Phenobarbitone-mediated translocation of the cytosolic proteins interacting with the 5 '-proximal region of rat liver CYP2B1/B2 gene into the nucleus

The positive element (PE) (-69 to -98 bp) within the 5'-proximal region of the CYP2B1B2 gene (+1 to -179 bp) of rat liver is essential for phenobarbitone (PB) response and gives a single major complex with the rat liver cytosol in gel shift analysis. This complex corresponds to complex I (top) of the three complexes given by the nuclear extracts. PB treatment of rats leads to a decrease in complex I formation with the cytosol and PE and an increase in the same with the nuclear extract in gel shift analysis. Both the changes are counteracted by simultaneous okadaic acid administration. The nuclear protein giving rise to complex I has been isolated and has an M-r of 26 kDa. The cytosolic counterpart consists of two species, 26 and 28 kDa, as revealed by Southwestern blot analysis using labeled PE. It is concluded that PB treatment leads to the translocation accompanied by processing of the cytosolic protein species into the nucleus that requires protein dephosphorylation. It is suggested that PB may exert a global regulation on the transcription of many genes by modulating the phosphorylation status of different protein factors involved in transcriptional regulation. (C) 2002 Elsevier Science (USA).

Two timescale analysis of the Alopex algorithm for optimization

Alopex is a correlation-based gradient-free optimization technique useful in many learning problems. However, there are no analytical results on the asymptotic behavior of this algorithm. This article presents a new version of Alopex that can be analyzed using techniques of two timescale stochastic approximation method. It is shown that the algorithm asymptotically behaves like a gradient-descent method, though it does not need (or estimate) any gradient information. It is also shown, through simulations, that the algorithm is quite effective.

A method of tracking the peak power points for a variable speed wind energy conversion system

In this paper, a method of tracking the peak power in a wind energy conversion system (WECS) is proposed, which is independent of the turbine parameters and air density. The algorithm searches for the peak power by varying the speed in the desired direction. The generator is operated in the speed control mode with the speed reference being dynamically modified in accordance with the magnitude and direction of change of active power. The peak power points in the P-omega curve correspond to dP/domega = 0. This fact is made use of in the optimum point search algorithm. The generator considered is a wound rotor induction machine whose stator is connected directly to the grid and the rotor is fed through back-to-back pulse-width-modulation (PWM) converters. Stator flux-oriented vector control is applied to control the active and reactive current loops independently. The turbine characteristics are generated by a dc motor fed from a commercial dc drive. All of the control loops are executed by a single-chip digital signal processor (DSP) controller TMS320F240. Experimental results show that the performance of the control algorithm compares well with the conventional torque control method.

Analysis of link-layer backoff schemes on point-to-point Markov fading links

Backoff algorithms are typically employed in multiple-access networks (e.g., Ethernet) to recover from packet collisions. In this letter, we propose and carry out the analysis for three types of link-layer backoff schemes, namely, linear backoff, exponential backoff, and geometric backoff, on point-to-point wireless fading links where packet errors occur nonindependently. In such a scenario, the backoff schemes are shown to achieve better energy efficiency without compromising much on the link layer throughput performance.

On an oscillatory point force in a rotating stratified fluid

The forced oscillations due to a point forcing effect in an infinite or contained, inviscid, incompressible, rotating, stratified fluid are investigated taking into account the density variation in the inertia terms in the linearized equations of motion. The solutions are obtained in closed form using generalized Fourier transforms. Solutions are presented for a medium bounded by a finite cylinder when the oscillatory forcing effect is acting at a point on the axis of the cylinder. In both the unbounded and bounded case, there exist characteristic cones emanating from the point of application of the force on which either the pressure or its derivatives are discontinuous. The perfect resonance existing at certain frequencies in an unbounded or bounded homogeneous fluid is avoided in the case of a confined stratified fluid.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Optimal scheduling of multiple chlorine sources in water distribution systems

The specified range of free chlorine residual (between minimum and maximum) in water distribution systems needs to be maintained to avoid deterioration of the microbial quality of water, control taste and/or odor problems, and hinder formation of carcino-genic disinfection by-products. Multiple water quality sources for providing chlorine input are needed to maintain the chlorine residuals within a specified range throughout the distribution system. The determination of source dosage (i.e., chlorine concentrations/chlorine mass rates) at water quality sources to satisfy the above objective under dynamic conditions is a complex process. A nonlinear optimization problem is formulated to determine the chlorine dosage at the water quality sources subjected to minimum and maximum constraints on chlorine concentrations at all monitoring nodes. A genetic algorithm (GA) approach in which decision variables (chlorine dosage) are coded as binary strings is used to solve this highly nonlinear optimization problem, with nonlinearities arising due to set-point sources and non-first-order reactions. Application of the model is illustrated using three sample water distribution systems, and it indicates that the GA,is a useful tool for evaluating optimal water quality source chlorine schedules.

Believe it or Not! Multicore CPUs can Match GPUs for FLOP-intensive Applications

In this work, we evaluate performance of a real-world image processing application that uses a cross-correlation algorithm to compare a given image with a reference one. The algorithm processes individual images represented as 2-dimensional matrices of single-precision floating-point values using O(n4) operations involving dot-products and additions. We implement this algorithm on a nVidia GTX 285 GPU using CUDA, and also parallelize it for the Intel Xeon (Nehalem) and IBM Power7 processors, using both manual and automatic techniques. Pthreads and OpenMP with SSE and VSX vector intrinsics are used for the manually parallelized version, while a state-of-the-art optimization framework based on the polyhedral model is used for automatic compiler parallelization and optimization. The performance of this algorithm on the nVidia GPU suffers from: (1) a smaller shared memory, (2) unaligned device memory access patterns, (3) expensive atomic operations, and (4) weaker single-thread performance. On commodity multi-core processors, the application dataset is small enough to fit in caches, and when parallelized using a combination of task and short-vector data parallelism (via SSE/VSX) or through fully automatic optimization from the compiler, the application matches or beats the performance of the GPU version. The primary reasons for better multi-core performance include larger and faster caches, higher clock frequency, higher on-chip memory bandwidth, and better compiler optimization and support for parallelization. The best performing versions on the Power7, Nehalem, and GTX 285 run in 1.02s, 1.82s, and 1.75s, respectively. These results conclusively demonstrate that, under certain conditions, it is possible for a FLOP-intensive structured application running on a multi-core processor to match or even beat the performance of an equivalent GPU version.