Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins

Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of `protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a `roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.

Space-Time Scales of Northward Propagation of Convection during Boreal Summer

This study uses precipitation estimates from the Tropical Rainfall Measuring Mission to quantify the spatial and temporal scales of northward propagation of convection over the Indian monsoon region during boreal summer. Propagating modes of convective systems in the intraseasonal time scales such as the Madden-Julian oscillation can interact with the intertropical convergence zone and bring active and break spells of the Indian summer monsoon. Wavelet analysis was used to quantify the spatial extent (scale) and center of these propagating convective bands, as well as the time period associated with different spatial scales. Results presented here suggest that during a good monsoon year the spatial scale of this oscillation is about 30 degrees centered around 10 degrees N. During weak monsoon years, the scale of propagation decreases and the center shifts farther south closer to the equator. A strong linear relationship is obtained between the center/scale of convective wave bands and intensity of monsoon precipitation over Indian land on the interannual time scale. Moreover, the spatial scale and its center during the break monsoon were found to be similar to an overall weak monsoon year. Based on this analysis, a new index is proposed to quantify the spatial scales associated with propagating convective bands. This automated wavelet-based technique developed here can be used to study meridional propagation of convection in a large volume of datasets from observations and model simulations. The information so obtained can be related to the interannual and intraseasonal variation of Indian monsoon precipitation.

Multilevel dodecagonal space-vector generation for induction motor drives by cascading three-level and two-level inverters

This study proposes an inverter circuit topology capable of generating multilevel dodecagonal (12-sided polygon) voltage space vectors by the cascaded connection of two-level and three-level inverters. By the proper selection of DC-link voltages and resultant switching states for the inverters, voltage space vectors whose tips lie on three concentric dodecagons, are obtained. A rectifier circuit for the inverter is also proposed, which significantly improves the power factor. The topology offers advantages such as the complete elimination of the fifth and seventh harmonics in phase voltages and an extension of the linear modulation range. In this study, a simple method for the calculation of pulse width modulation timing was presented along with extensive simulation and experimental results in order to validate the proposed concept.

Space-vector-based hybrid pulse width modulation technique to reduce line current distortion in induction motor drives

Pulse width modulation (PWM) techniques involving different switching sequences are used in space vector-based PWM generation for reducing line current ripple in induction motor drives. This study proposes a hybrid PWM technique employing five switching sequences. The proposed technique is a combination of continuous PWM, discontinuous PWM (DPWM) and advanced bus clamping PWM methods. Performance of the proposed PWM technique is evaluated and compared with those of the existing techniques on a constant volts per hertz induction motor drive. In terms of total harmonic distortion in the line current, the proposed method is shown to be superior to both conventional space vector PWM (CSVPWM) and DPWM over a fundamental frequency range of 32-50 Hz at a given average switching frequency. The reduction in harmonic distortion is about 42% over CSVPWM at the rated speed of the drive.

The Structural Characterization of Folded Peptides Containing the Conformationally Constrained beta-Amino Acid Residue beta(2,2)Ac(6)c

Backbone alkylation has been shown to result in a dramatic reduction in the conformational space that is sterically accessible to a-amino acid residues in peptides. By extension, the presence of geminal dialkyl substituents at backbone atoms also restricts available conformational space for beta and ? residues. Five peptides containing the achiral beta 2,2-disubstituted beta-amino acid residue, 1-(aminomethyl)cyclohexanecarboxylic acid (beta 2,2Ac6c), have been structurally characterized in crystals by X-ray diffraction. The tripeptide Boc-Aib-beta 2,2Ac6c-Aib-OMe (1) adopts a novel fold stabilized by two intramolecular H-bonds (C11 and C9) of opposite directionality. The tetrapeptide Boc-Aib-beta 2,2Ac6c]2-OMe (2) and pentapeptide Boc-Aib-beta 2,2Ac6c]2-Aib-OMe (3) form short stretches of a hybrid a beta C11 helix stabilized by two and three intramolecular H-bonds, respectively. The structure of the dipeptide Boc-Aib-beta 2,2Ac6c-OMe (5) does not reveal any intramolecular H-bond. The aggregation pattern in the crystal provides an example of an extended conformation of the beta 2,2Ac6c residue, forming a polar sheet like H-bond. The protected derivative Ac-beta 2,2Ac6c-NHMe (4) adopts a locally folded gauche conformation about the C beta?Ca bonds (?=-55.7 degrees). Of the seven examples of beta 2,2Ac6c residues reported here, six adopt gauche conformations, a feature which promotes local folding when incorporated into peptides. A comparison between the conformational properties of beta 2,2Ac6c and beta 3,3Ac6c residues, in peptides, is presented. Backbone torsional parameters of H-bonded a beta/beta a turns are derived from the structures presented in this study and earlier reports.

Spatial Modulation and Space Shift Keying in Single Carrier Communication

Spatial modulation (SM) and space shift keying (SSK) are relatively new modulation techniques which are attractive in multi-antenna communications. Single carrier (SC) systems can avoid the peak-to-average power ratio (PAPR) problem encountered in multicarrier systems. In this paper, we study SM and SSK signaling in cyclic-prefixed SC (CPSC) systems on MIMO-ISI channels. We present a diversity analysis of MIMO-CPSC systems under SSK and SM signaling. Our analysis shows that the diversity order achieved by (n(t), n(r)) SSK scheme and (n(t), n(r), Theta(M)) SM scheme in MIMO-CPSC systems under maximum-likelihood (ML) detection is n(r), where n(t), n(r) denote the number of transmit and receive antennas and Theta(M) denotes the modulation alphabet of size M. Bit error rate (BER) simulation results validate this predicted diversity order. Simulation results also show that MIMO-CPSC with SM and SSK achieves much better performance than MIMO-OFDM with SM and SSK.

Multilevel Dodecagonal Voltage Space Vector Generation using Flying Capacitor topology for Induction motor drives

In this paper, a multilevel flying capacitor inverter topology suitable for generating multilevel dodecagonal space vectors for an induction motor drive, is proposed. Because of the dodecagonal space vectors, it has increased modulation range with the absence of all 6n +/- 1, (n=odd) harmonics in the phase voltage and currents. The topology, realized by flying capacitor three level inverters feeding an open-end winding induction motor, does not suffer the neutral point voltage imbalance issues seen in NPC inverters and the capacitors have inherent charge-balancing capability with PWM control using switching state redundancies. Furthermore, the proposed technique uses lesser number of power supplies compared to cascaded H-bridge or NPC based dodecagonal schemes and has better ride-through capability. Finally, the voltage control is obtained through a simple carrier-based space vector PWM scheme implemented on a DSP.

A Space-Vector-Based Hysteresis Current Controller for a General n-Level Inverter-Fed Drive With Nearly Constant Switching Frequency Control

A current-error space-vector-based hysteresis current controller for a general n-level voltage-source inverter (VSI)-fed three-phase induction motor (IM) drive is proposed here, with control of the switching frequency variation for the full linear modulation range. The proposed current controller monitors the space-vector-based current error of an n-level VSI-fed IM to keep the current error within a parabolic boundary, using the information of the current triangular sector in which the tip of the reference vector lies. Information of the reference voltage vector is estimated using the measured current-error space vectors, along the alpha- and beta-axes. Appropriate dimension and orientation of this parabolic boundary ensure a switching frequency spectrum similar to that of a constant-switching-frequency voltage-controlled space vector pulsewidth modulation (PWM) (SVPWM)-based IM drive. Like SVPWM for multilevel inverters, the proposed controller selects inverter switching vectors, forming a triangular sector in which the tip of the reference vector stays, for the hysteresis PWM control. The sector in the n-level inverter space vector diagram, in which the tip of the fundamental stator voltage stays, is precisely detected, using the sampled reference space vector estimated from the instantaneous current-error space vectors. The proposed controller retains all the advantages of a conventional hysteresis controller such as fast current control, with smooth transition to the overmodulation region. The proposed controller is implemented on a five-level VSI-fed 7.5-kW IM drive.

A Hybrid Multilevel Inverter System Based on Dodecagonal Space Vectors for Medium Voltage IM Drives

Dodecagonal (12-sided) space vector pulsewidth modulation (PWM) schemes are characterized by the complete absence of (6n +/- 1)th-order harmonics (for odd n) in the phase voltages, within the linear modulation range and beyond, including over-modulation. This paper presents a new topology suitable for the realization of such multilevel inverter schemes for induction motor (IM) drives, by cascading two-level inverters with flying-capacitor-inverter fed floating H-bridge cells. Now, any standard IM may be used to get the dodecagonal operation which hitherto was possible only with open-end winding IM. To minimize the current total harmonic distortion (THD), a strategy for synchronous PWM is also proposed. It is shown that the proposed method is capable of obtaining better THD figures, compared to conventional dodecagonal schemes. The topology and the PWM strategy are validated through analysis and subsequently verified experimentally.

Medium Voltage Drive for Induction Motors Using Multilevel Octadecagonal Voltage Space Vectors

Multilevel inverters with hexagonal and dodecagonal voltage space vector structures have improved harmonic profile compared to two-level inverters. Further improvement in the quality of the waveform is possible using multilevel octadecagonal (18-sided polygon) voltage space vectors. This paper proposes an inverter circuit topology capable of generating multilevel octadecagonal voltage space vectors, by cascading two asymmetric three-level inverters. By the proper selection of dc-link voltages and the resultant switching states for the inverters, voltage space vectors, whose tips lie on three concentric octadecagons, are obtained. The advantages of octadecagonal voltage space vector-based pulsewidth modulation (PWM) techniques are the complete elimination of fifth, seventh, eleventh, and thirteenth harmonics in phase voltages and the extension of linear modulation range. In this paper, a simple PWM timing calculation method is also proposed. Experimental results have been presented in this paper to validate the proposed concept.

A Compact and Compliant External Pipe-Crawling Robot

The focus of this paper is on the practical aspects of design, prototyping, and testing of a compact, compliant external pipe-crawling robot that can inspect a closely spaced bundle of pipes in hazardous environments and areas that are inaccessible to humans. The robot consists of two radially deployable compliant ring actuators that are attached to each other along the longitudinal axis of the pipe by a bidirectional linear actuator. The robot imitates the motion of an inchworm. The novel aspect of the compliant ring actuator is a spring-steel compliant mechanism that converts circumferential motion to radial motion of its multiple gripping pads. Circumferential motion to ring actuators is provided by two shape memory alloy (SMA) wires that are guided by insulating rollers. The design of the compliant mechanism is derived from a radially deployable mechanism. A unique feature of the design is that the compliant mechanism provides the necessary kinematic function within the limited annular space around the pipe and serves as the bias spring for the SMA wires. The robot has a control circuit that sequentially activates the SMA wires and the linear actuator; it also controls the crawling speed. The robot has been fabricated, tested, and automated. Its crawling speed is about 45 mm/min, and the weight is about 150 g. It fits within an annular space of a radial span of 15 mm to crawl on a pipe of 60-mm outer diameter.

Distributed Space Time Coding for Wireless Two-Way Relaying

We consider the wireless two-way relay channel, in which two-way data transfer takes place between the end nodes with the help of a relay. For the Denoise-And-Forward (DNF) protocol, it was shown by Koike-Akino et al. that adaptively changing the network coding map used at the relay greatly reduces the impact of Multiple Access Interference at the relay. The harmful effect of the deep channel fade conditions can be effectively mitigated by proper choice of these network coding maps at the relay. Alternatively, in this paper we propose a Distributed Space Time Coding (DSTC) scheme, which effectively removes most of the deep fade channel conditions at the transmitting nodes itself without any CSIT and without any need to adaptively change the network coding map used at the relay. It is shown that the deep fades occur when the channel fade coefficient vector falls in a finite number of vector subspaces of, which are referred to as the singular fade subspaces. DSTC design criterion referred to as the singularity minimization criterion under which the number of such vector subspaces are minimized is obtained. Also, a criterion to maximize the coding gain of the DSTC is obtained. Explicit low decoding complexity DSTC designs which satisfy the singularity minimization criterion and maximize the coding gain for QAM and PSK signal sets are provided. Simulation results show that at high Signal to Noise Ratio, the DSTC scheme provides large gains when compared to the conventional Exclusive OR network code and performs better than the adaptive network coding scheme.

A game theoretic approach for feature clustering and its application to feature selection

In this paper, we develop a game theoretic approach for clustering features in a learning problem. Feature clustering can serve as an important preprocessing step in many problems such as feature selection, dimensionality reduction, etc. In this approach, we view features as rational players of a coalitional game where they form coalitions (or clusters) among themselves in order to maximize their individual payoffs. We show how Nash Stable Partition (NSP), a well known concept in the coalitional game theory, provides a natural way of clustering features. Through this approach, one can obtain some desirable properties of the clusters by choosing appropriate payoff functions. For a small number of features, the NSP based clustering can be found by solving an integer linear program (ILP). However, for large number of features, the ILP based approach does not scale well and hence we propose a hierarchical approach. Interestingly, a key result that we prove on the equivalence between a k-size NSP of a coalitional game and minimum k-cut of an appropriately constructed graph comes in handy for large scale problems. In this paper, we use feature selection problem (in a classification setting) as a running example to illustrate our approach. We conduct experiments to illustrate the efficacy of our approach.

A Savitzky-Golay Filtering Perspective of Dynamic Feature Computation

We address the classical problem of delta feature computation, and interpret the operation involved in terms of Savitzky- Golay (SG) filtering. Features such as themel-frequency cepstral coefficients (MFCCs), obtained based on short-time spectra of the speech signal, are commonly used in speech recognition tasks. In order to incorporate the dynamics of speech, auxiliary delta and delta-delta features, which are computed as temporal derivatives of the original features, are used. Typically, the delta features are computed in a smooth fashion using local least-squares (LS) polynomial fitting on each feature vector component trajectory. In the light of the original work of Savitzky and Golay, and a recent article by Schafer in IEEE Signal Processing Magazine, we interpret the dynamic feature vector computation for arbitrary derivative orders as SG filtering with a fixed impulse response. This filtering equivalence brings in significantly lower latency with no loss in accuracy, as validated by results on a TIMIT phoneme recognition task. The SG filters involved in dynamic parameter computation can be viewed as modulation filters, proposed by Hermansky.

Real-Space Manifestations of Bottlenecks in Turbulence Spectra

An energy-spectrum bottleneck, a bump in the turbulence spectrum between the inertial and dissipation ranges, is shown to occur in the nonturbulent, one-dimensional, hyperviscous Burgers equation and found to be the Fourier-space signature of oscillations in the real-space velocity, which are explained by boundary-layer-expansion techniques. Pseudospectral simulations are used to show that such oscillations occur in velocity correlation functions in one- and three-dimensional hyperviscous hydrodynamical equations that display genuine turbulence. DOI: 10.1103/PhysRevLett.110.064501