Inferring phylogenies of evolving sequences without multiple sequence alignment

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

A different kind of studio: Reflecting on the open studio and the artist-teacher

For more than 15 years, QUT’s Visual Arts discipline has employed a teaching model known as the ‘open studio’ in their undergraduate BFA program. Distinct from the other models of studio degrees in Australia, the open studio approach emphasizes individual practice by focusing on experimentation, collaboration and cross-disciplinary activities. However, while this activity proves to be highly relevant to exploring and participating in the ‘post medium’ nature of much contemporary art, the open studio also presents a complex of affecting challenges to the artist-teacher. The open studio, it can be argued, produces a different type of student than traditional, discipline-specific art programs – but it also produces a different kind of artist-teacher. In this paper, the authors will provide a reflection on their own experiences as artists and studio lecturers involved with the two ‘bookends’ of the QUT studio program – first year and third year. Using these separate contexts as case studies, the authors will discuss the transformative qualities of the open studio as it is adapted to the particularities of each cohort and the curricular needs of each year level. In particular, the authors will explore the way the teaching experience has influenced and positively challenged their individual (and paradoxically) discipline-focussed, studio practices. It is generally accepted that the teaching of art needs to be continually reconceptualised in response to the changing conditions of contemporary art, culture and technology. This paper will articulate how the authors have worked at that reconceptualisation within both their teaching and studio practices and so practically demonstrate the complex dialogic processes inherent to the teaching of the visual arts studio.

Can larger-bodied cemented femoral components reduce periprosthetic fractures? A biomechanical study

Introduction: The risk for late periprosthetic femoral fractures is higher in patients treated for a neck of femur fracture compared to osteoarthritis. It has been hypothesised that osteopenia and consequent decreased stiffness of the proximal femur are responsible for this. We investigated whether a femoral component with a bigger body would increase the torque to failure in a biaxially loaded composite Sawbone model. Material and methods: A biomechanical bone analogue was used. Two different body sizes (Exeter 44-1 vs 44-4) of a polished tapered cemented femoral stem were implanted by an experienced surgeon in 7 bone analogues each and internally rotated at 40°/s until failure. Torque to fracture and fracture energy were measured using a biaxial materials testing device (Instron 8874, MI, USA). The data were non-parametric and therefore tested with the Mann-Whitney U-test. Results: The median torque to fracture was 156.7 Nm (IQR 19.7) for the 44-1 stem and 237.1 Nm (IQR 52.9) for the 44-4 stem (p=0.001). The median fracture energy was 8.5J (IQR 7.3) for the 44-1 stem and 19.5J (IQR 8.8) for the 44-4 stem (p=0.014). Conclusions: The use of a large body polished tapered cemented stems for neck of femur fractures increases the torque to failure in a biomechanical model and therefore is likely to reduce late periprosthetic fracture risk in this vulnerable cohort.

Tailoring surface properties and structure of layered double hydroxides using silanes with different number of functional groups

Four silanes, trimethylchlorosilane (TMCS), dimethyldiethoxylsilane (DMDES), 3-aminopropyltriethoxysilane (APTES) and tetraethoxysilane (TEOS), were adopted to graft layered double hydroxides (LDH) via an induced hydrolysis silylation method (IHS). Fourier transform infrared spectra (FTIR) and 29Si MAS nuclear magnetic resonance spectra (29Si MAS NMR) indicated that APTES and TEOS can be grafted onto LDH surfaces via condensation with hydroxyl groups of LDH, while TMCS and DMDES could only be adsorbed on the LDH surface with a small quantity. A combination of X-ray diffraction patterns (XRD) and 29Si MAS NMR spectra showed that silanes were exclusively present in the external surface and had little influence on the long range order of LDH. The surfactant intercalation experiment indicated that the adsorbed and/or grafted silane could not fix the interlamellar spacing of the LDH. However, they will form crosslink between the particles and affect the further surfactant intercalation in the silylated samples. The replacement of water by ethanol in the tactoids and/or aggregations and the polysiloxane oligomers formed during silylation procedure can dramatically increase the value of BET surface area (SBET) and total pore volumes (Vp) of the products.

Influence of the structural characteristic of pyrolysis products on thermal stability of styrene-butadiene rubber composites reinforced by different particle sized kaolinites

A series of rubber composites were prepared by blending styrene-butadiene rubber (SBR) latex and the different particle sized kaolinites. The thermal stabilities of the rubber composites were characterized using thermogravimetry, digital photography, scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and Raman spectroscopy. Kaolinite SBR composites showed much greater thermal stability when compared with that of the pure SBR. With the increase of kaolinite particle size, the pyrolysis products became much looser; the char layer and crystalline carbon content gradually decreased in the pyrolysis residues. The pyrolysis residues of the SBR composites filled with the different particle sized kaolinites showed some remarkable changes in structural characteristics. The increase of kaolinite particle size was not beneficial to form the compact and stable crystalline carbon in the pyrolysis process, and resulted in a negative influence in improving the thermal stability of kaolinite/SBR composites.

Different correlation of Sphingosine-1-Phosphate receptor 1 with receptor activator of nuclear factor kappa B ligand and regulatory T cells in rat periapical lesions

Introduction Sphingosine-1-phosphate receptor 1 (S1P1) is crucial for regulation of immunity and bone metabolism. This study aimed to investigate the expression of S1P1 in rat periapical lesions and its relationship with receptor activator of nuclear factor kappa B ligand (RANKL) and regulatory T (Treg) cells. Methods Periapical lesions were induced by pulp exposure in the first lower molars of 55 Wistar rats. Thirty rats were killed on days 0, 7, 14, 21, 28, and 35, and their mandibles were harvested for x-ray imaging, micro–computed tomography scanning, histologic observation, immunohistochemistry, enzyme histochemistry, and double immunofluorescence analysis. The remaining 25 rats were killed on days 0, 14, 21, 28, and 35, and mandibles were harvested for flow cytometry. Results The volume and area of the periapical lesions increased from day 0 to day 21 and then remained comparably stable after day 28. S1P1-positive cells were observed in the inflammatory periapical regions; the number of S1P1-positive cells peaked at day 14 and then decreased from day 21 to day 35. The distribution of S1P1-positive cells was positively correlated with the dynamics of RANKL-positive cells but was negatively correlated with that of Treg cells. Conclusions S1P1 expression was differentially correlated with RANKL and Treg cell infiltration in the periapical lesions and is therefore a contributing factor to the pathogenesis of such lesions.

Pilot study comparing the influence of different types of exercise intervention on the fear of falling in older adults

Background: Individuals who fear falling may restrict themselves from performing certain activities and may increase their risk of falling. Such fear, reflected in the form of falls efficacy, has been measured in only a small number of studies measuring the effectiveness of exercise interventions in the elderly. This may be due to the various types of exercise that can be performed. Hence the effectiveness of exercise on falls efficacy is relatively understudied. Therefore, there is a need to measure falls efficacy as an outcome variable when conducting exercise interventions in the elderly. Methods: A total of 43 elderly community-dwelling volunteers were recruited and randomly allocated to a conventional exercise intervention, a holistic exercise intervention, or a control group. The interventions were performed 2 days per week for 10 weeks. Falls efficacy was measured at baseline and at the completion of the interventions using the Modified Falls Efficacy Scale (MFES). Results: Within group comparisons between baseline and follow-up indicated no significant improvements in falls efficacy, however, the difference for the conventional exercise group approached statistical significance (baseline 8.9 to follow-up 9.3; P = 0.058). Within group comparisons of mean difference MFES scores showed a significant difference between the conventional exercise group and the control group (conventional exercise group 0.4 vs control group −0.6; P < 0.05). Conclusion: Given the lack of significant improvements in falls efficacy found for any of the groups, it cannot be concluded whether a conventional or a holistic exercise intervention is the best approach for improving falls efficacy. It is possible that the characteristics of the exercise interventions including specificity, intensity, frequency and duration need to be manipulated if the purpose is to bring about improvements in falls efficacy.

Can different measures of intelligence be used interchangeably? A comparison of the Wechsler and Stanford-Binet scales

The Wechsler and Stanford Binet scales are among the most commonly used tests of intelligence. In clinical practice, they often seem to be used interchangeably. This paper reports the results of two studies that compared the most recent editions of two Wechsler scales (WPPSI-III and WISC-IV) with the Stanford-Binet Fifth Edition (SB5). The participants in the first study were 36 typically developing 4-year-old children who completed the WPPSI-III and SB5 in counter-balanced order. Although correlations of composite scores ranged from r = .59 to r = .82 and were similar to those reported for earlier versions of the two instruments, more than half the sample had a score discrepancy greater than 10 points across the two instruments. In the second study, the WISC-IV and SB5 were administered to 30 children aged 12-14 years. There was a significant difference between Full Scale IQs on the two measures, with scores being higher on the WISC-IV. Differences between the two verbal scales were also significant and favoured the WISC-IV. There were moderate correlations of Full Scale IQs (r = .58) and Nonverbal IQs (r = .54) but the relationship between the two Verbal scales was not significant. For some children, notable score differences led to different categorisations of their level of intellectual ability The findings suggest that the Wechsler and Stanford Binet scales cannot be presumed to be interchangeable. The discussion focuses on how psychologists might reconcile large differences in test scores and the need for caution when interpreting and comparing test results.

A new constraint handling method for wind farm layout optimization with lands owned by different owners

For wind farm optimizations with lands belonging to different owners, the traditional penalty method is highly dependent on the type of wind farm land division. The application of the traditional method can be cumbersome if the divisions are complex. To overcome this disadvantage, a new method is proposed in this paper for the first time. Unlike the penalty method which requires the addition of penalizing term when evaluating the fitness function, it is achieved through repairing the infeasible solutions before fitness evaluation. To assess the effectiveness of the proposed method on the optimization of wind farm, the optimizing results of different methods are compared for three different types of wind farm division. Different wind scenarios are also incorporated during optimization which includes (i) constant wind speed and wind direction; (ii) various wind speed and wind direction, and; (iii) the more realisticWeibull distribution. Results show that the performance of the new method varies for different land plots in the tested cases. Nevertheless, it is found that optimum or at least close to optimum results can be obtained with sequential land plot study using the new method for all cases. It is concluded that satisfactory results can be achieved using the proposed method. In addition, it has the advantage of flexibility in managing the wind farm design, which not only frees users to define the penalty parameter but without limitations on the wind farm division.

Genetic risk score analysis indicates migraine with and without comorbid depression are genetically different disorders

Migraine and major depressive disorder (MDD) are comorbid, moderately heritable and to some extent influenced by the same genes. In a previous paper, we suggested the possibility of causality (one trait causing the other) underlying this comorbidity. We present a new application of polygenic (genetic risk) score analysis to investigate the mechanisms underlying the genetic overlap of migraine and MDD. Genetic risk scores were constructed based on data from two discovery samples in which genome-wide association analyses (GWA) were performed for migraine and MDD, respectively. The Australian Twin Migraine GWA study (N = 6,350) included 2,825 migraine cases and 3,525 controls, 805 of whom met the diagnostic criteria for MDD. The RADIANT GWA study (N = 3,230) included 1,636 MDD cases and 1,594 controls. Genetic risk scores for migraine and for MDD were used to predict pure and comorbid forms of migraine and MDD in an independent Dutch target sample (NTR-NESDA, N = 2,966), which included 1,476 MDD cases and 1,058 migraine cases (723 of these individuals had both disorders concurrently). The observed patterns of prediction suggest that the 'pure' forms of migraine and MDD are genetically distinct disorders. The subgroup of individuals with comorbid MDD and migraine were genetically most similar to MDD patients. These results indicate that in at least a subset of migraine patients with MDD, migraine may be a symptom or consequence of MDD. © 2013 Springer-Verlag Berlin Heidelberg.

Field size consistency of nominally matched linacs

Given that there is increasing recognition of the effect that submillimetre changes in collimator position can have on radiotherapy beam dosimetry, this study aimed to evaluate the potential variability in small field collimation that may exist between otherwise matched linacs. Field sizes and field output factors were measured using radiochromic film and an electron diode, for jaw- and MLC-collimated fields produced by eight dosimetrically matched Varian iX linacs (Varian Medical Systems, Palo Alto, USA). This study used nominal sizes from 0.6×0.6 to 10×10 cm215 , for jaw-collimated fields,and from 1×1 to 10×10 cm216 , for MLC-collimated fields, delivered from a zero (head up, beam directed vertically downward) gantry angle. Differences between the field sizes measured for the eight linacs exceeded the uncertainty of the film measurements and the repositioning uncertainty of the jaws and MLCs on one linac. The dimensions of fields defined by MLC leaves were more consistent between linacs, while also differing more from their nominal values than fields defined by orthogonal jaws. The field output factors measured for the different linacs generally increased with increasing measured field size for the nominal 0.6×0.6 and 1×1 cm2 fields, and became consistent between linacs for nominal field sizes of 2×2 cm2 25 and larger. The inclusion in radiotherapy treatment planning system beam data of small field output factors acquired in fields collimated by jaws (rather than the more-reproducible MLCs), associated with either the nominal or the measured field sizes, should be viewed with caution. The size and reproducibility of the fields (especially the small fields) used to acquire treatment planning data should be investigated thoroughly as part of the linac or planning system commissioning process. Further investigation of these issues, using different linac models, collimation systems and beam orientations, is recommended.

Effects of different levels of refractive blur on night-time pedestrian visibility

Purpose The aim of this study was to systematically investigate the effect of different levels of refractive blur and driver age on night-time pedestrian recognition and determine whether clothing that has been shown to improve pedestrian conspicuity is robust to the effects of blur. Methods Night-time pedestrian recognition was measured for 24 visually normal participants (12 younger M=24.9±4.5 years and 12 older adults M=77.6±5.7 years) for three levels of binocular blur (+0.50 D, +1.00 D, +2.00 D) compared to baseline (optimal refractive correction). Pedestrians walked in place on a closed road circuit and wore one of three clothing conditions: i) everyday clothing, ii) a retro-reflective vest and iii) retro-reflective tape positioned on the extremities in a configuration that conveyed biological motion (known as “biomotion”); the order of conditions was randomized between participants. Pedestrian recognition distances were recorded for each blur and pedestrian clothing combination while participants drove an instrumented vehicle around a closed road course. Results The recognition distances for pedestrians were significantly reduced (p<0.05) by all levels of blur compared to baseline. Pedestrians wearing “biomotion” clothing were recognized at significantly longer distances than for the other clothing configurations in all blur conditions. However, these effects were smaller for the older adults, who had much shorter recognition distances for all conditions tested. Conclusions In summary, even small amounts of blur had a significant detrimental effect on night-time pedestrian recognition. Biomotion retro-reflective clothing was effective, even under moderately degraded visibility conditions, for both young and older drivers.

Design of a tablet sized human-computer interface and its effect on situation awareness

Emergency Response Teams increasingly use interactive technology to help manage information and communications. The challenge is to maintain a high situation awareness for different interactive devices sizes. This research specifically compared a handheld interactive device in the form of an iPad with a large interactive multi-touch tabletop. A search and rescue inspired simulator was designed to test operator situation awareness for the two sized devices. The results show that operators had better situation awareness on the tabletop device when the operation related to detecting of moving targets, searching target locations, distinguishing target types, and comprehending displayed information.

Active aging: Exploration into self-ratings of "being active," out-of-home physical activity, and participation among older Australian adults living in four different settings

We examined whether self-ratings of “being active” among older people living in four different settings (major city high and lower density suburbs, a regional city, and a rural area) were associated with out-of-home participation and outdoor physical activity. A mixed-methods approach (survey, travel diary, and GPS tracking over a one-week period) was used to gather data from 48 individuals aged over 55 years. Self-ratings of “being active” were found to be positively correlated with the number of days older people spent time away from home but unrelated to time traveled by active means (walking and biking). No significant differences in active travel were found between the four study locations, despite differences in their respective built environments.The findings suggest that additional strategies to the creation of “age-friendly” environments are needed if older people are to increase their levels of outdoor physical activity. “Active aging” promotion campaigns may need to explicitly identify the benefits of walking outdoors to ambulatory older people as a means of maintaining their overall health, functional ability, and participation within society in the long-term and also encourage the development of community-based programs in order to facilitate regular walking for this group.

Different approaches of applying single-objective binary genetic algorithm on the wind farm design

This paper discusses three different ways of applying the single-objective binary genetic algorithm into designing the wind farm. The introduction of different applications is through altering the binary encoding methods in GA codes. The first encoding method is the traditional one with fixed wind turbine positions. The second involves varying the initial positions from results of the first method, and it is achieved by using binary digits to represent the coordination of wind turbine on X or Y axis. The third is the mixing of the first encoding method with another one, which is by adding four more binary digits to represent one of the unavailable plots. The goal of this paper is to demonstrate how the single-objective binary algorithm can be applied and how the wind turbines are distributed under various conditions with best fitness. The main emphasis of discussion is focused on the scenario of wind direction varying from 0° to 45°. Results show that choosing the appropriate position of wind turbines is more significant than choosing the wind turbine numbers, considering that the former has a bigger influence on the whole farm fitness than the latter. And the farm has best performance of fitness values, farm efficiency, and total power with the direction between 20°to 30°.