sRNAscanner: A Computational Tool for Intergenic Small RNA Detection in Bacterial Genomes

Background:Bacterial non-coding small RNAs (sRNAs) have attracted considerable attention due to their ubiquitous nature and contribution to numerous cellular processes including survival, adaptation and pathogenesis. Existing computational approaches for identifying bacterial sRNAs demonstrate varying levels of success and there remains considerable room for improvement. Methodology/Principal Findings: Here we have proposed a transcriptional signal-based computational method to identify intergenic sRNA transcriptional units (TUs) in completely sequenced bacterial genomes. Our sRNAscanner tool uses position weight matrices derived from experimentally defined E. coli K-12 MG1655 sRNA promoter and rho-independent terminator signals to identify intergenic sRNA TUs through sliding window based genome scans. Analysis of genomes representative of twelve species suggested that sRNAscanner demonstrated equivalent sensitivity to sRNAPredict2, the best performing bioinformatics tool available presently. However, each algorithm yielded substantial numbers of known and uncharacterized hits that were unique to one or the other tool only. sRNAscanner identified 118 novel putative intergenic sRNA genes in Salmonella enterica Typhimurium LT2, none of which were flagged by sRNAPredict2. Candidate sRNA locations were compared with available deep sequencing libraries derived from Hfq-co-immunoprecipitated RNA purified from a second Typhimurium strain (Sittka et al. (2008) PLoS Genetics 4: e1000163). Sixteen potential novel sRNAs computationally predicted and detected in deep sequencing libraries were selected for experimental validation by Northern analysis using total RNA isolated from bacteria grown under eleven different growth conditions. RNA bands of expected sizes were detected in Northern blots for six of the examined candidates. Furthermore, the 5'-ends of these six Northern-supported sRNA candidates were successfully mapped using 5'-RACE analysis. Conclusions/Significance: We have developed, computationally examined and experimentally validated the sRNAscanner algorithm. Data derived from this study has successfully identified six novel S. Typhimurium sRNA genes. In addition, the computational specificity analysis we have undertaken suggests that similar to 40% of sRNAscanner hits with high cumulative sum of scores represent genuine, undiscovered sRNA genes. Collectively, these data strongly support the utility of sRNAscanner and offer a glimpse of its potential to reveal large numbers of sRNA genes that have to date defied identification. sRNAscanner is available from: http://bicmku.in:8081/sRNAscanner or http://cluster.physics.iisc.ernet.in/sRNAscanner/.

Weak consistency of read-only transactions: A tool to improve concurrency in heterogeneous locking protocols

Three different types of consistencies, viz., semiweak, weak, and strong, of a read-only transaction in a schedule s of a set T of transactions are defined and these are compared with the existing notions of consistencies of a read-only transaction in a schedule. We present a technique that enables a user to control the consistency of a read-only transaction in heterogeneous locking protocols. Since the weak consistency of a read-only transaction improves concurrency in heterogeneous locking protocols, the users can help to improve concurrency in heterogeneous locking protocols by supplying the consistency requirements of read-only transactions. A heterogeneous locking protocol P' derived from a locking protocol P that uses exclusive mode locks only and ensures serializability need not be deadlock-free. We present a sufficient condition that ensures the deadlock-freeness of Pprime, when P is deadlock-free and all the read-only transactions in Pprime are two phase.

Extended colored Petri net: An efficient tool for analyzing concurrent systems

This paper proposes a novel and simple definition of general colored Petri nets. This definition is coherent with that of (uncolored) Petri nets, preserves the reflexivity of the original net and is extended to represent inhibitors. Also suggested are systematic and formal merging rules to obtain a well-formed structure of the extended colored Petri net by folding a given uncolored net. Finally, we present a technique to compute colored invariants by selecting colored RP-subnets. On the average, the proposed technique performs better than the existing ones. The analysis procedure is explained through an illustrative example of a three-level interrupt-priority-handler scheme.

Infinite dimensional slow modulations in a well known delayed model for cutting tool vibrations

We apply the method of multiple scales (MMS) to a well-known model of regenerative cutting vibrations in the large delay regime. By ``large'' we mean the delay is much larger than the timescale of typical cutting tool oscillations. The MMS up to second order, recently developed for such systems, is applied here to study tool dynamics in the large delay regime. The second order analysis is found to be much more accurate than the first order analysis. Numerical integration of the MMS slow flow is much faster than for the original equation, yet shows excellent accuracy in that plotted solutions of moderate amplitudes are visually near-indistinguishable. The advantages of the present analysis are that infinite dimensional dynamics is retained in the slow flow, while the more usual center manifold reduction gives a planar phase space; lower-dimensional dynamical features, such as Hopf bifurcations and families of periodic solutions, are also captured by the MMS; the strong sensitivity of the slow modulation dynamics to small changes in parameter values, peculiar to such systems with large delays, is seen clearly; and though certain parameters are treated as small (or, reciprocally, large), the analysis is not restricted to infinitesimal distances from the Hopf bifurcation.

Transferability of Multipole Charge Density Parameters for Supramolecular Synthons: A New Tool for Quantitative Crystal Engineering

The modularity of the supramolecular synthon is used to obtain transferability of charge density derived multipolar parameters for structural fragments, thus creating an opportunity to derive charge density maps for new compounds. On the basis of high resolution X-ray diffraction data obtained at 100 K for three compounds methoxybenzoic acid, acetanilide, and 4-methyl-benzoic acid, multipole parameters for O-H center dot center dot center dot O carboxylic acid dimer and N-H center dot center dot center dot O amide infinite chain synthon fragments have been derived. The robustness associated with these supramolecular synthons has been used to model charge density derived multipolar parameters for 4-(acetylamino)benzoic acid and 4-methylacetanilide. The study provides pointers to the design and fabrication of a synthon library of high resolution X-ray diffraction data sets. It has been demonstrated that the derived charge density features can be exploited in both intra- and intermolecular space for any organic compound based on transferability of multipole parameters. The supramolecular synthon based fragments approach (SBFA) has been compared with experimental charge density data to check the reliability of use of this methodology for transferring charge density derived multipole parameters.

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios. Program summary Program title: edgecount Catalogue identifier: AEIA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66685 No. of bytes in distributed program, including test data, etc.: 485 381 Distribution format: tar.gz Programming language: FORTRAN 90/95 Computer: Most UNIX-based platforms Operating system: Linux, Mac OS Classification: 16.1, 7.8 Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice. Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern. Running time: Typically similar to second(s) for all examples. (C) 2010 Elsevier B.V. All rights reserved.

Ultrafast laser spectroscopy-A tool chemists and biologists

Application of ultrafast lasers to chemistry and biology has been an active area of research in the international scene for over a decade for physical and biophysical chemists. Perhaps, ultrafast laser spectroscopy is one of the most versatile tools available today to experimentally study structure and dynamics in the time domain of nanoseconds (10(-9) sec) to femtoseconds (10(-15) sec). In this article we attempt to highlight some of the recent developments in ultrafast laser spectroscopy with particular reference to vibrational spectroscopy, viz. infrared and Raman spectroscopy, in the above time domain.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Machine-tool selection and operation allocation in FMS: solving a fuzzy goal-programming model using a genetic algorithm

The decision-making process for machine-tool selection and operation allocation in a flexible manufacturing system (FMS) usually involves multiple conflicting objectives. Thus, a fuzzy goal-programming model can be effectively applied to this decision problem. The paper addresses application of a fuzzy goal-programming concept to model the problem of machine-tool selection and operation allocation with explicit considerations given to objectives of minimizing the total cost of machining operation, material handling and set-up. The constraints pertaining to the capacity of machines, tool magazine and tool life are included in the model. A genetic algorithm (GA)-based approach is adopted to optimize this fuzzy goal-programming model. An illustrative example is provided and some results of computational experiments are reported.

Tool for Identification of Duplicate Records Downloaded from Multiple Cd-Roms. A Case Study with Spirs Based Databases

As research becomes more and more interdisciplinary, literature search from CD-ROM databases is often carried out on more than one CD-ROM database. This results in retrieving duplicate records due to same literature being covered (indexed) in more than one database. The retrieval software does not identify such duplicate records. Three different programs have been written to accomplish the task of identifying the duplicate records. These programs are executed from a shell script to minimize manual intervention. The various fields that have been used (extracted) to identify the duplicate records include the article title, year, volume number, issue number and pagination. The shell script when executed prompts for input file that may contain duplicate records. The programs identify the duplicate records and write them to a new file.

A model for tool-use traditions in primates: implications for the coevolution of culture and cognition

Inspired by the demonstration that tool-use variants among wild chimpanzees and orangutans qualify as traditions (or cultures), we developed a formal model to predict the incidence of these acquired specializations among wild primates and to examine the evolution of their underlying abilities. We assumed that the acquisition of the skill by an individual in a social unit is crucially controlled by three main factors, namely probability of innovation, probability of socially biased learning, and the prevailing social conditions (sociability, or number of potential experts at close proximity). The model reconfirms the restriction of customary tool use in wild primates to the most intelligent radiation, great apes; the greater incidence of tool use in more sociable populations of orangutans and chimpanzees; and tendencies toward tool manufacture among the most sociable monkeys. However, it also indicates that sociable gregariousness is far more likely to produce the maintenance of invented skills in a population than solitary life, where the mother is the only accessible expert. We therefore used the model to explore the evolution of the three key parameters. The most likely evolutionary scenario is that where complex skills contribute to fitness, sociability and/or the capacity for socially biased learning increase, whereas innovative abilities (i.e., intelligence) follow indirectly. We suggest that the evolution of high intelligence will often be a byproduct of selection on abilities for socially biased learning that are needed to acquire important skills, and hence that high intelligence should be most common in sociable rather than solitary organisms. Evidence for increased sociability during hominin evolution is consistent with this new hypothesis. (C) 2003 Elsevier Science Ltd. All rights reserved.

Comparison of CVD and MOCVD-grown Al2O3 coatings in the performance of cemented carbide cutting tool inserts

Low-pressure MOCVD, with tris(2,4 pentanedionato)aluminum(III) as the precursor, was used in the present investigation to coat alumina on to cemented carbide cutting tools. To evaluate the MOCVD process, the efficiency in cutting operations of MOCVD-coated tools was compared with that of tools coated using the industry-standard CVD process.Three multilayer cemented carbide cutting tool inserts, viz., TiN/TiC/WC, CVD-coated Al2O3 on TiN/TiC/WC, and MOCVD-coated Al2O3 on TiN/TiC/WC, were compared in the dry turning of mild steel. Turning tests were conducted for cutting speeds ranging from 14 to 47 m/min, for a depth of cut from 0.25 to 1 mm, at the constant feed rate of 0.2 mm/min. The axial, tangential, and radial forces were measured using a lathe tool dynamometer for different cutting parameters, and the machined work pieces were tested for surface roughness. The results indicate that, in most of the cases examined, the MOCVD-coated inserts produced a smoother surface finish, while requiring lower cutting forces, indicating that MOCVD produces the best-performing insert, followed by the CVD-coated one. The superior performance of MOCVD-alumina is attributed to the co-deposition of carbon with the oxide, due to the very nature of the precursor used, leading to enhanced mechanical properties for cutting applications in harsh environment.

Interference Alignment as a Tool in Network Coding as Applied to Distributed Storage

In this paper, we outline an approach to the task of designing network codes in a non-multicast setting. Our approach makes use of the concept of interference alignment. As an example, we consider the distributed storage problem where the data is stored across the network in n nodes and where a data collector can recover the data by connecting to any k of the n nodes and where furthermore, upon failure of a node, a new node can replicate the data stored in the failed node while minimizing the repair bandwidth.

INTACTE: An Interconnect Area, Delay, and Energy Estimation Tool for Microarchitectural Explorations

Prior work on modeling interconnects has focused on optimizing the wire and repeater design for trading off energy and delay, and is largely based on low level circuit parameters. Hence these models are hard to use directly to make high level microarchitectural trade-offs in the initial exploration phase of a design. In this paper, we propose INTACTE, a tool that can be used by architects toget reasonably accurate interconnect area, delay, and power estimates based on a few architecture level parameters for the interconnect such as length, width (in number of bits), frequency, and latency for a specified technology and voltage. The tool uses well known models of interconnect delay and energy taking into account the wire pitch, repeater size, and spacing for a range of voltages and technologies.It then solves an optimization problem of finding the lowest energy interconnect design in terms of the low level circuit parameters, which meets the architectural constraintsgiven as inputs. In addition, the tool also provides the area, energy, and delay for a range of supply voltages and degrees of pipelining, which can be used for micro-architectural exploration of a chip. The delay and energy models used by the tool have been validated against low level circuit simulations. We discuss several potential applications of the tool and present an example of optimizing interconnect design in the context of clustered VLIW architectures. Copyright 2007 ACM.