bluuebunny/crossref_metadata_2025 huggingface dataset:
An infrared method to assess organoclay delamination and orientation in organoclay polymer nanocomposites
Authors: IJdo Wouter L. , Kemnetz Steven , Benderly Daphne
Published: July 2006

Assessing the degree of organoclay delamination and layer alignment is crucial to deliver consistent properties of nanocomposite materials. A simple infrared technique is discussed that permits quantitative determination of these organoclay dispersion parameters in a nanocomposite. This technique complements other existing methods to optimize process conditions to fully achieve the advantages that high purity hectorite nanoclays can bring to plastic nanocomposites. POLYM. ENG. SCI. 46:1031–1039, 2006. © 2006 Society of Plastics Engineers
Thickness dependence of optical properties of amorphous indium oxide thin films deposited by reactive evaporation
Authors: Ulutaş K. , Değer D. , Skarlatos Y.
Published: July 2006

The electrical conductivity and absorption coefficient of amorphous indium oxide thin films, thermally evaporated on glass substrates at room temperature, were evaluated. For direct transitions the variation of the optical band gap with thickness was determined and this variation was supposed to appear due to the variation of localized gap states, whereas the variation of conductivity with thickness was supposed to be due to the variation of carrier concentration. We attribute the variation of absorption coefficient with thickness to the variation of optical band gap energy rather than optical interference. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and low frequency noise properties of 4H‐SiC p+–n–n+ junction diodes
Authors: Arpatzanis N. , Tsormpatzoglou A. , Dimitriadis C. A. , Zekentes K. , Camara N. , Godlewski M.
Published: July 2006

The electrical and low frequency noise properties of 4H‐SiC p+–n–n+ junctions have been investigated at different temperatures. The forward current–voltage characteristics are described as the sum of a recombination current originating from carrier recombination on the sidewall of the circular mesa of the diodes and a diffusion volume current. In the current region where the recombination mechanism is dominant, the main noise sources are attributed to carrier recombination at the perimeter surface of the diode and to a generation‐recombination noise related to a local trap level. In the current region where the diffusion current becomes important, the noise originates from mobility and diffusivity fluctuations in the space charge region of the p+–n junction. Analysis of the current and noise data allowed us to determine the density of surface states and the Hooge factor, characterizing the surface and the bulk quality of the diode. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron transport through single alkane molecules with different contact geometries on gold
Authors: Lee Myeong H. , Speyer Gil , Sankey Otto F.
Published: July 2006

We report theoretical simulations of the effects of different binding sites and metal contact geometries on the conductance through single alkanedithiol molecules on gold. Examined are the current–voltage (I –V ) characteristics and the projected density of states when a one‐atom‐thick filament is formed at the molecule‐metal interface. Filaments similar to these are believed to be formed in gold STM break‐junction experiments. I –V characteristics with these contacts are compared to those of planar gold contacts at hollow or on‐top sites. The results reveal that a gold filament contact produces a large change in the Fermi level lineup which significantly affects its I –V curve. The conductance decreases by a factor of 4 ∼ 6 when gold atoms are placed between the molecule and the gold surface to form a filament, and non‐linearities develop. The hollow and on‐top planar contacts show similar conductivities to each other and produce linear I –V curve. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An accurate and efficient procedure of fitting electric field potential by point charges for QM/MM calculations
Authors: Makhov D. V. , Stuchebrukhov Alexei A.
Published: July 2006

An accurate and efficient computational procedure of fitting an electric field potential given on the grid in a finite QM cavity of arbitrary shape by point charges is described. The charges are located on the surface of the sphere that encloses the QM cavity, and also inside the sphere, but outside the QM cavity. The procedure is based on the use of spherical harmonics and singular value decomposition. An example of application of the procedure in QM/MM calculations of pKa values in proteins is discussed. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computer simulations of protein translocation
Authors: Kirmizialtin Serdal , Huang Lei , Makarov Dmitrii E.
Published: July 2006

Many biological processes, e.g. protein degradation by ATP dependent proteases and mitochondrial protein import, involve protein translocation through nanometer‐sized pores. In this paper, we report on computer simulations of two models of protein translocation. In the first model, a protein domain is pulled mechanically through a narrow neutral pore. We compare the free energy cost of squeezing an initially folded protein into the pore with that for a random‐coil‐like homopolymer and show that the former case involves several partially folded intermediates. The second model involves electrophoretically driven translocation of a β‐hairpin forming peptide across the α‐hemolysin protein pore. The distribution of the time the peptide spends inside the pore is exponential at low forces, suggesting a single rate limiting barrier crossing step for the translocation process, while at higher forces this distribution tends to be a bell shaped curve. The dependence of the average translocation time 〈t 〉 on the applied force f is well described by the exponential relationship: 〈t 〉 = af + b at low forces, while at high forces the inverse translocation time is a linear function of the force, 〈t 〉–1 = Af – B . (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using the PRIMME eigensolver in materials science applications
Authors: Stathopoulos Andreas
Published: July 2006

One of the outstanding computational problems in materials science is the solution of large, Hermitian eigenvalue problems. The dimension of these problems can grow to several millions, while thousands of eigenvalues and eigenvectors must be computed. Applications that must maintain orthogonality in the eigenvector basis scale quadratically to the number of eigenvectors. In this paper, we present an overview of the state‐of‐the‐art in methods and software for eigenvalue computations, and demonstrate why our new package PRIMME fills an important gap in both methods and software. Moreover, we show that PRIMME includes two nearly optimal methods, and that it can be significantly faster than any existing method. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Computer simulations of protein translocation
Authors: Kirmizialtin Serdal , Huang Lei , Makarov Dmitrii E.
Published: July 2006

Many biological processes involve translocation of protein molecules across pores. Shown in the cover picture of this issue is a snapshot from a computer simulation of the protein ubiquitin that is forced mechanically to enter a narrow cylindrical pore. As the force f applied at one end of the molecule pulls it along the pore, the confinement within the pore causes the protein to unfold. The ensuing changes in the protein's entropy and energy lead to a free energy barrier, which has to be surmounted for the translocation to occur. The magnitude of this barrier is estimated by Kirmizialtin et al. in the article [1]. The plot was generated by using the PyMol software.

This paper is a presentation from the 1st Institute for the Theory of Advanced Materials in Information Technology Workshop on Computational Materials and Electronics held 20–22 October 2005 in Austin, USA. The present issue has been guest‐edited by James Chelikowsky and Alex Demkov. The background of the cover shows a photograph of the tower of the University of Texas at Austin. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Disaggregating the State: Networks and Collective Resistance in Shanghai
Authors: Shi Fayong , Cai Yongshun
Published: July 2006

Collective action directed at the government is not rare in China, but why some actions endure and succeed whereas many others fail remains inadequately addressed. Based on a case of home owners' sustained collective resistance in Shanghai, this study finds that state power is fragmented at the local level. While the disparate priorities among different levels of state authorities provide opportunities for resistance, social networks between participants of collective action and officials or media workers may significantly help the former to achieve success.
The effect of FF-MAS on porcine cumulus–oocyte complex maturation, fertilization and pronucleus formation in vitro
Authors: Faerge Inger , Strejcek Frantisek , Laurincik Jozef , Rath Detlef , Niemann Heiner , Schellander Karl , Rosenkranz Christine , Hyttel Poul Maddox , Grøndahl Christian
Published: July 2006

Follicular fluid meiosis-activating sterol (FF-MAS) has been isolated from the follicular fluid (FF) of several species including man. FF-MAS increases the quality of in vitro oocyte maturation, and thus the developmental potential of oocytes exposed to FF-MAS during in vitro maturation is improved. The aim of the present study was to investigate the effects of FF-MAS on porcine oocyte maturation and pronucleus formation in vitro. Porcine cumulus–oocyte complexes (COCs) were isolated from abattoir ovaries and in vitro matured for 48 h in NCSU 37 medium supplemented with 1 mg/l cysteine, 10 ng/ml epidermal growth factor and 50 μM 2-mercaptoethanol with or without 10% porcine follicular fluid (pFF). For the first 22 h, 1 mM db-cAMP and 10 I.E PMSG/hCG was added. The medium was supplemented with 1 μM, 3 μM, 10 μM, 30 μM or 100 μM FF-MAS dissolved in ethanol. After maturation the COCs were denuded mechanically using a fine glass pipette under constant pH and in vitro fertilized with fresh semen (5 × 105 spermatozoa/ml). The presumptive zygotes were evaluated 18 h after fertilization. The addition of pFF increased the monospermic as well as the polyspermic penetration of oocytes. In the absence of pFF, the addition of FF-MAS decreased the polyspermic penetration rate, whereas FF-MAS in combination with pFF decreased monospermic and increased polyspermic penetration. The degeneration rate of ova decreased in the presence of FF-MAS irrespective of the presence or absence of pFF. In the absence of pFF, FF-MAS at 3–10 μM increased the number of zygotes with advanced maternal pronuclear stages. In supraphysiological doses, i.e. 30–100 μM, FF-MAS dose-dependently and reversibly inhibited nuclear maturation in the absence of pFF.
Fazang (643–712) and Wuzhensi: With a Special Reference to his Daoist Ties
Authors: Chen Jinhua
Published: July 2006

In his biography for the Avatamsaka master Fazang (643–712), Tang Tae Ch'ǒnboksa kosaju pǒn'gyǒng taedǒk Pǒpjang hwasang chǒn (Ch. Tang Da Jianfusi gu sizhu fanjing dade Fazang heshang zhuan) (Biography for Upādhyāya Fazang, the Late Bhadanta-translator and Abbot of Great Jianfusi of the Tang) composed ca. 904, the Korean author Ch'oe Ch'iwon (Ch. Cui Zhiyuan, 857–904) reports a ritual that Fazang performed to pray for snow in order to prevent an imminent drought. The ritual was executed in the winter of 711, barely one year before Fazang's death, beside a pond at the scenic mountain range fifty li west of Chang'an – Mount Zhongnan.
Welche Kinder und Jugendlichen nehmen Verhaltenstherapie im Leistungssystem der Gesetzlichen Krankenversicherung in Anspruch?
Authors: Blanz Susanne , Schmidt Martin H.
Published: July 2006

Zusammenfassung. Der Beitrag widmet sich der Inanspruchnahmeforschung auf dem Gebiet der ambulanten Verhaltenstherapie des Kindes- und Jugendalters im Leistungssystem der gesetzlichen Krankenkassen als Teilgebiet der inputorientierten Versorgungsforschung. Im Rahmen einer Dokumentenanalyse von 1021 Kurz- oder Langzeitanträgen auf Kostenübernahme einer Verhaltenstherapie durch die Krankenkassen der jeweiligen anfragenden Versicherten, die zur Begutachtung eingereicht worden waren, wurde die Intention verfolgt, die WER-Frage der Inanspruchnahme zu beantworten, wobei auf soziodemografische Merkmale der Antragsstichprobe fokussiert wurde. Es zeigte sich, dass bis zum Alter von 15 Jahren männliche Kinder und Jugendliche sowohl in der Antragsstichprobe als auch im Vergleich mit der Allgemeinbevölkerung überrepräsentiert waren, während sich das Geschlechterverhältnis mit steigendem Alter umkehrte. Gut drei Viertel der versicherten Jungen und Mädchen war zum Zeitpunkt der Antragstellung zwischen fünf und 15 Jahre (im Mittel 11;14 Jahre) alt, in der Mehrzahl erst- oder zweitgeborene Kinder und an dritter Stelle Einzelkinder. Während knapp sieben Prozent der Jungen und Mädchen auf eine Förderschule gingen, besuchte die große Mehrheit einen Regelschultyp mit unterschiedlicher Altersangemessenheit der jeweiligen Klasseneinstufung. Im Vergleich zur Allgemeinbevölkerung wurde überproportional häufig ein Antrag auf Verhaltenstherapie für die Kinder Alleinerziehender und nicht in einem Beschäftigungsverhältnis stehender, allein erziehender Eltern gestellt.
A theoretical study of He2ICl van der Waals cluster
Authors: Valdés Álvaro , Prosmiti Rita , Villarreal Pablo , Delgado-Barrio Gerardo
Published: July 2006

The structure, energetics, and dynamics of He2ICl complex in its ground state are studied by means of ab initio electronic structure and quantum-mechanical calculations. Interaction energies for selected He2ICl configurations are calculated at the coupled-cluster [CCSD(T)] level of theory using a large-core pseudopotential for the I atom and the aug-cc-pVTZ and aug-cc-pV5Z basis sets for the Cl and He atoms, respectively. The surface is characterized around its lower five minima and the minimum energy pathways through them. The global minimum of the potential corresponds to a “police-nightstick (1)” configuration, the second one to a linear, the next one to tetrahedral configuration, and the following two to “bifork” and “police-nightstick (2)” structures, with well depths of −99.12, −97.42, −88.32, −85.84, and −78.54cm−1, respectively. An analytical form based on the sum of the three-body parametrized HeICl interactions plus the He–He interaction is found to represent very well the tetra-atomic CSSD(T) results. The present potential expression is employed to perform variational five-dimensional quantum-mechanical calculations to study the vibrational bound states of the van der Waals He2ICl complex. Results for total angular momentum J=0 provide the binding energy D0 and the corresponding vibrationally averaged structure for different isomers of the cluster. Comparison of these results with recent experimental observations further justifies the potential used in this work.
Embedding wave function theory in density functional theory
Authors: Henderson Thomas M.
Published: July 2006

We present a framework for embedding a highly accurate coupled-cluster calculation within a larger density functional calculation. We use a perturbative buffer to help insulate the coupled-cluster region from the rest of the system. Regions are defined, not in real space, but in Hilbert space, though connection between the two can be made by spatial localization of single-particle orbitals. Relations between our embedding approach and some similar techniques are discussed. We present results for small sample systems for which we can extract essentially exact results, demonstrating that our approach seems to work quite well and is generally more reliable than some of the related approaches due to the introduction of additional interaction terms.
Simulation of photoelectron spectra with anharmonicity fully included: Application to the X̃A22←X̃A11 band of furan
Authors: Bonness Sean , Kirtman Bernard , Huix Miquel , Sanchez Angel J. , Luis Josep M.
Published: July 2006

Using a new unconventional procedure for calculating Franck-Condon factors with anharmonicity fully included the X̃A22←X̃A11 band in the photoelectron spectrum of furan (and deuterated furan) was simulated at the second-order perturbation theory level. All 21 vibrational modes were considered but, in the end, only 4 are required to accurately reproduce the spectrum. Except for our own recent work on ethylene such calculations have been previously limited to tri- or tetraatomic molecules. Most of the effect of anharmonicity is accounted for in first order, although second-order corrections to the vibrational frequencies are important. Based on these simulations we were able to improve upon and extend previous assignments as well as suggest further measurements.
High-resolution inner-shell excitation spectroscopy of H2-phthalocyanine
Authors: Kera S. , Casu M. B. , Schöll A. , Schmidt Th. , Batchelor D. , Rühl E. , Umbach E.
Published: July 2006

We report on a combined experimental and theoretical carbon and nitrogen K-edge near-edge x-ray absorption fine structure investigation on condensed metal-free phthalocyanine (H2Pc). Based on the results from improved virtual orbital calculations, all resonances in the experimental high-resolution data can be assigned to various electronic transitions. The comparison between experiments and calculations further shows that a significant influence of the core hole, which affects both the transition energies and the cross sections, is present and must be considered in theoretical approaches. Moreover, additional fine structure is clearly resolved for the first N 1s→π* transition, which can be interpreted as vibronic coupling to the electronic core excitation.
Exact Kohn-Sham versus Hartree-Fock in momentum space: Examples of two-fermion systems
Authors: Ragot Sébastien
Published: July 2006

The question of how density functional theory (DFT) compares with Hartree-Fock (HF) for the computation of momentum-space properties is addressed in relation to systems for which (near) exact Kohn-Sham (KS) and HF one-electron matrices are known. This makes it possible to objectively compare HF and exact KS and hence to assess the potential of DFT for momentum-space studies. The systems considered are the Moshinsky [Am. J. Phys. 36, 52 (1968)] atom, Hooke’s atom, and light two-electron ions, for which expressions for correlated density matrices or momentum densities have been derived in closed form. The results obtained show that it is necessary to make a distinction between true and approximate DFTs.
Enhanced electron diffusion length of mesoporous TiO2 film by using Nb2O5 energy barrier for dye-sensitized solar cells
Authors: Ahn Kwang-Soon , Kang Moon-Sung , Lee Jae-Kwan , Shin Byong-Cheol , Lee Ji-Won
Published: July 2006

Electron diffusion coefficient (D) and electron lifetime (τ) of mesoporous TiO2 films with Nb2O5 energy barrier were investigated by the stepped light-induced transient measurements of photocurrent and photovoltage, compared with that without the Nb2O5. Both the D and τ values were significantly increased with the Nb2O5 energy barrier, resulting in remarkable enhancements of electron diffusion length and optimum thickness of the TiO2 film. As a result, the Nb2O5 energy barrier could provide much more efficient dye-sensitized solar cells by the additional effect of the improved optimum thickness as well as the existing effect at the same TiO2 film thickness.
Enhanced optical second harmonic generation in hybrid polymer nanoassemblies based on coupled surface plasmon resonance of a gold nanoparticle array
Authors: Ishifuji Miki , Mitsuishi Masaya , Miyashita Tokuji
Published: July 2006

Effective utilization of coupled surface plasmon resonance from gold nanoparticles was demonstrated experimentally for optoelectronic applications based on second-order nonlinear optics. Hybrid polymer nanoassemblies were constructed by manipulating gold nanoparticle arrays with nonlinear optical active polymer nanosheets to investigate the second harmonic generation. The gold nanoparticle arrays were assembled on heterodeposited polymer nanosheets. The second harmonic light intensity was enhanced by a factor of 8. The observed enhancement was attributed to coupling of surface plasmons between two adjacent gold nanoparticles, thereby enhancing the surface electromagnetic field around the nanoparticles at the fundamental light wavelength (1064nm).
Unusual hydrogen distribution and its change in hydrogenated amorphous silicon prepared using bias electric-field molecular beam deposition
Authors: Matsuki Nobuyuki , Shimizu Satoshi , Kondo Michio , Matsuda Akihisa
Published: July 2006

Hydrogenated amorphous silicon (a-Si:H) films prepared using a molecular beam deposition (MBD) method show an unusually sharp, narrow infrared absorption peak at 2080–2090cm−1, which is thought to result from surface SiH species in the a-Si:H. The sharp, narrow peak is eliminated by a bias electric field of several kilovolts during deposition. The absence or presence of incoming high-energy silicon atoms or clusters accelerated by the field seems to be crucial for the resulting network structure and hydrogen distribution in a-Si:H prepared using MBD.
Propagation of surface water wave pulses over an uneven topographical bottom
Authors: Chen Liang-Shan , Li Sheng , George Thomas F. , Kuo Chao-Hsien , Sun Xin
Published: July 2006

The propagation of surface water wave pulses over a topographical bottom with randomly arranged cylindrical steps is investigated by multiple scattering theory. It is shown that the waves within a certain frequency range can be localized due to the strong multiple scattering process. In the localized state, the wave intensity decreases exponentially as the transmitted distance increases. By making use of this effect, some components contained in the pulse can be filtered or inhibited by the cylinder ensemble and trapped for a relatively long period of time until dissipation.
Loss of photocurrent efficiency in low mobility semiconductors: Analytic approach to space charge effects
Authors: Tessler Nir , Rappaport Noam
Published: July 2006

We derive an analytic expression for the photocurrent efficiency as a function of the optical excitation power within the framework of space charge limit of Mott and Gurney [Electronic Processes in Ionic Crystals (Oxford University Press, London, 1940)]. This complements the approach based on charge recombination and we show that the two give similar expressions. Namely, in low mobility and intrinsic semiconductors (as conjugated polymers) based photocell, where recombination follows Langevin’s expression, the onsets of space charge and of charge recombination coincide. The analysis shows that the onset of space charge or recombination depends only on the slow carrier mobility value and do not require imbalanced mobility values.
Organic thin-film transistors with poly(methyl silsesquioxane) modified dielectric interfaces
Authors: Wu Yiliang , Liu Ping , Ong Beng S.
Published: July 2006

Poly(methyl silsesquioxane) modification of SiO2 gate dielectric surface leads to significantly improved performance of polythiophene-based organic thin-film transistors. The beneficial effects of this surface modification on transistor performance are often significantly greater than those of other silane self-assembled monolayers (SAMs). This polymer modification approach can also be applied to solution-processed dielectric surfaces where the growth of silane SAMs is difficult, thus enabling fabrication of flexible organic thin-film transistor circuits on plastic substrates.
Urana subterranean clover (Trifolium subterraneum L. var. subterraneum)
Authors: Nichols P. G. H. , Barbetti M. J. , Sandral G. A. , Dear B. S. , de Koning C. T. , Lloyd D. L. , Evans P. M. , Craig A. D. , Si P. , You M. P.
Published: July 2006

Urana is a hardseeded, moderately early flowering F5-derived crossbred subterranean clover of var. subterraneum [(Katz. et Morley) Zohary and Heller] developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It has been selected for release as a new cultivar on the basis of its high winter and spring herbage production and overall field performance relative to other subterranean clovers of similar maturity. Urana is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. It is best suited to well-drained, moderately acidic soils in areas with a growing season of 5–7 months, which extends into mid-October. Urana is suited to phase farming and crop rotations. It has been granted Plant Breeders Rights in Australia.
The Plug Domain of Yeast Sec61p Is Important for Efficient Protein Translocation, but Is Not Essential for Cell Viability
Authors: Junne Tina , Schwede Torsten , Goder Veit , Spiess Martin
Published: July 2006

The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side. It was proposed to be important for gating the protein conducting channel and for maintaining the permeability barrier in its unoccupied state. Here, we analyzed in yeast the effect of introducing destabilizing point mutations in the plug domain or of its partial or complete deletion. Unexpectedly, even when the entire plug domain was deleted, cells were viable without growth phenotype. They showed an effect on signal sequence orientation of diagnostic signal-anchor proteins, a minor defect in cotranslational and a significant deficiency in posttranslational translocation. Steady-state levels of the mutant protein were reduced, and when coexpressed with wild-type Sec61p, the mutant lacking the plug competed poorly for complex partners. The results suggest that the plug is unlikely to be important for sealing the translocation pore in yeast but that it plays a role in stabilizing Sec61p during translocon formation.
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
Authors: Mokdad Ali , Leontis Neocles B.
Published: July 2006

Summary: RNA atomic resolution structures have revealed the existance of different families of basepair interactions, each of which with its own isosteric sub-families. Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position. Potential mistakes in the alignments can then be corrected using other sequence editing software. Ribostral has been developed and tested under Windows XP, and is capable of running on any PC or MAC platform with MATLAB 7.1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform.

Availability:  

Contact:  mali@bgsu.edu

Supplementary information: A user manual is available on Ribostral website.
High Expression of CD105 as a Prognostic Predictor of Early Tongue Cancer
Authors: Chuang Hui‐Ching , Su Chih‐Ying , Huang Hsuang‐Ying , Chien Chih‐Yen , Chen Ching‐Mei , Huang Chao‐Cheng
Published: July 2006

Objectives: The purpose of this article is to investigate the expressions of vascular endothelial growth factor (VEGF) and endoglin (CD105) in the biopsy tissues of squamous cell carcinoma of the tongue in early tumor stages and their relationship with the clinicopathologic features.

Study Design and Methods: The authors conducted retrospective clinical and biologic studies. Immunohistochemistry was used to study the expressions of VEGF and CD105 in the biopsy tissues taken from 94 patients with T1 and T2 tongue cancers. The expressions of VEGF and CD105 were analyzed and correlated to the clinicopathologic features of these patients.

Results: High expressions of VEGF and CD105 significantly correlated with a relatively advanced tumor stage (P = .001 and P < .001), positive nodal status (P < .001 and P < .001), presence of tumor necrosis (P = .022 and P = .01), and greater tumor thickness (P < .001 and P < .001), respectively. In addition, high expression of CD105 correlated with the presence of perineural invasion (P = .003). However, the expression of VEGF and CD105 did not significantly correlate with age, gender, vascular invasion, or histologic grading. The cumulative 5‐year disease‐free survival rate significantly correlated with low expression of VEGF (P = .003), CD105 (P < .001), positive nodal status (P < .001), a relatively advanced tumor stage (P = .024), greater tumor thickness (P = .023), and presence of tumor necrosis (P = .003). Nonetheless, Cox's regression analysis revealed that only the expression of CD105 was an independent prognostic predictor for survival (P < .001).

Conclusions: Higher expression of either CD105 or VEGF in the tumor bed implicates a more aggressive potential for T1 and T2 tongue cancers, and the expression of CD105 is a useful predictive prognostic factor in early tongue cancer.
Expression of RANKL and OPG in Middle Ear Cholesteatoma Tissue
Authors: Jeong Jin‐Hyeok , Park Chul‐Won , Tae Kyung , Lee Seung‐Hwan , Shin Dae‐Hyun , Kim Kyung‐Rae , Park Yong‐Wook
Published: July 2006

Objectives: The objective of this study was to investigate how the expression of the RANK‐RANKL‐OPG system mediates the formation and differentiation of osteoclasts and causes bone resorption in cholesteatoma.

Methods: An immunohistochemical analysis was carried out in 22 cholesteatoma tissues obtained during middle ear surgery and 15 normal postauricular skin tissues to examine the expression of RANKL and OPG.

Results: All 22 cases of cholesteatoma and the 15 cases of normal postauricular skin expressed RANKL and OPG. The count and rate of RANKL‐positive cells in cholesteatoma was significantly higher than in normal postauricular skin. The count and rate of OPG‐positive cells in normal postauricular skin was significantly higher than in cholesteatoma. The ratio of the positive expression rates of RANKL and OPG in cholesteatoma was statistically higher than in normal postauricular skin.

Conclusions: We provide evidence suggesting that RANKL, which activates osteoclasts, plays a significant role in the mechanism of bone destruction in cholesteatoma, and that the ratio of RANKL to OPG may be a reliable indicator of bone destruction in cholesteatoma.
Enterococcus caccae sp. nov., isolated from human stools
Authors: Carvalho Maria da Glória S. , Shewmaker P. Lynn , Steigerwalt Arnold G. , Morey Roger E. , Sampson A. J. , Joyce Kevin , Barrett Timothy J. , Teixeira Lucia M. , Facklam Richard R.
Published: July 2006

The National Antimicrobial Resistance Monitoring System Laboratory at the Centers for Disease Control and Prevention (CDC) isolated two enterococcus-like strains that were referred to the CDC Streptococcus Laboratory for further identification. The isolates were recovered from human stool samples collected on different occasions from the same individual in Portland (OR, USA) in July 2000. Conventional physiological tests distinguished these strains from all known species of enterococci. Analyses of whole-cell-protein electrophoretic profiles showed the same unique profile for the two isolates, being most similar those of Enterococcus moraviensis and Enterococcus haemoperoxidus albeit not close enough to allow conclusive inclusion in any enterococcal species. Both isolates gave positive results in tests using the AccuProbe Enterococcus genetic probe, and Lancefield extracts reacted with CDC group D antiserum. Comparative 16S rRNA gene sequencing studies also revealed that these strains were closely related to the species E. moraviensis (99.6 % identity). The results of DNA–DNA relatedness experiments confirmed that these strains represented a single novel taxon. The highest level of DNA–DNA relatedness found between the novel taxon and any of the currently recognized species of Enterococcus was 32 %, for both E. moraviensis and E. haemoperoxidus. On the basis of this evidence, it is proposed that these stool isolates constitute a novel species, for which the name Enterococcus caccae sp. nov. is proposed. The type strain is 2215-02T (=SS-1777T=ATCC BAA-1240T=CCUG 51564T).
Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan
Authors: Miyazaki Masayuki , Nogi Yuichi , Usami Ron , Horikoshi Koki
Published: July 2006

Six strains representing three novel species were isolated from deep-sea sediment in Suruga Bay, Japan, at a depth of 2406–2409 m. On the basis of 16S rRNA gene sequence analysis, the isolated strains, c931T, c941T, d943, c952, d954 and c959T, are closely affiliated with members of the genus Shewanella. The hybridization values for DNA–DNA relatedness between these strains and Shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition of a species. On the basis of their distinct taxonomic characteristics, the isolated strains represent three novel Shewanella species, for which the names Shewanella kaireitica sp. nov. (three strains, type strain c931T=JCM 11836T=DSM 17170T), Shewanella abyssi sp. nov. (two strains, type strain c941T=JCM 13041T=DSM 17171T) and Shewanella surugensis sp. nov. (type strain c959T=JCM 11835T=DSM 17177T) are proposed.
Salicola marasensis gen. nov., sp. nov., an extremely halophilic bacterium isolated from the Maras solar salterns in Peru
Authors: Maturrano Lenin , Valens-Vadell María , Rosselló-Mora Ramon , Antón Josefa
Published: July 2006

Six strains of extremely halophilic bacteria were isolated from several crystallizer ponds of the Maras solar salterns in the Peruvian Andes. On the basis of 16S rRNA gene sequence similarity, G+C contents and DNA–DNA hybridization results, the six isolates constituted a genomically homogeneous group affiliated with the Gammaproteobacteria. The closest relatives were members of the halophilic genera Halovibrio and Halospina, which showed 16S rRNA gene sequence similarities below 97 % and whole-genome hybridization levels below 33 % for the type strain, 7Sm5T. From the genomic and phenotypic properties of the six novel isolates and phylogenetic reconstruction based on 16S rRNA gene sequence analysis, they can be considered to represent a novel genus within the Gammaproteobacteria. On the basis of the taxonomic study, a novel genus, Salicola gen. nov., is proposed containing the single species Salicola marasensis sp. nov., which is the type species. The type strain of Salicola marasensis is 7Sm5T (=CECT 7107T=CIP 108835T).
Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea
Authors: Kim Byung-Yong , Weon Hang-Yeon , Cousin Sylvie , Yoo Seung-Hee , Kwon Soon-Wo , Go Seung-Joo , Stackebrandt Erko
Published: July 2006

Two yellow-pigmented, Gram-negative, rod-shaped bacterial strains, GH1-10T and GH29-5T, were isolated from greenhouse soils in Korea. 16S rRNA gene sequence analysis indicated that these strains were related to members of the genus Flavobacterium. Strain GH1-10T was most closely related to Flavobacterium psychrolimnae and Flavobacterium denitrificans, with sequence similarities of 95.9 and 95.2 %, respectively. Strain GH29-5T was most closely related to ‘Flavobacterium saliodium’, F. denitrificans and Flavobacterium frigoris, with sequence similarities of 94.3, 92.5 and 92.5 %, respectively. The major cellular fatty acids of GH1-10T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c) and iso-C17 : 0 3-OH, and those of GH29-5T were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Both strains contained menaquinone with six isoprene units (MK-6) as the sole quinone. The DNA G+C contents of GH1-10T and GH29-5T were 35 and 39 mol%, respectively. Based on the phylogenetic and phenotypic data presented, it is concluded that the two bacteria represent two separate novel species of the genus Flavobacterium. The names proposed to accommodate these organisms are Flavobacterium daejeonense sp. nov., with type strain GH1-10T (=KACC 11422T=DSM 17708T), and Flavobacterium suncheonense sp. nov., with type strain GH29-5T (=KACC 11423T=DSM 17707T).
Real-Time RT-PCR: cDNA Synthesis
Authors: Kusser Wolfgang , Javorschi Sandrine , Gleeson Martin A.
Published: July 2006

INTRODUCTION

This protocol uses the Superscript II First-Strand Synthesis System for the generation of cDNA from total RNA.
Simple electrostatic model improves designed protein sequences
Authors: Zollars Eric S. , Marshall Shannon A. , Mayo Stephen L.
Published: July 2006

Electrostatic interactions are important for both protein stability and function, including binding and catalysis. As protein design moves into these areas, an accurate description of electrostatic energy becomes necessary. Here, we show that a simple distance‐dependent Coulombic function parameterized by a comparison to Poisson‐Boltzmann calculations is able to capture some of these electrostatic interactions. Specifically, all three helix N‐capping interactions in the engrailed homeodomain fold are recovered using the newly parameterized model. The stability of this designed protein is similar to a protein forced by sequence restriction to have beneficial electrostatic interactions.
Regional differences in adhesive tape stripping of human skin
Authors: Tokumura Fumio , Yoshiura Yumi , Homma Takeyasu , Nukatsuka Hiroshi
Published: July 2006

Background/purpose: The regional differences in acrylic adhesive tape stripping of human skin were evaluated.

Methods: Two kinds of adhesive tape with different water vapor permeabilities were applied to the flexor side of the forearm and the cheek, palm and sole in eight healthy male volunteers. Dermal peeling force was measured at 1 and 6 h after application. Simultaneously, the electrical conductance of the skin beneath the applied tape and the amount of stripped corneocytes on the removed tape were measured.

Results and conclusion: The regional difference in dermal peeling force of the permeable tape was large and that of the occlusive tape was small. The dermal peeling force of the permeable tape was high in the order of the palm, sole, cheek and forearm and individual differences among subjects in dermal peeling force of tape applied to the palm was large. The regional difference in dermal peeling force was considered to be related to fluid accumulation beneath the applied tape and the amount of stripped corneocytes. On the other hand, that the dermal peeling force of the occlusive tape was low and the regional difference was small may have been caused by fluid accumulation from the skin beneath the applied tape on all regions.
Safety of sodium fluorescein for in vivo study of skin
Authors: O'goshi Ken‐ichiro , Serup Jørgen
Published: July 2006

Background/purpose: Epicutaneous labeling or intradermal injection of the fluorescent sodium fluorescein is being used increasingly to investigate skin conditions in vivo when using non‐invasive devices such as confocal scanning laser microscopy. Sodium fluorescein was used intravenously for decades for the examination of the vasculature of the ocular fundus (fluorescein angiography) and as eye drops for diagnosis of corneal erosions. The objective of this article is to systematically review the literature on fluorescein and conclude its safety in cutaneous research to support research planning and evaluations by ethics committees.

Methods: A number of databases and the literature about safety and toxicity of fluorescein in animal and human studies were searched and analyzed.

Results: Side effects or adverse events reported in the literature were related to intravenous bolus injection. Transient nausea and vomiting may occur. Other adverse events such as vasovagal reaction, cardiac or respiratory effects and anaphylaxes are extremely rare but may be fatal. Intradermal injection may cause mild itch or pain; systemic adverse event was reported. Epicutaneous labeling is associated with no reported problem. A typical local dose is several magnitudes of order smaller than a typical intravenous dose.

Conclusion: Fluorescein has been used for many years in medicine for diagnostic purposes and is widely safe, albeit intravenous bolus injection may cause serious adverse reactions. In the literature, we could not trace reports of local or systemic side effects of topical sodium fluorescein except itch and pain on intradermal injection, however, dependent on the fluorescein preparation used. Local dermal application of fluorescein for in vivo study of skin may be considered widely safe.
Inhibitory effect of coenzyme Q1 on eukaryotic DNA polymerase γ and DNA topoisomerase II activities on the growth of a human cancer cell line
Authors: Yonezawa Yuko , Kuriyama Isoko , Fukuoh Atsushi , Muta Tsuyoshi , Kang Dongchon , Takemura Masaharu , Kato Ikuo , Yoshida Hiromi , Mizushina Yoshiyuki
Published: July 2006

Coenzyme Q (CoQ) is an isoprenoid quinine that functions as an electron carrier in the mitochondrial respiratory chain in eukaryotes. CoQ having shorter isoprenoid chains, especially CoQ1 and CoQ2, selectively inhibited the in vitro activity of eukaryotic DNA polymerase (pol) γ, which is a mitochondrial pol. These compounds did not influence the activities of nuclear DNA replicative pols such as α, δ and ɛ, and nuclear DNA repair‐related pols such as β, η, ι, κ and λ. CoQ also inhibited DNA topoisomerase II (topo II) activity, although the enzymatic characteristics, including modes of action, amino acid sequences and three‐dimensional structures, were markedly different from those of pol γ. These compounds did not inhibit the activities of procaryotic pols such as Escherichia coli pol I, and other DNA metabolic enzymes such as human immunodeficiency virus reverse transcriptase, T7 RNA polymerase and bovine deoxyribonuclease I. CoQ1, which has the shortest isoprenoid chains, had the strongest inhibitory effect on pol γ and topo II activities among CoQ1–CoQ10, with 50% inhibitory concentration (IC50) values of 12.2 and 15.5 µM, respectively. CoQ1 could prevent the growth of human promyelocytic leukemia cells, HL‐60, and the 50% lethal dose (LD50) value was 14.0 µM. The cells were halted at S phase and G1 phase in the cell cycle, and suppressed mitochondrial proliferation. From these results, the relationship between the inhibition of pol γ/topo II and cancer cell growth by CoQ is discussed. (Cancer Sci 2006; 97: 716–723)
Effects of salbutamol and glyceryl trinitrate on large arterial stiffness are similar between patients with hypertension and adults with normal blood pressure
Authors: Waring W. Stephen , Sinclair Hannah M. , Webb David J.
Published: July 2006

What is already known about this subject

Assessment of endothelial function gives prognostic information and allows risk stratification among patients with hypertension.

Existing techniques for determining endothelial function involve invasive methods that are not widely applicable beyond a research environment.

A simple non‐invasive pulse wave analysis (PWA) method for assessing endothelial function has recently been described, but its applicability in clinical practice is uncertain.

What this study adds

Application of the PWA technique to patients with established hypertension is feasible, but endothelial dysfunction was not detected.

Possible discrepancies between different agonists used to assess endothelial function might be important and need further consideration.

Aims

Endothelial function is characteristically impaired in patients with hypertension. Endothelial function was assessed in men and women with hypertension using a recently described, non‐invasive method.

Methods

Twenty patients and 20 controls received salbutamol 400 µg and glyceryl trinitrate (GTN) 500 µg in a two‐way randomized, single‐blind study. Effects on augmentation index (AIx) were assessed using pulse wave analysis (PWA).

Results

Responses (absolute AIx reduction and 95% confidence interval) to salbutamol were 8.4% (6.2, 10.6) and 8.3% (7.0, 9.6) in patients and controls, respectively, and those to GTN were 13.6% (10.8, 16.4) and 15.5% (13.0, 17.0), respectively.

Conclusions

Systemic arterial responses to endothelium‐dependent and ‐independent vasodilators are preserved in patients with mild, uncomplicated hypertension, indicating normal large arterial endothelial function.
Peginterferon alpha‐2b plus ribavirin for treatment of chronic hepatitis C with severe fibrosis: a multicentre randomized controlled trial comparing two doses of peginterferon alpha‐2b
Authors: Abergel A. , Hezode C. , Leroy V. , Barange K. , Bronowicki J. P. , Tran A. , Alric L. , Castera L. , Bernard P.‐H. , Henquell C. , Lafeuille H. , Ughetto S. , Darcha C. , Chevallier M. , Martineau N. , Dubost S. , Randl K. , Dhumeaux D. , Bommelaer G. , Bonny C. ,   a French multicenter study group
Published: July 2006

Summary.  We compared sustained virological response (SVR) in chronic hepatitis C patients with severe fibrosis treated with pegylated interferon (Peg‐IFN) α‐2b 1.5 μg/kg/week or 0.75 μg/kg/week in combination with ribavirin 800 mg/day for 48 weeks. This was a multicentre randomized controlled study. SVR was observed in 44.5% (45/101) of patients treated with the standard dose of Peg‐IFN and 37.2% (38/102) of patients treated with the low dose (NS). In patients with genotypes 1, 4 and 5, SVR was observed in 25.0% of patients who received the standard dose and 16.9% of patients who received the low dose of Peg‐IFN (P = NS). In patients with genotypes 1, 4 and 5 and low viraemia, SVR was obtained in 27.3% of patients treated with the standard dose and 25.8% of patients treated with the low dose (P = NS). In the high‐viraemia subgroup, SVR was obtained in 24.0% and 9.1% of patients, respectively. In patients with genotypes 2 and 3, SVR was similar in both groups (73.2%vs 73.0%). Thus, (1) patients with genotypes 2 and 3 and severe fibrosis can be treated with low dose of Peg‐IFN and ribavirin, (2) this study suggests that patients with genotypes 1, 4 and 5 and high viraemia could receive a standard dose of Peg‐IFN associated with ribavirin for 48 weeks, (3) side effects limit the efficacy of the treatment with standard dose of Peg‐IFN in patients with genotypes 1, 4 and 5 and low viraemia, (4) more studies are needed for patients with genotype 2 or 3 to define the optimal duration (24 or 48 weeks) in patients with severe fibrosis.