Abstract

Traditional association rule mining based on the support–confidence framework provides the objective measure of the rules that are of interest to users. However, it does not reflect the semantic measure among the items. The semantic measure of an itemset is characterized with utility values that are typically associated with transaction items, where a user will be interested to an itemset only if it satisfies a given utility constraint. In this paper, we first define the problem of finding association rules using utility-confidence framework, which is a generalization of the amount-confidence measure. Using this semantic concept of rules, we then propose a compressed representation for association rules having minimal antecedent and maximal consequent. This representation is generated with the help of high utility closed itemsets (HUCI) and their generators. We propose the algorithms to generate the utility based non-redundant association rules and methods for reconstructing all association rules. Furthermore, we describe the algorithms which generate high utility itemsets (HUI) and high utility closed itemsets with their generators. These proposed algorithms are implemented using both synthetic and real datasets. The results demonstrate better efficiency and effectiveness of the proposed HUCI-Miner algorithm compared to other well-known existing algorithms. In addition, the experimental results show better quality in the compressed representation of the entire rule set under the considered framework.

Abstract

Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. ‘RNA Base Pair Count, Geometry and Stability’ ( http://bioinf.iiit.ac.in/RNABPCOGEST …

Abstract

The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid–base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ

Abstract

Improving the thermostability of industrial enzymes is an important protein engineering challenge. Point mutations, induced to increase thermostability, affect the structure and dynamics of the target protein in several ways and thus can also affect its activity. There appears to be no general rules for improving the thermostabilty of enzymes without adversely affecting their enzymatic activity. We report MD simulations, of wild type Bacillus subtilis lipase (WT) and its six progressively thermostable mutants (2M, 3M, 4M, 6M, 9M, and 12M), performed at different temperatures, to address this issue. Less thermostable mutants (LTMs), 2M to 6M, show WT-like dynamics at all simulation temperatures. However, the two more thermostable mutants (MTMs) show the required flexibility at appropriate temperature ranges and maintain conformational stability at high temperature. They show a deep and rugged free-energy

Abstract

Drought is one of the major environmental stress conditions affecting the yield of rice across the globe. Unraveling the functional roles of the drought-responsive genes and their underlying molecular mechanisms will provide important leads to improve the yield of rice. Co-expression relationships derived from condition-dependent gene expression data is an effective way to identify the functional associations between genes that are part of the same biological process and may be under similar transcriptional control. For this purpose, vast amount of freely available transcriptomic data can be used for functional annotation. In this study we consider gene expression data for different tissues and developmental stages in response to drought stress. We analyze the network of co-expressed genes to identify drought-responsive genes modules in a tissue and stage-specific manner based on differential expression and gene enrichment analysis. Taking cues from the systems-level behavior of these modules, we propose two approaches to identify clusters of tightly co-expressed/co-regulated genes. Using graph-centrality measures and differential gene expression, we identify biologically informative genes that lack any functional annotation. We show that using orthologous information from other plant species, the conserved co-expression patterns of the uncharacterized genes can be identified. Presence of a conserved neighborhood enables us to extrapolate functional annotation. Alternatively, we show that ‘guide-gene’ approach can help in understanding the tissue-specific transcriptional regulation of uncharacterized genes. Finally, we confirm the …

Abstract

In the last decade there has been considerable interest in a novel dynamical phenomenon of chimera states observed in an array of non-locally coupled oscillators where regions of coherence and incoherence coexist across the network. In this study we show how chimera states emerge in coupled logistic maps for certain specified initial conditions when the range and strength of coupling is varied. Here we show that these states are very robust and persist even in the presence of noise in the network parameters. On applying localized external perturbation to the incoherent regions, it is possible to obtain a completely coherent/incoherent dynamics in the whole network depending on the strength and sign of perturbation. This has important applications in the control of undesirable local dynamics, such as seizures in neural systems, or fibrillations in cardiac

Abstract

The current study evaluates the growing stock, biomass and carbon content of Andhra Pradesh state’s forest (India) along with its current status of forest degradation and loss. For this purpose, the study used the growing stock data collected by state forest department in 2010 for the calculation of biomass and carbon storage using the standard conversion and expansion factors given by IPCC. The analysis shows low biomass and carbon values for the state’s forest in comparison to the mean values recorded in different studies made for Andhra Pradesh. It is also observed to be lower when compared with the average carbon and biomass for Indian forests. Overall, the analysis showed degradation and loss of forest in the state, coupled with reduction in biomass and carbon sink.

Abstract

The Jaisalmer district of Rajasthan province of India was known to suffer with frequent drought due to poor and delayed monsoon, abnormally high summer-temperature and insufficient water resources. However fl ood-like situation prevails in the drought prone Jaisalmer district of Rajasthan as torrential rains are seen to affect the region in the recent years. In the present study, detailed analysis of meteorological, hydrological and satellite data of the Jaisalmer district has been carried out for the years 2006−2008. Standardized Precipitation Index (SPI), Consecutive Dry Days (CDD) and Effective Drought Index (EDI) have been used to quantify the precipitation defi cit. Standardized Water-Level Index (SWI) has been developed to assess ground-water recharge-defi cit. Vegetative drought indices like Vegetation Condition Index (VCI), Temperature Condition Index (TCI), Vegetation Health Index (VHI), Normalized Difference Vegetation Index (NDVI) and Modifi ed Soil-Adjusted Vegetation Index 2 have been calculated. We also introduce two new indices Soil based Vegetation Condition Index (SVCI) and Composite Drought Index (CDI) specifi cally for regions like Jaisalmer where aridity in soil and affects vegetation and water-level.

Abstract

Survival of plant species is governed by a number of functions. The participation of each function in species survival and the impact of the contrary behaviour of the species vary from function to function. The probability of extinction of species varies in all such scenarios and has to be calculated separately. Secondly, species follow different patterns of dispersal and localisation at different stages of occupancy state of the site, therefore, the scenarios of competition for resources with climatic shifts leading to deterioration and loss of biodiversity resulting in extinction needs to be studied. Furthermore, most possible deviations of species from climax community states needs to be calculated before species become extinct due to sudden environmental disruption. Globally, various types of anthropogenic disturbances threaten the diversity of biological systems. The impact of these anthropogenic activities needs to be analysed to identify extinction patterns with respect to these activities. All the analyses mentioned above have been tried to be achieved through probabilistic or graphical models in this study

Abstract

This research note focuses on the current climate change research scenario and discusses primarily what is required in the present global climate change conditions. Most of the climate change research and models predict adverse future conditions that have to be faced by humanity, with less emphasis on mitigation measures. Moreover, research ends as reports on the shelves of scientists and researchers and as publications in journals. At this juncture the major focus should be on research that helps in reducing the impact rather than on analysing future scenarios of climate change using different models. The article raises several questions and suggestions regards climate change research and lays emphasis on what we really need from climate change researchers.