Fibre diffraction of lithium DNA shows structural variability and deviation from a regular helical structure for the B-form

Recently, reports have appeared which show structural variations in B-DNA and indicate deviations from a uniform helical structure. We report for the first time that these indications are also present in the B-form fibre diffraction patterns for the lithium salt of natural DNA. We have used an improved method of controlling the salt concentration in the fibres. Our results are based on the appearance and disappearance of meridional reflections on different layer lines depending upon the salt.

Multipath Dissemination in Regular Mesh Topologies

Mesh topologies are important for large-scale peer-to-peer systems that use low-power transceivers. The Quality of Service (QoS) in such systems is known to decrease as the scale increases. We present a scalable approach for dissemination that exploits all the shortest paths between a pair of nodes and improves the QoS. Despite th presence of multiple shortest paths in a system, we show that these paths cannot be exploited by spreading the messages over the paths in a simple round-robin manner; nodes along one of these paths will always handle more messages than the nodes along the other paths. We characterize the set of shortest paths between a pair of nodes in regular mesh topologies and derive rules, using this characterization, to effectively spread the messages over all the available paths. These rules ensure that all the nodes that are at the same distance from the source handle roughly the same number of messages. By modeling the multihop propagation in the mesh topology as a multistage queuing network, we present simulation results from a variety of scenarios that include link failures and propagation irregularities to reflect real-world characteristics. Our method achieves improved QoS in all these scenarios.

Optimal maintenance and replacement via a semi-Markov decision model

Optimal bang-coast maintenance policies for a machine, subject to failure, are considered. The approach utilizes a semi-Markov model for the system. A simplified model for modifying the probability of machine failure with maintenance is employed. A numerical example is presented to illustrate the procedure and results.

Active nucleoprotein filaments of single-stranded binding protein and recA protein on single-stranded DNA have a regular repeating structure

When E. coli single-stranded DNA binding protein (SSB) coats single-stranded DNA (ssDNA) in the presence of 1 mM MgCl2 it inhibits the subsequent binding of recA protein, whereas SSB binding to ssDNA in 12 mM MgCl2 promotes the binding of recA protein. These two conditions correspond respectively to those which produce 'smooth' and 'beaded' forms of ssDNA-SSB filaments. By gel filtration and immunoprecipitation we observed active nucleoprotein filaments of recA protein and SSB on ssDNA that contained on average 1 monomer of recA protein per 4 nucleotides and 1 monomer of SSB per 20-22 nucleotides. Filaments in such a mixture, when digested with micrococcal nuclease produced a regular repeating pattern, approximately every 70-80 nucleotides, that differed from the pattern observed when only recA protein was bound to the ssDNA. We conclude that the beaded ssDNA-SSB nucleoprotein filament readily binds recA protein and forms an intermediate that is active in the formation of joint molecules and can retain substantially all of the SSB that was originally bound.

d-Regular Graphs of Acyclic Chromatic Index at Least d+2

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and is denoted by a'(G). It was conjectured by Alon, Suclakov and Zaks (and earlier by Fiamcik) that a'(G) <= Delta+2, where Delta = Delta(G) denotes the maximum degree of the graph. Alon et al. also raised the question whether the complete graphs of even order are the only regular graphs which require Delta+2 colors to be acyclically edge colored. In this article, using a simple counting argument we observe not only that this is not true, but in fact all d-regular graphs with 2n vertices and d>n, requires at least d+2 colors. We also show that a'(K-n,K-n) >= n+2, when n is odd using a more non-trivial argument. (Here K-n,K-n denotes the complete bipartite graph with n vertices on each side.) This lower bound for Kn,n can be shown to be tight for some families of complete bipartite graphs and for small values of n. We also infer that for every d, n such that d >= 5, n >= 2d+3 and dn even, there exist d-regular graphs which require at least d+2-colors to be acyclically edge colored. (C) 2009 Wiley Periodicals, Inc. J Graph Theory 63: 226-230, 2010.

Replacement of water on a steel substrate by a surrounding oil reservoir

With an objective to replace a water droplet from a steel surface by oil we study here the impact of injecting a hydrophilic/lipophilic surfactant into the droplet or into the surrounding oil reservoir. Contact angle goniometery, Grazing angle FTIR spectroscopy and Atomic force microscopy are used to record the oil/water interfacial tension, surface energetics of the substrate under the oil and water phases as well as the corresponding physical states of the substrates. Such energetics reflect the rate at which the excess surfactant molecules accumulate at the water/oil interface and desorb into the phases. The molecules diffuse into the substrate from the phases and build up specific molecular configurations which, with the interfacial tension, control the non-equilibrium progress of and the equilibrium status of the contact line. The study shows that the most efficient replacement of water by the surrounding oil happens when a surfactant is sparingly soluble in the supplier oil phase and highly soluble in the recipient water phase.

The effect of progesterone replacement on gene expression in the corpus luteum during induced regression and late luteal phase in the bonnet monkey (Macaca radiata)

Background: In higher primates, although LH/CG play a critical role in the control of corpus luteum (CL) function, the direct effects of progesterone (P4) in the maintenance of CL structure and function are unclear. Several experiments were conducted in the bonnet monkey to examine direct effects of P4 on gene expression changes in the CL, during induced luteolysis and the late luteal phase of natural cycles. Methods: To identify differentially expressed genes encoding PR, PR binding factors, cofactors and PR downstream signaling target genes, the genome-wide analysis data generated in CL of monkeys after LH/P-4 depletion and LH replacement were mined and validated by real-time RT-PCR analysis. Initially, expression of these P4 related genes were determined in CL during different stages of luteal phase. The recently reported model system of induced luteolysis, yet capable of responsive to tropic support, afforded an ideal situation to examine direct effects of P4 on structure and function of CL. For this purpose, P4 was infused via ALZET pumps into monkeys 24 h after LH/P4 depletion to maintain mid luteal phase circulating P4 concentration (P4 replacement). In another experiment, exogenous P4 was supplemented during late luteal phase to mimic early pregnancy. Results: Based on the published microarray data, 45 genes were identified to be commonly regulated by LH and P4. From these 19 genes belonging to PR signaling were selected to determine their expression in LH/P-4 depletion and P4 replacement experiments. These 19 genes when analyzed revealed 8 genes to be directly responsive to P4, whereas the other genes to be regulated by both LH and P4. Progesterone supplementation for 24 h during the late luteal phase also showed changes in expression of 17 out of 19 genes examined. Conclusion: These results taken together suggest that P4 regulates, directly or indirectly, expression of a number of genes involved in the CL structure and function.

Regular versus alternating (FeS4)(n) chains: Magnetism in KFeS2 and CsFeS2

We report crystal magnetic susceptibility results of two S = 1/2 one-dimensional Heisenberg antiferromagnets, KFeS2 and CsFeS2. Both compounds consist of (FeS4)(n) chains with an average Fe-Fe distance of 2.7 Angstrom. In KFeS2, all intrachain Fe-Fe distances are identical. Its magnetic susceptibility is typical of a regular antiferromagnetic chain with spin-spin exchange parameter J = -440.7 K. In CsFeS2, however, the Fe-Fe distances alternate between 2.61 and 2.82 Angstrom. This is reflected in its magnetic susceptibility, which could be fitted with J = -640 K, and the degree of alternation, alpha = 0.3. These compounds form a unique pair, and allow for a convenient experimental comparison of the magnetic properties of regular versus alternating Heisenberg chains.

Minimizing buffer requirements under rate-optimal schedule in regular dataflow networks

Large-grain synchronous dataflow graphs or multi-rate graphs have the distinct feature that the nodes of the dataflow graph fire at different rates. Such multi-rate large-grain dataflow graphs have been widely regarded as a powerful programming model for DSP applications. In this paper we propose a method to minimize buffer storage requirement in constructing rate-optimal compile-time (MBRO) schedules for multi-rate dataflow graphs. We demonstrate that the constraints to minimize buffer storage while executing at the optimal computation rate (i.e. the maximum possible computation rate without storage constraints) can be formulated as a unified linear programming problem in our framework. A novel feature of our method is that in constructing the rate-optimal schedule, it directly minimizes the memory requirement by choosing the schedule time of nodes appropriately. Lastly, a new circular-arc interval graph coloring algorithm has been proposed to further reduce the memory requirement by allowing buffer sharing among the arcs of the multi-rate dataflow graph. We have constructed an experimental testbed which implements our MBRO scheduling algorithm as well as (i) the widely used periodic admissible parallel schedules (also known as block schedules) proposed by Lee and Messerschmitt (IEEE Transactions on Computers, vol. 36, no. 1, 1987, pp. 24-35), (ii) the optimal scheduling buffer allocation (OSBA) algorithm of Ning and Gao (Conference Record of the Twentieth Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, Charleston, SC, Jan. 10-13, 1993, pp. 29-42), and (iii) the multi-rate software pipelining (MRSP) algorithm (Govindarajan and Gao, in Proceedings of the 1993 International Conference on Application Specific Array Processors, Venice, Italy, Oct. 25-27, 1993, pp. 77-88). Schedules generated for a number of random dataflow graphs and for a set of DSP application programs using the different scheduling methods are compared. The experimental results have demonstrated a significant improvement (10-20%) in buffer requirements for the MBRO schedules compared to the schedules generated by the other three methods, without sacrificing the computation rate. The MBRO method also gives a 20% average improvement in computation rate compared to Lee's Block scheduling method.

An efficient web cache replacement policy

Several replacement policies for web caches have been proposed and studied extensively in the literature. Different replacement policies perform better in terms of (i) the number of objects found in the cache (cache hit), (ii) the network traffic avoided by fetching the referenced object from the cache, or (iii) the savings in response time. In this paper, we propose a simple and efficient replacement policy (hereafter known as SE) which improves all three performance measures. Trace-driven simulations were done to evaluate the performance of SE. We compare SE with two widely used and efficient replacement policies, namely Least Recently Used (LRU) and Least Unified Value (LUV) algorithms. Our results show that SE performs at least as well as, if not better than, both these replacement policies. Unlike various other replacement policies proposed in literature, our SE policy does not require parameter tuning or a-priori trace analysis and has an efficient and simple implementation that can be incorporated in any existing proxy server or web server with ease.

On limiting cases in the flexure of simply supported regular polygonal plates

Limiting solutions are derived for the flexure of simply supported many-sided regular polygons, as the number of sides is increased indefinitely. It is shown that these solutions are different from those for simply supported circular plates. For axisymmetric loading, circular plate solutions overestimate the deflexions and the moments by significant factors.

Dynamically Reconfigurable Regular Expression Matching Architecture

Regular Expressions are generic representations for a string or a collection of strings. This paper focuses on implementation of a regular expression matching architecture on reconfigurable fabric like FPGA. We present a Nondeterministic Finite Automata based implementation with extended regular expression syntax set compared to previous approaches. We also describe a dynamically reconfigurable generic block that implements the supported regular expression syntax. This enables formation of the regular expression hardware by a simple cascade of generic blocks as well as a possibility for reconfiguring the generic blocks to change the regular expression being matched. Further,we have developed an HDL code generator to obtain the VHDL description of the hardware for any regular expression set. Our optimized regular expression engine achieves a throughput of 2.45 Gbps. Our dynamically reconfigurable regular expression engine achieves a throughput of 0.8 Gbps using 12 FPGA slices per generic block on Xilinx Virtex2Pro FPGA.

A Combinatorial Family of Near Regular LDPC Codes

An elementary combinatorial Tanner graph construction for a family of near-regular low density parity check (LDPC) codes achieving high girth is presented. These codes are near regular in the sense that the degree of a left/right vertex is allowed to differ by at most one from the average. The construction yields in quadratic time complexity an asymptotic code family with provable lower bounds on the rate and the girth for a given choice of block length and average degree. The construction gives flexibility in the choice of design parameters of the code like rate, girth and average degree. Performance simulations of iterative decoding algorithm for the AWGN channel on codes designed using the method demonstrate that these codes perform better than regular PEG codes and MacKay codes of similar length for all values of Signal to noise ratio.

Emulating Optimal Replacement with a Shepherd Cache

The inherent temporal locality in memory accesses is filtered out by the L1 cache. As a consequence, an L2 cache with LRU replacement incurs significantly higher misses than the optimal replacement policy (OPT). We propose to narrow this gap through a novel replacement strategy that mimics the replacement decisions of OPT. The L2 cache is logically divided into two components, a Shepherd Cache (SC) with a simple FIFO replacement and a Main Cache (MC) with an emulation of optimal replacement. The SC plays the dual role of caching lines and guiding the replacement decisions in MC. Our pro- posed organization can cover 40% of the gap between OPT and LRU for a 2MB cache resulting in 7% overall speedup. Comparison with the dynamic insertion policy, a victim buffer, a V-Way cache and an LRU based fully associative cache demonstrates that our scheme performs better than all these strategies.