Experimental observations of rapid maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background. Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ∼10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results. We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion. These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. © 2008 Walt et al; licensee BioMed Central Ltd.

Error and uncertainty of adult age estimation of the pubic symphysis in an Australian sub-population using computed tomography

After attending this presentation, attendees will gain awareness of: (1) the error and uncertainty associated with the application of the Suchey-Brooks (S-B) method of age estimation of the pubic symphysis to a contemporary Australian population; (2) the implications of sexual dimorphism and bilateral asymmetry of the pubic symphysis through preliminary geometric morphometric assessment; and (3) the value of three-dimensional (3D) autopsy data acquisition for creating forensic anthropological standards. This presentation will impact the forensic science community by demonstrating that, in the absence of demographically sound skeletal collections, post-mortem autopsy data provides an exciting platform for the construction of large contemporary ‘virtual osteological libraries’ for which forensic anthropological research can be conducted on Australian individuals. More specifically, this study assesses the applicability and accuracy of the S-B method to a contemporary adult population in Queensland, Australia, and using a geometric morphometric approach, provides an insight to the age-related degeneration of the pubic symphysis. Despite the prominent use of the Suchey-Brooks (1990) method of age estimation in forensic anthropological practice, it is subject to intrinsic limitations, with reports of differential inter-population error rates between geographical locations1-4. Australian forensic anthropology is constrained by a paucity of population specific standards due to a lack of repositories of documented skeletons. Consequently, in Australian casework proceedings, standards constructed from predominately American reference samples are applied to establish a biological profile. In the global era of terrorism and natural disasters, more specific population standards are required to improve the efficiency of medico-legal death investigation in Queensland. The sample comprises multi-slice computed tomography (MSCT) scans of the pubic symphysis (slice thickness: 0.5mm, overlap: 0.1mm) on 195 individuals of caucasian ethnicity aged 15-70 years. Volume rendering reconstruction of the symphyseal surface was conducted in Amira® (v.4.1) and quantitative analyses in Rapidform® XOS. The sample was divided into ten-year age sub-sets (eg. 15-24) with a final sub-set of 65-70 years. Error with respect to the method’s assigned means were analysed on the basis of bias (directionality of error), inaccuracy (magnitude of error) and percentage correct classification of left and right symphyseal surfaces. Morphometric variables including surface area, circumference, maximum height and width of the symphyseal surface and micro-architectural assessment of cortical and trabecular bone composition were quantified using novel automated engineering software capabilities. The results of this study demonstrated correct age classification utilizing the mean and standard deviations of each phase of the S-B method of 80.02% and 86.18% in Australian males and females, respectively. Application of the S-B method resulted in positive biases and mean inaccuracies of 7.24 (±6.56) years for individuals less than 55 years of age, compared to negative biases and mean inaccuracies of 5.89 (±3.90) years for individuals greater than 55 years of age. Statistically significant differences between chronological and S-B mean age were demonstrated in 83.33% and 50% of the six age subsets in males and females, respectively. Asymmetry of the pubic symphysis was a frequent phenomenon with 53.33% of the Queensland population exhibiting statistically significant (χ2 - p<0.01) differential phase classification of left and right surfaces of the same individual. Directionality was found in bilateral asymmetry, with the right symphyseal faces being slightly older on average and providing more accurate estimates using the S-B method5. Morphometric analysis verified these findings, with the left surface exhibiting significantly greater circumference and surface area than the right (p<0.05). Morphometric analysis demonstrated an increase in maximum height and width of the surface with age, with most significant changes (p<0.05) occurring between the 25-34 and 55-64 year age subsets. These differences may be attributed to hormonal components linked to menopause in females and a reduction in testosterone in males. Micro-architectural analysis demonstrated degradation of cortical composition with age, with differential bone resorption between the medial, ventral and dorsal surfaces of the pubic symphysis. This study recommends that the S-B method be applied with caution in medico-legal death investigations of unknown skeletal remains in Queensland. Age estimation will always be accompanied by error; therefore this study demonstrates the potential for quantitative morphometric modelling of age related changes of the pubic symphysis as a tool for methodological refinement, providing a rigor and robust assessment to remove the subjectivity associated with current pelvic aging methods.

Closing the case of APOE in multiple sclerosis : no association with disease risk in over 29,000 subjects

Background Single nucleotide polymorphisms (SNPs) rs429358 (ε4) and rs7412 (ε2), both invoking changes in the amino-acid sequence of the apolipoprotein E (APOE) gene, have previously been tested for association with multiple sclerosis (MS) risk. However, none of these studies was sufficiently powered to detect modest effect sizes at acceptable type-I error rates. As both SNPs are only imperfectly captured on commonly used microarray genotyping platforms, their evaluation in the context of genome-wide association studies has been hindered until recently. Methods We genotyped 12 740 subjects hitherto not studied for their APOE status, imputed raw genotype data from 8739 subjects from five independent genome wide association studies datasets using the most recent high-resolution reference panels, and extracted genotype data for 8265 subjects from previous candidate gene assessments. Results Despite sufficient power to detect associations at genome-wide significance thresholds across a range of ORs, our analyses did not support a role of rs429358 or rs7412 on MS susceptibility. This included meta-analyses of the combined data across 13 913 MS cases and 15 831 controls (OR=0.95, p=0.259, and OR 1.07, p=0.0569, for rs429358 and rs7412, respectively). Conclusion Given the large sample size of our analyses, it is unlikely that the two APOE missense SNPs studied here exert any relevant effects on MS susceptibility.

What can we learn from the crashes of learner riders?

In some parts of Australia, people wanting to learn to ride a motorcycle are required to complete an off-road training course before they are allowed to practice on the road. In the state of Queensland, they are only required to pass a short multiple-choice road rules knowledge test. This paper describes an analysis of police-reported crashes involving learner riders in Queensland that was undertaken as part of research investigating whether pre-learner training is needed and, if so, the issues that should be addressed in training.. The crashes of learner riders and other riders were compared to identify whether there are particular situations or locations in which learner motorcyclists are over-involved in crashes, which could then be targeted in the pre-learner package. The analyses were undertaken separately for riders aged under 25 (330 crashes) versus those aged 25 and over (237 crashes) to provide some insight into whether age or riding inexperience are the more important factors, and thus to indicate whether there are merits in having different licensing or training approaches for younger and older learner riders. Given that the average age of learner riders was 33 years, under 25 was chosen to provide a sufficiently large sample of younger riders. Learner riders appeared to be involved in more severe crashes and to be more often at fault than fully-licensed riders but this may reflect problems in reporting, rather than real differences. Compared to open licence holders, both younger and older learner riders had relatively more crashes in low speed zones and relatively fewer in high speed zones. Riders aged under 25 had elevated percentages of night-time crashes and fewer single unit (potentially involving rider error only) crashes regardless of the type of licence held. The contributing factors that were more prevalent in crashes of learner riders than holders of open licences were: inexperience (37.2% versus 0.5%), inattention (21.5% versus 15.6%), alcohol or drugs (12.0% versus 5.1%) and drink riding (9.9% versus 3.1%). The pattern of contributing factors was generally similar for younger and older learner riders, although younger learners were (not surprisingly) more likely to have inexperience coded as a contributing factor (49.7% versus 19.8%). Some of the differences in crashes between learner riders and fully-licensed riders appear to reflect relatively more riding in urban areas by learners, rather than increased risks relating to inexperience. The analysis of contributing factors in learner rider crashes suggests that hazard perception and risk management (in terms of speed and alcohol and drugs) should be included in a pre-learner program. Currently, most learner riders in Queensland complete pre-licence training and become licensed within one month of obtaining their learner permit. If the introduction of pre-learner training required that the learner permit was held for a minimum duration, then the immediate effect might be more learners riding (and crashing). Thus, it is important to consider how training and licensing initiatives work together in order to improve the safety of new riders (and how this can be evaluated).

The effects of flight speed on ranging performance of bats using frequency modulated echolocation pulses

Many species of bat use ultrasonic frequency modulated (FM) pulses to measure the distance to objects by timing the emission and reception of each pulse. Echolocation is mainly used in flight. Since the flight speed of bats often exceeds 1% of the speed of sound, Doppler effects will lead to compression of the time between emission and reception as well as an elevation of the echo frequencies, resulting in a distortion of the perceived range. This paper describes the consequences of these Doppler effects on the ranging performance of bats using different pulse designs. The consequences of Doppler effects on ranging performance described in this paper assume bats to have a very accurate ranging resolution, which is feasible with a filterbank receiver. By modeling two receiver types, it was first established that the effects of Doppler compression are virtually independent of the receiver type. Then, used a cross-correlation model was used to investigate the effect of flight speed on Doppler tolerance and range–Doppler coupling separately. This paper further shows how pulse duration, bandwidth, function type, and harmonics influence Doppler tolerance and range–Doppler coupling. The influence of each signal parameter is illustrated using calls of several bat species. It is argued that range–Doppler coupling is a significant source of error in bat echolocation, and various strategies bats could employ to deal with this problem, including the use of range rate information are discussed.

The influence of flight speed on the ranging performance of bats using frequency modulated echolocation pulses

Many species of bat use ultrasonic frequency modulated (FM) pulses to measure the distance to objects by timing the emission and reception of each pulse. Echolocation is mainly used in flight. Since the flight speed of bats often exceeds 1% of the speed of sound,Doppler effects will lead to compression of the time between emission and reception as well as an elevation of the echo frequencies, resulting in a distortion of the perceived range. This paper describes the consequences of these Doppler effects on the ranging performance of bats using different pulse designs. The consequences of Doppler effects on ranging performance described in this paper assume bats to have a very accurate ranging resolution, which is feasible with a filterbank receiver. By modeling two receiver types, it was first established that the effects of Doppler compression are virtually independent of the receiver type. Then, used a cross-correlation model was used to investigate the effect of flight speed on Doppler tolerance and range–Doppler coupling separately. This paper further shows how pulse duration, bandwidth, function type, and harmonics influence Doppler tolerance and range–Doppler coupling. The influence of each signal parameter is illustrated using calls of several bat species. It is argued that range–Doppler coupling is a significant source of error in bat echolocation, and various strategies bats could employ to deal with this problem, including the use of range rate information are discussed.

Conversion of n-type CuTCNQ into p-type nitrogen-doped CuO and the implication for room temperature gas sensing

Sensors to detect toxic and harmful gases are usually based on metal oxides that are operated at elevated temperature. However, enabling gas detection at room temperature (RT) is a significant ongoing challenge. Here, we address this issue by demonstrating that microrods of semiconducting CuTCNQ (TCNQ=7,7,8,8-tetracyanoquinodimethane) with nanostructured features can be employed as conductometric gas sensors operating at 50°C for detection of oxidizing and reducing gases such as NO2 and NH3. The sensor is evaluated at RT and up to 200°C. It was found that CuTCNQ is transformed into a N-doped CuO material with p-type conductivity when annealed at the maximum temperature. This is the first time that such a transformation, from a semiconducting charge transfer material into a N-doped metal oxide is detected. It is shown here that both the surface chemistry and the type of majority charge carrier within the sensing layer is critically important for the type of response towards oxidizing and reducing gases. A detailed physical description of NO2 and NH3 sensing mechanism at CuTCNQ and N-doped CuO is provided to explain the difference in the response. For the N-doped CuO sensor, a detection limit of 1 ppm for NO2 and 10 ppm for NH3 are achieved.

Analysis of physical activity in emmetropic and myopic university students during semester and holiday periods: A pilot study

Background Previous studies (mostly questionnaire-based in children) suggest that outdoor activity is protective against myopia. There are few studies on young adults investigating both the impact of simply being outdoors versus performing physical activity. The aim was to study the relationship between the refractive error of young adults and their physical activity patterns. Methods Twenty-seven university students, aged 18 to 25 years, wore a pedometer (Omron HJ720ITE) for seven days both during the semester and holiday periods. They simultaneously recorded the type of activity performed, its duration, the number of steps taken (from the pedometer) and their location (indoors/outdoors) in a logbook. Mean spherical refractive error was used to divide participants into three groups (emmetropes: +1.00 to -0.50 D, low myopes: -0.62 to -3.00 D, higher myopes: -3.12 D or greater myopia). Results There were no significant differences between the refractive groups during the semester or holiday periods; the average daily times spent outdoors, the duration of physical activity, the ratio of physical activity performed outdoors to indoors and amount of near work performed were similar. The peak exercise intensity was similar across all groups: approximately 100 steps perminute, a brisk walk. Up to one-third of all physical activity was performed outdoors. There were some significant differences in activities performed during semester and holiday times. For example, lowmyopes spent significantly less time outside (49 ± 47 versus 74 ± 41 minutes, p = 0.005) and performed less physical activity (6,388 ± 1,747 versus 6,779 ± 2,746 steps per day; p = 0.03) during the holidays compared to during semester. Conclusions The fact that all groups had similar low exercise intensity butmany were notmyopic suggests that physical activity levels are not critical. There were differences in the activity patterns of lowmyopes during semester and holiday periods. This study highlights the need for a larger longitudinal-based study with particular emphasis on how discretionary time is spent.

Effect of position on precision within the recording field of a markerless motion capture system

Introduction Markerless motion capture systems are relatively new devices that can significantly speed up capturing full body motion. A precision of the assessment of the finger’s position with this type of equipment was evaluated at 17.30 ± 9.56 mm when compare to an active marker system [1]. The Microsoft Kinect was proposed to standardized and enhanced clinical evaluation of patients with hemiplegic cerebral palsy [2]. Markerless motion capture systems have the potential to be used in a clinical setting for movement analysis, as well as for large cohort research. However, the precision of such system needs to be characterized. Global objectives • To assess the precision within the recording field of the markerless motion capture system Openstage 2 (Organic Motion, NY). • To compare the markerless motion capture system with an optoelectric motion capture system with active markers. Specific objectives • To assess the noise of a static body at 13 different location within the recording field of the markerless motion capture system. • To assess the smallest oscillation detected by the markerless motion capture system. • To assess the difference between both systems regarding the body joint angle measurement. Methods Equipment • OpenStage® 2 (Organic Motion, NY) o Markerless motion capture system o 16 video cameras (acquisition rate : 60Hz) o Recording zone : 4m * 5m * 2.4m (depth * width * height) o Provide position and angle of 23 different body segments • VisualeyezTM VZ4000 (PhoeniX Technologies Incorporated, BC) o Optoelectric motion capture system with active markers o 4 trackers system (total of 12 cameras) o Accuracy : 0.5~0.7mm Protocol & Analysis • Static noise: o Motion recording of an humanoid mannequin was done in 13 different locations o RMSE was calculated for each segment in each location • Smallest oscillation detected: o Small oscillations were induced to the humanoid mannequin and motion was recorded until it stopped. o Correlation between the displacement of the head recorded by both systems was measured. A corresponding magnitude was also measured. • Body joints angle: o Body motion was recorded simultaneously with both systems (left side only). o 6 participants (3 females; 32.7 ± 9.4 years old) • Tasks: Walk, Squat, Shoulder flexion & abduction, Elbow flexion, Wrist extension, Pronation / supination (not in results), Head flexion & rotation (not in results), Leg rotation (not in results), Trunk rotation (not in results) o Several body joint angles were measured with both systems. o RMSE was calculated between signals of both systems. Results Conclusion Results show that the Organic Motion markerless system has the potential to be used for assessment of clinical motor symptoms or motor performances However, the following points should be considered: • Precision of the Openstage system varied within the recording field. • Precision is not constant between limb segments. • The error seems to be higher close to the range of motion extremities.

Identifying advanced practice: A national survey of a nursing workforce

Background The size and flexibility of the nursing workforce has positioned nursing as central to the goals of health service improvement. Nursing's response to meeting these goals has resulted in proliferation of advanced practice nursing with a confusing array of practice profiles, titles and roles. Whilst numerous models and definitions of advanced practice nursing have been developed there is scant published research of significant scope that supports these models. Consequently there is an ongoing call in the literature for clarity and stability in nomenclature, and confusion in the health industry on how to optimise the utility of advanced practice nursing. Objectives To identify and delineate advanced practice from other levels of nursing practice through examination of a national nursing workforce. Design A cross-sectional electronic survey of nurses using the validated Advanced Practice Role Delineation tool based on the Strong Model of Advanced Practice. Participants Study participants were registered nurses employed in a clinical service environment across all states and territories of Australia. Methods A sample of 5662 registered nurses participated in the study. Domain means for each participant were calculated then means for nursing position titles were calculated. Position titles were grouped by delineation and were compared with one-way analysis of variance on domain means. The alpha for all tests was set at 0.05. Significant effects were examined with Scheffe post hoc comparisons to control for Type 1 error. Results The survey tool was able to identify position titles where nurses were practicing at an advanced level and to delineate this cohort from other levels of nursing practice, including nurse practitioner. The results show that nurses who practice at an advanced level are characterised by high mean scores across all Domains of the Strong Model of Advanced Practice. The mean scores of advanced practice nurses were significantly different from nurse practitioners in the Direct Care Domain and significantly different from other levels of nurse across all domains. Conclusions The study results show that the nurse practitioner, advanced practice nurse and foundation level registered nurse have different patterns of practice and the Advanced Practice Role Delineation tool has the capacity to clearly delineate and define advanced practice nursing. These findings make a significant contribution to the international debate and show that the profession can now identify what is and what is not advanced practice in nursing.

Computation of turbulent flow in an IFRF quarl burner

A computational model for isothermal axisymmetric turbulent flow in a quarl burner is set up using the CFD package FLUENT, and numerical solutions obtained from the model are compared with available experimental data. A standard k-e model and and two versions of the RNG k-e model are used to model the turbulence. One of the aims of the computational study is to investigate whether the RNG based k-e turbulence models are capable of yielding improved flow predictions compared with the standard k-e turbulence model. A difficulty is that the flow considered here features a confined vortex breakdown which can be highly sensitive to flow behaviour both upstream and downstream of the breakdown zone. Nevertheless, the relatively simple confining geometry allows us to undertake a systematic study so that both grid-independent and domain-independent results can be reported. The systematic study includes a detailed investigation of the effects of upstream and downstream conditions on the predictions, in addition to grid refinement and other tests to ensure that numerical error is not significant. Another important aim is to determine to what extent the turbulence model predictions can provide us with new insights into the physics of confined vortex breakdown flows. To this end, the computations are discussed in detail with reference to known vortex breakdown phenomena and existing theories. A major conclusion is that one of the RNG k-e models investigated here is able to correctly capture the complex forward flow region inside the recirculating breakdown zone. This apparently pathological result is in stark contrast to the findings of previous studies, most of which have concluded that either algebraic or differential Reynolds stress modelling is needed to correctly predict the observed flow features. Arguments are given as to why an isotropic eddy-viscosity turbulence model may well be able to capture the complex flow structure within the recirculating zone for this flow setup. With regard to the flow physics, a major finding is that the results obtained here are more consistent with the view that confined vortex breakdown is a type of axisymmetric boundary layer separation, rather than a manifestation of a subcritical flow state.

The clinical reasoning characteristics of diagnostic experts

The aim of this study was to identify and describe the clinical reasoning characteristics of diagnostic experts. A group of 21 experienced general practitioners were asked to complete the Diagnostic Thinking Inventory (DTI) and a set of 10 clinical reasoning problems (CRPs) to evaluate their clinical reasoning. Both the DTI and the CRPs were scored, and the CRP response patterns of each GP examined in terms of the number and type of errors contained in them. Analysis of these data showed that six GPs were able to reach the correct diagnosis using significantly less clinical information than their colleagues. These GPs also made significantly fewer interpretation errors but scored lower on both the DTI and the CRPs. Additionally, this analysis showed that more than 20% of misdiagnoses occurred despite no errors being made in the identification and interpretation of relevant clinical information. These results indicate that these six GPs diagnose efficiently, effectively and accurately using relatively few clinical data and can therefore be classified as diagnostic experts. They also indicate that a major cause of misdiagnoses is failure to properly integrate clinical data. We suggest that increased emphasis on this step in the reasoning process should prove beneficial to the development of clinical reasoning skill in undergraduate medical students.

From emotional suppression to regulated empathy : the changing face of control in the CES

Between the 1970s and the 1990s the level and type of emotionality in the Commonwealth Employment Service (the Australian national employment service) altered. Within a context of changing economic conditions and concomitant work intensification, it is argued that untenable working conditions resulted in new recruits adopting a coping strategy that led to the use rather than the suppression of emotions. The use of emotions provided workers with job satisfaction and greater control over service interactions. Management subsequently commandeered the use of emotions to complement the introduction of private sector management techniques and service delivery reforms, regaining control over worker-client interactions.

Particle number and mass emission factors from combustion of wood samples collected from Queensland forest

Knowledge of particle emission characteristics associated with forest fires and in general, biomass burning, is becoming increasingly important due to the impact of these emissions on human health. Of particular importance is developing a better understanding of the size distribution of particles generated from forest combustion under different environmental conditions, as well as provision of emission factors for different particle size ranges. This study was aimed at quantifying particle emission factors from four types of wood found in South East Queensland forests: Spotted Gum (Corymbia citriodora), Red Gum (Eucalypt tereticornis), Blood Gum (Eucalypt intermedia), and Iron bark (Eucalypt decorticans); under controlled laboratory conditions. The experimental set up included a modified commercial stove connected to a dilution system designed for the conditions of the study. Measurements of particle number size distribution and concentration resulting from the burning of woods with a relatively homogenous moisture content (in the range of 15 to 26 %) and for different rates of burning were performed using a TSI Scanning Mobility Particle Sizer (SMPS) in the size range from 10 to 600 nm and a TSI Dust Trak for PM2.5. The results of the study in terms of the relationship between particle number size distribution and different condition of burning for different species show that particle number emission factors and PM2.5 mass emission factors depend on the type of wood and the burning rate; fast burning or slow burning. The average particle number emission factors for fast burning conditions are in the range of 3.3 x 1015 to 5.7 x 1015 particles/kg, and for PM2.5 are in the range of 139 to 217 mg/kg.

Is philanthropy relevant? a study of professional advisers in Australia

CPNS’ new Working Paper examines the latest findings from a national survey of professional advisers on the topic of philanthropy assistance to high-net-worth individuals. Findings confirm a growing willingness within the Australian advisory sector to provide philanthropy advice to clients with means, although the rate of change has slowed since 2005. Advisers are now more likely to see benefits in providing this type of counselling, as well as benefits for their clients in engaging in philanthropy.