Nash equilibrium based semantic cache in mobile sensor grid database systems

Mobile applications are being increasingly deployed on a massive scale in various mobile sensor grid database systems. With limited resources from the mobile devices, how to process the huge number of queries from mobile users with distributed sensor grid databases becomes a critical problem for such mobile systems. While the fundamental semantic cache technique has been investigated for query optimization in sensor grid database systems, the problem is still difficult due to the fact that more realistic multi-dimensional constraints have not been considered in existing methods. To solve the problem, a new semantic cache scheme is presented in this paper for location-dependent data queries in distributed sensor grid database systems. It considers multi-dimensional constraints or factors in a unified cost model architecture, determines the parameters of the cost model in the scheme by using the concept of Nash equilibrium from game theory, and makes semantic cache decisions from the established cost model. The scenarios of three factors of semantic, time and locations are investigated as special cases, which improve existing methods. Experiments are conducted to demonstrate the semantic cache scheme presented in this paper for distributed sensor grid database systems.

Wave algorithms:Optimal database search and catalysis

Grover's database search algorithm, although discovered in the context of quantum computation, can be implemented using any physical system that allows superposition of states. A physical realization of this algorithm is described using coupled simple harmonic oscillators, which can be exactly solved in both classical and quantum domains. Classical wave algorithms are far more stable against decoherence compared to their quantum counterparts. In addition to providing convenient demonstration models, they may have a role in practical situations, such as catalysis.

CREMOFAC- a database of chromatin remodeling factors

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors.Results: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable.

Secure Concurrency Control in Firm Real-Time Database Systems

Many real-time database applications arise in electronic financial services, safety-critical installations and military systems where enforcing security is crucial to the success of the enterprise. For real-time database systems supporting applications with firm deadlines, we investigate here the performance implications, in terms of killed transactions, of guaranteeing multilevel secrecy. In particular, we focus on the concurrency control (CC) aspects of this issue. Our main contributions are the following: First, we identify which among the previously proposed real-time CC protocols are capable of providing covert-channel-free security. Second, using a detailed simulation model, we profile the real-time performance of a representative set of these secure CC protocols for a variety of security-classified workloads and system configurations. Our experiments show that a prioritized optimistic CC protocol, OPT-WAIT, provides the best overall performance. Third, we propose and evaluate a novel "dual-CC" approach that allows the real-time database system to simultaneously use different CC mechanisms for guaranteeing security and for improving real-time performance. By appropriately choosing these different mechanisms, concurrency control protocols that provide even better performance than OPT-WAIT are designed. Finally, we propose and evaluate GUARD, an adaptive admission-control policy designed to provide fairness with respect to the distribution of killed transactions across security levels. Our experiments show that GUARD efficiently provides close to ideal fairness for real-time applications that can tolerate covert channel bandwidths of upto one bit per second.

Artificial database for character recognition research

This paper describes a technique for artificial generation of learning and test sample sets suitable for character recognition research. Sample sets of English (Latin), Malayalam, Kannada and Tamil characters are generated easily through their prototype specifications by the endpoint co-ordinates, nature of segments and connectivity.

Drug epidemiology, interactions and pharmacogenetics : A post-mortem database study

Use of adverse drug combinations, abuse of medicinal drugs and substance abuse are considerable social problems that are difficult to study. Prescription database studies might fail to incorporate factors like use of over-the-counter drugs and patient compliance, and spontaneous reporting databases suffer from underreporting. Substance abuse and smoking studies might be impeded by poor participation activity and reliability. The Forensic Toxicology Unit at the University of Helsinki is the only laboratory in Finland that performs forensic toxicology related to cause-of-death investigations comprising the analysis of over 6000 medico-legal cases yearly. The analysis repertoire covers most commonly used drugs and drugs of abuse, and the ensuing database contains also background information and information extracted from the final death certificate. In this thesis, the data stored in this comprehensive post-mortem toxicology database was combined with additional metabolite and genotype analyses that were performed to complete the profile of selected cases. The incidence of drug combinations possessing serious adverse drug interactions was generally low (0.71%), but it was notable for the two individually studied drugs, a common anticoagulant warfarin (33%) and a new generation antidepressant venlafaxine (46%). Serotonin toxicity and adverse cardiovascular effects were the most prominent possible adverse outcomes. However, the specific role of the suspected adverse drug combinations was rarely recognized in the death certificates. The frequency of bleeds was observed to be elevated when paracetamol and warfarin were used concomitantly. Pharmacogenetic factors did not play a major role in fatalities related to venlafaxine, but the presence of interacting drugs was more common in cases showing high venlafaxine concentrations. Nicotine findings in deceased young adults were roughly three times more prevalent than the smoking frequency estimation of living population. Contrary to previous studies, no difference in the proportion of suicides was observed between nicotine users and non-nicotine users. However, findings of abused substances, including abused prescription drugs, were more common in the nicotine users group than in the non-nicotine users group. The results of the thesis are important for forensic and clinical medicine, as well as for public health. The possibility of drug interactions and pharmacogenetic issues should be taken into account in cause-of-death investigations, especially in unclear cases, medical malpractice suspicions and cases where toxicological findings are scarce. Post-mortem toxicological epidemiology is a new field of research that can help to reveal problems in drug use and prescription practises.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis x Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

WebGeSTer DB-a transcription terminator database

We present WebGeSTer DB, the largest database of intrinsic transcription terminators (http://pallab.serc.iisc.ernet.in/gester). The database comprises of a million terminators identified in 1060 bacterial genome sequences and 798 plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome. Analysis of the results, both at the whole-genome level and with respect to terminators downstream of specific genes, offers insight into the prevalence of canonical and non-canonical terminators across different phyla. The data in the database reinforce the paradigm that intrinsic termination is a conserved and efficient regulatory mechanism in bacteria. Our database is freely accessible.

Quantum Algorithms with Fixed Points: The Case of Database Search

The standard quantum search algorithm lacks a feature, enjoyed by many classical algorithms, of having a fixed-point, i.e. a monotonic convergence towards the solution. Here we present two variations of the quantum search algorithm, which get around this limitation. The first replaces selective inversions in the algorithm by selective phase shifts of $\frac{\pi}{3}$. The second controls the selective inversion operations using two ancilla qubits, and irreversible measurement operations on the ancilla qubits drive the starting state towards the target state. Using $q$ oracle queries, these variations reduce the probability of finding a non-target state from $\epsilon$ to $\epsilon^{2q+1}$, which is asymptotically optimal. Similar ideas can lead to robust quantum algorithms, and provide conceptually new schemes for error correction.

Creation of a Huge Annotated Database for Tamil and Kannada OHR

This paper describes the efforts at MILE lab, IISc, to create a 100,000-word database each in Kannada and Tamil for the design and development of Online Handwritten Recognition. It has been collected from over 600 users in order to capture the variations in writing style. We describe features of the scripts and how the number of symbols were reduced to be able to effectively train the data for recognition. The list of words include all the characters, Kannada and Indo-Arabic numerals, punctuations and other symbols. A semi-automated tool for the annotation of data from stroke to word level is used. It segments each word into stroke groups and also acts as a validation mechanism for segmentation. The tool displays the stroke, stroke groups and aksharas of a word and hence can be used to study the various styles of writing, delayed strokes and for assigning quality tags to the words. The tool is currently being used for annotating Tamil and Kannada data. The output is stored in a standard XML format.

Kannada WordNet - a lexical database

This paper presents the preliminary analysis of Kannada WordNet and the set of relevant computational tools. Although the design has been inspired by the famous English WordNet, and to certain extent, by the Hindi WordNet, the unique features of Kannada WordNet are graded antonyms and meronymy relationships, nominal as well as verbal compoundings, complex verb constructions and efficient underlying database design (designed to handle storage and display of Kannada unicode characters). Kannada WordNet would not only add to the sparse collection of machine-readable Kannada dictionaries, but also will give new insights into the Kannada vocabulary. It provides sufficient interface for applications involved in Kannada machine translation, spell checker and semantic analyser.

DoSA: Database of Structural Alignments

Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.

Real-time magnetic resonance imaging and electromagnetic articulography database for speech production research (TC)

USC-TIMIT is an extensive database of multimodal speech production data, developed to complement existing resources available to the speech research community and with the intention of being continuously refined and augmented. The database currently includes real-time magnetic resonance imaging data from five male and five female speakers of American English. Electromagnetic articulography data have also been presently collected from four of these speakers. The two modalities were recorded in two independent sessions while the subjects produced the same 460 sentence corpus used previously in the MOCHA-TIMIT database. In both cases the audio signal was recorded and synchronized with the articulatory data. The database and companion software are freely available to the research community. (C) 2014 Acoustical Society of America.

Haemophilus influenzae Genome Database (HIGDB): A single point web resource for Haemophilus influenzae

Background: Haemophilus influenzae (H. Influenzae) is the causative agent of pneumonia, bacteraemia and meningitis. The organism is responsible for large number of deaths in both developed and developing countries. Even-though the first bacterial genome to be sequenced was that of H. Influenzae, there is no exclusive database dedicated for H. Influenzae. This prompted us to develop the Haemophilus influenzae Genome Database (HIGDB). Methods: All data of HIGDB are stored and managed in MySQL database. The HIGDB is hosted on Solaris server and developed using PERL modules. Ajax and JavaScript are used for the interface development. Results: The HIGDB contains detailed information on 42,741 proteins, 18,077 genes including 10 whole genome sequences and also 284 three dimensional structures of proteins of H. influenzae. In addition, the database provides ``Motif search'' and ``GBrowse''. The HIGDB is freely accessible through the URL:http://bioserverl.physicslisc.ernetin/HIGDB/. Discussion: The HIGDB will be a single point access for bacteriological, clinical, genomic and proteomic information of H. influenzae. The database can also be used to identify DNA motifs within H. influenzae genomes and to compare gene or protein sequences of a particular strain with other strains of H. influenzae. (C) 2014 Elsevier Ltd. All rights reserved.