Structural Alignment based Kernels for Protein Structure Classification

Structural alignments are the most widely used tools for comparing proteins with low sequence similarity. The main contribution of this paper is to derive various kernels on proteins from structural alignments, which do not use sequence information. Central to the kernels is a novel alignment algorithm which matches substructures of fixed size using spectral graph matching techniques. We derive positive semi-definite kernels which capture the notion of similarity between substructures. Using these as base more sophisticated kernels on protein structures are proposed. To empirically evaluate the kernels we used a 40% sequence non-redundant structures from 15 different SCOP superfamilies. The kernels when used with SVMs show competitive performance with CE, a state of the art structure comparison program.

River water quality response under hypothetical climate change scenarios in Tunga-Bhadra river, India

Analysis of climate change impacts on streamflow by perturbing the climate inputs has been a concern for many authors in the past few years, but there are few analyses for the impacts on water quality. To examine the impact of change in climate variables on the water quality parameters, the water quality input variables have to be perturbed. The primary input variables that can be considered for such an analysis are streamflow and water temperature, which are affected by changes in precipitation and air temperature, respectively. Using hypothetical scenarios to represent both greenhouse warming and streamflow changes, the sensitivity of the water quality parameters has been evaluated under conditions of altered river flow and river temperature in this article. Historical data analysis of hydroclimatic variables is carried out, which includes flow duration exceedance percentage (e.g. Q90), single low- flow indices (e.g. 7Q10, 30Q10) and relationships between climatic variables and surface variables. For the study region of Tunga-Bhadra river in India, low flows are found to be decreasing and water temperatures are found to be increasing. As a result, there is a reduction in dissolved oxygen (DO) levels found in recent years. Water quality responses of six hypothetical climate change scenarios were simulated by the water quality model, QUAL2K. A simple linear regression relation between air and water temperature is used to generate the scenarios for river water temperature. The results suggest that all the hypothetical climate change scenarios would cause impairment in water quality. It was found that there is a significant decrease in DO levels due to the impact of climate change on temperature and flows, even when the discharges were at safe permissible levels set by pollution control agencies (PCAs). The necessity to improve the standards of PCA and develop adaptation policies for the dischargers to account for climate change is examined through a fuzzy waste load allocation model developed earlier. Copyright (C) 2011 John Wiley & Sons, Ltd.

Interference Alignment Algorithms for the K User Constant MIMO Interference Channel

This paper considers the degrees of freedom (DOF) for a K user multiple-input multiple-output (MIMO) M x N interference channel using interference alignment (IA). A new performance metric for evaluating the efficacy of IA algorithms is proposed, which measures the extent to which the desired signal dimensionality is preserved after zero-forcing the interference at the receiver. Inspired by the metric, two algorithms are proposed for designing the linear precoders and receive filters for IA in the constant MIMO interference channel with a finite number of symbol extensions. The first algorithm uses an eigenbeamforming method to align sub-streams of the interference to reduce the dimensionality of the interference at all the receivers. The second algorithm is iterative, and is based on minimizing the interference leakage power while preserving the dimensionality of the desired signal space at the intended receivers. The improved performance of the algorithms is illustrated by comparing them with existing algorithms for IA using Monte Carlo simulations.

Joint Performance Analysis of Channel Quality Indicator Feedback Schemes and Frequency-Domain Scheduling for LTE

Frequency-domain scheduling and rate adaptation enable next-generation orthogonal frequency-division multiple access (OFDMA) cellular systems such as Long-Term Evolution (LTE) to achieve significantly higher spectral efficiencies. LTE uses a pragmatic combination of several techniques to reduce the channel-state feedback that is required by a frequency-domain scheduler. In the subband-level feedback and user-selected subband feedback schemes specified in LTE, the user reduces feedback by reporting only the channel quality that is averaged over groups of resource blocks called subbands. This approach leads to an occasional incorrect determination of rate by the scheduler for some resource blocks. In this paper, we develop closed-form expressions for the throughput achieved by the feedback schemes of LTE. The analysis quantifies the joint effects of three critical components on the overall system throughput-scheduler, multiple-antenna mode, and the feedback scheme-and brings out its dependence on system parameters such as the number of resource blocks per subband and the rate adaptation thresholds. The effect of the coarse subband-level frequency granularity of feedback is captured. The analysis provides an independent theoretical reference and a quick system parameter optimization tool to an LTE system designer and theoretically helps in understanding the behavior of OFDMA feedback reduction techniques when operated under practical system constraints.

Performance analysis of subband-level channel quality indicator feedback scheme of LTE

Frequency-domain scheduling and rate adaptation enable next generation wireless cellular systems such as Long Term Evolution (LTE) to achieve significantly higher downlink throughput. LTE assigns subcarriers in chunks, called physical resource blocks (PRBs), to users to reduce control signaling overhead. To reduce the enormous feedback overhead, the channel quality indicator (CQI) report that is used to feed back channel state information is averaged over a subband, which, in turn, is a group of multiple PRBs. In this paper, we develop closed-form expressions for the throughput achieved by the subband-level CQI feedback mechanism of LTE. We show that the coarse frequency resolution of the CQI incurs a significant loss in throughput and limits the multi-user gains achievable by the system. We then show that the performance can be improved by means of an offset mechanism that effectively makes the users more conservative in reporting their CQI.

A generalized network alignment for three-source three-destination multiple unicast networks with delays

The concept of interference alignment when extended to three-source three-destination instantaneous multiple unicast network for the case where, each source-destination pair has a min-cut of 1 and zero-interference conditions are not satisfied, is known to achieve a rate of half for every source-destination pair under certain conditions [6]. This was called network alignment. We generalize this concept of network alignment to three-source three-destination multiple unicast (3S-3D-MU) networks with delays, without making use of memory at the intermediate nodes (i.e., nodes other than the sources and destinations) and using time varying Local Encoding Kernels (LEKs). This achieves half the rate corresponding to the individual source-destination min-cut for some classes of 3S-3D-MU network with delays which do not satisfy the zero-interference conditions.

Band alignment studies in InN/p-Si(100) heterojunctions by x-ray photoelectron spectroscopy

The band offsets in InN/p-Si heterojunctions are determined by high resolution x-ray photoemission spectroscopy. The valence band of InN is found to be 1.39 eV below that of Si. Given the bandgap of 0.7 eV for InN, a type-III heterojunction with a conduction band offset of 1.81 eV was found. Agreement between the simulated and experimental data obtained from the heterojunction spectra was found to be excellent, establishing that the method of determination was accurate. The charge neutrality level (CNL) model provided a reasonable description of the band alignment of the InN/p-Si interface and a change in the interface dipole by 0.06 eV was observed for InN/p-Si interface.

Magnetic arm-switch-based three-phase series-shunt compensated quality AC power supply

This study presents a novel magnetic arm-switch-based integrated magnetic circuit for a three-phase series-shunt compensated uninterruptible power supply (UPS). The magnetic circuit acts as a common interacting field for a number of energy ports, viz., series inverter, shunt inverter, grid and load. The magnetic arm-switching technique ensures equivalent series or shunt connection between the inverters. In normal grid mode (stabiliser mode), the series inverter is used for series voltage correction and the shunt one for current correction. The inverters and the load are effectively connected in parallel when the grid power is not available. These inverters are then used to share the load power. The operation of the inverters in parallel is ensured by the magnetic arm-switching technique. This study also includes modelling of the magnetic circuit. A graphical technique called bond graph is used to model the system. In this model, the magnetic circuit is represented in terms of gyrator-capacitors. Therefore the model is also termed as gyrator-capacitor model. The model is used to extract the dynamic equations that are used to simulate the system using MATLAB/SIMULINK. This study also discusses a synchronously rotating reference frame-based control technique that is used for the control of the series and shunt inverters in different operating modes. Finally, the gyrator-capacitor model is validated by comparing the simulated and experimental results.

Studies towards synthesis, evolution and alignment characteristics of dense, millimeter long multiwalled carbon nanotube arrays

We report the synthesis of aligned arrays of millimeter long carbon nanotubes (CNTs), from benzene and ferrocene as the molecular precursor and catalyst respectively, by a one-step chemical vapor deposition technique. The length of the grown CNTs depends on the reaction temperature and increases from similar to 85 mu m to similar to 1.4 mm when the synthesis temperature is raised from 650 to 1100 degrees C, while the tube diameter is almost independent of the preparation temperature and is similar to 80 nm. The parallel arrangement of the CNTs, as well as their tube diameter can be verified spectroscopically by small angle X-ray scattering (SAXS) studies. Based on electron diffraction scattering (EDS) studies of the top and the base of the CNT films, a root growth process can be deduced.

Interference Alignment in Regenerating Codes for Distributed Storage: Necessity and Code Constructions

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any arbitrary of nodes. However regenerating codes possess in addition, the ability to repair a failed node by connecting to any arbitrary nodes and downloading an amount of data that is typically far less than the size of the data file. This amount of download is termed the repair bandwidth. Minimum storage regenerating (MSR) codes are a subclass of regenerating codes that require the least amount of network storage; every such code is a maximum distance separable (MDS) code. Further, when a replacement node stores data identical to that in the failed node, the repair is termed as exact. The four principal results of the paper are (a) the explicit construction of a class of MDS codes for d = n - 1 >= 2k - 1 termed the MISER code, that achieves the cut-set bound on the repair bandwidth for the exact repair of systematic nodes, (b) proof of the necessity of interference alignment in exact-repair MSR codes, (c) a proof showing the impossibility of constructing linear, exact-repair MSR codes for d < 2k - 3 in the absence of symbol extension, and (d) the construction, also explicit, of high-rate MSR codes for d = k+1. Interference alignment (IA) is a theme that runs throughout the paper: the MISER code is built on the principles of IA and IA is also a crucial component to the nonexistence proof for d < 2k - 3. To the best of our knowledge, the constructions presented in this paper are the first explicit constructions of regenerating codes that achieve the cut-set bound.

Climate change induced risk in water quality control problems

A modeling framework is presented in this paper, integrating hydrologic scenarios projected from a General Circulation Model (GCM) with a water quality simulation model to quantify the future expected risk. Statistical downscaling with a Canonical Correlation Analysis (CCA) is carried out to develop the future scenarios of hydro-climate variables starting with simulations provided by a GCM. A Multiple Logistic Regression (MLR) is used to quantify the risk of Low Water Quality (LWQ) corresponding to a threshold quality level, by considering the streamflow and water temperature as explanatory variables. An Imprecise Fuzzy Waste Load Allocation Model (IFWLAM) presented in an earlier study is then used to develop adaptive policies to address the projected water quality risks. Application of the proposed methodology is demonstrated with the case study of Tunga-Bhadra river in India. The results showed that the projected changes in the hydro-climate variables tend to diminish DO levels, thus increasing the future risk levels of LWQ. (C) 2012 Elsevier B.V. All rights reserved.

Weakly ordered chiral alignment medium derived from 5 `-GMP: guanosine

A novel weakly ordered chiral lyotropic alignment medium, derived by the self-assembly of guanosine 5'-monophosphate (5'-GMP) : guanosine for scaling RDCs to desired strengths and for the discrimination of enantiomers, is reported. The preparation of this inexpensive mesophase is straightforward, requires less time (1 h), and is sustainable, reversible and tunable over a wide range of temperature (280-330 K) and concentration.

QUAD: quality assessment of documents

We propose a set of metrics that evaluate the uniformity, sharpness, continuity, noise, stroke width variance,pulse width ratio, transient pixels density, entropy and variance of components to quantify the quality of a document image. The measures are intended to be used in any optical character recognition (OCR) engine to a priori estimate the expected performance of the OCR. The suggested measures have been evaluated on many document images, which have different scripts. The quality of a document image is manually annotated by users to create a ground truth. The idea is to correlate the values of the measures with the user annotated data. If the measure calculated matches the annotated description,then the metric is accepted; else it is rejected. In the set of metrics proposed, some of them are accepted and the rest are rejected. We have defined metrics that are easily estimatable. The metrics proposed in this paper are based on the feedback of homely grown OCR engines for Indic (Tamil and Kannada) languages. The metrics are independent of the scripts, and depend only on the quality and age of the paper and the printing. Experiments and results for each proposed metric are discussed. Actual recognition of the printed text is not performed to evaluate the proposed metrics. Sometimes, a document image containing broken characters results in good document image as per the evaluated metrics, which is part of the unsolved challenges. The proposed measures work on gray scale document images and fail to provide reliable information on binarized document image.