bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental and theoretical investigations of the magnetocaloric effect of Ni2.15Mn0.85−xCuxGa (x=0.05,0.07) alloys
Authors: Duan J. F. , Long Y. , Bao B. , Zhang H. , Ye R. C. , Chang Y. Q. , Wan F. R. , Wu G. H.
Published: March 2008

Magnetocaloric effects of Ni2.15Mn0.85−xCuxGa (x=0.05,0.07) alloys were investigated with both experimental and theoretical approaches. The experiments show that these alloys have large entropy changes and refrigeration capacities with the field change of 2T. Further theoretical analysis indicates that both magnetic entropy changes and lattice entropy changes have the same sign during heating, while the main entropy change arises from the magnetic entropy change.
Transmission electron microscopy study of the oxidation of TiN layers during sputtering process
Authors: Wang Chun , Kryder Mark H.
Published: March 2008

Epitaxial SrRuO3∕SrTiO3 (001) thin films with a TiN template layer have been deposited on Si(001) single crystal substrates by rf sputtering. The epitaxial orientation relationship was determined to be cube on cube with respect to Si and the crystal quality of the SrRuO3∕SrTiO3 film is preserved even when the TiN template layer was oxidized into anatase phase of TiO2 during the sputtering process of SrRuO3. The effect of oxygen plasma on the oxidation and delamination of the TiN layer has been studied using transmission electron microscopy (TEM). The stress in the thin film of SrRuO3∕SrTiO3∕TiN structure was determined from the buckle shape in both plan view and cross-sectional TEM images. The critical stress and the compressive stress were estimated to be 2 and 4GPa.
Highly sensitive mass detection and identification using vibration localization in coupled microcantilever arrays
Authors: Spletzer Matthew , Raman Arvind , Sumali Hartono , Sullivan John P.
Published: March 2008

We study the use of vibration localization in large arrays of mechanically coupled, nearly identical microcantilevers for ultrasensitive mass detection and identification. We demonstrate that eigenmode changes in such an array can be two to three orders of magnitude greater than relative changes in resonance frequencies when an analyte mass is added. Moreover, the changes in eigenmodes are unique to the cantilever to which mass is added, thereby providing a characteristic “fingerprint” that identifies the particular cantilever where mass has been added. This opens the door to ultrasensitive detection and identification of multiple analytes with a single coupled array.
Spark plasma sintering-fabricated one-dimensional nanoscale “crystalline-amorphous” carbon heterojunction
Authors: Qi Xiang , Bao Qiaoliang , Li Chang Ming , Gan Ye , Song Qunliang , Pan Chunxu , Tang Ding Yuan
Published: March 2008

One-dimensional (1D) nanoscale “crystalline-amorphous” carbon heterojunction is fabricated by post-treatment of an amorphous carbon nanofiber in a spark plasma sintering (SPS) system. It is proposed that the unique SPS process is responsible for the heterojunction formation. Studies of the electrical transport property show that the nanoscale heterojunction exhibits a typical rectification behavior. The heterojunctions may have broad potential applications in nanoelectronics and optoelectronics and the SPS technique could be a distinctive approach to construct 1D functional nanomaterials with high throughput.
Spin relaxation in n-type GaAs quantum wells with transient spin grating
Authors: Weng M. Q. , Wu M. W. , Cui H. L.
Published: March 2008

By solving the kinetic spin Bloch equations, we study the time evolution of the transient spin grating, whose spin polarization periodically varies in real space, confined in (001) GaAs quantum wells. With this study, we can investigate the properties of both the spin transport and the spin relaxation at the same time. The Fourier component of the spin signal double exponentially decays with two decay rates 1∕τ+ and 1∕τ−. In the high temperature regime, the average of these two rates quadratically varies with the grating wave vector q, i.e., (1∕τ++1∕τ−)∕2=Dsq2+1∕τ̃s, with Ds and τ̃s representing the spin diffusion coefficient and the average of the out-of-plane and the in-plane spin relaxation times, respectively. τ± calculated from our theory are in good agreement with the experimental data by Weber et al. [Phys. Rev. Lett. 98, 076604 (2007)]. By comparing Ds with and without the electron-electron Coulomb scattering, we calculate the contribution of Coulomb drag to the spin diffusion coefficient. With the transient spin grating result, we further reveal the relations among different characteristic parameters such as spin diffusion coefficient Ds, spin relaxation time τs, and spin injection length Ls. We show that in the presence of the Dresselhaus and/or Rashba spin-orbit coupling, the widely used relation Ls=Dsτs is generally inaccurate and can even be very wrong in some special cases. We present an accurate way to extract the steady-state transport characteristic parameters from the transient spin grating signals.
Study of defects evolution in GaN layers grown by metal-organic chemical vapor deposition
Authors: Jang J. H. , Herrero A. M. , Gila B. , Abernathy C. , Craciun V.
Published: March 2008

GaN layers were grown on c-plane sapphire substrates by metal-organic chemical vapor deposition with a conventional two step growth method. The effect of the three-dimensional (3D) growth mode time (t3D), which depends on trimethylgallium flow rate and growth temperature, on the crystalline quality of the GaN layers was investigated by high resolution x-ray diffraction. Tilt and twist angles were estimated from full width at half maximum (FWHM) of the omega rocking curves (ω-RCs) recorded from the planes parallel and perpendicular to the sample surface. Grazing incidence x-ray diffraction was used for a direct measurement of the twist angle. The threading dislocation densities of GaN layers were estimated from the FWHM values of (0002) and (101¯0) ω-RCs. It was found that while the screw-type dislocations were independent of t3D, the edge-type dislocation density decreased with increasing t3D. Investigations of the structural defects using transmission electron microscopy showed that almost all dislocations generated during the growth of GaN were pure edge or mixed type.
Electron deflector in UHV system: Scattered electrons in ebeam evaporation
Authors: van Veenhuizen Marc J. , Moodera J.
Published: March 2008

The evaporating electron gun in UHV systems has a side-effect that it gives rise to large quantities of scattered and secondary electrons. These electrons may cause damage to sensitive samples and may yield lift-off problems of resist defined patterns. We designed an electron deflector to deflect the electrons and measured the current caused by the electrons during the evaporation of iron.
A source of a reference spherical wave based on a single mode optical fiber with a narrowed exit aperture
Authors: Chkhalo N. I. , Klimov A. Yu. , Rogov V. V. , Salashchenko N. N. , Toropov M. N.
Published: March 2008

A new type of a reference spherical wave source (SWS) based on a single mode optical fiber with a narrowed down up to the submicrometer size exit aperture is proposed. It is intended for the precision point diffraction interferometers as a source of a reference wave. Systematic experimental errors which influence the measurement accuracy of the quality of the wave fronts generated by the SWSs are considered. Experimental data on wave front deformations are given. The combined root-mean-square (rms) wave deformation for a couple of the SWSs measured in a numerical aperture of NA=0.27 reaches the value of rms=0.36nm that corresponds to rms=0.25nm of a single SWS or about λ∕2500 for the red He–Ne laser.
Čerenkov-type phase-matched second-harmonic emission from GaAs∕AlGaAs quantum-cascade lasers
Authors: Austerer M. , Detz H. , Schartner S. , Nobile M. , Schrenk W. , Andrews A. M. , Klang P. , Strasser G.
Published: March 2008

Second-harmonic (SH) emission in the form of Čerenkov-type phase-matched radiation has been measured for quantum-cascade lasers (QCLs) with built-in nonlinearities. The QCLs operate at 10.9μm wavelength and, due to material dispersion, show a high collinear phase mismatch, resulting in low SH external conversion efficiencies on the order of 2μW∕W2. Due to our waveguide design, we were able to couple out and measure the generated SH light in the form of Čerenkov-type phase-matched radiation from the substrate of the device. The SH power collected from the Čerenkov beam leads to an increased external conversion efficiency of ∼50μW∕W2.
Anamorphic microlens arrays based on breath-figure template with adaptive surface reconstruction
Authors: Chari Krishnan , Lander Charles W. , Sudol Ronald J.
Published: March 2008

We describe an approach for fabricating anamorphic microlens array films based on a microporous polymer film template created by self-assembly of condensed water droplets. By using a copolymer of hydrophobic and hydrophilic functionalities for the template material, we create an “environmentally responsive” surface. The hydrophilic groups attract water to create the microvoid pattern but upon heating and stretching in dry air the copolymer reorients to create a low surface energy “nonstick” surface. This enables a variety of polymer precursor materials to be coated on the template, cured, and released to provide anamorphic films with the proper mechanical and optical properties.
Ir
∕
Ta
N
as a bilayer diffusion barrier for advanced Cu interconnects
Authors: Leu L. C. , Norton D. P. , McElwee-White L. , Anderson T. J.
Published: March 2008

The properties of an Ir (5nm)∕TaN (5nm) stacked layer as a copper diffusion barrier on Si have been investigated. Ir∕TaN bilayer barriers were prepared at room temperature by magnetron sputtering followed by in situ Cu deposition for diffusion tests. Thermal annealing of the barrier stacks was carried out in vacuum at high temperatures for 1h. X-ray diffraction patterns, cross sectional transmission electron microscopy images, and energy-dispersive spectrometer line scans on the samples annealed at 600°C revealed no Cu diffusion through the barrier. The results indicate that the Ir∕TaN bilayer is an effective diffusion barrier for copper metallization.
High temperature stability of Hf-based gate dielectric stacks with rare-earth oxide layers for threshold voltage control
Authors: LeBeau James M. , Jur Jesse S. , Lichtenwalner Daniel J. , Craft H. Spalding , Maria Jon-Paul , Kingon Angus I. , Klenov Dmitri O. , Cagnon Joël , Stemmer Susanne
Published: March 2008

The thermal stability of DyOx∕HfSiON and HoOx∕HfSiON gate dielectric stacks on silicon was studied by scanning transmission electron microscopy techniques and correlated with their electrical characteristics. Intermixing of the rare-earth elements with the HfSiON was observed, but there was no diffusion into the interfacial SiO2. Rapid thermal annealing (1000°C) produced little detectable change in the concentration profile of the rare-earth elements but caused thinning of the interfacial SiO2 layer along with a corresponding increase in the rare-earth oxide layer thickness. These reactions could be explained with oxygen deficiency in the rare-earth oxide layer and its greater thermodynamic stability relative to SiO2. Negative flat band voltage shifts were observed relative to a control sample with no DyOx or HoOx. Mechanisms by which the observed microstructure changes could give rise to negative flatband voltage shifts are discussed.
The
Homo floresiensis
cranium (LB1): Size, scaling, and early
Homo
affinities
Authors: Gordon Adam D. , Nevell Lisa , Wood Bernard
Published: March 2008

The skeletal remains of a diminutive small-brained hominin found in Late Pleistocene cave deposits on the island of Flores, Indonesia were assigned to a new species,
Homo floresiensis
[Brown P,
et al.
(2004) A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia.
Nature
431: 1055–1061]. A dramatically different interpretation is that this material belongs not to a novel hominin taxon but to a population of small-bodied modern humans affected, or unaffected, by microcephaly. The debate has primarily focused on the size and shape of the endocranial cavity of the type specimen, LB1, with less attention being paid to the morphological evidence provided by the rest of the LB1 cranium and postcranium, and no study thus far has addressed the problem of how scaling would affect shape comparisons between a diminutive cranium like LB1 and the much larger crania of modern humans. We show that whether or not the effects of its small cranial size are accounted for, the external cranial morphology of the LB1 cranium cannot be accommodated within a large global sample of normal modern human crania. Instead, the shape of LB1, which is shown by multivariate analysis to differ significantly from that of modern humans, is similar to that of
Homo erectus sensu lato
, and, to a lesser extent,
Homo habilis
. Our results are consistent with hypotheses that suggest the Liang Bua specimens represent a diminutive population closely related to either early
H. erectus s. l.
from East Africa and/or Dmanisi or to
H. habilis
.
COPI coatomer complex proteins facilitate the translocation of anthrax lethal factor across vesicular membranes
in vitro
Authors: Tamayo Alfred G. , Bharti Ajit , Trujillo Carolina , Harrison Robert , Murphy John R.
Published: March 2008

The delivery of the diphtheria toxin catalytic domain (DTA) from acidified endosomes into the cytoplasm of eukaryotic cells requires protein–protein interactions between the toxin and a cytosolic translocation factor (CTF) complex. A conserved peptide motif, T1, within the DT transmembrane helix 1 mediates these interactions. Because the T1 motif is also present in the N-terminal segments of lethal factor (LF) and edema factor (EF) in anthrax toxin, we asked whether LF entry into the cell might also be facilitated by target cell cytosolic proteins. In this study, we have used LFnDTA and its associated ADP-ribosyltransferase activity (DTA) to determine the requirements for LF translocation from the lumen of endosomal vesicles to the external medium
in vitro
. Although low-level release of LFnDTA from enriched endosomal vesicles occurs in the absence of added factors, translocation was enhanced by the addition of cytosolic proteins and ATP to the reaction mixture. We show by GST-LFn pull-down assays that LFn specifically interacts with at least ζ-COP and β-COP of the COPI coatomer complex. Immunodepletion of COPI coatomer complex and associated proteins from cytosolic extracts blocks
in vitro
LFnDTA translocation. Translocation may be reconstituted by the addition of partially purified bovine COPI to the translocation assay mixture. Taken together, these data suggest that the delivery of LF to the cytosol requires either COPI coatomer complex or a COPI subcomplex for translocation from the endosomal lumen. This facilitated delivery appears to use a mechanism that is analogous to that of DT entry.
cis
-Jasmone induces
Arabidopsis
genes that affect the chemical ecology of multitrophic interactions with aphids and their parasitoids
Authors: Bruce Toby J. A. , Matthes Michaela C. , Chamberlain Keith , Woodcock Christine M. , Mohib Abdul , Webster Ben , Smart Lesley E. , Birkett Michael A. , Pickett John A. , Napier Johnathan A.
Published: March 2008

It is of adaptive value for a plant to prepare its defenses when a threat is detected, and certain plant volatiles associated with insect damage, such as
cis
-jasmone (CJ), are known to switch-on defense metabolism. We used aphid and aphid parasitoid responses to
Arabidopsis thaliana
as a model system for studying gene expression and defense chemistry and its impact at different trophic levels. Differential responses to volatiles of induced
Arabidopsis
occurred for specialist and generalist insects: the generalist aphid,
Myzus persicae
, was repelled, whereas the specialist,
Lipaphis erysimi
, was attracted; the generalist aphid parasitoid
Aphidius ervi
was attracted, but the specialist parasitoid
Diaeretiella rapae
was not affected.
A. ervi
also spent longer foraging on induced plants than on untreated ones. Transcriptomic analyses of CJ-induced
Arabidopsis
plants revealed that a limited number of genes, including a gene for a cytochrome P450,
CYP81D11
, were strongly up-regulated in the treated plants. We examined transgenic
Arabidopsis
lines constitutively overexpressing this gene in bioassays and found insect responses similar to those obtained for wild-type plants induced with CJ, indicating the importance of this gene in the CJ-activated defense response. Genes involved in glucosinolate biosynthesis and catabolism are unaffected by CJ and, because these genes relate to interactions with herbivores and parasitoids specific to this family of plants (Brassicaceae), this finding may explain the differences in behavioral response of specialist and generalist insects.
Distinct nuclear and cytoplasmic functions of androgen receptor cofactor p44 and association with androgen-independent prostate cancer
Authors: Peng Yi , Chen Fei , Melamed Jonathan , Chiriboga Luis , Wei Jianjun , Kong Xiangtian , Mcleod Maureen , Li Yirong , Li Caihong X. , Feng Alice , Garabedian Michael J. , Wang Zhengxin , Roeder Robert G. , Lee Peng
Published: March 2008

Androgen receptor (AR) mediates transcriptional activation of diverse target genes through interactions with various coactivators that may alter its function and help mediate the switch between prostate cell proliferation and differentiation. We recently identified p44/MEP50 as an AR coactivator and further showed that it is expressed primarily in the nucleus and cytoplasm of benign prostate epithelial and prostate cancer cells, respectively. We also showed that haploinsufficiency in p44
+/−
mice causes prostate epithelial cell proliferation. To establish direct cause-and-effect relationships, we have used p44 fusion proteins that are selectively expressed in the nucleus or cytoplasm of prostate cancer cells (LNCaP), along with RNAi analyses, to examine effects of p44 both
in vitro
and
in vivo
(in tumor xenografts). We show that preferential expression of p44 in the nucleus inhibits proliferation of LNCaP cells in an AR-dependent manner, whereas preferential expression of p44 in the cytoplasm enhances cell proliferation. These effects appear to be mediated, at least in part, through the regulation of distinct cell-cycle regulatory genes that include p21 (up-regulated by nuclear p44) and cyclin D2 and CDK6 (up-regulated by cytoplasmic p44). Importantly, we also demonstrate that altered p44 expression is associated with androgen-independent prostate cancer. Our results indicate that nuclear p44 and cytoplasmic p44 have distinct and opposing functions in the regulation of prostate cancer cell proliferation.
A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5
Authors: Ernst Robert , Kueppers Petra , Klein Cornelia M. , Schwarzmueller Tobias , Kuchler Karl , Schmitt Lutz
Published: March 2008

The yeast ABC transporter Pdr5 plays a major role in drug resistance against a large number of structurally unrelated compounds. Although Pdr5 has been extensively studied, many important aspects regarding its molecular mechanisms remain unresolved. For example, a striking degeneration of conserved amino acid residues exists in the nucleotide binding domains (NBDs), but their functional relevance is unknown. Here, we performed
in vivo
and
in vitro
experiments to address the functional asymmetry of NBDs. It became evident by ATPase activity and drug transport studies that catalysis at only one of the two NBD composite sites is crucial for protein function. Furthermore, mutations of the proposed “catalytic carboxylate” (E1036) and the “catalytic dyad histidine” (H1068) were characterized. Although a mutation of the glutamate abolished ATPase activity and substrate transport, mutation of H1068 had no influence on ATP consumption. However, the H1068A mutation abolished rhodamine transport
in vivo
and
in vitro
, while leaving the transport of other substrates unaffected. By contrast to mammalian P-glycoprotein (P-gp), the ATPase activity of yeast Pdr5 is not stimulated by the addition of substrates, indicating that Pdr5 is an uncoupled ABC transporter that constantly hydrolyses ATP to ensure active substrate transport. Taken together, our data provide important insights into the molecular mechanism of Pdr5 and suggest that not solely the transmembrane domains dictate substrate selection.
Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm
Authors: Wong Pak Kin , Yu Fuqu , Shahangian Arash , Cheng Genhong , Sun Ren , Ho Chih-Ming
Published: March 2008

A mixture of drugs is often more effective than using a single effector. However, it is extremely challenging to identify potent drug combinations by trial and error because of the large number of possible combinations and the inherent complexity of the underlying biological network. With a closed-loop optimization modality, we experimentally demonstrate effective searching for potent drug combinations for controlling cellular functions through a large parametric space. Only tens of iterations out of one hundred thousand possible trials were needed to determine a potent combination of drugs for inhibiting vesicular stomatitis virus infection of NIH 3T3 fibroblasts. In addition, the drug combination reduced the required dosage by ≈10-fold compared with individual drugs. In another example, a potent mixture was identified in thirty iterations out of a possible million combinations of six cytokines that regulate the activity of nuclear factor kappa B in 293T cells. The closed-loop optimization approach possesses the potential of being an effective approach for manipulating a wide class of biological systems.
Involvement of
Arabidopsis
HOS15 in histone deacetylation and cold tolerance
Authors: Zhu Jianhua , Jeong Jae Cheol , Zhu Yanmei , Sokolchik Irina , Miyazaki Saori , Zhu Jian-Kang , Hasegawa Paul M. , Bohnert Hans J. , Shi Huazhong , Yun Dae-Jin , Bressan Ray A.
Published: March 2008

Histone modification in chromatin is one of the key control points in gene regulation in eukaryotic cells. Protein complexes composed of histone acetyltransferase or deacetylase, WD40 repeat protein, and many other components have been implicated in this process. Here, we report the identification and functional characterization of HOS15, a WD40-repeat protein crucial for repression of genes associated with abiotic stress tolerance through histone deacetylation in
Arabidopsis
. HOS15 shares high sequence similarity with human transducin-beta like protein (TBL), a component of a repressor protein complex involved in histone deacetylation. Mutation of the
HOS15
gene renders mutant plants hypersensitive to freezing temperatures. HOS15 is localized in the nucleus and specifically interacts with histone H4. The level of acetylated histone H4 is higher in the
hos15
mutant than in WT plants. Moreover, the stress inducible
RD29A
promoter is hyperinduced and associated with a substantially higher level of acetylated histone H4 in the
hos15
mutant under cold stress conditions. Our results suggest a critical role for gene activation/repression by histone acetylation/deacetylation in plant acclimation and tolerance to cold stress.
Observing Tutorial Dialogues Collaboratively: Insights About Human Tutoring Effectiveness From Vicarious Learning
Authors: Chi Michelene T. H. , Roy Marguerite , Hausmann Robert G. M.
Published: March 2008

The goals of this study are to evaluate a relatively novel learning environment, as well as to seek greater understanding of why human tutoring is so effective. This alternative learning environment consists of pairs of students collaboratively observing a videotape of another student being tutored. Comparing this collaboratively observing environment to four other instructional methods—one‐on‐one human tutoring, observing tutoring individually, collaborating without observing, and studying alone—the results showed that students learned to solve physics problems just as effectively from observing tutoring collaboratively as the tutees who were being tutored individually. We explain the effectiveness of this learning environment by postulating that such a situation encourages learners to become active and constructive observers through interactions with a peer. In essence, collaboratively observing combines the benefit of tutoring with the benefit of collaborating. The learning outcomes of the tutees and the collaborative observers, along with the tutoring dialogues, were used to further evaluate three hypotheses explaining why human tutoring is an effective learning method. Detailed analyses of the protocols at several grain sizes suggest that tutoring is effective when tutees are independently or jointly constructing knowledge: with the tutor, but not when the tutor independently conveys knowledge.
The Role of Words and Sounds in Infants' Visual Processing: From Overshadowing to Attentional Tuning
Authors: Sloutsky Vladimir M. , Robinson Christopher W.
Published: March 2008

Although it is well documented that language plays an important role in cognitive development, there are different views concerning the mechanisms underlying these effects. Some argue that even early in development, effects of words stem from top‐down knowledge, whereas others argue that these effects stem from auditory input affecting attention allocated to visual input. Previous research (e.g., ) demonstrated that non‐speech sounds attenuate processing of corresponding visual input at 8, 12, and 16 months of age, whereas the current study demonstrates that words attenuate visual processing at 10 months but not at 16 months (Experiment 1). Furthermore, prefamiliarization with non‐speech sounds (Experiment 2) resulted in able processing of visual input by 16‐month‐olds. These findings suggest that some effects of labels found early in development may stem from familiarity with human speech. The possibility of general‐auditory factors underlying the effects of words on cognitive development is discussed.
Trade‐Offs Between Grounded and Abstract Representations: Evidence From Algebra Problem Solving
Authors: Koedinger Kenneth R. , Alibali Martha W. , Nathan Mitchell J.
Published: March 2008

This article explores the complementary strengths and weaknesses of grounded and abstract representations in the domain of early algebra. Abstract representations, such as algebraic symbols, are concise and easy to manipulate but are distanced from any physical referents. Grounded representations, such as verbal descriptions of situations, are more concrete and familiar, and they are more similar to physical objects and everyday experience. The complementary computational characteristics of grounded and abstract representations lead to trade‐offs in problem‐solving performance. In prior research with high school students solving relatively simple problems, demonstrated performance benefits of grounded representations over abstract representations—students were better at solving simple story problems than the analogous equations. This article extends this prior work to examine both simple and more complex problems in two samples of college students. On complex problems with two references to the unknown, a “symbolic advantage” emerged, such that students were better at solving equations than analogous story problems. Furthermore, the previously observed “verbal advantage” on simple problems was replicated. We thus provide empirical support for a trade‐off between grounded, verbal representations, which show advantages on simpler problems, and abstract, symbolic representations, which show advantages on more complex problems.
Effects of Attention on the Strength of Lexical Influences on Speech Perception: Behavioral Experiments and Computational Mechanisms
Authors: Mirman Daniel , McClelland James L. , Holt Lori L. , Magnuson James S.
Published: March 2008

The effects of lexical context on phonological processing are pervasive and there have been indications that such effects may be modulated by attention. However, attentional modulation in speech processing is neither well documented nor well understood. Experiment 1 demonstrated attentional modulation of lexical facilitation of speech sound recognition when task and critical stimuli were identical across attention conditions. We propose modulation of lexical activation as a neurophysiologically plausible computational mechanism that can account for this type of modulation. Contrary to the claims of critics, this mechanism can account for attentional modulation without violating the principle of interactive processing. Simulations of the interactive TRACE model extended to include two different ways of modulating lexical activation showed that each can account for attentional modulation of lexical feedback effects. Experiment 2 tested conflicting predictions from the two implementations and provided evidence that is consistent with bias input as the mechanism of attentional control of lexical activation.
A Probabilistic Model of Melody Perception
Authors: Temperley David
Published: March 2008

This study presents a probabilistic model of melody perception, which infers the key of a melody and also judges the probability of the melody itself. The model uses Bayesian reasoning: For any “surface” pattern and underlying “structure,” we can infer the structure maximizing P(structure|surface) based on knowledge of P(surface, structure). The probability of the surface can then be calculated as ∑ P(surface, structure), summed over all structures. In this case, the surface is a pattern of notes; the structure is a key. A generative model is proposed, based on three principles: (a) melodies tend to remain within a narrow pitch range; (b) note‐to‐note intervals within a melody tend to be small; and (c) notes tend to conform to a distribution (or key profile) that depends on the key. The model is tested in three ways. First, it is tested on its ability to identify the keys of a set of folksong melodies. Second, it is tested on a melodic expectation task in which it must judge the probability of different notes occurring given a prior context; these judgments are compared with perception data from a melodic expectation experiment. Finally, the model is tested on its ability to detect incorrect notes in melodies by assigning them lower probabilities than the original versions.
Diffusion Dynamics of CuxCluster on Cu(111) Surface
Authors: Tang Jian-feng , Xu Mai-chang , Li Xue-song , Long Wo-yun
Published: March 2008

The diffusion dynamics of small two-dimensional atomic clusters Cux (1 x 8) on Cu(111) surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K. The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented. Our simulations show that the diffusion migration energy of the Cu7 cluster is the highest and the prefactor for the Cu7 cluster is almost three orders of magnitude larger than that for single atom diffusion. This conclusion is consistent with the experimental results for similar metals. In addition, the dependence of cluster diffusion on film growth is also discussed.
Solvent Reorganization Energy and Electronic Coupling for Intramolecular Electron Transfer in Biphenyl-Acceptor Anion Radicals
Authors: Wang Jing-bo , Ma Jian-yi , Li Xiang-yuan , He Fu-cheng , Fu Ke-xiang
Published: March 2008

A novel algorithm was designed and implemented to realize the numerical calculation of the solvent reorganization energy for electron transfer reactions, on the basis of nonequilibrium solvation theory and the dielectric polarizable continuum model. Applying the procedure to the well-investigated intramolecular electron transfer in biphenyl-androstane-naphthyl and biphenyl-androstane-phenanthryl systems, the numerical results of solvent reorganization energy were determined to be around 60 kJ/mol, in good agreement with experimental data. Koopman's theorem was adopted for the calculation of the electron transfer coupling element, associated with the linear reaction coordinate approximation. The values for this quantity obtained are acceptable when compared with experimental results.
Diffusion of an Extra Ga Atom in GaAs(001)(2 4) Rich-As Surface
Authors: Li Kun , Pan Bi-cai
Published: March 2008

The potential energy surface for the migration of an extra Ga atom on the GaAs(001) 2(2 4) surface was mapped out by performing calculations at the level of analytical bond-order potential. Based on this calculations, we found some lower-energy sites for the adsorption of an extra Ga atom in the surface, which were in agreement with the experimental data. Moreover, many possible pathways for an extra Ga atom diffusing in this surface were revealed. According to the relative energies of the possible pathways, the individual Ga adatoms preferably keep their diffusion in two pathways parallel to the As dimers. This result can be understood using the strain caused by the diffusing Ga atom in the pathways. In addition, the simulated kinetic processes of the extra Ga atom diffusing in different pathways at finite temperatures support the prediction from our calculated potential energy surface.
Synthesis and Characterization of Cobalt-Carbon Core-Shell Microspheres in Supercritical Carbon Dioxide System
Authors: Yang Jun-song , Chen Qian-wang
Published: March 2008

The synthesis of cobalt-carbon core-shell microspheres in supercritical carbon dioxide system was investigated. Cobalt-carbon core-shell microspheres with diameter of about 1 m were prepared at 350 C for 12 h in a closed vessel containing an appropriate amount of bis(cyclopentadienyl)cobalt powder and dry ice. Characterization by a variety of techniques, including X-ray powder diffraction, X-ray photoelectron spectroscopy, Transmission electron microscope, Fourier transform infrared spectrum and Raman spectroscopy analysis reveals that each cobalt-carbon core-shell microsphere is made up of an amorphous cobalt core with diameter less than 1 m and an amorphous carbon shell with thickness of about 200 nm. The possible growth mechanism of cobalt-carbon core-shell microspheres is discussed, based on the pyrolysis of bis(cyclopentadienyl)cobalt in supercritical carbon dioxide and the deposition of carbon or carbon clusters with odd electrons on the surface of magnetic cobalt cores due to magnetic attraction. Magnetic measurements show 141.41 emu/g of saturation magnetization of a typical sample, which is lower than the 168 emu/g of the corresponding metal cobalt bulk material. This is attributed to the considerable mass of the carbon shell and amorphous nature of the magnetic core. Control of magnetism in the cobalt-carbon core-shell microspheres was achieved by annealing treatments.
Synthesis and Photocatalytic Activity of One-dimensional ZnO-Zn2SnO4 Mixed Oxide Nanowires
Authors: Bai Xue-lian , Pan Nan , Wang Xiao-ping , Wang Hai-qian
Published: March 2008

Mixed oxide photocatalysts, ZnO-Zn2SnO4 (ZnO-ZTO) nanowires with different sizes were prepared by a simple thermal evaporation method. The ZnO-ZTO nanowires were characterized with a scanning electron microscope, X-ray diffraction, high-resolution transmission electron microscopy, energy-dispersive spectrometer, and X-ray photoelectron spectra. The photocatalytic activity of the ZnO-ZTO mixed nanowires were studied by observing the photodegradation behaviors of methyl orange aqueous solution. The results suggest that the ZnO-ZTO mixed oxide nanowires have a higher photocatalytic activity than pure ZnO and Zn2SnO4 nanowires. The photocatalyst concentration in the solution distinctly affects the degradation rate, and our results show that higher photodegradation efficiency can be achieved with a smaller amount of ZnO-ZTO nanowire catalyst, as compared to the pure ZnO and ZTO nanowires. Moreover, the photocatalytic activity can also be enhanced by reducing the average diameter of the nanowires. The activity of pure ZnO and ZTO nanowires are also enhanced by physically mixing them. These results can be explained by the synergism between the two semiconductors.
MRN‐100, An Iron‐Based Compound, Possesses Anti‐HIV Activity In Vitro
Authors: Ghoneum Mamdooh , Shaheen Magda
Published: March 2008

We examined the in vitro anti‐human immunodeficiency virus (HIV) activity of MRN‐100, an iron‐based compound derived from bivalent and tervalent ferrates. MRN‐100 action against HIV‐1 (SF strain) was tested in primary cultures of peripheral blood mononuclear cells (MNC) by analyzing p24 antigen production and percent survival of MNC infected with HIV. MRN‐100 at a concentration of 10% (v/v) inhibited HIV‐1 replication in 11 out of 14 samples (79%). The percentage of suppression of p24 antigen was −12.3 to 100% at 10 days post‐treatment. MRN‐100 also exhibited a significant protective effect in the survival of HIV‐1‐infected MNC. MNC survival post‐treatment was dose dependent, 70.4% ± 8.4, 83.6% ± 10.7 and 90% ± 11.4, at concentrations 2.5, 5 and 10% (v/v), respectively, as compared with 53% ± 4 for HIV‐1‐infected MNC without treatment. The effect was detected as early as 4 days and continued up to 11 days. Treatment with MRN‐100 caused no significant change in proliferative response of MNC alone or cocultured with different mitogens: PHA and Con‐A (activators of T cell function) and PWM (activator of CD4+ T cell‐dependent B cells). We concluded that MRN‐100 possesses anti‐HIV activity in vitro and without an increase in lymphocyte proliferation, MRN‐100 may be a useful agent for treating patients with acquired immunodeficiency syndrome.
Soybeans Ameliolate Diabetic Nephropathy in Rats
Authors: Choi Young Eun , Ahn Soo Kyung , Lee Won Taek , Lee Jong Eun , Park Seung Hwa , Yoon Bang Bu , Park Kyung Ah
Published: March 2008

Diabetic nephropathy is one of the most frequent and serious complications of diabetes mellitus. Soybeans have been shown to reduce urinary albumin excretion and total cholesterol in non‐diabetic patients with nephrotic syndrome. However, reports focusing specifically on diabetic nephropathy are scarce and the available results are inconsistent. It was reported that soybean consumption reduced urinary protein excretion in type 1 diabetic patients with diabetic nephropathy, whereas it was found to elicit an increase in urinary protein excretion when soybeans were consumed by type 2 diabetic patients. This study aims to investigate the effects of soybean in diabetic nephropathy, particularly the effects of consuming soybeans on the histopathology of diabetic nephropathy, using aquaporin (AQP) and osteopontin (OPN) expression as diagnostic markers. Male Sprague‐Dawley rats were assigned to one of three groups: control, diabetic with red chow diet and diabetic with soybean diet. For histological examination, the expression of OPN and AQP, renal function and hemoglobin A1c were evaluated at the end of the study. Improvements in glomerular and tubulointerstitial lesions were demonstrated in the diabetic rat group given a soybean diet. OPN and AQP expression were suppressed in the kidney specimens of diabetic rats with the soybean diet. In conclusion, soybeans may prevent the weight loss and morphological disruption of the kidney associated with diabetes mellitus. Soybeans also may improve glycemic control. It seems likely that long‐term control of blood glucose levels using a soybean diet could prevent the progression of diabetes mellitus, and therefore, nephropathy could be prevented.
Power and SNP tagging in whole mitochondrial genome association studies
Authors: McRae Allan F. , Byrne Enda M. , Zhao Zhen Zhen , Montgomery Grant W. , Visscher Peter M.
Published: March 2008

The application of genetic association studies to detect mitochondrial variants responsible for phenotypic variation has recently been demonstrated. However, the only power estimates currently available are based on the use of mitochondrial haplogroups, which can only tag a small fraction of the common variation in the mitochondrial genome. Here, power estimates are derived for a SNP-based study design for both disease (case-control) and quantitative trait mapping studies. Power is estimated using simulations based on a collection of publicly available mitochondrial sequences of European origin. The power when testing all common mitochondrial SNPs is shown to be equivalent to that when testing only tagging SNPs, despite the relatively high ratio of tagging SNPs to total SNPs resulting from the tagging of all SNPs with a minor allele frequency greater than 1%. The sample size requirements of mitochondrial genome association studies are compared with that of nuclear whole-genome studies. Remarkably, the trade off between the number of tests being performed and the proportion of phenotypic variance explained for a fixed effect size results in approximately equal sample sizes required for both study types, although the per individual cost for the mitochondrial association study is much less. To test the representation of the sequences used in the power simulations, a sample of 3839 individuals from 1037 Australian families was genotyped for 69 tagging SNPs. The strong concordance in allele frequencies and linkage disequilibrium between the European sequences and the Australian sample indicates that the results presented here are transferable across populations of European descent.
The epitope space of the human proteome
Authors: Berglund Lisa , Andrade Jorge , Odeberg Jacob , Uhlén Mathias
Published: March 2008

In the post‐genome era, there is a great need for protein‐specific affinity reagents to explore the human proteome. Antibodies are suitable as reagents, but generation of antibodies with low cross‐reactivity to other human proteins requires careful selection of antigens. Here we show the results from a proteome‐wide effort to map linear epitopes based on uniqueness relative to the entire human proteome. The analysis was based on a sliding window sequence similarity search using short windows (8, 10, and 12 amino acid residues). A comparison of exact string matching (Hamming distance) and a heuristic method (BLAST) was performed, showing that the heuristic method combined with a grid strategy allows for whole proteome analysis with high accuracy and feasible run times. The analysis shows that it is possible to find unique antigens for a majority of the human proteins, with relatively strict rules involving low sequence identity of the possible linear epitopes. The implications for human antibody‐based proteomics efforts are discussed.
Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?
Authors: Chruszcz Maksymilian , Potrzebowski Wojciech , Zimmerman Matthew D. , Grabowski Marek , Zheng Heping , Lasota Piotr , Minor Wladek
Published: March 2008

A nonredundant set of 9081 protein crystal structures in the Protein Data Bank was used to examine the solvent content, the number of polypeptide chains, and the oligomeric states of proteins in crystals as a function of crystal symmetry (as classified by crystal systems and space groups). It was found that there is a correlation between solvent content and crystal symmetry. Surprisingly, proteins crystallizing in lower symmetry systems have lower solvent content compared to those crystallizing in higher symmetry systems. Nevertheless, there is no universal correlation between solvent content and preferences of macromolecules to crystallize in certain space groups. Crystal symmetry as a function of oligomeric state was examined, where trimers, tetramers, and hexamers were found to prefer to crystallize in systems where the oligomer symmetry could be incorporated in the crystal symmetry. Our analysis also shows that the frequency distribution within the enantiomorphous pairs of space groups does not differ significantly, in contrast to previous reports.
Quantitative analysis of multi‐protein interactions using FRET: Application to the SUMO pathway
Authors: Martin Sarah F. , Tatham Michael H. , Hay Ronald T. , Samuel Ifor D.W.
Published: March 2008

Protein–protein binding and signaling pathways are important fields of biomedical science. Here we report simple optical methods for the determination of the equilibrium binding constant Kd of protein–protein interactions as well as quantitative studies of biochemical cascades. The techniques are based on steady‐state and time‐resolved fluorescence resonance energy transfer (FRET) between ECFP and Venus‐YFP fused to proteins of the SUMO family. Using FRET has several advantages over conventional free‐solution techniques such as isothermal titration calorimetry (ITC): Concentrations are determined accurately by absorbance, highly sensitive binding signals enable the analysis of small quantities, and assays are compatible with multi‐well plate format. Most importantly, our FRET‐based techniques enable us to measure the effect of other molecules on the binding of two proteins of interest, which is not straightforward with other approaches. These assays provide powerful tools for the study of competitive biochemical cascades and the extent to which drug candidates modify protein interactions.
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2‐Cys subfamily without any formation of toroid‐shaped decamers
Authors: Smeets Aude , Loumaye Eléonore , Clippe André , Rees Jean‐François , Knoops Bernard , Declercq Jean‐Paul
Published: March 2008

The peroxiredoxins (PRDXs) define a superfamily of thiol‐dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high‐molecular‐weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2‐Cys, atypical 2‐Cys, and 1‐Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1‐Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2‐Cys PRDX subfamily. The protein is composed of two distinct domains: a C‐terminal domain and an N‐terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild‐type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid‐shaped decamers formed by dimer association and observed in most typical 2‐Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2‐Cys PRDXs without any formation of toroid‐shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide‐dependent cell signaling rather than a molecular chaperone.
Induced‐fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure‐based drug design
Authors: Xu Yechun , Colletier Jacques Ph. , Jiang Hualiang , Silman Israel , Sussman Joel L. , Weik Martin
Published: March 2008

Crystal structures of acetylcholinesterase complexed with ligands are compared with side‐chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ligand binding thus involve preexisting equilibrium dynamics. Consequently, rational drug design could benefit significantly from conformations monitored by MD simulations of native targets.