bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal vapor bubble and pressure dynamics during infrared laser ablation of tissue
Authors: Wagner Wolfgang , Sokolow Adam , Pearlstein Robert , Edwards Glenn
Published: January 2009

Free-electron laser irradiation can superheat tissue water, driving thermal vapor bubbles confined by tissue matrix and leading to mechanical tissue failure (ablation). Acoustic transients propagating from an ablation cavity were recorded with a polarization quadrature, interferometric vibrometer. For 3.0 μm infrared irradiation, the shocklike transients with peak pressures in the megapascal range indicate amplification due to bubble collapse. In contrast, for 6.45 μm irradiation, elastic transients with peak pressures in the 0.1 MPa range indicate tissue failure during bubble growth.
Transient electro-osmotic flow in cylindrical microcapillaries containing salt-free medium
Authors: Chang Shih-Hsiang
Published: January 2009

A theoretical study on the transient electro-osmotic flow through a cylindrical microcapillary containing a salt-free medium is presented for both constant surface charge density and constant surface potential. The exact analytical solutions for the electric potential distribution and the transient electro-osmotic flow velocity are derived by solving the nonlinear Poisson-Boltzmann equation and the Navier-Stokes equation. Based on these results, a systematic parametric study on the characteristics of the transient electro-osmotic flow is detailed. The general behavior of transient electro-osmotic flow in a cylindrical tube is similar to that observed in a microchannel containing an electrolyte solution. However, the steady-state electro-osmotic flow significantly deviates from the typical plug flow at higher surface charge and the rate of increase in the electro-osmotic mobility is strongly suppressed due to the effect of counterion condensation. In addition, the applicability limit of these solutions is also discussed.
Understanding exceptional thermodynamic and kinetic stability of amorphous sulfur obtained by rapid compression
Authors: Yu P. , Wang W. H. , Wang R. J. , Lin S. X. , Liu X. R. , Hong S. M. , Bai H. Y.
Published: January 2009

Amorphous sulfur (a-S) with excellent stability is obtained by rapid compression method. The prepared a-S has a single glassy phase and exhibits a wide supercooled liquid region of 112 K and much high thermal and kinetic stability at room temperature compared to that of conventional a-S fabricated by quenched method. The substantial improved thermal and kinetic stability is attributed to low energy state induced by rapid compressing process. The stable a-S is a model system for facilitating the studies of the nature of glasses and supercooled liquids.
Optical properties of Mn1.56Co0.96Ni0.48O4 films studied by spectroscopic ellipsometry
Authors: Gao Y. Q. , Huang Z. M. , Hou Y. , Wu J. , Ge Y. J. , Chu J. H.
Published: January 2009

Spectroscopic ellipsometry is used to determine the optical properties of the noncrystalline and crystalline Mn1.56Co0.96Ni0.48O4 (MCN) films prepared by chemical solution deposition method in the range of 250–1100 nm. A pronounced difference in the optical functions is found between 500 and 600 °C. Two distinctive peaks, attributed to the critical points of the MCN films, appear in the optical constant spectra for the films annealed at 600 °C while they are not obvious for the films annealed at 500 °C. The presented results are instructive, further understanding the physical properties of transition metal oxides in theory.
Remote dynamic acoustoelastic testing: Elastic and dissipative acoustic nonlinearities measured under hydrostatic tension and compression
Authors: Renaud Guillaume , Callé Samuel , Defontaine Marielle
Published: January 2009

Remote dynamic acoustoelastic testing is proposed to provide a noninvasive and regional measurement of elastic and dissipative acoustic nonlinearities in fluids and solids. The probed medium is dynamically stressed by a low-frequency sinusoidal variation in the hydrostatic pressure in the surrounding fluid. Simultaneously, ultrasound pulses propagate undergoing time of flight and energy modulations, associated with elastic and dissipative nonlinearities, respectively. Acoustic nonlinearities in tension phases can be distinguished from those measured in compression phases. Instantaneous modulations of ultrasound time of flight and energy are analyzed as functions of the instantaneous low-frequency acoustic pressure, similar to a quasistatic acoustoelastic testing.
Photopatternable self-assembled monolayers as micron scale templates for polymer based field effect transistors
Authors: Avnon Eran , Paz Yaron , Tessler Nir
Published: January 2009

We study the use of photopatternable self-assembled monolayers (SAMs) as a template for self-localizing patterns of conducting-polymer based transistors. To allow the use of standard SAMs, we studied and optimized the photocatalytic effect of TiO2, so that it can render the SAMs photopatternable by direct UV light imaging down to micron scale resolution. The resulting template produces high resolution patterns of conducting polymer without resorting to high resolution inkjet printing. This process is used to demonstrate 2 μm channel length organic field effect transistors.
Deep ultraviolet and near infrared photodiode based on n-ZnO/p-silicon nanowire heterojunction fabricated at low temperature
Authors: Zhou Hai , Fang Guojia , Yuan Longyan , Wang Chong , Yang Xiaoxia , Huang Huihui , Zhou Conghua , Zhao Xingzhong
Published: January 2009

n -ZnO / p -silicon nanowire (SiNW) photodiodes were prepared by radio frequency reactive magnetron sputtering of n-type zinc oxide at room temperature on photoresist filled p-SiNWs, which were fabricated by electroless metal deposition method at 323 K. Our n-ZnO/p-SiNW photodiodes showed good temperature- and light-intensity dependence. They exhibited strong responsivities of 19.2 and 2.5 A/W for 254 and 1000 nm photons, respectively, under a reverse bias of 2 V with a strong peak of responsivity near 390 nm, the wavelength corresponding to the band gap of ZnO. These results present potential applications of n-ZnO/p-SiNW photodetectors in deep ultraviolet and near infrared regions.
High resolution fluorescence imaging of damage regions in H+ ion implanted Nd:MgO:LiNbO3 channel waveguides
Authors: Jaque Daniel , Chen Feng
Published: January 2009

We report on the fluorescence imaging of channel waveguides fabricated by light ion (H+) implantation in neodymium (Nd) doped MgO:LiNbO3 crystals. The spectroscopic properties of Nd ions have been found to be modified only at the nuclear damage region while remaining unaltered at the electronic one. The fluorescence image of the light ion implanted waveguide has been found to be completely different from that obtained by medium-mass ion implantation, revealing the different waveguide formation mechanisms taking place in each case.
Size dependence of lattice deformation induced by growth stress in Sn nanowires
Authors: Shin Ho Sun , Yu Jin , Song Jae Yong , Park Hyun Min
Published: January 2009

We report on size-dependent lattice expansion of single crystalline Sn nanowires (NWs) with the wire radius (rNW=6.9–34.7 nm), where the NWs are deposited under confinement of a nanotemplate. The longitudinal lattice expansion in the NWs increases up to approximately 1.0% with the reciprocal radius (1/rNW), contrary to the general theoretical prediction that the surface relaxation causes lattice contraction of nanomaterials. The longitudinal dilatation of the NW lattice can be understood by the Poisson effect induced by the compressive growth stress in the radial direction, which increases with the reciprocal radius.
Effects of rare earth manganites on structural, ferroelectric, and magnetic properties of BiFeO3 thin films
Authors: Lahmar A. , Habouti S. , Dietze M. , Solterbeck C.-H. , Es-Souni M.
Published: January 2009

The results of structural studies of pure-phase perovskite thin films of BiFeO3–10% RMnO3 (R=La, Eu, Gd, Tb, and Dy) are presented. Raman scattering studies show line broadening similar to what is reported for RMnO3; they were attributed to Jahn–Teller distortion and orthorhombic structural change. Evidence of an anomaly of the orthorhombic distortion at GdMnO3 could be obtained. Interestingly the addition of GdMnO3 leads to a substantial increase in magnetization, combined with moderate ferroelectric polarization. All other compositions are characterized by higher ferroelectric polarization but almost no magnetization.
Mechanism of grain growth during severe plastic deformation of a nanocrystalline Ni–Fe alloy
Authors: Wang Y. B. , Ho J. C. , Liao X. Z. , Li H. Q. , Ringer S. P. , Zhu Y. T.
Published: January 2009

Deformation induced grain growth has been widely reported in nanocrystalline materials. However, the grain growth mechanism remains an open question. This study applies high-pressure torsion to severely deform bulk nanocrystalline Ni-20 wt % Fe disks and uses transmission electron microscopy to characterize the grain growth process. Our results provide solid evidence suggesting that high pressure torsion induced grain growth is achieved primarily via grain rotation for grains much smaller than 100 nm. Dislocations are mainly seen at small-angle subgrain boundaries during the grain growth process but are seen everywhere in grains after the grains have grown large.
On dielectric breakdown in silicon-rich silicon nitride thin films
Authors: Habermehl S. , Apodaca R. T. , Kaplar R. J.
Published: January 2009

Observations of dielectric breakdown in Si-rich silicon nitride indicate that it is initiated by threshold field trap ionization. The films exhibit the charge transport mechanism of Poole–Frenkel emission with a compositionally dependent ionization potential ranging from 0.58 to 1.22 eV. Similar to silicon oxynitride, the barrier lowering energy at the point of dielectric breakdown is correlated with within ∼2kT of the ionization potential, thus revealing a dual role for bulk traps in the film: regulating charge transport and retarding hot electron generation. Additionally, a semiempirical expression is developed that accurately predicts the compositional dependence of the breakdown field.
Stabilization of lateral mode transients in high-power broad area semiconductor lasers
Authors: Chen Chen , Leisher Paul , Patterson Steve , Crump Paul , Kim Yong Kwan , Choquette Kent
Published: January 2009

The lateral modes in high-power broad area gain-guided semiconductor lasers suffer from instabilities that can lead to self-focusing of the optical modes resulting in the formation of beam filaments. The introduction of cold-cavity index guiding, by means of etched holes, has been previously shown to reduce filament formation in the optical near field. In this work, a simple measurement technique is presented and utilized to characterize the behavior of local intensity fluctuations in the time domain. The use of etched holes to provide index guiding is shown to provide a significant improvement in the temporal stability of the lateral optical modes.
Quantifying the number of color centers in single fluorescent nanodiamonds by photon correlation spectroscopy and Monte Carlo simulation
Authors: Hui Yuen Yung , Chang Yi-Ren , Lim Tsong-Shin , Lee Hsu-Yang , Fann Wunshain , Chang Huan-Cheng
Published: January 2009

The number of negatively charged nitrogen-vacancy centers (N-V)− in fluorescent nanodiamond (FND) has been determined by photon correlation spectroscopy and Monte Carlo simulations at the single particle level. By taking account of the random dipole orientation of the multiple (N-V)− fluorophores and simulating the probability distribution of their effective numbers (Ne), we found that the actual number (Na) of the fluorophores is in linear correlation with Ne, with correction factors of 1.8 and 1.2 in measurements using linearly and circularly polarized lights, respectively. We determined Na=8±1 for 28 nm FND particles prepared by 3 MeV proton irradiation.
Effects of impurity scattering on the quantized conductance of a quasi-one-dimensional quantum wire
Authors: Chen J. C. , Lin Yiping , Lin Kuan Ting , Ueda T. , Komiyama S.
Published: January 2009

We report an experimental observation of how the presence of an impurity in a quasi-one-dimensional wire influences the quantized conductance. The impurity is a chemically etched nanohole, relative to which the walls of the wire can be tuned via external gate voltages. Depending on the positions of the sidewalls, resonance features are observed in the quantized conductance due to either the multiple scatterings between the impurity and the wall of wire or the channel interference. Meanwhile, the differential conductance exhibits the well-known half-plateau features in a single channel wire or saturates in a wire with coupled two channels.
Graded Structure in Odour Categories: A Cross-Cultural Case Study
Authors: Chrea Christelle , Valentin Dominique , Abdi Hervé
Published: January 2009

The existence of graded structure in fruit and flower odour categories and its stability in different cultures is examined. Groups of students from France, the United States, and Vietnam performed a typicality rating task, a similarity judgment task, a membership verification task, a recognition memory task, a familiarity rating task, and a free identification task using a set of 40 odorants (20 fruit odorants and 20 flower odorants). Overall, our results demonstrate that fruit and flower odour categories possess graded structure. Moreover, principal component analyses of the data revealed the implication of typicality in a variety of cognitive tasks where typical odours receive a preferential processing compared to atypical ones. Finally, our results suggest that typicality can be predicted to a certain extent by experiential knowledge but that other determinants play a role in odour category structure. Altogether, this study confirms that graded structure is a universal property of categories and suggests that universals and cultural specifics can both constrain the emergence of odour category structures.
Caricature and Contrast in the Upper Palaeolithic: Morphometric Evidence from Cave Art
Authors: Cheyne James Allan , Meschino Lisa , Smilek Daniel
Published: January 2009

The earliest known explicit and unambiguous employment of representation in external media is in the form of figurative depictions of large mammals during the Upper Palaeolithic. These images, though often created with evident technical skill and intimate knowledge of the subject matter, are frequently characterised by curious and pronounced distortions. We provide evidence, based on quantitative analysis of parietal graphic images of two commonly depicted species, for the hypothesis that certain of these distortions are neither errors nor idiosyncratic variations, but systematic deviations from veridicality in the form of caricatures consistent with cognitive principles of graded typicality and contrast in categorisation. Our analysis provides evidence that the first apparent conventions of representational art by humans were informed by basic cognitive-perceptual principles of categorisation.
Chemical magnetoreception in birds: The radical pair mechanism
Authors: Rodgers Christopher T. , Hore P. J.
Published: January 2009

Migratory birds travel vast distances each year, finding their way by various means, including a remarkable ability to perceive the Earth's magnetic field. Although it has been known for 40 years that birds possess a magnetic compass, avian magnetoreception is poorly understood at all levels from the primary biophysical detection events, signal transduction pathways and neurophysiology, to the processing of information in the brain. It has been proposed that the primary detector is a specialized ocular photoreceptor that plays host to magnetically sensitive photochemical reactions having radical pairs as fleeting intermediates. Here, we present a physical chemist's perspective on the “radical pair mechanism” of compass magnetoreception in birds. We outline the essential chemical requirements for detecting the direction of an Earth-strength ≈50 μT magnetic field and comment on the likelihood that these might be satisfied in a biologically plausible receptor. Our survey concludes with a discussion of cryptochrome, the photoactive protein that has been put forward as the magnetoreceptor molecule.
Rb/Cdk2/Cdk4 triple mutant mice elicit an alternative mechanism for regulation of the G
1
/S transition
Authors: Li Weimin , Kotoshiba Shuhei , Berthet Cyril , Hilton Mary Beth , Kaldis Philipp
Published: January 2009

The G
1
/S-phase transition is a well-toned switch in the mammalian cell cycle. Cdk2, Cdk4, and the rate-limiting tumor suppressor retinoblastoma protein (Rb) have been studied in separate animal models, but interactions between the kinases and Rb in vivo have yet to be investigated. To further dissect the regulation of the G
1
to S-phase progression, we generated Cdk2
−/−
Cdk4
−/−
Rb
−/−
(TKO) mutant mice. TKO mice died at midgestation with major defects in the circulatory systems and displayed combined phenotypes of Rb
−/−
and Cdk2
−/−
Cdk4
−/−
mutants. However, TKO mouse embryonic fibroblasts were not only resistant to senescence and became immortal but displayed enhanced S-phase entry and proliferation rates similar to wild type. These effects were more remarkable in hypoxic compared with normoxic conditions. Interestingly, depletion of the pocket proteins by HPV-E7 or p107/p130 shRNA in the absence of Cdk2/Cdk4 elicited a mechanism for the G
1
/S regulation with increased levels of p27
Kip1
binding to Cdk1/cyclin E complexes. Our work indicates that the G
1
/S transition can be controlled in different ways depending on the situation, resembling a regulatory network.
Nkx2–5 transactivates the
Ets-related protein 71
gene and specifies an endothelial/endocardial fate in the developing embryo
Authors: Ferdous Anwarul , Caprioli Arianna , Iacovino Michelina , Martin Cindy M. , Morris Jesse , Richardson James A. , Latif Shuaib , Hammer Robert E. , Harvey Richard P. , Olson Eric N. , Kyba Michael , Garry Daniel J.
Published: January 2009

Recent studies support the existence of a common progenitor for the cardiac and endothelial cell lineages, but the underlying transcriptional networks responsible for specification of these cell fates remain unclear. Here we demonstrated that Ets-related protein 71 (Etsrp71), a newly discovered ETS family transcription factor, was a novel downstream target of the homeodomain protein, Nkx2–5. Using genetic mouse models and molecular biological techniques, we demonstrated that Nkx2–5 binds to an evolutionarily conserved Nkx2–5 response element in the
Etsrp71
promoter and induces the
Etsrp71
gene expression in vitro and in vivo.
Etsrp71
was transiently expressed in the endocardium/endothelium of the developing embryo (E7.75-E9.5) and was extinguished during the latter stages of development. Using a gene disruption strategy, we found that
Etsrp71
mutant embryos lacked endocardial/endothelial lineages and were nonviable. Moreover, using transgenic technologies and transcriptional and chromatin immunoprecipitation (ChIP) assays, we further established that Tie2 is a direct downstream target of Etsrp71. Collectively, our results uncover a novel functional role for Nkx2–5 and define a transcriptional network that specifies an endocardial/endothelial fate in the developing heart and embryo.
Toward a genetics of cancer resistance
Authors: Klein George
Published: January 2009

Two of three humans never get cancer. Even the majority of heavy smokers remain cancer free. Is this a matter of chance, or are there cancer-resistant genotypes? Based on the evidence discussed, it would appear that evolution has favored a limited number of relatively common resistance genes that may nip incipient cancerous foci in the bud, i.e., to stop them at their inception. It is further suggested that resistance genes may act at the level of tissue organization in a dominant fashion.
Differential impact of the CD45 juxtamembrane wedge on central and peripheral T cell receptor responses
Authors: Hermiston Michelle L. , Zikherman Julie , Tan Allison L. , Lam Viola C. , Cresalia Nicole M. , Oksenberg Nir , Goren Nira , Brassat David , Oksenberg Jorge R. , Weiss Arthur
Published: January 2009

The cooperative activity of protein tyrosine kinases and phosphatases plays a central role in regulation of T cell receptor (TCR) signal strength. Perturbing this balance, and thus the threshold for TCR signals, has profound impacts on T cell development and function. We previously generated mice containing a point mutation in the juxtamembrane wedge of the receptor-like protein tyrosine phosphatase CD45. Demonstrating the critical negative regulatory function of the wedge, the CD45 E613R (WEDGE) mutation led to a lymphoproliferative disorder (LPD) and a lupus-like autoimmune syndrome. Using genetic, cellular, and biochemical approaches, we now demonstrate that the CD45 wedge influences T cell development and function. Consistent with increased TCR signal strength, WEDGE mice have augmented positive selection and enhanced sensitivity to the CD4-mediated disease experimental autoimmune encephalitis (EAE). These correspond with hyperresponsive calcium and pERK responses to TCR stimulation in thymocytes, but surprisingly, not in peripheral T cells, where these responses are actually depressed. Together, the data support a role for the CD45 wedge in regulation of T cell responses in vivo and suggest that its effects depend on cellular context.
Identification ofRhodococcus fascianscytokinins and their modus operandi to reshape the plant
Authors: Pertry Ine , Václavíková Kateřina , Depuydt Stephen , Galuszka Petr , Spíchal Lukáš , Temmerman Wim , Stes Elisabeth , Schmülling Thomas , Kakimoto Tatsuo , Van Montagu Marc C. E. , Strnad Miroslav , Holsters Marcelle , Tarkowski Petr , Vereecke Danny
Published: January 2009

Decades ago, the importance of cytokinins (CKs) duringRhodococcus fascianspathology had been acknowledged, and an isopentenyltransferase gene had been characterized in thefasoperon of the linear virulence plasmid, but hitherto, no specific CK(s) could be associated with virulence. We show that the CK receptors AHK3 and AHK4 ofArabidopsis thalianaare essential for symptom development, and that the CK perception machinery is induced upon infection, underlining its central role in the symptomatology. Three classical CKs [isopentenyladenine,trans-zeatin, andcis-zeatin (cZ)] and their 2-methylthio (2MeS)-derivatives were identified by CK profiling of both the pathogenicR. fasciansstrain D188 and its nonpathogenic derivative D188–5. However, the much higher CK levels in strain D188 suggest that the linear plasmid is responsible for the virulence-associated production. AllR. fasciansCKs were recognized by AHK3 and AHK4, and, although they individually provoked typical CK responses in several bioassays, the mixture of bacterial CKs exhibited clear synergistic effects. Thecis- and 2MeS-derivatives were poor substrates of the apoplastic CK oxidase/dehydrogenase enzymes and the latter were not cytotoxic at high concentrations. Consequently, the accumulating 2MeScZ (and cZ) in infectedArabidopsistissue contribute to the continuous stimulation of tissue proliferation. Based on these results, we postulate that theR. fascianspathology is based on the local and persistent secretion of an array of CKs.
F2 +-X2+ Band System of Cobalt Carbide
Authors: Guo Jing-ru , Zhang Zhao-xia , Wang Ting-ting , Chen Cong-xiang , Chen Yang
Published: January 2009

The laser-induced fluorescence excitation spectrum of CoC was recorded in the spectral region from 13500 cm1 to 22000 cm1, in which the CoC molecules were produced by the reaction of sputtered cobalt atoms with methanol under supersonic jet cooled conditions. Much of the visible spectrum was assigned to transitions between the X2+ ground state and F2+ state. The 11 bands assigned as (v = 313, 0) transitions of the F2+-X2+ band system were observed and rotationally analyzed. Equilibrium constants for the F2+ state were Te = 13628 cm1, e = 669 cm1, ee = 4.3 cm1, Be = 0.546 cm1, and Re = 1.758 A. Some new bands were observed.
Spectral Characteristics of White Organic Light-emitting Diodes Based on Novel Phosphorescent Sensitizer
Authors: Tang Xiao-qing , Yu Jun-sheng , Li Lu , Wen Wen , Jiang Ya-dong
Published: January 2009

White organic light-emitting diodes were fabricated by using a novel phosphorescence bis(1,2-dipheny1-1H-benzoimidazole)iridium(acetylacetonate)[(pbi)2Ir(acac)] as sensitizer and a fluorescent dye of 4-(dicyanomethylene)-2-t-butyl-6-(1,1,7,7-tetramethyljulolidyl-9-enyl)-4H-pyran (DCJTB) codoped into a car-bazole polymer of poly(N-vinylcarbazole) (PVK). Through characterizing the UV-Vis absorption spectra, the photoluminescence spectra of (pbi)2Ir(acac) and DCJTB, and the electroluminescence spectral properties of the WOLEDs, the energy transfer mechanisms of the codoped polymer system were deduced. The results demonstrate that the luminescent spectra with different intensity of (pbi)2Ir(acac) and DCJTB were co-existent in the EL spectra of the blended system, which is ascribed to an incomplete energy transfer process in the EL process. The efficient Forster and Dexter energy transfer between the host and the guests enabled a strong yellow emission from (pbi)2Ir(acac) and DCJTB, where (pbi)2Ir(acac) plays an important role as a phosphorescent sensitizer for DCJTB. With the blue emitting-layer of N,N-diphenyl-N,N-bis(1-naphthyl)(1,1-biphenyl)-4,4-diamine, the codoped system device achieved white emission. The codoped system showed that its Commissions Internationale de 1Eclairage coordinates were more independent of the variation of bias voltage than those of phosphorescent doped PVK systems.
Electron Momentum Spectroscopy of Ethanethiol Complete Valence Shell
Authors: Xue Xin-xia , Yan Mi , Wu Fang , Shan Xu , Xu Ke-zun , Chen Xiang-jun
Published: January 2009

The binding energy spectra and electron momentum distributions for the complete valence orbitals of ethanethiol were measured for the first time by binary (e, 2e) electron momentum spectroscopy employing non-coplanar symmetric kinematics at an impact energy of 1200 eV plus binding energy. The experimental results are generally consistent with the theoretical calculations using density functional theory and HartreeFock methods with various basis sets. A possible satellite line at 17.8 eV in binding energy spectrum was observed and studied by electron momentum spectroscopy.
System Size Resonance Associated with Canard Phenomenon in a Biological Cell System
Authors: Ma Juan , Li Hong-ying , Hou Zhong-huai , Xin Hou-wen
Published: January 2009

The influence of internal noise on the calcium oscillations is studied. It is found that stochastic calcium oscillations occur when the internal noise is considered, while the corresponding deterministic dynamics only yields a steady state. Also, the performance of such oscillations shows two maxima with the variation of the system size, indicating the occurrence of system size resonance. This behavior is found to be intimately connected with the canard phenomenon. Interestingly, it is also found that one of the optimal system sizes matches well with the real cell size, and such a match is robust to the variation of the control parameters.
Substituent Effect on Infrared Spectra and Thermodynamic Properties of Polynitroamino Substituted Cyclopentane and Cyclohexane
Authors: Qiu Ling , Gong Xue-dong , Xiao He-ming
Published: January 2009

Density functional theory method was employed to study the effect of the nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct polycyclic or caged nitramines. Based on the optimized molecular structures of two groups of monocyclic nitramines at the B3LYP/6-31G** level, the infrared (IR) spectra were obtained and assigned by harmonic vibrational analysis. The calculated results agree reasonably with the available experimental data. According to the principles of statistic thermodynamics, thermodynamic properties were derived from the IR spectra, which were linearly correlated with the number of nitroamino groups as well as the temperature. The contributions of nitroamino groups to thermodynamic properties are in accord with the group additivity.
Density Functional Theory Study of Infrared and Ultraviolet Spectra of Urea L-Malic Acid
Authors: Zhang Yan-lan , Wang Hong-yan , Jiao Dong-sheng , Hu Yong-hong
Published: January 2009

Urea L-malic acid, a new second order nonlinear optical crystal, was studied using density functional theory (DFT). PBEPBE/6-31+G(d,p) method, the optimal method for comparing the results from the several DFT methods, was chosen to study the molecular structure. Infrared and ultraviolet-visible spectra were obtained and compared with experiments. The ultraviolet-visible spectrum was also analyzed by the molecular orbital population. The geometries, and the infrared and ultraviolet-visible spectra in water were studied using DFT methods in combination with the polarized continuum model to predict the perturbations by the solvent effect.
Theoretical Study of the AlEt3-Promoted Tandem Reductive Rearrangement of Epoxides
Authors: Zhang Li-dong , Guo Hui-jun , Pan Yang , Qi Fei
Published: January 2009

The AlEt3-promoted tandem reductive rearrangement reactions of epoxides was studied at B3LYP/6-31G(d,p) level. For the model compound -hydroxy epoxides, two possible reaction pathways I and II were calculated. The main difference is the order of ethylene release and six- to five-member ring rearrangement. The ring contraction rearrangement in pathway I is the first step and this step is the rate controlling step with a free energy barrier of 116.62 kJ/mol. For pathway II, the ethylene release occurs first, and is followed by a six-member ring opening reaction which is the rate controlling step, and the barrier is 251.38 kJ/mol. The reason for such high barrier is that the ethylene release results in the following reaction being more difficult. The results show that pathway I (CC rearrangement and then ethylene release) is more favorable, which is consistent with experimental results.
Translocation of Polymer Chains Through a Channel with Complex Geometries
Authors: Yang Zhi-yong , Zhang Lin-xi , Cheng Jun
Published: January 2009

The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels (left channel, middle channel, and right channel, respectively) is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f (f > 0) versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observed with the elastic force f 0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the translocation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the component translocation time is not the same for different channels can be presented.
Thermodynamic Calculation on the Formation of Titanium Hydride
Authors: Zhao Jing-wei , Ding Hua , Tian Xue-feng , Zhao Wen-juan , Hou Hong-liang
Published: January 2009

A modified Miedema model, using interrelationship among the basic properties of elements Ti and H, is employed to calculate the standard enthalpy of formation of titanium hydride TiHx (1 x 2). Based on Debye theories of solid thermal capacity, the vibrational entropy, as well as electronic entropy, is acquired by quantum mechanics and statistic thermodynamics methods, and a new approach is presented to calculate the standard entropy of formation of TiH2. The values of standard enthalpy of formation of TiHx decrease linearly with increase of x. The calculated results of standard enthalpy, entropy, and free energy of formation of TiH2 at 298.16 K are 142.39 kJ/mol, 143.0 J/(molK) and 99.75 kJ/mol, respectively, which is consistent with the previously-reported data obtained by either experimental or theoretical calculation methods. The results show that the thermodynamic model for titanium hydride is reasonable.
Elimination of Anti-spiral Waves by Local Inhomogeneity in Oscillatory Systems
Authors: Liu Fu-cheng , Wang Xiao-fei
Published: January 2009

Anti-spiral waves are controlled in an oscillatory system by using a local inhomogeneity. The inhomogeneity acts as a wave source, and gives rise to the propagating plane waves. It is found that there is a critical pacemaking domain size below which no wave will be created at all. Two types of ordered waves (target waves and traveling waves) are created depending on the geometry of the local inhomogeneity. The competition between the anti-spiral waves and the ordered waves is discussed. Two different competition mechanisms were observed, which are related to the ordered waves obtained from different local inhomogeneities. It is found that traveling waves with either lower frequency or higher frequency can both eliminate the anti-spiral waves, while only the target waves with lower absolute value of frequency can eliminate the anti-spiral waves. This method also applies to outwardly rotating spiral waves. The control mechanism is intuitively explained and the control method is easily operative.
Damping of Magnetorheological Elastomers
Authors: Chen Lin , Gong Xing-long , Li Wei-hua
Published: January 2009

The damping property of magnetorheological (MR) elastomers is characterized by a modified dynamic mechanical-magnetic coupled analyzer. The influences of the external magnetic flux density, damping of the matrix, content of iron particles, dynamic strain, and driving frequency on the damping properties of MR elastomers were investigated experimentally. The experimental results indicate that the damping properties of MR elastomers greatly depend on the interfacial slipping between the inner particles and the matrix. Different from general composite materials, the interfacial slipping in MR elastomers is affected by the external applied magnetic field.
Chloride Assisted Growth of Aluminum Nitride Nanobelts and Their Enhanced Dielectric Responses
Authors: Xie Ting , Ye Min , Jiang Zhi , Qin Yong , Wu Yu-cheng , Meng Guo-wen , Zhang Li-de
Published: January 2009

Aluminum nitride (AlN) nanobelts were successfully synthesized in high yield through a chloride assisted vapor-solid process. X-ray diffraction, transmission electron microscopy, and selected area electronic diffraction demonstrate that the as-prepared nanobelts are pure, structurally uniform and single crystalline, and can be indexed to hexagonal wurtzite structure. The micro observations show that there exist no defects in the obtained nanobelts. The growth direction of the nanobelts is along [0001]. The frequency spectra of the relative dielectric constant and of the dielectric loss were measured in the frequency range of 50 Hz to 5 MHz. Analysis of these spectra indicates that the interface in samples has great influence on the dielectric behavior of samples. As compared with AlN micropowders, AlN nanobelts have much higher relative dielectric constant, especially at low frequencies at room temperature.
Influence of Chemical Effect on the K/K Intensity Ratios and K Energy Shift of Co, Ni, Cu, and Zn Complexes
Authors: Apaydn G. , Aylk V. , Byklolu Z. , Tralu E. , Kantekin H.
Published: January 2009

Chemical effects on the K/K intensity ratios and E energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV -rays from a 241Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the K/K intensity ratios and E energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of K/K were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.
Centrosome/Spindle Pole–associated Protein Regulates Cytokinesis via Promoting the Recruitment of MyoGEF to the Central Spindle
Authors: Asiedu Michael , Wu Di , Matsumura Fumio , Wei Qize
Published: January 2009

Cooperative communications between the central spindle and the contractile ring are critical for the spatial and temporal regulation of cytokinesis. Here we report that MyoGEF, a guanine nucleotide exchange factor that localizes to the central spindle and cleavage furrow, interacts with centrosome/spindle pole-associated protein (CSPP), which is concentrated at the spindle pole and central spindle during mitosis and cytokinesis. Both in vitro and in vivo pulldown assays show that MyoGEF interacts with CSPP. The C-terminus of MyoGEF and N-terminus of CSPP are required for their interaction. Immunofluorescence analysis indicates that MyoGEF and CSPP colocalize at the central spindle. Depletion of CSPP or MyoGEF by RNA-interference (RNAi) not only causes defects in mitosis and cytokinesis, such as metaphase arrest and furrow regression, but also mislocalization of nonmuscle myosin II with a phosphorylated myosin regulatory light chain (p-MRLC). Importantly, CSPP depletion by RNAi interferes with MyoGEF localization at the central spindle. Finally, MyoGEF interacts with ECT2, and RNAi-mediated depletion of MyoGEF leads to mislocalization of ECT2 and RhoA during cytokinesis. Therefore, we propose that CSPP interacts with and recruits MyoGEF to the central spindle, where MyoGEF contributes to the spatiotemporal regulation of cytokinesis.
Heterotrimerization of Heat-Shock Factors 1 and 2 Provides a Transcriptional Switch in Response to Distinct Stimuli
Authors: Sandqvist Anton , Björk Johanna K. , Åkerfelt Malin , Chitikova Zhanna , Grichine Alexei , Vourc'h Claire , Jolly Caroline , Salminen Tiina A. , Nymalm Yvonne , Sistonen Lea
Published: January 2009

Organisms respond to circumstances threatening the cellular protein homeostasis by activation of heat-shock transcription factors (HSFs), which play important roles in stress resistance, development, and longevity. Of the four HSFs in vertebrates (HSF1-4), HSF1 is activated by stress, whereas HSF2 lacks intrinsic stress responsiveness. The mechanism by which HSF2 is recruited to stress-inducible promoters and how HSF2 is activated is not known. However, changes in the HSF2 expression occur, coinciding with the functions of HSF2 in development. Here, we demonstrate that HSF1 and HSF2 form heterotrimers when bound to satellite III DNA in nuclear stress bodies, subnuclear structures in which HSF1 induces transcription. By depleting HSF2, we show that HSF1-HSF2 heterotrimerization is a mechanism regulating transcription. Upon stress, HSF2 DNA binding is HSF1 dependent. Intriguingly, when the elevated expression of HSF2 during development is mimicked, HSF2 binds to DNA and becomes transcriptionally competent. HSF2 activation leads to activation of also HSF1, revealing a functional interdependency that is mediated through the conserved trimerization domains of these factors. We propose that heterotrimerization of HSF1 and HSF2 integrates transcriptional activation in response to distinct stress and developmental stimuli.
Oxysterol Binding Protein–related Protein 9 (ORP9) Is a Cholesterol Transfer Protein That Regulates Golgi Structure and Function
Authors: Ngo Mike , Ridgway Neale D.
Published: January 2009

Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) constitute a large gene family that differentially localize to organellar membranes, reflecting a functional role in sterol signaling and/or transport. OSBP partitions between the endoplasmic reticulum (ER) and Golgi apparatus where it imparts sterol-dependent regulation of ceramide transport and sphingomyelin synthesis. ORP9L also is localized to the ER–Golgi, but its role in secretion and lipid transport is unknown. Here we demonstrate that ORP9L partitioning between the trans-Golgi/trans-Golgi network (TGN), and the ER is mediated by a phosphatidylinositol 4-phosphate (PI-4P)-specific PH domain and VAMP-associated protein (VAP), respectively. In vitro, both OSBP and ORP9L mediated PI-4P–dependent cholesterol transport between liposomes, suggesting their primary in vivo function is sterol transfer between the Golgi and ER. Depletion of ORP9L by RNAi caused Golgi fragmentation, inhibition of vesicular somatitus virus glycoprotein transport from the ER and accumulation of cholesterol in endosomes/lysosomes. Complete cessation of protein transport and cell growth inhibition was achieved by inducible overexpression of ORP9S, a dominant negative variant lacking the PH domain. We conclude that ORP9 maintains the integrity of the early secretory pathway by mediating transport of sterols between the ER and trans-Golgi/TGN.
bioDBnet: the biological database network
Authors: Mudunuri Uma , Che Anney , Yi Ming , Stephens Robert M.
Published: January 2009

Summary: bioDBnet is an online web resource that provides interconnected access to many types of biological databases. It has integrated many of the most commonly used biological databases and in its current state has 153 database identifiers (nodes) covering all aspects of biology including genes, proteins, pathways and other biological concepts. bioDBnet offers various ways to work with these databases including conversions, extensive database reports, custom navigation and has various tools to enhance the quality of the results. Importantly, the access to bioDBnet is updated regularly, providing access to the most recent releases of each individual database.

Availability:  http://biodbnet.abcc.ncifcrf.gov

Contact:  stephensr@mail.nih.gov

Supplementary information:  Supplementary data are available at Bioinformatics online
A novel method for large tree visualization
Authors: Heard Jeff , Kaufmann William , Guan Xiaojun
Published: January 2009

Summary: Many genomic and proteomic analyses generate as a result a tree of genes or proteins. These trees are often large (containing tens of thousands of nodes and edges), and need a visualization tool to fully display all the information contained in the tree. Clustering analysis can be performed on these trees to obtain clusters of proteins, and we need an efficient way to visualize the clustering results. We present a novel tree visualization tool to help with such analyses.

Availability:  http://www2.renci.org/~jeff/software/bin/win32/ProteinVis-2.1.6-win32.zip

Contact:  jeff@renci.org; xguan@renci.org
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes
Authors: Guralnick Robert , Hill Andrew
Published: January 2009

Motivation: Data about biodiversity have been scattered in different formats in natural history collections, survey reports and the literature. A central challenge for the biodiversity informatics community is to provide the means to share and rapidly synthesize these data and the knowledge they provide us to build an easily accessible, unified global map of biodiversity. Such a map would provide raw and summary data and information on biodiversity and its change across the world at multiple scales.

Results: We discuss a series of steps required to create a unified global map of biodiversity. These steps include: building biodiversity repositories; creating scalable species distribution maps; creating flexible, user-programmable pipelines which enable biodiversity assessment; and integrating phylogenetic approaches into biodiversity assessment. We show two case studies that combine phyloinformatic and biodiversity informatic approaches to document large scale biodiversity patterns. The first case study uses data available from the Barcode of Life initiative in order to make species conservation assessment of North American birds taking into account evolutionary uniqueness. The second case study uses full genomes of influenza A available from Genbank to provide an auto-updating documentation of the evolution and geographic spread of these viruses.

Availability: Both the website for tracking evolution and spread of influenza A and the website for applying phyloinformatics analysis to Barcode of Life data are available as outcomes of case studies (http://biodiversity.colorado.edu).

Contact:  robert.guralnick@colorado.edu
Erratum: sample size determination for the false discovery rate
Authors: Pounds Stan , Cheng Cheng
Published: January 2009

Contact: stanley.pounds@stjude.org
Steeper biomass spectra of demersal fish communities after trawler exclusion in Sicily
Authors: Sweeting Christopher J. , Badalamenti Fabio , D'Anna Giovanni , Pipitone Carlo , Polunin N. V. C.
Published: January 2009

Sweeting, C. J., Badalamenti, F., D'Anna, G., Pipitone, C., and Polunin, N. V. C. 2009. Steeper biomass spectra of demersal fish communities after trawler exclusion in Sicily. – ICES Journal of Marine Science, 66: 195–202. The effects of trawling on Mediterranean demersal fish communities were assessed by comparing them with the normalized biomass spectra among three gulfs on the north Sicilian coast, one of which had been subject to 15 years of trawler exclusion. Comparisons were conducted across seasons and among depth strata. Biomass-spectra slopes were significantly steeper in the gulf that was closed to trawling than in the unprotected gulfs. This was attributed to the exclusion of trawlers, which lacked catch-size selectivity, and to the continued fishing by artisanal gears that are more size selective. The biomass of all size classes was higher in the protected gulf than in unprotected areas, and increases were greatest in smaller size classes. Community mean individual fish mass was similar among all areas with a wider range of body masses present in the trawl exclusion area, compensating for the greater abundance of small fish. Size-spectra slopes were generally shallower and midpoint heights lower with increasing depth and were greater in autumn than spring; the effect of these seasonal and depth factors was as great as that of protection. Depth patterns are explainable by bathymetric trends in within- and among-species fish size. Seasonal differences were attributed to variation in spawning behaviour and fishery recruitment, with seasonal differences being greater in unprotected locations as a result of recruitment overfishing.