Parametric study of the behavior of double toggle switching mechanisms

The paper identified and characterized a special multi-degree of freedom toggle behavior, called double toggle, observed in a typical MCCB switching mechanism. For an idealized system, the condition of toggle sequence is derived geometrically. The existing tools available in a multi-body dynamics package are used for exploring the dynamic behavior of such systems parametrically. The double toggle mechanism is found to make the system insensitive to the operator's behavior; however, the system is vulnerable under extreme usage. The linkage kinematics and stopper locations are found to have dominant role on the behavior of the system. It is revealed that the operating time is immune to the inertial property of the input link and sensitive to that of the output link. Novel designs exploiting this observation, in terms of spring and toggle placements, to enhance switching performance have also been reported in the paper. Detailed study revealed that strategic placement of the spring helps in selective alteration of system performance. Thus, the study establishes the critical importance of the kinematic design of MCCB over the dynamic parameters. (C) 2013 Elsevier Ltd. All rights reserved.

Effect of amplitude correlations on coherence in the local field potential

Neural activity across the brain shows both spatial and temporal correlations at multiple scales, and understanding these correlations is a key step toward understanding cortical processing. Correlation in the local field potential (LFP) recorded from two brain areas is often characterized by computing the coherence, which is generally taken to reflect the degree of phase consistency across trials between two sites. Coherence, however, depends on two factors-phase consistency as well as amplitude covariation across trials-but the spatial structure of amplitude correlations across sites and its contribution to coherence are not well characterized. We recorded LFP from an array of microelectrodes chronically implanted in the primary visual cortex of monkeys and studied correlations in amplitude across electrodes as a function of interelectrode distance. We found that amplitude correlations showed a similar trend as coherence as a function of frequency and interelectrode distance. Importantly, even when phases were completely randomized between two electrodes, amplitude correlations introduced significant coherence. To quantify the contributions of phase consistency and amplitude correlations to coherence, we simulated pairs of sinusoids with varying phase consistency and amplitude correlations. These simulations confirmed that amplitude correlations can significantly bias coherence measurements, resulting in either over-or underestimation of true phase coherence. Our results highlight the importance of accounting for the correlations in amplitude while using coherence to study phase relationships across sites and frequencies.

Importance of structural distortions in enhancement of transition temperature in FeSe1-xTex superconductors

Temperature (12 K <= T <= 300 K) dependent extended x-ray absorption fine structure (EXAFS) studies at the Fe K edge in FeSe1-xTex (x = 0, 0.5 and 1.0) compounds have been carried out to understand the reasons for the increase in T-C upon Te doping in FeSe. While local distortions are present near superconducting onset in FeSe and FeSe0.5Te0.5, they seem to be absent in non superconducting FeTe. Of crucial importance is the variation of anion height. In FeSe0.5Te0.5, near the superconducting onset, the two heights, h(Fe-Se) and h(Fe-Te) show a nearly opposite behaviour. These changes indicate a possible correlation between Fe-chalcogen hybridization and the superconducting transition temperature in these Fe-chalcogenides.

Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

Towards an Understanding of the Influence of Sedimentation on Colloidal Aggregation by Peclet Number

The Peclet number is a useful index to estimate the importance of sedimentation as compared to the Brownian motion. However, how to choose the characteristic length scale for the Peclet number evaluation is rather critical because the diffusion length increases as the square root of the time whereas the drifting length is linearly related to time. Our Brownian dynamics simulation shows that the degree of sedimentation influence on the coagulation decreases when the dispersion volume fraction increases. Therefore using a fixed length, such as the diameter of particle, as the characteristic length scale for Peclet number evaluation is not a good choice when dealing with the influence of sedimentation on coagulation. The simulations demonstrated that environmental factors in the coagulation process, such as dispersion volume fraction and size distribution, should be taken into account for more reasonable evaluation of the sedimentation influence.

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

19 p.

Three-dimensional models of mantle convection : influence of phase transitions and temperature-dependent viscosity

Two of the most important questions in mantle dynamics are investigated in three separate studies: the influence of phase transitions (studies 1 and 2), and the influence of temperature-dependent viscosity (study 3).

(1) Numerical modeling of mantle convection in a three-dimensional spherical shell incorporating the two major mantle phase transitions reveals an inherently three-dimensional flow pattern characterized by accumulation of cold downwellings above the 670 km discontinuity, and cylindrical 'avalanches' of upper mantle material into the lower mantle. The exothermic phase transition at 400 km depth reduces the degree of layering. A region of strongly-depressed temperature occurs at the base of the mantle. The temperature field is strongly modulated by this partial layering, both locally and in globally-averaged diagnostics. Flow penetration is strongly wavelength-dependent, with easy penetration at long wavelengths but strong inhibition at short wavelengths. The amplitude of the geoid is not significantly affected.

(2) Using a simple criterion for the deflection of an upwelling or downwelling by an endothermic phase transition, the scaling of the critical phase buoyancy parameter with the important lengthscales is obtained. The derived trends match those observed in numerical simulations, i.e., deflection is enhanced by (a) shorter wavelengths, (b) narrower up/downwellings (c) internal heating and (d) narrower phase loops.

(3) A systematic investigation into the effects of temperature-dependent viscosity on mantle convection has been performed in three-dimensional Cartesian geometry, with a factor of 1000-2500 viscosity variation, and Rayleigh numbers of 10^5-10^7. Enormous differences in model behavior are found, depending on the details of rheology, heating mode, compressibility and boundary conditions. Stress-free boundaries, compressibility, and temperature-dependent viscosity all favor long-wavelength flows, even in internally heated cases. However, small cells are obtained with some parameter combinations. Downwelling plumes and upwelling sheets are possible when viscosity is dependent solely on temperature. Viscous dissipation becomes important with temperature-dependent viscosity.

The sensitivity of mantle flow and structure to these various complexities illustrates the importance of performing mantle convection calculations with rheological and thermodynamic properties matching as closely as possible those of the Earth.

Metallogenic Provinces of the Southwestern United States and Northern Mexico

Some of the metallogenic provinces of the southwestern United States and northern Mexico are defined by the geographic distribution of trace elements in the primary sulfide minerals chalcopyrite and sphalerite. The elements investigated include antimony, arsenic, bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, molybdenum, nickel, silver, tellurium, thallium, and tin. Of these elements, cobalt, gallium, germanium, indium, nickel, silver, and tin exhibit the best defined geographic distribution.

The data indicate that chalcopyrite is the preferred host for tin and perhaps molybdenum; sphalerite is the preferred host for cadmium, gallium, germanium, indium, and manganese; galena is the preferred host for antimony, bismuth, silver, tellurium, and thallium; and pyrite is the preferred host for cobalt, nickel, and perhaps arsenic. With respect to the two minerals chalcopyrite and sphalerite, antimony, arsenic, molybdenum, nickel, silver, and tin prefer chalcopyrite; and bismuth, cadmium, cobalt, gallium, germanium, indium, manganese, and thallium prefer sphalerite. This distribution probably is the result of the interaction of several factors, among which are these: the various radii of the elements, the association due to chemical similarities of the major and trace elements, and the degree of ionic versus covalent and metallic character of the metal-sulfur bonds in chalcopyrite and sphalerite. The type of deposit, according to a temperature classification, appears to be of minor importance in determining the trace element content of chalcopyrite and sphalerite.

A preliminary investigation of large single crystals of sphalerite and chalcopyrite indicates that the distribution within a single crystal of some elements such as cadmium in sphalerite and indium and silver in chalcopyrite is relatively uniform, whereas the distribution of some other elements such as cobalt and manganese in sphalerite is somewhat less uniform and the distribution of tin in sphalerite is extremely erratic. The variations in trace element content probably are due largely to variations in the composition of the fluids during the growth of the crystals, but the erratic behavior of tin in sphalerite perhaps is related to the presence of numerous cavities and inclusions in the crystal studied.

Maps of the geographic distribution of trace elements in chalcopyrite and sphalerite exhibit three main belts of greater than average trace element content, which are called the Eastern, Central, and Western belts. These belts are consistent in trend and position with a beltlike distribution of copper, gold, lead, zinc, silver, and tungsten deposits and with most of the major tectonic features. However, there appear to be no definite time relationships, for as many as four metallogenic epochs, from Precambrian to late Tertiary, are represented by ore deposits within the Central belt.

The evidence suggests that the beltlike features have a deep seated origin, perhaps in the sub-crust or outer parts of the mantle, and that the deposits within each belt might be genetically related through a beltlike compositional heterogeneity in the source regions of the ores. Hence, the belts are regarded as metallogenic provinces.

Predicting the distribution of Vibrio vulnificus in Chesapeake Bay

Vibrio vulnificus is a gram-negative pathogenic bacterium endemic to coastal waters worldwide, and a leading cause of seafood related mortality. Because of human health concerns, understanding the ecology of the species and potentially predicting its distribution is of great importance. We evaluated and applied a previously published qPCR assay to water samples (n = 235) collected from the main-stem of the Chesapeake Bay (2007 – 2008) by Maryland and Virginia State water quality monitoring programs. Results confirmed strong relationships between the likelihood of Vibrio vulnificus presence and both temperature and salinity that were used to develop a logistic regression model. The habitat model demonstrated a high degree of concordance (93%), and robustness as subsequent bootstrapping (n=1000) did not change model output (P > 0.05). We forced this empirical habitat model with temperature and salinity predictions generated by a regional hydrodynamic modeling system to demonstrate its utility in future pathogen forecasting efforts in the Chesapeake Bay.

Assessment and monitoring of marine debris in Gray's Reef National Marine Sanctuary

Gray’s Reef National Marine Sanctuary (GRNMS) is located 32.4 km offshore of Sapelo Island, Georgia. The ecological importance of this area is related to the transition between tropical and temperate waters, and the existence of a topographically complex system of ledges. Due to its central location, GRNMS can be used as a focal site to study the accumulation and impacts of marine debris on the Atlantic continental shelf offshore of the Southeast United States. Previously, researchers characterized marine debris in GRNMS and reported that incidence of the debris at the limited densely colonized ledge sites was significantly greater than at sand or sparsely colonized live bottom, and is further influenced by the level of boating activity and physiographic characteristics (e.g., ledge height). Information gleaned from the initial marine debris characterization was used to devise a strategy for prioritizing cleanup and monitoring efforts. However, a significant gap in knowledge was the rate of debris accumulation. The primary objective of this study was to select, mark, and perform initial marine debris surveys at permanent monitoring sites within GRNMS to quantify long-term trends in types, abundance, impacts, and accumulation rates of debris. Ledge sites were selected to compare types, abundance, and accumulation rates of marine debris between a) areas of high and low use and b) short and tall ledges. Nine permanent monitoring sites were marked and initially surveyed in 2007/2008. Surveys were conducted within a 50 x 4 m transect for a total survey area of 200 square meters. All debris was removed and detailed information was taken on the types of debris, quantity, and associations with benthic fauna. Information on associations with benthic fauna included degree of entanglement, type of organism with which it is entangled or resting on, degree of fouling, and visible impacts such as tissue abrasions. Sites were re-surveyed approximately one year later to quantify new accumulation. During the initial survey, a total of ten debris items, totaling 16.3 kg in weight, were removed from two monitoring stations, both “tall” sites within the area of high boat use. Year-one accumulation totaled five items and approximately 7 kg in weight. Similar to the initial survey, all debris was found at sites in the area of high boat use. However, in contrast to the initial survey, two of these items were found on medium-height ledges. Removed items included fishing line, leaders, rope, plastic, and fabric. Although items were often encrusted in benthic biota or entangled on the ledge, impacts such as abrasions or other injuries were not observed. During the 2009 monitoring efforts, volunteer divers were trained to conduct the survey. Monitoring protocols were documented for GRNMS staff and included as an appendix of this report to enable long-term monitoring of sites. Additionally, national reconnaissance data (e.g. satellite, radar, aerial surveys) and other information on known fishing locations were examined for patterns of resource use and correlations with debris occurrence patterns. A previous model predicting the density of marine debris based on ledge features and boat use was refined and the results were used to generate a map of predicted debris density for all ledges.

The Ic behavior of 2G YBCO tapes under DC/AC magnetic fields at various temperatures

In order to design a High Temperature Superconducting (HTS) machine that is able to operate safely and reliably, studies on the characterization of Second Generation (2G) HTS tapes are of paramount importance. This paper presents an experimental setup to measure critical current of 2G HTS tapes in high DC magnetic fields (up to 5 Tesla) with an AC current ripple superimposed, as well as various temperatures ranging from 25 K to 77 K. The 2G tape measured is the SGS12050 coated conductor made by SuperPower. The critical current is measured by a flux vector with reference to the widest sample face from 0 to 90 degrees in 10 degree steps. Smaller steps are required close to 0 . A Variable Temperature Insert (VTI) is utilized to control temperature change. © 2010 IEEE.

Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey

Physiological functions of human genes may be studied by gene-knockout experiments in model organisms such as the mouse. This strategy relies on the existence of one-to-one gene orthology between the human and mouse. When lineage-specific gene duplication occurs and paralogous genes share a certain degree of functional redundancy, knockout mice may not provide accurate functional information on human genes. Angiogenin is a small protein that stimulates blood-vessel growth and promotes tumor development. Humans and related primates only have one angiogenin gene, while mice have three paralogous genes. This makes it difficult to generate angiogenin-knockout mice and even more difficult to interpret the genotype-phenotype relation from such animals should they be generated. We here show that in the douc langur (Pygathrix nemaeus), an Asian leaf-eating colobine monkey, the single-copy angiogenin gene has a one-nucleotide deletion in the sixth codon of the mature peptide, generating a premature stop codon. This nucleotide deletion is found in five unrelated individuals sequenced, and therefore is likely to have been fixed in the species. Five colobine species that are closely related to the douc langur have intact angiogenin genes, suggesting that the pseudogenization event was recent and unique to the douc langur lineage. This natural knockout experiment suggests that primate angiogenin is dispensable even in the wild. Further physiological studies of douc largurs may offer additional information on the role of this cancer-related gene in normal physiology of primates, including humans. Our findings also provide a strong case for the importance of evolutionary analysis in biomedical studies of gene functions. (C) 2003 Elsevier Science B.V. All rights reserved.

Characterization of TRPC2, an Essential Genetic Component of VNS Chemoreception, Provides Insights into the Evolution of Pheromonal Olfaction in Secondary-Adapted Marine Mammals

Pheromones are chemical cues released and sensed by individuals of the same species, which are of major importance in regulating reproductive and social behaviors of mammals. Generally, they are detected by the vomeronasal system (VNS). Here, we first investigated and compared an essential genetic component of vomeronasal chemoreception, that is, TRPC2 gene, of four marine mammals varying the degree of aquatic specialization and related terrestrial species in order to provide insights into the evolution of pheromonal olfaction in the mammalian transition from land to water. Our results based on sequence characterizations and evolutionary analyses, for the first time, show the evidence for the ancestral impairment of vomeronasal pheromone signal transduction pathway in fully aquatic cetaceans, supporting a reduced or absent dependence on olfaction as a result of the complete adaptation to the marine habitat, whereas the amphibious California sea lion was found to have a putatively functional TRPC2 gene, which is still under strong selective pressures, reflecting the reliance of terrestrial environment on chemical recognition among the semiadapted marine mammals. Interestingly, our study found that, unlike that of the California sea lion, TRPC2 genes of the harbor seal and the river otter, both of which are also semiaquatic, are pseudogenes. Our data suggest that other unknown selective pressures or sensory modalities might have promoted the independent absence of a functional VNS in these two species. In this respect, the evolution of pheromonal olfaction in marine mammals appears to be more complex and confusing than has been previously thought. Our study makes a useful contribution to the current understanding of the evolution of pheromone perception of mammals in response to selective pressures from an aquatic environment.

Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

The attrition behaviour of oxygen-carriers under inert and reacting conditions

The attrition of two potential oxygen-carriers for chemical-looping, 100. wt% mechanically-mixed, unsupported iron oxide (400-600 μm diameter) and 25. wt% copper oxide impregnated on alumina (600-900 μm diameter), has been studied. The rates of attrition of batches of these particles whilst they were being fluidised and subjected to successive cycles of reduction and oxidation were determined by measuring the rate of production of fine particles elutriated from the bed, as well as progressive changes in the distribution of particle sizes retained in the bed. The ability of the particles to withstand impacts was also investigated by examining the degree of fragmentation of 1. g of reacted particles of known size on projecting them at a target at various velocities. It was found that the mechanical strength of the iron oxide particles deteriorated significantly after repeated cycles of oxidation and reduction. Thus, the rate of elutriation increased ~35-fold between the 1st and 10th cycle. At an impact velocity of 38. m/s, the amount of fragmentation in the impact test, viz. mass fraction of particles after impact having a size less than that before impact, increased from ~2.3. wt% (fresh particles) to 98. wt% after the 10th cycle. The CuO particles, in comparison, were able to withstand repeated reaction: no signs of increased rates of elutriation or fragmentation were observed over ten cycles. These results highlight the importance of selecting a durable support for oxygen-carriers. © 2011 Elsevier Ltd.