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.

When good neighbors don't need fences: temporal landscape partitioning among baboon social groups

Intraspecific competition is a key factor shaping space-use strategies and movement decisions in many species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely unknown. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for similar to 900 days, and we used behavioral, demographic, and life history data to measure factors affecting use of overlap areas. Annual home ranges of neighboring groups overlapped substantially, as predicted (baboons are considered non-territorial), but home ranges overlapped less when space use was assessed over shorter time scales. Moreover, neighboring groups were in close spatial proximity to one another on fewer days than predicted by a null model, suggesting an avoidance-based spacing pattern. At all time scales examined (monthly, biweekly, and weekly), time spent in overlap areas was greater during time periods when groups fed on evenly dispersed, low-quality foods. The percent of fertile females in social groups was negatively correlated with time spent in overlap areas only during weekly time intervals. This suggests that broad temporal changes in ecological resources are a major predictor of how intensively overlap areas are used, and groups modify these ecologically driven spacing patterns at short time scales based on female reproductive status. Together, these findings offer insight into the economics of territoriality by highlighting the dynamics of spacing patterns at differing time scales.

Community-managed forests and wildlife-friendly agriculture play a subsidiary but not substitutive role to protected areas for the endangered Asian elephant

Global conservation policy is increasingly debating the feasibility of reconciling wildlife conservation and human resource requirements in land uses outside protected areas (PAs). However, there are few quantitative assessments of whether or to what extent these `wildlife-friendly' land uses fulfill a fundamental function of PAs-to separate biodiversity from anthropogenic threats. We distinguish the role of wildlife-friendly land uses as being (a) subsidiary, whereby they augment PAs with secondary habitat, or (b) substitutive, wherein they provide comparable habitat to PAs. We tested our hypotheses by investigating the influence of land use and human presence on space-use intensity of the endangered Asian elephant (Elephas maximus) in a fragmented landscape comprising PAs and wildlife-friendly land uses. We applied multistate occupancy models to spatial data on elephant occurrence to estimate and model the overall probability of elephants using a site, and the conditional probability of high-intensity use given that elephants use a site. The probability of elephants using a site regardless of intensity did not vary between PAs and wildlife-friendly land uses. However, high-intensity use declined with distance to PM, and this effect was accentuated by an increase in village density. Therefore, while wildlife-friendly land uses did play a subsidiary conservation role, their potential to substitute for PAs was offset by a strong human presence. Our findings demonstrate the need to evaluate the role of wildlife-friendly land uses in landscape-scale conservation; for species that have conflicting resource requirements with people, PAs are likely to provide crucial refuge from growing anthropogenic threats. (C) 2014 Elsevier Ltd. All rights reserved.

Divvying up an incubator: How parasitic and mutualistic fig wasps use space within their nursery microcosm

Differential occupancy of space can lead to species coexistence. The fig-fig wasp pollination system hosts species-specific pollinating and parasitic wasps that develop within galls in a nursery comprising a closed inflorescence, the syconium. This microcosm affords excellent opportunities for investigating spatial partitioning since it harbours a closed community in which all wasp species are dependent on securing safe sites inside the syconium for their developing offspring while differing in life history, egg deposition strategies and oviposition times relative to nursery development. We determined ontogenetic changes in oviposition sites available to the seven-member fig wasp community of Ficus racemosa comprising pollinators, gallers and parasitoids. We used species distribution models (SDMs) for the first time at a microcosm scale to predict patterns of spatial occurrence of nursery occupants. SDMs gave high true-positive and low false-positive site occupancy rates for most occupants indicating species specificity in oviposition sites. The nursery microcosm itself changed with syconium development and sequential egg-laying by different wasp species. The number of sites occupied by offspring of the different wasp species was negatively related to the risk of syconium abortion by the plant host following oviposition. Since unpollinated syconia are usually aborted, parasitic wasps ovipositing into nurseries at the same time as the pollinator targeted many sites, suggesting response to lower risk of syconium abortion owing to reduced risk of pollination failure compared to those species ovipositing before pollination. Wasp life history and oviposition time relative to nursery development contributed to the co-existence of nursery occupants.

Denoising neural data with state-space smoothing: Method and application

Neural data are inevitably contaminated by noise. When such noisy data are subjected to statistical analysis, misleading conclusions can be reached. Here we attempt to address this problem by applying a state-space smoothing method, based on the combined use of the Kalman filter theory and the Expectation–Maximization algorithm, to denoise two datasets of local field potentials recorded from monkeys performing a visuomotor task. For the first dataset, it was found that the analysis of the high gamma band (60–90 Hz) neural activity in the prefrontal cortex is highly susceptible to the effect of noise, and denoising leads to markedly improved results that were physiologically interpretable. For the second dataset, Granger causality between primary motor and primary somatosensory cortices was not consistent across two monkeys and the effect of noise was suspected. After denoising, the discrepancy between the two subjects was significantly reduced.

Space-Time Codes Achieving the DMD Tradeoff of the MIMO-ARQ Channel

For the quasi-static, Rayleigh-fading multiple-input multiple-output (MIMO) channel with n(t) transmit and n(r) receive antennas, Zheng and Tse showed that there exists a fundamental tradeoff between diversity and spatial-multiplexing gains, referred to as the diversity-multiplexing gain (D-MG) tradeoff. Subsequently, El Gamal, Caire, and Damen considered signaling across the same channel using an L-round automatic retransmission request (ARQ) protocol that assumes the presence of a noiseless feedback channel capable of conveying one bit of information per use of the feedback channel. They showed that given a fixed number L of ARQ rounds and no power control, there is a tradeoff between diversity and multiplexing gains, termed the diversity-multiplexing-delay (DMD) tradeoff. This tradeoff indicates that the diversity gain under the ARQ scheme for a particular information rate is considerably larger than that obtainable in the absence of feedback. In this paper, a set of sufficient conditions under which a space-time (ST) code will achieve the DMD tradeoff is presented. This is followed by two classes of explicit constructions of ST codes which meet these conditions. Constructions belonging to the first class achieve minimum delay and apply to a broad class of fading channels whenever n(r) >= n(t) and either L/n(t) or n(t)kslashL. The second class of constructions do not achieve minimum delay, but do achieve the DMD tradeoff of the fading channel for all statistical descriptions of the channel and for all values of the parameters n(r,) n(t,) L.

Continuation of limit cycles near saddle homoclinic points using splines in phase space

We present a new algorithm for continuation of limit cycles of autonomous systems as a system parameter is varied. The algorithm works in phase space with an ordered set of points on the limit cycle, along with spline interpolation. Currently popular algorithms in bifurcation analysis packages compute time-domain approximations of limit cycles using either shooting or collocation. The present approach seems useful for continuation near saddle homoclinic points, where it encounters a corner while time-domain methods essentially encounter a discontinuity (a relatively short period of rapid variation). Other phase space-based algorithms use rescaled arclength in place of time, but subsequently resemble the time-domain methods. Compared to these, we introduce additional freedom through a variable stretching of arclength based on local curvature, through the use of an auxiliary index-based variable. Several numerical examples are presented. Comparisons with results from the popular package, MATCONT, are favorable close to saddle homoclinic points.

Distributed space-time codes for cooperative networks with partial CSI

Design criteria and full-diversity Distributed Space Time Codes (DSTCs) for the two phase transmission based cooperative diversity protocol of Jing-Hassibi and the Generalized Nonorthogonal Amplify and Forward (GNAF) protocol are reported, when the relay nodes are assumed to have knowledge of the phase component of the source to relay channel gains. It is shown that this under this partial channel state information (CSI), several well known space time codes for the colocated MIMO (Multiple Input Multiple Output) channel become amenable for use as DSTCs. In particular, the well known complex orthogonal designs, generalized coordinate interleaved orthogonal designs (GCIODs) and unitary weight single symbol decodable (UW-SSD) codes are shown to satisfy the required design constraints for DSTCs. Exploiting the relaxed code design constraints, we propose DSTCs obtained from Clifford Algebras which have low ML decoding complexity.

Four group decodable differential scaled unitary linear space-time codes

Differential Unitary Space-Time Block codes (STBCs) offer a means to communicate on the Multiple Input Multiple Output (MIMO) channel without the need for channel knowledge at both the transmitter and the receiver. Recently Yuen-Guan-Tjhung have proposed Single-Symbol-Decodable Differential Space-Time Modulation based on Quasi-Orthogonal Designs (QODs) by replacing the original unitary criterion by a scaled unitary criterion. These codes were also shown to perform better than differential unitary STBCs from Orthogonal Designs (ODs). However the rate (as measured in complex symbols per channel use) of the codes of Yuen-Guan-Tjhung decay as the number of transmit antennas increase. In this paper, a new class of differential scaled unitary STBCs for all even number of transmit antennas is proposed. These codes have a rate of 1 complex symbols per channel use, achieve full diversity and moreover they are four-group decodable, i.e., the set of real symbols can be partitioned into four groups and decoding can be done for the symbols in each group separately. Explicit construction of multidimensional signal sets that yield full diversity for this new class of codes is also given.

Noncoherent low-decoding-complexity space-time codes for wireless relay networks

The differential encoding/decoding setup introduced by Kiran et at, Oggier et al and Jing et al for wireless relay networks that use codebooks consisting of unitary matrices is extended to allow codebooks consisting of scaled unitary matrices. For such codebooks to be used in the Jing-Hassibi protocol for cooperative diversity, the conditions that need to be satisfied by the relay matrices and the codebook are identified. A class of previously known rate one, full diversity, four-group encodable and four-group decodable Differential Space-Time Codes (DSTCs) is proposed for use as Distributed DSTCs (DDSTCs) in the proposed set up. To the best of our knowledge, this is the first known low decoding complexity DDSTC scheme for cooperative wireless networks.

A systematic design of high-rate full-diversity space-frequency codes for MIMO-OFDM systems

This paper presents a systematic construction of high-rate and full-diversity space-frequency block codes for MIMO-OFDM systems. While all prior constructions offer only a maximum rate of one complex symbol per channel use, our construction yields rate equal to the number of transmit antennas and simultaneously achieves full-diversity. The proposed construction works for arbitrary number of transmit antennas and arbitrary channel power delay profile. A key step in this construction is the generalization of the stacked matrix code design criteria given by Bolcskei et.al., (IEEE WCNC 2000). Explicit equivalence of our generalized code design criteria with the Hadamard-product based criteria of W. Su et.al., (lEEE Trans. Sig. Proc. Nov 2003) is established and new high-rate codes are constructed using our criteria.

A unified construction of space-time codes with optimal rate-diversity tradeoff

The problem of constructing space-time (ST) block codes over a fixed, desired signal constellation is considered. In this situation, there is a tradeoff between the transmission rate as measured in constellation symbols per channel use and the transmit diversity gain achieved by the code. The transmit diversity is a measure of the rate of polynomial decay of pairwise error probability of the code with increase in the signal-to-noise ratio (SNR). In the setting of a quasi-static channel model, let n(t) denote the number of transmit antennas and T the block interval. For any n(t) <= T, a unified construction of (n(t) x T) ST codes is provided here, for a class of signal constellations that includes the familiar pulse-amplitude (PAM), quadrature-amplitude (QAM), and 2(K)-ary phase-shift-keying (PSK) modulations as special cases. The construction is optimal as measured by the rate-diversity tradeoff and can achieve any given integer point on the rate-diversity tradeoff curve. An estimate of the coding gain realized is given. Other results presented here include i) an extension of the optimal unified construction to the multiple fading block case, ii) a version of the optimal unified construction in which the underlying binary block codes are replaced by trellis codes, iii) the providing of a linear dispersion form for the underlying binary block codes, iv) a Gray-mapped version of the unified construction, and v) a generalization of construction of the S-ary case corresponding to constellations of size S-K. Items ii) and iii) are aimed at simplifying the decoding of this class of ST codes.

Improved switching frequency variation control of hysteresis controlled voltage source inverter-fed IM drives using current error space vector

A constant switching frequency current error space vector-based hysteresis controller for two-level voltage source inverter-fed induction motor (IM) drives is proposed in this study. The proposed controller is capable of driving the IM in the entire speed range extending to the six-step mode. The proposed controller uses the parabolic boundary, reported earlier, for vector selection in a sector, but uses simple, fast and self-adaptive sector identification logic for sector change detection in the entire modulation range. This new scheme detects the sector change using the change in direction of current error along the axes jA, jB and jC. Most of the previous schemes use an outer boundary for sector change detection. So the current error goes outside the boundary six times during sector change, in one cycle,, introducing additional fifth and seventh harmonic components in phase current. This may cause sixth harmonic torque pulsations in the motor and spread in the harmonic spectrum of phase voltage. The proposed new scheme detects the sector change fast and accurately eliminating the chance of introducing additional fifth and seventh harmonic components in phase current and provides harmonic spectrum of phase voltage, which exactly matches with that of constant switching frequency voltage-controlled space vector pulse width modulation (VC-SVPWM)-based two-level inverter-fed drives.

Low PAPR full-diversity space-frequency codes for MIMO-OFDM systems

Use of precoding transforms such as Hadamard Transforms and Phase Alteration for Peak to Average Power Ratio (PAPR) reduction in OFDM systems are well known. In this paper we propose use of Inverse Discrete Fourier Transform (IDFT) and Hadamard transform as precoding transforms in MIMO-OFDM systems to achieve low peak to average power ratio (PAPR). We show that while our approach using IDFT does not disturb the diversity gains of the MIMO-OFDM systems (spatial, temporal and frequency diversity gains), it offers a better trade-off between PAPR reduction and ML decoding complexity compared to that of the Hadamard transform precoding. We study in detail the amount of PAPR reduction achieved for the following two recently proposed full-diversity Space-Frequency coded MIMO-OFDM systems using both the IDFT and the Hadamard transform: (i) W. Su. Z. Safar, M. Olfat, K. J. R. Liu (IEEE Trans. on Signal Processing, Nov. 2003), and (ii) W. Su, Z. Safar, K. J. R. Liu (IEEE Trans. on Information Theory, Jan. 2005).

A non-orthogonal distributed space-time coded protocol - Part 1:Signal model and design criteria

In this two-part series of papers, a generalized non-orthogonal amplify and forward (GNAF) protocol which generalizes several known cooperative diversity protocols is proposed. Transmission in the GNAF protocol comprises of two phases - the broadcast phase and the cooperation phase. In the broadcast phase, the source broadcasts its information to the relays as well as the destination. In the cooperation phase, the source and the relays together transmit a space-time code in a distributed fashion. The GNAF protocol relaxes the constraints imposed by the protocol of Jing and Hassibi on the code structure. In Part-I of this paper, a code design criteria is obtained and it is shown that the GNAF protocol is delay efficient and coding gain efficient as well. Moreover GNAF protocol enables the use of sphere decoders at the destination with a non-exponential Maximum likelihood (ML) decoding complexity. In Part-II, several low decoding complexity code constructions are studied and a lower bound on the Diversity-Multiplexing Gain tradeoff of the GNAF protocol is obtained.