Better prediction of protein contact number using a support vector regression analysis of amino acid sequence

Background: Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C-beta atoms in other residues within a sphere around the C-beta atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. Results: We predict contact number from protein sequence using a novel support vector regression algorithm. Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. If residues are classified as being either contacted or non-contacted, the prediction accuracies are all greater than 77%, regardless of the choice of classification thresholds. Conclusion: The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary sequence and higher order consecutive protein structural and functional properties.

Interindividual Differences in Leg Muscle Mass and Pyruvate Kinase Activity Correlate with Interindividual Differences in Jumping Performance of Hyla multilineata

Frog jumping is an excellent model system for examining the structural basis of interindividual variation in burst locomotor performance. Some possible factors that affect jump performance, such as total body size, hindlimb length, muscle mass, and muscle mechanical and biochemical properties, were analysed at the interindividual (intraspecies) level in the tree frog Hyla multilineata. The aim of this study was to determine which of these physiological and anatomical variables both vary between individuals and are correlated with interindividual variation in jump performance. The model produced via stepwise linear regression analysis of absolute data suggested that 62% of the interindividual variation in maximum jump distance could be explained by a combination of interindividual variation in absolute plantaris muscle mass, total hindlimb muscle mass ( excluding plantaris muscle), and pyruvate kinase activity. When body length effects were removed, multiple regression indicated that the same independent variables explained 43% of the residual interindividual variation in jump distance. This suggests that individuals with relatively large jumping muscles and high pyruvate kinase activity for their body size achieved comparatively large maximal jump distances for their body size.

Estimating percolation and lateral water flow on sloping land in rainfed lowland rice ecosystem

Quantifying water losses in paddy fields assists estimation of water availability in rainfed lowland rice ecosystem. Little information is available on water balance in different toposequence positions of sloped rainfed lowland. Therefore, the aim of this work was to quantify percolation and the lateral water flow with special reference to the toposequential variation. Data used for the analysis was collected in Laos and northeast Thailand. Percolation and water tables were measured on a daily basis using a steel cylindrical tube with a lid and perforated PVC tubes, respectively. Percolation rate was determined using linear regression analysis of cumulative percolation. Assuming that the total amount of evaporation and transpiration was equivalent to potential evapotranspiration, the lateral water flow was estimated using the water balance equation. Separate perched water and groundwater tables were observed in paddy fields on coarse-textured soils. The percolation rate varied between 0 and 3 mm/day across locations, and the maximum water loss by lateral movement was more than 20 mm/day. Our results are in agreement with the previously reported findings, and the methodology of estimating water balance components appears reasonably acceptable. With regard to the toposequential variation, the higher the position in the topoesquence, the greater potential for water loss because of higher percolation and lateral flow rates.

Carotid artery intimal medial thickness, brachial artery flow-mediated vasodilation and cardiovascular risk factors in diabetic and non-diabetic indigenous Australians

Background: Indigenous Australians are at high risk for cardiovascular disease and type 2 diabetes. Carotid artery intimal medial thickness (CIMT) and brachial artery flow-mediated vasodilation (FMD) are ultrasound imaging based surrogate markers of cardiovascular risk. This study examines the relative contributions of traditional cardiovascular risk factors on CIMT and FMD in adult Indigenous Australians with and without type 2 diabetes mellitus. Method: One hundred and nineteen Indigenous Australians were recruited. Physical and biochemical markers of cardiovascular risk, together with CIMT and FMD were meausred for all subjects. Results: Fifty-three Indigenous Australians subjects (45%) had type 2 diabetes mellitus. There was a significantly greater mean CIMT in diabetic versus non-diabetic subjects (p = 0.049). In the non-diabetic group with non-parametric analyses, there were significant correlations between CIMT and: age (r = 0.64, p < 0.001), systolic blood pressure (r = 0.47, p < 0.001) and non-smokers (r = -0.30, p = 0.018). In the diabetic group, non-parametric analysis showed correlations between CIMT, age (r = 0.36, p = 0.009) and duration of diabetes (r = 0.30, p = 0.035) only. Adjusting forage, sex, smoking and history of cardiovascular disease, Hb(A1c) became the sole significant correlate of CIMT (r = 0.35,p = 0.01) in the diabetic group. In non-parametric analysis, age was the sole significant correlate of FMD (r = -0.31,p = 0.013), and only in non-diabetic subjects. Linear regression analysis showed significant associations between CIMT and age (t = 4.6,p < 0.001), systolic blood pressure (t = 2.6, p = 0.010) and Hb(A1c) (t = 2.6, p = 0.012), smoking (t = 2.1, p = 0.04) and fasting LDL-cholesterol (t = 2.1, p = 0.04). There were no significant associations between FMD and examined cardiovascular risk factors with linear regression analysis Conclusions: CIMT appears to be a useful surrogate marker of cardiovascular risk in this sample of Indigenous Australian subjects, correlating better than FMD with established cardiovascular risk factors. A lifestyle intervention programme may alleviate the burden of cardiovascular disease in Indigenous Australians by reducing central obesity, lowering blood pressure, correcting dyslipidaemia and improving glycaemic control. CIMT may prove to be a useful tool to assess efficacy of such an intervention programme. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

Association of public support for survival of wildlife species with their likeability

We surveyed 204 individuals from the general public in Brisbane, Australia, to ascertain the extent to which they liked or disliked 24 species of wildlife (belonging to three classes: mammals, birds and reptiles) present in tropical Australia. We calculated likeability indices for each species. We also asked respondents if they favored the survival of each of these species, and were able to calculate the percentage of respondents favoring survival of each. Using linear regression analysis, we could relate the percentage of respondents favoring survival of each of the species to their indices of likeability. In addition, we compared the mean likeability of species in the three classes (mammals, birds and reptiles) with the respondents' allocation of funds (hypothetical 1,000 Australian dollars) between conservation of species and a human charity. From this, we were able to assess how important stated likeability is for preferences to conserve species by animal class, and reconsidered the hypothesis in the literature that there is likely to be more public support for the survival of mammals than for birds, and more support for the survival of birds than for reptiles.

Protein contamination of the laryngeal mask airway and its relationship to re-use

The Laryngeal Mask Airway is a reusable device for maintaining the patency of a patient's airway during general anaesthesia. The device can be reused after it has been cleaned and sterilized. Protein contamination of medical instruments is a concern and has been found to occur despite standard sterilization techniques. The reason for the concern relates to the possibility of the transmission of prions and the risk of developing a neurodegenerative disorder such as Creutzveldt-Jacob disease. The purpose of this study was to quantify the amount of protein contamination that occurs, and to relate this to the number of times the Laryngeal Mask Airway has been used. Fifty previously used Classic Laryngeal Masks were collected after routine sterilization and packaging. The devices were immersed in protein detecting stain and then visual inspection performed to assess the degree and distribution of the staining. The researcher was blinded to the number of times the Laryngeal Mask Airway had been used. Linear regression analysis of the degrees of staining of the airway revealed that protein contamination occurs after the first use of the device and this increases with each subsequent use. This finding highlights the concern that the currently used cleaning and sterilization methods do not prevent the accumulation of proteinaceous material on Laryngeal Mask Airways. Consideration should be given to the search for more efficient cleaning and sterilization techniques or the use of disposable devices.

The water balance on sloping land in rainfed lowland rice ecosystem

Quantifying water losses in paddy fields assists estimation of water availability in rainfed lowland rice ecosystem. There is, however, no definite method for determining the water losses, and little information is available on water balance in different toposequence positions of a sloped rainfed lowland. Therefore, the aim of this work was to quantify percolation and the lateral water flow with special reference to the toposequential variation. Data used for the analysis was collected in Laos and northeast Thailand. Percolation and water tables were measured on a daily basis. The percolator is a steel cylindrical tube with a lid to prevent water loss from evapotranspiration. The water table meter is a short PVC tube for determination of perched water table and a long PVC tube for groundwater table, and the side is perforated with 5-mm diameter holes at 20-mm distance. Percolation rate was determined using linear regression analysis of cumulative percolation. Assuming that the total amount of evaporation and transpiration was equivalent to potential evapotranspiration, the lateral water flow was estimated using the water balance equation. Our results are in agreement with the previously reported findings, and the methodology of estimating water balance components appears reasonably acceptable. With regard to the toposequential variation, the higher position in the topoesquence, the greater potential of the water losses because of higher percolation and lateral flow rates.

Effects of rock properties on specific cutting energy in linear cutting of sandstones by picks

Specific cutting energy (SE) has been widely used to assess the rock cuttability for mechanical excavation purposes. Some prediction models were developed for SE through correlating rock properties with SE values. However, some of the textural and compositional rock parameters i.e. texture coefficient and feldspar, mafic, and felsic mineral contents were not considered. The present study is to investigate the effects of previously ignored rock parameters along with engineering rock properties on SE. Mineralogical and petrographic analyses, rock mechanics, and linear rock cutting tests were performed on sandstone samples taken from sites around Ankara, Turkey. Relationships between SE and rock properties were evaluated using bivariate correlation and linear regression analyses. The tests and subsequent analyses revealed that the texture coefficient and feldspar content of sandstones affected rock cuttability, evidenced by significant correlations between these parameters and SE at a 90% confidence level. Felsic and mafic mineral contents of sandstones did not exhibit any statistically significant correlation against SE. Cementation coefficient, effective porosity, and pore volume had good correlations against SE. Poisson's ratio, Brazilian tensile strength, Shore scleroscope hardness, Schmidt hammer hardness, dry density, and point load strength index showed very strong linear correlations against SE at confidence levels of 95% and above, all of which were also found suitable to be used in predicting SE individually, depending on the results of regression analysis, ANOVA, Student's t-tests, and R2 values. Poisson's ratio exhibited the highest correlation with SE and seemed to be the most reliable SE prediction tool in sandstones.

Effects of rock properties on specific cutting energy in linear cutting of sandstones by picks

Specific cutting energy (SE) has been widely used to assess the rock cuttability for mechanical excavation purposes. Some prediction models were developed for SE through correlating rock properties with SE values. However, some of the textural and compositional rock parameters i.e. texture coefficient and feldspar, mafic, and felsic mineral contents were not considered. The present study is to investigate the effects of previously ignored rock parameters along with engineering rock properties on SE. Mineralogical and petrographic analyses, rock mechanics, and linear rock cutting tests were performed on sandstone samples taken from sites around Ankara, Turkey. Relationships between SE and rock properties were evaluated using bivariate correlation and linear regression analyses. The tests and subsequent analyses revealed that the texture coefficient and feldspar content of sandstones affected rock cuttability, evidenced by significant correlations between these parameters and SE at a 90% confidence level. Felsic and mafic mineral contents of sandstones did not exhibit any statistically significant correlation against SE. Cementation coefficient, effective porosity, and pore volume had good correlations against SE. Poisson's ratio, Brazilian tensile strength, Shore scleroscope hardness, Schmidt hammer hardness, dry density, and point load strength index showed very strong linear correlations against SE at confidence levels of 95% and above, all of which were also found suitable to be used in predicting SE individually, depending on the results of regression analysis, ANOVA, Student's t-tests, and R-2 values. Poisson's ratio exhibited the highest correlation with SE and seemed to be the most reliable SE prediction tool in sandstones.