bluuebunny/crossref_metadata_2025 huggingface dataset:
Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems
Authors: Zhang Hong-Xuan , Goutsias John
Published: March 2011

Sensitivity analysis is a valuable task for assessing the effects of biological variability on cellular behavior. Available techniques require knowledge of nominal parameter values, which cannot be determined accurately due to experimental uncertainty typical to problems of systems biology. As a consequence, the practical use of existing sensitivity analysis techniques may be seriously hampered by the effects of unpredictable experimental variability. To address this problem, we propose here a probabilistic approach to sensitivity analysis of biochemical reaction systems that explicitly models experimental variability and effectively reduces the impact of this type of uncertainty on the results. The proposed approach employs a recently introduced variance-based method to sensitivity analysis of biochemical reaction systems [Zhang et al., J. Chem. Phys. 134, 094101 (2009)] and leads to a technique that can be effectively used to accommodate appreciable levels of experimental variability. We discuss three numerical techniques for evaluating the sensitivity indices associated with the new method, which include Monte Carlo estimation, derivative approximation, and dimensionality reduction based on orthonormal Hermite approximation. By employing a computational model of the epidermal growth factor receptor signaling pathway, we demonstrate that the proposed technique can greatly reduce the effect of experimental variability on variance-based sensitivity analysis results. We expect that, in cases of appreciable experimental variability, the new method can lead to substantial improvements over existing sensitivity analysis techniques.
Interaction between LiH molecule and Li atom from state-of-the-art electronic structure calculations
Authors: Skomorowski Wojciech , Pawłowski Filip , Korona Tatiana , Moszynski Robert , Żuchowski Piotr S. , Hutson Jeremy M.
Published: March 2011

State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born–Oppenheimer approximation. The interaction potential was obtained using a combination of the explicitly correlated unrestricted coupled-cluster method with single, double, and noniterative triple excitations [UCCSD(T)-F12] for the core–core and core–valence correlation and full configuration interaction for the valence–valence correlation. The potential energy surface has a global minimum 8743 cm−1 deep if the Li–H bond length is held fixed at the monomer equilibrium distance or 8825 cm−1 deep if it is allowed to vary. In order to evaluate the performance of the conventional CCSD(T) approach, calculations were carried out using correlation-consistent polarized valence X-tuple-zeta basis sets, with X ranging from 2 to 5, and a very large set of bond functions. Using simple two-point extrapolations based on the single-power laws X−2 and X−3 for the orbital basis sets, we were able to reproduce the CCSD(T)–F12 results for the characteristic points of the potential with an error of 0.49% at worst. The contribution beyond the CCSD(T)–F12 model, obtained from full configuration interaction calculations for the valence–valence correlation, was shown to be very small, and the error bars on the potential were estimated. At linear LiH–Li geometries, the ground-state potential shows an avoided crossing with an ion-pair potential. The energy difference between the ground-state and excited-state potentials at the avoided crossing is only 94 cm−1. Using both adiabatic and diabatic pictures, we analyze the interaction between the two potential energy surfaces and its possible impact on the collisional dynamics. When the Li–H bond is allowed to vary, a seam of conical intersections appears at C2v geometries. At the linear LiH–Li geometry, the conical intersection is at a Li–H distance which is only slightly larger than the monomer equilibrium distance, but for nonlinear geometries it quickly shifts to Li–H distances that are well outside the classical turning points of the ground-state potential of LiH. This suggests that the conical intersection will have little impact on the dynamics of Li–LiH collisions at ultralow temperatures. Finally, the reaction channels for the exchange and insertion reactions are also analyzed and found to be unimportant for the dynamics.
A microfluidic vibrating wire viscometer for operation at high pressure and high temperature
Authors: Dehestru Guillaume , Leman Marie , Jundt Jacques , Dryden Phil , Sullivan Matthew , Harrison Christopher
Published: March 2011

This article discusses a microfluidic vibrating wire viscometer with an internal volume of a few microliters. Accuracy of order ±10% for viscosities ranging from 0.1 to 100 cP is demonstrated for temperatures (10 °C–175 °C) and pressures (10–24 000 psi) suitable for oilfield use by prior calibration in air and toluene. Comparison between multiple data sets indicates that a large fraction of the discrepancy between literature values is systematic, indicating that future refinements may be possible with better interpretation. Confinement effects are evaluated and are not found to play a significant role, which is surprising since the ratio (6.6) of the fluid channel width to the wire diameter is very low.
Cell model of hydrogen liquid at megabar pressures
Authors: Vorob'ev V. S. , Novikov V. G.
Published: March 2011

We present a new model for the quantum fluid resulting from the melting of crystal hydrogen at megabar pressures. This model is based on a cell approach that takes into account of localized electron states and the effect of proton degeneration. The predictions of our model are in good agreement with recent experimental results on the anomalies in the melting process.
Negative refractive index in symmetric cut-wire pair metamaterial
Authors: Ourir Abdelwaheb , Ouslimani Habiba Hafdallah
Published: March 2011

Plasmonic metamaterial with a negative refractive index is achieved in a periodical symmetric cut-wire pair without any structural asymmetry. The main control parameter is the lateral lattice size. The designed structure presents two discrete resonance modes due to hybridization. The electric resonance depends strongly on the structural parameter, while the magnetic resonance remains unchanged with this parameter. The hybridization scheme can be inverted by increasing the lateral lattice width. Theoretical and experimental results demonstrate a negative refraction index for the designed structure when the electric resonance frequency occurs below the magnetic one. This spatial arrangement presents many advantages since it is easier, repetitive and well-adapted for realizations in microwave and optical regimes.
Theory of optical emission enhancement by coupled metal nanoparticles: An analytical approach
Authors: Sun G. , Khurgin J. B.
Published: March 2011

We present an analytical “coupled mode” model explaining enhancement of emission by an emitter placed within complexes of metal nanoparticles and apply it for an important case of an emitter placed inside the gap of two coupled Au nanospheres. This approach has dual advantages of exposing the underling physics of the enhancement and revealing a straightforward path toward optimization.
Sticking and desorption of hydrogen on graphite: A comparative study of different models
Authors: Lepetit Bruno , Lemoine Didier , Medina Zuleika , Jackson Bret
Published: March 2011

We study the physisorption of atomic hydrogen on graphitic surfaces with four different quantum mechanical methods: perturbation and effective Hamiltonian theories, close coupling wavepacket, and reduced density matrix propagation methods. Corrugation is included in the modeling of the surface. Sticking is a fast process which is well described by all methods. Sticking probabilities are of the order of a few percent in the collision energy range 0–25 meV, but are enhanced for collision energies close to those of diffraction resonances. Sticking also increases with surface temperature. Desorption is a slow process which involves multiphonon processes. We show, however, how to correct the close coupling wavepacket method to account for such phenomena and obtain correct time constants for initial state decay. Desorption time constants are in the range of 20–50 ps for a surface temperature of 300 K.
Multiple excitation of silicon nanoclusters during erbium sensitization process in silicon rich oxide host
Authors: Huda M. Q. , Subrina S.
Published: March 2011

Sensitization of erbium through silicon nanocluster (Si-nc) in silicon rich oxide host has been analyzed through a statistical approach. Our analysis shows that significant fraction of Si-ncs can experience multiple excitations during the Er lifecycle. The probability of Si-nc being excited at every alternate cycles of excitation increases from small fractions to percentage levels for incident flux levels above 1018/cm2 s. We show that, for typical values of Er and Si-nc incorporation, saturating effects in Er luminescence starts at flux levels much lower than that for Si-nc excitation. Occurrence of multiple excitation of Si-nc has been correlated with the deteriorating effects in Er sensitization at higher flux incidence.
A quantum defect model for the s, p, d, and f Rydberg series of CaF
Authors: Kay Jeffrey J. , Coy Stephen L. , Wong Bryan M. , Jungen Christian , Field Robert W.
Published: March 2011

We present an improved quantum defect theory model for the “s,” “p,” “d,” and “f” Rydberg series of CaF. The model, which is the result of an exhaustive fit of high-resolution spectroscopic data, parameterizes the electronic structure of the ten (“s”Σ, “p”Σ, “p”Π, “d”Σ, “d”Π, “d”Δ, “f”Σ, “f”Π, “f”Δ, and “f”Φ) Rydberg series of CaF in terms of a set of twenty $\mu _{\ell \ell^{\prime} }^{(\iLambda)}$μℓℓ′(Λ) quantum defect matrix elements and their dependence on both internuclear separation and on the binding energy of the outer electron. Over 1000 rovibronic Rydberg levels belonging to 131 observed electronic states of CaF with n* ≥ 5 are included in the fit. The correctness and physical validity of the fit model are assured both by our intuition-guided combinatorial fit strategy and by comparison with R-matrix calculations based on a one-electron effective potential. The power of this quantum defect model lies in its ability to account for the rovibronic energy level structure and nearly all dynamical processes, including structure and dynamics outside of the range of the current observations. Its completeness places CaF at a level of spectroscopic characterization similar to NO and H2.
Information entropy of conditionally exactly solvable potentials
Authors: Dutta D. , Roy P.
Published: March 2011

We evaluate Shannon entropy for the position and momentum eigenstates of some conditionally exactly solvable potentials which are isospectral to harmonic oscillator and whose solutions are given in terms of exceptional orthogonal polynomials. The Bialynicki–Birula–Mycielski inequality has also been tested for a number of states.
Impact of Cu/III ratio on the near-surface defects in polycrystalline CuGaSe2 thin films
Authors: Islam M. M. , Uedono A. , Ishibashi S. , Tenjinbayashi K. , Sakurai T. , Yamada A. , Ishizuka S. , Matsubara K. , Niki S. , Akimoto K.
Published: March 2011

Polycrystalline CuGaSe2 thin films grown with various Cu/III(=Cu/Ga) ratios were investigated by positron annihilation spectroscopy (PAS). The line-shape parameter S of the spectra was used to characterize defects in CuGaSe2 films. The S-parameter in positron annihilation spectra increased with decreasing bulk Cu/III ratio in the CuGaSe2 film. Experimental results combined with theoretical calculation show the formation of multiple vacancy-type defect complexes in the near-surface region of the CuGaSe2 film when Cu-content in the film is decreased. These point defects appear to cause the higher S-parameter in PAS measurement.
Large deviations of the current in stochastic collisional dynamics
Authors: Lefevere Raphaël , Mariani Mauro , Zambotti Lorenzo
Published: March 2011

We consider a class of deterministic local collisional dynamics, showing how to approximate them by means of stochastic models and then studying the fluctuations of the current of energy. We show first that the variance of the time-integrated current is finite and related to the conductivity by the Green–Kubo relation. Next we show that the law of the empirical average current satisfies a large deviations principle and compute explicitly the rate functional in a suitable scaling limit. We observe that this functional is not strictly convex.
Role of fluid elasticity on the dynamics of rinsing flow by an impinging jet
Authors: Hsu Tienyi T. , Walker Travis W. , Frank Curtis W. , Fuller Gerald G.
Published: March 2011

Rinsing flows are common processes where a jet of one liquid impinges upon a layer of a second liquid for the purpose of removing the second liquid. An imaging setup has been developed to obtain both qualitative and quantitative data on the rinsing flow of a jet of water impinging on either layers of Newtonian or elastic fluids. Three classes of test fluids have been investigated: a Newtonian glycerol-water solution, a semidilute aqueous solution of high molecular weight polyacrylamide solution displaying both elasticity and shear thinning, and an elastic but non-shear thinning Boger fluid. The fluids were designed to have approximately equal zero-shear viscosities. For all cases, a circular hydraulic jump occurs and Saffman–Taylor instabilities were observed at the interface between the low viscosity jet and the higher viscosity coating liquids. Results show that the elasticity (extensional viscosity) of the samples influences the pattern of the instabilities and contributes to dampening surface disturbances in the vicinity of the hydraulic jump. Quantitative measurements of liquid layer thicknesses were obtained using a laser triangulation technique. We observed that shear thinning contributes to increasing the velocity of the hydraulic jump circle growth, and the growth profile appears to be linear instead of logarithmic-like as in the Newtonian fluids. Shear thinning characteristics of the samples also contribute to a larger vertical height of the hydraulic jump and an undercutting phenomenon. The elasticity of the fluids contributes to a “recoil” of the hydraulic jump circle, causing the circle, after initial expansion, to shrink in size before expanding again.
Comparison of the spectral and temporal emission characteristics of homoepitaxial and heteroepitaxial ZnO nanowires
Authors: Pfüller C. , Brandt O. , Flissikowski T. , Grahn H. T. , Ive T. , Speck J. S. , DenBaars S. P.
Published: March 2011

Using metalorganic chemical vapor deposition, we have grown ZnO nanowires (NWs) on ZnO(0001) as well as on Al2O3(0001) and Si(111) substrates. The optical properties of these NWs are studied by continuous-wave and time-resolved photoluminescence spectroscopy. Both the spectral and the temporal characteristics of the NWs are found to be virtually identical despite the different substrates and the different morphology of the NWs. This study thus provides strong experimental evidence for the hypothesis that NWs remove the constraints introduced by the substrate.
Manipulation of optical field distribution in layered composite polymeric-inorganic waveguides
Authors: Hiltunen Jussi , Uusitalo Sanna , Karioja Pentti , Pearce Stuart , Charlton Martin , Wang Meng , Puustinen Jarkko , Lappalainen Jyrki
Published: March 2011

We discuss the manipulation of optical field distribution in a low-refractive index polymeric waveguide by depositing a thin high refractive index Ta2O5 film on top of the waveguide. According to microstructure studies, the sputtered Ta2O5 thin films deposited on the polymer layer were very smooth with root mean square surface roughness value of 0.58 nm, had amorphous phase, and were optimal for integrated optical devices. Both computational and experimental optical studies suggest that the inorganic-polymeric composite waveguide design greatly increases the intensity distribution of the propagating mode at the surface. Consequently, the interaction of the optical field with the ambient surrounding medium is enhanced by a factor of about 1.7 in order of magnitude.
Magnetic and calorimetric investigations of inverse magnetocaloric effect in Pr0.46Sr0.54MnO3
Authors: Naik V. B. , Barik S. K. , Mahendiran R. , Raveau B.
Published: March 2011

We investigated magnetic entropy change (ΔSm) in the A-type antiferromagnet Pr0.46Sr0.54MnO3 by magnetic and differential scanning calorimetry (DSC) methods. The field-induced antiferromagnetic to ferromagnetic transition is first-order in nature and is accompanied by a large change in the latent heat as evidenced by the DSC data. The ΔSm shows an inverse magnetocaloric effect (ΔSm=+9 J kg−1 K−1 for ΔH=7 T) around the Neel temperature (TN=210±2 K) by magnetic measurement, which closely agrees with the calorimetric results. It is suggested that the large positive ΔSm results from a field-induced structural transition that accompanies the destruction of antiferromagnetism.
Extensional flow of blood analog solutions in microfluidic devices
Authors: Sousa P. C. , Pinho F. T. , Oliveira M. S. N. , Alves M. A.
Published: March 2011

In this study, we show the importance of extensional rheology, in addition to the shear rheology, in the choice of blood analog solutions intended to be used in vitro for mimicking the microcirculatory system. For this purpose, we compare the flow of a Newtonian fluid and two well-established viscoelastic blood analog polymer solutions through microfluidic channels containing both hyperbolic and abrupt contractions/expansions. The hyperbolic shape was selected in order to impose a nearly constant strain rate at the centerline of the microchannels and achieve a quasihomogeneous and strong extensional flow often found in features of the human microcirculatory system such as stenoses. The two blood analog fluids used are aqueous solutions of a polyacrylamide (125 ppm w/w) and of a xanthan gum (500 ppm w/w), which were characterized rheologically in steady-shear flow using a rotational rheometer and in extension using a capillary breakup extensional rheometer (CaBER). Both blood analogs exhibit a shear-thinning behavior similar to that of whole human blood, but their relaxation times, obtained from CaBER experiments, are substantially different (by one order of magnitude). Visualizations of the flow patterns using streak photography, measurements of the velocity field using microparticle image velocimetry, and pressure-drop measurements were carried out experimentally for a wide range of flow rates. The experimental results were also compared with the numerical simulations of the flow of a Newtonian fluid and a generalized Newtonian fluid with shear-thinning behavior. Our results show that the flow patterns of the two blood analog solutions are considerably different, despite their similar shear rheology. Furthermore, we demonstrate that the elastic properties of the fluid have a major impact on the flow characteristics, with the polyacrylamide solution exhibiting a much stronger elastic character. As such, these properties must be taken into account in the choice or development of analog fluids that are adequate to replicate blood behavior at the microscale.
Reduced surface leakage current and trapping effects in AlGaN/GaN high electron mobility transistors on silicon with SiN/Al2O3 passivation
Authors: Liu Z. H. , Ng G. I. , Zhou H. , Arulkumaran S. , Maung Y. K. T.
Published: March 2011

The surface leakage currents and the surface trapping effects of the AlGaN/GaN high electron mobility transistors (HEMTs) on silicon with different passivation schemes, namely, a 120 nm plasma enhanced chemical vapor deposited SiN, a 10 nm atomic layer deposited (ALD) Al2O3 and a bilayer of SiN/Al2O3 (120/10 nm) have been investigated. After SiN passivation, the surface leakage current of the GaN HEMT was found to increase by about six orders; while it only increased by three orders after the insertion of Al2O3 between SiN and AlGaN/GaN. The surface conduction mechanism is believed to be the two-dimensional variable range hopping for all the samples. The leakage current in the etched GaN buffer layer with SiN/Al2O3 bilayer passivation was also much smaller than that with only SiN passivation. The pulse measurement shows that the bilayer of SiN/Al2O3 passivation scheme can effectively reduce the surface states and suppress the trapping effects.
Hall resistivity of Fe doped Si film at low temperatures
Authors: Xu Y. Q. , Su W. F. , Nie T. X. , Cui J. , Shao Y. M. , Jiang Z. M.
Published: March 2011

Nonmonotonically magnetic-field-dependent and sensitively temperature-dependent Hall resistivity of Fe doped Si film has been systematically studied at low temperatures. Two-band of holes conduction mechanism is proposed to be responsible for the observed extraordinary Hall resistivity, as well as magnetoresistance characteristics. Holes in the valence band are generated by thermal activation of electrons from the valence band to shallow acceptor levels with an activation energy of 41.2 meV while holes in acceptor impurity band transport by hopping processes with an activation energy of 2.5 meV. This work shows that even very complicated behavior of Hall resistivity may be understood under a two-band conduction mechanism.
Spatially resolved lasers using a glassy cholesteric liquid crystal film with lateral pitch gradient
Authors: Wei Simon K. H. , Chen Shaw H.
Published: March 2011

To fabricate spatially resolved glassy cholesteric liquid crystal (CLC) lasers, a lateral pitch gradient was introduced by thermally activated diffusion across the interface of two films comprising nematic and cholesteric oligofluorene doped with a red-emitting oligifluorene. The formation of spatially resolved Grandjean–Cano bands was accountable by strong surface anchoring at substrates and the qualitative chiral concentration profile. Across each band there was a common stop band, and a set of bands produced multiple lasing peaks across the spectral range determined by light-emitter’s fluorescence spectrum. The resultant lasing thresholds, 6.6–7.6 mJ/cm2, and slope efficiencies, 0.2%–1.5%, are superior to those reported to date for gradient-pitch CLC lasers.
Room-temperature nonsaturating magnetoresistance of intrinsic bulk silicon in high pulsed magnetic fields
Authors: Wu L. H. , Zhang X. , Vanacken J. , Schildermans N. , Wan C. H. , Moshchalkov V. V.
Published: March 2011

Nonsaturating positive magnetoresistance (MR) of intrinsic bulk silicon (i-Si) was observed at forward bias, exhibiting an almost linear behavior at high magnetic fields (5 T<B<40 T). The MR reaches 180% at 40 T at room temperature using a bias of 1.5 V, and there is no indication that this MR would saturate at even stronger fields. The nonsaturating large MR of i-Si supports experimentally the hypothesis that the MR of silicon may be induced by inhomogeneous current flows.
Effect of maternal age on mitochondrial DNA copy number, ATP content and IVF outcome of bovine oocytes
Authors: Iwata Hisataka , Goto Hiroya , Tanaka Hiroshi , Sakaguchi Yosuke , Kimura Koji , Kuwayama Takehito , Monji Yashunori
Published: March 2011

The primary aim of the present study was to examine the effect of maternal age (in months) on mitochondrial DNA copy number (Mt number), ATP content and IVF outcome of bovine oocytes. We also compared the Mt number of oocytes with fertilisation outcome and ATP content. Oocytes were collected from cows aged 20–204 months and the Mt number was determined by real-time polymerase chain reaction. The Mt number in immature and mature oocytes was determined to be 368 118 and 807 794, respectively; the ATP content in these oocytes was 1.2 and 2.0 pM, respectively. Both Mt number and ATP content increased during oocyte maturation. However, after 90 months of age, the Mt number of mature oocytes decreased with increasing maternal age, whereas the ATP content of mature oocytes was positively correlated with maternal age (P < 0.01); there was no obvious relationship observed between Mt number and ATP content. Furthermore, maternal age was positively correlated with the abnormal fertilisation rate (P < 0.01). Mt number and fertilisation outcome were unrelated, but the nature of this relationship differed between young (21–89 months) and old (>89 months) cows. Thus, we conclude that Mt number, the ATP content and fertilisation outcome of bovine oocytes are affected by maternal age.
A sensory subpopulation depends on vesicular glutamate transporter 2 for mechanical pain, and together with substance P, inflammatory pain
Authors: Lagerström Malin C. , Rogoz Katarzyna , Abrahamsen Bjarke , Lind Anne-Li , Ölund Caroline , Smith Casey , Mendez José Alfredo , Wallén-Mackenzie Åsa , Wood John N. , Kullander Klas
Published: March 2011

Ablating or functionally compromising sets of sensory neurons has provided important insights into peripheral modality-specific wiring in the somatosensory system. Inflammatory hyperalgesia, cold pain, and noxious mechanosensation have all been shown to depend upon Na
v
1.8-positive sensory neurons. The release of fast-acting neurotransmitters, such as glutamate, and more slowly released neuropeptides, such as substance P (SP), contribute to the diversified responses to external stimuli. Here we show that deleting
Vglut2
in

Na
v
1.8
Cre

-positive neurons compromised mechanical pain and NGF-induced thermal hyperalgesia, whereas tactile-evoked sensation, thermal, formalin-evoked, and chronic neuropathic pain were normal. However, when

Vglut2
f/f
;Na
v
1.8
Cre

mice were injected with a SP antagonist before the formalin test, the second phase pain response was nearly completely abolished, whereas in control mice, the pain response was unaffected. Our results suggest that VGLUT2-dependent signaling originating from Na
v
1.8-positive neurons is a principal sensing mechanism for mechanical pain and, together with SP, inflammatory pain. These data define sets of primary afferents associated with specific modalities and provide useful genetic tools with which to analyze the pathways that are activated by functionally distinct neuronal populations and transmitters.
Design, synthesis, and evaluation of potent bryostatin analogs that modulate PKC translocation selectivity
Authors: Wender Paul A. , Baryza Jeremy L. , Brenner Stacey E. , DeChristopher Brian A. , Loy Brian A. , Schrier Adam J. , Verma Vishal A.
Published: March 2011

Modern methods for the identification of therapeutic leads include chemical or virtual screening of compound libraries. Nature’s library represents a vast and diverse source of leads, often exhibiting exquisite biological activities. However, the advancement of natural product leads into the clinic is often impeded by their scarcity, complexity, and nonoptimal properties or efficacy as well as the challenges associated with their synthesis or modification. Function-oriented synthesis represents a strategy to address these issues through the design of simpler and therefore synthetically more accessible analogs that incorporate the activity-determining features of the natural product leads. This study illustrates the application of this strategy to the design and synthesis of functional analogs of the bryostatin marine natural products. It is specifically directed at exploring the activity-determining role of bryostatin A-ring functionality on PKC affinity and selectivity. The resultant functional analogs, which were prepared by a flexible, modular synthetic strategy, exhibit excellent affinity to PKC and differential isoform selectivity. These and related studies provide the basic information needed for the design of simplified and thus synthetically more accessible functional analogs that target PKC isoforms, major targets of therapeutic interest.
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method
Authors: Ma Haisu , Schadt Eric E. , Kaplan Lee M. , Zhao Hongyu
Published: March 2011

Motivation: The identification of condition specific sub-networks from gene expression profiles has important biological applications, ranging from the selection of disease-related biomarkers to the discovery of pathway alterations across different phenotypes. Although many methods exist for extracting these sub-networks, very few existing approaches simultaneously consider both the differential expression of individual genes and the differential correlation of gene pairs, losing potentially valuable information in the data.

Results: In this article, we propose a new method, COSINE (COndition SpecIfic sub-NEtwork), which employs a scoring function that jointly measures the condition-specific changes of both ‘nodes’ (individual genes) and ‘edges’ (gene–gene co-expression). It uses the genetic algorithm to search for the single optimal sub-network which maximizes the scoring function. We applied COSINE to both simulated datasets with various differential expression patterns, and three real datasets, one prostate cancer dataset, a second one from the across-tissue comparison of morbidly obese patients and the other from the across-population comparison of the HapMap samples. Compared with previous methods, COSINE is more powerful in identifying truly significant sub-networks of appropriate size and meaningful biological relevance.

Availability: The R code is available as the COSINE package on CRAN: http://cran.r-project.org/web/packages/COSINE/index.html.

Contact:  hongyu.zhao@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
ogaraK: a population genetics simulator for malaria
Authors: Antao Tiago , Hastings Ian M.
Published: March 2011

Motivation: The evolution of resistance in Plasmodium falciparum malaria against most available treatments is a major global health threat. Population genetics approaches are commonly used to model the spread of drug resistance. Due to uncommon features in malaria biology, existing forward-time population genetics simulators cannot suitably model Plasmodium falciparum malaria.

Results: Here we present ogaraK, a population genetics simulator for modelling the spread of drug-resistant malaria. OgaraK is designed to make malaria simulation computationally tractable as it models infections, not individual parasites. OgaraK is also able to model the life cycle of the parasite which includes both haploid and diploid phases and sexual and asexual reproduction. We also allow for the simulation of different inbreeding levels, an important difference between high and low transmission areas and a fundamental factor influencing the outcome of strategies to control or eliminate malaria.

Availability: OgaraK is available as free software (GPL) from the address http://popgen.eu/soft/ogaraK.

Contact:  tra@popgen.eu

Supplementary information:  Supplementary data is available at Bioinformatics online.
MrBayes on a Graphics Processing Unit
Authors: Zhou Jianfu , Liu Xiaoguang , Stones Douglas S. , Xie Qiang , Wang Gang
Published: March 2011

Motivation: Bayesian phylogenetic inference can be used to propose a ‘tree of life’ for a collection of species whose DNA sequences are known. While there are many packages available that implement Bayesian phylogenetic inference, such as the popular MrBayes, running these programs poses significant computational challenges. Parallelized versions of the Metropolis coupled Markov chain Monte Carlo (MC3) algorithm in MrBayes have been presented that can run on various platforms, such as a graphics processing unit (GPU). The GPU has been used as a cost-effective means for computational research in many fields. However, until now, some limitations have prevented the GPU from being used to run MrBayes MC3 effectively.

Results: We give an appraisal of the possibility of realistically implementing MrBayes MC3 in parallel on an ordinary four-core desktop computer with a GPU. An earlier proposed algorithm for running MrBayes MC3 in parallel on a GPU has some significant drawbacks (e.g. too much CPU–GPU communication) which we resolve. We implement these improvements on the NVIDIA GeForce GTX 480 as most other GPUs are unsuitable for running MrBayes MC3 due to a range of reasons, such as having insufficient support for double precision floating-point arithmetic. Experiments indicate that run-time can be decreased by a factor of up to 5.4 by adding a single GPU (versus state-of-the-art multicore parallel algorithms). We can also achieve a speedup (versus serial MrBayes MC3) of more than 40 on a sufficiently large dataset using two GPUs.

Availability: GPU MrBayes (i.e. the proposed implementation of MrBayes MC3 for the GPU) is available from http://mrbayes-gpu.sourceforge.net/.

Contact:  liuxg74@yahoo.com.cn

Supplementary information:  Supplementary data are avaliable at Bioinformatics online.
Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA
Authors: Dey Abhinav , Verma Amit Kumar , Chatterji Dipankar
Published: March 2011

The protein MsRbpA fromMycobacterium smegmatisrescues RNA polymerase (RNAP) from the inhibitory effect of rifampicin (Rif). We have reported previously that MsRbpA interacts with the β-subunit of RNAP and that the effect of MsRbpA on Rif-resistant (RifR) RNAP is minimal. Here we attempted to gain molecular insights into the mechanism of action of this protein with respect to its role in rescuing RNAP from Rif-mediated transcription inhibition. Our experimental approach comprised multiple-round transcription assays, fluorescence spectroscopy, MS and surface plasmon resonance in order to meet the above objective. Based on our molecular studies we propose here that Rif is released from its binding site in the RNAP–Rif complex in the presence of MsRbpA. Biophysical studies reveal that the location of MsRbpA on RNAP is at the junction of the β- and β′-subunits, close to the Rif-binding site and the (i+1) site on RNAP.
The effect of lipid emulsion on depth of anaesthesia following thiopental administration to rabbits
Authors: Kazemi A. , Harvey M. , Cave G. , Lahner D.
Published: March 2011

Intravenous lipid emulsion has proven benefit in lipophilic drug‐induced cardiotoxicity. Its effect in reversal of central nervous system depression secondary to overdose with lipophilic psychotropic agents remains uncertain. Twenty adult New Zealand White rabbits were anaesthetised with 20 mg.kg−1 thiopental and randomised to receive either 4 ml.kg−1 saline 0.9% or 4 ml.kg−1 lipid emulsion 20% immediately afterwards. Depth of anaesthesia was monitored using bispectral index (BIS) at 1‐min intervals. Duration of anaesthesia was measured as time to regain the righting reflex (ability of the animal to right spontaneously from dorsal recumbency to sternal recumbency). The BIS was greater in the control group (p = 0.011). The greatest BIS differential was observed immediately following treatment (mean (SD) BIS 75.0 (9.5) for saline vs 58.6 (10.4) for lipid, 95% CI 5.75–27.1; p < 0.001). No difference was observed in duration of anaesthesia (mean (SD) 15.5 (0.8) min for saline vs 15.6 (0.7) min for lipid, p = 0.86). Lipid emulsion administration may serve to increase central nervous system depression in the early phase of lipophilic toxin distribution.
Anaplastic large cell Ki‐1 lymphoma. Delineation of two morphological types
Authors: Chan J. K. C. , Ng C. S. , Hui P. K. , Leung T. W. , Lo E. S. F. , Lau W. H. , Mcguire L. J.
Published: March 2011

This report describes 16 cases of the recently recognized anaplastic large cell Ki‐1 lymphoma. The disease showed a male:female ratio of 2.2:1 and a bimodal age distribution with peaks in the third and eighth decades. The clinical presentation was highly variable, with lymph node, skin, bone and gastrointestinal tract being the most commonly affected sites. The lymph nodes usually showed subtotal or sinusoidal involvement, and parenchymal fibrosis was common. The large neoplastic cells were almost invariably admixed with many reactive small lymphocytes, histiocytes and/or neutrophils. Two cytological types could be delineated: type I (pale cell, four cases) consisted of large polygonal cells with distinct pink‐staining cell membrane and pale cytoplasm and pleomorphic nuclei showing marked chromatin clearing; and type II (basophilic cell, 12 cases) consisted of round or oval cells with basophilic cytoplasm and/or paranuclear pale hof, pleomorphic nuclei often reniform or lobulated and with frequent multinucleated wreath‐like and Reed‐Sternberg‐like cells. Immunohistochemical studies showed that nine cases (56.3%) exhibited a T‐cell phenotype, three cases (18.8%) each exhibited a B‐cell or null‐cell phenotype, while one case exhibited both T‐ and B‐cell markers. Cutaneous involvement at presentation was associated with a favourable outcome, and spontaneous regression was common. For patients with non‐cutaneous presentation, the prognosis was relatively good for young patients treated with aggressive chemotherapy, but was grave for old patients.
Immunohistochemical detection of the c‐erbB‐2 proto‐oncogene product in normal, benign and malignant cartilage tissues
Authors: Wrba F. , Gullick W. J. , Fertl H. , Amann G. , Salzer‐Kuntschik M.
Published: March 2011

Benign and malignant cartilage tumours as well as normal cartilage were stained immunohistochemically with antibodies raised to a synthetic peptide from the sequence of the c‐erbB‐2 protein. Positive staining was present in 18/23 of the chondrosarcomas and in one case of osteochondroma. Normal and benign neoplastic cartilage tissues revealed negative results. It is concluded that expression of the c‐erbB‐2 protein may contribute to cell transformation in chondrosarcomas; it is not apparent whether the expression of c‐erbB‐2 protein in chondrosarcomas characterizes a subpopulation of different prognostic significance.
A cytokeratin immunohistochemical study of cholestatic liver disease: Evidence that hepatocytes can express “bile duct‐type” cytokeratins
Authors: Van Eyken P. , Sciot R. , Desmet V. J.
Published: March 2011

A cytokeratin immunohistochemical study was performed on 38 liver biopsies from cases of primary biliary cirrhosis, primary sclerosing cholangitis, extrahepatic biliary obstruction or drug‐induced liver disease in order to analyse the cytoskeletal changes in detail. On paraffin sections of 27 cases, a variable number of hepatocytes were reactive with a polyclonal anti‐cytokeratin antiserum that, in the normal liver, stains bile duct cells only. On cryostat sections of 23 cases, a variable number of hepatocytes were immunoreactive with a monoclonal antibody specifically directed against cytokeratin no. 7 and were most numerous in cases of long‐standing cholestasis irrespective of the aetiology. In three cases of primary sclerosing cholangitis and two cases of primary biliary cirrhosis a few hepatocytes were also weakly positive with a monoclonal antibody specific for cytokeratin no. 19. Since cytokeratins no. 7 and no. 19 are, in the normal liver, restricted to bile duct cells, these results further support the concept of “ductular metaplasia” of hepatocytes, the mechanism of which remains unclear.
Prognosis of ovarian carcinomas: Prediction by histoquantitative methods
Authors: Haapasalo H. , Collan Y. , Atkin N. B. , Pesonen E. , Seppä A.
Published: March 2011

Prognosis of ovarian carcinomas: prediction by histoquantitative methods

Prediction of prognosis of ovarian carcinomas by morphometric, histopathological and clinical indices was estimated in 105 tumours. Morphometric parameters included mitotic activity index, volume‐corrected mitotic index (M/V index), volume fraction of neoplastic epithelium, nuclear area, nuclear perimeter, shortest and longest nuclear axis and form factor of nucleus. Cox's multivariate regression model showed that the clinical stage was the best predictor of prognosis followed by the M/V index, which expresses the mitotic activity as the number of mitotic figures per square millimeter of neoplastic epithelium in the microscope field. In all tumour subgroups studied the M/V index was the best prognostic factor and for stage I tumours it was the only parameter selected by the Cox's model as a significant and independent prognostic predictor. We conclude that the M/V index can be used as a significant prognostic factor in ovarian carcinomas.
Malignant epithelioid haemangioendothelioma of the liver: A clinicopathological and histochemical study of 12 cases
Authors: Dietze O. , Davies S. E. , Williams R. , Portmann B.
Published: March 2011

We describe the clinicopathological findings in 12 cases of hepatic epithelioid haemangioendothelioma in order to identify diagnostic and prognostic features of this unusual vascular neoplasm. Three main tumour patterns were observed histologically: (1) a peripheral pattern with neoplastic cells scattered between fairly normal liver cell plates; (2) a cellular pattern showing a confusing admixture of pleomorphic tumour cells and atrophied hepatocytes set in a small amount of fibrous stroma; and (3) a scarred pattern with sparse tumour cells in a dense fibrous matrix. There were two types of vascular invasion: tuft‐like intravascular proliferations of epithelioid cells and fibro‐thrombotic venous occlusions. Awareness of these different aspects is important, as they are variably sampled by biopsy needles. The clinical course in this series was less favourable than that previously reported. Eight patients have died, in six instances of liver failure within 4–41 months of diagnosis. Extensive involvement of both lobes of the liver heralds imminent hepatic failure. The slow growth of metastases may justify liver transplantation in order to prolong life.
Digital Pacinian neuroma: A distinctive hyperplastic lesion
Authors: Fletcher C. D. M. , Theaker J. M.
Published: March 2011

Neural tumours composed solely of Pacinian corpuscles or showing focal Pacinian differentiation are extremely rare and have only occasionally been reported in the literature. All such lesions to date have been benign. Three lesions are described herein which presented as painful digital masses in middle‐aged adults and which were composed of abnormal aggregates of morphologically mature Pacinian corpuscles and intervening small nerves. Only five similar cases have been previously recorded. Possible pathogenetic mechanisms of this unusual hyperplastic phenomenon are discussed.
Modulation of the antigenicity of amylase in cervical glandular atypia, adenocarcinoma in situ and invasive adenocarcinoma
Authors: Griffin N. R. , Wells M. , Fox H.
Published: March 2011

Using a polyclonal anti‐salivary α‐amylase antibody and a biotin‐avidin‐peroxidase detection system immunoreactive amylase was detected in 39/40 cases of invasive cervical adenocarcinoma, 6/7 cases of adenocarcinoma in situ, 6/6 cases of high‐grade cervical glandular atypia and 12/14 cases of low‐grade cervical glandular atypia. Expression was seen in only 2/18 normal endocervices and this was weak and patchy. In contrast, strong amylase activity was demonstrated in 18/18 normal endocervices using a starch film assay on frozen sections. It is proposed that antigenic modulation of amylase occurs during endocervical neoplastic transformation.
Optimisation of lipase production by a mutant of Candida antarctica DSM‐3855 using response surface methodology
Authors: Liu Junhong , Zhang Yuanyuan
Published: March 2011

Response surface methodology (RSM) was used to determine the optimum cultivation conditions for lipase production by a mutant strain of Candida antarctica DSM‐3855. Among four variables, initial pH, soybean meal, and temperature were identified as significant variables for lipase production by full factorial design. A mathematical model was developed to investigate the influences of three factors on lipase activity and to predict their optimum value. According to RSM, the optimum cultivation conditions for the maximum lipase production were found to be: initial pH 6.0, soybean meal 3.38% (w/v), and temperature 26 °C. Under the optimum conditions, the maximum lipase yields of 27.34 U mL−1 was obtained after 58 h of cultivation in a 15 L fermenter.
The compositional quality and volatile compounds of samples from the blend of monovarietal olive oils cultivated in Tunisia
Authors: Youssef Ouni , Guido Flamini , Mokhar Guerfel , Nabil Ben Youssef , Daoud Douja , Mokhtar Zarrouk
Published: March 2011

Chemlali olive oil has been blended with oils obtained from Oueslati and Chetoui varieties to improve the quality of the former one. Parameters such as acidity, acids compositions, phenol content, oxidative stability and volatile compounds were characterised for various blends Chemlali × Oueslati and Chemlali × Chetoui.

The accumulation of volatiles originating from the lipoxygenase pathway in the monovarietal oils was different and closely dependent on the genetic store of each variety. The concentrations appeared to proportionally vary according to the relative proportion of each monovarietal oil in the mixtures. The blending process improved fatty acids by increasing the oleic acid content and decreasing the palmitic and linoleic acids levels of Chemlali oil. At 40% blending, oleic acid increased from 54% to 62%, while palmitic acid decreased from 18.59% to 16% when Oueslati and Chetoui olive oil was used.
Kinetics of colour change of bamboo shoot slices during microwave drying
Authors: Bal Lalit M. , Kar Abhijit , Satya Santosh , Naik Satya N.
Published: March 2011

The effect of microwave power on colour change kinetics of bamboo shoot slices was investigated during microwave drying. Colour changes were quantified by tri‐stimulus Hunter L (whiteness/darkness), a (redness/greenness), and b (yellowness/blueness) system. These values were also used for calculation of total colour change (ΔE), chroma, hue angle, and browning index (BI). Microwave drying as expected changed colour parameters because of browning. The values of L and b decreased, while values of a and ΔE increased during drying. Mathematical modelling of colour change kinetics indicated that L, b, chroma and BI could be defined using a first‐order kinetic model, while a, ΔE and hue angle could be defined using a zero‐order kinetic model. Considering together colour deterioration and quality of dried bamboo shoot slices at higher power reveals the need of process standardisation for getting good quality product.
Interpretation of viscoelastic behaviour of sweet cherries using rheological models
Authors: Moghimi Ali , Saiedirad Mohammad Hosaien , Moghadam Ebrahim Ganji
Published: March 2011

Viscoelastic behaviour of some commercial sweet cherry cultivars of Iran has been studied in current research. For this purpose, stress relaxation test was conducted on five cultivars of sweet cherry including Siah Mashhad, Abarde, Victoria, Dovom Ras and Tak Dane. Two common models (Generalised Maxwell model and Peleg model) were fitted to the experimental data. Both models could describe stress relaxation behaviour of cherries (R2 = 0.99), but Generalised Maxwell model had lower root mean square error (RMSE) than Peleg model. Based on analysis of stress relaxation data using models constants, Tak Dane exhibited more solid properties, while Victoria showed less elastic behaviour than other cultivars. The results revealed that relaxation ratio (R%) and the area under the stress relaxation curve could be effective alternative to models with easier mathematical procedure.
Sensory aspects of liquid smoking of giant river prawn: comparison with traditional smoking
Authors: Portella Carolina G. , Sant’Ana Léa S. , Valenti Wagner C.
Published: March 2011

The purpose of this paper is to investigate the impact of liquid smoke on the sensory characteristics of giant river prawn (Macrobrachium rosenbergii). The sensorial profile was plotted using quantitative descriptive analysis and assessment of the acceptability of samples of beheaded and peeled and only beheaded freshwater prawns smoked using the traditional method or liquid smoke (LS). The prawns subjected to LS were characterised by their aroma, artificial flavour and bitter flavour. The beheaded, peeled prawns were found to be more acceptable, confirming that the presence of the shell is a limiting factor in the acceptability of smoked prawns.