Prediction of HLA-DQ3.2 beta ligands: evidence of multiple registers in class II binding peptides

Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and hypersensitivity reactions. Sequence-based computational techniques for predicting HLA-DQ binding peptides have encountered limited success, with few prediction techniques developed using three-dimensional models. Methods: We describe a structure-based prediction model for modeling peptide-DQ3.2 beta complexes. We have developed a rapid and accurate protocol for docking candidate peptides into the DQ3.2 beta receptor and a scoring function to discriminate binders from the background. The scoring function was rigorously trained, tested and validated using experimentally verified DQ3.2 beta binding and non-binding peptides obtained from biochemical and functional studies. Results: Our model predicts DQ3.2 beta binding peptides with high accuracy [area under the receiver operating characteristic (ROC) curve A(ROC) > 0.90], compared with experimental data. We investigated the binding patterns of DQ3.2 beta peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders.

Explaining landholders' decisions about riparian zone management: The role of behavioural, normative, and control beliefs

Water quality is a key concern in the current global environment, with the need to promote practices that help to protect water quality, such as riparian zone management, being paramount. The present study used the theory of planned behaviour as a framework for understanding how beliefs influence decisions about riparian zone management. Respondents completed a survey that assessed their behavioural, normative, and control beliefs in relation to intentions to manage riparian zones on their property. The results of the study showed that, overall, landholders with strong intentions to manage their riparian zones differed significantly in terms of their beliefs compared to landholders who had weak intentions to manage their riparian zones. Strong intentions to manage riparian zones were associated with a favourable cost-benefit analysis, greater perceptions of normative support for the practice and lower perceptions of the extent to which barriers would impede management of riparian zones. It was also evident that willingness to comply with the recommendations of salient referents, beliefs about the benefits of riparian zone management and perceptions of the extent to which barriers would impede riparian zone management were most important for determining intentions to manage riparian zones. Implications for policy and extension practice are discussed. (c) 2005 Elsevier Ltd. All rights reserved.

Minimising cold damage during reproductive development among temperate rice genotypes. I. Avoiding low temperature with the use of appropriate sowing time and photoperiod-sensitive varieties

Multiple-sown field trials in 4 consecutive years in the Riverina region of south-eastern Australia provided 24 different combinations of temperature and day length, which enabled the development of crop phenology models. A crop model was developed for 7 cultivars from diverse origins to identify if photoperiod sensitivity is involved in determining phenological development, and if that is advantageous in avoiding low-temperature damage. Cultivars that were mildly photoperiod-sensitive were identified from sowing to flowering and from panicle initiation to flowering. The crop models were run for 47 years of temperature data to quantify the risk of encountering low temperature during the critical young microspore stage for 5 different sowing dates. Cultivars that were mildly photoperiod-sensitive, such as Amaroo, had a reduced likelihood of encountering low temperature for a wider range of sowing dates compared with photoperiod-insensitive cultivars. The benefits of increased photoperiod sensitivity include greater sowing flexibility and reduced water use as growth duration is shortened when sowing is delayed. Determining the optimal sowing date also requires other considerations, e. g. the risk of cold damage at other sensitive stages such as flowering and the response of yield to a delay in flowering under non-limiting conditions. It was concluded that appropriate sowing time and the use of photoperiod-sensitive cultivars can be advantageous in the Riverina region in avoiding low temperature damage during reproductive development.

Scramjet lift, thrust and pitching-moment characteristics measured in a shock tunnel

Lift, pitching moment, and thrust/drag on a supersonic combustion ramjet were measured in the T4 free-piston shock tunnel using a three-component stress-wave force balance. The scramjet model was 0.567 m long and weighed approximately 6 kg. Combustion occurred at a nozzle-supply enthalpy of 3.3 MJ/kg and nozzle-supply pressure of 32 MPa at Mach 6.6 for equivalence ratios up to 1.4. The force coefficients varied approximately linearly with equivalence ratio. The location of the center of pressure changed by 10% of the chord of the model over the range of equivalence ratios tested. Lift and pitching-moment coefficients remained constant when the nozzle-supply enthalpy was increased to 4.9 MJ/kg at an equivalence ratio of 0.8, but the thrust coefficient decreased rapidly. When the nozzle-supply pressure was reduced at a nozzle-supply enthalpy of 3.3 MJ/kg and an equivalence ratio of 0.8, the combustion-generated increment of lift and thrust was maintained at 26 MPa, but disappeared at 16 MPa. Measured lift and thrust forces agreed well with calculations made using a simplified force prediction model, but the measured pitching moment substantially exceeded predictions. Choking occurred at nozzle-supply enthalpies of less than 3.0 MJ/kg with an equivalence ratio of 0.8. The tests failed to yield a positive thrust because of the skin-friction drag that accounted for up to 50% of the fuel-off drag.

Statistical tests of load-unload response ratio signals by lattice solid model: Implication to tidal triggering and earthquake prediction

Statistical tests of Load-Unload Response Ratio (LURR) signals are carried in order to verify statistical robustness of the previous studies using the Lattice Solid Model (MORA et al., 2002b). In each case 24 groups of samples with the same macroscopic parameters (tidal perturbation amplitude A, period T and tectonic loading rate k) but different particle arrangements are employed. Results of uni-axial compression experiments show that before the normalized time of catastrophic failure, the ensemble average LURR value rises significantly, in agreement with the observations of high LURR prior to the large earthquakes. In shearing tests, two parameters are found to control the correlation between earthquake occurrence and tidal stress. One is, A/(kT) controlling the phase shift between the peak seismicity rate and the peak amplitude of the perturbation stress. With an increase of this parameter, the phase shift is found to decrease. Another parameter, AT/k, controls the height of the probability density function (Pdf) of modeled seismicity. As this parameter increases, the Pdf becomes sharper and narrower, indicating a strong triggering. Statistical studies of LURR signals in shearing tests also suggest that except in strong triggering cases, where LURR cannot be calculated due to poor data in unloading cycles, the larger events are more likely to occur in higher LURR periods than the smaller ones, supporting the LURR hypothesis.

Prediction of vapor-moisture equilibriums for a wood-moisture system using a modified UNIQUAC model

A modified UNIQUAC model has been extended to describe and predict the equilibrium relative humidity and moisture content for wood. The method is validated over a range of moisture content from oven-dried state to fiber saturation point, and over a temperature range of 20-70 degrees C. Adjustable parameters and binary interaction parameters of the UNIQUAC model were estimated from experimental data for Caribbean pine and Hoop pine as well as data available in the literature. The two group-interaction parameters for the wood-moisture system were consistent with using function group contributions for H2O, -OH and -CHO. The result reconfirms that the main contributors to water adsorption in cell walls are the hydroxyl groups of the carbohydrates in cellulose and hemicelluloses. This provides some physical insight into the intermolecular force and energy between bound water and the wood material. (c) 2006 Elsevier Ltd. All rights reserved.