Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Experimental and finite element analysis of a double strap joint between steel plates and normal modulus CFRP

Strengthening of steel structures using externally-bonded carbon fibre reinforced polymers ‘CFRP’ is a rapidly developing technique. This paper describes the behaviour of axially loaded flat steel plates strengthened using carbon fibre reinforced polymer sheets. Two steel plates were joined together with adhesive and followed by the application of carbon fibre sheet double strap joint with different bond lengths. The behaviour of the specimens was further investigated by using nonlinear finite element analysis to predict the failure modes and load capacity. In this study, bond failure is the dominant failure mode for normal modulus (240 GPa) CFRP bonding which closely matched the results of finite elements. The predicted ultimate loads from the FE analysis are found to be in good agreement with experimental values.

Vibration characteristics of concrete-steel composite floor structures

This paper discusses the vibration characteristics of a concrete-steel composite multi-panel floor structure; the use of these structures is becoming more common. These structures have many desirable properties but are prone to excessive and complex vibration, which is not currently well understood. Existing design codes and practice guides provide generic advice or simple techniques that cannot address the complex vibration in these types of low-frequency structures. The results of this study show the potential for an adverse dynamic response from higher and multi-modal excitation influenced by human-induced pattern loading, structural geometry, and activity frequency. Higher harmonics of the load frequency are able to excite higher modes in the composite floor structure in addition to its fundamental mode. The analytical techniques used in this paper can supplement the current limited code and practice guide provisions for mitigating the impact of human-induced vibrations in these floor structures.

Structural and thermal performance of cold-formed steel stud wall systems under fire conditions

Cold-formed steel stud walls are a major component of Light Steel Framing (LSF) building systems used in commercial, industrial and residential buildings. In the conventional LSF stud wall systems, thin steel studs are protected from fire by placing one or two layers of plasterboard on both sides with or without cavity insulation. However, there is very limited data about the structural and thermal performance of stud wall systems while past research showed contradicting results, for example, about the benefits of cavity insulation. This research was therefore conducted to improve the knowledge and understanding of the structural and thermal performance of cold-formed steel stud wall systems (both load bearing and non-load bearing) under fire conditions and to develop new improved stud wall systems including reliable and simple methods to predict their fire resistance rating. Full scale fire tests of cold-formed steel stud wall systems formed the basis of this research. This research proposed an innovative LSF stud wall system in which a composite panel made of two plasterboards with insulation between them was used to improve the fire rating. Hence fire tests included both conventional steel stud walls with and without the use of cavity insulation and the new composite panel system. A propane fired gas furnace was specially designed and constructed first. The furnace was designed to deliver heat in accordance with the standard time temperature curve as proposed by AS 1530.4 (SA, 2005). A compression loading frame capable of loading the individual studs of a full scale steel stud wall system was also designed and built for the load-bearing tests. Fire tests included comprehensive time-temperature measurements across the thickness and along the length of all the specimens using K type thermocouples. They also included the measurements of load-deformation characteristics of stud walls until failure. The first phase of fire tests included 15 small scale fire tests of gypsum plasterboards, and composite panels using different types of insulating material of varying thickness and density. Fire performance of single and multiple layers of gypsum plasterboards was assessed including the effect of interfaces between adjacent plasterboards on the thermal performance. Effects of insulations such as glass fibre, rock fibre and cellulose fibre were also determined while the tests provided important data relating to the temperature at which the fall off of external plasterboards occurred. In the second phase, nine small scale non-load bearing wall specimens were tested to investigate the thermal performance of conventional and innovative steel stud wall systems. Effects of single and multiple layers of plasterboards with and without vertical joints were investigated. The new composite panels were seen to offer greater thermal protection to the studs in comparison to the conventional panels. In the third phase of fire tests, nine full scale load bearing wall specimens were tested to study the thermal and structural performance of the load bearing wall assemblies. A full scale test was also conducted at ambient temperature. These tests showed that the use of cavity insulation led to inferior fire performance of walls, and provided good explanations and supporting research data to overcome the incorrect industry assumptions about cavity insulation. They demonstrated that the use of insulation externally in a composite panel enhanced the thermal and structural performance of stud walls and increased their fire resistance rating significantly. Hence this research recommends the use of the new composite panel system for cold-formed LSF walls. This research also included steady state tensile tests at ambient and elevated temperatures to address the lack of reliable mechanical properties for high grade cold-formed steels at elevated temperatures. Suitable predictive equations were developed for calculating the yield strength and elastic modulus at elevated temperatures. In summary, this research has developed comprehensive experimental thermal and structural performance data for both the conventional and the proposed non-load bearing and load bearing stud wall systems under fire conditions. Idealized hot flange temperature profiles have been developed for non-insulated, cavity insulated and externally insulated load bearing wall models along with suitable equations for predicting their failure times. A graphical method has also been proposed to predict the failure times (fire rating) of non-load bearing and load bearing walls under different load ratios. The results from this research are useful to both fire researchers and engineers working in this field. Most importantly, this research has significantly improved the knowledge and understanding of cold-formed LSF walls under fire conditions, and developed an innovative LSF wall system with increased fire rating. It has clearly demonstrated the detrimental effects of using cavity insulation, and has paved the way for Australian building industries to develop new wall panels with increased fire rating for commercial applications worldwide.

The flammability of metallic materials in normal and reduced gravity

Metallic materials exposed to oxygen-enriched atmospheres – as commonly used in the medical, aerospace, aviation and numerous chemical processing industries – represent a significant fire hazard which must be addressed during design, maintenance and operation. Hence, accurate knowledge of metallic materials flammability is required. Reduced gravity (i.e. space-based) operations present additional unique concerns, where the absence of gravity must also be taken into account. The flammability of metallic materials has historically been quantified using three standardised test methods developed by NASA, ASTM and ISO. These tests typically involve the forceful (promoted) ignition of a test sample (typically a 3.2 mm diameter cylindrical rod) in pressurised oxygen. A test sample is defined as flammable when it undergoes burning that is independent of the ignition process utilised. In the standardised tests, this is indicated by the propagation of burning further than a defined amount, or „burn criterion.. The burn criterion in use at the onset of this project was arbitrarily selected, and did not accurately reflect the length a sample must burn in order to be burning independent of the ignition event and, in some cases, required complete consumption of the test sample for a metallic material to be considered flammable. It has been demonstrated that a) a metallic material.s propensity to support burning is altered by any increase in test sample temperature greater than ~250-300 oC and b) promoted ignition causes an increase in temperature of the test sample in the region closest to the igniter, a region referred to as the Heat Affected Zone (HAZ). If a test sample continues to burn past the HAZ (where the HAZ is defined as the region of the test sample above the igniter that undergoes an increase in temperature of greater than or equal to 250 oC by the end of the ignition event), it is burning independent of the igniter, and should be considered flammable. The extent of the HAZ, therefore, can be used to justify the selection of the burn criterion. A two dimensional mathematical model was developed in order to predict the extent of the HAZ created in a standard test sample by a typical igniter. The model was validated against previous theoretical and experimental work performed in collaboration with NASA, and then used to predict the extent of the HAZ for different metallic materials in several configurations. The extent of HAZ predicted varied significantly, ranging from ~2-27 mm depending on the test sample thermal properties and test conditions (i.e. pressure). The magnitude of the HAZ was found to increase with increasing thermal diffusivity, and decreasing pressure (due to slower ignition times). Based upon the findings of this work, a new burn criterion requiring 30 mm of the test sample to be consumed (from the top of the ignition promoter) was recommended and validated. This new burn criterion was subsequently included in the latest revision of the ASTM G124 and NASA 6001B international test standards that are used to evaluate metallic material flammability in oxygen. These revisions also have the added benefit of enabling the conduct of reduced gravity metallic material flammability testing in strict accordance with the ASTM G124 standard, allowing measurement and comparison of the relative flammability (i.e. Lowest Burn Pressure (LBP), Highest No-Burn Pressure (HNBP) and average Regression Rate of the Melting Interface(RRMI)) of metallic materials in normal and reduced gravity, as well as determination of the applicability of normal gravity test results to reduced gravity use environments. This is important, as currently most space-based applications will typically use normal gravity information in order to qualify systems and/or components for reduced gravity use. This is shown here to be non-conservative for metallic materials which are more flammable in reduced gravity. The flammability of two metallic materials, Inconel® 718 and 316 stainless steel (both commonly used to manufacture components for oxygen service in both terrestrial and space-based systems) was evaluated in normal and reduced gravity using the new ASTM G124-10 test standard. This allowed direct comparison of the flammability of the two metallic materials in normal gravity and reduced gravity respectively. The results of this work clearly show, for the first time, that metallic materials are more flammable in reduced gravity than in normal gravity when testing is conducted as described in the ASTM G124-10 test standard. This was shown to be the case in terms of both higher regression rates (i.e. faster consumption of the test sample – fuel), and burning at lower pressures in reduced gravity. Specifically, it was found that the LBP for 3.2 mm diameter Inconel® 718 and 316 stainless steel test samples decreased by 50% from 3.45 MPa (500 psia) in normal gravity to 1.72 MPa (250 psia) in reduced gravity for the Inconel® 718, and 25% from 3.45 MPa (500 psia) in normal gravity to 2.76 MPa (400 psia) in reduced gravity for the 316 stainless steel. The average RRMI increased by factors of 2.2 (27.2 mm/s in 2.24 MPa (325 psia) oxygen in reduced gravity compared to 12.8 mm/s in 4.48 MPa (650 psia) oxygen in normal gravity) for the Inconel® 718 and 1.6 (15.0 mm/s in 2.76 MPa (400 psia) oxygen in reduced gravity compared to 9.5 mm/s in 5.17 MPa (750 psia) oxygen in normal gravity) for the 316 stainless steel. Reasons for the increased flammability of metallic materials in reduced gravity compared to normal gravity are discussed, based upon the observations made during reduced gravity testing and previous work. Finally, the implications (for fire safety and engineering applications) of these results are presented and discussed, in particular, examining methods for mitigating the risk of a fire in reduced gravity.

ICT as core business: will we prosper or drown?

Recent changes in IT organisations have resulted in changes to library IT support. Concurrently, new tools and systems for service delivery, have become available, but these require a move away from the traditional ICT model. Many libraries are investigating new models, including Software as a Service (SaaS), cloud computing and open source software. This paper considers whether the adoption of these tools and environments by libraries has occurred as a result of a lack of suitable ICT solutions and support ICT organisations. It also considers what skills library staff need in order to ensure sustainability, supportability, and ultimately, success.

Determination of stress-strain characteristics of railhead steel using image analysis

True stress-strain curve of railhead steel is required to investigate the behaviour of railhead under wheel loading through elasto-plastic Finite Element (FE) analysis. To reduce the rate of wear, the railhead material is hardened through annealing and quenching. The Australian standard rail sections are not fully hardened and hence suffer from non-uniform distribution of the material property; usage of average properties in the FE modelling can potentially induce error in the predicted plastic strains. Coupons obtained at varying depths of the railhead were, therefore, tested under axial tension and the strains were measured using strain gauges as well as an image analysis technique, known as the Particle Image Velocimetry (PIV). The head hardened steel exhibit existence of three distinct zones of yield strength; the yield strength as the ratio of the average yield strength provided in the standard (σyr=780MPa) and the corresponding depth as the ratio of the head hardened zone along the axis of symmetry are as follows: (1.17 σyr, 20%), (1.06 σyr, 20%- 80%) and (0.71 σyr, > 80%). The stress-strain curves exhibit limited plastic zone with fracture occurring at strain less than 0.1.

Central Queensland Mining Supplies Pty Ltd v Columbia Steel Casting Co Ltd

In Central Queensland Mining Supplies Pty Ltd v Columbia Steel Casting Co Ltd [2011] QSC 183 Applegarth J considered complaints made by the defendant about the approach the plaintiff had taken in its endeavour to comply with its disclosure obligation under r 211 of the Uniform Civil Procedure Rules 1999 (Qld). The judgment also provides an indication of the direction the court is taking in relation to disclosure and document management in matters involving large numbers of documents.

Sale of property gifted under a will by an attorney acting under an enduring power of attorney : does the gift adeem and what is the attorney's duty?

The authors examine Moylan v Rickard and how the case illustrates the effectiveness of the Powers of Attorney Act 1998 (Qld) to provide remedies and other possible avenues of redress

Numerical modelling of non-load bearing light gauge cold-formed steel frame walls under fire conditions

Recently an innovative composite panel system was developed, where a thin insulation layer was used externally between two plasterboards to improve the fire performance of light gauge cold-formed steel frame walls. In this research, finite-element thermal models of both the traditional light gauge cold-formed steel frame wall panels with cavity insulation and the new light gauge cold-formed steel frame composite wall panels were developed to simulate their thermal behaviour under standard and realistic fire conditions. Suitable apparent thermal properties of gypsum plasterboard, insulation materials and steel were proposed and used. The developed models were then validated by comparing their results with available fire test results. This article presents the details of the developed finite-element models of small-scale non-load-bearing light gauge cold-formed steel frame wall panels and the results of the thermal analysis. It has been shown that accurate finite-element models can be used to simulate the thermal behaviour of small-scale light gauge cold-formed steel frame walls with varying configurations of insulations and plasterboards. The numerical results show that the use of cavity insulation was detrimental to the fire rating of light gauge cold-formed steel frame walls, while the use of external insulation offered superior thermal protection to them. The effects of real fire conditions are also presented.

Simulation of AE wave propagation in thin plate for source identification

In most materials, short stress waves are generated during the process of plastic deformation, phase transformation, crack formation and crack growth. These phenomena are applied in acoustic emission (AE) for the detection of material defects in wide spectrum areas, ranging from non-destructive testing for the detection of materials defects to monitoring of microeismical activity. AE technique is also used for defect source identification and for failure detection. AE waves consist of P waves (primary/longitudinal waves), S waves (shear/transverse waves) and Rayleight (surface) waves as well as reflected and diffracted waves. The propagation of AE waves in various modes has made the determination of source location difficult. In order to use the acoustic emission technique for accurate identification of source location, an understanding of wave propagation of the AE signals at various locations in a plate structure is essential. Furthermore, an understanding of wave propagation can also assist in sensor location for optimum detection of AE signals. In real life, as the AE signals radiate from the source it will result in stress waves. Unless the type of stress wave is known, it is very difficult to locate the source when using the classical propagation velocity equations. This paper describes the simulation of AE waves to identify the source location in steel plate as well as the wave modes. The finite element analysis (FEA) is used for the numerical simulation of wave propagation in thin plate. By knowing the type of wave generated, it is possible to apply the appropriate wave equations to determine the location of the source. For a single plate structure, the results show that the simulation algorithm is effective to simulate different stress waves.

Behaviour and design of cold-formed steel beams subject to lateral-torsional buckling

Cold-formed steel beams are increasingly used as floor joists and bearers in buildings. Their behaviour and moment capacities are influenced by lateral-torsional buckling when they are not laterally restrained adequately. Past research on lateral-torsional buckling has concentrated on hot-rolled steel beams. Hence a numerical study was undertaken to investigate the lateral-torsional buckling behaviour of simply supported cold-formed steel lipped channel beams subjected to uniform bending. For this purpose a finite element model was developed using ABAQUS and its accuracy was verified using available numerical and experimental results. It was then used in a detailed parametric study to simulate the lateral-torsional buckling behaviour and capacity of cold-formed steel beams under varying conditions. The moment capacity results were compared with the predictions from the current design rules in many cold-formed steel codes and suitable recommendations were made. European design rules were found to be conservative while Australian/New Zealand and North American design rules were unconservative. Hence the moment capacity design equations in these codes were modified in this paper based on the available finite element analysis results. This paper presents the details of the parametric study, recommendations to current design rules and the new design rules proposed in this research for lateral-torsional buckling of cold-formed steel lipped channel beams.

Numerical study of cold-formed steel beam subject to lateral-torsional buckling

The use of cold-formed steel members as structural columns and beams in residential, industrial and commercial buildings has increased significantly in recent times. This study is focused on the use of cold-formed steel sections as flexural members subject to lateral-torsional buckling. For this purpose a finite element model of a simply supported lipped channel beam under uniform bending was developed, validated using available numerical and experimental results, and used in a detailed parametric study. The moment capacity results were then compared with the predictions from the current ambient temperature design rules in the cold-formed steel structures codes of Australia, New Zealand, North America and Europe. European design rules were found to be conservative while Australian and American design rules were unsafe. This paper presents the results of the numerical study, the comparison with the current design rules and the new proposed design rules.

Lateral torsional buckling behaviour of cold-formed steel beams at elevated temperatures

Abstract: This paper presents the details of a study into the behaviour and moment capacities of cold-formed steel lipped channel beams (LCB) subject to lateral-torsional buckling at elevated temperatures. It was based on a validated numerical model of a simply supported and laterally unrestrained LCB subjected to a uniform moment. The ultimate moment capacities from this study were compared with the predicted values using ambient and fire design methods. This study showed that the lateral torsional buckling capacity is strongly influenced by the level of non-linearity in the stress-strain curves of steel at elevated temperatures. Hence most of the current design methods based on a single buckling curve were not adequate to determine the moment capacities. This paper proposes a new design method for the cold-formed steel LCBs subject lateral-torsional buckling at elevated temperatures.

Geostatistical analysis of adult Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae) in wheat stored at constant temperatures

Insect monitoring and sampling programmes are used in the stored grains industry for the detection and estimation of insect pests. At the low pest densities dictated by economic and commercial requirements, the accuracy of both detection and abundance estimates can be influenced by variations in the spatial structure of pest populations over short distances. Geostatistical analysis of Rhyzopertha dominica populations in 2 dimensions showed that, in both the horizontal and vertical directions and at all temperatures examined, insect numbers were positively correlated over short (0-5cm) distances, and negatively correlated over longer (≥10cm) distances. Analysis in 3 dimensions showed a similar pattern, with positive correlations over short distances and negative correlations at longer distances. At 35°C, insects were located significantly further from the grain surface than at 25 and 30°C. Dispersion metrics showed statistically significant aggregation in all cases. This is the first research using small sample units, high sampling intensities, and a range of temperatures, to show spatial structuring of R. dominica populations over short distances. This research will have significant implications for sampling in the stored grains industry.