RPS: Repeats in Protein Sequences

Repeats are two or more contiguous segments of amino acid residues that are believed to have arisen as a result of intragenic duplication, recombination and mutation events. These repeats can be utilized for protein structure prediction and can provide insights into the protein evolution and phylogenetic relationship. Therefore, to aid structural biologists and phylogeneticists in their research, a computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats (of varying lengths) in protein sequences. In addition, users can check the frequency of occurrence of the repeats in sequence databases such as the Genome Database, PIR and SWISS-PROT and among the protein sequences available in the Protein Data Bank archive. Furthermore, users can view the three-dimensional structure of the repeats using the Java visualization plug-in Jmol. The proposed computing resource can be accessed over the World Wide Web at http://bioserver1.physics.iisc.ernet.in/rps/.

A Procedure for the 3D Reconstruction of Biological Organs from 2D Image Sequences

In this work, a procedure is presented for the reconstruction of biological organs from image sequences obtained through CT-scan. Although commercial software, which can accomplish this task, are readily available, the procedure presented here needs only free software. The procedure has been applied to reconstruct a liver from the scan data available in literature. 3D biological organs obtained this way can be used for the finite element analysis of biological organs and this has been demonstrated by carrying out an FE analysis on the reconstructed liver.

Maintaining dynamic sequences under equality tests in polylogarithmic time

We present a randomized and a deterministic data structure for maintaining a dynamic family of sequences under equality tests of pairs of sequences and creations of new sequences by joining or splitting existing sequences. Both data structures support equality tests in O(1) time. The randomized version supports new sequence creations in O(log(2) n) expected time where n is the length of the sequence created. The deterministic solution supports sequence creations in O(log n (log m log* m + log n)) time for the mth operation.

Sex-specific organisation of middle repetitive DNA sequences in the mealybug Planococcus lilacinus

Differential organisation of homologous chromosomes is related to both sex determination and genomic imprinting in coccid insects, the mealybugs. We report here the identification of two middle repetitive sequences that are differentially organised between the two sexes and also within the same diploid nucleus. These two sequences form a part of the male-specific nuclease-resistant chromatin (NRC) fraction of a mealybug Planococcus lilacinus. To understand the phenomenon of differential organisation we have analysed the components of NRC by cloning the DNA sequences present, deciphering their primary sequence, nucleosomal organisation, genomic distribution and cytological localisation, Our observations suggest that the middle repetitive sequences within NRC are functionally significant and we discuss their probable involvement in male-specific chromatin organisation.

A checking method for probabilistic seismic-hazard assessment: case studies on three cities

The conventional Cornell's source-based approach of probabilistic seismic-hazard assessment (PSHA) has been employed all around the world, whilst many studies often rely on the use of computer packages such as FRISK (McGuire FRISK-a computer program for seismic risk analysis. Open-File Report 78-1007, United States Geological Survey, Department of Interior, Washington 1978) and SEISRISK III (Bender and Perkins SEISRISK III-a computer program for seismic hazard estimation, Bulletin 1772. United States Geological Survey, Department of Interior, Washington 1987). A ``black-box'' syndrome may be resulted if the user of the software does not have another simple and robust PSHA method that can be used to make comparisons. An alternative method for PSHA, namely direct amplitude-based (DAB) approach, has been developed as a heuristic and efficient method enabling users to undertake their own sanity checks on outputs from computer packages. This paper experiments the application of the DAB approach for three cities in China, Iran, and India, respectively, and compares with documented results computed by the source-based approach. Several insights regarding the procedure of conducting PSHA have also been obtained, which could be useful for future seismic-hazard studies.

Low correlation interleaved QAM sequences

A low correlation interleaved QAM sequence family is presented here. In a CDMA setting, these sequences have the ability to transport a large amount of data as well as enable variable-rate signaling on the reverse link. The new interleaved selected family INQ has period N, normalized maximum correlation parameter thetasmacrmax bounded above by lsim a radicN, where a ranges from 1.17 in the 16-QAM case to 1.99 for large M2-QAM, where M = 2m, m ges 2. Each user is enabled to transfer m + 1 bits of data per period of the spreading sequence. These constructions have the lowest known value of maximum correlation of any sequence family with the same alphabet.

Pruned Universal Symbol Sequences for LZW based Language identification

We present a improved language modeling technique for Lempel-Ziv-Welch (LZW) based LID scheme. The previous approach to LID using LZW algorithm prepares the language pattern table using LZW algorithm. Because of the sequential nature of the LZW algorithm, several language specific patterns of the language were missing in the pattern table. To overcome this, we build a universal pattern table, which contains all patterns of different length. For each language it's corresponding language specific pattern table is constructed by retaining the patterns of the universal table whose frequency of appearance in the training data is above the threshold.This approach reduces the classification score (Compression Ratio [LZW-CR] or the weighted discriminant score[LZW-WDS]) for non native languages and increases the LID performance considerably.

On the Decidability of Model-Checking Information Flow Properties

Current standard security practices do not provide substantial assurance about information flow security: the end-to-end behavior of a computing system. Noninterference is the basic semantical condition used to account for information flow security. In the literature, there are many definitions of noninterference: Non-inference, Separability and so on. Mantel presented a framework of Basic Security Predicates (BSPs) for characterizing the definitions of noninterference in the literature. Model-checking these BSPs for finite state systems was shown to be decidable in [8]. In this paper, we show that verifying these BSPs for the more expressive system model of pushdown systems is undecidable. We also give an example of a simple security property which is undecidable even for finite-state systems: the property is a weak form of non-inference called WNI, which is not expressible in Mantel’s BSP framework.

Sequences for Phase-Encoded Optical CDMA

In phase-encoded optical CDMA (OCDMA) spreading is achieved by encoding the phase of signal spectrum. Here, a mathematical model for the output signal of a phase-encoded OCDMA system is first derived. This is shown to lead to a performance metric for the design of spreading sequences for asynchronous transmission. Generalized bent functions are used to construct a family of efficient phase-encoding sequences. It is shown how M-ary modulation of these spreading sequences is possible. The problem of designing efficient phaseencoded sequences is then related to the problem of minimizing PMEPR (peak-to-mean envelope power ratio) in an OFDM communication system.

Optimality of orthogonal sequences with multi-dimensional signaling

The sum capacity on a symbol-synchronous CDMA system having processing gain N and supporting K power constrained users is achieved by employing any set of N orthogonal sequences if a few users are allowed to signal along multiple dimensions. Analogously, the minimum received power (energy-per-chip) on the symbolsynchronous CDMA system supporting K users that demand specified data rates is attained by employing any set of N orthogonal sequences. At most (N - 1) users need to be split and if there are no oversized users, these split users need to signal only in two dimensions each. These results show that sum capacity or minimum sum power can be achieved with minimal downlink signaling.

Modified Stability Checking for On-Line Error Detection

The paper propose a unified error detection technique, based on stability checking, for on-line detection of delay, crosstalk and transient faults in combinational circuits and SEUs in sequential elements. The proposed method, called modified stability checking (MSC), overcomes the limitations of the earlier stability checking methods. The paper also proposed a novel checker circuit to realize this scheme. The checker is self-checking for a wide set of realistic internal faults including transient faults. Extensive circuit simulations have been done to characterize the checker circuit. A prototype checker circuit for a 1mm2 standard cell array has been implemented in a 0.13mum process.

Spreading Sequences for Asynchronous Spectrally Phase Encoded Optical CDMA

In phase encoding optical CDMA (OCDMA) the spreading is achieved by encoding the phase of signal spectrum. In this paper we first derive a mathematical model for the output of phase encoding OCDMA systems. Based on this model we introduce a metric to design spreading sequences for asynchronous transmission. Then we connect the phase encoding sequence design problem to OFDM PMEPR (peak to mean envelope power ratio) problem. Using this connection we conclude that designing sequences with good properties for samples of timing delay guarantees that the same sequence to be good for all timing delays. Finally using generalized bent function we manage to construct a family of sequences which are good for asynchronous phase encoding OCDMA systems and using these sequences we introduce an M-ary modulation scheme for phase encoding OCDMA

Novel Switching Sequences for a Space-Vector-Modulated Three-Level Inverter

A three-level inverter produces six active vectors, each of normalized magnitudes 1, 0.866, and 0.5, besides a zero vector. The vectors of relative length 0.5 are termed pivot vectors.The three nearest voltage vectors are usually used to synthesize the reference vector. In most continuous pulsewidth-modulation(PWM) schemes, the switching sequence begins from a pivot vector and ends with the same pivot vector. Thus, the pivot vector is applied twice in a subcycle or half-carrier cycle. This paper proposes and investigates alternative switching sequences, which use the pivot vector only once but employ one of the other two vectors twice within the subcycle. The total harmonic distortion(THD) in the fundamental line current pertaining to these novel sequences is studied theoretically as well as experimentally over the whole range of modulation. Compared with centered space vector PWM, two of the proposed sequences lead to reduced THD at high modulation indices at a given average switching frequency.

Improving Superscalar Instruction Dispatch And Issue By Exploiting Dynamic Code Sequences

Superscalar processors currently have the potential to fetch multiple basic blocks per cycle by employing one of several recently proposed instruction fetch mechanisms. However, this increased fetch bandwidth cannot be exploited unless pipeline stages further downstream correspondingly improve. In particular,register renaming a large number of instructions per cycle is diDcult. A large instruction window, needed to receive multiple basic blocks per cycle, will slow down dependence resolution and instruction issue. This paper addresses these and related issues by proposing (i) partitioning of the instruction window into multiple blocks, each holding a dynamic code sequence; (ii) logical partitioning of the registerjle into a global file and several local jles, the latter holding registers local to a dynamic code sequence; (iii) the dynamic recording and reuse of register renaming information for registers local to a dynamic code sequence. Performance studies show these mechanisms improve performance over traditional superscalar processors by factors ranging from 1.5 to a little over 3 for the SPEC Integer programs. Next, it is observed that several of the loops in the benchmarks display vector-like behavior during execution, even if the static loop bodies are likely complex for compile-time vectorization. A dynamic loop vectorization mechanism that builds on top of the above mechanisms is briefly outlined. The mechanism vectorizes up to 60% of the dynamic instructions for some programs, albeit the average number of iterations per loop is quite small.

Fast algorithms for frequent episode discovery in event sequences

In this paper we consider the process of discovering frequent episodes in event sequences. The most computationally intensive part of this process is that of counting the frequencies of a set of candidate episodes. We present two new frequency counting algorithms for speeding up this part. These, referred to as non-overlapping and non-inteleaved frequency counts, are based on directly counting suitable subsets of the occurrences of an episode. Hence they are different from the frequency counts of Mannila et al [1], where they count the number of windows in which the episode occurs. Our new frequency counts offer a speed-up factor of 7 or more on real and synthetic datasets. We also show how the new frequency counts can be used when the events in episodes have time-durations as well.