Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

Numerical modelling of light gauge cold-formed steel compression members subjected to distortional buckling at elevated temperatures

Fire safety design of building structures has received greater attention in recent times due to continuing loss of properties and lives during fires. However, fire performance of light gauge cold-formed steel structures is not well understood despite its increased usage in buildings. Cold-formed steel compression members are susceptible to various buckling modes such as local and distortional buckling and their ultimate strength behaviour is governed by these buckling modes. Therefore a research project based on experimental and numerical studies was undertaken to investigate the distortional buckling behaviour of light gauge cold-formed steel compression members under simulated fire conditions. Lipped channel sections with and without additional lips were selected with three thicknesses of 0.6, 0.8, and 0.95 mm and both low and high strength steels (G250 and G550 steels). More than 150 compression tests were undertaken first at ambient and elevated temperatures. Finite element models of the tested compression members were then developed by including the degradation of mechanical properties with increasing temperatures. Comparison of finite element analysis and experimental results showed that the developed finite element models were capable of simulating the distortional buckling and strength behaviour at ambient and elevated temperatures up to 800 °C. The validated model was used to determine the effects of mechanical properties, geometric imperfections and residual stresses on the distortional buckling behaviour and strength of cold-formed steel columns. This paper presents the details of the numerical study and the results. It demonstrated the importance of using accurate mechanical properties at elevated temperatures in order to obtain reliable strength characteristics of cold-formed steel columns under fire conditions.

Wider reinforced masonry shear walls subjected to cyclic lateral loading

Partially grouted wider reinforced masonry wall, built predominantly with the use of face shell bedded hollow concrete blocks, is adopted extensively in the cyclonic areas due to its economy. Its out-of-plane response to lateral pressure loading is well definied; however its in-plane shear behaviour is less well understood, in particular it is unclear how the grouted reinforced cores affect the load paths within the wall. For the rational design of the walls, clarification is sought as to whether the wall acts as a composite of unreinforced panels surrounded by the reinforced cores or simply as a continuum embedded with reinforcement at wider spacing. This paper reports four full scale walls tested under in-place cyclic shear loading to provide some insight into the effect of the grout cores in altering the load paths within the wall. The global lateral load - lateral deflection hysteretic curves as well as the local responses of some critical zones of the shear walls are presented. It is shown that the aspect ratio of the unreinforced masonry panels surrounded by the reinforced grouted cores within the shear walls have profound effect in ascertaining the behaviour of the shear walls.

Structural behaviour and design of cold-formed steel wall systems under fire conditions

In recent times, light gauge steel framed (LSF) structures, such as cold-formed steel wall systems, are increasingly used, but without a full understanding of their fire performance. Traditionally the fire resistance rating of these load-bearing LSF wall systems is based on approximate prescriptive methods developed based on limited fire tests. Very often they are limited to standard wall configurations used by the industry. Increased fire rating is provided simply by adding more plasterboards to these walls. This is not an acceptable situation as it not only inhibits innovation and structural and cost efficiencies but also casts doubt over the fire safety of these wall systems. Hence a detailed fire research study into the performance of LSF wall systems was undertaken using full scale fire tests and extensive numerical studies. A new composite wall panel developed at QUT was also considered in this study, where the insulation was used externally between the plasterboards on both sides of the steel wall frame instead of locating it in the cavity. Three full scale fire tests of LSF wall systems built using the new composite panel system were undertaken at a higher load ratio using a gas furnace designed to deliver heat in accordance with the standard time temperature curve in AS 1530.4 (SA, 2005). Fire tests included the measurements of load-deformation characteristics of LSF walls until failure as well as associated time-temperature measurements across the thickness and along the length of all the specimens. Tests of LSF walls under axial compression load have shown the improvement to their fire performance and fire resistance rating when the new composite panel was used. Hence this research recommends the use of the new composite panel system for cold-formed LSF walls. The numerical study was undertaken using a finite element program ABAQUS. The finite element analyses were conducted under both steady state and transient state conditions using the measured hot and cold flange temperature distributions from the fire tests. The elevated temperature reduction factors for mechanical properties were based on the equations proposed by Dolamune Kankanamge and Mahendran (2011). These finite element models were first validated by comparing their results with experimental test results from this study and Kolarkar (2010). The developed finite element models were able to predict the failure times within 5 minutes. The validated model was then used in a detailed numerical study into the strength of cold-formed thin-walled steel channels used in both the conventional and the new composite panel systems to increase the understanding of their behaviour under nonuniform elevated temperature conditions and to develop fire design rules. The measured time-temperature distributions obtained from the fire tests were used. Since the fire tests showed that the plasterboards provided sufficient lateral restraint until the failure of LSF wall panels, this assumption was also used in the analyses and was further validated by comparison with experimental results. Hence in this study of LSF wall studs, only the flexural buckling about the major axis and local buckling were considered. A new fire design method was proposed using AS/NZS 4600 (SA, 2005), NAS (AISI, 2007) and Eurocode 3 Part 1.3 (ECS, 2006). The importance of considering thermal bowing, magnified thermal bowing and neutral axis shift in the fire design was also investigated. A spread sheet based design tool was developed based on the above design codes to predict the failure load ratio versus time and temperature for varying LSF wall configurations including insulations. Idealised time-temperature profiles were developed based on the measured temperature values of the studs. This was used in a detailed numerical study to fully understand the structural behaviour of LSF wall panels. Appropriate equations were proposed to find the critical temperatures for different composite panels, varying in steel thickness, steel grade and screw spacing for any load ratio. Hence useful and simple design rules were proposed based on the current cold-formed steel structures and fire design standards, and their accuracy and advantages were discussed. The results were also used to validate the fire design rules developed based on AS/NZS 4600 (SA, 2005) and Eurocode Part 1.3 (ECS, 2006). This demonstrated the significant improvements to the design method when compared to the currently used prescriptive design methods for LSF wall systems under fire conditions. In summary, this research has developed comprehensive experimental and numerical thermal and structural performance data for both the conventional and the proposed new load bearing LSF wall systems under standard fire conditions. Finite element models were developed to predict the failure times of LSF walls accurately. Idealized hot flange temperature profiles were developed for non-insulated, cavity and externally insulated load bearing wall systems. Suitable fire design rules and spread sheet based design tools were developed based on the existing standards to predict the ultimate failure load, failure times and failure temperatures of LSF wall studs. Simplified equations were proposed to find the critical temperatures for varying wall panel configurations and load ratios. The results from this research are useful to both structural and fire engineers and researchers. Most importantly, this research has significantly improved the knowledge and understanding of cold-formed LSF loadbearing walls under standard fire conditions.

Numerical and experimental studies of cold-formed steel floor systems under standard fire conditions

Light gauge cold-formed steel frame (LSF) structures are increasingly used in industrial, commercial and residential buildings because of their non-combustibility, dimensional stability, and ease of installation. A floor-ceiling system is an example of its applications. LSF floor-ceiling systems must be designed to serve as fire compartment boundaries and provide adequate fire resistance. Fire rated floor-ceiling assemblies formed with new materials and construction methodologies have been increasingly used in buildings. However, limited research has been undertaken in the past and hence a thorough understanding of their fire resistance behaviour is not available. Recently a new composite panel in which an external insulation layer is used between two plasterboards has been developed at QUT to provide a higher fire rating to LSF floors under standard fire conditions. But its increased fire rating could not be determined using the currently available design methods. Research on LSF floor systems under fire conditions is relatively recent and the behaviour of floor joists and other components in the systems is not fully understood. The present design methods thus require the use of expensive fire protection materials to protect them from excessive heat increase during a fire. This leads to uneconomical and conservative designs. Fire rating of these floor systems is provided simply by adding more plasterboard sheets to the steel joists and such an approach is totally inefficient. Hence a detailed fire research study was undertaken into the structural and thermal performance of LSF floor systems including those protected by the new composite panel system using full scale fire tests and extensive numerical studies. Experimental study included both the conventional and the new steel floor-ceiling systems under structural and fire loads using a gas furnace designed to deliver heat in accordance with the standard time- temperature curve in AS 1530.4 (SA, 2005). Fire tests included the behavioural and deflection characteristics of LSF floor joists until failure as well as related time-temperature measurements across the section and along the length of all the specimens. Full scale fire tests have shown that the structural and thermal performance of externally insulated LSF floor system was superior than traditional LSF floors with or without cavity insulation. Therefore this research recommends the use of the new composite panel system for cold-formed LSF floor-ceiling systems. The numerical analyses of LSF floor joists were undertaken using the finite element program ABAQUS based on the measured time-temperature profiles obtained from fire tests under both steady state and transient state conditions. Mechanical properties at elevated temperatures were considered based on the equations proposed by Dolamune Kankanamge and Mahendran (2011). Finite element models were calibrated using the full scale test results and used to further provide a detailed understanding of the structural fire behaviour of the LSF floor-ceiling systems. The models also confirmed the superior performance of the new composite panel system. The validated model was then used in a detailed parametric study. Fire tests and the numerical studies showed that plasterboards provided sufficient lateral restraint to LSF floor joists until their failure. Hence only the section moment capacity of LSF floor joists subjected to local buckling effects was considered in this research. To predict the section moment capacity at elevated temperatures, the effective section modulus of joists at ambient temperature is generally considered adequate. However, this research has shown that it leads to considerable over- estimation of the local buckling capacity of joist subject to non-uniform temperature distributions under fire conditions. Therefore new simplified fire design rules were proposed for LSF floor joist to determine the section moment capacity at elevated temperature based on AS/NZS 4600 (SA, 2005), NAS (AISI, 2007) and Eurocode 3 Part 1.3 (ECS, 2006). The accuracy of the proposed fire design rules was verified with finite element analysis results. A spread sheet based design tool was also developed based on these design rules to predict the failure load ratio versus time, moment capacity versus time and temperature for various LSF floor configurations. Idealised time-temperature profiles of LSF floor joists were developed based on fire test measurements. They were used in the detailed parametric study to fully understand the structural and fire behaviour of LSF floor panels. Simple design rules were also proposed to predict both critical average joist temperatures and failure times (fire rating) of LSF floor systems with various floor configurations and structural parameters under any given load ratio. Findings from this research have led to a comprehensive understanding of the structural and fire behaviour of LSF floor systems including those protected by the new composite panel, and simple design methods. These design rules were proposed within the guidelines of the Australian/New Zealand, American and European cold- formed steel structures standard codes of practice. These may also lead to further improvements to fire resistance through suitable modifications to the current composite panel system.

How important is length? : mechanical testing and measurement of a cemented, polished, tapered femoral implant

Total hip arthroplasty (THA) has a proven clinical record for providing pain relief and return of function to patients with disabling arthritis. There are many successful options for femoral implant design and fixation. Cemented, polished, tapered femoral implants have been shown to have excellent results in national joint registries and long-term clinical series. These implants are usually 150mm long at their lateral aspect. Due to their length, these implants cannot always be offered to patients due to variations in femoral anatomy. Polished, tapered implants as short as 95mm exist, however their small proximal geometry (neck offset and body size) limit their use to smaller stature patients. There is a group of patients in which a shorter implant with a maintained proximal body size would be advantageous. There are also potential benefits to a shorter implant in standard patient populations such as reduced bone removal due to reduced reaming, favourable loading of the proximal femur, and the ability to revise into good proximal bone stock if required. These factors potentially make a shorter implant an option for all patient populations. The role of implant length in determining the stability of a cemented, polished, tapered femoral implant is not well defined by the literature. Before changes in implant design can be made, a better understanding of the role of each region in determining performance is required. The aim of the thesis was to describe how implant length affects the stability of a cemented, polished, tapered femoral implant. This has been determined through an extensive body of laboratory testing. The major findings are that for a given proximal body size, a reduction in implant length has no effect on the torsional stability of a polished, tapered design, while a small reduction in axial stability should be expected. These findings are important because the literature suggests that torsional stability is the major determinant of long-term clinical performance of a THA system. Furthermore, a polished, tapered design is known to be forgiving of cement-implant interface micromotion due to the favourable wear characteristics. Together these findings suggest that a shorter polished, tapered implant may be well tolerated. The effect of a change in implant length on the geometric characteristics of polished, tapered design were also determined and applied to the mechanical testing. Importantly, interface area does play a role in stability of the system; however it is the distribution of the interface and not the magnitude of the area that defines stability. Taper angle (at least in the range of angles seen in this work) was shown not to be a determinant of axial or torsional stability. A range of implants were tested, comparing variations in length, neck offset and indication (primary versus cement-in-cement revision). At their manufactured length, the 125mm implants were similar to their longer 150mm counterparts suggesting that they may be similarly well tolerated in the clinical environment. However, the slimmer cement-in-cement revision implant was shown to have a poorer mechanical performance, suggesting their use in higher demand patients may be hazardous. An implant length of 125mm has been shown to be quite stable and the results suggest that a further reduction to 100mm may be tolerated. However, further work is required. A shorter implant with maintained proximal body size would be useful for the group of patients who are unable to access the current standard length implants due to variations in femoral anatomy. Extending the findings further, the similar function with potential benefits of a shorter implant make their application to all patients appealing.

Lateral movements in composite high-rise buildings under seismic action

Daring human nature has already led to the construction of high-rise buildings in naturally challenging geological regions and in worse environments of the world. However; literature review divulges that there is a lag in research of certain generic principles and rules for the prediction of lateral movement in multistorey construction. The present competitive trend orders the best possible used of available construction material and resources. Hence; the mixed used of reinforced concrete with structural steel is gaining prevalence day by day. This paper investigates the effects of Seismic load on composite multistorey building provided with core wall and trusses through FEM modelling. The results showed that increased rigidity corresponds to lower period of vibration and hence higher seismic forces. Since Seismic action is a function of mass and response acceleration, therefore; mass increment generate higher earthquake load and thus cause higher impact base shear and overturning movement. Whereas; wind force depends on building exposed, larger the plan dimension greater is the wind impact. Nonetheless; outriggers trusses noticeably contribute, in improving the serviceability of structure subjected to wind and earthquake forces.

Quantitative studies of lower motor neuron degeneration in amyotrophic lateral sclerosis : Evidence for exponential decay of motor unit numbers and greatest rate of loss at the site of onset

Objective: To use our Bayesian method of motor unit number estimation (MUNE) to evaluate lower motor neuron degeneration in ALS. Methods: In subjects with ALS we performed serial MUNE studies. We examined the repeatability of the test and then determined whether the loss of MUs was fitted by an exponential or Weibull distribution. Results: The decline in motor unit (MU) numbers was well-fitted by an exponential decay curve. We calculated the half life of MUs in the abductor digiti minimi (ADM), abductor pollicis brevis (APB) and/or extensor digitorum brevis (EDB) muscles. The mean half life of the MUs of ADM muscle was greater than those of the APB or EDB muscles. The half-life of MUs was less in the ADM muscle of subjects with upper limb than in those with lower limb onset. Conclusions: The rate of loss of lower motor neurons in ALS is exponential, the motor units of the APB decay more quickly than those of the ADM muscle and the rate of loss of motor units is greater at the site of onset of disease. Significance: This shows that the Bayesian MUNE method is useful in following the course and exploring the clinical features of ALS. 2012 International Federation of Clinical Neurophysiology.

Role of kilometer-scale weak circular heterogeneities on upper crustal deformation patterns: Evidence from scaled analogue modeling and the Sudbury Basin, Canada

The Sudbury Basin is a non-cylindrical fold basin occupying the central portion of the Sudbury Impact Structure. The impact structure lends itself excellently to explore the structural evolution of continental crust containing a circular region of long-term weakness. In a series of scaled analogue experiments various model crustal configurations were shortened horizontally at a constant rate. In mechanically weakened crust, model basins formed that mimic several first-order structural characteristics of the Sudbury Basin: (1) asymmetric, non-cylindrical folding of the Basin, (2) structures indicating concentric shortening around lateral basin termini and (3) the presence of a zone of strain concentration near the hinge zones of model basins. Geometrically and kinematically this zone corresponds to the South Range Shear Zone of the Sudbury Basin. According to our experiments, this shear zone is a direct mechanical consequence of basin formation, rather than the result of thrusting following folding. Overall, the models highlight the structurally anomalous character of the Sudbury Basin within the Paleoproterozoic Eastern Penokean Orogen. In particular, our models suggest that the Basin formed by pure shear thickening of crust, whereas transpressive deformation prevailed elsewhere in the orogen. The model basin is deformed by thickening and non-cylindrical synformal buckling, while conjugate transpressive shear zones propagated away from its lateral tips. This is consistent with pure shear deformation of a weak circular inclusion in a strong matrix. The models suggest that the Sudbury Basin formed as a consequence of long-term weakening of the upper crust by meteorite impact.

Comparative study of depth-dependent characteristics of equine and human osteochondral tissue from the medial and lateral femoral condyles

Articular cartilage defects are common after joint injuries. When left untreated, the biomechanical protective function of cartilage is gradually lost, making the joint more susceptible to further damage, causing progressive loss of joint function and eventually osteoarthritis (OA). In the process of translating promising tissue-engineering cartilage repair approaches from bench to bedside, pre-clinical animal models including mice, rabbits, goats, and horses, are widely used. The equine species is becoming an increasingly popular model for the in vivo evaluation of regenerative orthopaedic approaches. As there is also an increasing body of evidence suggesting that successful lasting tissue reconstruction requires an implant that mimics natural tissue organization, it is imperative that depth-dependent characteristics of equine osteochondral tissue are known, to assess to what extent they resemble those in humans. Therefore, osteochondral cores (4-8 mm) were obtained from the medial and lateral femoral condyles of equine and human donors. Cores were processed for histology and for biochemical quantification of DNA, glycosaminoglycan (GAG) and collagen content. Equine and human osteochondral tissues possess similar geometrical (thickness) and organizational (GAG, collagen and DNA distribution with depth) features. These comparable trends further underscore the validity of the equine model for the evaluation of regenerative approaches for articular cartilage.