How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Prediction of flame liftoff height of diffusion/partially premixed jet flames and modeling of mild combustion burners

In this article, a new flame extinction model based on the k/epsilon turbulence time scale concept is proposed to predict the flame liftoff heights over a wide range of coflow temperature and O-2 mass fraction of the coflow. The flame is assumed to be quenched, when the fluid time scale is less than the chemical time scale ( Da < 1). The chemical time scale is derived as a function of temperature, oxidizer mass fraction, fuel dilution, velocity of the jet and fuel type. The present extinction model has been tested for a variety of conditions: ( a) ambient coflow conditions ( 1 atm and 300 K) for propane, methane and hydrogen jet flames, ( b) highly preheated coflow, and ( c) high temperature and low oxidizer concentration coflow. Predicted flame liftoff heights of jet diffusion and partially premixed flames are in excellent agreement with the experimental data for all the simulated conditions and fuels. It is observed that flame stabilization occurs at a point near the stoichiometric mixture fraction surface, where the local flow velocity is equal to the local flame propagation speed. The present method is used to determine the chemical time scale for the conditions existing in the mild/ flameless combustion burners investigated by the authors earlier. This model has successfully predicted the initial premixing of the fuel with combustion products before the combustion reaction initiates. It has been inferred from these numerical simulations that fuel injection is followed by intense premixing with hot combustion products in the primary zone and combustion reaction follows further downstream. Reaction rate contours suggest that reaction takes place over a large volume and the magnitude of the combustion reaction is lower compared to the conventional combustion mode. The appearance of attached flames in the mild combustion burners at low thermal inputs is also predicted, which is due to lower average jet velocity and larger residence times in the near injection zone.

Prediction of fatigue strength in plain and reinforced concrete beams

A fatigue crack propagation model for concrete is proposed based on the concepts of fracture mechanics. This model takes into account the loading history, frequency of applied load, and size, effect parameters. Using this model, a method is described based on linear elastic fracture mechanics to assess the residual strength of cracked plain and reinforced concrete (RC) beams. This could be used to predict the residual strength (load carrying capacity) of cracked or damaged plain and reinforced concrete beams at a given level of damage. It has been seen that the fatigue crack propagation rate increases as. the size of plain concrete, beam increases indicating an increase in brittleness. In reinforced concrete (RC) beams, the fracture process becomes stable only when the beam is sufficiently reinforced.

Nonlinear ensemble prediction of chaotic daily rainfall

The significance of treating rainfall as a chaotic system instead of a stochastic system for a better understanding of the underlying dynamics has been taken up by various studies recently. However, an important limitation of all these approaches is the dependence on a single method for identifying the chaotic nature and the parameters involved. Many of these approaches aim at only analyzing the chaotic nature and not its prediction. In the present study, an attempt is made to identify chaos using various techniques and prediction is also done by generating ensembles in order to quantify the uncertainty involved. Daily rainfall data of three regions with contrasting characteristics (mainly in the spatial area covered), Malaprabha, Mahanadi and All-India for the period 1955-2000 are used for the study. Auto-correlation and mutual information methods are used to determine the delay time for the phase space reconstruction. Optimum embedding dimension is determined using correlation dimension, false nearest neighbour algorithm and also nonlinear prediction methods. The low embedding dimensions obtained from these methods indicate the existence of low dimensional chaos in the three rainfall series. Correlation dimension method is done on th phase randomized and first derivative of the data series to check whether the saturation of the dimension is due to the inherent linear correlation structure or due to low dimensional dynamics. Positive Lyapunov exponents obtained prove the exponential divergence of the trajectories and hence the unpredictability. Surrogate data test is also done to further confirm the nonlinear structure of the rainfall series. A range of plausible parameters is used for generating an ensemble of predictions of rainfall for each year separately for the period 1996-2000 using the data till the preceding year. For analyzing the sensitiveness to initial conditions, predictions are done from two different months in a year viz., from the beginning of January and June. The reasonably good predictions obtained indicate the efficiency of the nonlinear prediction method for predicting the rainfall series. Also, the rank probability skill score and the rank histograms show that the ensembles generated are reliable with a good spread and skill. A comparison of results of the three regions indicates that although they are chaotic in nature, the spatial averaging over a large area can increase the dimension and improve the predictability, thus destroying the chaotic nature. (C) 2010 Elsevier Ltd. All rights reserved.

Prediction of estrus cyclicity in Asian elephants (Elephas maximus) through estimation of fecal progesterone metabolite: development of an enzyme-linked immuno-sorbent assay

Asian elephants (Dephas maximus), prominent ``flagship species'', arelisted under the category of endangered species (EN - A2c, ver. 3.1, IUCN Red List 2009) and there is a need for their conservation This requires understanding demographic and reproductive dynamics of the species. Monitoring reproductive status of any species is traditionally being carried out through invasive blood sampling and this is restrictive for large animals such as wild or semi-captive elephants due to legal. ethical, and practical reasons Hence. there is a need for a non-invasive technique to assess reproductive cyclicity profiles of elephants. which will help in the species' conservation strategies In this study. we developed an indirect competitive enzyme linked immuno-sorbent assay (ELISA) to estimate the concentration of one of the progesterone-metabolites i.e, allopregnanolone (5 alpha-P-3OH) in fecal samples of As elephants We validated the assay which had a sensitivity of 0.25 mu M at 90% binding with an EC50 value of 1 37 mu M Using female elephants. kept under semi-captive conditions in the forest camps of Mudumalar Wildlife Sanctuary, Tamil Nadu and Bandipur National Park, Karnataka, India. we measured fecal progesterone-metabolite (5 alpha-P-3OH) concentrations in six an and showed their clear correlation with those of scrum progesterone measured by a standard radio-immuno assay. Statistical analyses using a Linear Mixed Effect model showed a positive correlation (P < 0 1) between the profiles of fecal 5 alpha-P-3OH (range 0 5-10 mu g/g) and serum progesterone (range: 0 1-1 8 ng/mL) Therefore, our studies show, for the first time, that the fecal progesterone-metabolite assay could be exploited to predict estrus cyclicity and to potentially assess the reproductive status of captive and free-ranging female Asian elephants, thereby helping to plan their breeding strategy (C) 2010 Elsevier Inc.All rights reserved.

Prediction of solid block masonry prism compressive strength using FE model

Masonry strength is dependent upon characteristics of the masonry unit,the mortar and the bond between them. Empirical formulae as well as analytical and finite element (FE) models have been developed to predict structural behaviour of masonry. This paper is focused on developing a three dimensional non-linear FE model based on micro-modelling approach to predict masonry prism compressive strength and crack pattern. The proposed FE model uses multi-linear stress-strain relationships to model the non-linear behaviour of solid masonry unit and the mortar. Willam-Warnke's five parameter failure theory developed for modelling the tri-axial behaviour of concrete has been adopted to model the failure of masonry materials. The post failure regime has been modelled by applying orthotropic constitutive equations based on the smeared crack approach. Compressive strength of the masonry prism predicted by the proposed FE model has been compared with experimental values as well as the values predicted by other failure theories and Eurocode formula. The crack pattern predicted by the FE model shows vertical splitting cracks in the prism. The FE model predicts the ultimate failure compressive stress close to 85 of the mean experimental compressive strength value.

Essays on the Modeling and Prediction of Volatility and Higher Moments of Stock Returns (summary section only)

One of the most fundamental and widely accepted ideas in finance is that investors are compensated through higher returns for taking on non-diversifiable risk. Hence the quantification, modeling and prediction of risk have been, and still are one of the most prolific research areas in financial economics. It was recognized early on that there are predictable patterns in the variance of speculative prices. Later research has shown that there may also be systematic variation in the skewness and kurtosis of financial returns. Lacking in the literature so far, is an out-of-sample forecast evaluation of the potential benefits of these new more complicated models with time-varying higher moments. Such an evaluation is the topic of this dissertation. Essay 1 investigates the forecast performance of the GARCH (1,1) model when estimated with 9 different error distributions on Standard and Poor’s 500 Index Future returns. By utilizing the theory of realized variance to construct an appropriate ex post measure of variance from intra-day data it is shown that allowing for a leptokurtic error distribution leads to significant improvements in variance forecasts compared to using the normal distribution. This result holds for daily, weekly as well as monthly forecast horizons. It is also found that allowing for skewness and time variation in the higher moments of the distribution does not further improve forecasts. In Essay 2, by using 20 years of daily Standard and Poor 500 index returns, it is found that density forecasts are much improved by allowing for constant excess kurtosis but not improved by allowing for skewness. By allowing the kurtosis and skewness to be time varying the density forecasts are not further improved but on the contrary made slightly worse. In Essay 3 a new model incorporating conditional variance, skewness and kurtosis based on the Normal Inverse Gaussian (NIG) distribution is proposed. The new model and two previously used NIG models are evaluated by their Value at Risk (VaR) forecasts on a long series of daily Standard and Poor’s 500 returns. The results show that only the new model produces satisfactory VaR forecasts for both 1% and 5% VaR Taken together the results of the thesis show that kurtosis appears not to exhibit predictable time variation, whereas there is found some predictability in the skewness. However, the dynamic properties of the skewness are not completely captured by any of the models.

Prediction of swelling pressure of soil using artificial intelligence techniques

The swelling pressure of soil depends upon various soil parameters such as mineralogy, clay content, Atterberg's limits, dry density, moisture content, initial degree of saturation, etc. along with structural and environmental factors. It is very difficult to model and analyze swelling pressure effectively taking all the above aspects into consideration. Various statistical/empirical methods have been attempted to predict the swelling pressure based on index properties of soil. In this paper, the computational intelligence techniques artificial neural network and support vector machine have been used to develop models based on the set of available experimental results to predict swelling pressure from the inputs; natural moisture content, dry density, liquid limit, plasticity index, and clay fraction. The generalization of the model to new set of data other than the training set of data is discussed which is required for successful application of a model. A detailed study of the relative performance of the computational intelligence techniques has been carried out based on different statistical performance criteria.

Prediction of swelling pressure of soil using artificial intelligence techniques

The swelling pressure of soil depends upon various soil parameters such as mineralogy, clay content, Atterberg's limits, dry density, moisture content, initial degree of saturation, etc. along with structural and environmental factors. It is very difficult to model and analyze swelling pressure effectively taking all the above aspects into consideration. Various statistical/empirical methods have been attempted to predict the swelling pressure based on index properties of soil. In this paper, the computational intelligence techniques artificial neural network and support vector machine have been used to develop models based on the set of available experimental results to predict swelling pressure from the inputs; natural moisture content, dry density, liquid limit, plasticity index, and clay fraction. The generalization of the model to new set of data other than the training set of data is discussed which is required for successful application of a model. A detailed study of the relative performance of the computational intelligence techniques has been carried out based on different statistical performance criteria.

Robust prediction of residual velocities and ballistic limits of projectiles for impact on thin aluminium plates

This paper deals with the simulation-driven study of the impact of hardened steel projectiles on thin aluminium target plates using explicit finite element analysis as implemented in LS-DYNA. The evaluation of finite element modelling includes a comprehensive mesh convergence study using shell elements for representing target plates and the solid element-based representation of ogivalnosed projectiles. A user-friendly automatic contact detection algorithm is used for capturing interaction between the projectile and the target plate. It is shown that the proper choice of mesh density and strain rate-dependent material properties is crucial as these parameters significantly affect the computed residual velocity. The efficacy of correlation with experimental data is adjudged in terms of a 'correlation index' defined in the present study for which values close to unity are desirable.By simulating laboratory impact tests on thin aluminium plates carried out by earlier investigators, extremely good prediction of experimental ballistic limits has been observed with correlation indices approaching unity. Additional simulation-based parametric studies have been carried out and results consistent with test data have been obtained. The simulation procedures followed in the present study can be applied with confidence in designing thin aluminium armour plates for protection against low calibre projectiles.

Prediction of inplane damping from deterministic and stochastic models

This paper reviews computational reliability, computer algebra, stochastic stability and rotating frame turbulence (RFT) in the context of predicting the blade inplane mode stability, a mode which is at best weakly damped. Computational reliability can be built into routine Floquet analysis involving trim analysis and eigenanalysis, and a highly portable special purpose processor restricted to rotorcraft dynamics analysis is found to be more economical than a multipurpose processor. While the RFT effects are dominant in turbulence modeling, the finding that turbulence stabilizes the inplane mode is based on the assumption that turbulence is white noise.

Intelligent prediction of the stress-strain response of intact and jointed rocks

An application of Artificial Neural Networks for predicting the stress-strain response of jointed rocks under different confining pressures is presented in this paper. Rocks of different compressive strength with different joint properties (frequency, orientation and strength of joints) are considered in this study. The database for training the neural network is formed from the results of triaxial compression tests on different intact and jointed rocks with different joint properties tested at different confining pressures reported by various researchers in the literature. The network was trained using a three-layered network with the feed-forward back propagation algorithm.About 85% of the data was used for training and the remaining 15% was used for testing the network. Results from the analyses demonstrated that the neural network approach is effective in capturing the stress-strain behaviour of intact rocks and the complex stress-strain behaviour of jointed rocks. A single neural network is demonstrated to be capable of predicting the stress-strain response of different jointed rocks, whose intact strength varies from 11.32 MPa to 123 MPa, spacing of joints varies from 10 cm to 100 cm. and confining pressures range from 0 to 13.8 MPa. (C) 2010 Elsevier Ltd. All rights reserved.

Prediction of breakout noise from an elliptical duct of finite length

This paper describes a predictive model for breakout noise from an elliptical duct or shell of finite length. The transmission mechanism is essentially that of ``mode coupling'', whereby higher structural modes in the duct walls get excited because of non-circularity of the wall. Effect of geometry has been taken care of by evaluating Fourier coefficients of the radius of curvature. The noise radiated from the duct walls is represented by that from a finite vibrating length of a semi infinite cylinder in a free field. Emphasis is on understanding the physics of the problem as well as analytical modeling. The analytical model is validated with 3-D FEM. Effects of the ovality, curvature, and axial terminations of the duct have been demonstrated. (C) 2010 Institute of Noise Control Engineering.

Improved prediction of plane transverse jets in supersonic crossflows

THE flowfield due to transverse injection of a round sonic jet into a supersonic flowis a configuration of interest in the design of supersonic combustors or thrust vector control of supersonic jets. The flow is also of fundamental interest because it presents separation from a smooth surface, embedded subsonic regions, curved shear layers, strong shocks, an unusual development of the injected jet into a kidney-shaped streamwise vortex pair, and a wake behind the jet. Although the geometry is simple, the flow is complex and is a good candidate for assessing the behavior of turbulence models for high-speed flow, beginning with the corresponding two-dimensional flow shown in Fig. 1. At the slot, an underexpanded sonic jet expands rapidly into the supersonic crossflow. Expansion waves reflect at the jet boundary, coalesce, and give rise to a Mach surface (Mach disk for round jets).