Optimal scheduling of a processor executing a communication protocol stack

We consider the problem of optimally scheduling a processor executing a multilayer protocol in an intelligent Network Interface Controller (NIC). In particular, we assume a typical LAN environment with class 4 transport service, a connectionless network service, and a class 1 link level protocol. We develop a queuing model for the problem. In the most general case this becomes a cyclic queuing network in which some queues have dedicated servers, and the others have a common schedulable server. We use sample path arguments and Markov decision theory to determine optimal service schedules. The optimal throughputs are compared with those obtained with simple policies. The optimal policy yields upto 25% improvement in some cases. In some other cases, the optimal policy does only slightly better than much simpler policies.

Role of oestradiol-17β in the regulation of synthesis and secretion of human chorionic gonadotrophin by first trimester human placenta

Inhibition of aromatase, a key enzyme in the biosynthesis of oestradiol-17 beta, by the addition of 1,4,6-androstatrien-3,17-dione resulted in a significant increase in the levels of immunoreactive human chorionic gonadotrophin (hCG) in the medium and tissue. This increase was partially reversed by the simultaneous addition of oestradiol-17 beta. These effects on the levels of immunoreactive hCG were also reflected by the increased levels of mRNA specific for the alpha and beta subunits of hCG following the addition of the aromatase inhibitor. However, addition of tamoxifen resulted in a drastic decrease in the levels of both the messages. Based on these results, it is suggested that the synthesis of hCG is negatively modulated by oestradiol-17 beta in the human placenta.

Specificity in the regulation of eukaryotic gene transcription

The regulation of eukaryotic gene transcription poses major challenges in terms of the innumerable protein factors required to ensure tissue or cell-type specificity. While this specificity is sought to be explained by the interaction of cis-acting DNA elements and thetrans-acting protein factor(s), considerable amount of degeneracy has been observed in this interaction. Immunoglobulin heavy chain gene expression in B cells and liver-specific gene expression are discussed as examples of this complexity in this article. Heterodimerization and post-translational modification of transcription factors and the organization of composite promoter elements are strategies by which diverse sets of genes can be regulated in a specific manner using a finite number of protein factors

Translational Up-Regulation and High-Level Protein Expression from Plasmid Vectors by mTOR Activation via Different Pathways in PC3 and 293T Cells

Background: Though 293T cells are widely used for expression of proteins from transfected plasmid vectors, the molecular basis for the high-level expression is yet to be understood. We recently identified the prostate carcinoma cell line PC3 to be as efficient as 293T in protein expression. This study was undertaken to decipher the molecular basis of high-level expression in these two cell lines. Methodology/Principal Findings: In a survey of different cell lines for efficient expression of platelet-derived growth factor-B (PDGF-B), beta-galactosidase (beta-gal) and green fluorescent protein (GFP) from plasmid vectors, PC3 was found to express at 5-50-fold higher levels compared to the bone metastatic prostate carcinoma cell line PC3BM and many other cell lines. Further, the efficiency of transfection and level of expression of the reporters in PC3 were comparable to that in 293T. Comparative analyses revealed that the high level expression of the reporters in the two cell lines was due to increased translational efficiency. While phosphatidic acid (PA)-mediated activation of mTOR, as revealed by drastic reduction in reporter expression by n-butanol, primarily contributed to the high level expression in PC3, multiple pathways involving PA, PI3K/Akt and ERK1/2 appear to contribute to the abundant reporter expression in 293T. Thus the extent of translational upregulation attained through the concerted activation of mTOR by multiple pathways in 293T could be achieved through its activation primarily by the PA pathway in PC3. Conclusions/Significance: Our studies reveal that the high-level expression of proteins from plasmid vectors is effected by translational up-regulation through mTOR activation via different signaling pathways in the two cell lines and that PC3 is as efficient as 293T for recombinant protein expression. Further, PC3 offers an advantage in that the level of expression of the protein can be regulated by simple addition of n-butanol to the culture medium.

Functions Of Cytochrome-C In Regulation Of Electron-Transfer And Protein Folding

Cytochrome c, a "mobile electron carrier" of the mitochondrial respiratory chain, also occurs in detectable amounts in the cytosol, and can receive electrons from cytochromes present in endoplasmic reticulum and plasma membranes as well as from superoxide and ascorbate. The pigment was found to dissociate from mitochondrial membranes in liver and kidney when rats were subjected to heat exposure and starvation, respectively. Treating cytochrome c with hydroxylamine gives a partially deaminated product with altered redox properties; decreased stimulation of respiration by deficient mitochondria, increased reduction by superoxide, and complete loss of reducibility by plasma membranes. Mitochondria isolated from brown adipose tissue of cold-exposed rats are found to be sub-saturated with cytochrome c. The ability of cytochrome c to reactivate reduced ribonuclease is now reinterpreted as a molecular chaperone role for the hemoprotein.

Optimal pulse spacing for dynamical decoupling in the presence of a purely dephasing spin bath

Maintaining quantum coherence is a crucial requirement for quantum computation; hence protecting quantum systems against their irreversible corruption due to environmental noise is an important open problem. Dynamical decoupling (DD) is an effective method for reducing decoherence with a low control overhead. It also plays an important role in quantum metrology, where, for instance, it is employed in multiparameter estimation. While a sequence of equidistant control pulses the Carr-Purcell-Meiboom-Gill (CPMG) sequence] has been ubiquitously used for decoupling, Uhrig recently proposed that a nonequidistant pulse sequence the Uhrig dynamic decoupling (UDD) sequence] may enhance DD performance, especially for systems where the spectral density of the environment has a sharp frequency cutoff. On the other hand, equidistant sequences outperform UDD for soft cutoffs. The relative advantage provided by UDD for intermediate regimes is not clear. In this paper, we analyze the relative DD performance in this regime experimentally, using solid-state nuclear magnetic resonance. Our system qubits are C-13 nuclear spins and the environment consists of a H-1 nuclear spin bath whose spectral density is close to a normal (Gaussian) distribution. We find that in the presence of such a bath, the CPMG sequence outperforms the UDD sequence. An analogy between dynamical decoupling and interference effects in optics provides an intuitive explanation as to why the CPMG sequence performs better than any nonequidistant DD sequence in the presence of this kind of environmental noise.

MOSAICS: Multiplexed Optimal Signal Acquisition Involving Compressed Sensing

It is possible to sample signals at sub-Nyquist rate and still be able to reconstruct them with reasonable accuracy provided they exhibit local Fourier sparsity. Underdetermined systems of equations, which arise out of undersampling, have been solved to yield sparse solutions using compressed sensing algorithms. In this paper, we propose a framework for real time sampling of multiple analog channels with a single A/D converter achieving higher effective sampling rate. Signal reconstruction from noisy measurements on two different synthetic signals has been presented. A scheme of implementing the algorithm in hardware has also been suggested.

Explicit and Optimal Exact-Regenerating Codes for the Minimum-Bandwidth Point in Distributed Storage

In the distributed storage setting that we consider, data is stored across n nodes in the network such that the data can be recovered by connecting to any subset of k nodes. Additionally, one can repair a failed node by connecting to any d nodes while downloading beta units of data from each. Dimakis et al. show that the repair bandwidth d beta can be considerably reduced if each node stores slightly more than the minimum required and characterize the tradeoff between the amount of storage per node and the repair bandwidth. In the exact regeneration variation, unlike the functional regeneration, the replacement for a failed node is required to store data identical to that in the failed node. This greatly reduces the complexity of system maintenance. The main result of this paper is an explicit construction of codes for all values of the system parameters at one of the two most important and extreme points of the tradeoff - the Minimum Bandwidth Regenerating point, which performs optimal exact regeneration of any failed node. A second result is a non-existence proof showing that with one possible exception, no other point on the tradeoff can be achieved for exact regeneration.

Effect of mutations on the p53 IRES RNA structure Implications for de-regulation of the synthesis of p53 isoforms

Earlier we have demonstrated the presence of internal ribosome entry site (IRES) within tumor suppressor p53 mRNA. Here we have mapped the putative secondary structure of p53-IRES RNA using information from chemical probing and nuclease mapping experiments. Additionally, the secondary structure of the IRES element of the wild-type RNA was compared with cancer-derived silent mutant p53 RNAs. These mutations might result in the conformational alterations of p53-IRES RNAs. The results also indicate decreased IRES activities of the mutants as compared to wild-type RNA. Further, it was observed that some of the cytoplasmic trans-acting factors, critical for enhancing IRES function, were unable to bind mutant RNAs as efficiently as to wild-type. Our results suggest that hnRNP C1/C2 binds to p53-IRES and siRNA mediated partial silencing of hnRNP C1/C2 showed appreciable decrease in IRES function and consequent decrease in the level of the corresponding p53 isoform. Interestingly mutant p53 IRES showed lesser binding with hnRNP C1/C2 protein. Finally, upon doxorubicin treatment, the mutant RNAs were unable to show enhanced p53 synthesis to similar extent compared to wild type. Taken together, these observations suggest that mutations occurring in the p53 IRES might have profound implications for de-regulation of its expression and activity.

Tunable Locally-Optimal Geographical Forwarding in Wireless Sensor Networks with Sleep-Wake Cycling Nodes

We consider a wireless sensor network whose main function is to detect certain infrequent alarm events, and to forward alarm packets to a base station, using geographical forwarding. The nodes know their locations, and they sleep-wake cycle, waking up periodically but not synchronously. In this situation, when a node has a packet to forward to the sink, there is a trade-off between how long this node waits for a suitable neighbor to wake up and the progress the packet makes towards the sink once it is forwarded to this neighbor. Hence, in choosing a relay node, we consider the problem of minimizing average delay subject to a constraint on the average progress. By constraint relaxation, we formulate this next hop relay selection problem as a Markov decision process (MDP). The exact optimal solution (BF (Best Forward)) can be found, but is computationally intensive. Next, we consider a mathematically simplified model for which the optimal policy (SF (Simplified Forward)) turns out to be a simple one-step-look-ahead rule. Simulations show that SF is very close in performance to BF, even for reasonably small node density. We then study the end-to-end performance of SF in comparison with two extremal policies: Max Forward (MF) and First Forward (FF), and an end-to-end delay minimising policy proposed by Kim et al. 1]. We find that, with appropriate choice of one hop average progress constraint, SF can be tuned to provide a favorable trade-off between end-to-end packet delay and the number of hops in the forwarding path.

Optimal polygon placement by translation

Let M be an m-sided simple polygon and N be an n-sided polygon with holes. In this paper we consider the problem of computing the feasible region, i.e., the set of all placements by translation of M so that M lies inside N without intersecting any hole. First we propose an O (mn(2)) time algorithm for computing the feasible region for the case when M is a monotone polygon. Then we consider the general case when M is a simple polygon and propose an O(m(2)n(2)) time algorithm for computing the feasible region. Both algorithms are optimal upto a constant factor.

Regulation of diacylglycerol kinase in rat brain membranes by docosahexaenoic acid

The effect of docosahexaenoic acid (DHA) on the diacylglycerol kinase (DG kinase) activity in rat brain membranes was investigated. DHA at 500 mu M concentration, stimulated the enzyme activity by about 2 fold. This effect was concentration-and time-dependent and was observed after very short periods of incubation (one min). DHA stimulation of DG kinase was observed only with rat brain membranes, and not with rat brain cytosol or rat liver membranes. Treating the rat brain membranes with phospholipase A(2) which released free fatty acids including DHA, significantly stimulated the DG kinase activity. It is concluded that DHA through its stimulatory effect on DG kinase may regulate the signalling events in growth-related situations in the brain such as synaptogenesis.

Robust/Optimal Temperature Profile Control of a High-Speed Aerospace Vehicle Using Neural Networks

An approximate dynamic programming (ADP)-based suboptimal neurocontroller to obtain desired temperature for a high-speed aerospace vehicle is synthesized in this paper. A I-D distributed parameter model of a fin is developed from basic thermal physics principles. "Snapshot" solutions of the dynamics are generated with a simple dynamic inversion-based feedback controller. Empirical basis functions are designed using the "proper orthogonal decomposition" (POD) technique and the snapshot solutions. A low-order nonlinear lumped parameter system to characterize the infinite dimensional system is obtained by carrying out a Galerkin projection. An ADP-based neurocontroller with a dual heuristic programming (DHP) formulation is obtained with a single-network-adaptive-critic (SNAC) controller for this approximate nonlinear model. Actual control in the original domain is calculated with the same POD basis functions through a reverse mapping. Further contribution of this paper includes development of an online robust neurocontroller to account for unmodeled dynamics and parametric uncertainties inherent in such a complex dynamic system. A neural network (NN) weight update rule that guarantees boundedness of the weights and relaxes the need for persistence of excitation (PE) condition is presented. Simulation studies show that in a fairly extensive but compact domain, any desired temperature profile can be achieved starting from any initial temperature profile. Therefore, the ADP and NN-based controllers appear to have the potential to become controller synthesis tools for nonlinear distributed parameter systems.