Improvement of protein structure comparison using a structural alphabet

The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBS) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment. (C) 2011 Elsevier Masson SAS. All rights reserved.

A comparison of the structure of liquid alloys derived from thermodynamic and diffraction studies

A significant amount of research on the thermodynamic properties of molten alloys is undertaken for obtaining insights into their structure . The partial and integral molar enthalpies, entropies and volumes of mixing provide some general information on the nature and strength of atomic bonds and the distribution of atoms. However, until recently it has been difficult to derive specific quantitative information because the excess entropy of mixing contains configurational , vibrational , electronic , and sometimes magnetic contributions which cannot be easily separated.

New possibilities in amplitude- and phase-comparison techniques for distance relays

The paper reports further work on the amplitude-comparison technique described by the same authors in a previous paper. This technique is extended to develop improved polar characteristics. Discontinuous polar characteristics, like directional parallelograms, are obtained by a single measuring gate with a simple mode of relay circuitry, whereas two measuring gates are required to provide a directional-quadrilateral characteristic of potentially general application. The paper also describes some new possibilities in phase-comparison methods for distance-protection schemes. Comparator models which effect the amplitude and phase comparison of the relaying signals are described in their schematic form. A comprehensive theoretical basis for comparison is also presented.

Dry tribology and nanomechanics of gaseous flame soot in comparison with carbon black and diesel soot

Ethylene gas is burnt and the carbon soot particles are thermophoretically collected using a home-built equipment where the fuel air injection and intervention into the 7.5-cm long flame are controlled using three small pneumatic cylinders and computer-driven controllers. The physical and mechanical properties and tribological performance of the collected soot are compared with those of carbon black and diesel soot. The crystalline structures of the nanometric particles generated in the flame, as revealed by high-resolution transmission electron studies, are shown to vary from the flame root to the exhaust. As the particle journeys upwards the flame, through a purely amorphous coagulated phase at the burner nozzle, it leads to a well-defined crystalline phase shell in the mid-flame zone and to a disordered phase consisting of randomly distributed short-range crystalline order at the exhaust. In the mid-flame region, a large shell of radial-columnar order surrounds a dense amorphous core. The hardness and wear resistance as well as friction coefficient of the soot extracted from this zone are low. The mechanical properties characteristics of this zone may be attributed to microcrystalline slip. Moving towards the exhaust, the slip is inhibited and there is an increase in hardness and friction compared to those in the mid-flame zone. This study of the comparison of flame soot to carbon black and diesel soot is further extended to suggest a rationale based on additional physico-chemical study using micro-Raman spectroscopy.

Quantifying Vocal Mimicry in the Greater Racket-Tailed Drongo: A Comparison of Automated Methods and Human Assessment

Objective identification and description of mimicked calls is a primary component of any study on avian vocal mimicry but few studies have adopted a quantitative approach. We used spectral feature representations commonly used in human speech analysis in combination with various distance metrics to distinguish between mimicked and non-mimicked calls of the greater racket-tailed drongo, Dicrurus paradiseus and cross-validated the results with human assessment of spectral similarity. We found that the automated method and human subjects performed similarly in terms of the overall number of correct matches of mimicked calls to putative model calls. However, the two methods also misclassified different subsets of calls and we achieved a maximum accuracy of ninety five per cent only when we combined the results of both the methods. This study is the first to use Mel-frequency Cepstral Coefficients and Relative Spectral Amplitude - filtered Linear Predictive Coding coefficients to quantify vocal mimicry. Our findings also suggest that in spite of several advances in automated methods of song analysis, corresponding cross-validation by humans remains essential.

Long-Term Monitoring of Ecological Conditions In Gray’s Reef National Marine Sanctuary: Comparison of soft-bottom benthic assemblages and contaminant levels in sediments and biota in Spring 2000 and 2005

As part of an ongoing program of benthic sampling and related assessments of sediment quality at Gray’s Reef National Marine Sanctuary (GRNMS) off the coast of Georgia, a survey of soft-bottom benthic habitats was conducted in spring 2005 to characterize condition of macroinfaunal assemblages and levels of chemical contaminants in sediments and biota relative to a baseline survey carried out in spring 2000. Distribution and abundance of macrobenthos were related foremost to sediment type (median particle size, % gravel), which in turn varied according to bottom-habitat mesoscale features (e.g., association with live bottom versus flat or rippled sand areas). Overall abundance and diversity of soft-bottom benthic communities were similar between the two years, though dominance patterns and relative abundances of component species were less repeatable. Seasonal summer pulses of a few taxa (e.g., the bivalve Ervilia sp. A) observed in 2000 were not observed in 2005. Concentrations of chemical contaminants in sediments and biota, though detectable in both years, were consistently at low, background levels and no exceedances of sediment probable bioeffect levels or FDA action levels for edible fish or shellfish were observed. Near-bottom dissolved oxygen levels and organic-matter content of sediments also have remained within normal ranges. Highly diverse benthic assemblages were found in both years, supporting the premise that GRNMS serves as an important reservoir of marine biodiversity. A total of 353 taxa (219 identified to species) were collected during the spring 2005 survey. Cumulatively, 588 taxa (371 identified to species) have been recorded in the sanctuary from surveys in 2000, 2001, 2002, and 2005. Species Accumulation Curves indicate that the theoretical maximum should be in excess of 600 species. Results of this study will be of value in advancing strategic science and management goals for GRNMS, including characterization and long-term monitoring of sanctuary resources and processes, as well as supporting evolving interests in ecosystem-based management of the surrounding South Atlantic Bight (SAB) ecosystem. (PDF contains 46 pages)

Biotic vs. Abiotic Control of Decomposition: A Comparison of the Effects of Simulated Extinctions and Changes in Temperature

The loss of species is known to have significant effects on ecosystem functioning, but only recently has it been recognized that species loss might rival the effects of other forms of environmental change on ecosystem processes. There is a need for experimental studies that explicitly manipulate species richness and environmental factors concurrently to determine their relative impacts on key ecosystem processes such as plant litter decomposition. It is crucial to understand what factors affect the rate of plant litter decomposition and the relative magnitude of such effects because the rate at which plant litter is lost and transformed to other forms of organic and inorganic carbon determines the capacity for carbon storage in ecosystems and the rate at which greenhouse gasses such as carbon dioxide are outgassed. Here we compared how an increase in water temperature of 5 degrees C and loss of detritivorous invertebrate and plant litter species affect decomposition rates in a laboratory experiment simulating stream conditions. Like some prior studies, we found that species identity, rather than species richness per se, is a key driver of decomposition, but additionally we showed that the loss of particular species can equal or exceed temperature change in its impact on decomposition. Our results indicate that the loss of particular species can be as important a driver of decomposition as substantial temperature change, but also that predicting the relative consequences of species loss and other forms of environmental change on decomposition requires knowledge of assemblages and their constituent species' ecology and ecophysiology.

Chemical and mineralogical characterization of micro-inclusions in diamonds

Secondary-ion mass spectrometry (SIMS), electron probe analysis (EPMA), analytical scanning electron microscopy (SEM) and infrared (IR) spectroscopy were used to determine the chemical composition and the mineralogy of sub-micrometer inclusions in cubic diamonds and in overgrowths (coats) on octahedral diamonds from Zaire, Botswana, and some unknown localities.

The inclusions are sub-micrometer in size. The typical diameter encountered during transmission electron microscope (TEM) examination was 0.1-0.5 µm. The micro-inclusions are sub-rounded and their shape is crystallographically controlled by the diamond. Normally they are not associated with cracks or dislocations and appear to be well isolated within the diamond matrix. The number density of inclusions is highly variable on any scale and may reach 10^(11) inclusions/cm^3 in the most densely populated zones. The total concentration of metal oxides in the diamonds varies between 20 and 1270 ppm (by weight).

SIMS analysis yields the average composition of about 100 inclusions contained in the sputtered volume. Comparison of analyses of different volumes of an individual diamond show roughly uniform composition (typically ±10% relative). The variation among the average compositions of different diamonds is somewhat greater (typically ±30%). Nevertheless, all diamonds exhibit similar characteristics, being rich in water, carbonate, SiO_2, and K_2O, and depleted in MgO. The composition of micro-inclusions in most diamonds vary within the following ranges: SiO_2, 30-53%; K_2O, 12-30%; CaO, 8-19%; FeO, 6-11%; Al_2O_3, 3-6%; MgO, 2-6%; TiO_2, 2-4%; Na_2O, 1-5%; P_2O_5, 1-4%; and Cl, 1-3%. In addition, BaO, 1-4%; SrO, 0.7-1.5%; La_2O_3, 0.1-0.3%; Ce_2O_3, 0.3-0.5%; smaller amounts of other rare-earth elements (REE), as well as Mn, Th, and U were also detected by instrumental neutron activation analysis (INAA). Mg/(Fe+Mg), 0.40-0.62 is low compared with other mantle derived phases; K/ AI ratios of 2-7 are very high, and the chondrite-normalized Ce/Eu ratios of 10-21 are also high, indicating extremely fractionated REE patterns.

SEM analyses indicate that individual inclusions within a single diamond are roughly of similar composition. The average composition of individual inclusions as measured with the SEM is similar to that measured by SIMS. Compositional variations revealed by the SEM are larger than those detected by SIMS and indicate a small variability in the composition of individual inclusions. No compositions of individual inclusions were determined that might correspond to mono-mineralic inclusions.

IR spectra of inclusion- bearing zones exhibit characteristic absorption due to: (1) pure diamonds, (2) nitrogen and hydrogen in the diamond matrix; and (3) mineral phases in the micro-inclusions. Nitrogen concentrations of 500-1100 ppm, typical of the micro-inclusion-bearing zones, are higher than the average nitrogen content of diamonds. Only type IaA centers were detected by IR. A yellow coloration may indicate small concentration of type IB centers.

The absorption due to the micro-inclusions in all diamonds produces similar spectra and indicates the presence of hydrated sheet silicates (most likely, Fe-rich clay minerals), carbonates (most likely calcite), and apatite. Small quantities of molecular CO_2 are also present in most diamonds. Water is probably associated with the silicates but the possibility of its presence as a fluid phase cannot be excluded. Characteristic lines of olivine, pyroxene and garnet were not detected and these phases cannot be significant components of the inclusions. Preliminary quantification of the IR data suggests that water and carbonate account for, on average, 20-40 wt% of the micro-inclusions.

The composition and mineralogy of the micro-inclusions are completely different from those of the more common, larger inclusions of the peridotitic or eclogitic assemblages. Their bulk composition resembles that of potassic magmas, such as kimberlites and lamproites, but is enriched in H_2O, CO_3, K_2O, and incompatible elements, and depleted in MgO.

It is suggested that the composition of the micro-inclusions represents a volatile-rich fluid or a melt trapped by the diamond during its growth. The high content of K, Na, P, and incompatible elements suggests that the trapped material found in the micro-inclusions may represent an effective metasomatizing agent. It may also be possible that fluids of similar composition are responsible for the extreme enrichment of incompatible elements documented in garnet and pyroxene inclusions in diamonds.

The origin of the fluid trapped in the micro-inclusions is still uncertain. It may have been formed by incipient melting of a highly metasomatized mantle rocks. More likely, it is the result of fractional crystallization of a potassic parental magma at depth. In either case, the micro-inclusions document the presence of highly potassic fluids or melts at depths corresponding to the diamond stability field in the upper mantle. The phases presently identified in the inclusions are believed to be the result of closed system reactions at lower pressures.

Value Estimation and Comparison in Multi-Attribute Choice

The following work explores the processes individuals utilize when making multi-attribute choices. With the exception of extremely simple or familiar choices, most decisions we face can be classified as multi-attribute choices. In order to evaluate and make choices in such an environment, we must be able to estimate and weight the particular attributes of an option. Hence, better understanding the mechanisms involved in this process is an important step for economists and psychologists. For example, when choosing between two meals that differ in taste and nutrition, what are the mechanisms that allow us to estimate and then weight attributes when constructing value? Furthermore, how can these mechanisms be influenced by variables such as attention or common physiological states, like hunger?

In order to investigate these and similar questions, we use a combination of choice and attentional data, where the attentional data was collected by recording eye movements as individuals made decisions. Chapter 1 designs and tests a neuroeconomic model of multi-attribute choice that makes predictions about choices, response time, and how these variables are correlated with attention. Chapter 2 applies the ideas in this model to intertemporal decision-making, and finds that attention causally affects discount rates. Chapter 3 explores how hunger, a common physiological state, alters the mechanisms we utilize as we make simple decisions about foods.

A comparison of the costs of operation of the motor bus, Birney safety car, and trolley bus on the local transportation routes in Pasadena

With the installation by the Pacific Electric Railway of a bus system in Pasadena to supplant most of its trolley lines, the problem of the comparison of the costs of the two systems naturally presented itself. The study here undertaken was originally started as just a comparison of the motor bus and Birney Safety Car, but as the work progressed it seemed advisable to include the trolley bus as well - a method of transportation that is comparatively new as far as development is concerned, but which seems to be finding increasing favor in the East.

I. Fundamental limitations in microelectronics. II. Power Schottky diode design and comparison with the junction diode. III. Permittivity of strontium titanate

Part I

The physical phenomena which will ultimately limit the packing density of planar bipolar and MOS integrated circuits are examined. The maximum packing density is obtained by minimizing the supply voltage and the size of the devices. The minimum size of a bipolar transistor is determined by junction breakdown, punch-through and doping fluctuations. The minimum size of a MOS transistor is determined by gate oxide breakdown and drain-source punch-through. The packing density of fully active bipolar or static non-complementary MOS circuits becomes limited by power dissipation. The packing density of circuits which are not fully active such as read-only memories, becomes limited by the area occupied by the devices, and the frequency is limited by the circuit time constants and by metal migration. The packing density of fully active dynamic or complementary MOS circuits is limited by the area occupied by the devices, and the frequency is limited by power dissipation and metal migration. It is concluded that read-only memories will reach approximately the same performance and packing density with MOS and bipolar technologies, while fully active circuits will reach the highest levels of integration with dynamic MOS or complementary MOS technologies.

Part II

Because the Schottky diode is a one-carrier device, it has both advantages and disadvantages with respect to the junction diode which is a two-carrier device. The advantage is that there are practically no excess minority carriers which must be swept out before the diode blocks current in the reverse direction, i.e. a much faster recovery time. The disadvantage of the Schottky diode is that for a high voltage device it is not possible to use conductivity modulation as in the p i n diode; since charge carriers are of one sign, no charge cancellation can occur and current becomes space charge limited. The Schottky diode design is developed in Section 2 and the characteristics of an optimally designed silicon Schottky diode are summarized in Fig. 9. Design criteria and quantitative comparison of junction and Schottky diodes is given in Table 1 and Fig. 10. Although somewhat approximate, the treatment allows a systematic quantitative comparison of the devices for any given application.

Part III

We interpret measurements of permittivity of perovskite strontium titanate as a function of orientation, temperature, electric field and frequency performed by Dr. Richard Neville. The free energy of the crystal is calculated as a function of polarization. The Curie-Weiss law and the LST relation are verified. A generalized LST relation is used to calculate the permittivity of strontium titanate from zero to optic frequencies. Two active optic modes are important. The lower frequency mode is attributed mainly to motion of the strontium ions with respect to the rest of the lattice, while the higher frequency active mode is attributed to motion of the titanium ions with respect to the oxygen lattice. An anomalous resonance which multi-domain strontium titanate crystals exhibit below 65°K is described and a plausible mechanism which explains the phenomenon is presented.

Solar flare particle propagation--comparison of a new analytic solution with spacecraft measurements

A new analytic solution has been obtained to the complete Fokker-Planck equation for solar flare particle propagation including the effects of convection, energy-change, corotation, and diffusion with ĸ_r = constant and ĸ_Ɵ ∝ r². It is assumed that the particles are injected impulsively at a single point in space, and that a boundary exists beyond which the particles are free to escape. Several solar flare particle events have been observed with the Caltech Solar and Galactic Cosmic Ray Experiment aboard OGO-6. Detailed comparisons of the predictions of the new solution with these observations of 1-70 MeV protons show that the model adequately describes both the rise and decay times, indicating that ĸ_r = constant is a better description of conditions inside 1 AU than is ĸ_r ∝ r. With an outer boundary at 2.7 AU, a solar wind velocity of 400 km/sec, and a radial diffusion coefficient ĸ_r ≈ 2-8 x 10²⁰ cm²/sec, the model gives reasonable fits to the time-profile of 1-10 MeV protons from "classical" flare-associated events. It is not necessary to invoke a scatter-free region near the sun in order to reproduce the fast rise times observed for directly-connected events. The new solution also yields a time-evolution for the vector anisotropy which agrees well with previously reported observations.

In addition, the new solution predicts that, during the decay phase, a typical convex spectral feature initially at energy T_o will move to lower energies at an exponential rate given by T_KINK = T_oexp(-t/Ƭ_KINK). Assuming adiabatic deceleration and a boundary at 2.7 AU, the solution yields Ƭ_KINK ≈ 100h, which is faster than the measured ~200h time constant and slower than the adiabatic rate of ~78h at 1 AU. Two possible explanations are that the boundary is at ~5 AU or that some other energy-change process is operative.

Biotic vs. Abiotic Control of Decomposition: A Comparison of the Effects of Simulated Extinctions and Changes in Temperature

The loss of species is known to have significant effects on ecosystem functioning, but only recently has it been recognized that species loss might rival the effects of other forms of environmental change on ecosystem processes. There is a need for experimental studies that explicitly manipulate species richness and environmental factors concurrently to determine their relative impacts on key ecosystem processes such as plant litter decomposition. It is crucial to understand what factors affect the rate of plant litter decomposition and the relative magnitude of such effects because the rate at which plant litter is lost and transformed to other forms of organic and inorganic carbon determines the capacity for carbon storage in ecosystems and the rate at which greenhouse gasses such as carbon dioxide are outgassed. Here we compared how an increase in water temperature of 5 degrees C and loss of detritivorous invertebrate and plant litter species affect decomposition rates in a laboratory experiment simulating stream conditions. Like some prior studies, we found that species identity, rather than species richness per se, is a key driver of decomposition, but additionally we showed that the loss of particular species can equal or exceed temperature change in its impact on decomposition. Our results indicate that the loss of particular species can be as important a driver of decomposition as substantial temperature change, but also that predicting the relative consequences of species loss and other forms of environmental change on decomposition requires knowledge of assemblages and their constituent species' ecology and ecophysiology

Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation

We analysed the whole-genome transcriptional profile of 6 cell lines of dark melanocytes (DM) and 6 of light melanocytes (LM) at basal conditions and after ultraviolet-B (UVB) radiation at different time points to investigate the mechanisms by which melanocytes protect human skin from the damaging effects of UVB. Further, we assessed the effect of different keratinocyte-conditioned media (KCM+ and KCM-) on melanocytes. Our results suggest that an interaction between ribosomal proteins and the P53 signaling pathway may occur in response to UVB in both DM and LM. We also observed that DM and LM show differentially expressed genes after irradiation, in particular at the first 6h after UVB. These are mainly associated with inflammatory reactions, cell survival or melanoma. Furthermore, the culture with KCM+ compared with KCM- had a noticeable effect on LM. This effect includes the activation of various signaling pathways such as the mTOR pathway, involved in the regulation of cell metabolism, growth, proliferation and survival. Finally, the comparison of the transcriptional profiles between LM and DM under basal conditions, and the application of natural selection tests in human populations allowed us to support the significant evolutionary role of MIF and ATP6V0B in the pigmentary phenotype.

Mechanisms of Toxicity of Ag Nanoparticles in Comparison to Bulk and Ionic Ag on Mussel Hemocytes and Gill Cells

Silver nanoparticles (Ag NPs) are increasingly used in many products and are expected to end up in the aquatic environment. Mussels have been proposed as marine model species to evaluate NP toxicity in vitro. The objective of this work was to assess the mechanisms of toxicity of Ag NPs on mussel hemocytes and gill cells, in comparison to ionic and bulk Ag. Firstly, cytotoxicity of commercial and maltose stabilized Ag NPs was screened in parallel with the ionic and bulk forms at a wide range of concentrations in isolated mussel cells using cell viability assays. Toxicity of maltose alone was also tested. LC50 values were calculated and the most toxic Ag NPs tested were selected for a second step where sublethal concentrations of each Ag form were tested using a wide array of mechanistic tests in both cell types. Maltose-stabilized Ag NPs showed size-dependent cytotoxicity, smaller (20 nm) NPs being more toxic than larger (40 and 100 nm) NPs. Maltose alone provoked minor effects on cell viability. Ionic Ag was the most cytotoxic Ag form tested whereas bulk Ag showed similar cytotoxicity to the commercial Ag NPs. Main mechanisms of action of Ag NPs involved oxidative stress and genotoxicity in the two cell types, activation of lysosomal AcP activity, disruption of actin cytoskeleton and stimulation of phagocytosis in hemocytes and increase of MXR transport activity and inhibition of Na-K-ATPase in gill cells. Similar effects were observed after exposure to ionic and bulk Ag in the two cell types, although generally effects were more marked for the ionic form. In conclusion, results suggest that most observed responses were due at least in part to dissolved Ag.