bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth of embedded Ge nanocrystals on different substrates
Authors: Yan Wensheng , Li Zhongrui , Sun Zhihu , Pan Zhiyu , Wei Shiqiang , Kolobov A. V.
Published: June 2007

The formation mechanism of Ge nanocrystals embedded in a SiO2 matrix on Si(100) and quartz substrates was systemically studied with multiple techniques, including x-ray diffraction, transmission electron microscopy, and fluorescence x-ray absorption fine structure. It was found that, on the quartz substrate, the content of GeO2-like species keeps no change during the annealing process. On the contrary, on the Si(100) substrate, the segregated GeO2 from the supersaturated GeO2-SiO2 solid solution can be reduced by Si atoms diffused from the substrate to form Ge nanocrystals. However, the Ge atoms in the stable GeO2-SiO2 solid solution cannot be reduced by the Si substrate under the annealing temperature of 1073 K.
Effect of confinement on the liquid-liquid phase transition of supercooled water
Authors: Brovchenko I. , Oleinikova A.
Published: June 2007

We report on an observation of the phase transition between two liquid phases of supercooled confined water in simulations. The temperature of the liquid-liquid transition of water at zero pressure slightly decreases due to confinement in the hydrophobic pore. The hydrophilic confinement affects this temperature in the opposite direction and shifts the critical point of the liquid-liquid transition to a higher pressure. As a result, in a strongly hydrophilic pore the liquid-liquid phase transition becomes continuous at zero pressure, indicating the shift of its critical point from negative to a positive pressure. These findings indicate that experimental studies of water confined in the pores of various hydrophobicity/hydrophilicity may clarify the location of the liquid-liquid critical point of bulk water.
Equilibrium and nonequilibrium molecular dynamics simulations of the thermal conductivity of molten alkali halides
Authors: Galamba N. , Nieto de Castro C. A. , Ely James F.
Published: June 2007

The thermal conductivity of molten NaCl and KCl was calculated through the Evans-Gillan nonequilibrium molecular dynamics (NEMD) algorithm and Green-Kubo equilibrium molecular dynamics (EMD) simulations. The EMD simulations were performed for a “binary” ionic mixture and the NEMD simulations assumed a pure system for reasons discussed in this work. The cross thermoelectric coefficient obtained from Green-Kubo EMD simulations is discussed in terms of the homogeneous thermoelectric power or Seebeck coefficient of these materials. The thermal conductivity obtained from NEMD simulations is found to be in very good agreement with that obtained through Green-Kubo EMD simulations for a binary ionic mixture. This result points to a possible cancellation between the neglected “partial enthalpy” contribution to the heat flux associated with the interdiffusion of one species through the other and that part of the thermal conductivity related to the coupled fluxes of charge and heat in “binary” ionic mixtures.
Qualitative analysis of a diamondlike carbon film by angle-resolved x-ray photoelectron spectroscopy
Authors: Takabayashi Susumu , Motomitsu Kunihiko , Takahagi Takayuki , Terayama Akira , Okamoto Keishi , Nakatani Tatsuyuki
Published: June 2007

Angle-resolved x-ray photoelectron spectroscopy was used to investigate the surface of a diamondlike carbon film prepared by the ionized deposition method. We then analyzed the C 1s spectra using the Doniach-Šunjić (DŠ) [J. Phys. C 3, 285 (1970)] function convoluted with a Gaussian function. Consequently, we obtained four fitting curves for the carbon components in each spectrum, regardless of the assumption of the singularity index (α) in the DŠ function, which expresses the asymmetry of the C 1s spectrum. The curves were assigned in the order of binding energy to bulk sp3 carbon (283.7–283.8eV), bulk sp2 carbon (284.2–284.3eV), surface sp2 carbon (284.7–284.8eV), and surface sp3 (285.3–285.4eV) carbon. We further considered the influence of the assumption of α. Consequently, we suggest that the C 1s spectra can be quantitatively analyzed without considering the influences of α when the ratio of α for sp2 carbon to that for sp3 carbon [α(sp2):α(sp3)] is between 10:0 and 5:5. The distribution in the α ratio may indicate that the sp2 and the sp3 carbon atoms can interact with each other (hybridization) and differ from those highly oriented pyrolytic graphite and diamond, respectively.
Lattice vibration fundamentals of nanocrystalline anatase: Temperature-dependent study using micro-Raman scattering spectroscopy
Authors: Wang Deliang , Chen Bo , Zhao Jianhua
Published: June 2007

A detailed temperature-dependent Raman scattering study was carried out from 83 to 723 K for nanocrystalline anatase with nanocrystal size of 19.4 nm. All six Raman-active modes, including the hardly observed Eg(2) mode, were observed, and each had its own unique temperature-dependent characteristic. The softest and the second softest modes, namely the Eg(1) and Eg(2), each showed hardening with increasing temperatures. The B1g(1) mode, which is between the Eg(1) and Eg(3), showed weak hardening from 83 to ∼330 K, and then its frequency decreased with increasing temperatures. Very good fittings were obtained for both the Raman frequencies and peak linewidths by using the Klemens model. The fitting results show that for the Eg(1) and Eg(2) modes, the hardening behavior came mostly from three-phonon processes, while for the A1g and Eg(3) modes, both three- and four-phonon processes contributed to the Raman softening.
Optical characterization of Cd1−x−yBexZnySe mixed crystals
Authors: Wang J. Z. , Huang P. J. , Hsu H. P. , Huang Y. S. , Firszt F. , Łęgowski S. , Męczyńska H. , Marasek A. , Tiong K. K.
Published: June 2007

A detailed optical characterization of a series of wurtzite-type Cd1−x−yBexZnySe mixed crystals grown by the modified high pressure Bridgman method has been carried out via photoluminescence (PL) and contactless electroreflectance (CER) in the temperature range of 15–300 K. Room temperature surface photovoltage spectroscopy has been used as a diagnostic technique for checking the surface condition of the sample. For the mechanically polished sample, the surface photovoltage spectrum at room temperature recorded a below band edge broad feature which is most likely related to the surface states induced by mechanical defect. This feature can be eliminated via mechanical polishing and followed by chemical etching, and hence, only the exciton line was observed for the damage-removed sample. Typical PL spectrum at low temperature consists of an exciton line, an edge emission due to recombination of shallow donor-acceptor pairs, and a broadband related to recombination through deep level defects. Various interband transitions, originating from the band edge and spin-orbit splitting critical points, of the samples have been observed in the CER spectra. Comparison of PL and CER data for the Cd1−x−yBexZnySe samples shows that for a low Zn and Be content the peak positions of the excitonic emission lines in the PL spectra correspond quite well to the transition energies of the A exciton from the CER data. For samples with higher Be and Zn contents, the results indicate that localization of excitons has taken place at low temperatures. The parameters that describe the temperature dependence of the transition energy and broadening parameter of the fundamental band edge exciton have been evaluated and discussed.
Glass transition temperature of bulk metallic glasses: A linear connection with the mixing enthalpy
Authors: Li Xuelian , Bian Xiufang , Hu Lina , Wu Yuqin , Guo Jing , Zhang Junyan
Published: June 2007

A linear relationship is found between the glass transition temperature Tg and the absolute value of the mixing enthalpy, |ΔHchem|, for bulk metallic glass systems. The increasing (or lowering) of Tg with an admixture of metals or other elements manifests itself in the larger (or smaller) of |ΔHchem| in a given system. The results indicate that the composition dependence of Tg results from the change of excess entropy (Sex) during thermal excitation. The |ΔHchem|, which relates to the strength of interaction among different atoms, corresponds to part of the Sex at Tg [Sex(Tg)]. The glass transition temperatures for Cu-Zr (Hf)-, Zr-Cu-, and La-Al-based glassy alloys are correlated with the interaction intensity between their based binary eutectic compositions, respectively.
Further analysis of the dynamically averaged vibrational spectrum for the “magic” protonated 21-water cluster
Authors: Iyengar Srinivasan S.
Published: June 2007

A temperature dependent analysis of the vibrational spectrum of the protonated 21-water cluster is provided using the ab initio molecular dynamics method called atom-centered density matrix propagation. It is found that even at low temperatures, finite temperature dynamical averaging greatly influences the spectral results. While the current publication deals with an analysis of the vibrational spectrum at many internal temperatures, the general conclusions are consistent with those in an earlier publication [Iyengar et al., J. Chem. Phys.123, 084309 (2005)]. Furthermore, a critical spectral region (below 1500cm−1) is found for this system, where the key vibrations of the protonated species can be detected.
Four-component relativistic theory for nuclear magnetic shielding constants: Critical assessments of different approaches
Authors: Xiao Yunlong , Liu Wenjian , Cheng Lan , Peng Daoling
Published: June 2007

Both formal and numerical analyses have been carried out on various exact and approximate variants of the four-component relativistic theory for nuclear magnetic shielding constants. These include the standard linear response theory (LRT), the full or external field-dependent unitary transformations of the Dirac operator, as well as the orbital decomposition approach. In contrast with LRT, the latter schemes take explicitly into account both the kinetic and magnetic balances between the large and small components of the Dirac spinors, and are therefore much less demanding on the basis sets. In addition, the diamagnetic contributions, which are otherwise “missing” in LRT, appear naturally in the latter schemes. Nevertheless, the definitions of paramagnetic and diamagnetic terms are not the same in the different schemes, but the difference is only of O(c−2) and thus vanishes in the nonrelativistic limit. It is shown that, as an operator theory, the full field-dependent unitary transformation approach cannot be applied to singular magnetic fields such as that due to the magnetic point dipole moment of a nucleus. However, the inherent singularities can be avoided by the corresponding matrix formulation (with a partial closed summation). All the schemes are combined with the Dirac-Kohn-Sham ansatz for ground state calculations, and by using virtually complete basis sets a new and more accurate set of absolute nuclear magnetic resonance shielding scales for the rare gases He–Rn have been established.
Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides
Authors: Murarka Rajesh K. , Head-Gordon Teresa
Published: June 2007

We have conducted extensive molecular dynamics simulations to study the single particle and collective dynamics of water in solutions of N-acetyl-glycine-methylamide, a model hydrophilic protein backbone, and N-acetyl-leucine-methylamide, a model (amphiphilic) hydrophobic peptide, as a function of peptide concentration. Various analytical models commonly used in the analysis of incoherent quasielastic neutron scattering (QENS), are tested against the translational and rotational intermediate scattering function, the mean square displacement of the water molecule center of mass, and fits to the second-order rotational correlation function of water evaluated directly from the simulation data. We find that while the agreement between the model-free analysis and analytical QENS models is quantitatively poor, the qualitative feature of dynamical heterogeneity due to caging is captured well by all approaches. The center of mass collective and single particle intermediate scattering functions of water calculated for these peptide solutions show that the crossover from collective to single particle-dominated motions occurs at a higher value of Q for high concentration solutions relative to low concentration because of the greater restriction in movement of water molecules due to confinement. Finally, we have shown that at the same level of confinement of the two peptides, the aqueous amphiphilic amino acid solution shows the strongest deviation between single particle and collective dynamics relative to the hydrophilic amino acid, indicating that chemical heterogeneity induces even greater spatial heterogeneity in the water dynamics.
Tools and strategies for visualization of large image data sets in high-resolution imaging mass spectrometry
Authors: Klinkert Ivo , McDonnell Liam A. , Luxembourg Stefan L. , Maarten Altelaar A. F. , Amstalden Erika R. , Piersma Sander R. , Heeren Ron M. A.
Published: June 2007

Mass spectrometry based proteomics is one of the scientific domains in which experiments produce a large amount of data that need special environments to interpret the results. Without the use of suitable tools and strategies, the transformation of the large data sets into information is not easily achievable. Therefore, in the context of the virtual laboratory of enhanced science, software tools are developed to handle mass spectrometry data sets. Using different data processing strategies for visualization, it enables fast mass spectrometric imaging of large surfaces at high-spatial resolution and thus aids in the understanding of various diseases and disorders. This article describes how to optimize the handling and processing of the data sets, including the selection of the most optimal data formats and the use of parallel processing. It also describes the tools and solutions and their application in mass spectrometric imaging strategies, including new measurement principles, image enhancement, and image artifact suppression.
Magnetic trapping of nanometer- and micrometer-sized particles
Authors: Huh Seung H. , Kim Chang Y. , Jeong Hyun S. , Nakajima Atsushi
Published: June 2007

Nanometer- and micrometer-sized particles (NPs and MPs) of gas-phase Co, Fe, and Fe–Nd–Dy–B were magnetically trapped on a substrate. For the magnetic trapping of NPs, two stepwise evolutions were investigated: (1) the formation of NP aggregates above a critical diameter of 8nm and (2) increase in the length to a few micrometers, which is the result of the equilibrium between the magnetostatic and thermal energies of NPs and the granular linear chains such as granular nanorods and nanofibers. The magnetic trapping of MPs or MPs∕NPs is particularly interesting because of the sequential pearl-necklace-like growth and magnetic separation in the linear chains.
Resonance and magnetic study of polycrystalline La0.9Ca0.1MnO3: Evidence of nonstoichiometry induced inhomogeneous magnetic ground state
Authors: Shames A. I. , Rozenberg E. , Gorodetsky G. , Tsindlekht M. I. , Felner I. , Mogilyansky D. , Pestun A. , Mukovskii Ya. M.
Published: June 2007

Electron magnetic resonance and ac and dc magnetic measurements in respective temperature intervals 75–600 and 5–300K were employed to probe and to compare magnetic ordering in two manganite ceramics with close composition: La0.9Ca0.1MnO3 and (La0.9Ca0.1)0.99MnO3. X-ray powder diffraction and dc low field magnetic measurements proved that lattice parameters and Curie temperatures of both compounds are close to each other. However, ac susceptibility, high field dc magnetic measurements, and resonance experiments have shown that the (La0.9Ca0.1)0.99MnO3 sample is characterized by stronger ferromagnetic correlations, higher spontaneous magnetization at low temperatures, and weaker effective magnetic anisotropy than the La0.9Ca0.1MnO3 one. The results obtained are discussed in the frame of experimentally proven inherent nonstoichiometry model, which takes into account cation vacancies in La and Ca sites appearing in low-doped La–Ca–Mn–O samples sintered in an air atmosphere. The studied samples are supposedly characterized by random distribution of cation vacancies and represent an intermediate case between fully stoichiometric and nonstoichiometric ones. This may explain strong and unpredictable influence of weak compositional change on the magnetic ordering. The nonstoichiometry seems to be generally responsible for previously reported difference in magnetic ordering between low-doped La–Ca–Mn–O ceramics and single crystals of the same nominal composition.
Transition amplitudes and sewing properties for bosons on the Riemann sphere
Authors: Dimock J.
Published: June 2007

We consider scalar quantum fields on the sphere, both massive and massless. In the massive case we show that the correlation functions define amplitudes which are trace class operators between tensor products of a fixed Hilbert space. We also establish certain sewing properties between these operators. In the massless case we consider exponential fields and have a conformal field theory. In this case the amplitudes are only bilinear forms but still we establish sewing properties. Our results are obtained in a functional integral framework.
Nanocomposite field effect transistors based on zinc oxide/polymer blends
Authors: Xu Zong-Xiang , Roy V. A. L. , Stallinga Peter , Muccini Michele , Toffanin Stefano , Xiang Hei-Feng , Che Chi-Ming
Published: June 2007

The authors have examined the field effect behavior of nanocomposite field effect transistors containing ZnO (zinc oxide) tetrapods or nanocrystals dispersed in a polymer matrix of poly[2-methoxy,5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV). The electrical characteristics of ZnO tetrapods/MEH-PPV composite devices exhibit an increase in hole mobility up to three orders of magnitude higher than the polymer MEH-PPV device.
The electronic properties of potassium doped copper-phthalocyanine studied by electron energy-loss spectroscopy
Authors: Flatz K. , Grobosch M. , Knupfer M.
Published: June 2007

The authors have studied the electronic structure of potassium doped copper-phthalocyanine using electron energy-loss spectroscopy. The evolution of the loss function indicates the formation of distinct KxCuPc phases. Taking into account the C1s and K2p core level excitations and recent results by Giovanelli et al. [J. Chem. Phys. 126, 044709 (2007)], they conclude that these are K2CuPc and K4CuPc. They discuss the changes in the electronic excitations upon doping on the basis of the molecular electronic levels and the presence of electronic correlations.
Does phenomenological kinetics provide an adequate description of heterogeneous catalytic reactions?
Authors: Temel Burcin , Meskine Hakim , Reuter Karsten , Scheffler Matthias , Metiu Horia
Published: June 2007

Phenomenological kinetics (PK) is widely used in the study of the reaction rates in heterogeneous catalysis, and it is an important aid in reactor design. PK makes simplifying assumptions: It neglects the role of fluctuations, assumes that there is no correlation between the locations of the reactants on the surface, and considers the reacting mixture to be an ideal solution. In this article we test to what extent these assumptions damage the theory. In practice the PK rate equations are used by adjusting the rate constants to fit the results of the experiments. However, there are numerous examples where a mechanism fitted the data and was shown later to be erroneous or where two mutually exclusive mechanisms fitted well the same set of data. Because of this, we compare the PK equations to “computer experiments” that use kinetic Monte Carlo (kMC) simulations. Unlike in real experiments, in kMC the structure of the surface, the reaction mechanism, and the rate constants are known. Therefore, any discrepancy between PK and kMC must be attributed to an intrinsic failure of PK. We find that the results obtained by solving the PK equations and those obtained from kMC, while using the same rate constants and the same reactions, do not agree. Moreover, when we vary the rate constants in the PK model to fit the turnover frequencies produced by kMC, we find that the fit is not adequate and that the rate constants that give the best fit are very different from the rate constants used in kMC. The discrepancy between PK and kMC for the model of CO oxidation used here is surprising since the kMC model contains no lateral interactions that would make the coverage of the reactants spatially inhomogeneous. Nevertheless, such inhomogeneities are created by the interplay between the rate of adsorption, of desorption, and of vacancy creation by the chemical reactions.
Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics
Authors: Chung Hoi Sung , Khalil Munira , Smith Adam W. , Tokmakoff Andrei
Published: June 2007

We have developed a Fourier transform two-dimensional infrared (2D IR) spectrometer to probe chemical reactions and biophysical processes triggered by a nanosecond temperature jump (T jump). The technical challenges for such a spectrometer involve (1) synchronization of a nanosecond T-jump laser and femtosecond laser system, (2) overcoming the decreased signal-to-noise ratio from low repetition rate data acquisition, and (3) performing an interferometric measurement through a sample with a density and index of refraction that varies with time delay after the T jump. The first challenge was overcome by synchronizing the two lasers to a clock derived from the Ti:sapphire oscillator, leading to timing accuracy of 2ns for delays up to 50ms. The data collection time is reduced by using undersampling with the improved signal-to-noise ratio obtained from a balanced detection scheme with a dual stripe array detector. Transient dispersed vibrational echo and 2D IR spectroscopy are applied to N-methylacetamide and ubiquitin, as examples, and the spectral responses by a temperature elevation and by structural changes of the protein are compared. The synchronization of 2D IR spectroscopy with a nanosecond temperature jump without losing its sensitivity at a low repetition rate opens a new applicability of the nonlinear spectroscopy to probe a variety of molecular structure changes induced by a nanosecond perturbation.
Theory for symmetric toggle magnetic random access memory
Authors: Worledge D. C. , Trouilloud P. L. , Gallagher W. J.
Published: June 2007

The authors analyze the critical switching curve for two identical coupled magnetic free layers, as used in toggle magnetic random access memory. The continuous and discontinuous transitions between different magnetic states are described. A general criteria for toggling is derived by summing up the number of clockwise and counterclockwise transitions, leading to a larger toggle region than previously reported. It also leads to a significant chirality effect, wherein the toggle region shifts depending on the order in which the word and bit line fields are applied. Finally, the authors discuss a type of switching useful for experimentally measuring the critical switching curve.
Short-wavelength intersubband electroabsorption modulation based on electron tunneling between GaN∕AlN coupled quantum wells
Authors: Nevou L. , Kheirodin N. , Tchernycheva M. , Meignien L. , Crozat P. , Lupu A. , Warde E. , Julien F. H. , Pozzovivo G. , Golka S. , Strasser G. , Guillot F. , Monroy E. , Remmele T. , Albrecht M.
Published: June 2007

Room temperature intersubband electroabsorption modulation in GaN∕AlN coupled quantum wells is demonstrated at short infrared wavelengths, covering the fiber-optics telecommunication wavelength range. Electroabsorption modulation with opposite sign is observed at λ=1.2–1.67μm and λ=2.1–2.4μm. The electromodulation originates from electron tunneling between a wide well (reservoir) and a narrow well separated by an ultrathin AlN barrier. Both the intersubband absorption and the modulation spectroscopic measurements are in good agreement with the simulations. The maximum modulation depth is ∼44% at λ=2.2μm. The −3dB cutoff frequency limited by the RC time constant is 11.5MHz for 700×700μm2 mesas.
Nonvolatile polycrystalline silicon thin film transistor memory using silicon-rich silicon nitride as charge storage layer
Authors: Pei Z. , Chung A. , Hwang H. L.
Published: June 2007

In this work, the authors report a memory device based on a Si thin film transistor (TFT) structure by incorporating silicon-rich silicon nitride (SRSN) film in the gate dielectric stacks as the charge storage layer. The SRSN film has a lower barrier for hole injection than the barrier for electron injection. Therefore, the memory window is dominated by hole injection. The memory window for TFT nonvolatile memory at steady state as large as 6.8V is observed, and the memory window is around 3V under pulse operation. In addition, this TFT memory has no significant degradation after 500 times of switching operation.
Organosilane-functionalized wide band gap semiconductor surfaces
Authors: Petoral R. M. , Yazdi G. R. , Lloyd Spetz A. , Yakimova R. , Uvdal K.
Published: June 2007

Surface functionalization of wide band gap semiconductors, SiC, ZnO, and GaN, with organosilane is reported. Formation of self-assembled monolayers of mercaptopropyltrimethoxysilane is confirmed by x-ray photoelectron spectroscopy and atomic force microscopy. The molecules are adsorbed on the surfaces through the silane groups with the free thiol groups molecularly oriented away from the surface. Moreover, chemisorption via the thiolate is observed for the ZnO surface. Immobilization of a model biomolecule to the functionalized surface is demonstrated. An amino acid derivative, i.e., phosphotyrosine derived thiol, is linked on the functionalized ZnO and GaN surfaces via formation of disulfide bridges.
Metabolic control of seedling development by invertases
Authors: Bonfig Katharina B. , Berger Susanne , Fatima Tahira , González Mari-Cruz , Roitsch Thomas
Published: June 2007

Invertases are important enzymes in higher plants, which are involved in regulating developmental processes and responses to external factors. In a functional approach the role of invertases was investigated using transgenic plants ectopically expressing inhibitor proteins to decrease invertase activity. For generating specific effects, these inhibitor proteins were expressed in Arabidopsis under the control of synthetic promoters consisting of tetramers of pathogen-inducible elements, which were reported to yield low constitutive expression. Unexpectedly, seedling growth of putative transgenic plants was arrested at the four-leaf stage. Analysis of β-glucuronidase activity of corresponding reporter gene lines showed a correlation of the growth arrest with high activity of these promoters in seedlings grown under tissue culture conditions. The negative effect of invertase inhibition on seedling growth was substantiated by transgenic tobacco plants expressing an invertase inhibitor under control of a tetracycline inducible promoter. Ectopic induction of the invertase inhibitor during early seedling development resulted in a reduced fresh weight of seedlings. The importance of invertase in seedling development is further supported by results of expression profiling of invertases in Arabidopsis, which was confirmed by expression analyses. The mRNA for the vacuolar invertases Atßfruct3 and Atßfruct4 and cell wall invertase AtcwINV1 are specifically and strongly expressed during seedling development. These complementing results show that invertase activity is required for normal seedling development.
Mechanical limits of viral capsids
Authors: Buenemann Mathias , Lenz Peter
Published: June 2007

We studied the elastic properties and mechanical stability of viral capsids under external force-loading with computer simulations. Our approach allows the implementation of specific geometries corresponding to specific phages, such as φ29 and cowpea chlorotic mottle virus. We demonstrate how, in a combined numerical and experimental approach, the elastic parameters can be determined with high precision. The experimentally observed bimodality of elastic spring constants is shown to be of geometrical origin, namely the presence of pentavalent units in the viral shell. We define a criterion for capsid breakage that explains well the experimentally observed rupture. From our numerics we find a crossover from γ
2/3
to γ
1/2
for the dependence of the rupture force on the Föppl-von Kármán number, γ. For filled capsids, high internal pressures lead to a stronger destabilization for viruses with buckled ground states versus viruses with unbuckled ground states. Finally, we show how our numerically calculated energy maps can be used to extract information about the strength of protein–protein interactions from rupture experiments.
The selection of acceptable protein mutations
Authors: Sasidharan Rajkumar , Chothia Cyrus
Published: June 2007

We have determined the general constraints that govern sequence divergence in proteins that retain entirely, or very largely, the same structure and function. To do this we collected data from three different groups of orthologous sequences: those found in humans and mice, in humans and chickens, and in
Escherichia coli
and
Salmonella enterica
. In total, these organisms have 21,738 suitable pairs of orthologs, and these contain nearly 2 million mutations. The three groups differ greatly in the taxa from which they come and/or in the time that separates them from their last common ancestor. Nevertheless, the results we obtain from the three different groups are strikingly similar. For each group, the orthologous sequence pairs were assigned to six different divergence categories on the basis of their sequence identities. For categories with the same divergence, common accepted mutations have similar frequencies and rank orders in the three groups. With divergence, the width of the range of common mutations grows in the same manner in each group. We examined the distribution of mutations in protein structures. With increasing divergence, mutations increase at different rates in the buried, intermediate, and exposed regions of protein structures in a manner that explains the exponential relationship between the divergence of structure and sequence. This work implies that commonly allowed mutations are selected by a set of general constraints that are well defined and whose nature varies with divergence.
Reduced Sensitivity of Older Adults to Affective Mismatches
Authors: Jiang Yang , Vagnini Victoria , Clark Jessica , Zhang Qin
Published: June 2007

The present study investigated age-related differences in emotional processing by using a paradigm of affective priming. Eighteen, right-handed, younger (mean age 22) and 15 older (mean age 68) subjects pressed buttons to indicate pleasantness of target words. The valence of each prime-target pair was congruent (e.g., win-love), incongruent (e.g., love-loss), or neutral (time-flower). Two sets of 720 prime-target pairs used either affective words or pictures as primes, and affect words as targets. We included well-matched positive and negative valence pairs in all congruent, neutral, and incongruent conditions, and controlled for possible contamination by semantic meaning, word frequency, and repetition effects. The response time (RT) results revealed that young participants responded faster to the targets in affectively congruent conditions than in incongruent conditions. In older participants, the responses to target words were indifferent to all valence congruency conditions. The age effect in affective priming largely reflects reduced sensitivity to affective mismatches among older adults. Intriguingly, emotional Stroop effect and some perceptual priming have been linked to increased interferences and mismatches in older adults. The age-related changes in affective, perceptual, and semantic processes are discussed.
Temporally Dissociated, Trait-Specific Modifications Underlie Phenotypic Polyphenism inSpea multiplicataTadpoles, Which Suggests Modularity
Authors: Storz Brian L. , Travis Joseph
Published: June 2007

Many organisms that develop in a variable environment show correlated patterns of phenotypic plasticity in several traits. Any individual trait modification can be beneficial, neutral, or deleterious in any particular environment; the organism's total fitness, which determines if the plasticity is adaptive, is the sum of these changes. Although much is known about how plastic traits contribute to fitness, less is known about the extent to which the various trait changes involved in the plastic responses share their developmental control. Shared control suggests that the various responses evolved in unison, but independent control suggests independent evolution of many components. Spadefoot toads have evolved adaptive polyphenism to cope with developing in rapidly drying ephemeral ponds. Larvae hatch as omnivores, but on exposure to an environmental cue, may develop into carnivores. We compared trait development in the two morphs and found that differences in jaw musculature, head dimensions, and intestines emerged early in development, whereas differences in shape of the tail emerged later. In omnivores, all traits except intestine length and hind-limb length were negatively allometric with body length; in carnivores, two of three jaw muscles displayed positive allometry and, among those that were negatively allometric, all except head width showed larger allometric coefficients in carnivores. Hind-limb length was positively allometric in both forms, but the allometric coefficients did not differ significantly. Intestine length was positively allometric to body length in both forms, but in this case, omnivores exhibited the higher coefficient. These results suggest that spadefoot plasticity is trait specific and the responses are suggestive of the existence of at least two modules: a suite of trophic traits that responds early in development and a suite of tail traits that responds later. The developmental control of these suites is the subject of further investigation.
Accurate quantitation of allele-specific expression patterns by analysis of DNA melting
Authors: Jeong Sangkyun , Hahn Yoonsoo , Rong Qi , Pfeifer Karl
Published: June 2007

Epigenetic and genetic mechanisms can result in large differences in expression levels of the two alleles in a diploid organism. Furthermore, these differences may be critical to phenotypic variations among individuals. In this study, we present a novel procedure and algorithm to precisely and accurately quantitate the relative expression of each allele. This method uses the differential melting properties of DNAs differing at even a single base pair. By referring to the melting characteristics of the two pure alleles, the fractional contribution of the two alleles to any unknown mixture can be mathematically resolved. These methods are highly accurate and precise because each single melting reaction yields multiple data points for analysis. Finally, we discuss how this approach can be used more generally to accurately quantitate gene expression relative to known standards.
Inoculation and Passaging of Mammalian Cell Suspension Cultures
Authors: Darlington Gretchen J.
Published: June 2007

INTRODUCTION

This protocol describes the growth and passaging of mammalian cells in suspension culture using a simple dilution procedure. In situations in which total replacement of medium is desired, the cells can be gently pelleted by centrifugation and resuspended in the appropriate medium.
Xenopus laevis Animal Cap/Vegetal Endoderm Conjugates: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: June 2007

INTRODUCTION

In Xenopus laevis, mesoderm can be induced in animal cap cells by contact with vegetal cells (presumptive endoderm). This juxtaposition of tissues was the first indication that the process of mesoderm induction could be separated from neural induction. This protocol describes how to set up a conjugate using Xenopus animal cap and vegetal tissue. In theory, a single embryo can provide both animal and vegetal cells; however, in practice, this is difficult to achieve.
Xenopus laevis Animal Cap/Dorsal Mesoderm Conjugates: Figure 1.
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: June 2007

INTRODUCTION

In Xenopus laevis, dorsal mesoderm is also called “organizer” tissue or Spemann’s organizer. It is fated to form the prechordal plate and notochord, as well as some somitic tissue. This protocol presents a method for the preparation of dorsal mesoderm conjugates, which can be useful in assessing whether test genes or promoters are responsive to dorsal mesodermal signals and, if so, by what region of the mesoderm they are induced. The example presented here is an animal cap/dorsal mesoderm conjugate.
An Expedient and Versatile Protocol for Extracting High-Quality DNA from Plant Leaves
Authors: Vallejos C. Eduardo
Published: June 2007

INTRODUCTION

Protocols for extracting plant genomic DNA have to contend with two major challenges: preventing the oxidation of phenolic substances that can react with nucleic acids and proteins, and eliminating polysaccharides that interfere with downstream enzymatic manipulations of DNA. A protocol has been developed in which the above-mentioned substances are removed from the sample before the DNA is removed from the chromatin structure. This protocol requires only two tubes during extraction and a single precipitation step to yield high-quality DNA. DNA extracted with this method has virtually no protein or phenolic contaminants (A260/A280>1.8), is RNA-free, contains high-molecular-weight fragments according to CHEF electrophoresis, and is fully digestible by restriction enzymes. This protocol has been successfully tested with leaf samples from common bean and corn; with leaves known to be rich in phenolics (tomato and bell pepper), pectins (sweet orange, grapefruit, and peach), or both substances (Muscadine grape); and with leaves that contain latex in the sap (papaya).
PCR-Based Analysis of Immunoprecipitated Chromatin: Figure 1.
Authors: Wagschal Alexandre , Delaval Katia , Pannetier Maëlle , Arnaud Philippe , Feil Robert
Published: June 2007

INTRODUCTION

After chromatin immunoprecipitation (ChIP), different PCR-based approaches can be used to determine how much DNA is precipitated at a locus of interest. Real-time PCR amplification is often the preferred technique. One can also use duplex PCR amplification, which is the coamplification of a fragment from the region of interest and a control fragment (e.g., the actin gene, or the tubulin gene). This approach allows for estimating relative levels of specific histone modifications along chromosomal domains. For allele-specific studies (for instance, on dosage-compensation mechanisms or on genomic imprinting), electrophoretic detection of single-strand conformation polymorphisms (SSCP) or similar strategies such as hot-stop PCR can differentiate PCR products that represent the silent allele from those amplified from the active allele. If a polymorphic restriction site is present in one allele and absent in the other, the method of choice is hot-stop PCR. If no polymorphic restriction sites are available, but there are single nucleotide polymorphisms (SNPs) that distinguish the alleles of interest, the best approach is to separate the PCR products derived from the two different alleles using SSCP. In SSCP, it is possible to discriminate denatured PCR products derived from one allele or the other because the secondary structure of each single strand will be directly dependent on the sequence itself. Hence, in nondenaturing gel conditions, each single strand will migrate differently. These four PCR-based methodologies to analyze immunoprecipitated chromatin (real-time PCR, duplex PCR, hot-stop PCR, and SSCP) are presented here.
Viability Staining of Mammalian Cell Cultures
Authors: Darlington Gretchen J.
Published: June 2007

INTRODUCTION

Various manipulations of cells, including passaging, freezing, and dissociation from primary tissue, can result in cell death. To determine the number of surviving cells in a population, exclusion of the dye trypan blue can be used. Normal healthy cells are able to exclude the dye, but trypan blue will diffuse into cells in which membrane integrity has been lost. This dye-exclusion method provides a rough estimate of cell viability and often does not distinguish within a 10%-20% difference. Additionally, cells that exclude dye are not necessarily capable of attachment and prolonged survival or proliferation.
Microdissection: Explant and Transplant Assays in Xenopus laevis
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: June 2007

INTRODUCTION

When analyzing any developmental process, important questions are those relating to the formation of different cell types. What makes a cell decide to become a particular cell type? What cell interactions are involved in this decision? The “commitment” of cells to a particular lineage is also called “specification” or “determination.” Analysis of the cell interactions, or inductions, required for tissue-type determination is a critical step in the identification of the genes that control the process. Lineage commitment and inductive interactions can be assessed by explant or transplant assays with embryos from Xenopus laevis.
Localization of Members of the γ-Glutamyl Transpeptidase Family Identifies Sites of Glutathione and Glutathione S-Conjugate Hydrolysis
Authors: Martin Melinda N. , Saladores Pilar H. , Lambert Elton , Hudson Andre O. , Leustek Thomas
Published: June 2007

γ-Glutamyl transpeptidases (GGTs) are essential for hydrolysis of the tripeptide glutathione (γ-glutamate-cysteine-glycine) and glutathione S-conjugates since they are the only enzymes known to cleave the amide bond linking the γ-carboxylate of glutamate to cysteine. In Arabidopsis thaliana, four GGT genes have been identified based on homology with animal GGTs. They are designated GGT1 (At4g39640), GGT2 (At4g39650), GGT3 (At1g69820), and GGT4 (At4g29210). By analyzing the expression of each GGT in plants containing GGT:β-glucuronidase fusions, the temporal and spatial pattern of degradation of glutathione and its metabolites was established, revealing appreciable overlap among GGTs. GGT2 exhibited narrow temporal and spatial expression primarily in immature trichomes, developing seeds, and pollen. GGT1 and GGT3 were coexpressed in most organs/tissues. Their expression was highest at sites of rapid growth including the rosette apex, floral stem apex, and seeds and might pinpoint locations where glutathione is delivered to sink tissues to supplement high demand for cysteine. In mature tissues, they were expressed only in vascular tissue. Knockout mutants of GGT2 and GGT4 showed no phenotype. The rosettes of GGT1 knockouts showed premature senescence after flowering. Knockouts of GGT3 showed reduced number of siliques and reduced seed yield. Knockouts were used to localize and assign catalytic activity to each GGT. In the standard GGT assay with γ-glutamyl p-nitroanilide as substrate, GGT1 accounted for 80% to 99% of the activity in all tissues except seeds where GGT2 was 50% of the activity. Protoplasting experiments indicated that both GGT1 and GGT2 are localized extracellularly but have different physical or chemical associations.
Physical Function and Quality of Life in Older Women With Diastolic Heart Failure: Effects of a Progressive Walking Program on Sleep Patterns
Authors: Gary Rebecca , Lee Shih Yu (Sylvia)
Published: June 2007

This preliminary study tested the effects of a home‐based walking intervention on total sleep time (TST), nocturnal awakenings, depressive symptoms, physical function, and quality of life (QOL) in older women with diastolic heart failure (DHF). Twenty‐three women (mean age, 68±11 years) with New York Heart Association class II or III DHF were randomized to either a 12‐week home‐based walking intervention (n=13) or education‐only program (control, n=10). No between‐group differences were found in women in the intervention and control groups on any of the outcome variables. When outcomes were compared within each group at baseline and 12 weeks, intervention‐group patients had improvement in TST (P<.01) and heart failure‐related QOL (P<.05) and a trend for decreased depressive symptoms (P<.07). Women randomized to the control group had no change in any outcomes. These preliminary findings suggest that a progressive walking program may improve TST and QOL in older women with DHF. Findings from this study support the need for larger studies to evaluate the long‐term benefits of a walking program on sleep patterns, QOL, and psychologic function in this population.
Expression of ERα and ERβ in lobular carcinoma in situ
Authors: Middleton L P , Perkins G H , Tucker S L , Sahin A A , Singletary S E
Published: June 2007

Aims:  Oestrogen is a modulator of cell growth and differentiation in the breast. It mediates most of its function through members of the oestrogen receptor (ER) family, ERα and ERβ. Lobular carcinoma in situ (LCIS) is a known risk factor for the development of breast cancer; however, the use of tamoxifen for prevention is based upon data for ER+ (ERα) LCIS associated with invasion, but limited data exist on the use of tamoxifen in cases of ER+ (ERα) LCIS occurring in the absence of invasive carcinoma. The aim of this study was to examine ER expression in LCIS to determine the relationship of ERα to ERβ and, thereby, to determine whether it is of clinical value to measure ERβ along with ERα.

Methods and results:  Core biopsy specimens from 50 patients were examined retrospectively. Histology was reviewed and histological parameters were assessed. Formalin‐fixed paraffin‐embedded tissue was available for E‐cadherin, ERα and ERβ immunohistochemistry. The degree of ERα and ERβ nuclear reactivity was quantified. The patients' mean age was 55 years. The mean follow‐up duration was 48 months. All 50 cases of LCIS were E‐cadherin‐negative. All cases were ERα+ and ERβ+. The staining intensity of ERβ was strong and included staining of periductal stromal cells. The median percentage of cells immunoreactive for ERα was 75% and for ERβ 70% (range 10% weak positive to 100% strong positive). There was a statistically significant relationship between ERβ staining intensity and incidence of ipsilateral breast cancer (P = 0.010).

Conclusions:  The presence and intensity of both stromal and glandular ERβ immunoreactivity suggest that the action of oestrogen on LCIS is on both stromal and glandular cells. Future studies are needed to determine whether the presence of ERβ in LCIS could be targeted to influence the treatment of this disease and perhaps alter its natural history.
Flat epithelial atypia (DIN 1a, atypical columnar change): an underdiagnosed entity very frequently coexisting with lobular neoplasia
Authors: Leibl S , Regitnig P , Moinfar F
Published: June 2007

Aims:  Flat epithelial atypia of the breast [FEA; synonyms: ductal intraepithelial neoplasia (DIN) 1a, atypical columnar change] is increasingly recognized by pathologists and shows distinct genetic alterations. The aim of this study was to determine its biological significance as an incidental finding in breast biopsy specimens.

Methods and results:  On the assumption that both FEA and lobular neoplasia (LN) derive from progenitor cells in the terminal ductal‐lobular unit, we investigated the association between FEA and LN semiquantitatively in 111 excisional breast biopsy specimens which contained LN, but did not contain ductal carcinoma in situ (DCIS) or invasive carcinoma. Ninety‐six cases (86.5%) revealed coexistence of LN and FEA (P < 0001). The distribution of LN was focal in 41 cases (37%), multifocal in 50 (45%) and extensive in 20 (18%) cases. FEA was identified as focal, multifocal and extensive in 29 (26%), 42 (38%) and 25 (23%) cases, respectively. Distribution patterns of LN and FEA showed no statistically significant correlation.

Conclusions:  Due to the striking association between LN and FEA in our material, one may speculate that these two lesions are biologically related and that FEA is an early but non‐obligate precursor lesion similar to LN. Based on this assumption, regular clinical and mammographic follow‐up of patients with FEA would be prudent.