Sparsely populated residue conformations in protein structures: Revisiting ``experimental'' Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (phi-) space for amino acid residues in proteins. Experimental distributions of phi, values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely arid, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of phi- space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in hairpins. The strand-helix motif with the Type II turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101-1112. (c) 2013 Wiley Periodicals, Inc.

PROPER HOLOMORPHIC MAPS BETWEEN BOUNDED SYMMETRIC DOMAINS REVISITED

We prove that a proper holomorphic map between two nonplanar bounded symmetric domains of the same dimension, one of them being irreducible, is a biholomorphism. Our methods allow us to give a single, all-encompassing argument that unifies the various special cases in which this result is known. We discuss an application of these methods to domains having noncompact automorphism groups that are not assumed to act transitively.

Dendritic atrophy constricts functional maps in resonance and impedance properties of hippocampal model neurons

A gradient in the density of hyperpolarization-activated cyclic-nucleotide gated (HCN) channels is necessary for the emergence of several functional maps within hippocampal pyramidal neurons. Here, we systematically analyzed the impact of dendritic atrophy on nine such functional maps, related to input resistance and local/transfer impedance properties, using conductance-based models of hippocampal pyramidal neurons. We introduced progressive dendritic atrophy in a CA1 pyramidal neuron reconstruction through a pruning algorithm, measured all functional maps in each pruned reconstruction, and arrived at functional forms for the dependence of underlying measurements on dendritic length. We found that, across frequencies, atrophied neurons responded with higher efficiency to incoming inputs, and the transfer of signals across the dendritic tree was more effective in an atrophied reconstruction. Importantly, despite the presence of identical HCN-channel density gradients, spatial gradients in input resistance, local/transfer resonance frequencies and impedance profiles were significantly constricted in reconstructions with dendrite atrophy, where these physiological measurements across dendritic locations converged to similar values. These results revealed that, in atrophied dendritic structures, the presence of an ion channel density gradient alone was insufficient to sustain homologous functional maps along the same neuronal topograph. We assessed the biophysical basis for these conclusions and found that this atrophy-induced constriction of functional maps was mediated by an enhanced spatial spread of the influence of an HCN-channel cluster in atrophied trees. These results demonstrated that the influence fields of ion channel conductances need to be localized for channel gradients to express themselves as homologous functional maps, suggesting that ion channel gradients are necessary but not sufficient for the emergence of functional maps within single neurons.

Seismic hazard maps and spectrum for Patna considering region-specific seismotectonic parameters

The objective of this paper was to develop the seismic hazard maps of Patna district considering the region-specific maximum magnitude and ground motion prediction equation (GMPEs) by worst-case deterministic and classical probabilistic approaches. Patna, located near Himalayan active seismic region has been subjected to destructive earthquakes such as 1803 and 1934 Bihar-Nepal earthquakes. Based on the past seismicity and earthquake damage distribution, linear sources and seismic events have been considered at radius of about 500 km around Patna district center. Maximum magnitude (M (max)) has been estimated based on the conventional approaches such as maximum observed magnitude (M (max) (obs) ) and/or increment of 0.5, Kijko method and regional rupture characteristics. Maximum of these three is taken as maximum probable magnitude for each source. Twenty-seven ground motion prediction equations (GMPEs) are found applicable for Patna region. Of these, suitable region-specific GMPEs are selected by performing the `efficacy test,' which makes use of log-likelihood. Maximum magnitude and selected GMPEs are used to estimate PGA and spectral acceleration at 0.2 and 1 s and mapped for worst-case deterministic approach and 2 and 10 % period of exceedance in 50 years. Furthermore, seismic hazard results are used to develop the deaggregation plot to quantify the contribution of seismic sources in terms of magnitude and distance. In this study, normalized site-specific design spectrum has been developed by dividing the hazard map into four zones based on the peak ground acceleration values. This site-specific response spectrum has been compared with recent Sikkim 2011 earthquake and Indian seismic code IS1893.

NON-DIMENSIONAL KINETOELASTOSTATIC MAPS FOR COMPLIANT MECHANISMS

How do we assess the capability of a compliant mechanism of given topology and shape? The kinetoelastostatic maps proposed in this paper help answer this question. These maps are drawn in 2D using two non-dimensional quantities, one capturing the nonlinear static response and the other the geometry, material, and applied forces. Geometrically nonlinear finite element analysis is used to create the maps for compliant mechanisms consisting of slender beams. In addition to the topology and shape, the overall proportions and the proportions of the cross-sections of the beam segments are kept fixed for a map. The finite region of the map is parameterized using a non-dimensional quantity defined as the slenderness ratio. The shape and size of the map and the parameterized curves inside it indicate the complete kinetoelastostatic capability of the corresponding compliant mechanism of given topology, shape, and fixed proportions. Static responses considered in this paper include input/output displacement, geometric amplification, mechanical advantage, maximum stress, etc. The maps can be used to compare mechanisms, to choose a suitable mechanism for an application, or re-design as may be needed. The usefulness of the non-dimensional maps is presented with multiple applications of different variety. Non-dimensional portrayal of snap-through mechanisms is one such example. The effect of the shape of the cross-section of the beam segments and the role of different segments in the mechanism as well as extension to 3D compliant mechanisms, the cases of multiple inputs and outputs, and moment loads are also explained. The effects of disproportionate changes on the maps are also analyzed.

Synchronous chaos in the coupled system of two logistic maps

Synchronous chaos is investigated in the coupled system of two Logistic maps. Although the diffusive coupling admits all synchronized motions, the stabilities of their configurations are dependent on the transverse Lyapunov exponents while independent of the longitudinal Lyapunov exponents. It is shown that synchronous chaos is structurally stable with respect to the system parameters. The mean motion is the pseudo-orbit of an individual local map so that its dynamics can be described by the local map. (C) 2004 Elsevier Ltd. All rights reserved.

Tracking the evolution of waste recycling research using overlay maps of science

Tracking the evolution of research in waste recycling science (WRS) can be valuable for environmental agencies, as well as for recycling businesses. Maps of science are visual, easily readable representations of the cognitive structure of a branch of science, a particular area of research or the global spectrum of scientific production. They are generally built upon evidence collected from reliable sources of information, such as patent and scientific publication databases. This study uses the methodology developed by Rafols et al. (2010) to make a “double overlay map” of WRS upon a basemap reflecting the cognitive structure of all journal-published science, for the years 2005 and 2010. The analysis has taken into account the cognitive areas where WRS articles are published and the areas from where it takes its intellectual nourishing, paying special attention to the growing trends of the key areas. Interpretation of results lead to the conclusion that extraction of energy from waste will probably be an important research topic in the future, along with developments in general chemistry and chemical engineering oriented to the recovery of valuable materials from waste. Agricultural and material sciences, together with the combined economics, politics and geography field, are areas with which WRS shows a relevant and ever increasing cognitive relationship.

An Extension of Self-Organizing Maps to Categorical Data

Self-organizing maps (SOM) have been recognized as a powerful tool in data exploratoration, especially for the tasks of clustering on high dimensional data. However, clustering on categorical data is still a challenge for SOM. This paper aims to extend standard SOM to handle feature values of categorical type. A batch SOM algorithm (NCSOM) is presented concerning the dissimilarity measure and update method of map evolution for both numeric and categorical features simultaneously.

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example, management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things a description of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)