On the prediction of simultaneous inbreeding coefficients at multiple loci

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

The difference of thermal stability between Fe-substituted palygorskite and Al-rich palygorskite

Sedimentary palygorskite (SP) and hydrothermal palygorskite (HP) were characterized by XRF, TG/DSC, andXRD. The total iron and dissociative iron in palygorskite were detected using spectrophotometry. The results showed that about 3.57 wt% of Fe2O3 was detected in SP in contrast with 0.4 wt% in HP. SP was a Fe-substituted palygorskite, and HP was an Al-rich palygorskite. The occurrence of Fe substitution in SP resulted in two mass loss steps of coordinated water and resulted in a larger d spacing. The SP showed greater thermal stability than the HP. It was proposed the change of (200) diffraction peak and (240) diffraction peak reflect changes of tetrahedral and octahedral structures in palygorskite.

Thermogravimetric analysis of selected layered double hydroxides

Thermogravimetric analysis (TG) and powder X-ray diffraction (PXRD) were used to study some selected Mg/Al and Zn/Al layered double hydroxides (LDHs) prepared by co-precipitation. A Mg/Al hydrotalcite was investigated before and after reformation in fluoride and nitrate solutions. Little change in the TG or PXRD patterns was observed. It was proposed that successful intercalation of nitrate anions has occurred. However, the absence of any change in the d(003) interlayer spacing suggests that fluoride anions were not intercalated between the LDH layers. Any fluoride anions that were removed from solution are most likely adsorbed onto the outer surfaces of the hydrotalcite. As fluoride removal was not quantified it is not possible to confirm that this has happened without further experimentation. Carbonate is probably intercalated into the interlayer of these hydrotalcites, as well as fluoride or nitrate. The carbonate most likely originates from either incomplete decarbonation during thermal activation or adsorption from the atmosphere or dissolved in the deionised water. Small and large scale co-precipitation syntheses of a Zn/Al LDH were also investigated to determine if there was any change in the product. While the small scale experiment produced a good quality LDH of reasonable purity; the large scale synthesis resulted in several additional phases. Imprecise measurement and difficulty in handling the large quantities of reagents appeared to be sufficient to alter the reaction conditions causing a mixture of phases to be formed.

Load bearing improves the limits of agreement for repeated in vivo measures of the speed of sound in human Achilles tendon

Axial acoustic wave propagation has been widely used in evaluating the mechanical properties of human bone in vivo. However, application of this technique to monitor soft tissues, such as tendon, has received comparatively little scientific attention. Laboratory-based research has established that axial acoustic wave transmission is not only related to the physical properties of equine tendon but is also proportional to tensile load to which it is exposed (Miles et al., 1996; Pourcelot et al., 2005). The reproducibility of the technique for in vivo measurements in human tendon, however, has not been established. The aim of this study was to evaluate the limits of agreement for repeated measures of the speed of sound (SoS) in human Achilles tendon in vivo. Methods: A custom built ultrasound device, consisting of an A-mode 1MHz emitter and two regularly spaced receivers, was used to measure the SoS in the mid-portion of the Achilles tendon in ten healthy males and ten females (mean age: 33.8 years, range 23-56 yrs; height: 1.73±0.08 m; weight: 68.4±15.3 kg). The emitter and receivers were held at fixed positions by a polyethylene frame and maintained in close contact with the skin overlying the tendon by means of elasticated straps. Repeated SoS measurements were taken with the subject prone (non-weightbearing and relaxed Achilles tendon) and during quiet bipedal and unipedal stance. In each instance, the device was detached and repositioned prior to measurement. Results: Limits of agreement for repeated SoS measures during non-weightbearing and bipedal and unipedal stance were ±53, ±28 and ±21 m/s, respectively. The average SoS in the non-weightbearing Achilles tendon was 1804±198 m/s. There was a significant increase in the average SoS during bilateral (2122±135 m/s) (P < 0.05) and unilateral (2221±79 m/s) stance (P < 0.05). Conclusions: Repeated SoS measures in human Achilles tendon were more reliable during stance than under non-weightbearing conditions. These findings are consistent with previous research in equine tendon in which lower variability in SoS was observed with increasing tensile load (Crevier-Denoix et al, 2009). Since the limits of agreement for Achilles tendon SoS are nearly 5% of the changes previously observed during walking and therapeutic heel raise exercises, acoustic wave transmission provides a promising new non-invasive method for determining tendon properties during sports and rehabilitation related activities.

An analysis of the KEEP CLEAR pavement markings effects on queuing vehicles dynamic performance at urban signalised intersections

KEEP CLEAR pavement markings are widely used at urban signalised intersections to indicate to drivers to avoid entering blocked intersections. For example, ‘Box junctions’ are most widely used in the United Kingdom and other European countries. However, in Australia, KEEP CLEAR markings are mostly used to improve access from side roads onto a main road, especially when the side road is very close to a signalised intersection. This paper aims to reveal how the KEEP CLEAR markings affect the dynamic performance of the queuing vehicles on the main road, where the side road access is near a signalised intersection. Raw traffic field data was collected from an intersection at the Gold Coast, Australia, and the Kanade–Lucas–Tomasi (KLT) feature tracker approach was used to extract dynamic vehicle data from the raw video footage. The data analysis reveals that the KEEP CLEAR markings generate positive effects on the queuing vehicles in discharge on the main road. This finding refutes the traditional viewpoint that the KEEP CLEAR pavement markings will cause delay for the queuing vehicles’ departure due to the enlarged queue spacing. Further studies are suggested in this paper as well.

Susceptibility of the critical structural components of railway bridges to the changes in train speed

Modern trains with different axle configurations, speeds and loads are used in railway networks. As a result, one of the most important questions of the mangers involved in bridge managements systems (BMS) is how these changes affect the structural behavior of the critical components of the railway bridges. Although researchers have conducted, many investigations on the dynamic effects of the moving loads on bridges, the influence of the changes in the speed of the train on the demand by capacity ratios of the different critical components of the bridge have not yet been properly studied. This study is important, because different components with different capacities and roles for carrying loads in the structure may be affected differently. To investigate the above phenomenon in this research, a structural model of a simply supported bridge is developed. It will be verified that the dynamic behavior of this bridge is similar to a group of railway bridges in Australia. Demand by capacity ratios of the critical components of the bridge, when it is subjected to a train load with different speeds will be calculated. The results show that the effect of increase or decrease of speed should not be underestimated. The outcome is very significant as it is contrary to what is currently expected, i.e. by reducing the speed of the train, the demand by capacity ratio of components may increase and make the bridge unsafe for carrying live load.

Effect of Reynolds numbers on flow past four square cylinders in an in-line square configuration for different gap spacings

In this paper two-dimensional (2-D) numerical investigation of flow past four square cylinders in an in-line square configuration are performed using the lattice Boltzmann method. The gap spacing g=s/d is set at 1, 3 and 6 and Reynolds number ranging from Re=60 to 175. We observed four distinct wake patterns: (i) a steady wake pattern (Re=60 and g=1) (ii) a stable shielding wake pattern (80≤Re≤175 and g=1) (iii) a wiggling shielding wake pattern (60≤Re≤175 and g=3) (iv) a vortex shedding wake pattern (60≤Re≤175 and g=6) At g=1, the Reynolds number is observed to have a strong effect on the wake patterns. It is also found that at g=1, the secondary cylinder interaction frequency significantly contributes for drag and lift coefficients signal. It is found that the primary vortex shedding frequency dominates the flow and the role of secondary cylinder interaction frequency almost vanish at g=6. It is observed that the jet between the gaps strongly influenced the wake interaction for different gap spacing and Reynolds number combination. To fully understand the wake transformations the details vorticity contour visualization, power spectra of lift coefficient signal and time signal analysis of drag and lift coefficients also presented in this paper.

Thermal stability and hot-stage Raman spectroscopic study of Ca-montmorillonite modified with different surfactants : a comparative study

Three long chain cationic surfactants were intercalated into Ca-montmorillonite through ion exchangeand the obtained organoclays were characterized by X-ray diffraction (XRD), high resolution thermo-gravimetric analysis (TG) and Raman spectroscopy. The intercalation of surfactants not only changes thesurface properties of clay from hydrophilic to hydrophobic but also greatly increases the basal spacing ofthe interlayers based on XRD analysis. The thermal stability of organoclays intercalated with three sur-factants (TTAB, DTAB and CTAB) and the different arrangements of the surfactant molecules intercalatedinto Ca-montmorillonite were determined by TG-DTG analysis. A Raman spectroscopic study on the Ca-montmorillonite modified by three surfactants prepared at different concentrations provided the detailedconformational ordering of different intercalated long-chain surfactants under different conditions. Thewavenumber of the antisymmetric stretching mode is more sensitive than that of the symmetric stretch-ing mode to the mobility of the tail of the amine chain. At room temperature, the conformational orderingis more easily affected by the packing density in the lateral model. With the increase of the temperature,the positions of both the antisymmetric and symmetric stretching bands shift to higher wavenumbers,which indicates a decrease of conformational ordering. This study offers new insights into the struc-ture and properties of Ca-montmorillonite modified with different long chain surfactants. Moreover, theexperimental results confirm the potential applications of organic Ca-montmorillonites for the removalof organic impurities from aqueous media.

Numerical characterization of the mechanical properties of metal nanowires

Nanowires (NWs) have attracted appealing and broad application owing to their remarkable mechanical, optical, electrical, thermal and other properties. To unlock the revolutionary characteristics of NWs, a considerable body of experimental and theoretical work has been conducted. However, due to the extremely small dimensions of NWs, the application and manipulation of the in situ experiments involve inherent complexities and huge challenges. For the same reason, the presence of defects appears as one of the most dominant factors in determining their properties. Hence, based on the experiments' deficiency and the necessity of investigating different defects' influence, the numerical simulation or modelling becomes increasingly important in the area of characterizing the properties of NWs. It has been noted that, despite the number of numerical studies of NWs, significant work still lies ahead in terms of problem formulation, interpretation of results, identification and delineation of deformation mechanisms, and constitutive characterization of behaviour. Therefore, the primary aim of this study was to characterize both perfect and defected metal NWs. Large-scale molecular dynamics (MD) simulations were utilized to assess the mechanical properties and deformation mechanisms of different NWs under diverse loading conditions including tension, compression, bending, vibration and torsion. The target samples include different FCC metal NWs (e.g., Cu, Ag, Au NWs), which were either in a perfect crystal structure or constructed with different defects (e.g. pre-existing surface/internal defects, grain/twin boundaries). It has been found from the tensile deformation that Young's modulus was insensitive to different styles of pre-existing defects, whereas the yield strength showed considerable reduction. The deformation mechanisms were found to be greatly influenced by the presence of defects, i.e., different defects acted in the role of dislocation sources, and many affluent deformation mechanisms had been triggered. Similar conclusions were also obtained from the compressive deformation, i.e., Young's modulus was insensitive to different defects, but the critical stress showed evident reduction. Results from the bending deformation revealed that the current modified beam models with the considerations of surface effect, or both surface effect and axial extension effect were still experiencing certain inaccuracy, especially for the NW with ultra small cross-sectional size. Additionally, the flexural rigidity of the NW was found to be insensitive to different pre-existing defects, while the yield strength showed an evident decrease. For the resonance study, the first-order natural frequency of the NW with pre-existing surface defects was almost the same as that from the perfect NW, whereas a lower first-order natural frequency and a significantly degraded quality factor was observed for NWs with grain boundaries. Most importantly, the <110> FCC NWs were found to exhibit a novel beat phenomenon driven by a single actuation, which was resulted from the asymmetry in the lattice spacing in the (110) plane of the NW cross-section, and expected to exert crucial impacts on the in situ nanomechanical measurements. In particular, <110> Ag NWs with rhombic, truncated rhombic, and triangular cross-sections were found to naturally possess two first-mode natural frequencies, which were envisioned with applications in NEMS that could operate in a non-planar regime. The torsion results revealed that the torsional rigidity of the NW was insensitive to the presence of pre-existing defects and twin boundaries, but received evident reduction due to grain boundaries. Meanwhile, the critical angle decreased considerably for defected NWs. This study has provided a comprehensive and deep investigation on the mechanical properties and deformation mechanisms of perfect and defected NWs, which will greatly extend and enhance the existing knowledge and understanding of the properties/performance of NWs, and eventually benefit the realization of their full potential applications. All delineated MD models and theoretical analysis techniques that were established for the target NWs in this research are also applicable to future studies on other kinds of NWs. It has been suggested that MD simulation is an effective and excellent tool, not only for the characterization of the properties of NWs, but also for the prediction of novel or unexpected properties.

Characterisation of microvasulature changes after closed soft tissue trauma by contrast enhanced micro-CT imaging

INTRODUCTION It is known that the vascular morphology and functionality are changed following closed soft tissue trauma (CSTT) [1], and bone fractures [2]. The disruption of blood vessels may lead to hypoxia and necrosis. Currently, most clinical methods for the diagnosis and monitoring of CSTT with or without bone fractures are primarily based on qualitative measures or practical experience, making the diagnosis subjective and inaccurate. There is evidence that CSTT and early vascular changes following the injury delay the soft tissue tissue and bone healing [3]. However, a precise qualitative and quantitative morphological assessment of vasculature changes after trauma is currently missing. In this research, we aim to establish a diagnostic framework to assess the 3D vascular morphological changes after standardized CSTT in a rat model qualitatively and quantitatively using contrast-enhanced micro-CT imaging. METHODS An impact device was used for the application of a controlled reproducible CSTT to the left thigh (Biceps Femoris) of anaesthetized male Wistar rats. After euthanizing the animals at 6 hours, 24 hours, 3 days, 7 days, or 14 days after trauma, CSTT was qualitatively evaluated by macroscopic visual observation of the skin and muscles. For visualization of the vasculature, the blood vessels of sacrificed rats were flushed with heparinised saline and then perfused with a radio-opaque contrast agent (Microfil, MV 122, Flowtech, USA) using an infusion pump. After allowing the contrast agent to polymerize overnight, both hind-limbs were dissected, and then the whole injured and contra-lateral control limbs were imaged using a micro-CT scanner (µCT 40, Scanco Medical, Switzerland) to evaluate the vascular morphological changes. Correlated biopsy samples were also taken from the CSTT region of both injured and control legs. The morphological parameters such as the vessel volume ratio (VV/TV), vessel diameter (V.D), spacing (V.Sp), number (V.N), connectivity (V.Conn) and the degree of anisotropy (DA) were then quantified by evaluating the scans of biopsy samples using the micro-CT imaging system. RESULTS AND DISCUSSION A qualitative evaluation of the CSTT has shown that the developed impact protocols were capable of producing a defined and reproducible injury within the region of interest (ROI), resulting in a large hematoma and moderate swelling in both lateral and medial sides of the injured legs. Also, the visualization of the vascular network using 3D images confirmed the ability to perfuse the large vessels and a majority of the microvasculature consistently (Figure 1). Quantification of the vascular morphology obtained from correlated biopsy samples has demonstrated that V.D and V.N and V.Sp were significantly higher in the injured legs 24 hours after impact in comparison with the control legs (p<0.05). The evaluation of the other time points is currently progressing. CONCLUSIONS The findings of this research will contribute to a better understanding of the changes to the vascular network architecture following traumatic injuries and during healing process. When interpreted in context of functional changes, such as tissue oxygenation, this will allow for objective diagnosis and monitoring of CSTT and serve as validation for future non-invasive clinical assessment modalities.

Can vasculature changes be characterised morphologically after closed soft tissue trauma?

INTRODUCTION Closed soft tissue trauma (CSTT) can be the result of a blunt impact, or a prolonged crush injury and involves damage to the skin, muscles and the neurovascular system. It causes a variety of symptoms such as haematoma and in severe cases may result in hypoxia and necrosis. There is evidence that early vasculature changes following the injury delays the tissue healing [1]. However, a precise qualitative and quantitative morphological assessment of vasculature changes after trauma and the effect of this on CSTT healing is currently missing. Research aims: Developing an experimental rat model to characterise the structural changes to the vasculature after trauma qualitatively and quantitatively using micro CT. MATERIAL AND METHODS An impact device was developed to apply a controlled reproducible CSTT to the left thigh (Biceps Femoris) of anaesthetised rats [3]. After euthanizing the animals at 6 hours after trauma, CSTT was qualitatively evaluated by macroscopic observations of the skin and muscles. For vasculature visualisation, the blood vessels of sacrificed rats were flushed with heparinised saline and then perfused with a radio-opaque contrast agent (Microfil) using an infusion pump (Figure 4). The overall changes to the vasculature as a result of impact trauma were characterised qualitatively based on the 3D reconstructed images of the vasculature (Figure 5). For a smaller region of interest, the morphological parameters such as vessel thickness (diameter), spacing, and average number per volume were quantified using the scanner’s software. RESULTS AND DISCUSSION Visual observation of CSTT has revealed a haematoma in some animals (Figure 3). Micro CT images indicate good perfusion of the vasculature with contrast agent, allowing the major vessels to be identified (Figure 5). Qualitatively and quantitatively, no differences between injured and non-injured legs were observed at 6 h after trauma. Further time points of 12h, 24h, 3 days and 14 days after trauma will be characterised for identifying temporal changes of the vasculature during healing. Histomorphometical studies are required for validation of the results derived from the micro CT imaging. CONCLUSION AND FUTURE DIRECTION Findings of this research may contribute towards the establishment of a fundamental basis for the quantitative assessment and monitoring of CSTT based on microvasculature changes after trauma, which will ultimately allow for optimising the clinical treatment and improve patient outcomes.

An IEEE 802.11p empirical performance model for cooperative systems applications

IEEE 802.11p is the new standard for Inter-Vehicular Communications (IVC) using the 5.9 GHz frequency band, as part of the DSRC framework; it will enable applications based on Cooperative Systems. Simulation is widely used to estimate or verify the potential benefits of such cooperative applications, notably in terms of safety for the drivers. We have developed a performance model for 802.11p that can be used by simulations of cooperative applications (e.g. collision avoidance) without requiring intricate models of the whole IVC stack. Instead, it provide a a straightforward yet realistic modelisation of IVC performance. Our model uses data from extensive field trials to infer the correlation between speed, distance and performance metrics such as maximum range, latency and frame loss. Then, we improve this model to limit the number of profiles that have to be generated when there are more than a few couples of emitter-receptor in a given location. Our model generates realistic performance for rural or suburban environments among small groups of IVC-equipped vehicles and road side units.

On the periodicity of traffic oscillations and capacity drop : the role of driver characteristics

This paper shows that traffic hysteresis, a manifestation of driver characteristics, has a profound impact on the development of traffic oscillations and the bottleneck discharge rate. Findings suggest that aggressive driver behavior (with small response times and jammed spacing) leads to spontaneous formations of stop-and-go disturbances. Furthermore, the aggressive behavior, coupled with a late response to adopt less aggressive behavior, generates large hysteresis that leads to oscillations’ transformation from localized to substantial disturbances and growth. The larger the magnitude of hysteresis is, the larger the growth is. Our finding also suggests that the bottleneck discharge rate can diminish by 8-23% when driver adopts a less aggressive reaction to a disturbance (characterized by a larger response time). This finding is particularly notable since lane-changes have been believed to be the major cause of a reduction in bottleneck discharge rate.

Design, construction, and analysis of cell line arrays and tissue microarrays for gene expression analysis

Cell line array (CMA) and tissue microarray (TMA) technologies are high-throughput methods for analysing both the abundance and distribution of gene expression in a panel of cell lines or multiple tissue specimens in an efficient and cost-effective manner. The process is based on Kononen's method of extracting a cylindrical core of paraffin-embedded donor tissue and inserting it into a recipient paraffin block. Donor tissue from surgically resected paraffin-embedded tissue blocks, frozen needle biopsies or cell line pellets can all be arrayed in the recipient block. The representative area of interest is identified and circled on a haematoxylin and eosin (H&E)-stained section of the donor block. Using a predesigned map showing a precise spacing pattern, a high density array of up to 1,000 cores of cell pellets and/or donor tissue can be embedded into the recipient block using a tissue arrayer from Beecher Instruments. Depending on the depth of the cell line/tissue removed from the donor block 100-300 consecutive sections can be cut from each CMA/TMA block. Sections can be stained for in situ detection of protein, DNA or RNA targets using immunohistochemistry (IHC), fluorescent in situ hybridisation (FISH) or mRNA in situ hybridisation (RNA-ISH), respectively. This chapter provides detailed methods for CMA/TMA design, construction and analysis with in-depth notes on all technical aspects including tips to deal with common pitfalls the user may encounter. © Springer Science+Business Media, LLC 2011.

Dietetic practice by Australian and Canadian dietitians with people with Parkinson's disease

Although Parkinson’s disease (PD) is a complex disease for which appropriate nutrition management is important, limited evidence is currently available to support dietetic practice. Existing PD-specific guidelines do not span all phases of the Nutrition Care Process (NCP). This study aimed to document PD-specific nutrition management practice by Australian and Canadian dietitians. DAA members and PEN subscribers were invited to participate in an online survey (late 2011). Eighty-four dietitians responded (79.8% Australian). The majority (70.2%) worked in the clinical setting. Existing non-PD guidelines were used by 52.4% while 53.6% relied on self-initiated literature reviews. Weight loss/malnutrition, protein intake, dysphagia and constipation were common issues in all NCP phases. Respondents also requested more information/evidence for these topics. Malnutrition screening (82.1%) and assessment (85.7%) were routinely performed. One-third did not receive referrals for weight loss for overweight/obesity. Protein intake meeting gender/age recommendations (69.0%), and high energy/high protein diets to manage malnutrition (82.1%) were most commonly used. Constipation management was through high fibre diets (86.9%). Recommendations for spacing of meals and PD medications varied with 34.5% not making recommendations. Nutritional diagnosis (70.2%) and stage of disease (61.9%) guided monitoring frequency. Common outcome measures included appropriate weight change (97.6%) and regular bowel movements (88.1%). With limited PD-specific guidance, dietitians applied best available evidence for other groups with similar issues. Dietitians requested evidence-based guidelines specifically for the nutritional management of PD. Guideline development should focus on those areas reported as commonly encountered. This process can identify the gaps in evidence to guide future research.