Abstract

Base pairs belonging to the cis Hoogsteen: sugar-edge (H:S) family play important structural roles in folded RNA molecules. Several of these are present in internal loops, where they are involved in interactions leading to planar dinucleotide platforms which stabilize higher order structures such as base triplets and quartets. We report results of analysis of 30 representative examples spanning 16 possible base pair combinations, with several of them showing multimodality of base pairing geometry. The geometries of 23 of these base pairs were modeled directly from coordinates extracted from RNA crystal structures. The other seven were predicted structures which were modeled on the basis of observed isosteric analogues. After appropriate satisfaction of residual valencies, these structures were relaxed using the B3LYP/6-31G(d,p) method and interaction energies were derived at the RIMP2/aug-cc-pVDZ level of theory. The geometries for each of the studied base pairs have been characterized in terms of the number and nature of H-bonds, rmsd values observed on optimization, base pair geometrical parameters, and sugar pucker analysis. In addition to its evaluation, the nature of intermolecular interaction in these complexes was also analyzed using Morokuma decomposition. The gas phase interaction energies range between −5.2 and −20.6 kcal/mol and, in contrast to the H:S trans base pairs, show enhanced relative importance of the electron correlation component, indicative of the greater role of dispersion energy in stabilization of these base pairs. The rich variety of hydrogen bonding pattern, involving the flexible sugar edge, appears to hold the key to several features of structural motifs, such as planarity and propensity to participate in triplets, observed in this family of base pairs. This work explores these aspects by integrating database analysis, and detailed base pairing geometry analysis at the atomistic level, with ab initio computation of interaction energies. The study, involving alternative classification of base pairs and triplets, provides insights into intrinsic properties of these base pairs and their possible structural and functional roles.

Abstract

We study the interplay of network connectivity and the issues related to the 'possibility', 'feasibility' and 'optimality' for unconditionally reliable message transmission (URMT) and unconditionally secure message transmission (USMT) in an undirected synchronous network, under the influence of an adaptive mixed adversary having unbounded computing power, who can corrupt some of the nodes in the network in Byzantine, omission, fail-stop and passive fashion respectively. We consider two types of adversary, namely threshold and non-threshold. One of the important conclusions we arrive at from our study is that allowing a negligible error probability significantly helps in the 'possibility', 'feasibility' and 'optimality' of both reliable and secure message transmission protocols. To design our protocols, we propose several new techniques which are of independent interest.

Abstract

This paper provides a solution to the issue:“How can we use Wikipedia based concepts in document clustering with lesser human involvement, accompanied by effective improvements in result?” In the devised system, we propose a method to exploit the importance of N-grams in a document and use Wikipedia based additional knowledge for GAAC based document clustering. The importance of N-grams in a document depends on a many features including, but not limited to: frequency, position of their occurrence in a sentence and the position of the sentence in which they occur, in the document. First, we introduce a new similarity measure, which takes the weighted N-gram importance into account, in the calculation of similarity measure while performing document clustering. As a result, the chances of topical similarity in clustering are improved. Second, we use Wikipedia as an additional knowledge base both, to remove noisy entries from the extracted N-grams and to reduce the information gap between N-grams that are conceptually-related, which do not have a match owing to differences in writing scheme or strategies. Our experimental results on the publicly available text dataset clearly show that our devised system has a significant improvement in performance over bag-of-words based state-of-the-art systems in this area.

Abstract

In the recent past composability has emerged as a key requirement for various distributed protocols. It is not enough for a protocol to be robust when it runs in isolation or in a “stand-alone” setting but it should be robust even in an environment where several copies of the same protocol or other protocol(s) are running simultaneously. In this work, we investigate the composability for protocols that tolerate a bounded adversary modeled as a probabilistic polynomial time Turing machine. We examine composability of protocols for two fundamental problems in distributed computing - reliable unicast and reliable broadcast. We show that any composable protocol – for reliable unicast tolerating an adversary, that corrupts up to any t nodes, requires 2t + 1 connectivity and for reliable broadcast tolerating an adversary, that corrupts up to any t nodes, requires n > 3t and 2t + 1 connectivity.

Abstract

Sensor networks consist of small motes attached with sensors to measure ambient parameters like temperature, humidity and light. As these motes are unreliable due to wireless link quality and also the data measuring sensors cannot be calibrated accurately for a given applications need. The unique data fusion needs are that parameter being measured is distributed across the network and needs to be computed reliably and with minimum overhead and redundancy due to data value being correlated. We show the asymptotic complexity of topology control when applied to power-aware routing is scalable and argue that the accuracy and reliability of the estimated sensor values can be accurately predicted for the physical value being sensed and aggregating. A prefix-based routing protocol is used for data-centric storage, which allows querying distributed parameters using a KEY, VALUE pairs without the need of the sensor node to know its exact geographic information. Intelligent sensor information processing, which is driven by these requirements, is discussed under the framework INSPIRE-DB.

Abstract

Glottal closure instants (GCI) are the instants of significant excitation of the vocal tract system during the production of speech. The performance of many speech analysis and synthesis approaches depends on accurate estimation of GCIs. A new method for detection of GCI locations in speech utterances using Fourier-Bessel (FB) expansion and amplitude and frequency modulated (AM-FM) signal model is proposed in this paper. The inherent filtering property of the FB expansion is used to weaken the effect of formants in the speech utterances. The band-limited signal reconstructed using FB coefficients has been considered as an AM-FM signal. The discrete-energy separation algorithm (DESA) has been used to estimate the amplitude envelope (AE) function of the AM-FM signal model. The estimated AE function is explored for detection of GCIs. The CMU-Arctic database is used in this work for the validation of the proposed method for GCI detection with the electro-glottograph (EGG) as a reference. It has been observed that the detected GCI by the proposed method seems to provide accurate location of GCIs.

Abstract

The voice onset time (VOT) combines the temporal and frequency structure over very short duration. This makes the VOT detection task difficult. But the VOT is an important temporal feature. In this paper we propose a new method for the detection of VOT in speech utterances. The method uses Fourier-Bessel (FB) expansion followed by amplitude and frequency modulated (AM-FM) signal model. The FB expansion is used to emphasize the vowel and consonant regions of stop consonant vowel (SCV) units (/ka/, /ta/, and /pa/). The emphasized signals using selected range of FB coefficients have been considered narrow-band AM-FM signals. The discrete energy separation algorithm (DESA) has been used to estimate amplitude envelope (AE) function of the AM-FM model. The estimated AE function is explored for the detection of VOT. The VOT detection studies are carried out using the speech corpus consists of utterances of various male and female speakers.

Abstract

In this paper, we consider the problem of mining the special proper-ties of a given record in a relational dataset. In our formulation, a property is a combination of multiple attribute-value pairs. The support of a property is the number of records that satisfy it. We consider a property as special if its support occurs to us as a shockand the measure of this shock factor is more than a userdefined thresholdη. We provide a way to define this notion of shock based on en-tropy. We also output the shock factor for records in the dataset in a convenient,easily-interpretable manner. An illustrated example is provided on how users can interpret the results. Experiments on real and synthetic data sets reveal interesting properties of data records that cannot be mined using traditional approaches.

Abstract

We have developed a web based integrated platform for the identification of genomic islands in which various measures that capture bias in nucleotide compositions have been implemented, viz., GC content (both at the whole genome and at three codon positions in genes), genomic signature, k-mer distribution (k=2–6), codon usage bias and amino acid usage bias. The analysis carried out in sliding windows (default size 10Kb) is compared with the genomic average for each measure. The output is displayed in a tabular format for each window which may be filtered if the values of the measures differ by 1.5σ (standard deviations) from the genomic average.

Abstract

Cool roof is one of the important strategies of energy savings in the tropical climate especially for low rise buildings. Standardization of the possible energy savings for a measure like cool roof would be quite difficult due to availability of various technologies and materials, as well as due to difference in building forms and climatic conditions. This paper talks about the development of an online tool for estimating energy saving through cool roof strategy using Energy Plus v4 as the backend simulation engine. Energy savings are calculated through simulating two identical buildings with different roof reflectivity values. Using this tool, simulations are run for the base case roof reflectivity of 0.3 and proposed case roof reflectivity of 0.75 for various major cities in India for a single floor, daytime use building. An average saving of 6.2% in cooling energy and 2.4% in total energy consumption was obtained using this tool.