bluuebunny/crossref_metadata_2025 huggingface dataset:
Scoring models of a diet quality index and the predictive capability of mortality in a population-based cohort of Swedish men and women
Authors: Drake Isabel , Gullberg Bo , Sonestedt Emily , Wallström Peter , Persson Margaretha , Hlebowicz Joanna , Nilsson Jan , Hedblad Bo , Wirfält Elisabet
Published: May 2012

Objective

To examine how different scoring models for a diet quality index influence associations with mortality outcomes.

Design

A study within the Malmö Diet and Cancer cohort. Food and nutrient intakes were estimated using a diet history method. The index included six components: SFA, PUFA, fish and shellfish, fibre, fruit and vegetables, and sucrose. Component scores were assigned using predefined (based on dietary recommendations) and population-based cut-offs (based on median or quintile intakes). Multivariate Cox regression was used to model associations between index scores (low, medium, high) and all-cause and cause-specific mortality by sex.

Setting

Malmö, the third largest city in Sweden.

Subjects

Men (n 6940) and women (n 10 186) aged 44–73 years. During a mean follow-up of 14·2 years, 2450 deaths occurred, 1221 from cancer and 709 from CVD.

Results

The predictive capability of the index for mortality outcomes varied with type of scoring model and by sex. Stronger associations were seen among men using predefined cut-offs. In contrast, the quintile-based scoring model showed greater predictability for mortality outcomes among women. The scoring model using median-based cut-offs showed low predictability for mortality among both men and women.

Conclusions

The scoring model used for dietary indices may have a significant impact on observed associations with disease outcomes. The rationale for selection of scoring model should be included in studies investigating the association between dietary indices and disease. Adherence to the current dietary recommendations was in the present study associated with decreased risk of all-cause and cause-specific mortality, particularly among men.
Identifying Hexagonal Boron Nitride Monolayers by Transmission Electron Microscopy
Authors: Odlyzko Michael L. , Mkhoyan K. Andre
Published: May 2012

Multislice simulations in the transmission electron microscope (TEM) were used to examine changes in annular-dark-field scanning TEM (ADF-STEM) images, conventional bright-field TEM (BF-CTEM) images, and selected-area electron diffraction (SAED) patterns as atomically thin hexagonal boron nitride (h-BN) samples are tilted up to 500 mrad off of the [0001] zone axis. For monolayer h-BN the contrast of ADF-STEM images and SAED patterns does not change with tilt in this range, while the contrast of BF-CTEM images does change; h-BN multilayer contrast varies strongly with tilt for ADF-STEM imaging, BF-CTEM imaging, and SAED. These results indicate that tilt series analysis in ADF-STEM image mode or SAED mode should permit identification of h-BN monolayers from raw TEM data as well as from quantitative post-processing.
The relationship between El Niño and the western North Pacific summer climate in a coupled GCM: Role of the transition of El Niño decaying phases
Authors: Chen Wei , Park Jong‐Kil , Dong Buwen , Lu Riyu , Jung Woo‐Sik
Published: May 2012

This study investigates the impacts of the transition of El Niño decaying phases on the western North Pacific anticyclone (WNPAC) anomalies in the subsequent summer with a coupled GCM. The modeling results suggest that the El Niños with short decaying phases lead to significant WNPAC anomalies in the following summer, which are contributed to mainly by the El Niños followed by La Niñas, in comparison with those not followed by La Niñas. In contrast, the long decaying cases are associated with the disappearance of WNPAC anomalies in the summer. These differences in the WNP circulation anomalies can be explained by the different configurations of simultaneous SSTs in the Indian Ocean and in the central and eastern tropical Pacific: positive SSTs in the former region and negative ones in the latter region constructively induce significant WNPAC anomalies for the short decaying cases, while the roles of positive SSTs in both regions for the long decaying cases work destructively and lead to weak WNP circulation anomalies. Further analysis indicates that the different lengths of El Niño decaying phases are predicted by the strength of Indian Ocean SSTs in the mature winter. The warmer wintertime Indian Ocean SSTs favor the anomalous easterly wind over the western and central equatorial Pacific in the subsequent summer, leading to a short decaying of El Niño. Thus, the strength of wintertime Indian Ocean SSTs is one of the important factors that affect the length of El Niño decaying phase and resultant WNPAC anomalies in the following summer.
Mincle polarizes human monocyte and neutrophil responses to Candida albicans
Authors: Vijayan Dipti , Radford Kristen J , Beckhouse Anthony G , Ashman Robert B , Wells Christine A
Published: May 2012

The distribution and function of the C‐type lectin Mincle has not previously been investigated in human cells, although mouse models have demonstrated a non‐redundant role for Mincle in the host response to fungal infections. This study identified an unusual pattern of reciprocal expression of Mincle on peripheral blood monocytes or neutrophils isolated from the same donor. Expression on monocytes was inversely correlated with phagocytosis and yeast killing, but was necessary for the induction of inflammatory cytokines in response to ex vivo Candida challenge. In contrast, Mincle expression on neutrophils was associated with phagocytic and candidacidal potential of those cells. Candida challenge upregulated Mincle expression but only in Mincle+ cells. These data highlight species‐specific differences between the regulation of Mincle expression in mouse and man. Reciprocal expression of Mincle modified the candidacidal potential of monocytes or neutrophils, suggesting it may also polarize the type of host response to fungal infection.
Co-ordination of cell cycle and differentiation in the developing nervous system
Authors: Hindley Christopher , Philpott Anna
Published: May 2012

During embryonic development, cells must divide to produce appropriate numbers, but later must exit the cell cycle to allow differentiation. How these processes of proliferation and differentiation are co-ordinated during embryonic development has been poorly understood until recently. However, a number of studies have now given an insight into how the cell cycle machinery, including cyclins, CDKs (cyclin-dependent kinases), CDK inhibitors and other cell cycle regulators directly influence mechanisms that control cell fate and differentiation. Conversely, examples are emerging of transcriptional regulators that are better known for their role in driving the differentiated phenotype, which also play complementary roles in controlling cell cycle progression. The present review will summarise our current understanding of the mechanisms co-ordinating the cell cycle and differentiation in the developing nervous system, where these links have been, perhaps, most extensively studied.
Hydroelastic response and energy harvesting potential of flexible piezoelectric beams in viscous flow
Authors: Akcabay Deniz Tolga , Young Yin Lu
Published: May 2012

Electroactive polymers such as piezoelectric elements are able to generate electric potential differences from induced mechanical deformations. They can be used to build devices to harvest ambient energy from natural flow-induced deformations, e.g., as flapping flags subject to flowing wind or artificial seaweed subject to waves or underwater currents. The objectives of this study are to (1) investigate the transient hydroelastic response and energy harvesting potential of flexible piezoelectric beams fluttering in incompressible, viscous flow, and (2) identify critical non-dimensional parameters that govern the response of piezoelectric beams fluttering in viscous flow. The fluid-structure interaction response is simulated using an immersed boundary approach coupled with a finite volume solver for incompressible, viscous flow. The effects of large beam deformation, membrane tension, and coupled electromechanical responses are all considered. Validation studies are shown for the motion of a flexible filament in uniform flow, and for a piezoelectric beam subject to base vibration. The predicted flutter velocities and frequencies also compared well with published experimental and numerical data over a range of Reynolds numbers for varying fluid and solid combinations. The results showed that for a heavy beam in a light fluid (i.e., high βρ regime), flutter incepts at a lower critical speed with a lower reduced frequency than for a light beam in a heavy fluid (i.e., low βρ regime). In the high βρ regime, flutter develops at the second mode and is only realized when the fluid inertial forces are in balance with the solid elastic restoring forces, which leads to large amplitude oscillations and complex wake patterns; the flutter speed is practically independent of the Reynolds number (Re) and solid to fluid mass ratio (βρ), because the response is dominated by the solid inertial forces. In the low βρ regime, fluid inertial forces dominate, flutter develops at higher modes and is only realized when the solid inertial forces are proportioned to the solid elastic restoring forces; the flutter speed depends on both Re and βρ, and viscous force and beam tension effects tend to delay flutter and reduce vibration amplitudes, leading to thinner, more simplified wake patterns. The results demonstrate that energy extraction via fluttering piezoelectric beams is possible. The overall efficiency was observed to be influenced by the piezoelectric circuit resistance, which is known to be directly related to the square of the piezoelectric coupling factor. The results show that the maximum strain limit of piezoelectrics may be exceeded, and hence careful optimization of the material and geometry is recommended to maximize the energy capture for a given range of expected flow conditions while satisfying safety and reliability requirements.
Influence of an anisotropic slip-length boundary condition on turbulent channel flow
Authors: Busse A. , Sandham N. D.
Published: May 2012

The effects of an anisotropic Navier slip-length boundary condition on turbulent channel flow are investigated parametrically by direct numerical simulations. The slip-length boundary condition is made direction dependent by specifying the value of the slip length independently for the streamwise and spanwise direction. The change in drag is mapped versus a wide range of streamwise and spanwise slip-length combinations at two different friction Reynolds numbers, \documentclass[12pt]{minimal}\begin{document}$Re_{\tau _0}=180$\end{document}Reτ0=180 and \documentclass[12pt]{minimal}\begin{document}$Re_{\tau _0}=360$\end{document}Reτ0=360. For moderate slip lengths both drag-reducing and drag-increasing slip-length combinations are found. The percentage drag increase saturates at approximately 60% for high spanwise slip. Once a threshold value for the streamwise slip length is exceeded, drag is reduced in all cases irrespective of the value of the spanwise slip length. The Reynolds number appears to have only little influence on the change in drag for the moderate Reynolds numbers studied here. A detailed comparison with the implicit theoretical formula of Fukagata et al. [Phys. Fluids 18, 051703 (2006)], which relates the change in drag with the streamwise and spanwise slip length, has been made. In general, this formula gives a fair representation of the change in drag; a modified version of this relation is presented, which improves the prediction for the change in drag for small slip length values and reduces the number of free parameters contained in the model. The effects of the slip-length boundary condition on the flow are further investigated using mean flow and turbulence statistics. For drag-neutral slip-length combinations the level of turbulent fluctuations is approximately unchanged. The presence of a slip-length boundary condition affects both the level of wall-shear stress fluctuations and the degree of intermittency of the wall-shear stress probability density function. The correlation statistics of the velocity field show that a high spanwise slip length causes a disruption of the near-wall streaks, while high streamwise slip favours an increasing streak regularity.
Control and femtosecond time-resolved imaging of torsion in a chiral molecule
Authors: Hansen Jonas L. , Nielsen Jens H. , Madsen Christian Bruun , Lindhardt Anders Thyboe , Johansson Mikael P. , Skrydstrup Troels , Madsen Lars Bojer , Stapelfeldt Henrik
Published: May 2012

We study how the combination of long and short laser pulses can be used to induce torsion in an axially chiral biphenyl derivative (3,5-difluoro-3′,5′-dibromo-4′-cyanobiphenyl). A long, with respect to the molecular rotational periods, elliptically polarized laser pulse produces 3D alignment of the molecules, and a linearly polarized short pulse initiates torsion about the stereogenic axis. The torsional motion is monitored in real-time by measuring the dihedral angle using femtosecond time-resolved Coulomb explosion imaging. Within the first 4 picoseconds (ps), torsion occurs with a period of 1.25 ps and an amplitude of 3° in excellent agreement with theoretical calculations. At larger times, the quantum states of the molecules describing the torsional motion dephase and an almost isotropic distribution of the dihedral angle is measured. We demonstrate an original application of covariance analysis of two-dimensional ion images to reveal strong correlations between specific ejected ionic fragments from Coulomb explosion. This technique strengthens our interpretation of the experimental data.
Estimating statistical distributions using an integral identity
Authors: Zhang Cheng , Ma Jianpeng
Published: May 2012

We present an identity for an unbiased estimate of a general statistical distribution. The identity computes the distribution density from dividing a histogram sum over a local window by a correction factor from a mean-force integral, and the mean force can be evaluated as a configuration average. We show that the optimal window size is roughly the inverse of the local mean-force fluctuation. The new identity offers a more robust and precise estimate than a previous one by Adib and Jarzynski [J. Chem. Phys. 122, 014114 (2005)]10.1063/1.1829631. It also allows a straightforward generalization to an arbitrary ensemble and a joint distribution of multiple variables. Particularly we derive a mean-force enhanced version of the weighted histogram analysis method. The method can be used to improve distributions computed from molecular simulations. We illustrate the use in computing a potential energy distribution, a volume distribution in a constant-pressure ensemble, a radial distribution function, and a joint distribution of amino acid backbone dihedral angles.
Fano-type resonance through a time-periodic potential in graphene
Authors: Lu Wei-Tao , Wang Shun-Jin , Li Wen , Wang Yong-Long , Ye Cheng-Zhi , Jiang Hua
Published: May 2012

Based on Floquet scattering matrix theory, the electron transmission through a periodic time-dependent potential in monolayer graphene is studied. It is found that the quantum interference between the bound states and continuum states due to the interaction of electron with oscillating field can result in the occurrence of asymmetric Fano-type resonance in transmission. The Fano-type resonance could be controlled by adjusting the momentum parallel to the potential well, the oscillation frequency, and amplitude. These results may be useful for probing the energy spectrum, the internal potential, and the geometric structure of graphene.
A comparative investigation on sub-micrometer InN and GaN Gunn diodes working at terahertz frequency
Authors: Yang Lin’an , Long Shuang , Guo Xin , Hao Yue
Published: May 2012

We report on a simulation for wurtzite-InN and GaN Gunn diodes with notch-doping and uniform-doping structural transit regions. Results show that 0.3–1.0 μm Gunn diodes with a diode area of 500 μm2 can generate fundamental frequencies of around 0.2–0.8 THz and rf currents of several hundred mA. InN diodes exhibit more stable oscillations, whereas GaN diodes generate higher oscillation frequencies at both dipole-domain mode and accumulation-domain mode due to different negative differential resistance (NDR) characteristics of high-field transport. The sharp NDR region of InN makes it more suitable for short transit region Gunn diode. Higher Irf/Iav and lower bias voltage in InN Gunn diode imply its conversion efficiency significantly higher than GaN diode.
Study on α-β quartz phase transition and its effect on dielectric properties
Authors: Xie Xiaojun , Cheng Yonghong , Wu Kai , Xiao Bing
Published: May 2012

In this paper, the Landau theory and ab initio molecular dynamics are applied to study the temperature induced α-β quartz phase transition, and its influences on dielectric properties are measured experimentally. Based on the Landau theory, the quartz phase transition is found to be a displacive second order transition. Moreover, the atomic displacements in different directions during the phase transition are obtained. The phase transition temperature is accurately estimated from the calculated structural parameters based on ab initio molecular dynamics. The dielectric experiments are carried out to study the effects of phase transition on dielectric properties, and strong anisotropy in different directions is observed. In [100] direction, a strong peak in the real part of dielectric function occurs near the phase transition temperature especially at the low frequency. However, the dielectric properties in [001] direction are hardly affected by phase transition. These phenomena can be interpreted successfully based on the calculated atomic displacements in different directions. In addition, the observed peaks of experimental dielectric spectra near the transition temperature can be also explained in terms of the dipole orientation polarization caused by atomic displacements during the phase transition.
Increased density and coverage uniformity of viruses on a sensor surface by using U-type, T-type, and W-type microfluidic devices
Authors: Wu Chia-Che , Tseng Ping-Kuo , Tsai Ching-Hsiu , Liu Yao-Lung
Published: May 2012

Microorganisms, molecules, or viruses in the fluidic environment are usually at considerably low Reynolds numbers because of small diameters. The viscous forces of molecules and viruses dominate at considerably low Reynolds numbers. This study developed three microfluidic devices, that is, T type, U type, and W type devices, to control the flow movement, which can increase the adhesion density of viruses on the surface of the sensor. The linker 11-mercaptoundecanoic acid (11-MUA) and Turnip yellow mosaic virus (TYMV) were used in this study and measured by a confocal microscope. Fluorescent intensity and coverage of 11-MUA and TYMV were used to identify the adhesion density quantitatively. Results indicate that 11-MUA layers and TYMV disperse randomly by the dipping method. Attachment tests for T-, U-, and W-type devices demonstrated average fluorescence intensities of 1.56, 2.18, and 2.67, respectively, and average fluorescence coverage of 1.31, 1.87, and 2.55 times those of dipping techniques, respectively. The T-type device produced the lowest fluorescence coverage uniformity (10%–80%), whereas the W-type device produced the highest fluorescence coverage uniformity (80%–90%). Fluorescence intensity correlates positively with flow within a specified flow range; however, the exact relationship between fluorescence intensity and flow requires further study. Attachment tests for TYMV virus samples indicated that the W-type device produced an average fluorescence intensity of 3.59 and average fluorescence coverage of 19.13 times greater than those achieved through dipping techniques. Traditional immersion methods achieved fluorescence coverage of 0%–10%, whereas that of the W-type device reached 70%–90%.
Metamaterial near-field sensor for deep-subwavelength thickness measurements and sensitive refractometry in the terahertz frequency range
Authors: Reinhard Benjamin , Schmitt Klemens M. , Wollrab Viktoria , Neu Jens , Beigang René , Rahm Marco
Published: May 2012

We present a metamaterial-based terahertz (THz) sensor for thickness measurements of subwavelength-thin materials and refractometry of liquids and liquid mixtures. The sensor operates in reflection geometry and exploits the frequency shift of a sharp Fano resonance minimum in the presence of dielectric materials. We obtained a minimum thickness resolution of 12.5 nm (1/16 000 times the wavelength of the THz radiation) and a refractive index sensitivity of 0.43 THz per refractive index unit. We support the experimental results by an analytical model that describes the dependence of the resonance frequency on the sample material thickness and the refractive index.
The Ã-state dissociation continuum of NO-Ar and its near infrared spectrum
Authors: Meyer H.
Published: May 2012

After preparing NO-Ar in a vibrational state correlating with the first overtone vibration in NO, we recorded its hot band UV spectrum by monitoring simultaneously the intensity in the NO+ and the NO+-Ar ion channels. In this way, the bound as well as the continuous part of the electronic \documentclass[12pt]{minimal}\begin{document}$\tilde{A}\leftarrow \tilde{X}$\end{document}Ã←X̃ spectrum are observed directly. Below the dissociation threshold, the intensity is found exclusively in the NO+-Ar ion channel while above it is found in the NO fragment ion channel. We observe simultaneously intensity in both ion channels only for a very narrow frequency range near the dissociation threshold. Structures in the dissociation spectrum correlate well with the thresholds for production of NO(A) in different rotational states. At frequencies well above the dissociation threshold, NO-Ar is detected efficiently as a NO fragment. This fact has been exploited to record the near IR spectrum of NO-Ar with significantly increased sensitivity. The dissociation detected spectra are essentially identical to our previous constant photon energy sum (CONPHOENERS) scans [B. Wen, Y. Kim, H. Meyer, J. Kłos, and M. H. Alexander, J. Phys. Chem. A 112, 9483 (2008)]10.1021/jp802765z. Several hot band spectra have been remeasured with improved sensitivity enabling a comprehensive analysis yielding for the first time spectroscopic constants for levels associated with the potential surfaces of NO-Ar correlating with NO(vNO = 0 and 2). Since many NO-X complexes do not have a strong bound Ã-state spectrum, although they do have a Ã-state dissociation continuum, there is the possibility to record their near IR spectra by employing dissociation detection.
Enhanced electrocaloric effect in poly(vinylidene fluoride-trifluoroethylene)-based terpolymer/copolymer blends
Authors: Chen Xiang-zhong , Qian Xiao-shi , Li Xinyu , Lu S. G. , Gu Hai-ming , Lin Minren , Shen Qun-dong , Zhang Q. M.
Published: May 2012

The electrocaloric effect in the blends of poly(vinylidene fluoride–trifluoroethylene–chlorofluoroethylene) (P(VDF-TrFE-CFE)) with small amount of poly(vinylidene fluoride–trifluoroethylene) (P(VDF-TrFE)) is investigated. It was found that small amount of P(VDF-TrFE) (∼10 wt. %) can cause a more than 10% increase in the crystallinity in the blends. Although the two polymers form separate crystalline phases, the interfacial couplings to the random defects in the terpolymer convert the normal ferroelectric P(VDF-TrFE) into a relaxor ferroelectric. As a result, the blends with 10 wt. % of P(VDF-TrFE) exhibit a 30% increase in the adiabatic temperature change over the entire experimental temperature range (20 °C–60 °C).
Polarization-tunable polariton excitation in a compound plasmonic crystal
Authors: Zhou Lin , Tang Xia-Mei , Huang Cheng-Ping , Zhang Yi , Zhu Yong-Yuan
Published: May 2012

Propagation of an electromagnetic (EM) wave through a compound plasmonic crystal composed of perpendicularly arranged gold nanorod pairs has been studied. Because of the strong coupling between the EM wave and vibrations of free electrons inside nanorod pairs, the polarization-tunable polariton stop band as well as pronounced polarization conversion can be achieved in the compound plasmonic crystal. A theory based on Huang-Kun-like equations is presented to reveal the mechanism, which agrees well with the simulations. Our results may shed light on the structure design and physical understandings on the anisotropic metamaterials.
Crystalline order of polymer nanoparticles over large areas at solid/liquid interfaces
Authors: Hellsing M. S. , Kapaklis V. , Rennie A. R. , Hughes A. V. , Porcar L.
Published: May 2012

We report on the formation of large two-dimensional domains (about 20 cm2) of oriented and ordered structures of polystyrene particles dispersed in water at a solid/liquid interface. Gentle flow of the dispersed sample into the holder at a shear strain rate of about 0.1 s−1 caused particles at the air/latex meniscus to self-assemble in a regular structure on both solid silica or alumina surfaces. Scattering experiments show that the particle separation at the surface was the same as in the bulk and determined by repulsion arising from the charges on the particles. Close-packed planes formed parallel to the interface.
Isolation and Molecular Characterization of a Novel Infectious Pancreatic Necrosis Virus Strain in Returning Atlantic Salmon Salmo salar from the Connecticut River, USA
Authors: Glenney Gavin W. , Barbash Patricia A. , Coll John A. , Quartz William M.
Published: May 2012

After 22 years of negative viral screening results, the viral pathogen infectious pancreatic necrosis virus (IPNV) was isolated from the ovarian fluid of two pooled samples of returning Connecticut River Atlantic salmon Salmo salar during the 2007 spawning season at Richard Cronin National Salmon Station (RCNSS), Hadley, Massachusetts. Cytopathic effect was observed in Chinook salmon embryo (CHSE-214) cells, and IPNV was confirmed by reverse transcriptase–polymerase chain reaction (RT–PCR). Sequence analysis conducted by the U.S. Geological Survey's Western Fisheries Research Center determined that the isolate closely resembled the Canada_3 strain, falling into Genogroup 4 rather than Genogroup 1, which is more common in the United States. This allowed us to speculate that the Atlantic salmon were not infected during their freshwater life stage in the Connecticut River watershed but somewhere on their migratory route or feeding grounds in the Northwest Atlantic. On November 20, 2007, the Connecticut River Atlantic Salmon Commission voted to depopulate the infected stock at RCNSS and the entire suspect egg lots held at White River National Fish Hatchery, Vermont. Approximately one and a half months later, the 121 Connecticut River Atlantic salmon were euthanized and sampled for a follow-up investigation to determine the prevalence of infection. Only one kidney–spleen homogenate (male) was confirmed IPNV positive via cell culture and RT–PCR. A total of 2,983 base pairs from segment A of the RNA genome were sequenced from this fish and determined to be from a new strain (Connecticut-1) of IPNV that closely resembles Canada_2 and Canada_3 in Genogroup 4. The new strain is genetically identical to one of the first ovarian fluid isolates over a shared 130-nucleotide region, possibly indicating original transmission from a single source. The absence of IPNV from the Connecticut River's subsequent four returning Atlantic salmon year-classes may indicate that the aggressive corrective action was prudent.

Received April 5, 2011; accepted December 9, 2011
Effects of Metomidate Hydrochloride Sedation on Blood Glucose and Marketability of Transported Threespot Gourami Trichogaster trichopterus
Authors: Crosby Tina C. , Hill Jeffrey E. , Hartman Kathleen H. , Yanong Roy P. E.
Published: May 2012

Our objectives were to determine whether sedation with metomidate hydrochloride (hereafter, “metomidate”) during transportation of threespot gourami Trichogaster trichopterus would prevent an increase in blood glucose levels and improve fish marketability (i.e., based on appearance and behavior) in comparison with unsedated controls. Threespot gourami are obligate air-breathers that possess a labyrinth organ, enabling the fish to respire air above the water surface; these fish should be lightly sedated during transport. Fish were transported for approximately 24 h via truck and domestic airline. Blood was sampled at 0, 2, 6, and 12 h posttransportation, and appearance and behavior were observed at 0, 2, 4, 6, and 12 h and 7 d posttransportation. Metomidate concentrations tested were 0.0 (control), 0.1, 0.2, 0.3, and 0.4 mg/L. At the concentrations tested, metomidate neither inhibited elevations in blood glucose nor improved marketability. Fish that were transported with 0.3-mg/L metomidate were less marketable based on behavioral indices, and fish that were transported with 0.4-mg/L metomidate had higher glucose levels than control fish. Use of metomidate as a transport sedative for threespot gourami should be considered with caution and may be problematic at the concentrations tested; however, further research examining additional indices of stress may clarify metomidate use for this species.

Received February 16, 2011; accepted December 18, 2011.
Numerical and physical magnitudes are mapped into time
Authors: Ben-Meir Shachar , Ganor-Stern Dana , Tzelgov Joseph
Published: May 2012

In two experiments we investigated mapping of numerical and physical magnitudes with temporal order. Pairs of digits were presented sequentially for a size comparison task. An advantage for numbers presented in ascending order was found when participants were comparing the numbers' physical and numerical magnitudes. The effect was more robust for comparisons of physical size, as it was found using both select larger and select smaller instructions, while for numerical comparisons it was found only for select larger instructions. Varying both the digits' numerical and physical sizes resulted in a size congruity effect, indicating automatic processing of the irrelevant magnitude dimension. Temporal order and the congruency between numerical and physical magnitudes affected comparisons in an additive manner, thus suggesting that they affect different stages of the comparison process.
BATMAN—an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model
Authors: Hao Jie , Astle William , De Iorio Maria , Ebbels Timothy M D
Published: May 2012

Motivation: Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject to human error. Conversely, alignment and binning can introduce artefacts and limit immediate biological interpretation of models.

Results: We present the Bayesian automated metabolite analyser for NMR spectra (BATMAN), an R package that deconvolutes peaks from one-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples. It applies a Markov chain Monte Carlo algorithm to sample from a joint posterior distribution of the model parameters and obtains concentration estimates with reduced error compared with conventional numerical integration and comparable to manual deconvolution by experienced spectroscopists.

Availability and implementation:  http://www1.imperial.ac.uk/medicine/people/t.ebbels/

Contact:  t.ebbels@imperial.ac.uk
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies
Authors: Kofler Robert , Schlötterer Christian
Published: May 2012

Summary: An analysis of gene set [e.g. Gene Ontology (GO)] enrichment assumes that all genes are sampled independently from each other with the same probability. These assumptions are violated in genome-wide association (GWA) studies since (i) longer genes typically have more single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters. Herein, we introduce Gowinda, a software specifically designed to test for enrichment of gene sets in GWA studies. We show that GO tests on GWA data could result in a substantial number of false-positive GO terms. Permutation tests implemented in Gowinda eliminate these biases, but maintain sufficient power to detect enrichment of GO terms. Since sufficient resolution for large datasets requires millions of permutations, we use multi-threading to keep computation times reasonable.

Availability and implementation: Gowinda is implemented in Java (v1.6) and freely available on http://code.google.com/p/gowinda/

Contact:  christian.schloetterer@vetmeduni.ac.at

Supplementary information: Manual: http://code.google.com/p/gowinda/wiki/Manual. Test data and tutorial: http://code.google.com/p/gowinda/wiki/Tutorial. Validation: http://code.google.com/p/gowinda/wiki/Validation.
Bringing together linguistic and genetic evidence to test the Bantu expansion
Authors: de Filippo Cesare , Bostoen Koen , Stoneking Mark , Pakendorf Brigitte
Published: May 2012

The expansion of Bantu languages represents one of the most momentous events in the history of Africa. While it is well accepted that Bantu languages spread from their homeland (Cameroon/Nigeria) approximately 5000 years ago (ya), there is no consensus about the timing and geographical routes underlying this expansion. Two main models of Bantu expansion have been suggested: The ‘early-split’ model claims that the most recent ancestor of Eastern languages expanded north of the rainforest towards the Great Lakes region approximately 4000 ya, while the ‘late-split’ model proposes that Eastern languages diversified from Western languages south of the rainforest approximately 2000 ya. Furthermore, it is unclear whether the language dispersal was coupled with the movement of people, raising the question of language shift versus demic diffusion. We use a novel approach taking into account both the spatial and temporal predictions of the two models and formally test these predictions with linguistic and genetic data. Our results show evidence for a demic diffusion in the genetic data, which is confirmed by the correlations between genetic and linguistic distances. While there is little support for the early-split model, the late-split model shows a relatively good fit to the data. Our analyses demonstrate that subsequent contact among languages/populations strongly affected the signal of the initial migration via isolation by distance.
Modelling the interaction of keratinocytes and fibroblasts during normal and abnormal wound healing processes
Authors: Menon Shakti N. , Flegg Jennifer A. , McCue Scott W. , Schugart Richard C. , Dawson Rebecca A. , McElwain D. L. Sean
Published: May 2012

The crosstalk between fibroblasts and keratinocytes is a vital component of the wound healing process, and involves the activity of a number of growth factors and cytokines. In this work, we develop a mathematical model of this crosstalk in order to elucidate the effects of these interactions on the regeneration of collagen in a wound that heals by second intention. We consider the role of four components that strongly affect this process: transforming growth factor-β, platelet-derived growth factor, interleukin-1 and keratinocyte growth factor. The impact of this network of interactions on the degradation of an initial fibrin clot, as well as its subsequent replacement by a matrix that is mainly composed of collagen, is described through an eight-component system of nonlinear partial differential equations. Numerical results, obtained in a two-dimensional domain, highlight key aspects of this multifarious process, such as re-epithelialization. The model is shown to reproduce many of the important features of normal wound healing. In addition, we use the model to simulate the treatment of two pathological cases: chronic hypoxia, which can lead to chronic wounds; and prolonged inflammation, which has been shown to lead to hypertrophic scarring. We find that our model predictions are qualitatively in agreement with previously reported observations and provide an alternative pathway for gaining insight into this complex biological process.
A cascade of evolutionary change alters consumer-resource dynamics and ecosystem function
Authors: Walsh Matthew R. , DeLong John P. , Hanley Torrance C. , Post David M.
Published: May 2012

It is becoming increasingly clear that intraspecific evolutionary divergence influences the properties of populations, communities and ecosystems. The different ecological impacts of phenotypes and genotypes may alter selection on many species and promote a cascade of ecological and evolutionary change throughout the food web. Theory predicts that evolutionary interactions across trophic levels may contribute to hypothesized feedbacks between ecology and evolution. However, the importance of ‘cascading evolutionary change’ in a natural setting is unknown. In lakes in Connecticut, USA, variation in migratory behaviour and feeding morphology of a fish predator, the alewife (
Alosa pseudoharengus
), drives life-history evolution in a species of zooplankton prey (
Daphnia ambigua
). Here we evaluated the reciprocal impacts of
Daphnia
evolution on ecological processes in laboratory mesocosms. We show that life-history evolution in
Daphnia
facilitates divergence in rates of population growth, which in turn significantly alters consumer-resource dynamics and ecosystem function. These experimental results parallel trends observed in lakes. Such results argue that a cascade of evolutionary change, which has occurred over contemporary timescales, alters community and ecosystem processes.
Protection of the Extracts ofLentinus edodesMycelia against Carbon-Tetrachloride-Induced Hepatic Injury in Rats
Authors: Chen Mei-Fen , Chung Hsien-Hui , Lu Han-Lin
Published: May 2012

Lentinus edodesis the medicinal macrofungus showing potential for therapeutic applications in infectious disorders including hepatitis. In an attempt to develop the agent for handling hepatic injury, we used the extracts ofLentinus edodesmycelia (LEM) to screen the effect on hepatic injury in rats induced by carbon tetrachloride (CCl4). Intraperitoneal administration of CCl4not only increased plasma glutamic oxaloacetic transaminase (GOT) and glutamic pyruvic transaminase (GPT) but also decreased hepatic superoxide dismutase (SOD) and glutathione peroxidase (GPx) levels in rats. Similar to the positive control silymarin, oral administration (three times daily) of this product (LEM) for 8 weeks significantly reduced plasma GOT and GPT. Also, the activities of antioxidant enzymes of SOD and GPx were elevated by LEM. in liver from CCl4-treated rats, indicating that mycelium can increase antioxidant-like activity. Moreover, the hepatic mRNA and protein levels of SOD and GPx were both markedly raised by LEM. The obtained results suggest that oral administration of the extracts ofLentinus edodesmycelia (LEM) has the protective effect against CCl4-induced hepatic injury in rats, mainly due to an increase in antioxidant-like action.
Optical Method for Cardiovascular Risk Marker Uric Acid Removal Assessment during Dialysis
Authors: Holmar Jana , Fridolin Ivo , Uhlin Fredrik , Lauri Kai , Luman Merike
Published: May 2012

The aim of this study was to estimate the concentration of uric acid (UA) optically by using the original and processed ultraviolet (UV) absorbance spectra of spent dialysate. Also, the effect of using several wavelengths (multi-wavelength algorithms) for estimation was examined. This paper gives an overview of seven studies carried out in Linköping, Sweden, and Tallinn, Estonia. A total of 60 patients were monitored over their 188 dialysis treatment procedures. Dialysate samples were taken and analysed by means of UA concentration in a chemical laboratory and with a double-beam spectrophotometer. The measured UV absorbance spectra were processed. Three models for the original and three for the first derivate of UV absorbance were created; concentrations of UA from the different methods were finally compared in terms of mean values and SD. The mean concentration (micromol/L) of UA was49.7±23.0measured in the chemical laboratory, and48.9±22.4calculated with the best estimate among all models. The concentrations were not significantly different (P≥0.17). It was found that using a multi-wavelength and processed signal approach leads to more accurate results, and therefore these approaches should be used in future.
Dose Effect Evaluation and Therapeutic Window of the Neuro-EPO Nasal Application for the Treatment of the Focal Ischemia Model in the Mongolian Gerbil
Authors: Teste Iliana Sosa , Tamos Yuneidys Mengana , Cruz Yamila Rodríguez , Cernada Adriana Muñoz , Rodríguez Janette Cruz , Martínez Nelvis Subirós , Antich Rosa Maria Coro , González-Quevedo Alina , Rodríguez Julio Cesar García
Published: May 2012

Cerebrovascular disease is the third leading cause of death and the leading cause of disability in Cuba and in several developed countries. A possible neuroprotective agent is the rHu-EPO, whose effects have been demonstrated in models of brain ischemia. The Neuro-EPO is a derivative of the rHu-EPO that avoids the stimulation of erythropoiesis. The aim of this study was to determine the Neuro-EPO delivery into the central nervous system (CNS) to exert a neuroprotective effect in cerebral ischemia model of the Mongolian gerbil. The Neuro-EPO in a rate of 249.4 UI every 8 hours for 4 days showed 25% higher viability efficacy (), improving neurological score and behavior of the spontaneous exploratory activity, the preservation of CA3 areas of the hippocampus, the cortex, and thalamic nuclei in the focal ischemia model of the Mongolian gerbil. In summary, this study, the average dose-used Neuro-EPO (249.4 UI/10 μL/every 8 hours for 4 days), proved to be valid indicators of viability, neurological status, and spontaneous exploratory activity, being significantly lower than that reported for the systemically use of the rHu-EPO as a neuroprotectant. Indeed, up to 12 h after brain ischemia is very positive Neuro-EPO administration by the nasal route as a candidate for neuroprotection.
Growth and Anatomical Parameters of Adventitious Roots Formed on Mung Bean Hypocotyls Are Correlated with Galactoglucomannan Oligosaccharides Structure
Authors: Kollárová K. , Zelko I. , Henselová M. , Capek P. , Lišková D.
Published: May 2012

The effect of galactoglucomannan oligosaccharides (GGMOs) compared with chemically modified oligosaccharides, GGMOs-g (with reduced number of D-galactose side chains) and GGMOs-r (with reduced reducing ends) on mung bean (Vigna radiata(L.) Wilczek) adventitious roots formation, elongation, and anatomical structure have been studied. All types of oligosaccharides influenced adventitious root formation in the same way: stimulation in the absence of exogenous auxin and inhibition in the presence of exogenous auxin. Both reactions are probably related with the presence/content of endogenous auxin in plant cuttings. However, the adventitious root length was inhibited by GGMOs both in the absence as well as in the presence of auxin (IBA or NAA), while GGMOs-g inhibition was significantly weaker compared with GGMOs. GGMOs-r were without significant difference on both processes, compared with GGMOs. GGMOs affected not only the adventitious root length but also their anatomy in dependence on the combination with certain type of auxin. The oligosaccharides influenced cortical cells division, which was reflected in the cortex area and in the root diameter. All processes followed were dependent on oligosaccharides chemical structure. The results suggest also that GGM-derived oligosaccharides may play an important role in adventitious roots elongation but not in their formation.
Physiological and Growth Responses of Six Turfgrass Species Relative to Salinity Tolerance
Authors: Uddin Md. Kamal , Juraimi Abdul Shukor , Ismail Mohd. Razi , Hossain Md. Alamgir , Othman Radziah , Abdul Rahim Anuar
Published: May 2012

The demand for salinity-tolerant turfgrasses is increasing due to augmented use of effluent or low-quality water (sea water) for turf irrigation and the growing turfgrass industry in coastal areas. Experimental plants, grown in plastic pots filled with a mixture of river sand andKOSASRpeat (9 : 1), were irrigated with sea water at different dilutions imparting salinity levels of 0, 8, 16, 24, 32, 40, or 48 dS m-1. Salinity tolerance was evaluated on the basis of leaf firing, shoot and root growth reduction, proline content, and relative water content.Paspalum vaginatumwas found to be most salt tolerant followed byZoysia japonicaandZoysia matrella, whileDigitaria didactyla,Cynodon dactylon“Tifdwarf,” andCynodon dactylon“Satiri” were moderately tolerant. The results indicate the importance of turfgrass varietal selection for saline environments.
Biology and Biotechnology of Follicle Development
Authors: Palma Gustavo Adolfo , Argañaraz Martin Eduardo , Barrera Antonio Daniel , Rodler Daniela , Mutto Adrian Ángel , Sinowatz Fred
Published: May 2012

Growth and development of ovarian follicles require a series of coordinated events that induce morphological and functional changes within the follicle, leading to cell differentiation and oocyte development. The preantral early antral follicle transition is the stage of follicular development during which gonadotropin dependence is obtained and the progression into growing or atresia of the follicle is made. Follicular growth during this period is tightly regulated by oocyte-granulosatheca cell interactions. A cluster of early expressed genes is required for normal folliculogenesis. Granulosa cell factors stimulate the recruitment of theca cells from cortical stromal cells. Thecal factors promote granulosa cell proliferation and suppress granulosa cell apoptosis. Cell-cell and cell-extracellular matrix interactions influence the production of growth factors in the different follicular compartments (oocyte, granulosa, and theca cells). Several autocrine and paracrine factors are involved in follicular growth and differentiation; their activity is present even at the time of ovulation, decreasing the gap junction communication, and stimulating the theca cell proliferation. In addition, the identification of the factors that promote follicular growth from the preantral stage to the small antral stage may provide important information for the identification for assisted reproduction techniques.