Persistence of multiple genetic lineages within intra-host populations of Ross River virus

We examined the structure and extent of genetic diversity in intrahost populations of Ross River virus (RRV) in samples from six human patients, focusing on the nonstructural (nsP3) and structural (E2) protein genes. Strikingly, although the samples were collected from contrasting ecological settings 3,000 kilometers apart in Australia, we observed multiple viral lineages in four of the six individuals, which is indicative of widespread mixed infections. In addition, a comparison with previously published RRV sequences revealed that these distinct lineages have been in circulation for at least 5 years, and we were able to document their long-term persistence over extensive geographical distances

Turbulence and suspended sediment measurements in an urban environment during the Brisbane River flood of January 2011

In urbanised areas, the flood flows constitute a hazard to populations and infrastructure as illustrated during major floods in 2011. During the 2011 Brisbane River flood, some turbulent velocity data were collected using acoustic Doppler velocimetry in an inundated street. The field deployment showed some unusual features of flood flow in the urban environment. That is, the water elevations and velocities fluctuated with distinctive periods between 50 and 100 s linked with some local topographic effects. The instantaneous velocity data were analysed using a triple decomposition. The velocity fluctuations included a large energy component in the slow fluctuation range, while the turbulent motion components were much smaller. The suspended sediment data showed some significant longitudinal flux. Altogether the results highlighted that the triple decomposition approach originally developed for period flows is well suited to complicated flows in an inundated urban environment.

Delta opioid-receptor function in the dorsal striatum plays a role in high levels of ethanol consumption in rats

Binge-like patterns of excessive drinking during young adulthood increase the propensity for alcohol use disorders (AUDs) later in adult life; however, the mechanisms that drive this are not completely understood. Previous studies showed that the δ-opioid peptide receptor (DOP-R) is dynamically regulated by exposure to ethanol and that the DOP-R plays a role in ethanol-mediated behaviors. The aim of this study was to determine the role of the DOP-R in high ethanol consumption from young adulthood through to late adulthood by measuring DOP-R-mediated [(35)S]GTPγS binding in brain membranes and DOP-R-mediated analgesia using a rat model of high ethanol consumption in Long Evans rats. We show that DOP-R activity in the dorsal striatum and DOP-R-mediated analgesia changes during development, being highest during early adulthood and reduced in late adulthood. Intermittent access to ethanol but not continuous ethanol or water from young adulthood leads to an increase in DOP-R activity in the dorsal striatum and DOP-R-mediated analgesia into late adulthood. Multiple microinfusions of naltrindole into the dorsal striatum or multiple systemic administration of naltrindole reduces ethanol consumption, and following termination of treatment, DOP-R activity in the dorsal striatum is attenuated. These findings suggest that DOP-R activity in the dorsal striatum plays a role in high levels of ethanol consumption and suggest that targeting the DOP-R is an alternative strategy for the treatment of AUDs.

The delta opioid receptor antagonist, SoRI-9409, decreases yohimbine stress-induced reinstatement of ethanol-seeking

A major problem in treating alcohol use disorders (AUDs) is the high rate of relapse due to stress and re-exposure to cues or an environment previously associated with alcohol use. Stressors can induce relapse to alcohol-seeking in humans or reinstatement in rodents. Delta opioid peptide receptors (DOP-Rs) play a role in cue-induced reinstatement of ethanol-seeking; however, their role in stress-induced reinstatement of ethanol-seeking is not known. The objective of this study was to determine the role of DOP-Rs in yohimbine-stress-induced reinstatement of ethanol-seeking. Male, Long-Evans rats were trained to self-administer 10% ethanol in daily 30-minute operant self-administration sessions using a FR3 schedule of reinforcement, followed by extinction training. Once extinction criteria were met, we examined the effects of the DOP-R antagonist, SoRI-9409 (0–5 mg/kg, i.p.) on yohimbine (2 mg/kg, i.p.) stress-induced reinstatement. Additionally, DOP-R-stimulated [35S]GTPS binding was measured in brain membranes and plasma levels of corticosterone (CORT) were determined. Pre-treatment with SoRI-9409 decreased yohimbine stress-induced reinstatement of ethanol-seeking but did not affect yohimbine-induced increases in plasma CORT levels. Additionally, yohimbine increased DOP-R-stimulated 35[S]GTPS binding in brain membranes of ethanol-trained rats, an effect that was inhibited by SoRI-9409. This suggests that the DOP-R plays an important role in yohimbine-stress-induced reinstatement of ethanol-seeking behavior, and DOP-R antagonists may be promising candidates for further development as a treatment for AUDs.

JFA based Speaker Recognition using Delta-Phase and MFCC features

This paper investigates the use of mel-frequency deltaphase (MFDP) features in comparison to, and in fusion with, traditional mel-frequency cepstral coefficient (MFCC) features within joint factor analysis (JFA) speaker verification. MFCC features, commonly used in speaker recognition systems, are derived purely from the magnitude spectrum, with the phase spectrum completely discarded. In this paper, we investigate if features derived from the phase spectrum can provide additional speaker discriminant information to the traditional MFCC approach in a JFA based speaker verification system. Results are presented which provide a comparison of MFCC-only, MFDPonly and score fusion of the two approaches within a JFA speaker verification approach. Based upon the results presented using the NIST 2008 Speaker Recognition Evaluation (SRE) dataset, we believe that, while MFDP features alone cannot compete with MFCC features, MFDP can provide complementary information that result in improved speaker verification performance when both approaches are combined in score fusion, particularly in the case of shorter utterances.

Cytokine synthesis by intestinal intraepithelial lymphocytes. Both gamma/delta T cell receptor-positive and alpha/beta T cell receptor-positive T cells in the G1 phase of cell cycle produce IFN-gamma and IL-5

Murine intestinal intraepithelial lymphocytes (IEL) have been shown to contain subsets of alpha/beta TCR+ and gamma/delta TCR+ T cells that spontaneously produce cytokines such as IFN-gamma and IL-5. We have now determined the nature and cell cycle stage of these cytokine-producing T lymphocytes in EIL by using IFN-gamma- and IL-5-specific ELISPOT assay, cytokine-specific mRNA-cDNA dot-blot hybridization and polymerase chain reaction, and flow cytometry (FACS) for DNA analysis. When CD3+ T cells from IEL of normal C3H/HeN mice were separated into low and high density fractions by discontinuous Percoll gradients, IFN-gamma and IL-5 spot-forming cells were only found in the former population. Analysis of mRNA for these cytokines by both IFN-gamma- and IL-5-specific dot-blot hybridization and polymerase chain reaction revealed that higher levels of message for IFN-gamma and IL-5 were also seen in the low density fraction. However, cell cycle analysis of these two fractions by FACS using propidium iodide showed a similar pattern of cell cycle stages in both low and high density populations (G0 + G1 approximately 96 to 98% and S/G2 + M approximately 2 to 4%). Finally, mRNA from gamma/delta TCR+ and alpha/beta TCR+ T cells in both low and high density fractions of IEL were analyzed for IFN-gamma and IL-5 message by polymerase chain reaction. After 35 cycles of amplification, both gamma/delta TCR+ and alpha/beta TCR+ T cells in the low density fraction expressed higher levels of message for these two cytokines when compared with the high density population. These results have now shown that both gamma/delta and alpha/beta TCR+ IEL can be separated into low and high density subsets and both fractions possess a similar stage of cell cycle. However, only the low density cells (in G1 phase) of both gamma/delta and alpha/beta TCR types possess increased cytokine-specific mRNA and produce the cytokines IFN-gamma and IL-5. Our results suggest that alpha/beta TCR+ and gamma/delta TCR+ IEL can produce cytokines without cell proliferation.

Application of a digital elevation model for flood modeling for the Pagsangaan River in Leyte

Flood related scientific and community-based data are rarely systematically collected and analysed in the Philippines. Over the last decades the Pagsangaan River Basin, Leyte, has experienced several flood events. However, documentation describing flood characteristics such as extent, duration or height of these floods are close to non-existing. To address this issue, computerized flood modelling was used to reproduce past events where there was data available for at least partial calibration and validation. The model was also used to provide scenario-based predictions based on A1B climate change assumptions for the area. The most important input for flood modelling is a Digital Elevation Model (DEM) of the river basin. No accurate topographic maps or Light Detection And Ranging (LIDAR)-generated data are available for the Pagsangaan River. Therefore, the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Global Digital Elevation Map (GDEM), Version 1, was chosen as the DEM. Although the horizontal spatial resolution of 30 m is rather desirable, it contains substantial vertical errors. These were identified, different correction methods were tested and the resulting DEM was used for flood modelling. The above mentioned data were combined with cross-sections at various strategic locations of the river network, meteorological records, river water level, and current velocity to develop the 1D-2D flood model. SOBEK was used as modelling software to create different rainfall scenarios, including historic flooding events. Due to the lack of scientific data for the verification of the model quality, interviews with local stakeholders served as the gauge to judge the quality of the generated flood maps. According to interviewees, the model reflects reality more accurately than previously available flood maps. The resulting flood maps are now used by the operations centre of a local flood early warning system for warnings and evacuation alerts. Furthermore these maps can serve as a basis to identify flood hazard areas for spatial land use planning purposes.

A case study of interactions between flood flow and buildings in an urban environment : Gardens Point during the 12-13 January 2011 flood of the Brisbane River (Australia)

Flood flows in inundated urban environment constitute a natural hazard. During the 12- 13 January 2011 flood of the Brisbane River, detailed water elevation, velocity and suspended sediment data were recorded in an inundated street at the peak of the flood. The field observations highlighted a number of unusual flow interactions with the urban surroundings. These included some slow fluctuations in water elevations and velocity with distinctive periods between 50 and 100 s caused by some local topographic effect (choking), superposed with some fast turbulent fluctuations. The suspended sediment data highlighted some significant suspended sediment loads in the inundated zone.

Ross River virus evolution : implications for vaccine development

Ross River virus is a mosquito-borne alphavirus that causes approximately 5000 cases of epidemic polyarthritis in Australia each year and has direct medical-associated costs of approximately US$15 million annually. While mosquito control programs are able, at best, to contain rather than prevent this disease, natural infection with Ross River virus confers lifelong protection against subsequent clinical infection. A killed-virus vaccine has been developed, which is in Phase III clinical trials. Analyses of intra-host genetic diversity and of long-term evolutionary changes in Ross River virus populations suggest that antigenic variation is unlikely to pose a threat to the efficacy of this vaccine.

“Would you; could you; on a boat?” Wait-time and travel-time activities during river ferry journeys and their relationship to overall satisfaction in Brisbane Queensland

This study investigates travel behaviour and wait-time activities as a component of passenger satisfaction with public transport in Brisbane, Australia. Australian transport planners recognise a variety of benefits to encouraging a mode shift away from automobile travel in favour of active and public transport use. Efforts to increase public transport ridership have included introducing state of the art passenger information systems, improving physical station access, and integrating system pricing, routes and scheduling for train, bus and ferry. Previous research regarding satisfaction with public transport emphasizes technical dimensions of service quality, including the timing and reliability of service. Those factors might be especially significant for frequent (commuting) travellers who look to balance the cost and efficiency of their travel options. In contrast, infrequent (leisure) passengers may be more concerned with way finding and the sensory experience of the journey. Perhaps due to the small relative proportion of trips made by river ferry compared to bus and rail, this mode of public transport has not received as much attention in travel-behaviour research. This case study of Brisbane’s river ferry system examines ferry passengers at selected terminals during peak and off-peak travel times to find out how travel behaviours and activities correlate to satisfaction with ferry travel. Data include 416 questionnaires completed by passengers intercepted during wait times at seven CityCat terminals in Brisbane. Descriptive statistical analysis revealed associations between specific wait time activities and satisfaction levels that could inform planners seeking to increase ridership and quality of life through ferry-oriented development.

Characterisation and source apportionment of polycyclic aromatic hydrocarbons in the sediments of Brisbane River

The thesis was a step forward in predicting the levels and sources of polycyclic aromatic hydrocarbons (PAHs) in sediments of Brisbane river, especially after the Brisbane floods in 2011. It employed different statistical techniques to provide valuable information that may assist source control and formulation of pollution mitigation measures for the river.

Differential entrainment of neuroelectric delta oscillations in developmental dyslexia

Oscillatory entrainment to the speech signal is important for language processing, but has not yet been studied in developmental disorders of language. Developmental dyslexia, a difficulty in acquiring efficient reading skills linked to difficulties with phonology (the sound structure of language), has been associated with behavioural entrainment deficits. It has been proposed that the phonological ‘deficit’ that characterises dyslexia across languages is related to impaired auditory entrainment to speech at lower frequencies via neuroelectric oscillations (<10 Hz, ‘temporal sampling theory’). Impaired entrainment to temporal modulations at lower frequencies would affect the recovery of the prosodic and syllabic structure of speech. Here we investigated event-related oscillatory EEG activity and contingent negative variation (CNV) to auditory rhythmic tone streams delivered at frequencies within the delta band (2 Hz, 1.5 Hz), relevant to sampling stressed syllables in speech. Given prior behavioural entrainment findings at these rates, we predicted functionally atypical entrainment of delta oscillations in dyslexia. Participants performed a rhythmic expectancy task, detecting occasional white noise targets interspersed with tones occurring regularly at rates of 2 Hz or 1.5 Hz. Both groups showed significant entrainment of delta oscillations to the rhythmic stimulus stream, however the strength of inter-trial delta phase coherence (ITC, ‘phase locking’) and the CNV were both significantly weaker in dyslexics, suggestive of weaker entrainment and less preparatory brain activity. Both ITC strength and CNV amplitude were significantly related to individual differences in language processing and reading. Additionally, the instantaneous phase of prestimulus delta oscillation predicted behavioural responding (response time) for control participants only.

Ross River virus arthritis

“Epidemics” of a benign disease causing polyarthralgia and rash were first described in Australia in 1927.63 Following the recovery of the causative agent and the advent of serologic tests able to diagnose Ross River virus infection, epidemic polyarthritis has been recognized as endemic in Australia and has occurred as epidemics in numerous Pacific nations. Approximately 4000 cases of epidemic polyarthritis are reported in Australia each year, with a peak of 7800 cases in 1996. Some confusion has been generated recently by use of the term Ross River fever to describe clinical Ross River virus infections because fever does not develop in more than half of those with clinical disease.59 Additional confusion has been generated by efforts to describe any polyarthritis caused by an Australian arbovirus as epidemic polyarthritis. The term epidemic polyarthritis should be used to describe only clinical disease caused by Ross River virus.