bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigations on the Stability of the Flow Characteristics in a Bubble Column
Authors: Lucas D. , Krepper E. , Prasser H.‐M. , Manera A.
Published: August 2006

The role of the lift force in the stability of the homogeneous flow regime in a bubble column is investigated. Instabilities caused by the lift force may be one important reason for the transition from a homogeneous to a heterogeneous bubble column. The lift force acts on rising bubbles in a lateral direction when gradients of the liquid velocity are present. Such gradients may result from circulation cells in the bubble column as well as from local disturbances. Depending on the sign of the lift force, such local disturbances in a homogeneous flow may be damped or enhanced. The corresponding feedback mechanism was analyzed by means of linear stability analyses. As a result, criteria for stability were obtained for mono‐dispersed flow, for a flow with two bubble size groups, and, finally, with some additional approximations also for the case of N bubble size groups or a given bubble size distribution. In a next step, the effects were investigated by CFD calculations. The obtained criteria for stability fit well with the observed effects in CFD simulations. Recently, two different groups confirmed the stability criteria experimentally.
Effect of Liquid Velocity on Axial Mixing in Gas‐Liquid Dispersions: A CFD Simulation
Authors: Roy S. , Joshi J. B.
Published: August 2006

A CFD analysis has been carried out to elucidate the characteristic features of axial mixing in gas‐liquid dispersed upflow when the flow changes between two extremes: from bubble column, with very low/no liquid velocity, to pipe flow with very high liquid velocity. The CFD model was validated by simulating flow both in multiphase and in single phase. An agreement was observed between the predictions and the experimental data available in the published literature. The validated CFD model has been extended for the simulation of the axial dispersion coefficient for both multiphase and single phase. CFD predictions of the axial dispersion coefficient show good agreement with experimental values published in the literature. A systematic numerical study was done by varying the superficial liquid velocity, from a very low value to a very high value, to understand its effect on axial dispersion.
Detailed 3D Modeling of Mass Transfer Processes in Two‐Phase Flows with Dynamic Interfaces
Authors: Darmana D. , Deen N. G. , Kuipers J. A. M.
Published: August 2006

A model is presented which allows a priori computation of mass transfer coefficients for bubbles (droplets) rising in quiescent Newtonian fluids. The proposed model is based on the front tracking technique and explicitly accounts for the bubble‐liquid mass transfer process. The dissolved species concentration in the liquid phase is computed from a species conservation equation while the value of the concentration at the interface is imposed via an immersed boundary technique. Simulations are carried out to demonstrate the capabilities of the model to predict bubble shape, flow field as well as transport of a species from the bubble to the liquid phase.
Correction of the Penetration Theory applied to the Prediction of kLa in a Bubble Column with Organic Liquids
Authors: Nedeltchev S. , Jordan U. , Schumpe A.
Published: August 2006

When Higbie's penetration theory is applied to calculate kL‐values for ellipsoidal rather than spherical bubbles, some correction factor needs to be introduced. In a recent paper, such a correction factor (less than unity) was derived for the homogeneous flow regime, based on kLa‐data measured in 1‐butanol, toluene, ethanol, and tap water: fc = 0.211 Eo0.63. In the present work, the validity of this approach is further tested on kLa‐data published for ethylbenzene, xylene, tetralin, anilin, nitrobenzene, 1,2‐dichloroethane, 1,4‐dioxane, 2‐propanol, benzene, ligroin, and ethyl acetate. The full data set involving 79 experimental kLa‐values at homogeneous flow in 14 organic liquids and tap water, is correlated with a 8.7 % mean error in the following modified form: fc = 0.185 Eo0.737.
Flow Regime Identification in a Bubble Column Based on Both Statistical and Chaotic Parameters Applied to Computed Tomography Data
Authors: Nedeltchev S. , Shaikh A. , Al‐Dahhan M.
Published: August 2006

The Kolmogorov entropy (KE) algorithm was applied successfully to single source γ‐ray Computed Tomography (CT) data measured in a 0.162 m ID bubble column equipped with a perforated plate distributor (163 holes · ∅︁ 1.32 mm). Dried air was used as the gas phase and Therminol LT (ρL = 886 kg m–3, μL = 0.88 · 10–3 Pa  s, σ = 17 · 10–3 N m–1) was used as a liquid phase. Three different pressures, P, of 0.1, 0.4, and 1.0 MPa were examined. At each pressure the superficial gas velocity, uG, was increased stepwise by steps of 0.01 m s–1 up to 0.2 m s–1. The average absolute deviation (AAD) was also used as a robust statistical criterion for regime transition. At all three pressures, based on the sudden changes in both the AAD and KE values, the boundaries of the following five regimes were identified: dispersed bubble regime, first and second transition regimes, coalesced bubble regime consisting of four regions (called 4‐region flow), and coalesced bubble regime consisting of three regions (called 3‐region flow). The existence of these regimes has already been documented. As the pressure increases, the transition velocity between the dispersed bubble and first transition regimes and the transition velocity between coalesced bubble (4‐region flow) and coalesced bubble (3‐region flow) regimes shift to higher uG values. On the other hand, at P = 0.4 MPa the second transition regime starts earlier. In addition, at P = 1 MPa the transition to coalesced bubble (4‐region flow) is delayed.
Hydrodynamics and Mixer‐Induced Bubble Formation in Micro Bubble Columns with Single and Multiple‐Channels
Authors: Haverkamp V. , Hessel V. , Löwe H. , Menges G. , Warnier M. J. F. , Rebrov E. V. , de Croon M. H. J. M. , Schouten J. C. , Liauw M. A.
Published: August 2006

A hydrodynamic characterization of an industrially used gas‐liquid contacting microchannel device is discussed, viz. the micro bubble column of IMM. Furthermore, similar characterization of a gas‐liquid flow microchip of TU/e, with two tailored mixer designs, is used to solve fundamental issues on hydrodynamics, and therefore, to achieve further design and operating optimization of that chip and the IMM device. Flow pattern maps are presented in a dimensionless fashion for further predictions on new fluidic systems for optimum single‐channel multiphase operation. Bubble formation was investigated in the two types of mixers and pinch‐off and hydrodynamic decay mechanisms are observed. The impact of these mechanisms on bubble size, bubble size distributions, and on the corresponding flow patterns, i.e., the type of mixer design, can be decisive for the flow pattern map and thus, may be used to alter flow pattern maps. The bubble sizes and their distribution were improved for the tailored designs, i.e., smaller and more regular bubbles were generated. Finally, the impact of multi‐channel distribution for gas and liquid flow is demonstrated. Intermediate flow patterns such as slug‐annular flow, also found for single‐phase operation, and the simultaneous coexistence of flow regimes are presented, with the latter providing evidence of flow maldistribution.
The Effect of Nozzle Shape on Bubble Formation from a Downward Nozzle
Authors: Tsuge H. , Mitsudani M. , Tezuka Y.
Published: August 2006

A lot of research has been conducted on the gas injection methods; especially bubble formation from the upward orifice or nozzle, whereas few studies on bubble formation from the downward nozzle have been reported. In this study, the effects of both nozzle shape and diameter on the bubble formation mechanism from the vertically downward nozzle were investigated. The theoretical results obtained by applying the revised two‐stage spherical bubble formation model for the downward nozzle was compared with the experimental results for small metal downward nozzles. The bubble formation mechanism and the bubble size were influenced by the edge angle and diameter of the nozzle, respectively, and the gas flow rate.
Synthesis, Structure, and in vitro Antitumor Activity of Some Glycoside Derivatives of Ferrocenyl‐Chalcones and Ferrocenyl‐Pyrazolines
Authors: Zsoldos‐Mády Virág , Csámpai Antal , Szabó Rita , Mészáros‐Alapi Erika , Pásztor Judit , Hudecz Ferenc , Sohár Pál
Published: August 2006

Some new glycosides of 3‐ferrocenyl‐1‐(4′‐hydroxyphenyl)‐prop‐2‐en‐1‐one were prepared and transformed into the corresponding pyrazoline and pyrazole derivatives. Using methyl‐hydrazine, formation of regioisomers was observed. DDQ was found to be a mild and efficient reagent for the pyrazoline‐pyrazole dehydroaromatization process. The structure of the new compounds was proved by IR and NMR spectroscopy. The in vitro antitumor activity of the substances was investigated against human leukemia (HL‐60) cells by the MTT method. Among these new compounds some chalcone derivatives (3 a, 3 b, 5 a, and 5 b) showed attractive in vitro antitumor effects on human leukemia cells. These molecules contained ferrocenyl moieties and a p‐hydroxy‐phenolic ring or a size‐independent apolar substitution of that.
6‐Alkylthio‐4‐[1‐(2,6‐difluorophenyl)alkyl]‐1H‐[1,3,5]triazin‐2‐ones (ADATs): Novel Regulators of Cell Differentiation and Proliferation
Authors: Sbardella Gianluca , Bartolini Sara , Castellano Sabrina , Artico Marino , Paesano Nicola , Rotili Dante , Spadafora Corrado , Mai Antonello
Published: August 2006

Novel triazine analogues of 5‐alkyl‐2‐alkylthio‐6‐[1‐(2,6‐difluorophenyl)alkyl]‐3,4‐dihydropyrimidin‐4(3H)‐ones (F2‐DABOs), previously described by us as nonnucleoside HIV‐1 reverse transcriptase inhibitors (NNRTIs), were tested for their antiproliferative and cytodifferentiating activity on the A‐375 human melanoma cell line. Most of the tested derivatives were effective in decreasing cell proliferation, facilitating morphological differentiation, and reprogramming gene expression. All these effects were reversible upon withdrawal of RT inhibitors. Among the compounds tested, 3 f showed the highest antiproliferative effect, whereas compound 6 c, although not affecting cell proliferation, is endowed with a strong cytodifferentiating effect, which is probably related to a marked upregulation of the e‐cad gene. These results support the potential of NNRTIs as valuable antitumor agents.
Novel approaches in the treatment of systemic mastocytosis
Authors: Quintas‐Cardama Alfonso , Aribi Ahmed , Cortes Jorge , Giles Francis J. , Kantarjian Hagop , Verstovsek Srdan
Published: August 2006

In the absence of curative options, therapy for aggressive forms of systemic mastocytosis (SM) has relied in the use of cytoreductive agents, mainly interferon‐α (IFN‐α) and cladribine. However, responses are transient and only occur in a subset of patients. Gain‐of‐function mutations at codon 816 of the KIT protooncogene lead to constitutively active Kit receptor molecules, which are central to the pathogenesis of SM. Recent advances in the understanding of the molecular underpinnings of SM have led to the development of small molecules targeting mutant Kit tyrosine kinase isoforms that significantly have widened the range of therapeutic options for patients with SM. Some of these promising agents, such as dasatinib, AMN107, and PKC412, currently are under investigation in clinical trials whereas, others are at different stages of preclinical development. In addition, monoclonal antibodies directed to neoplastic mast cell‐restricted surface antigens constitute a viable option for the treatment of SM that warrants further investigation. Cancer 2006. © 2006 American Cancer Society.
Noninvasive imaging for evaluation of the systemic delivery of capsid‐modified adenoviruses in an orthotopic model of advanced lung cancer
Authors: Sarkioja Merja , Kanerva Anna , Salo Jarmo , Kangasniemi Lotta , Eriksson Minna , Raki Mari , Ranki Tuuli , Hakkarainen Tanja , Hemminki Akseli
Published: August 2006

BACKGROUND.

Variable expression of the coxsackie and adenovirus receptor (CAR) has limited gene transfer efficacy to many types of tumors. Consequently, tropism‐modified adenoviruses have been developed for enhanced infectivity. To the authors' knowledge, targeting approaches for nonsmall cell lung cancer (NSCLC) have not been comprehensively evaluated. The current hypothesis was that modified adenoviruses could be used for increasing gene transfer to and killing of NSCLC cells in vitro and in vivo.

METHODS.

Ten NSCLC cell lines were analyzed to represent the different NSCLC histologies. Because clinical tumors may differ from established cell lines, 6 clinical specimens fresh from patients were analyzed. For in vivo studies, a novel orthotopic murine model of advanced lung cancer was developed. Because tumor response is difficult to quantitate in orthotopic models, noninvasive imaging of green fluorescent protein (GFP) was utilized as a surrogate for tumor size measurements.

RESULTS.

Adenoviruses whose capsids were modified with RGD‐4C, the serotype 3 knob, or polylysine displayed increased gene transfer to NSCLC cell lines and clinical samples in comparison to serotype 5 viruses. Conditionally replicating oncolytic adenoviruses (CRAds) with the same modifications showed enhanced therapeutic efficiency in vitro and in vivo. The median survival of mice treated with Ad5.pK7‐Δ24 or Ad5‐Δ24RGD increased 37% (P<.01). GFP imaging allowed noninvasive individualized detection of response and recurrence.

CONCLUSIONS.

Targeting of adenovirus to heterologous receptors can improve killing of NSCLC cells. Utilization of clinical samples and an orthotopic model of advanced lung cancer may provide clinically relevant translational data. Cancer 2006. © 2006 American Cancer Society.
1,4‐Diazabicyclo[2.2.2]octane (DABCO) as an Efficient Reagent for the Synthesis of Isoxazole Derivatives from Primary Nitro Compounds and Dipolarophiles: The Role of the Base
Authors: Cecchi Luca , De Sarlo Francesco , Machetti Fabrizio
Published: August 2006

The dehydration of primary nitro compounds can be performed by bases in the presence of dipolarophiles. The reactivity of several tertiary amines or azaheteroaromatic compounds containing one or two basic centres is shown to be related to the ability of the protonated base to establish H‐bonded ion pairs with the adduct that is formed from the nitronate and the dipolarophile in chloroform. Among the organic bases examined, caged tertiary diamine 1,4‐diazabicyclo[2.2.2]octane (DABCO) gave the best results. The reaction is applicable to activated nitro compounds and to phenylnitromethane and affords isoxazoline derivatives in higher yields compared with those of other methods. The reaction, however, is not compatible with nitroalkanes. The proposed mechanism of the reaction is based on the collapse of the H‐bonded ion pair. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
A Formal Total Synthesis of Virantmycin: A Modular Approach towards Tetrahydroquinoline Natural Products
Authors: Keck Daniel , Vanderheiden Sylvia , Bräse Stefan
Published: August 2006

A synthesis of an advanced intermediate towards the racemic form of the antiviral agent virantmycin has been developed featuring an intramolecular aza‐xylylene Diels–Alder reaction. The required arylthiocarbamate has been constructed using an efficient oxidative cyclization strategy. A novel synthetic approach to chlorine‐substituted allylic alcohols using an unprecedented palladium‐catalyzed cross‐coupling reaction of α,β‐unsaturated ketones and protected propargylic alcohols is reported.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
RGD peptide‐conjugated poly(dimethylsiloxane) promotes adhesion, proliferation, and collagen secretion of human fibroblasts
Authors: Li Bin , Chen Jianxin , Wang James H.‐C.
Published: August 2006

A novel technique for conjugating Arg‐Gly‐Asp (RGD) peptides to poly(dimethylsiloxane) (PDMS) surfaces as well as its application to cell culture is presented in this paper. This technique performs RGD conjugation to PDMS through photochemical immobilization of functional NHS groups to PDMS surface followed with linking RGD peptide to the surface via coupling reaction with NHS. A bifunctional photolinker, N‐sulfosuccinimidyl‐6‐(4′‐azido‐2′‐nitrophenylamino)hexanoate (sulfo‐SANPAH), was used to conjugate RGD peptide to the surface. Compared to existing methods for peptide conjugation to PDMS, this technique is convenient, efficient, and free of organic contamination to PDMS surfaces. It can also be used to conjugate other peptides or proteins to most polymeric materials. In addition, cell culture studies showed that the RGD‐conjugated PDMS surfaces promoted the adhesion, proliferation, and collagen production of human skin fibroblasts (HSFs). Finally, the RGD‐conjugated PDMS surfaces are resistant to autoclaving and UV irradiation, which enables them to be repeatedly used in cell culture studies. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Gradient substrate assembly for quantifying cellular response to biomaterials
Authors: Mei Ying , Elliott John T. , Smith Jack R. , Langenbach Kurt J. , Wu Tao , Xu Chang , Beers Kathryn L. , Amis Eric J. , Henderson Lori
Published: August 2006

Using quantitative fluorescence microscopy in conjunction with a method of gradient substrate assembly established in their group, the authors were able to introduce and measure reproducible changes in cellular morphology and cell density by manipulating polymer grafting density. The mechanism behind this change in cellular behavior was explained by a semiempirical, geometric model that describes the effect of the spatial distribution of the polymer on protein attachment. A 10‐fold increase in graft density of poly(2‐hydroxyethyl methacrylate) [PHEMA] along the surface of a gradient sample, preexposed to bovine fibronectin, caused a change in the size of fibroblasts on the surface (i.e., cell spreading) from (1238 ± 704) to (377 ± 216) μm2. The results were in quantitative agreement with those obtained on three separate gradient samples. Both cellular response and fibronectin adsorption (as measured via ellipsometry) were found to vary sigmoidally with graft density of PHEMA, demonstrating the high degree of correlation between the two phenomena. A simple, rigid‐disk model accounting for the surface coverage of PHEMA was able to predict the amount of adsorbed fibronectin with a correlation coefficient of 0.97. Maximal cell adhesion and cell spreading were found to occur at fibronectin surface densities of 50 and 100 ng/cm2, respectively. The results demonstrate the role of gradient substrate assembly as a method for quantifying the relationship between protein and cellular response to technologically relevant polymeric materials. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006
Cultivation of MC3T3‐E1 cells on a newly developed material (Sponceram®) using a rotating bed system bioreactor
Authors: Suck Kirstin , Behr Larissa , Fischer Marcel , Hoffmeister Hans , van Griensven Martijn , Stahl Frank , Scheper Thomas , Kasper Cornelia
Published: August 2006

The influence of a 3D macroporous scaffold (Sponceram®) on the differentiation process into bone cells was investigated under static conditions in cell culture dishes. Furthermore, cultivations were performed using a new bioreactor system in the presence or absence of bone morphogenetic protein 2 (BMP‐2). Preosteoblastic MC3T3‐E1 cells were first cultured on Sponceram scaffolds in 96‐well dishes using standard medium, differentiation medium and BMP‐2 medium. Cell proliferation showed a similar course for all conditions used. Alkaline phosphatase (AP) activity resulted in a maximum at day 5 in the presence of BMP‐2. Two bioreactor cultivations were performed in a BIOSTAT® Bplus RBS (rotating bed system) 500 on Sponceram carrier discs. One cultivation was performed using standard medium. The second one was used with the same medium with BMP‐2 substituted. Significant calcification of the extracellular matrix in the presence of BMP‐2 occurred but even in the absence of BMP‐2 mineralization was observed. mRNA expression of collagen I, osteocalcin and bone sialoprotein was detected after both reactor cultivations. This study demonstrates that macroporous Sponceram is suitable for the cultivation and differentiation of MC3T3‐E1 cells into the osteoblastic phenotype. The results of the bioreactor cultivation revealed that the scaffold promoted the differentiation process even in the absence of BMP‐2. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2007
MRI of the kidney and urinary tract
Authors: Israel Gary M.
Published: August 2006

MRI of the kidney and urinary tract has evolved with advancements in MR technology combined with further radiologic experience. A combination of simple pulse sequences and the use of gadolinium (Gd) allow a comprehensive evaluation of the genitourinary system and facilitate the detection and accurate characterization of renal and urinary tract masses. In this review an MRI technique used to evaluate the kidneys and urinary tract is presented with an emphasis on the characterization of renal masses. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
A proteomic analysis during serial subculture and osteogenic differentiation of human mesenchymal stem cell
Authors: Sun Hyun Jin , Bahk Young Yil , Choi Yon Rak , Shim Jung Hye , Han Seung Hwan , Lee Jin Woo
Published: August 2006

Although previous studies have reported the effects of extensive subculturing on proliferation rates and osteogenic potential of human mesenchymal stem cells (hMSCs), the results remain controversial. The aim of our study was to characterize the proliferation and osteogenic potential of hMSCs during serial subculture, and also to identify proteins that are differentially regulated in hMSCs during serial subculture and osteogenic differentiation using proteome analysis. Here we show that the proliferation and osteogenic capacity of hMSCs decrease during serial subculturing. Several proteins were shown to be differentially regulated during serial subculture; among these the expression of T‐complex protein 1 α subunit (TCP‐1α), a protein known to be associated with cell proliferation, cell cycle, morphological changes, and apoptosis, gradually decreased during serial subculture. Among proteins that were differentially regulated during osteogenic differentiation, chloride intracellular channel 1 (CLIC1) was downregulated only during the early passages eukaryotic translation elongation factor, and acidic ribosomal phosphoprotein P0 was downregulated during the middle passages, while annexin V, LIM, and SH3 domain protein 1 (LASP‐1), and 14‐3‐3 protein gamma (YWHAG) were upregulated during the later passage. These studies suggest that differentially regulated passage‐specific proteins may play a role in the decrease of osteogenic differentiation potential under serial subculturing. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:2059–2071, 2006
Late Pleistocene and Holocene environmental changes in the coastal zone of northwestern Portugal
Authors: de Carvalho G. Soares , Granja H. M. , Loureiro E. , Henriques R.
Published: August 2006

This paper examines the Quaternary changes in the coastal zone of northwestern Portugal through the relationship between sediments and landforms. By interpolating the available data from geomorphology, lithostratigraphy, sedimentology and geochronology, it was possible to reconstruct existing palaeoenvironments, the oldest of which date back to the last interglacial. The main landforms are a high and a low platform bounded by scarps. River sands and silty sediments formed in a lacustrine environment (Antas Formation, MIS 5) are associated with the high platform. Two deposits are associated with the low platform: the Cepães Formation (MIS 3) consisting of a lower set of river sand beds and an upper gravel beach bed, and the Aguçadoura Formation (MIS 1) consisting of Holocene lagoonal beds. Copyright © 2006 John Wiley & Sons, Ltd.
Rheology Pathway to Macroscale Ordered Nanostructures of Polymeric Nanotemplates: Nanopores, Nanosheets and Nanofibers
Authors: Fahmi Amir W. , Gutmann Jochen S. , Vogel Roland , Gindy Nabil , Stamm Manfred
Published: August 2006

Summary: The creation of nanotemplates under dynamic shear flow conditions is described. The structures used are based on the self‐organization of comb‐coil‐like diblock copolymer systems with two intrinsic length scales, resulting from combining diblock copolymers with hydrogen‐bonding amphiphiles. Rheological data of polymeric supramolecular order formation are studied under oscillating shear flow conditions and it was observed that the order of the polymeric nanodomains can be extended to macroscopic distances. It is proposed that the key success factor to obtain highly ordered samples is to perform the orientation process using appropriate rheological conditions (temperature, frequency and strain) selected such that the ratio of the elastic component G′ to the viscous component G″ is larger than 1. This observation was used to select the rheological parameters for the three different samples investigated, where three different types of nanotemplates are observed after extracting the hydrogen‐bonding amphiphile; nanosheets, hollow cylinders and nanofibres. SAXS is primarily used to inspect the resulting structures. Additionally, AFM and TEM were utilized to image the morphologies and to further act as visual proof for the efficiency of the rheological orientation process.

AFM phase image of PS‐b‐P4VP nanosheets on Si wafer substrate after extracting the PDP.

magnified image

AFM phase image of PS‐b‐P4VP nanosheets on Si wafer substrate after extracting the PDP.
Kinetics of Cationic Photopolymerizations of UV‐Curable Epoxy‐Based SU8‐Negative Photoresists With and Without Silica Nanoparticles
Authors: Cho Jung‐Dae , Ju Hyoung‐Tae , Park Young‐Sik , Hong Jin‐Who
Published: August 2006

Summary: This paper reports on the photocuring kinetics of protonic‐acid‐initiated cationic polymerizations of UV‐curable epoxy‐based SU8‐negative photoresist systems with and without silica nanoparticles, as assessed using photo‐DSC, FTIR spectroscopy, UV‐vis spectroscopy, and SEM. Photo‐DSC analysis using an autocatalytic kinetic model demonstrated that the cross‐link density and cure rate increased as the concentration of silica nanoparticles with surface silanol groups increased to 2.5 wt.‐%. This result was confirmed by FTIR spectroscopy, and suggests that the presence of silica nanoparticles of up to 2.5 wt.‐% promoted the cure conversion and cure rate of the UV‐curable hybrid organic/inorganic negative photoresists due to the synergistic effect of silica nanoparticles acting both as an effective flow or diffusion‐aid agent and as a proton‐donor cocatalyst during the cationic photopolymerization process. The decrease in the cross‐link density that occurred when the silica content was higher than 2.5 wt.‐% was attributed to aggregation between silica nanoparticles due to their high surface energy.

SEM photograph at the film‐air interface of the UV‐cured hybrid organic/inorganic photoresist containing 10 wt.‐% silica nanoparticles.

magnified image

SEM photograph at the film‐air interface of the UV‐cured hybrid organic/inorganic photoresist containing 10 wt.‐% silica nanoparticles.
Front Cover: Macromol. Rapid Commun. 17/2006
Authors: Jinnai Hiroshi , Hasegawa Hirokazu , Nishikawa Yukihiro , Sevink G. J. Agur , Braunfeld Michael B. , Agard David A. , Spontak Richard J.
Published: August 2006

Front Cover: A block copolymer/homopolymer (AB/hA) blend exhibits coexisting bicontinuous morphologies, one ordered and the other disordered. Transmission electron microtomography is used to analyze the 3D features of both morphologies (right images), and complementary Mesodyn simulations identify the distributions of hA, A and B within the morphologies (lower images). Further details can be found in the article by H. Jinnai, H. Hasegawa,* Y. Nishikawa, G. J. A. Sevink, M. B. Braunfeld, D. A. Agard, and R. J. Spontak* on page 1424.
Back Cover: Macromol. Rapid Commun. 17/2006
Authors: Kudo Kazuaki , Yoshizawa Takuya , Hamada Takashi , Li Jun , Sakamoto Seiji , Shiraishi Shinsaku
Published: August 2006

Back Cover: Owing to a unique regiodifferentiating nature of an unsymmetric spirocyclic dianhydride, alternating copoly‐ (amide acid)s and copolyimides could be obtained in one‐pot. Constitutionally isomeric polymers were synthesized from common monomers by only changing the method of addition. Further details can be found in the article by K. Kudo,* T. Yoshizawa, T. Hamada, J. Li, S. Sakamoto, and S. Shiraishi on page 1430.
Effect of diffusion in inhomogeneous magnetic fields on balanced steady‐state free precession
Authors: Bieri O. , Scheffler K.
Published: August 2006

In this work, the effects of susceptibility variation from dilute, micron‐sized spherical field perturbers and diffusion on balanced steady‐state free precession (bSSFP) are analyzed. Predictions from Monte Carlo simulations are in good agreement with experiments and reveal that, for diffusing protons, susceptibility variation becomes apparent as a reduction in the overall bSSFP signal intensity. This reduction depends on microsphere parameters (radius and susceptibility difference), as well as on sequence‐related parameters (repetition time and flip angle) and on relaxation times. Specific Monte Carlo results from one set of parameter values can be extrapolated to another set of values by means of a scaling law and a substitution model. The scaling law, derived from the Bloch–Torrey equation, captures the dependencies of bSSFP signal reduction on susceptibility and diffusion‐related changes and on repetition time, whereas the substitution model describes those on flip angle and relaxation times. Copyright © 2006 John Wiley & Sons, Ltd.
Clustered generalized finite element methods for mesh unrefinement, non‐matching and invalid meshes
Authors: Duarte C. A. , Liszka T. J. , Tworzydlo W. W.
Published: August 2006

In spite of significant advancements in automatic mesh generation during the past decade, the construction of quality finite element discretizations on complex three‐dimensional domains is still a difficult and time demanding task.

In this paper, the partition of unity framework used in the generalized finite element method (GFEM) is exploited to create a very robust and flexible method capable of using meshes that are unacceptable for the finite element method, while retaining its accuracy and computational efficiency. This is accomplished not by changing the mesh but instead by clustering groups of nodes and elements. The clusters define a modified finite element partition of unity that is constant over part of the clusters. This so‐called clustered partition of unity is then enriched to the desired order using the framework of the GFEM.

The proposed generalized finite element method can correctly and efficiently deal with: (i) elements with negative Jacobian; (ii) excessively fine meshes created by automatic mesh generators; (iii) meshes consisting of several sub‐domains with non‐matching interfaces. Under such relaxed requirements for an acceptable mesh, and for correctly defined geometries, today's automated tetrahedral mesh generators can practically guarantee successful volume meshing that can be entirely hidden from the user. A detailed technical discussion of the proposed generalized finite element method with clustering along with numerical experiments and some implementation details are presented. Copyright © 2006 John Wiley & Sons, Ltd.
Exact dynamic stiffness matrix for a thin‐walled beam of doubly asymmetric cross‐section filled with shear sensitive material
Authors: Rafezy B. , Howson W. P.
Published: August 2006

An exact dynamic stiffness matrix is developed for the flexural motion of a three‐dimensional, bi‐material beam of doubly asymmetric cross‐section. The beam comprises a thin walled outer layer that encloses and works compositely with its shear sensitive core material. The outer layer may have the form of an open or closed section and provides flexural, warping and Saint‐Venant rigidity, while the core material provides Saint‐Venant and shear rigidity. The uniform distribution of mass in the member is accounted for exactly and thus necessitates the solution of a transcendental eigenvalue problem. This is accomplished using the Wittrick–Williams algorithm, which enables the required natural frequencies to be converged upon to any required accuracy with the certain knowledge that none have been missed. Such a formulation enables the powerful modelling features associated with the finite element technique to be utilized when establishing structural models. Three examples are included to validate and illustrate the method. The work also holds considerable potential in its application to the approximate analysis of asymmetric, multi‐storey, three‐dimensional wall‐frame structures. Copyright © 2006 John Wiley & Sons, Ltd.
Comparative proteomic studies on the pathogenesis of human ulcerative colitis
Authors: Hsieh Sen‐Yung , Shih Tsung‐Chieh , Yeh Chien‐Yuh , Lin Chun‐Jung , Chou Yun‐Ying , Lee Ying‐Shiung
Published: August 2006

Ulcerative colitis (UC) is a chronic inflammatory disorder primarily affecting the colon mucosa. Its etiology and pathogenesis remain unclear. We used 2‐DE and MS to identify differentially expressed proteins among the UC active, UC inactive, nonspecific colitis, and normal colon mucosa. Thirteen down‐regulated and six up‐regulated proteins were identified. Of the down‐expressed proteins, eight (heat‐shock protein 90 (HSPA9B), heat‐shock protein 60 (HSPD1), H+‐transporting two‐sector ATPase (ATP5B), prohibitin (PHB), mitochondrial malate dehydrogenase (MDH2), voltage‐dependent anion‐selective channel protein 1 (VDAC1), thioredoxin peroxidase (PRDX1), and thiol‐specific antioxidant (PRDX2)) were mitochondrial proteins, three (ATP5B, MDH2, triosephosphate isomerase) were involved in energy generation, three (PRDX1, PRDX2, SELENBP1) were cellular antioxidants, and six (HSPD1, HSPA9B, PRDX1, PRDX2, PHB, VDAC1) were stress‐response proteins. Transmission electron microscopy revealed pathological alterations of mitochondrial ultrastructures even before the global colonocyte changes in the UC colon mucosa. PHB, an essential mitochondrial component protein, was down‐expressed in the disease active as well as inactive colon mucosa from the patients of UC, indicative of an early event of mitochondrial changes during UC development. In contrast, aberrant activation of NFAT and ectopic expression of potential immunogenic proteins (tumor rejection antigen 1 and poliovirus receptor related protein 1) were found in the UC‐diseased colon mucosa. Our findings suggest the implications of colonocyte mitochondrial dysfunction and perturbed mucosa immune regulation in the pathogenesis of UC and provide potential targets for the development of a new therapy.
Effect of fungal polysaccharides on the modulation of plasma proteins in streptozotocin‐induced diabetic rats
Authors: Kim Sang Woo , Hwang Hye Jin , Kim Hyun Mi , Lee Myung Chul , Shik Lee Myung , Choi Jang Won , Yun Jong Won
Published: August 2006

To search out novel biomarkers for monitoring diabetes prognosis, we examined the effect of hypoglycemic fungal exopolysaccharides (EPS) on the differential levels of plasma proteins in streptozotocin‐induced diabetic rats. The orally administrated EPS exhibited an excellent hypoglycemic effect, lowering the average plasma glucose level, and increasing insulin secretion in diabetic rats. The 2‐DE analysis of rat plasma demonstrated that about 500 visualized spots were differentially regulated, of which 20 spots were identified as principal diabetes‐associated proteins. The distinct effect of diabetes induction on the pattern of rat plasma proteins includes the down‐regulation of albumin, apolipoprotein E (Apo E), α1‐inhibitor‐3, fetuin β, Gc‐globulin, hemopexin, vitronectin, and transthyretin (TTR) monomer, and the up‐regulation of Apo A‐I, Apo A‐IV, ceruloplasmin, α1‐antitrypsin, serine protease inhibitor III, and transferrin. Those protein levels were interestingly restored to those of healthy rats by EPS treatment, although the order of magnitude of the changes differed widely. Two proteins of interest showed distinct differential expression with opposite trends: TTR tetramer was significantly down‐regulated and immunoglobulin (Ig) kappa light chain was significantly up‐regulated upon diabetes induction, both of which were also normalized to those of healthy groups after EPS treatment.
Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis
Authors: Zhang Xuequn , Guo Yuanbiao , Song Yanping , Sun Wei , Yu Chaohui , Zhao Xiaohang , Wang Hongyang , Jiang Hongchi , Li Youming , Qian Xiaohong , Jiang Ying , He Fuchu
Published: August 2006

Normal Chinese Liver Proteome Expression Profile is one of the major parts of Human Liver Proteome Project. Before starting the studies, it is necessary to examine the interindividual variation of normal liver proteome and evaluate the minimal size of samples for proteomic analysis. In this study, normal liver samples from ten individual volunteers were collected and the proteome profiles of these samples were analyzed using 2‐D difference gel electrophoresis (DIGE) combined with MALDI‐TOF/TOF MS. The individual liver tissue lysates were labeled with Cy3 and Cy5 while the pooled sample was labeled with Cy2 as an internal standard, which minimized gel‐to‐gel variation. After analysis by the DeCyder software, up to 2056 protein spots were detected on the master gel. The CV of standardized abundance was calculated for the protein spots that were matched across all ten gels. The CV values of these protein spots ranged from 6.4 to 108.5% and the median CV was ∼19%, which demonstrated that the protein expression of normal liver among different individuals was relatively stable. The eight proteins with CV values over 50% were identified which would be a caveat when considering these proteins as potential disease‐related markers. Moreover, the one‐way ANOVA feature showed a correlation between sample size and individual variations. The results showed that when the sample size exceeded 7, the individual variations were not significant to the whole pool. Our results are an important basis for liver protein expression profiles and comparative proteomics of liver disease.
Mechanism and kinetics of dithiobenzoate‐mediated RAFT polymerization. I. The current situation
Authors: Barner‐Kowollik Christopher , Buback Michael , Charleux Bernadette , Coote Michelle L. , Drache Marco , Fukuda Takeshi , Goto Atsushi , Klumperman Bert , Lowe Andrew B. , Mcleary James B. , Moad Graeme , Monteiro Michael J. , Sanderson Ronald D. , Tonge Matthew P. , Vana Philipp
Published: August 2006

Investigations into the kinetics and mechanism of dithiobenzoate‐mediated Reversible Addition–Fragmentation Chain Transfer (RAFT) polymerizations, which exhibit nonideal kinetic behavior, such as induction periods and rate retardation, are comprehensively reviewed. The appreciable uncertainty in the rate coefficients associated with the RAFT equilibrium is discussed and methods for obtaining RAFT‐specific rate coefficients are detailed. In addition, mechanistic studies are presented, which target the elucidation of the fundamental cause of rate retarding effects. The experimental and theoretical data existing in the literature are critically evaluated and apparent discrepancies between the results of different studies into the kinetics of RAFT polymerizations are discussed. Finally, recommendations for further work are given. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5809–5831, 2006
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins
Authors: Yu Haibo , Kohl Andreas , Binz H. Kaspar , Plückthun Andreas , Grütter Markus G. , van Gunsteren Wilfred F.
Published: August 2006

Two designed ankyrin repeat (AR) proteins (E3_5 and E3_19) are high homologous (with about 87% sequence identity) and their crystal structures have a Cα atom‐positional root‐mean‐square difference of about 0.14 nm. However, it was found that E3_5 is considerably more stable than E3_19 in guanidinium hydrochloride and thermal denaturation experiments. With the goal of providing insights into the various factors contributing to the stabilities of the designed AR proteins and suggesting possible mutations to enhance their stabilities, homology modeling and molecular dynamics (MD) simulations with explicit solvent have been performed. Because the crystal structure of E3_19 was solved later than that of E3_5, a homology model of E3_19 based on the crystal structure of E3_5 was also used in the simulations. E3_5 shows a very stable trajectory in both crystal and solution simulations. In contrast, the C‐terminal repeat of E3_19 unfolds in the simulations starting from either the modeled structure or the crystal structure, although it has a sequence identical to that of E3_5. A continuum electrostatic model was used to estimate the effect of single mutations on protein stability and to study the interaction between the internal ARs and the C‐terminal capping AR. Mutations involving charged residues were found to have large effects on stability. Due to the difference in charge distribution in the internal ARs of E3_19 and E3_5, their interaction with the C‐terminal capping AR is less favorable in E3_19. The simulation trajectories suggest that the stability of the designed AR proteins can be increased by optimizing the electrostatic interactions within and between the different repeats. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Specificity of molecular interactions in transient protein–protein interaction interfaces
Authors: Cho Kyu‐il , Lee KiYoung , Lee Kwang H. , Kim Dongsup , Lee Doheon
Published: August 2006

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein–protein heterocomplexes. This is the first approach to analyze protein–protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein–protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein–protein interface. We analyze the 131 interfaces of transient protein–protein heterocomplexes in PDB: 33 protease‐inhibitors, 52 antibody‐antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G‐protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are Cα H···OC interaction, cation···anion interaction, amine···amine interaction, and amine···cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave‐one‐out cross‐validation at k = 15. Of these four interaction types, CαH···OC shows binding specificity for protease‐inhibitor complexes, while cation–anion interaction is predominant in signaling complexes. The amine ··· amine and amine···cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody–antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease‐inhibitors and sig‐naling proteins have optimized their interfaces to suit their biological functions, antibody–antigen interactions are the happenstance, implying that antibody–antigen complexes do not show distinctive interaction types. Persistent interaction types such as π···π, amide‐carbonyl, and hydroxyl‐carbonyl interaction, are also investigated. Analyzing the structural orientations of the π···π stacking interactions, we find that herringbone shape is a major configuration in transient protein–protein interfaces. This result is different from that of protein core, where parallel‐displaced configurations are the major configuration. We also analyze overall trend of amide‐carbonyl and hydroxyl‐carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl‐carbonyl interactions. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Spectroscopic ellipsometry study of FePt nanoparticle films
Authors: Lee S. J. , Lo C. C. H. , Yu A. C. C. , Fan M.
Published: August 2006

The optical properties of a FePt nanoparticle film were investigated using spectroscopic ellipsometry. The FePt nanoparticle film of thickness about 15 nm was prepared by deposition of FePt nanoparticles directly on a Si substrate. The nanoparticle film was annealed at 600 °C in vacuum for two hours before the measurements. The optical properties of the FePt nanoparticle film showed distinctively different spectra from those obtained from the bulk and thin film FePt samples, in particular in the low photon energy range (below 3.5 eV) where the nanoparticle film exhibited a relatively flat refractive index and a substantially lower extinction coefficient than the bulk and epitaxial thin film samples. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Studies of quantum levels in GaInNAs single quantum wells
Authors: Shirakata Sho , Kondow Masahiko , Kitatani Takeshi
Published: August 2006

Spectroscopic studies have been carried out on the quantum levels in GaInNAs/GaAs single quantum wells (SQWs). Photoluminescence (PL), PL excitation (PLE), photoreflectance (PR), and high‐density‐excited PL (HDE‐PL) were measured on high quality GaInNAs SQWs, Ga0.65In0.35N0.01As0.99/GaAs (well thickness: l z = 10 nm) and Ga0.65In0.35N0.005As0.995/GaAs (l z = 3∼10 nm), grown by molecular‐beam epitaxy. For Ga0.65In0.35N0.01As0.99/GaAs (l z = 10 nm), PL at 8 K exhibited a peak at 1.07 eV due to the exciton‐related transition between quantum levels of ground states (e1–hh1). Both PR and PLE exhibited three transitions (1.17, 1.20 and 1.32 eV), and the former two transitions were assigned to as either of e1–lh1 and e2–hh2 transitions, while the transition at 1.32 eV was assigned to as the e2–lh2 transition. For HDE‐PL, a new PL peak was observed at about 1.2 eV, and it was assigned to the unresolved e1–lh1 and e2–hh2 transitions. Similar optical measurements have been done on the Ga0.65In0.35N0.005As0.995/GaAs with various l z (3∼10 nm). Dependence of optical spectra and energies of quantum levels on l z have been studied. It has been found that HDE‐PL in combination with PLE is a good tool for the study of the quantum level of GaInNAs SQW. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)