Advances in Image Reconstruction Methods for Real-Time Magnetic Resonance Thermometry

Magnetic Resonance Imaging (MRI) has been widely used in cancer treatment planning, which takes the advantage of high-resolution and high-contrast provided by it. The raw data collected in the MRI can also be used to obtain the temperature maps and has been explored for performing MR thermometry. This review article describes the methods that are used in performing MR thermometry, with an emphasis on reconstruction methods that are useful to obtain these temperature maps in real-time for large region of interest. This article also proposes a prior-image constrained reconstruction method for temperature reconstruction in MR thermometry, and a systematic comparison using ex-vivo tissue experiments with state of the art reconstruction method is presented.

Application of Qualitative Imaging Methods to Electrical Performance-Aware Package Board Design

Package-board co-design plays a crucial role in determining the performance of high-speed systems. Although there exist several commercial solutions for electromagnetic analysis and verification, lack of Computer Aided Design (CAD) tools for SI aware design and synthesis lead to longer design cycles and non-optimal package-board interconnect geometries. In this work, the functional similarities between package-board design and radio-frequency (RF) imaging are explored. Consequently, qualitative methods common to the imaging community, like Tikhonov Regularization (TR) and Landweber method are applied to solve multi-objective, multi-variable package design problems. In addition, a new hierarchical iterative piecewise linear algorithm is developed as a wrapper over LBP for an efficient solution in the design space.

Estimating the volume of glaciers in the Himalayan-Karakoram region using different methods

Ice volume estimates are crucial for assessing water reserves stored in glaciers. Due to its large glacier coverage, such estimates are of particular interest for the Himalayan-Karakoram (HK) region. In this study, different existing methodologies are used to estimate the ice reserves: three area-volume relations, one slope-dependent volume estimation method, and two ice-thickness distribution models are applied to a recent, detailed, and complete glacier inventory of the HK region, spanning over the period 2000-2010 and revealing an ice coverage of 40 775 km(2). An uncertainty and sensitivity assessment is performed to investigate the influence of the observed glacier area and important model parameters on the resulting total ice volume. Results of the two ice-thickness distribution models are validated with local ice-thickness measurements at six glaciers. The resulting ice volumes for the entire HK region range from 2955 to 4737 km(3), depending on the approach. This range is lower than most previous estimates. Results from the ice thickness distribution models and the slope-dependent thickness estimations agree well with measured local ice thicknesses. However, total volume estimates from area-related relations are larger than those from other approaches. The study provides evidence on the significant effect of the selected method on results and underlines the importance of a careful and critical evaluation.

Quorum Sensing and Biofilm Formation in Mycobacteria: Role of c-di-GMP and Methods to Study This Second Messenger

Bacteria have evolved to survive the ever-changing environment using intriguing mechanisms of quorum sensing (QS). Very often, QS facilitates formation of biofilm to help bacteria to persist longer and the formation of such biofilms is regulated by c-di-GMP. It is a well-known second messenger also found in mycobacteria. Several methods have been developed to study c-di-GMP signaling pathways in a variety of bacteria. In this review, we have attempted to highlight a connection between c-di-GMP and biofilm formation and QS in mycobacteria and several methods that have helped in better understanding of c-di-GMP signaling. (c) 2014 IUBMB Life, 66(12):823-834, 2014

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

A Smooth Discretization Bridging Finite Element and Mesh-free Methods Using Polynomial Reproducing Simplex Splines

This work sets forth a `hybrid' discretization scheme utilizing bivariate simplex splines as kernels in a polynomial reproducing scheme constructed over a conventional Finite Element Method (FEM)-like domain discretization based on Delaunay triangulation. Careful construction of the simplex spline knotset ensures the success of the polynomial reproduction procedure at all points in the domain of interest, a significant advancement over its precursor, the DMS-FEM. The shape functions in the proposed method inherit the global continuity (Cp-1) and local supports of the simplex splines of degree p. In the proposed scheme, the triangles comprising the domain discretization also serve as background cells for numerical integration which here are near-aligned to the supports of the shape functions (and their intersections), thus considerably ameliorating an oft-cited source of inaccuracy in the numerical integration of mesh-free (MF) schemes. Numerical experiments show the proposed method requires lower order quadrature rules for accurate evaluation of integrals in the Galerkin weak form. Numerical demonstrations of optimal convergence rates for a few test cases are given and the method is also implemented to compute crack-tip fields in a gradient-enhanced elasticity model.

Novel Transmit Precoding Methods for Rayleigh Fading Multiuser TDD-MIMO Systems With CSIT and No CSIR

In this paper, we present novel precoding methods for multiuser Rayleigh fading multiple-input-multiple-output (MIMO) systems when channel state information (CSI) is available at the transmitter (CSIT) but not at the receiver (CSIR). Such a scenario is relevant, for example, in time-division duplex (TDD) MIMO communications, where, due to channel reciprocity, CSIT can be directly acquired by sending a training sequence from the receiver to the transmitter(s). We propose three transmit precoding schemes that convert the fading MIMO channel into a fixed-gain additive white Gaussian noise (AWGN) channel while satisfying an average power constraint. We also extend one of the precoding schemes to the multiuser Rayleigh fading multiple-access channel (MAC), broadcast channel (BC), and interference channel (IC). The proposed schemes convert the fading MIMO channel into fixed-gain parallel AWGN channels in all three cases. Hence, they achieve an infinite diversity order, which is in sharp contrast to schemes based on perfect CSIR and no CSIT, which, at best, achieve a finite diversity order. Further, we show that a polynomial diversity order is retained, even in the presence of channel estimation errors at the transmitter. Monte Carlo simulations illustrate the bit error rate (BER) performance obtainable from the proposed precoding scheme compared with existing transmit precoding schemes.

Evaluating Methods to Predict Streamflow at Ungauged Sites using Regional Flow Duration Curves: A Case Study

Precise information on streamflows is of major importance for planning and monitoring of water resources schemes related to hydro power, water supply, irrigation, flood control, and for maintaining ecosystem. Engineers encounter challenges when streamflow data are either unavailable or inadequate at target locations. To address these challenges, there have been efforts to develop methodologies that facilitate prediction of streamflow at ungauged sites. Conventionally, time intensive and data exhaustive rainfall-runoff models are used to arrive at streamflow at ungauged sites. Most recent studies show improved methods based on regionalization using Flow Duration Curves (FDCs). A FDC is a graphical representation of streamflow variability, which is a plot between streamflow values and their corresponding exceedance probabilities that are determined using a plotting position formula. It provides information on the percentage of time any specified magnitude of streamflow is equaled or exceeded. The present study assesses the effectiveness of two methods to predict streamflow at ungauged sites by application to catchments in Mahanadi river basin, India. The methods considered are (i) Regional flow duration curve method, and (ii) Area Ratio method. The first method involves (a) the development of regression relationships between percentile flows and attributes of catchments in the study area, (b) use of the relationships to construct regional FDC for the ungauged site, and (c) use of a spatial interpolation technique to decode information in FDC to construct streamflow time series for the ungauged site. Area ratio method is conventionally used to transfer streamflow related information from gauged sites to ungauged sites. Attributes that have been considered for the analysis include variables representing hydrology, climatology, topography, land-use/land- cover and soil properties corresponding to catchments in the study area. Effectiveness of the presented methods is assessed using jack knife cross-validation. Conclusions based on the study are presented and discussed. (C) 2015 The Authors. Published by Elsevier B.V.

Simulations using meshfree methods

In this paper, attempt is made to solve a few problems using the Polynomial Point Collocation Method (PPCM), the Radial Point Collocation Method (RPCM), Smoothed Particle Hydrodynamics (SPH), and the Finite Point Method (FPM). A few observations on the accuracy of these methods are recorded. All the simulations in this paper are three dimensional linear elastostatic simulations, without accounting for body forces.

Study of Multilevel Sinusoidal PWM methods for Cascaded H-Bridge Multilevel Inverters

This paper is a study of Multilevel Sinusoidal Pulse Width Modulation (MSPWM) methods; Phase Disposition (PD), Alternate Phase Opposition Disposition (APOD), Phase Opposition Disposition (POD) on a single phase Cascaded H-Bridge Multilevel inverter. Various factors such as amplitude modulation index (Ma), frequency modulation index (M-f), phase angle between carrier and reference modulating wave (phi) have been considered for simulation. Variation in these factors and their effect on inverter performance is evaluated. Factors such as DC bus utilization, output r.m.s voltage, total harmonic distortion (%THD), dominant harmonic order, switching losses are evaluated based on simulation results.

Multi-transform based spectral element to include first order shear deformation in plates

For obtaining dynamic response of structure to high frequency shock excitation spectral elements have several advantages over conventional methods. At higher frequencies transverse shear and rotary inertia have a predominant role. These are represented by the First order Shear Deformation Theory (FSDT). But not much work is reported on spectral elements with FSDT. This work presents a new spectral element based on the FSDT/Mindlin Plate Theory which is essential for wave propagation analysis of sandwich plates. Multi-transformation method is used to solve the coupled partial differential equations, i.e., Laplace transforms for temporal approximation and wavelet transforms for spatial approximation. The formulation takes into account the axial-flexure and shear coupling. The ability of the element to represent different modes of wave motion is demonstrated. Impact on the derived wave motion characteristics in the absence of the developed spectral element is discussed. The transient response using the formulated element is validated by the results obtained using Finite Element Method (FEM) which needs significant computational effort. Experimental results are provided which confirms the need to having the developed spectral element for the high frequency response of structures. (C) 2015 Elsevier Ltd. All rights reserved.

A Remark on the A Posteriori Error Analysis of Discontinuous Galerkin Methods for the Obstacle Problem

We revisit the a posteriori error analysis of discontinuous Galerkin methods for the obstacle problem derived in 25]. Under a mild assumption on the trace of obstacle, we derive a reliable a posteriori error estimator which does not involve min/max functions. A key in this approach is an auxiliary problem with discrete obstacle. Applications to various discontinuous Galerkin finite element methods are presented. Numerical experiments show that the new estimator obtained in this article performs better.

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.