bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disulfide structures of highly bridged peptides: A new strategy for analysis
Authors: Gray William R. 
Published: February 2009

AbstractA new approach is described for analyzing disulfide linkage patterns in peptides containing tightly clustered cystines. Such peptides are very difficult to analyze with traditional strategies, which require that the peptide chain be split between close or adjacent Cys residues. The water‐soluble tris‐(2‐carboxyethyl)‐phosphine (TCEP) reduced disulfides at pH 3, and partially reduced peptides were purified by high performance liquid chromatography with minimal thiol–disulfide exchange. Alkylation of free thiols, followed by sequencer analysis, provided explicit assignment of disulfides that had been reduced. Thiol–disulfide exchange occurred during alkylation of some peptides, but correct deductions were still possible. Alkylation competed best with exchange when peptide solution was added with rapid mixing to 2.2 M iodoacetamide. Variants were developed in which up to three alkylating agents were used to label different pairs of thiols, allowing a full assignment in one sequencer analysis. Model peptides used included insulin (three bridges, intra‐ and interchain disulfides; ‐Cys·Cys‐ pair), endothelin and apamin (two disulfides; ‐Cys·x·Cys‐ pair), conotoxin GI and isomers (two disulfides; ‐Cys·Cys‐ pair), and bacterial enterotoxin (three bridges within 13 residues; two ‐Cys·Cys‐ pairs). With insulin, all intermediates in the reduction pathway were identified; with conotoxin GI, analysis was carried out successfully for all three disulfide isomers. In addition to these known structures, the method has been applied successfully to the analysis of several previously unsolved structures of similar complexity. Rates of reduction of disulfide bonds varied widely, but most peptides did not show a strongly preferred route for reduction.
Mechanical unfolding of covalently linked GroES: Evidence of structural subunit intermediates
Authors: Sakane Isao , Hongo Kunihiro , Mizobata Tomohiro , Kawata Yasushi 
Published: February 2009

AbstractIt is difficult to determine the structural stability of the individual subunits or protomers of many proteins in the cell that exist in an oligomeric or complexed state. In this study, we used single‐molecule force spectroscopy on seven subunits of covalently linked cochaperonin GroES (ESC7) to evaluate the structural stability of the subunit. A modified form of ESC7 was immobilized on a mica surface. The force‐extension profile obtained from the mechanical unfolding of this ESC7 showed a distinctive sawtooth pattern that is typical for multimodular proteins. When analyzed according to the worm‐like chain model, the contour lengths calculated from the peaks in the profile suggested that linked‐GroES subunits unfold in distinct steps after the oligomeric ring structure of ESC7 is disrupted. The evidence that structured subunits of ESC7 withstand external force to some extent even after the perturbation of the oligomeric ring structure suggests that a stable monomeric intermediate is an important component of the equilibrium unfolding reaction of GroES.
Effects of the sesquiterpene lactone parthenolide on prostate tumor‐initiating cells: An integrated molecular profiling approach
Authors: Kawasaki Brian T. , Hurt Elaine M. , Kalathur Madhuri , Duhagon Maria Ana , Milner John A. , Kim Young S. , Farrar William L. 
Published: February 2009

AbstractRecent evidence suggests tumor‐initating cells (TICs), also called cancer stem cells, are responsible for tumor initiation and progression; therefore, they represent an important cell population for development of future anti‐cancer therapies. In this study, we show that the sesquiterpene lactone parthenolide (PTL) is cytotoxic to prostate TICs isolated from prostate cancer cell lines: DU145, PC3, VCAP, and LAPC4, as well as primary prostate TICs. Furthermore, PTL inhibited TIC‐driven tumor formation in mouse xenografts. Using an integrated molecular profiling approach encompassing proteomics, profiles of activated transcription factors and genomics we ascertained the effects of PTL on prostate cancer cells. In addition to the previously described effects of PTL, we determined that the non‐receptor tyrosine kinase src, and many src signaling components, including: Csk, FAK, β1‐arrestin, FGFR2, PKC, MEK/MAPK, CaMK, ELK‐1, and ELK‐1‐dependent genes are novel targets of PTL action. Furthermore, PTL altered the binding of transcription factors important in prostate cancer including: C/EBP‐α, fos related antigen‐1 (FRA‐1), HOXA‐4, c‐MYB, SNAIL, SP1, serum response factor (SRF), STAT3, X‐box binding protein‐1 (XBP1), and p53. In summary, we show PTL is cytotoxic to prostate TICs and describe the molecular events of PTL‐mediated cytotoxicity. Therefore, PTL represents a promising therapeutic for prostate cancer treatment. Prostate 69: 827–837, 2009. © 2009 Wiley‐Liss, Inc.
Gene expression changes are age‐dependent and lobe‐specific in the brown Norway rat model of prostatic hyperplasia
Authors: Bethel Carlise R. , Chaudhary Jaideep , Anway Matthew D. , Brown Terry R. 
Published: February 2009

AbstractBACKGROUNDBenign prostatic hyperplasia (BPH) is an age‐related enlargement of the prostate, characterized by increased proliferation of stromal and epithelial cells. Despite its prevalence, the etiology of BPH is unknown.METHODSThe Brown Norway rat is a model for age‐dependent, lobe‐specific hyperplasia of the prostate. Histological analyses of the dorsal and lateral lobes from aged rats reveal focal areas characterized by increased numbers of luminal epithelial cells, whereas the ventral lobe is unaffected. This study examined differential gene expression by lobe and age in the Brown Norway rat prostate. The objective was to identify genes with different levels of expression in the prostate lobes from 4‐month (young) and 24‐month (old) animals, and to subsequently link changes in gene expression to mechanisms of prostate aging.RESULTSThe number of age‐dependent differentially expressed genes was greatest in the dorsal compared to the ventral and lateral lobes. Minimal redundancy was observed among the differentially expressed genes in the three lobes. Age‐related changes in the expression levels of 14 candidate genes in the dorsal, lateral and ventral lobes were confirmed by quantitative RT‐PCR. Genes that exhibited age‐related differences in their expression were associated with proliferation, oxidative stress, and prostate cancer progression, including topoisomerase II alpha (Topo2a), aurora kinase B (Aurkb), stathmin 1 (Stmn1), and glutathione S‐transferase pi. Immunohistochemistry for Topo2a, Aurkb, and Stmn1 confirmed age‐related changes in protein localization in the lateral lobe of young and aged prostates.CONCLUSIONThese findings provide clues to the molecular events associated with aging in the prostate. Prostate 69: 838–850, 2009. © 2009 Wiley‐Liss, Inc.
Lab‐on‐substrate technology platform
Authors: Braun Tanja , Böttcher Lars , Bauer Jörg , Jung Erik , Becker Karl‐Friedrich , Ostmann Andreas , Aschenbrenner Rolf , Reichl Herbert 
Published: February 2009

AbstractA technology platform based on standard PCB technology has been developed for cost‐effective fabrication of biological and medical test devices. Aluminum, polyimide and Pyralux have been selected as materials with focus on bio‐ and process compatibility. A process flow consisting of lamination, Al structuring by wet etching, microwell and via formation by laser drilling and via metallization was developed. Surface treatments have been evaluated for hydrophobic and hydrophilic modification of the materials. The technology was demonstrated with a dielectrophoresis enhanced microwell device for single cell handling and detection of cell‐to‐cell interaction as needed for the improvement of tumor therapy. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Oxide removal from GaN(0001) surfaces
Authors: Schulz Ch. , Schmidt Th. , Flege J. I. , Berner N. , Tessarek Ch. , Hommel D. , Falta J. 
Published: February 2009

AbstractX‐ray photoelectron spectroscopy has been used to study two different two‐step cleaning methods of MOVPE grown GaN(0001). Carbon and oxygen were identified as the major contaminants, even though the samples were stored in a glove box after growth and transferred under nitrogen atmosphere. By thermal annealing of the samples a significant oxygen decrease and a complete removal of the carbon was achieved. To remove the residual oxygen, subsequently Ga deposition/re‐desorption cycles and N‐plasma treatment were performed (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Thermal characterization of light‐emitting diodes in the frequency domain
Authors: Vitta Pranciškus , Žukauskas Artūras 
Published: February 2009

AbstractWe report on a method for measurement of thermal relaxation time constants within light‐emitting diodes (LEDs) using harmonic modulation of the driving current. The method is based on the phase shift of the forward voltage waveform in respect to that of the modulated current. The phase shift is due to the sensitivity of the forward voltage to junction temperature, which responds to the modulation of the heat generation depending on the thermal relaxation rate. The frequency dependence of the phase shift was shown to exhibit characteristic dips at angular frequencies equal to inverse thermal time constants. Such an approach for thermal characterization was demonstrated for common GaP, AlGaAs, AlInGaP, and InGaN LEDs. In particular, low‐power p‐n and double‐heterostructure LEDs as well as high‐power truncated‐inverted‐pyramid and flip‐chip LEDs were investigated. The measured thermal time constants (∼ 0.1–100 ms) were tentatively assigned to heat flows within the multilayer structure of the LEDs and collated with the numerical estimates based on thermal resistance and heat capacitance of the LED components. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of compositional changes of source materials on AlN synthesis using Li‐Al‐N solvent
Authors: Nagano T. , Kangawa Y. , Kakimoto K. 
Published: February 2009

AbstractWe carried out AlN synthesis using Li‐Al‐N solvent. In the present work, Al and Li3N were used as source materials. In this paper, we discuss the variation in phase stability of the products with change in Li‐Al‐N composition, i.e., Al/Li3N molar ratio. The results suggest that LiAlO2 extra phase was formed in the products under an Al‐rich synthesis condition. The oxide formation seems to be caused by oxidation of the nitrogen source. That is, some of the Li3N reacted with H2O in the ambient and to be LiOH, though preparation of the source materials was performed in a glove‐box. On the other hand, scanning electron microscopy (SEM) images indicate the possibility of reducing nucleation sites and increasing grain size by optimizing the Al/Li3N molar ratio. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Incorporation of QD ensembles in separate confinement heterostructures for long wavelength emission
Authors: Aschenbrenner T. , Tessarek C. , Figge S. , Hommel D. 
Published: February 2009

AbstractThis paper deals with the incorporation of temperature‐sensitive InGaN quantum dot (QD) ensembles into separate confinement double heterostructures grown on free‐standing GaN substrates. The laser diode (LD) structures were processed as ridge waveguide devices. The emission wavelength in electroluminescence (EL) of the 3 fold QD layers is around 485 nm.The structural quality and state of strain of the layers has been determined by high resolution X‐ray diffraction (HRXRD) measurements. Current‐voltage characteristics, light output power measurements and EL‐spectra demonstrate the good stability of the device. A comparable small blue shift was observed with increasing excitation current (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coulomb blockade effects in the electrical characteristics of mesoporous silicon
Authors: Borini Stefano , Boarino Luca , Amato Giampiero 
Published: February 2009

AbstractWe report on a study of the conductivity threshold voltage which is observed in the electrical characteristics of (100)‐oriented mesoporous silicon, when a particular measurement configuration is used. By varying the temperature and the atmosphere (i.e. presence of NO2 and NH3 gas), the evolution of the conductivity gap is observed, and the origin of the blockade effect is investigated. It is argued that the conductivity gap arises from positive charges trapped in nanoconstrictions, which inhibit, by Coulomb interaction, the hole current along the longitudinal direction (parallel to the sample surface), where silicon nanocrystals are poorly interconnected. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Prospects for a waveguide Raman amplifier in porous silicon at 1.5 μm
Authors: Sirleto Luigi , Ferrara Maria Antonietta , Rendina Ivo , Jalali B. 
Published: February 2009

AbstractRecently, the possibility of light generation and/or amplification in silicon, based on Raman emission, has achieved significant results. However, limitations inherent to the physics of silicon have been pointed out, too. In order to overcome these limitations, a possible option is to consider low dimensional silicon. In this paper, an approach based on Raman scattering in porous silicon is investigated. First, we point out two significant advantages with respect to silicon: the broadening of the spontaneous Raman emission and the tuning of the Stokes shift. Then, we discuss about the prospect of Raman amplifier in porous silicon. Finally the design of a Raman amplifier in porous silicon waveguide is proposed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polymer nanopillars using self‐ordered nanoporous alumina templates
Authors: Palacios R. , Formentín P. , Ferré‐Borrull J. , Pallarés J. , Marsal L. F. 
Published: February 2009

AbstractThe fabrication of polymer nanostructures by replication process using self‐ordered nanoporous alumina with different pore depth and pore diameter as template is reported here. The method entails vacuum infiltration of a Poly(methyl methacrylate) (PMMA) solution into the pores of the template, which was fabricated by using a two‐step anodization process in 0.3 M oxalic acid at 50 V and 15 °C. We have studied how the aspect ratio of the nanopores influence the PMMA nanopillars fabrication. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Porous silicon/polysilicon for improved sensitivity pressure sensors
Authors: Sujatha L. , Bhattacharya Enakshi 
Published: February 2009

AbstractThis paper describes the technique of improving the sensitivity of bulk micromachined silicon pressure sensors with judicious use of porous silicon (PS) and porous polysilicon (PPS). Since PS has a much lower Young's modulus than Si, pressure sensors with Si/PS composite membranes show higher sensitivity. The sensitivity also increases as the porosity of the PS layer increases. Further improvement in sensitivity can be achieved by replacing the conventional polysilicon piezoresistors with porous polysilicon ones. Though the composite membranes exhibit higher sensitivity, they suffer from higher offset voltage due to the stress developed by the formation of porous silicon. Pressure sensors with silicon membrane and porous polysilicon piezoresistors yield modest improvement in sensitivity without increase in offset voltage. A combination of porous polysilicon piezoresistors and composite membranes with microporous silicon gave the highest sensitivity value as well as the highest offset. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carrier transport mechanisms in cathodically biased meso‐porous p+‐Si against solutions containing Fe2+ and Co2+ species
Authors: Hamadache Farida , Gelloz Bernard 
Published: February 2009

AbstractThis work reports on the use of the cyclic voltametry technique to study the electrochemical behavior of porous p+‐type silicon (PS) contacted by aqueous solutions containing Fe2+ and Co2+ electro‐actives species. Current‐potential (I‐V) measurements were performed on both flat and porous silicon substrates and different Fe2+ concentrations were considered. With flat Si, similar I‐V characteristic behaviors were obtained in 0.1 M Fe2+ and 0. 1 M Co2+ solutions, except that iron can be deposited from a potential more cathodic than cobalt. With porous Si, different I‐V characteristic behaviors were observed and a diffusion‐like current peak was detected in the presence of Fe2+ species. The observed current peak is located near the standard redox potential of iron. However, its intensity is lower than that of Fe2+ ions diffusion current peak and it does not increase as Fe2+ concentration increases. A three‐step carrier transport mechanism was proposed to show that the current peak could be attributed to iron nucleation on the pore walls via electroless deposition. Accordingly the difference observed in PS I‐V characteristics was attributed to the fact that electroless deposition on pore walls occurs at a potential for which the reduction of Co2+ ions is faster than that of Fe2+ ones and it can also occur at the pore bottom via electrodeposition. These results are used to explain the poor pore filling rate with iron, reported elsewhere. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hybrid metal/silicon nanocomposite systems and their catalytic activity
Authors: Polisski Sergej , Goller Bernhard , Lapkin Alexei , Kovalev Dmitry 
Published: February 2009

AbstractIn this work we studied the reduction of metal salts and their mixtures on extended hydrogen‐terminated porous silicon surfaces. For these experiments we employed salts of Au, Ag, Pt and their mixtures. We show that the size and shape of resulting metal and metal alloy nanoparticles depends on the pore morphology. This has been confirmed by transmission electron microscopy measurements and plasmon resonance experiments. Finally we demonstrate catalytic activity of formed Pt nanoparticles in PSi matrix via monitoring the conversion of carbon monoxide. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoinduced fluorescence enhancement and energy transfer effects of quantum dots porous silicon
Authors: DeLouise Lisa A. , Ouyang Huimin 
Published: February 2009

AbstractWe investigate photoinduced fluorescence enhancement (PFE) and energy transfer effects of surfactant capped Cd/Se core and CdSe/ZnS core/shell quantum dots (QD) that emit at 630‐650 nm adsorbed in and onto porous silicon (PSi) single layer films and microcavity devices. Evidence is presented for fluorescence resonance energy transfer (FRET) from the QD (emitter) to mesoPSi nanostructures (acceptor) that photoluminess between 650‐850 nm. We also observe a strong PFE of QD emission adsorbed into meso porous silicon (mesoPSi) under continuous irradiation with 532 nm excitation light. New insight into the mechanism of PFE is gleaned from studies of PSi pore size and surface chemistry including native, H2O2, UV‐ozone, and thermal oxides, and aminosilane coated thermal oxide mesoPSi. These treatments alter the photoluminescent characteristics of the mesoPSi and QD. The PFE effect on QD PL is largest on thermally oxidized microcavities. PFE is considerably weaker for CdSe QD adsorbed onto macroPSi, silicon wafer surfaces and especially for ZnS capped QD suggesting the PFE effect requires a close interaction of the QD core with oxidized substrate. It is plausible that mesoPSi (10‐20 nm dia) mediates a more intimate contact compared to macro or planar Si wafer. The PFE effect dynamically increases the QD PL by passivating nonradiative state through oxidation and possibly through increasing the lifetime of nonradiative trapped state by coupling to surface vibrations. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adaptive modelling of dose–response relationships using smoothing splines
Authors: Kirby Simon , Colman Peter , Morris Mark 
Published: February 2009

AbstractWe consider the use of smoothing splines for the adaptive modelling of dose–response relationships. A smoothing spline is a nonparametric estimator of a function that is a compromise between the fit to the data and the degree of smoothness and thus provides a flexible way of modelling dose–response data. In conjunction with decision rules for which doses to continue with after an interim analysis, it can be used to give an adaptive way of modelling the relationship between dose and response. We fit smoothing splines using the generalized cross‐validation criterion for deciding on the degree of smoothness and we use estimated bootstrap percentiles of the predicted values for each dose to decide upon which doses to continue with after an interim analysis. We compare this approach with a corresponding adaptive analysis of variance approach based upon new simulations of the scenarios previously used by the PhRMA Working Group on Adaptive Dose‐Ranging Studies. The results obtained for the adaptive modelling of dose–response data using smoothing splines are mostly comparable with those previously obtained by the PhRMA Working Group for the Bayesian Normal Dynamic Linear model (GADA) procedure. These methods may be useful for carrying out adaptations, detecting dose–response relationships and identifying clinically relevant doses. Copyright © 2009 John Wiley & Sons, Ltd.
Nanotopographic characterization of spotted micro arrays on polyvinyl alcohol films by high‐resolution long‐range nanoprofiling
Authors: Thete Aniket R. , Gross G. Alexander , Hausotte Tino , Jäger Gerd , Dorozhovets Nataliya , Köhler J. Michael 
Published: February 2009

AbstractThe nanopositioning and nanomeasuring machine was applied for the nanotopographic characterization of polymer micro spot arrays of fluorimetric chemochips. Chemochips are arrays of fluorescence dyes in a hydrogel matrix with different response behaviors of chemical components determination of chemical and physico‐chemical properties of analytes by a pattern recognition approach. For the characterization and quality control of the spots, a nanometer resolution is needed over a scan range of several millimeters. This challenge could be met by use of a scanning probe sensor in connection with a laser interferometer controlled high‐precision positioning and measuring device. This way, topographic scans with the resolution of atomic force microscope could be achieved over these demandingly large ranges. The technique was used in order to determine the quality of thin film micro spots made from fluorescence dye solutions on preformed polymer films and also tested for characterization of monomolecular films in the form of micro spots. The nanotopographic measurements reflect the strong influence of solvent/matrix interaction, wetting, swelling and material transport during the application of picoliter droplets in the spotting process. The measurement clarifies the reason for the formation of roughness in the nanometer range by nano‐crystal formation in the upper part of polymer film and the rim formation of micro spots during solvent evaporation. The studies show the effect of application of different numbers of droplets in a dispensing series for spot formation and prove the high importance of polymer/solvent interaction for the quality of formed micro spots as well as for spot arrays of monomolecular films. SCANNING 31: 35–48, 2009. © 2009 Wiley Periodicals, Inc.