Abstract

RNA structural bioinformatics has developed, into a vibrant interdisciplinary area, in response to the emergence of noncoding RNA molecules as key regulatory players in nearly all important biological processes. Here we introduce the different conceptual tools and available resources, related to this new area. We also review its application in studying the role of RNA-protein interactions.

Abstract

This paper proposes a method for automatic detection of breathy voiced vowels in continuous Gujarati speech. As breathy voice is a specific phonetic feature predominantly present in Gujarati among Indian languages, it can be used for identifying Gujarati language. The objective of this paper is to differentiate breathy voiced vowels from modal voiced vowels based on loudness measure. Excitation source characteristics represented by loudness measure are used for differentiating the voice quality. In the proposed method, initially vowel regions in continuous speech are determined by using the knowledge of vowel onset points and epochs. Later, hypothesized vowel segments are classified by using loudness measure. Performance of the proposed method is evaluated on Gujarati speech utterances containing around 47 breathy and 192 modal vowels spoken by 5 male and 5 female speakers. Classification of vowels into breathy or modal voice is achieved with an accuracy of around 94 %.

Abstract

In this paper, the non-uniform duration modification is exploited along with other prosody features for neutral speech to anger speech conversion. The non-uniform duration modification method modifies the durations of vowel and pause segments by different modification factors. Vowel segments are modified by factors based on their identities, and pause segments by uniform factors. Consonant and transition segments are not modified. These modification factors are derived from the analysis of neutral and anger speech. For this purpose, a well known Indian database named as the Indian Institute of Technology Kharagpur Simulated Emotion Speech Corpus (IITKGP-SESC) is chosen for analysis of emotions and synthesis of emotions from neutral speech. The prosodic features used in this study for emotion conversion are pitch contour, intensity contour, and duration contour. Subjective listening test results show that the effectiveness of perception of emotion is better in case of non-uniform duration modification than uniform duration modification

Abstract

DNA–RNA hybrids are heterogeneous nucleic acid duplexes consisting of a DNA strand and a RNA strand, and are formed as key intermediates in many important biological processes. They serve as substrates for the RNase H enzymatic activity, which has been exploited for several biomedical technologies such as antiviral and antisense therapies. To understand the relation of structural properties with the base composition in DNA–RNA hybrids, molecular dynamics (MD) simulations were performed on selected model systems by systematically varying the deoxypyrimidine (dPy) content from 0 to 100% in the DNA strand. The results suggest that the hybrid duplex properties are highly dependent on their deoxypyrimidine content of the DNA strand. However, such variations are not seen in their corresponding pure DNA and RNA duplex counterparts. It is also noticed that the systematic variation in deoxypyrimidine …

Abstract

Gold cluster–nucleobase complexes have potential applications in designing and fabrication of novel electronic nano-devices, and there has been a surge in research activities in this area recently. Binding of gold clusters (Au3 and Au4) with DNA bases and size-expanded DNA bases (x-bases) have been studied using density functional theory employing high quality basis set. A comprehensive attempt has been made to examine several gold–nucleobase complexes with respect to change in the orientation of Au clusters with respect to all the titratable sites of the bases. Geometric and electronic features of these complexes provided evidences for existence of non-conventional hydrogen bonds, which was further substantiated via vibrational frequency and natural bond orbital (NBO) analysis. The nucleobases, both canonical and size-expanded forms, form stable complexes with both the gold clusters considered …

Abstract

The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu – modeled and validated based on available experimental data – umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

Abstract

In this paper we introduce a new histogram equalization based contrast enhancement method called High Speed Quantile Based Histogram Equalization (HSQHE) suitable for high contrast digital images. The proposed method is an effective tool to deal with the “mean-shift” problem, which is a usual problem with the histogram equalization based contrast enhancement methods. The main idea of HSQHE is to divide input image histogram into two or more sub-histograms, where segmentation is based on quantile values. Since the histogram segmentation is based on the quantile values, the entire spectrum of gray level will always play an important role in enhancement process. Also the proposed method does not require the recursive segmentation of the histogram as in many other methods, and hence proposed method requires less time for segmentation. The experimental results show that the performance of proposed HSQHE method is better as compared to other existing methods available in literature. Also this method preserves image brightness more accurately than the prevailing state of art and takes less time as compared to the other methods.

Abstract

This paper describes our submission for FIRE 2014 Shared Task on Transliterated Search. The shared task features two sub-tasks: Query word labeling and Mixed-script Ad hoc retrieval for Hindi Song Lyrics. Query Word Labeling is on token level language identification of query words in code-mixed queries and back-transliteration of identified Indian language words into their native scripts. We have developed letter based language models for the token level language identification of query words and a structured perceptron model for back-transliteration of Indic words. The second subtask for Mixed-script Ad hoc retrieval for Hindi Song Lyrics is to retrieve a ranked list of songs from a corpus of Hindi song lyrics given an input query in Devanagari or transliterated Roman script. We have used edit distance based query expansion and language modeling followed by relevance based reranking for the retrieval of relevant Hindi Song lyrics for a given query.

Abstract

GPUs with their massive Single Instruction Multiple Data (SIMD) capability have become attractive for scientific computation. The Kirchhoff-Helmholtz Transform (KHT) is a two dimensional integral commonly used in numerical reconstruction of the object from its experimentally measured diffraction pattern (called hologram). We explore the evaluation of KHT using GPU at various levels of optimisation. These optimisations are of two types:(a) algorithmic: exploiting the symmetries inherent in KHT, and (b) programmatic: optimizations that are specific to the GPU architecture like the lookup tables, scheduling of read/writes. From the numerical experiments, we report the speedup for each level of optimisation.

Abstract

A novel compliant robot is proposed for traversing on unstructured terrains. The robot consists of modules, each containing a link and an active wheel-pair, and neighboring modules are connected using a passive joint. This type of robots are lighter and provide high durability due to the absence of link-actuators. However, they have limited climbing ability due to tendency of tipping over while climbing big obstacles. To overcome this disadvantage, the use of compliant joints is proposed in this work. Stiffness of each compliant joint is estimated by formulating an optimization problem with an objective to minimize link joint moments while maintaining static-equilibrium. This is one of the key novelties of the proposed work. A design methodology is also proposed for developing an n-module compliant robot for climbing a given height on a known surface. The efficacy of the proposed formulation is illustrated using numerical simulations of the three and five module robots. The robot is successfully able to climb maximum heights upto three times and six times the wheel diameter using three and five modules, respectively. A working prototype was developed and the simulation results were successfully validated on it.