Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (phi, ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (phi, ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (phi, ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins.

CONFORMATIONAL FEATURES OF SIGMA FACTOR/ANTI-SIGMA COMPLEXES

The association of a factors with the RNA polymerase dictates the expression profile of a bacterial cell. Major changes to the transcription profile are achieved by the use of multiple sigma factors that confer distinct promoter selectivity to the holoenzyme. The cellular concentration of a sigma factor is regulated by diverse mechanisms involving transcription, translation and post-translational events. The number of sigma factors varies substantially across bacteria. The diversity in the interactions between sigma factors also vary-ranging from collaboration, competition or partial redundancy in some cellular or environmental contexts. These interactions can be rationalized by a mechanistic model referred to as the partitioning of a space model of bacterial transcription. The structural similarity between different sigma/anti-sigma complexes despite poor sequence conservation and cellular localization reveals an elegant route to incorporate diverse regulatory mechanisms within a structurally conserved scaffold. These features are described here with a focus on sigma/anti-sigma complexes from Mycobacterium tuberculosis. In particular, we discuss recent data on the conditional regulation of sigma/anti-sigma factor interactions. Specific stages of M. tuberculosis infection, such as the latent phase, as well as the remarkable adaptability of this pathogen to diverse environmental conditions can be rationalized by the synchronized action of different a factors.

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.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Space vector based modulation scheme for reducing capacitor RMS current in three-level diode-clamped inverter

The DC capacitor is an important component in a voltage source inverter.The RMS current flowing through the capacitor determines the capacitor size and losses. The losses, in turn, influence the capacitor life. This paper proposes a space vector based modulation strategy for reducing the capacitor RMS current in a three-level diode-clamped inverter. An analytical closed-form expression is derived for the DC capacitor RMS current with the proposed PWM strategy. The analytical expression is validated through simulations and also experimentally. Theoretical and experimental results are presented, comparing the proposed strategy with conventional space vector PWM (CSVPWM). It is shown that the proposed strategy reduces the capacitor RMS current significantly at high modulation indices and high power factors. (C) 2014 Elsevier B.V. All rights reserved.

OFDM-Aided Differential Space-Time Shift Keying Using Iterative Soft Multiple-Symbol Differential Sphere Decoding

Soft-decision multiple-symbol differential sphere decoding (MSDSD) is proposed for orthogonal frequency-division multiplexing (OFDM)-aided differential space-time shift keying (DSTSK)-aided transmission over frequency-selective channels. Specifically, the DSTSK signaling blocks are generated by the channel-encoded source information and the space-time (ST) blocks are appropriately mapped to a number of OFDM subcarriers. After OFDM demodulation, the DSTSK signal is noncoherently detected by our soft-decision MSDSD detector. A novel soft-decision MSDSD detector is designed, and the associated decision rule is derived for the DSTSK scheme. Our simulation results demonstrate that an SNR reduction of 2 dB is achieved by the proposed scheme using an MSDSD window size of N-w = 4 over the conventional soft-decision-aided differential detection benchmarker, while communicating over dispersive channels and dispensing with channel estimation (CE).

Distribution, Demography, and Conservation of Lion-tailed Macaques (Macaca silenus) in the Anamalai Hills Landscape, Western Ghats, India

The status of the endemic and endangered lion-tailed macaque (Macaca silenus) has not been properly assessed in several regions of the Western Ghats of southern India. We conducted a study in Parambikulam Forest Reserve in the state of Kerala to determine the distribution, demography, and status of lion-tailed macaques. We laid 5km(2) grid cells on the map of the study area (644km(2)) and made four replicated walks in each grid cell using GPS. We gathered data on lion-tailed macaque group locations, demography, and site covariates including trail length, duration of walk, proportion of evergreen forest, height of tallest trees, and human disturbance index. We also performed occupancy modeling using PRESENCE ver. 3.0. We estimated a minimum of 17 groups of macaques in these hills. Low detection and occupancy probabilities indicated a low density of lion-tailed macaques in the study area. Height of the tallest trees correlated positively whereas human disturbance and proportion of evergreen forest correlated negatively with occupancy in grid cells. We also used data from earlier studies carried out in the surrounding Anamalai Tiger Reserve and Nelliyampathy Hills to discuss the conservation status in the large Anamalai Hills Landscape. This landscape harbors an estimated population of 1108 individuals of lion-tailed macaques, which is about one third of the entire estimated wild population of this species. A conservation plan for this landscape could be used as a model for conservation in other regions of the Western Ghats.

Collective eigenstates of emission in an N-entity heterostructure and the evaluation of its Green tensors and self-energy components

Optical emission from emitters strongly interacting among themselves and also with other polarizable matter in close proximity has been approximated by emission from independent emitters. This is primarily due to our inability to evaluate the self-energy matrices and radiative properties of the collective eigenstates of emitters in heterogeneous ensembles. A method to evaluate self-energy matrices that is not limited by the geometry and material composition is presented to understand and exploit such collective excitations. Numerical evaluations using this method are used to highlight the significant differences between independent and the collective modes of emission in nanoscale heterostructures. A set of N Lorentz emitters and other polarizable entities is used to represent the coupled system of a generalized geometry in a volume integral approach. Closed form relations between the Green tensors of entity pairs in free space and their correspondents in a heterostructure are derived concisely. This is made possible for general geometries because the global matrices consisting of all free-space Green dyads are subject to conservation laws. The self-energy matrix can then be assembled using the evaluated Green tensors of the heterostructure, but a decomposition of its components into their radiative and nonradiative decay contributions is nontrivial. The relations to compute the observables of the eigenstates (such as quantum efficiency, power/energy of emission, radiative and nonradiative decay rates) are presented. A note on extension of this method to collective excitations, which also includes strong interactions with a surface in the near-field, is added. (C) 2014 Optical Society of America

Medium-Voltage Drive for Induction Machine With Multilevel Dodecagonal Voltage Space Vectors With Symmetric Triangles

Multilevel inverters with dodecagonal (12-sided polygon) voltage space vector structure have advantages, such as complete elimination of fifth and seventh harmonics, reduction in electromagnetic interference, reduction in device voltage ratings, reduction of switching frequency, extension of linear modulation range, etc., making it a viable option for high-power medium-voltage drives. This paper proposes two power circuit topologies capable of generating multilevel dodecagonal voltage space vector structure with symmetric triangles (for the first time) with minimum number of dc-link power supplies and floating capacitor H-bridges. The first power topology is composed of two hybrid cascaded five-level inverters connected to either side of an open-end winding induction machine. Each inverter consists of a three-level neutral-point-clamped inverter, which is cascaded with an isolated H-bridge making it a five-level inverter. The second topology is for a normal induction motor. Both of these circuit topologies have inherent capacitor balancing for floating H-bridges for all modulation indexes, including transient operations. The proposed topologies do not require any precharging circuitry for startup. A simple pulsewidth modulation timing calculation method for space vector modulation is also presented in this paper. Due to the symmetric arrangement of congruent triangles within the voltage space vector structure, the timing computation requires only the sampled reference values and does not require any offline computation, lookup tables, or angle computation. Experimental results for steady-state operation and transient operation are also presented to validate the proposed concept.

A Grassmann path from AdS(3) to flat space

We show that interpreting the inverse AdS(3) radius 1/l as a Grassmann variable results in a formal map from gravity in AdS(3) to gravity in flat space. The underlying reason for this is the fact that ISO(2, 1) is the Inonu-Wigner contraction of SO(2, 2). We show how this works for the Chern-Simons actions, demonstrate how the general (Banados) solution in AdS(3) maps to the general flat space solution, and how the Killing vectors, charges and the Virasoro algebra in the Brown-Henneaux case map to the corresponding quantities in the BMS3 case. Our results straightforwardly generalize to the higher spin case: the recently constructed flat space higher spin theories emerge automatically in this approach from their AdS counterparts. We conclude with a discussion of singularity resolution in the BMS gauge as an application.

Identifying regions for conservation of sloth bears through occupancy modelling in north-eastern Karnataka, India

In the absence of information on species in decline with contracting ranges, management should emphasize remaining populations and protection of their habitats. Threatened by anthropogenic pressure including habitat degradation and loss, sloth bears (Melursus ursinus) in India have become limited in range, habitat, and population size. We identified ecological and anthropogenic determinants of occurrence within an occupancy framework to evaluate habitat suitability of non-protected regions (with sloth bears) in northeastern Karnataka, India. We employed a systematic sampling methodology to yield presence absence data to examine a priori hypotheses of determinants that affected occupancy. These covariates were broadly classified as habitat or anthropogenic factors. Mean number of termite mounds and trees positively influenced sloth bear occupancy, and grazing pressure expounded by mean number of livestock dung affected it negatively. Also, mean percentage of shrub coverage had no impact on bear inhabitance. The best fitting model further predicted habitats in Bukkasagara, Agoli, and Benakal reserved forests to have 38%, 75%, and 88%, respectively, of their sampled grid cells with high occupancies (>0.70) albeit little or no legal protection. We recommend a conservation strategy that includes protection of vegetation stand-structure, maintenance of soil moisture, and enrichment of habitat for the long-term welfare of this species.

Monitoring urbanization and its implications in a mega city from space: Spatiotemporal patterns and its indicators

Rapid and invasive urbanization has been associated with depletion of natural resources (vegetation and water resources), which in turn deteriorates the landscape structure and conditions in the local environment. Rapid increase in population due to the migration from rural areas is one of the critical issues of the urban growth. Urbanisation in India is drastically changing the land cover and often resulting in the sprawl. The sprawl regions often lack basic amenities such as treated water supply, sanitation, etc. This necessitates regular monitoring and understanding of the rate of urban development in order to ensure the sustenance of natural resources. Urban sprawl is the extent of urbanization which leads to the development of urban forms with the destruction of ecology and natural landforms. The rate of change of land use and extent of urban sprawl can be efficiently visualized and modelled with the help of geo-informatics. The knowledge of urban area, especially the growth magnitude, shape geometry, and spatial pattern is essential to understand the growth and characteristics of urbanization process. Urban pattern, shape and growth can be quantified using spatial metrics. This communication quantifies the urbanisation and associated growth pattern in Delhi. Spatial data of four decades were analysed to understand land over and land use dynamics. Further the region was divided into 4 zones and into circles of 1 km incrementing radius to understand and quantify the local spatial changes. Results of the landscape metrics indicate that the urban center was highly aggregated and the outskirts and the buffer regions were in the verge of aggregating urban patches. Shannon's Entropy index clearly depicted the outgrowth of sprawl areas in different zones of Delhi. (C) 2014 Elsevier Ltd. All rights reserved.

Performance Analysis of Space-Shift Keying in Decode-and-Forward Multihop MIMO Networks

In this paper, space-shift keying (SSK) is considered for multihop multiple-input-multiple-output (MIMO) networks. In SSK, only one among n(s) = 2(m) available transmit antennas, chosen on the basis of m information bits, is activated during transmission. We consider two different systems of multihop co-operation, where each node has multiple antennas and employs SSK. In system I, a multihop diversity relaying scheme is considered. In system II, a multihop multibranch relaying scheme is considered. In both systems, we adopt decode-and-forward (DF) relaying, where each relay forwards the signal only when it correctly decodes. We analyze the end-to-end bit error rate (BER) and diversity order of both the systems with SSK. For binary SSK (n(s) = 2), our analytical BER expression is exact, and our numerical results show that the BERs evaluated through the analytical expression overlap with those obtained through Monte Carlo simulations. For nonbinary SSK (n(s) > 2), we derive an approximate BER expression, where the analytically evaluated BER results closely follow the simulated BER results. We show the comparison of the BERs of SSK and conventional phase-shift keying (PSK) and also show the instances where SSK outperforms PSK. We also present the diversity analyses for SSK in systems I and II, which predict the achievable diversity orders as a function of system parameters.

Space-Vector-Based Hybrid PWM Technique to Reduce Peak-to-Peak Torque Ripple in Induction Motor Drives

Special switching sequences involving division of active state time are used in space-vector-based generation of pulse width modulation (PWM) waveforms. This paper proposes a hybrid PWM technique which is a combination of the conventional and special switching sequences. The proposed hybrid PWM technique reduces the peak-to-peak torque ripple at high speeds of an induction motor drive. Supporting simulation and experimental results are presented from a closed-loop controlled motor drive.

Space-Time Coded Spatial Modulated Physical Layer Network Coding for Two-Way Relaying

Using the spatial modulation approach, where only one transmit antenna is active at a time, we propose two transmission schemes for two-way relay channel using physical layer network coding with space time coding using coordinate interleaved orthogonal designs (CIODs). It is shown that using two uncorrelated transmit antennas at the nodes, but using only one RF transmit chain and space-time coding across these antennas can give a better performance without using any extra resources and without increasing the hardware implementation cost and complexity. In the first transmission scheme, two antennas are used only at the relay, adaptive network coding (ANC) is employed at the relay and the relay transmits a CIOD space time block code (STBC). This gives a better performance compared to an existing ANC scheme for two-way relay channel which uses one antenna each at all the three nodes. It is shown that for this scheme at high SNR the average end-to-end symbol error probability (SEP) is upper bounded by twice the SEP of a point-to-point fading channel. In the second transmission scheme, two transmit antennas are used at all the three nodes, CIOD STBCs are transmitted in multiple access and broadcast phases. This scheme provides a diversity order of two for the average end-to-end SEP with an increased decoding complexity of O(M-3) for an arbitrary signal set and O(M-2 root M) for square QAM signal set. Simulation results show that the proposed schemes performs better than the existing ANC schemes under perfect and imperfect channel state information.