, however, back pain was less at six weeks and quality of life was higher at six months in the SiCaP group than the rhBMP-2 group. Conclusions SiCaP and rhBMP-2 were comparable in terms of achieving successful bone growth and fusion. Both groups similarly alleviated pain and improved quality of life, neurological, satisfaction and return to work outcomes following PLF surgery.

The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas

he composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.

Regional and seasonal variation in airborne grass pollen levels between cities of Australia and New Zealand

Although grass pollen is widely regarded as the major outdoor aeroallergen source in Australia and New Zealand (NZ), no assemblage of airborne pollen data for the region has been previously compiled. Grass pollen count data collected at 14 urban sites in Australia and NZ over periods ranging from 1 to 17 years were acquired, assembled and compared, revealing considerable spatiotemporal variability. Although direct comparison between these data is problematic due to methodological differences between monitoring sites, the following patterns are apparent. Grass pollen seasons tended to have more than one peak from tropics to latitudes of 37°S and single peaks at sites south of this latitude. A longer grass pollen season was therefore found at sites below 37°S, driven by later seasonal end dates for grass growth and flowering. Daily pollen counts increased with latitude; subtropical regions had seasons of both high intensity and long duration. At higher latitude sites, the single springtime grass pollen peak is potentially due to a cooler growing season and a predominance of pollen from C3 grasses. The multiple peaks at lower latitude sites may be due to a warmer season and the predominance of pollen from C4 grasses. Prevalence and duration of seasonal allergies may reflect the differing pollen seasons across Australia and NZ. It must be emphasized that these findings are tentative due to limitations in the available data, reinforcing the need to implement standardized pollen-monitoring methods across Australasia. Furthermore, spatiotemporal differences in grass pollen counts indicate that local, current, standardized pollen monitoring would assist with the management of pollen allergen exposure for patients at risk of allergic rhinitis and asthma. © 2015 Springer Science+Business Media Dordrecht

Differences in grass pollen allergen exposure across Australia

Objective Allergic rhinitis and allergic asthma are important chronic diseases posing serious public health issues in Australia with associated medical, economic, and societal burdens. Pollen are significant sources of clinically relevant outdoor aeroallergens, recognised as both a major trigger for, and cause of, allergic respiratory diseases. This study aimed to provide a national, and indeed international, perspective on the state of Australian pollen data using a large representative sample. Methods Atmospheric grass pollen concentration is examined over a number of years within the period 1995 to 2013 for Brisbane, Canberra, Darwin, Hobart, Melbourne, and Sydney, including determination of the clinical' grass pollen season and grass pollen peak. Results The results of this study describe, for the first time, a striking spatial and temporal variability in grass pollen seasons in Australia, with important implications for clinicians and public health professionals, and the Australian grass pollen-allergic community. Conclusions These results demonstrate that static pollen calendars are of limited utility and in some cases misleading. This study also highlights significant deficiencies and limitations in the existing Australian pollen monitoring and data. Implications: Establishment of an Australian national pollen monitoring network would help facilitate advances in the clinical and public health management of the millions of Australians with asthma and allergic rhinitis.

Pharmacology in one semester [Version 3, Semester 1, 2014]

- For use in Introductory Units/Courses to Biomedical/Science Students - For use with Allied Health Students who are taking pharmacology as a Unit/Course or a part Unit/Course

Hydrothermal liquefaction of bagasse using ethanol and black liquor as solvents

The objective of this study was to examine the hydrothermal liquefaction of sugarcane bagasse using ethanol and black liquor (BL) in a pilot scale. Combinations of co-solvents (ethanol/ water, ethanol/BL) were studied at various concentrations and reaction conditions. The maximum oil yield of 61% was achieved with a reaction temperature of 300 °C for 30 min and using pure BL as a solvent, while the highest higher heating value (HHV) was obtained from a 50:50 ethanol-BL mixture. The oils contained alcohols, esters, phenolic compounds, aromatics, and heterocyclics. The O/C and H/C ratios of the oil were comparable with traditional biodiesel and commercial diesel. Although this study showed there are some improvements to be made to improve the chemical composition, the approach has potential for large-scale production of a substitute for fossil-fuel-based diesel.

The Arctic Summer Cloud Ocean Study (ASCOS): overview and experimental design

The climate in the Arctic is changing faster than anywhere else on earth. Poorly understood feedback processes relating to Arctic clouds and aerosol–cloud interactions contribute to a poor understanding of the present changes in the Arctic climate system, and also to a large spread in projections of future climate in the Arctic. The problem is exacerbated by the paucity of research-quality observations in the central Arctic. Improved formulations in climate models require such observations, which can only come from measurements in situ in this difficult-to-reach region with logistically demanding environmental conditions. The Arctic Summer Cloud Ocean Study (ASCOS) was the most extensive central Arctic Ocean expedition with an atmospheric focus during the International Polar Year (IPY) 2007–2008. ASCOS focused on the study of the formation and life cycle of low-level Arctic clouds. ASCOS departed from Longyearbyen on Svalbard on 2 August and returned on 9 September 2008. In transit into and out of the pack ice, four short research stations were undertaken in the Fram Strait: two in open water and two in the marginal ice zone. After traversing the pack ice northward, an ice camp was set up on 12 August at 87°21' N, 01°29' W and remained in operation through 1 September, drifting with the ice. During this time, extensive measurements were taken of atmospheric gas and particle chemistry and physics, mesoscale and boundary-layer meteorology, marine biology and chemistry, and upper ocean physics. ASCOS provides a unique interdisciplinary data set for development and testing of new hypotheses on cloud processes, their interactions with the sea ice and ocean and associated physical, chemical, and biological processes and interactions. For example, the first-ever quantitative observation of bubbles in Arctic leads, combined with the unique discovery of marine organic material, polymer gels with an origin in the ocean, inside cloud droplets suggests the possibility of primary marine organically derived cloud condensation nuclei in Arctic stratocumulus clouds. Direct observations of surface fluxes of aerosols could, however, not explain observed variability in aerosol concentrations, and the balance between local and remote aerosols sources remains open. Lack of cloud condensation nuclei (CCN) was at times a controlling factor in low-level cloud formation, and hence for the impact of clouds on the surface energy budget. ASCOS provided detailed measurements of the surface energy balance from late summer melt into the initial autumn freeze-up, and documented the effects of clouds and storms on the surface energy balance during this transition. In addition to such process-level studies, the unique, independent ASCOS data set can and is being used for validation of satellite retrievals, operational models, and reanalysis data sets.

VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's Esophagus

Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (P combined = 4.09 × 10-9; odds ratio (OR) = 1.21, 95% confidence interval (CI) =1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (P combined = 2.74 × 10-10; OR = 1.14, 95% CI = 1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus. © 2012 Nature America, Inc. All rights reserved.

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10−8). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10−4, Bonferroni corrected), of which six reached P < 5 × 10−8, including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.

Functional activation during the Rapid Visual Information Processing task in a middle aged cohort: An fMRI study

The Rapid Visual Information Processing (RVIP) task, a serial discrimination task where task performance believed to reflect sustained attention capabilities, is widely used in behavioural research and increasingly in neuroimaging studies. To date, functional neuroimaging research into the RVIP has been undertaken using block analyses, reflecting the sustained processing involved in the task, but not necessarily the transient processes associated with individual trial performance. Furthermore, this research has been limited to young cohorts. This study assessed the behavioural and functional magnetic resonance imaging (fMRI) outcomes of the RVIP task using both block and event-related analyses in a healthy middle aged cohort (mean age = 53.56 years, n = 16). The results show that the version of the RVIP used here is sensitive to changes in attentional demand processes with participants achieving a 43% accuracy hit rate in the experimental task compared with 96% accuracy in the control task. As shown by previous research, the block analysis revealed an increase in activation in a network of frontal, parietal, occipital and cerebellar regions. The event related analysis showed a similar network of activation, seemingly omitting regions involved in the processing of the task (as shown in the block analysis), such as occipital areas and the thalamus, providing an indication of a network of regions involved in correct trial performance. Frontal (superior and inferior frontal gryi), parietal (precuenus, inferior parietal lobe) and cerebellar regions were shown to be active in both the block and event-related analyses, suggesting their importance in sustained attention/vigilance. These networks and the differences between them are discussed in detail, as well as implications for future research in middle aged cohorts.