bluuebunny/crossref_metadata_2025 huggingface dataset:
Existence and non-uniqueness of constant scalar curvature toric Sasaki metrics
Authors: Legendre Eveline
Published: July 2011

We study compatible toric Sasaki metrics with constant scalar curvature on co-oriented compact toric contact manifolds of Reeb type of dimension at least five. These metrics come in rays of transversal homothety due to the possible rescaling of the Reeb vector fields. We prove that there exist Reeb vector fields for which the transversal Futaki invariant (restricted to the Lie algebra of the torus) vanishes. Using an existence result of E. Legendre [Toric geometry of convex quadrilaterals, J. Symplectic Geom. 9 (2011), 343–385], we show that a co-oriented compact toric contact 5-manifold whose moment cone has four facets admits a finite number of rays of transversal homothetic compatible toric Sasaki metrics with constant scalar curvature. We point out a family of well-known toric contact structures on S2×S3 admitting two non-isometric and non-transversally homothetic compatible toric Sasaki metrics with constant scalar curvature.
On anticyclotomic μ-invariants of modular forms
Authors: Pollack Robert , Weston Tom
Published: July 2011

We prove the μ-part of the main conjecture for modular forms along the anticyclotomic Zp-extension of a quadratic imaginary field. Our proof consists of first giving an explicit formula for the algebraic μ-invariant, and then using results of Ribet and Takahashi showing that our formula agrees with Vatsal’s formula for the analytic μ-invariant.
Transient Two-Phase Flow Patterns by Application of a High Voltage Pulse Width Modulated Signal and the Effect on Condensation Heat Transfer
Authors: Ng Kevin , Ching Chan Y. , Cotton James S.
Published: July 2011

The objectives of this study are (i) to determine the transient phase redistributions of a two-phase flow in a smooth horizontal annular channel by applying high voltage pulses to induce electric fields and (ii) to quantify the resultant changes in the condensation heat transfer. The experiments were performed using refrigerant R-134a flowing in the annular channel that was cooled on the outside by a counter-current flow of water. The electric fields are established by applying high voltage to a concentric rod electrode inside a grounded tube. The effect of the electrohydrodynamic (EHD) forces on the changes to the initial stratified/stratified wavy flow pattern was visualized using a high speed camera. The EHD effect results in the redistribution of the liquid–vapor phase within the channel and unique flow structures, such as twisted liquid cones and entrained droplets, are observed. These structures only appear during the initial application of EHD and are absent in the steady state. Experiments were performed using a 8 kV pulse width modulated (PWM) signal with duty cycles ranging from 0% to 100% to evaluate the heat transfer and pressure drop characteristics of the transient EHD flow patterns. The resultant heat transfer increased with the duty cycle to approximately 2.7-fold at a mass flux of 45–55 kg/m2s and 1.2-fold at a mass flux of 110 kg/m2s. The enhancement was higher as the pulse width was increased.
Magnetohydrodynamic Free Convective Couette Flow With Suction and Injection
Authors: Jha Basant K. , Apere Clement A.
Published: July 2011

This paper considers the unsteady MHD free convective Couette flow of a viscous incompressible electrically conducting fluid between two parallel vertical porous plates. Both cases of the applied magnetic field being fixed either to the fluid or to the moving porous plate are considered. The solution of the governing equations has been obtained by using a Laplace transform technique. However, the Riemann-sum approximation method is used to invert the Laplace domain to the time domain. The unified solution obtained for the velocity have been used to compute the skin friction, while the temperature has been used to compute the Nusselt number. The effect of various flow parameters entering into the problem such as Prandtl number, Grashof number, and the suction/injection parameter are discussed with the aid of line graphs. The skin friction have been seen to decrease with both suction and injection on the surface of the moving plate when the channel is being cooled, while on the stationary plate, the magnitude of the skin friction increases with injection.
Mixed Convection in a Vertical Channel Containing Porous and Viscous Fluid Regions With Viscous Dissipation and Inertial Effects: A Perturbation Solution
Authors: Hajipour Mastaneh , Dehkordi Asghar Molaei
Published: July 2011

In this paper, combined forced and natural convection in a vertical channel containing both porous and viscous regions taking into account the influences of inertial force and viscous dissipation has been studied. In this regard, fully developed fluid flow in the porous region was modeled using the Brinkman–Forchheimer extended Darcy model. To solve governing equations of both the porous and viscous regions including thermal energy and momentum equations, a two-parameter perturbation method was applied. The velocity and temperature distributions of both the regions were obtained in terms of various parameters such as inertial force, Grashof, Reynolds, and Brinkman numbers, as well as various types of viscous dissipation models. In addition, numerical solution was conducted using finite difference method to compare the results. The predicted results clearly indicate that the type of viscous dissipation model has significant effect on the temperature and velocity distributions. The acquired knowledge in this study can be used by designers to control channel flow as suitable for a certain application.
Study of Bulk-Loaded Liquid Propellant Combustion Propulsion Processes With Stepped-Wall Combustion Chamber
Authors: Yu Yonggang , Chang Xuexia , Zhao Na , Mang Shanshan , Zhou Yanhuang
Published: July 2011

The multilevel stepped-wall chamber is designed to study the combustion stability control mechanism of the bulk-loaded liquid propellant gun (BLPG). The cold state experiment of the interaction of the high speed gas jet with liquid medium is conducted by means of high speed digital camera system. The simulated small caliber bulk-loaded liquid propellant combustion propulsion device is designed to study the effect of the stepped-wall chamber size on the combustion stability. The experimental results indicate that, the stepped-wall structure can restrain the expansion randomness of the Taylor cavity and leads smooth expansion at each step. In 4 stepped-wall chamber with ΔD/L = 3/40, the interior ballistic performance of BLPG is stable and the consistency of the p-t curves is good. Two-dimensional unsteady model is developed based on the BLPG combustion propulsion experiment. The numerical simulation results coincide well with the experiment.
Experimental and Numerical Investigations on Traveling Charge Gun Using Liquid Fuels
Authors: Lu Xin , Zhou Yanhuang , Yu Yonggang
Published: July 2011

The traveling charge (TC) concept is theoretically capable of producing higher muzzle velocities without a large increase in maximum operating pressure, compared with the conventional charge. This work presents experimental and numerical studies on a 35 mm test gun system using liquid fuels as traveling charge. Eight firings with 2 different configurations of booster charge and traveling charge are performed in this paper. The firing experimental results indicate that the liquid traveling charge configuration performs better, in terms of increased muzzle velocity, than a conventional propellant charge by approximately 94 m/s, corresponding to about 8% velocity increase. A mathematical model for the two-phase flows in the 35 mm test gun system using liquid fuels as traveling charge is established and simulated by using the two-phase flow method and computational fluid dynamics technology. The mathematical model for the two-phase gas-dynamical processes consists of a system of first-order, nonlinear coupled partial differential equations. An adaptive grid generation algorithm is developed to account for the expansion of the computational domain due to the motion of the system’s payload in the tube. The numerical code is well validated by comparing its predictions with the experimental results. The calculated pressure-time profiles and projectile muzzle velocity are in good agreement with the experimental data. The numerical results show that the mathematical model developed gives the correct trend and can provide useful calculated parameters for the structural design of liquid traveling charge.
A Computational Constitutive Model for Glass Subjected to Large Strains, High Strain Rates and High Pressures
Authors: Holmquist Timothy J. , Johnson Gordon R.
Published: July 2011

This article presents a computational constitutive model for glass subjected to large strains, high strain rates and high pressures. The model has similarities to a previously developed model for brittle materials by Johnson, Holmquist and Beissel (JHB model), but there are significant differences. This new glass model provides a material strength that is dependent on the location and/or condition of the material. Provisions are made for the strength to be dependent on whether it is in the interior, on the surface (different surface finishes can be accommodated), adjacent to failed material, or if it is failed. The intact and failed strengths are also dependent on the pressure and the strain rate. Thermal softening, damage softening, time-dependent softening, and the effect of the third invariant are also included. The shear modulus can be constant or variable. The pressure-volume relationship includes permanent densification and bulking. Damage is accumulated based on plastic strain, pressure and strain rate. Simple (single-element) examples are presented to illustrate the capabilities of the model. Computed results for more complex ballistic impact configurations are also presented and compared to experimental data.
Magnus Effect: Physical Origins and Numerical Prediction
Authors: Cayzac Roxan , Carette Eric , Denis Pascal , Guillen Philippe
Published: July 2011

An overview of the Magnus effect of projectiles and missiles is presented. The first part of the paper is devoted to the description of the physical mechanisms governing the Magnus effect. For yawing and spinning projectiles, at small incidences, the spin induces a weak asymmetry of the boundary layer profiles. At high incidences, increased spin causes the separated vortex sheets to be altered. Vortex asymmetry generates an additional lateral force which gives a vortex contribution to the total Magnus effect. For finned projectiles or missiles, the origin of the Magnus effect on fins is the main issue. There are two principal sources contributing to the Magnus effect. Firstly, the interaction between the asymmetric boundary layer-wake of the body and the fins, and secondly, the spin induced modifications of the local incidences and of the flow topology around the fins. The second part of the paper is devoted to the numerical prediction and validation of these flow phenomena. A state of the art is presented including classical CFD methods based on Reynolds-averaged Navier–Stokes (RANS) and unsteady rans (URANS) equations, and also hybrid RANS/LES approach called ZDES. This last method is a recent advance in turbulence modeling methodologies that allows to take into account the unsteadiness of the flow in the base region. For validation purposes computational results were compared with wind tunnel tests. A wide range of angles of attack, spin rates, Reynolds and Mach numbers (subsonic, transonic and supersonic) have been investigated.
Effectiveness of Explosive Reactive Armor
Authors: Mayseless Meir
Published: July 2011

Explosive reactive armor (ERA) is a type of add-on armor that usually consists of tiles made of two metal plates with an explosive layer in between. The ERA is placed at a certain distance from the main armor to enhance its performance. ERA design is optimized based on the required effectiveness of the tiles. Various methods of defining ERA effectiveness are described. The effectiveness parameters of the mass-flux model and its derivatives, the effect of material properties, the escape length of the jet tip precursor, the explosive layer thickness, and the edge effects are analyzed, and correlations between them are presented. Analysis results are compared with available experimental data and a very good correlation is found.
Design and Control of a Pneumatic Artificial Muscle Actuated Above-Knee Prosthesis
Authors: Waycaster Garrett , Wu Sai-Kit , Shen Xiangrong
Published: July 2011

This paper presents the authors’ investigation results of applying the pneumatic artificial muscle actuation to above-knee prostheses. As a well-known muscle actuator, the pneumatic artificial muscle actuator features a number of unique advantages, including high power density, and similar elastic characteristics to biological muscles. Despite multiple applications in related areas, the application of pneumatic artificial muscle in above-knee prostheses has not been explored. Inspired by this fact, the research presented in this paper aims to develop a pneumatic artificial muscle-actuated above-knee prosthesis, with three specific objectives: (1) demonstrate the pneumatic artificial muscle actuation’s capability in generating sufficient torque output to meet the locomotive requirements; (2) develop an effective control approach to enable the restoration of locomotive functions; (3) conduct preliminary testing of the prosthesis prototype on a healthy subject through a specially designed able-body adaptor. In the prosthesis design, an agonist–antagonist layout is utilized to obtain a bidirectional motion. To minimize the radial profile, an open-frame structure is used, with the purpose of allowing the expansion of the muscle actuators into the center space without interference. Also, the muscle actuator parameters are calculated to provide sufficient torque capacity (up to 140 N m) to meet the requirements of level walking. According to this design, the fabricated prototype weighs approximately 3 kg, with a range of motion of approximately 100°. For the control of the prosthesis, a model-based torque control algorithm is developed based on the sliding mode control approach, which provides robust torque control for this highly nonlinear system. Combining this torque control algorithm with an impedance-based torque command generator (higher-level control algorithm), the fabricated prosthesis prototype has demonstrated a capability of providing a natural gait during treadmill walking experiments.
Experimental Evaluation and Modeling Analysis of Micromilling of Hardened H13 Tool Steels
Authors: Ding Hongtao , Shen Ninggang , Shin Yung C.
Published: July 2011

This study is focused on experimental evaluation and numerical modeling of micromilling of hardened H13 tool steels. Multiple tool wear tests are performed in a microside cutting condition with 100 μm diameter endmills. The machined surface integrity, part dimension control, size effect, and tool wear progression in micromachining of hardened tool steels are experimentally investigated. A strain gradient plasticity model is developed for micromachining of hardened H13 tool steel. Novel 2D finite element (FE) models are developed in software ABAQUS to simulate the continuous chip formation with varying chip thickness in complete micromilling cycles under two configurations: microslotting and microside cutting. The steady-state cutting temperature is investigated by a heat transfer analysis of multi micromilling cycles. The FE model with the material strain gradient plasticity is validated by comparing the model predictions of the specific cutting forces with the measured data. The FE model results are discussed in chip formation, stress, temperature, and velocity fields to great details. It is shown that the developed FE model is capable of modeling a continuous chip formation in a complete micromilling cycle, including the size effect. It is also shown that the built-up edge in micromachining can be predicted with the FE model.
Radiation hardness of the storage phosphor europium doped potassium chloride for radiation therapy dosimetry
Authors: Driewer Joseph P. , Chen Haijian , Osvet Andres , Low Daniel A. , Li H. Harold
Published: July 2011

Purpose

: An important property of a reusable dosimeter is its radiation hardness, that is, its ability to retain its dosimetric merits after irradiation. The radiation hardness of europium doped potassium chloride (KCl:Eu2+), a storage phosphor material recently proposed for radiation therapy dosimetry, is examined in this study.

Methods

: Pellet‐style KCl:Eu2+ dosimeters, 6 mm in diameter, and 1 mm thick, were fabricated in‐house for this study. The pellets were exposed by a 6 MV photon beam or in a high dose rate 137Cs irradiator. Macroscopic properties, such as radiation sensitivity, dose response linearity, and signal stability, were studied with a laboratory photostimulated luminescence (PSL) readout system. Since phosphor performance is related to the state of the storage centers and the activator, Eu2+, in the host lattice, spectroscopic and temporal measurements were carried out in order to explore radiation‐induced changes at the microscopic level.

Results

: KCl:Eu2+ dosimeters retained approximately 90% of their initial signal strength after a 5000 Gy dose history. Dose response was initially supralinear over the dose range of 100–700 cGy but became linear after 60 Gy. Linearity did not change significantly in the 0–5000 Gy dose history spanned in this study. Annealing high dose history chips resulted in a return of supralinearity and a recovery of sensitivity. There were no significant changes in the PSL stimulation spectra, PSL emission spectra, photoluminescence spectra, or luminescence lifetime, indicating that the PSL signal process remains intact after irradiation but at a reduced efficiency due to reparable radiation‐induced perturbations in the crystal lattice.

Conclusions

: Systematic studies of KCl:Eu2+ material are important for understanding how the material can be optimized for radiation therapy dosimetry purposes. The data presented here indicate that KCl:Eu2+ exhibits strong radiation hardness and lends support for further investigations of this novel material.
Maxwellian relaxation of elastic particles in one dimension
Authors: Mohazzabi Pirooz , Schmidt Jeffrey R.
Published: July 2011

The statistical mechanics of one-dimensional binary mixtures is discussed from both a theoretical and simulation point of view at a level suitable for senior and introductory graduate level courses in statistical mechanics. By using a simple mathematical technique, the nonlinear Boltzmann equation is solved exactly in Fourier space. An efficient simulation algorithm is presented which yields results that are in excellent agreement with theory. We show that the velocity distribution of each type of particle relaxes to a Maxwellian for all mass ratios other than unity and infinity, and the relaxation time is a minimum for the mass ratio of 3+22.
Locating the source of projectile fluid droplets
Authors: Varney Christopher R. , Gittes Fred
Published: July 2011

The ill-posed projectile problem of finding the source height from spattered droplets of viscous fluid is a longstanding obstacle to accident reconstruction and crime-scene analysis. It is widely known how to infer the impact angle of droplets on a surface from the elongation of their impact profiles. However, the lack of velocity information makes finding the height of the origin from the impact position and angle of individual drops not possible. From aggregate statistics of the spatter and basic equations of projectile motion, we introduce a reciprocal correlation plot that is effective when the polar launch angle is concentrated in a narrow range. The vertical coordinate depends on the orientation of the spattered surface and equals the tangent of the impact angle for a level surface. When the horizontal plot coordinate is twice the reciprocal of the impact distance, we can infer the source height as the slope of the data points in the reciprocal correlation plot. If the distribution of launch angles is not narrow, failure of the method is evident in the lack of linear correlation. We perform a number of experimental trials, as well as numerical calculations and show that the height estimate is relatively insensitive to aerodynamic drag. Besides its possible relevance for crime investigation, reciprocal-plot analysis of spatter may find application to volcanism and other topics and is most immediately applicable for undergraduate science and engineering students in the context of crime-scene analysis.
Dynamic dipoles
Authors: Griffiths David J.
Published: July 2011

We study stationary but time-dependent ideal (point) electric and magnetic dipoles, both the conventional type consisting of electric charges and currents and the hypothetical kind composed of magnetic monopoles and their currents. We derive their potentials and fields, and calculate the energy, momentum, and angular momentum they radiate.
Reparametrization-invariant formulation of classical mechanics and the Schrödinger equation
Authors: Deriglazov A. , Rizzuti B. F.
Published: July 2011

Any classical-mechanics system can be formulated in reparametrization-invariant form. That is, we use the parametric representation for the trajectories, x=x(τ) and t=t(τ) instead of x=x(t). We discuss the quantization rules in this formulation and show that some of the rules become clearer. In particular, both the temporal and the spatial coordinates are subject to quantization, and the canonical Hamiltonian in the reparametrization-invariant formulation is proportional to H̃=pt+H, where H is the usual Hamiltonian and pt is the momentum conjugate to the variable t. Due to reparametrization invariance, H̃ vanishes for any solution, and hence the corresponding quantum-mechanical operator has the property H̃∧Ψ=0, which is the time-dependent Schrödinger equation, iℏ∂tΨ=H∧Ψ. We discuss the quantum mechanics of a relativistic particle as an example.
Is the electrostatic force between a point charge and a neutral metallic object always attractive?
Authors: Levin Michael , Johnson Steven G.
Published: July 2011

We give an example of a geometry in which the electrostatic force between a point charge and a neutral metallic object is repulsive. The example consists of a point charge centered above a thin metallic hemisphere, positioned concave up. We show that this geometry has a repulsive regime using both a simple analytical argument and an exact calculation for an analogous two-dimensional geometry. Analogues of this geometry-induced repulsion appear in many other contexts, including Casimir systems.
Wronskian method for one-dimensional quantum scattering
Authors: Fernández Francisco M.
Published: July 2011

The use of Wronskians with properly chosen linearly independent solutions of the Schrödinger equation greatly facilitates the calculation of the transmission probability for scattering in one dimension and also provides a reliable test for the accuracy of the calculation. We apply the approach to a Gaussian barrier and a Gaussian well, and test its accuracy for an exactly solvable model.
Targeting TLRs Expands the Antibody Repertoire in Response to a Malaria Vaccine
Authors: Wiley Steven R. , Raman Vanitha S. , Desbien Anthony , Bailor Hilton R. , Bhardwaj Rukmini , Shakri Ahmed Rushdi , Reed Steven G. , Chitnis Chetan E. , Carter Darrick
Published: July 2011

The use of TLR agonists in vaccination broadens the range of polymorphic variants against which the antibodies can be effective.
Antibody Repertoire: Embracing Diversity
Authors: Pollard Andrew J. , Hill Adrian V. S.
Published: July 2011

Adjuvanted formulations expand the vaccine-induced antibody repertoires against a virus and a parasite.
Preventing HIV Transmission: Early Therapy Is Key
Authors: Nyendak Melissa
Published: July 2011

Early combination antiretroviral drug therapy reduces virus transmission to the uninfected partner in HIV serodiscordant couples.
A Death by a Thousand Cuts
Authors: Hong David S.
Published: July 2011

Nearly 4% of lung cancers exhibit mutations in the DDR2 kinase gene and are susceptible to dasatinib, adding to the 14% that are already known to respond to this drug.
Current situation and future challenges of tobacco control policy in Thailand
Authors: Sangthong Rassamee , Wichaidit Wit , Ketchoo Chittawet
Published: July 2011

In Thailand, the prevalence of smoking has steadily declined over the past 20 years, suggesting an effective tobacco control policy. However, the prevalence has recently stabilised and youth smoking now appears to be on the rise. Tobacco use is the third highest risk factor contributing to the burden of disease in the country. This is an issue of concern and led to the present review of tobacco control measures in Thailand.

The present evidence-based review shows that Thailand's tobacco control measures are relatively strong and comply well with the WHO Framework Convention on Tobacco Control in terms of taxation, advertisement through popular media, and warning labels on cigarettes and other tobacco product packages. However, challenges remain in dealing with highly prevalent roll-your-own cigarettes, strict prohibition of tobacco sale to underage youths, household smoking, illicit trade of tobacco products, viable tobacco crop diversification for domestic tobacco growers and liability. If these challenges are met, the prevalence of tobacco consumption could possibly be further reduced.
Suspected side effects of doxycycline use in dogs – a retrospective study of 386 cases
Authors: Schulz B. S. , Hupfauer S. , Ammer H. , Sauter‐Louis C. , Hartmann K.
Published: July 2011

This study investigated doxycycline‐related side effects in a large population of dogs. Data from 386 dogs that had received doxycycline for the treatment of various infectious diseases were analysed retrospectively. Potential side effects that developed during treatment were documented, and correlations with signalment, dose, duration of treatment, frequency of application, doxycycline preparation and use of additional drugs were investigated. Vomiting was reported in 18.3 per cent of dogs, 7.0 per cent developed diarrhoea and 2.5 per cent developed anorexia. While being treated with doxycycline, 39.4 per cent of dogs showed an increase in alanine aminotransferase (ALT) activity and 36.4 per cent showed an increase in alkaline phosphatase (ALP) activity. There was a dose‐related risk of an increase in ALP activity (P=0.011, odds ratio [OR]=1.27, 95 per cent confidence interval [CI] 1.06 to 1.53), and older dogs treated with doxycycline were more likely to develop an increase in ALT activity (P=0.038, OR=1.23, 95 per cent CI 1.01 to 1.50) and vomiting (P=0.017, OR=1.11, 95 per cent CI 1.02 to 1.21).
Detection of high serological prevalence and comparison of different tests forSalmonellain pigs in Northern Ireland
Authors: Belsué J. B. , Alujas A. M. , Porter R.
Published: July 2011

Thirty‐one farrow‐to‐finish pig units with a Zoonoses National Control Programme (ZNCP) forSalmonellaabove the UK target of 10 per cent during the previous 12 months were selected for the study. Pooled faecal samples were collected from different groups of pigs. Furthermore, mice, rat and bird faeces and carcases were collected, if found on the unit. In total, 937 samples were collected on‐farm and analysed forSalmonella. The four carcases selected monthly per producer by the slaughterhouse for the British Pig Executive ZNCPSalmonellaProgramme were tested for antibodies to groups B and C with a mix‐ELISA test. The same four carcases were swabbed externally and internally, mesenteric lymph nodes (MLNs) were collected and colonic contents were swabbed. A wide variety ofSalmonellaserovars was isolated from the samples. Most of the isolates were detected in the rearing herd (on‐farm) and in the MLNs (slaughterhouse). There was no correlation between ELISA results from the meat juice and bacteriological isolations using Spearman correlation analyses. Furthermore, no significant association was found between positive results of ELISA and positive results from the bacteriological samples taken.
Assessment of stable isotopic signatures as a means to track the exchange of sea lice (Lepeophtheirus salmonis) between host fish populations
Authors: Dean Susan , DiBacco Claudio , McKinley Robert Scott
Published: July 2011

The viability of stable isotopic carbon (δ13C) and nitrogen (δ15N) signatures to track the exchange of sea lice, Lepeophtheirus salmonis , between hosts was tested. It was predicted that nonfeeding sea lice would experience lowered δ13C signatures and enriched δ15N signatures owing, at least in part, to moulting during development. It was also predicted that newly settled parasitic first generation sea lice (late stage copepodids) would retain isotopic signatures indistinguishable from their natal host fish population. During this laboratory study, δ13C signatures of nonfeeding sea lice developmental stages declined over time, while the δ13C signature of chalimus III sea lice was not significantly different from fin and gill signatures of their natal hosts, thus providing an isotopic link to their natal host fish population. In contrast, δ15N analysis did not show promise as a tracer in this study, as host fish populations did not display distinct δ15N signatures. These results suggest that δ13C signatures may be applied to identify sources of sea lice epizootics and potentially quantify the exchange of sea lice between cultured and wild salmon populations.
Fatty acid signatures of Lake Michigan prey fish and invertebrates: among-species differences and spatiotemporal variability
Authors: Czesny Sergiusz J. , Rinchard Jacques , Hanson S. Dale , Dettmers John M. , Dabrowski Konrad
Published: July 2011

Lipid concentration and fatty acid composition of common prey species or taxonomic groups from four distinct regions of Lake Michigan were quantified (n = 894). We used a combination of parametric and nonparametric statistics to assess the differences in fatty acid signatures (FAS) among species and to evaluate intraspecies variation relative to interspecies variation in FAS. Discriminant function analysis performed on 13 species or taxa groups using the 18 most abundant fatty acids revealed clear separation among taxa, with overall classification success reaching 89%. Species were readily distinguished based on their overall fatty acid profile in spite of intraspecies variation (temporal, regional, and size-related). Among species sampled, pelagic and benthic clusters were formed based on the degree of fatty acid profile similarity. In alewife ( Alosa pseudoharengus ) and round goby ( Neogobius melanostomus ), fatty acid compositions differed with fish size, sampling location, and temporal variation; however, the magnitude of these differences was small relative to differences between species. Our results demonstrate the utility of fatty acid signatures in studies of food webs in large freshwater ecosystems. This study is also a necessary first step toward development of mechanistic research that investigates the effects of variation in fatty acids within the prey base on top predators.
Using acoustic data from fishing vessels to estimate walleye pollock (Theragra chalcogramma) abundance in the eastern Bering Sea
Authors: Honkalehto Taina , Ressler Patrick H. , Towler Richard H. , Wilson Christopher D.
Published: July 2011

Eastern Bering Sea walleye pollock ( Theragra chalcogramma ) support one of the world’s largest fisheries. Because of walleye pollock’s high recruitment variability and relatively short life span, timely and accurate abundance indices are needed for fisheries management. Walleye pollock are surveyed biennially with an acoustic-trawl (AT) survey and annually with a bottom trawl (BT) survey. The latter tracks the demersal portion of the population using chartered fishing vessels, whereas the AT survey tracks the younger, midwater portion using research vessels and is critical for evaluating prerecruit abundances. Acoustic data collected from commercial fishing vessels conducting the BT survey were analyzed to provide information on midwater walleye pollock abundance at relatively low cost. A retrospective analysis of AT survey data identified a suitable index area to track midwater walleye pollock abundance. The BT survey acoustic data in that area tracked the AT survey abundance and captured its broad spatial patterns. This study is unique because commercial vessel acoustic data were used to estimate a new annual abundance index whose performance can be evaluated by a biennial research vessel survey. The new index will benefit managers by providing more accurate information on near-term abundance trends when dedicated research ship time is not available.
Estimating multifleet catchability coefficients and natural mortality from fishery catch and effort data: comparison of Bayesian state–space and observation error models
Authors: Zhou Shijie , Punt André E. , Deng Roy , Bishop Janet
Published: July 2011

Catchability and natural mortality are key quantities in fisheries stock assessment. However, it is difficult to estimate these two parameters simultaneously using only fishery catch and effort data. A Bayesian state–space modified delay–difference model is outlined that can estimate time series of catchability by fleet as well as natural mortality. This model, and three variants thereof, is fitted to data for grooved tiger prawns ( Penaeus semisulcatus ) in Australia’s Northern Prawn Fishery during the period of the year when there is little recruitment. A model that allows for both observation and process error and estimates natural mortality is best, in terms of model selection criteria as well as fit diagnostics. The posterior median estimate for catchability for the primary target fleet ranges from 6.15 × 10−4to 1.09 × 10−4during 1980–2007, while the posterior median estimate for catchability for a fleet with P. semisulcatus as its byproduct is about 20% of that for the primary fleet. Fishing efficiency increased at approximately 2% annually during 1980–2007, while the weekly natural mortality is estimated to be 0.053 week–1.
A state–space multistage life cycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt (Hyposmesus transpacificus)
Authors: Maunder Mark N. , Deriso Richard B.
Published: July 2011

Multiple factors acting on different life stages influence population dynamics and complicate the assessment and management of populations. To provide appropriate management advice, the data should be used to determine which factors are important and what life stages they impact. It is also important to consider density dependence because it can modify the impact of some factors. We develop a state–space multistage life cycle model that allows for density dependence and environmental factors to impact different life stages. Models are ranked using a two-covariates-at-a-time stepwise procedure based on AICcmodel averaging to reduce the possibility of excluding factors that are detectable in combination, but not alone. Impact analysis is used to evaluate the impact of factors on the population. The framework is illustrated by application to delta smelt ( Hyposmesus transpacificus ), a threatened species that is potentially impacted by multiple anthropogenic factors. Our results indicate that density dependence and a few key factors impact the delta smelt population. Temperature, prey, and predators dominated the factors supported by the data and operated on different life stages. The included factors explain the recent declines in delta smelt abundance and may provide insight into the cause of the pelagic species decline in the San Francisco Estuary.
Painting the rye genome with genome-specific sequences
Authors: González-García Miriam , Cuacos María , González-Sánchez Mónica , Puertas María J. , Vega Juan M.
Published: July 2011

We used rye-specific repetitive DNA sequences in fluorescence in situ hybridization (FISH) to paint the rye genome and to identify rye DNA in a wheat background. A 592 bp fragment from the rye-specific dispersed repetitive family R173 (named UCM600) was cloned and used as a FISH probe. UCM600 is dispersed over the seven rye chromosomes, being absent from the pericentromeric and subtelomeric regions. A similar pattern of distribution was also observed on the rye B chromosomes, but with weaker signals. The FISH hybridization patterns using UCM600 as probe were comparable with those obtained with the genomic in situ hybridization (GISH) procedure. There were, however, sharper signals and less background with FISH. UCM600 was combined with the rye-specific sequences Bilby and pSc200 to obtain a more complete painting. With these probes, the rye chromosomes were labeled with distinctive patterns; thus, allowing the rye cultivar ‘Imperial’ to be karyotyped. It was also possible to distinguish rye chromosomes in triticale and alien rye chromatin in wheat–rye addition and translocation lines. The distribution of UCM600 was similar in cultivated rye and in the wild Secale species Secale vavilovii Grossh., Secale sylvestre Host, and Secale africanum Stapf. Thus, UCM600 can be used to detect Secale DNA introgressed from wild species in a wheat background.
The complete genome sequence ofClostridium botulinumF str. 230613, insertion sites, and recombination of BoNT gene clusters
Authors: Tian Ren-Mao , Li Tao , Hou Xiao-Jun , Wang Qin , Cai Kun , Liu Yue-Nan , Gao Xiang , Liu Hao , Xiao Le , Tu Wei , Shi Jing , Cao Wu-Chun , Wang Hui
Published: July 2011

The genomic DNA of Clostridium botulinum F str. 230613 includes a chromosome (3 993 083 bp, 3502 coding sequences (CDs)) and a plasmid (17 531 bp, 25 CDs). The arrangement of the botulinum neurotoxin serotype F (BoNT/F) gene cluster, a 15-kb (or longer) fragment including the bont gene and other relevant genes, and its different insertion sites in C. botulinum A2 and C. botulinum F were formulated. Mobile elements and virulence factors were analysed. We also found a cell adhesion and pectin lyase domain–containing protein, which may function in attaching to the host and as a pectin lyase. The nine BoNT gene clusters of group I C. botulinum strains were located at three sites in the chromosome of C. botulinum F str. 230613. This study showed the inserting inclination of BoNT/A1 tend to have gene clusters inserted at site 3, BoNT/F at site 2, and BoNT/A2 at site 1. Additionally, we found the recombination event between the BoNT gene clusters of sites 2 and 3, a mechanism that contributed to the diversity of the BoNT gene cluster arrangement.
Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.)
Authors: Gupta Sarika , Kumari Kajal , Das Jyotirmoy , Lata Charu , Puranik Swati , Prasad Manoj
Published: July 2011

Introns are noncoding sequences in a gene that are transcribed to precursor mRNA but spliced out during mRNA maturation and are abundant in eukaryotic genomes. The availability of codominant molecular markers and saturated genetic linkage maps have been limited in foxtail millet (Setaria italica (L.) P. Beauv.). Here, we describe the development of 98 novel intron length polymorphic (ILP) markers in foxtail millet using sequence information of the model plant rice. A total of 575 nonredundant expressed sequence tag (EST) sequences were obtained, of which 327 and 248 unique sequences were from dehydration- and salinity-stressed suppression subtractive hybridization libraries, respectively. The BLAST analysis of 98 EST sequences suggests a nearly defined function for about 64% of them, and they were grouped into 11 different functional categories. All 98 ILP primer pairs showed a high level of cross-species amplification in two millets and two nonmillets species ranging from 90% to 100%, with a mean of ∼97%. The mean observed heterozygosity and Nei’s average gene diversity 0.016 and 0.171, respectively, established the efficiency of the ILP markers for distinguishing the foxtail millet accessions. Based on 26 ILP markers, a reasonable dendrogram of 45 foxtail millet accessions was constructed, demonstrating the utility of ILP markers in germplasm characterizations and genomic relationships in millets and nonmillets species.
Occurrence of LINE,gypsy-like, andcopia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatasL.)
Authors: Okpul Tom , Harding Robert M. , Dieters Mark J. , Godwin Ian D.
Published: July 2011

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.
Synthesis, characterization, X-ray structure, and mixed-valence states of trans-dichlorotin(IV)-5,10,15,20-tetraferrocenylporphyrin
Authors: Solntsev Pavlo V. , Neisen Ben D. , Sabin Jared R. , Gerasimchuk Nikolay N. , Nemykin Victor N.
Published: July 2011

Reaction between H2TFcP (TFcP2- is a dianion of 5,10,15,20-tetraferrocenylporphyrin) with tin(II) chloride results in formation of the trans- Cl2SnTFcP complex, which was characterized by UV-vis, MCD, 1H and 13C NMR, and APCI MS methods. X-ray single crystal analysis was used to determine the structure of the target compound. Crystallography reveals a very unusual α,α,β,β-conformation of the ferrocene groups and largely planar structure of the porphyrin macrocycle. Density functional theory calculations predict that the HOMO in trans- Cl2SnTFcP is predominantly ferrocene centered, while LUMO is primarily localized over the porphyrin core. Redox properties of the trans- Cl2SnTFcP complex were investigated using electrochemical (CV and DPV), spectroelectrochemical, and chemical oxidation approaches. Electrochemical experiments conducted in low-polarity solvent using non-coordinating electrolyte reveal the sequential oxidation of ferrocene substituents along with porphyrin-based single-electron oxidation and reduction processes. The first ferrocene oxidation process is separated by 130 mV from the next three ferrocene based oxidations, which are more closely spaced. Mixed-valence [trans- Cl2SnTFcP]+ was generated in situ by spectroelectrochemical and chemical oxidation approaches and characterized by UV-vis-NIR spectroscopy.
Leucine-stimulated mTOR signaling is partly attenuated in skeletal muscle of chronically uremic rats
Authors: Chen Yu , Sood Sumita , McIntire Kevin , Roth Richard , Rabkin Ralph
Published: July 2011

The branched-chain amino acid leucine stimulates muscle protein synthesis in part by directly activating the mTOR signaling pathway. Furthermore, leucine, if given in conjunction with resistance exercise, enhances the exercise-induced mTOR signaling and protein synthesis. Here we tested whether leucine can activate the mTOR anabolic signaling pathway in uremia and whether it can enhance work overload (WO)-induced signaling through this pathway. Chronic kidney disease (CKD) and control rats were studied after 7 days of surgically induced unilateral plantaris muscle WO and a single leucine or saline load. In the basal state, 4E-BP1 phosphorylation was modestly depressed in non-WO muscle of CKD rats, whereas rpS6 phosphorylation was nearly completely suppressed. After oral leucine mTOR, S6K1 and rpS6 phosphorylation increased similarly in both groups, whereas the phospho-4E-BP1 response was modestly attenuated in CKD. WO alone activated the mTOR signaling pathway in control and CKD rats. In WO CKD, muscle leucine augmented mTOR and 4E-BP1 phosphorylation, but its effect on S6K1 phosphorylation was attenuated. Taken together, this study has established that the chronic uremic state impairs basal signaling through the mTOR anabolic pathway, an abnormality that may contribute to muscle wasting. However, despite this abnormality, leucine can stimulate this signaling pathway in CKD, although its effectiveness is partially attenuated, including in skeletal muscle undergoing sustained WO. Thus, although there is some resistance to leucine in CKD, the data suggest a potential role for leucine-rich supplements in the management of uremic muscle wasting.
Simultaneous measurement of glucose transport and utilization in the human brain
Authors: Shestov Alexander A. , Emir Uzay E. , Kumar Anjali , Henry Pierre-Gilles , Seaquist Elizabeth R. , Öz Gülin
Published: July 2011

Glucose is the primary fuel for brain function, and determining the kinetics of cerebral glucose transport and utilization is critical for quantifying cerebral energy metabolism. The kinetic parameters of cerebral glucose transport, KMtand Vmaxt, in humans have so far been obtained by measuring steady-state brain glucose levels by proton (1H) NMR as a function of plasma glucose levels and fitting steady-state models to these data. Extraction of the kinetic parameters for cerebral glucose transport necessitated assuming a constant cerebral metabolic rate of glucose ( CMRglc) obtained from other tracer studies, such as13C NMR. Here we present new methodology to simultaneously obtain kinetic parameters for glucose transport and utilization in the human brain by fitting both dynamic and steady-state1H NMR data with a reversible, non-steady-state Michaelis-Menten model. Dynamic data were obtained by measuring brain and plasma glucose time courses during glucose infusions to raise and maintain plasma concentration at ∼17 mmol/l for ∼2 h in five healthy volunteers. Steady-state brain vs. plasma glucose concentrations were taken from literature and the steady-state portions of data from the five volunteers. In addition to providing simultaneous measurements of glucose transport and utilization and obviating assumptions for constant CMRglc, this methodology does not necessitate infusions of expensive or radioactive tracers. Using this new methodology, we found that the maximum transport capacity for glucose through the blood-brain barrier was nearly twofold higher than maximum cerebral glucose utilization. The glucose transport and utilization parameters were consistent with previously published values for human brain.