An Efficient Simulated Annealing With a Valid Solution Mechanism For TDMA Brodcast Scheduling problem

This paper presents an efficient Simulated Annealing with valid solution mechanism for finding an optimum conflict-free transmission schedule for a broadcast radio network. This is known as a Broadcast Scheduling Problem (BSP) and shown as an NP-complete problem, in earlier studies. Because of this NP-complete nature, earlier studies used genetic algorithms, mean field annealing, neural networks, factor graph and sum product algorithm, and sequential vertex coloring algorithm to obtain the solution. In our study, a valid solution mechanism is included in simulated annealing. Because of this inclusion, we are able to achieve better results even for networks with 100 nodes and 300 links. The results obtained using our methodology is compared with all the other earlier solution methods.

Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein

The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished, A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.

The cDNA sequence of cytochrome b5 associated with cytokinin-induced haustoria formation in Cuscuta reflexa

A cDNA clone isolated by differentially screening a cytokinin-induced haustorial cDNA library of Cuscuta reflexa was sequenced and identified as the gene coding for cytochrome b(5), based on the similarity of the deduced amino-acid sequence with that of the cauliflower (60% identity) and tobacco (78% identity) proteins. The 5'-UTR is unusually long (720 bp) and contains 14 potential start codons (ATG) and 10 short ORFs.

Comparative Nucleotide and Amino Acid Sequence Analysis of the Sequence-Specific RNA-Binding Rotavirus Nonstructural Protein NSP3

NSP3, an acidic nonstructural protein, encoded by gene 7 has been implicated as the key player in the assembly of the 11 viral plus-strand RNAs into the early replication intermediates during rotavirus morphogenesis. To date, the sequence or NSP3 from only three animal rotaviruses (SA11, SA114F, and bovine UK) has been determined and that from a human strain has not been reported. To determine the genetic diversity among gene 7 alleles from group A rotaviruses, the nucleotide sequence of the NSP3 gene from 13 strains belonging to nine different G serotypes, from both humans and animals, has been determined. Based on the amino acid sequence identity as well as phylogenetic analysis, NSP3 from group A rotaviruses falls into three evolutionarily related groups, i.e., the SA11 group, the Wa group, and the S2 group. The SA 11/SA114F gene appears to have a distant ancestral origin from that of the others and codes for a polypeptide of 315 amino acids (aa) in length. NSP3 from all other group A rotaviruses is only 313 aa in length because of a 2-amino-acid deletion near the carboxy-terminus, While the SA114F gene has the longest 3' untranslated region (UTR) of 132 nucleotides, that from other strains suffered deletions of varying lengths at two positions downstream of the translational termination codon. In spite of the divergence of the nucleotide (nt) sequence in the protein coding region, a stretch of about 80 nt in the 3' UTR is highly conserved in the NSP3 gene from all the strains. This conserved sequence in the 3' UTR might play an important role in the regulation of expression of the NSP3 gene. (C) 1995 Academic Press, Inc.

Demographic history of India and mtDNA-sequence diversity

The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion or steady growth. The low-ranking Mukri caste, however, may have either maintained a roughly constant population size or undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with ah other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in southern Asia, taking place at some point after modern humans initially left Africa.

S-nets: A Petri net based model for performance evaluation of real-time scheduling algorithms

A new class of nets, called S-nets, is introduced for the performance analysis of scheduling algorithms used in real-time systems Deterministic timed Petri nets do not adequately model the scheduling of resources encountered in real-time systems, and need to be augmented with resource places and signal places, and a scheduler block, to facilitate the modeling of scheduling algorithms. The tokens are colored, and the transition firing rules are suitably modified. Further, the concept of transition folding is used, to get intuitively simple models of multiframe real-time systems. Two generic performance measures, called �load index� and �balance index,� which characterize the resource utilization and the uniformity of workload distribution, respectively, are defined. The utility of S-nets for evaluating heuristic-based scheduling schemes is illustrated by considering three heuristics for real-time scheduling. S-nets are useful in tuning the hardware configuration and the underlying scheduling policy, so that the system utilization is maximized, and the workload distribution among the computing resources is balanced.

Scheduling expression trees with reusable registers on delayed-load architectures

In this paper, we look at the problem of scheduling expression trees with reusable registers on delayed load architectures. Reusable registers come into the picture when the compiler has a data-flow analyzer which is able to estimate the extent of use of the registers. Earlier work considered the same problem without allowing for register variables. Subsequently, Venugopal considered non-reusable registers in the tree. We further extend these efforts to consider a much more general form of the tree. We describe an approximate algorithm for the problem. We formally prove that the code schedule produced by this algorithm will, in the worst case, generate one interlock and use just one more register than that used by the optimal schedule. Spilling is minimized. The approximate algorithm is simple and has linear complexity.

DNA Condensation by the Rat Spermatidal Protein TP2 Shows GC-Rich Sequence Preference and Is Zinc Dependent

Transition protein-2 (TP2), isolated from rat testes, was recently shown to be a zinc metalloprotein. We have now carried out a detailed analysis of the DNA condensing properties of TP2 with various polynucleotides using circular dichroism spectroscopy. The condensation of the alternating copolymers by TP2 (incubated with 10 mu M ZnSO4), namely, poly(dG-dC). poly(dG-dC) and poly(dA-dT). poly(dA-dT), was severalfold higher than condensation of either of the homoduplexes poly(dG). poly-(dC) and poly(dA). poly(dT) or rat oligonucleosomal DNA. Between the two alternating copolymers, poly(dG-dC). poly(dG-dC) was condensed 3.2-fold more effectively than poly(dA-dT). poly(dA-dT). Preincubation of TP2 with 5 mM EDTA significantly reduced its DNA-condensing property. Interestingly, condensation of the alternating copolymer poly(dI-dC). poly(dI-dC) by TP2 was much less as compared to that of poly(dG-dC). poly(dG-dC). The V8 protease-derived N-terminal fragment (88 aa) condensed poly(dA-dT). poly(dA-dT) to a very small extent but did not have any effect on poly(dG-dC). poly-(dG-dC). The C-terminal fragment (28 aa) was able to condense poly(dA-dT) . poly(dA-dT) more effectively than poly(dG-dC). poly(dG-dC). These results suggest that TP2 in its zinc-coordinated form condenses GC-rich polynucleotides much more effectively than other types of polynucleotides. Neither the N-terminal two-thirds of TP2 which is the zinc-binding domain nor the C-terminal basic domain are as effective as intact TP2 in bringing about condensation of DNA.

Isomerisation of 4-aryl-4-methylhex-5-en-2-ones to 5-aryl-4-methylhex-5-en-2-ones by an intramolecular ene-retro ene reaction sequence

Acid-catalysed thermal rearrangement of 4-aryl-4-methylhex-5-en-2-ones (products of the Claisen rearrangement of beta-methylcinnamyl alcohols and 2-methoxypropene) to isomeric 5-aryl-4-methylhex-5-en-2-ones via an intramolecular ene reaction of the enol tautomer followed by a retro ene reaction of the resultant acetylcyclopropane is described. Formation of the known diketone 13 via the ozonolysis of the rearrangement product 10, confirmed the structures of the rearranged enones, whereas formation of the enone 15 containing an extra methyl group on the styrene double bond confirmed the proposed mechanism. Finally, the rearrangement has been extended to the formal synthesis of beta-cuparenone 20 via the enones 22 and 23.

Primary Sequence That Determines the Functional Overlap between Mitochondrial Heat Shock Protein 70 Ssc1 and Ssc3 of Saccharomyces cerevisiae

The evolutionary diversity of the HSP70 gene family at the genetic level has generated complex structural variations leading to altered functional specificity and mode of regulation in different cellular compartments. By utilizing Saccharomyces cerevisiae as a model system for better understanding the global functional cooperativity between Hsp70 paralogs, we have dissected the differences in functional properties at the biochemical level between mitochondrial heat shock protein 70 (mtHsp70) Ssc1 and an uncharacterized Ssc3 paralog. Based on the evolutionary origin of Ssc3 and a high degree of sequence homology with Ssc1, it has been proposed that both have a close functional overlap in the mitochondrial matrix. Surprisingly, our results demonstrate that there is no functional cross-talk between Ssc1 and Ssc3 paralogs. The lack of in vivo functional overlap is due to altered conformation and significant lower stability associated with Ssc3. The substrate-binding domain of Ssc3 showed poor affinity toward mitochondrial client proteins and Tim44 due to the open conformation in ADP-bound state. In addition to that, the nucleotide-binding domain of Ssc3 showed an altered regulation by the Mge1 co-chaperone due to a high degree of conformational plasticity, which strongly promotes aggregation. Besides, Ssc3 possesses a dysfunctional inter-domain interface thus rendering it unable to perform functions similar to generic Hsp70s. Moreover, we have identified the critical amino acid sequence of Ssc1 and Ssc3 that can ``make or break'' mtHsp70 chaperone function. Together, our analysis provides the first evidence to show that the nucleotide-binding domain of mtHsp70s plays a critical role in determining the functional specificity among paralogs and orthologs across kingdoms.

Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution

In this paper, we report an analysis of the protein sequence length distribution for 13 bacteria, four archaea and one eukaryote whose genomes have been completely sequenced, The frequency distribution of protein sequence length for all the 18 organisms are remarkably similar, independent of genome size and can be described in terms of a lognormal probability distribution function. A simple stochastic model based on multiplicative processes has been proposed to explain the sequence length distribution. The stochastic model supports the random-origin hypothesis of protein sequences in genomes. Distributions of large proteins deviate from the overall lognormal behavior. Their cumulative distribution follows a power-law analogous to Pareto's law used to describe the income distribution of the wealthy. The protein sequence length distribution in genomes of organisms has important implications for microbial evolution and applications. (C) 1999 Elsevier Science B.V. All rights reserved.

Providing quality of service via opportunistic splitting using stochastic approximation

We consider the problem of wireless channel allocation to multiple users. A slot is given to a user with a highest metric (e.g., channel gain) in that slot. The scheduler may not know the channel states of all the users at the beginning of each slot. In this scenario opportunistic splitting is an attractive solution. However this algorithm requires that the metrics of different users form independent, identically distributed (iid) sequences with same distribution and that their distribution and number be known to the scheduler. This limits the usefulness of opportunistic splitting. In this paper we develop a parametric version of this algorithm. The optimal parameters of the algorithm are learnt online through a stochastic approximation scheme. Our algorithm does not require the metrics of different users to have the same distribution. The statistics of these metrics and the number of users can be unknown and also vary with time. Each metric sequence can be Markov. We prove the convergence of the algorithm and show its utility by scheduling the channel to maximize its throughput while satisfying some fairness and/or quality of service constraints.

Profile-Based Load Scheduling in Wireless Energy Harvesting Sensors for Data Rate Maximization

In this paper, power management algorithms for energy harvesting sensors (EHS) that operate purely based on energy harvested from the environment are proposed. To maintain energy neutrality, EHS nodes schedule their utilization of the harvested power so as to save/draw energy into/from an inefficient battery during peak/low energy harvesting periods, respectively. Under this constraint, one of the key system design goals is to transmit as much data as possible given the energy harvesting profile. For implementational simplicity, it is assumed that the EHS transmits at a constant data rate with power control, when the channel is sufficiently good. By converting the data rate maximization problem into a convex optimization problem, the optimal load scheduling (power management) algorithm that maximizes the average data rate subject to energy neutrality is derived. Also, the energy storage requirements on the battery for implementing the proposed algorithm are calculated. Further, robust schemes that account for the insufficiency of battery storage capacity, or errors in the prediction of the harvested power are proposed. The superior performance of the proposed algorithms over conventional scheduling schemes are demonstrated through computations using numerical data from solar energy harvesting databases.