Blind equalization and sequence estimation using Markov chain Monte Carlo methods

This paper discusses the problem of restoring a digital input signal that has been degraded by an unknown FIR filter in noise, using the Gibbs sampler. A method for drawing a random sample of a sequence of bits is presented; this is shown to have faster convergence than a scheme by Chen and Li, which draws bits independently. ©1998 IEEE.

Adaptive control of combustion instabilities for unknown sign of the high frequency gain

A type of adaptive, closed-loop controllers known as self-tuning regulators present a robust method of eliminating thermoacoustic oscillations in modern gas turbines. These controllers are able to adapt to changes in operating conditions, and require very little pre-characterisation of the system. One piece of information that is required, however, is the sign of the system's high frequency gain (or its 'instantaneous gain'). This poses a problem: combustion systems are infinite-dimensional, and so this information is never known a priori. A possible solution is to use a Nussbaum gain, which guarantees closed-loop stability without knowledge of the sign of the high frequency gain. Despite the theory for such a controller having been developed in the 1980s, it has never, to the authors' knowledge, been demonstrated experimentally. In this paper, a Nussbaum gain is used to stabilise thermoacoustic instability in a Rijke tube. The sign of the high frequency gain of the system is not required, and the controller is robust to large changes in operating conditions - demonstrated by varying the length of the Rijke tube with time. Copyright © 2008 by Simon J. Illingworth & Aimee S. Morgans.

Adaptive diversification of bitter taste receptor genes in mammalian evolution

The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome sequences, respectively, in addition to the 23 and 6 previously known T2R genes from the two species. A phylogenetic analysis of the T2R genes suggests that they can be classified into three main groups, which are designated A, B, and C. Interestingly, while the one-to-one gene orthology between the human and mouse is common to group B and C genes, group A genes show a pattern of species- or lineage-specific duplication. It is possible that group B and C genes are necessary for detecting bitter tastants common to both humans and mice, whereas group A genes are used for species-specific bitter tastants. The analysis also reveals that phylogenetically closely related T2R genes are close in their chromosomal locations, demonstrating tandem gene duplication as the primary source of new T2Rs. For closely related paralogous genes, a rate of nonsynonymous nucleotide substitution significantly higher than the rate of synonymous substitution was observed in the extracellular regions of T2Rs, which are presumably involved in tastant-binding. This suggests the role of positive selection in the diversification of newly duplicated T2R genes. Because many natural poisonous substances are bitter, we conjecture that the mammalian T2R genes are under diversifying selection for the ability to recognize a diverse array of poisons that the organisms may encounter in exploring new habitats and diets.

Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Shoor and Inche-Borun lakes in Golestan, Hoze-Soltan and Namak lakes in Qom, Maharloo and Bakhteghan lakes in Fars, Nough pool in Kerman and Mighan pool in Markazi and DNA extracted by phenol-chloroform method. Primers designed on a ribosomal fragment (16s rRNA) of mt DNA sequence and PCR was done. Digestion of the 1566 bp segment PCR product by 10 restriction endonuclease (Alu I, EcoR I, Eco47 I, Hae III, Hind III, Hinf I, Mbo I, Msp I, Rsa I, TaqI) showed 25 different haplotypes: 9 in Urmia, 4 in Shoor and Inche- Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan, 1 in Bakhtegan Maharlo, 3 in Maharloo and 4 in Nough. Measurement of haplotype and nucleotide diversity intra population and nucleotide diversity and divergence inter populations and evolutionary distance between haplotypes showed a high diversity in mitochondrial genome of Artemia in studied regions whose results are similar to those explained for highly geographic expansion organism. In addition, results showed considerable heterogeneity between different populations and there are enough evidences in haplotypic level for separation of studied samples and division of Iranian Artemia to seven populations including Urmia, Shoor and Inche-Borun, Hoze-Soltan and Namak, Maharloo, Bakhteghan, Nough and Mighan. Phylogenetic analysis of the 16S rRNA data set resulted strict consensus and neighbor joining distance trees, demonstrated that all samples were monophyletic and parthenogenetic form derivation from bisexual populations and genetically high resemblance to those of A. urmiana. Study of 270 specimens from different region showed the genus Artemia in Iran clustered into three clades including: 1- Shoor, Inche-Burun, Hoze-Soltan, Namak, Bakhtegan and Maharloo 2- Nough and Mighan 3- Urmia. Totally, obtained results indicated to ability of used techniques for study of inter species diversity, population structure, reveal of phylogenic relationship and dividing of different populations of Artemia in Iran.

Adaptive BDDC in Three Dimensions

The adaptive BDDC method is extended to the selection of face constraints in three dimensions. A new implementation of the BDDC method is presented based on a global formulation without an explicit coarse problem, with massive parallelism provided by a multifrontal solver. Constraints are implemented by a projection and sparsity of the projected operator is preserved by a generalized change of variables. The effectiveness of the method is illustrated on several engineering problems.

Optical tweezing beam control using liquid crystal adaptive optical elements

Liquid crystal (LC) adaptive optical elements are described, which provide an alternative to existing micropositioning technologies in optical tweezing. A full description of this work is given in [1]. An adaptive LC prism supplies tip/tilt to the phase profile of the trapping beam, giving rise to an available steering radius within the x-y plane of 10 μm. Additionally, a modally addressed adaptive LC lens provides defocus, offering a z-focal range for the trapping site of 100 μm. The result is full three-dimensional positional control of trapped particle(s) using a simple and wholly electronic control system. Compared to competing technologies, these devices provide a lower degree of controllability, but have the advantage of simplicity, cost and light efficiency. Furthermore, due to their birefringence, LC elements offer the opportunity of the creation of dual optical traps with controllable depth and separation.

Adaptive sequential Monte Carlo approach for real-time applications

This paper presents an adaptive Sequential Monte Carlo approach for real-time applications. Sequential Monte Carlo method is employed to estimate the states of dynamic systems using weighted particles. The proposed approach reduces the run-time computation complexity by adapting the size of the particle set. Multiple processing elements on FPGAs are dynamically allocated for improved energy efficiency without violating real-time constraints. A robot localisation application is developed based on the proposed approach. Compared to a non-adaptive implementation, the dynamic energy consumption is reduced by up to 70% without affecting the quality of solutions. © 2012 IEEE.

A body force-based method for prediction of multiple-pure-tone noise: Validation

Emissions, fuel burn, and noise are the main drivers for innovative aircraft design. Embedded propulsion systems, such as for example used in hybrid-wing body aircraft, can offer fuel burn and noise reduction benefits but the impact of inlet flow distortion on the generation and propagation of turbomachinery noise has yet to be assessed. A novel approach is used to quantify the effects of non-uniform flow on the creation and propagation of multiple pure tone (MPT) noise. The ultimate goal is to conduct a parametric study of S-duct inlets to quantify the effects of inlet design parameters on the acoustic signature. The key challenge is that the effects of distortion transfer, noise source generation and propagation through the non-uniform flow field are inherently coupled such that a simultaneous computation of the aerodynamics and acoustics is required to capture the mechanisms at play. The technical approach is based on a body force description of the fan blade row that is able to capture the distortion transfer and the blade-to-blade flow variations that cause the MPT noise while reducing computational cost. A single, 3-D full-wheel CFD simulation, in which the Euler equations are solved to second-order spatial and temporal accuracy, simultaneously computes the MPT noise generation and its propagation in distorted inlet flow. A new method of producing the blade-to-blade variations in the body force field for MPT noise generation has been developed and validated. The numerical dissipation inherent to the solver is quantified and used to correct for non-physical attenuation in the far-field noise spectra. Source generation, acoustic propagation and acoustic energy transfer between modes is examined in detail. The new method is validated on NASA's Source Diagnostic Test fan and inlet, showing good agreement with experimental data for aerodynamic performance, acoustic source generation, and far-field noise spectra. The next steps involve the assessment of MPT noise in serpentine inlet ducts and the development of a reduced order formulation suitable for incorporation into NASA's ANOPP framework. © 2010 by Jeff Defoe, Alex Narkaj & Zoltan Spakovszky.

Heterogeneous reconfigurable system for adaptive particle filters in real-time applications

This paper presents a heterogeneous reconfigurable system for real-time applications applying particle filters. The system consists of an FPGA and a multi-threaded CPU. We propose a method to adapt the number of particles dynamically and utilise the run-time reconfigurability of the FPGA for reduced power and energy consumption. An application is developed which involves simultaneous mobile robot localisation and people tracking. It shows that the proposed adaptive particle filter can reduce up to 99% of computation time. Using run-time reconfiguration, we achieve 34% reduction in idle power and save 26-34% of system energy. Our proposed system is up to 7.39 times faster and 3.65 times more energy efficient than the Intel Xeon X5650 CPU with 12 threads, and 1.3 times faster and 2.13 times more energy efficient than an NVIDIA Tesla C2070 GPU. © 2013 Springer-Verlag.

Improved bounds for subband-adaptive iterative shrinkage/thresholding algorithms.

This paper presents new methods for computing the step sizes of the subband-adaptive iterative shrinkage-thresholding algorithms proposed by Bayram & Selesnick and Vonesch & Unser. The method yields tighter wavelet-domain bounds of the system matrix, thus leading to improved convergence speeds. It is directly applicable to non-redundant wavelet bases, and we also adapt it for cases of redundant frames. It turns out that the simplest and most intuitive setting for the step sizes that ignores subband aliasing is often satisfactory in practice. We show that our methods can be used to advantage with reweighted least squares penalty functions as well as L1 penalties. We emphasize that the algorithms presented here are suitable for performing inverse filtering on very large datasets, including 3D data, since inversions are applied only to diagonal matrices and fast transforms are used to achieve all matrix-vector products.

A six sensor method for measuring acoustic properties in ducts.

An accurate description of sound propagation in a duct is important to obtain the sound power radiating from a source in both near and far fields. A technique has been developed and applied to decompose higher-order modes of sound emitted into a duct. Traditional experiments and theory based on two-sensor methods are limited to the plane-wave contribution to the sound field at low frequency. Due to the increase in independent measurements required, a computational method has been developed to simulate sensitivities of real measurements (e.g., noise) and optimize the set-up. An experimental rig has been constructed to decompose the first two modes using six independent measurements from surface, flush-mounted microphones. Experiments were initially performed using a loudspeaker as the source for validation. Subsequently, the sound emitted by a mixed-flow fan has been investigated and compared to measurements made in accordance with the internationally standardized in-duct fan measurement method. This method utilizes large anechoic terminations and a procedure involving averaging over measurements in space and time to account for the contribution from higher-order modes. The new method does not require either of these added complications and gives detail about the underlying modal content of the emitted sound.

Estimation of soil properties and deformations in staged constructions based on mcmc method

This paper presents a Bayesian probabilistic framework to assess soil properties and model uncertainty to better predict excavation-induced deformations using field deformation data. The potential correlations between deformations at different depths are accounted for in the likelihood function needed in the Bayesian approach. The proposed approach also accounts for inclinometer measurement errors. The posterior statistics of the unknown soil properties and the model parameters are computed using the Delayed Rejection (DR) method and the Adaptive Metropolis (AM) method. As an application, the proposed framework is used to assess the unknown soil properties of multiple soil layers using deformation data at different locations and for incremental excavation stages. The developed approach can be used for the design of optimal revisions for supported excavation systems. © 2010 ASCE.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Aeroacoustic source measurement methods for characterizing the sound generated by ducted flow devices with higher-order modes.

The International Organization for Standardization (ISO) method 5136 is widely used in industry and academia to determine the sound power radiated into a duct by fans and other flow devices. The method involves placing the device at the center of a long cylindrical duct with anechoic terminations at each end to eliminate reflections. A single off-axis microphone is used on the inlet and outlet sides that can theoretically capture the plane-wave mode amplitudes but this does not provide enough information to fully account for higher-order modes. In this study, the "two-port" source model is formulated to include higher-order modes and applied for the first three modes. This requires six independent surface pressure measurements on each side or "port." The resulting experimental set-up is much shorter than the ISO rig and does not require anechoic terminations. An array of six external loudspeaker sources is used to characterize the passive part of the two-port model and the set-up provides a framework to account for transmission of higher-order modes through a fan. The relative importance of the higher-order modes has been considered and their effect on inaccuracies when using the ISO method to find source sound power has been analyzed.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.