bluuebunny/crossref_metadata_2025 huggingface dataset:
Extraction with Spinodal Decomposition – Experiment and Simulation
Authors: Arce J. C. , Schaadt A. , Bart H.‐J.
Published: March 2006

Experimental results on the growth and velocity of droplets (up to 0.45 mm/s) during the temperature‐induced phase separation of the 3‐methoxypropionitrile/water solvent system as well as a variety of theoretical methods used to study the demixing dynamics are presented. Due to computational costs, the simulation with Molecular Dynamics (MD) is feasible only for very short times (ps) and miniscule boxes (Å). Dissipative Particle Dynamics (DPD), where a coarse‐grained model of the system is employed, allows nanosecond simulations in a box with more than 13 million atoms in a diffusion‐dominated regime. Finally, the influence of the diffusion/convection ratio during the separation in the μs scale is studied by use of a code based on Model H for both instantaneous and non‐instantaneous quenching cases. Structural information and macroscopic parameters, such as interfacial tension, can be derived from the molecular simulations.
Experimental Investigation and Modeling of Adsorption of Water and Ethanol on Cornmeal in an Ethanol‐Water Binary Vapor System
Authors: Chang H. , Yuan X.‐G. , Tian H. , Zeng A.‐W.
Published: March 2006

The adsorption capacity of water and ethanol on cornmeal in an ethanol‐water binary vapor system was investigated in a fixed‐bed apparatus for ethanol dehydration. Experiments were performed at temperatures of 82–100 °C for different relative humidities of ethanol‐water vapor. Adsorption equilibrium models, including those based on the adsorption potential theory of Polanyi and Sircar's model, have been used to fit the experimental data for water adsorption on cornmeal, and all gave good fits. For ethanol adsorption, pseudo‐equilibrium was defined as the mass adsorbed on the cornmeal within the time needed for the equilibrium for water on the same adsorbent. Based on this limiting condition, adsorption behaviors and mechanisms were analyzed.
Synthesis of Small Tripeptide Molecules through a Catalysis Sequence Comprising Metathesis and Aminohydroxylation
Authors: Streuff Jan , Nieger Martin , Muñiz Kilian
Published: March 2006

Tripeptidic structures were synthesized by using a combination of two independent consecutive catalytic procedures. Cross‐metathesis of N‐acroyl amino acid esters yields fumaric amide compounds with exclusive E double‐bond geometry. This represents an unprecedented example of complete double‐bond selectivity in this kind of reaction. A subsequent asymmetric aminohydroxylation of the chiral fumaric amides was carried out without the need of any further ligand and gave high yields and no side products. This reaction transforms the central fumaric amide unit into a hydroxy aspartic acid moiety and relies on the inherent stereochemistry of the starting fumaric diamides. An additional feature of our sequence is the ease of generating stereochemical diversification within the aminohydroxylation reaction. As a consequence, rapid conformational and configurational diversification can be achieved from the overall two‐step catalytic sequence. The versatility of this approach is demonstrated by starting from two different N‐acroyl amino esters, which led to the synthesis of eight structurally and stereochemically different tripeptides that could all be identified individually. As such, the present two‐step catalytic approach should serve to efficiently synthesize large families of tripeptidic molecular probes.
Addition of Carbenes to the Sidewalls of Single‐Walled Carbon Nanotubes
Authors: Bettinger Holger F.
Published: March 2006

The addition of carbenes CX2 (X=H, Cl) to single‐walled carbon nanotubes (SWNTs) was investigated by density functional theory and finite, hydrogen‐terminated nanotube clusters or periodic boundary conditions in conjunction with basis sets of up to polarized triple‐ζ quality. For armchair [(3,3) to (12,12)] and zigzag tubes [(3,0) to (18,0)], reaction of CH2 with the CC bond oriented along the tube axis (A) is less exothermic than with those CC bonds having circumferential (C) orientation. This preference decreases monotonically with increasing tube diameter for armchair, but not for zigzag tubes; here, tubes with small band gaps have a very low preference for circumferential addition. Axial addition results in cyclopropane products, while circumferential addition produces “open” structures for both armchair and zigzag tubes. The barriers for addition of dichlorocarbene to a (5,5) SWNT, studied for a finite C90H20 cluster, are higher than that for addition to C60, in spite of similar diameters of the carbon materials. Whereas addition of CCl2 to [60]fullerene proceeds in a concerted fashion, addition to a (5,5) armchair SWNT is predicted to occur stepwise and involve a diradicaloid intermediate according to B3LYP, PBE, and GVB‐PP computations. Addition to C bonds of (5,5) armchair tubes resulting in the thermodynamically more stable insertion products is kinetically less favorable than that to A bonds yielding cyclopropane derivatives.
Structure and Total Synthesis of Aspernigerin: A Novel Cytotoxic Endophyte Metabolite
Authors: Shen Li , Ye Yong‐Hao , Wang Xiao‐Ting , Zhu Hai‐Liang , Xu Chen , Song Yong‐Cun , Li Hai , Tan Ren‐Xiang
Published: March 2006

Aspernigerin (1), a novel cytotoxic alkaloid consisting of an unprecedented structural framework has been isolated from the extract of a culture of Aspergillus niger IFB‐E003, an endophyte in Cyndon dactylon. Its structure was elucidated on the basis of comprehensive NMR spectral analysis and confirmed by single‐crystal X‐ray analysis. Aspernigerin (1) has been shown to be cytotoxic to the tumor cell lines nasopharynyeal epidermoid KB, cervical carcinoma Hela, and colorectal carcinoma SW1116 with corresponding IC50 values of 22, 46, and 35 μM, respectively. A feasible total synthetic route for aspernigerin (1) has been established for further pharmacological research.
Vacuum‐ultraviolet circular dichroism analysis of biomolecules
Authors: Gekko Kunihiko , Matsuo Koichi
Published: March 2006

The vacuum‐ultraviolet circular dichroism (VUVCD) spectra of various amino acids, saccharides, and proteins were measured using a synchrotron‐radiation CD spectrophotometer at HiSOR/HSRC that is capable of measuring the CD spectra down to 140 nm in aqueous solution. L‐Isomers of amino acids show two successive positive peaks at around 200 and 180 nm depending on the side chain. The ab initio assignment by time‐dependent density functional theory predicts that these peaks are attributed to n–π* and π–π* transitions of the carboxyl group, respectively. Most mono‐ and disaccharides exhibit characteristic peaks at around 170 nm, sensitively depending on the anomeric and axial/equatorial configurations of hydroxyl groups, trans‐gauche conformations of the hydroxymethyl group, and the type of glycosidic linkage. The VUVCD spectra of 31 globular proteins allow us to estimate more accurately the content and number of α‐helix and β‐strand segments by extending the short‐wavelength limit of the analytical program SELCON3 down to 160 nm. These results demonstrate that synchrotron‐radiation VUVCD spectroscopy is a useful tool for structure analyses of biomolecules in solution based on the higher energy transitions of chromophores. Chirality, 2006. © 2006 Wiley‐Liss, Inc.
Absolute configurations of brominated sesquiterpenes determined by vibrational circular dichroism
Authors: Monde Kenji , Taniguchi Tohru , Miura Nobuaki , Vairappan Charles S. , Suzuki Minoru
Published: March 2006

Two brominated sesquiterpenes, majapolene B (1) and acetylmajapolene B (2), isolated from the red algal genus Laurencia were investigated using vibrational circular dichroism (VCD). The ab initio theoretical VCD and IR calculations of 1 and 2 were performed by density functional theory (DFT) using the B3PW91/6–31G(d,p) basis set. The experimental VCD spectra and corresponding population‐weighted theoretical VCD spectra were found to be in excellent agreement in CCl4 solution in the 1800–850 cm−1 region, which allowed unambiguous determination of the absolute configurations of (−)‐1 and (−)‐2 as 7S,10S and 7S,10S, respectively. Chirality, 2006. © 2006 Wiley‐Liss, Inc.
First‐principles calculations of protein circular dichroism in the far‐ultraviolet and beyond
Authors: Oakley Mark T. , Bulheller Benjamin M. , Hirst Jonathan D.
Published: March 2006

Understanding the relationship between the amino acid sequence of a protein and its unique, compact three‐dimensional structure is one of the grand challenges in molecular biophysics. One exciting approach to the protein‐folding problem is fast time‐resolved spectroscopy in the ultra‐violet (UV). Time‐resolved electronic circular dichroism (CD) spectroscopy offers resolution on a nanosecond (or faster) timescale, but does not provide the spatial resolution of techniques like X‐ray crystallography or NMR. There is a need to underpin fast timescale spectroscopic studies of protein folding with a stronger theoretical foundation. We review some recent studies in this regard and briefly highlight how modern quantum chemical models of aromatic groups have improved the accuracy of calculations of protein CD spectra near‐UV. On the other side of the far‐UV, we describe calculations indicating that charge‐transfer transitions are likely to be responsible for bands observed in the vacuum UV in protein CD. Chirality 18:340–347, 2006. © 2006 Wiley‐Liss, Inc.
Protocols for the analysis of theoretical optical rotations
Authors: Polavarapu Prasad L.
Published: March 2006

The availability of sophisticated quantum mechanical methods for predicting molecular optical rotations has revolutionized the determination of molecular stereochemistry. However, the objectives and approaches used for the applications of optical rotation vary from one laboratory to the other. With the number of applications of optical rotation increasing at an unprecedented rate, it is considered necessary to discuss the protocols for the general use of optical rotations predicted with quantum mechanical methods. A summary of the quantum mechanical methods for predicting optical rotations and protocols for the use of predicted optical rotations are presented in this article. Chirality, 2006. © 2006 Wiley‐Liss, Inc.
For most large underdetermined systems of linear equations the minimal 𝓁1‐norm solution is also the sparsest solution
Authors: Donoho David L.
Published: March 2006

We consider linear equationsy= Φxwhereyis a given vector in ℝnand Φ is a givenn×mmatrix withn 0 so that for largenand for all Φ's except a negligible fraction, the following property holds:For every y having a representation y= Φx0by a coefficient vector x0∈ ℝmwith fewer than ρ · n nonzeros, the solution x1of the𝓁1‐minimization problemis unique and equal to x0. In contrast, heuristic attempts to sparsely solve such systems—greedy algorithms and thresholding—perform poorly in this challenging setting. The techniques include the use of random proportional embeddings and almost‐spherical sections in Banach space theory, and deviation bounds for the eigenvalues of random Wishart matrices. © 2006 Wiley Periodicals, Inc.
Coordination Mode of the Zinc(II) and Cadmium(II) Cations with N‐(Diisopropoxyphosphoryl)thiobenzamide
Authors: Sokolov Felix D. , Safin Damir A. , Zabirov Nail G. , Brusko Vasiliy V. , Khairutdinov Bulat I. , Krivolapov Dmitry B. , Litvinov Igor A.
Published: March 2006

Reaction of the potassium salt of N‐(diisopropoxyphosphoryl)thiobenzamide (iPrO)2P(O)NHC(S)C6H5 (HL) with ZnII and CdII cations in aqueous EtOH leads to three different complexes: [Zn(L‐O,S)2] (1), [Cd2(L‐O,S)4] (2) and [Cd(HL‐O)2(L‐O,S)2] (3). The structures of these compounds were investigated by single‐crystal X‐ray diffraction analysis, EI‐MS and ES‐MS, IR, 1H, 13C and 31P NMR spectroscopy and microanalysis. The zinc(II) atom in complex 1 is in a distorted tetrahedral ZnO2S2 environment formed by the C=S sulfur atoms and the P=O oxygen atoms of two deprotonated ligands. The cadmium(II) complex 2 is centrosymmetric and consists of dimeric species. Two [Cd(L‐O,S)2] moieties are connected by two bridging [S–Cd–S] units through the sulfur atoms of the ligand C=S groups. Complex 2 has a distorted trigonal‐bipyramidal Cd(Oax)2(Seq)3 core. Complex 3 has a tetragonal‐bipyramidal environment, Cd(Oax)2(Oeq)2(Seq)2, and two neutral ligand molecules are coordinated in the axial positions through the oxygen atoms of the P=O groups. The base of the bipyramid is formed by two anionic ligands in a typical 1,5‐O,S coordination mode. The ligands are in a trans configuration. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Proteomics‐driven progress in neurodegeneration research
Authors: Fountoulakis Michael , Kossida Sophia
Published: March 2006

Proteomics technologies have been widely used in the investigation of neurodegenerative and psychiatric disorders, and in particular in the detection of differences between healthy individuals and patients suffering from such diseases. Thus, brain and cerebrospinal fluid (CSF) samples from patients with Alzheimer's disease, Down syndrome, Pick's disease, Parkinson's disease, schizophrenia, and other disorders as well as brain and CSF from animals serving as models of neurological disorders have been analyzed by proteomics. 2‐DE followed by MALDI‐TOF‐MS has been mainly applied as this proteomics approach provides the possibility of convenient quantification of protein levels and detection of post‐translational modifications. About 330 unique proteins with deranged levels and modifications have been detected by proteomics approaches to be related to neurodegeneration and psychiatric disorders. They are mainly involved in metabolism pathways, cytoskeleton formation, signal transduction, guidance, detoxification, transport, and conformational changes. In this article, we provide a summary of the major contributions of proteomics technologies in the study of neurodegenerative and psychiatric diseases, in particular, in the detection of changes in protein levels and modifications related to these disorders.
Ligand exchange capillary electrophoresis by cyclodextrin derivatives, a powerful tool for enantiomeric separations
Authors: Cucinotta Vincenzo , Giuffrida Alessandro , Maccarrone Giuseppe , Messina Marianna , Vecchio Graziella
Published: March 2006

Five pure CD derivatives synthesized in our laboratory were used as chiral selectors in the presence of copper(II) ion. Three enantiomeric pairs of amino acids were submitted to separation experiments in CE, by exploiting the ligand exchange mechanism. The results obtained in the investigated systems, together with those of the analogous systems previously studied, clearly show the usefulness of this technique in chiral separations. By comparing the ligand exchange CE results with potentiometric results, either reported elsewhere or studied here for the first time (system Cu/CDampy/tyrosine), it has been possible to rationalise the separation results. The importance of the availability of pure selectors, and to characterise them both spectroscopically and thermodynamically is discussed.
Reactor Performance in the Presence of Catalyst Deactivation
Authors: Flaschel E.
Published: March 2006

The main variable of enzymatic processes is often found to be the operating temperature. An increase in temperature leads to higher rates for the catalytic transformation. However, beyond a certain temperature catalyst deactivation is winning the game. Therefore, processes should be optimized in order to determine the temperature which leads to a minimal demand of enzyme preparation. For the prediction of such optimal reactor operation, modeling of the temperature dependence of the process has to be performed. Examples of such modeling are given for the hydrolysis of lactose in UHT milk by means of three different β‐galactosidases – those from Aspergillus oryzae, Kluyveromyces lactis, and Escherichia coli. The reaction kinetics for a constant initial lactose concentration can be described by a model of two parameters, of which only one depends on temperature. For the lactase of E. coli the reaction can be described as a simple reaction with first order kinetics. The deactivation mechanism includes a reversible as well as an irreversible path of denaturation. The temperature dependent parameters follow Arrhenius' and van't Hoff's law, respectively. On the basis of their particular reaction models all three enzymes can be compared with respect to their optimum use. The models have been verified under laboratory conditions and have shown their usefulness for the prediction of optimum operating variables. Quite remarkable features have been found for the lactase of E. coli.
Optimization and Control of Industrial Microbial Cultivation Processes
Authors: Jenzsch M. , Simutis R. , Lübbert A.
Published: March 2006

Compared to the immense achievements in fundamental molecular biological sciences, the improvements in the fermentation and downstream processing technologies used in industry have been less spectacular over the last decade. Hence, there is a misbalance between new cellular systems and production technologies, resulting in a decreasing annual rate of approved production processes. In its PAT initiative the U.S. Food and Drug Administration identifies the potential for continuous improvement and makes concrete suggestions how this can be achieved. Here, some of these suggestions were applied to recombinant protein production with Escherichia coli and Pichia pastoris cultures. Concretely, the development of process operational procedures is discussed that allow a more tight supervision of the processes and the automatic control in cases where processes deviate from their set‐point profiles.
Optimization of Reaction Parameters and Cultivation Conditions for Biocatalytic Hydrogen Transfer Employing Overexpressed ADH‐‘A’ from Rhodococcus ruber DSM 44541 in E. coli
Authors: Edegger K. , Gruber C. C. , Faber K. , Hafner A. , Kroutil W.
Published: March 2006

The alcohol dehydrogenase ADH‐‘A’ from Rhodococcus ruber DSM 44541 represents a highly efficient catalyst for biocatalytic hydrogen transfer reactions. Starting from an exceedingly low level of active ADH‐‘A’ in Escherichia coli, the apparent specific activity of ADH‐‘A’ overexpressed in E. coli cells could be drastically enhanced by a factor of 550 by optimizing the host and induction/growth conditions. The influence of reaction parameters like pH, cosubstrate (2‐propanol, acetone) concentration, substrate concentration temperature and additional cofactor on the apparent activity was investigated. In contrast to the purified enzyme, the pH optimum for oxidation and reduction were identical. Due to the employment of whole cells of E. coli/ADH‐‘A’ as catalyst lower operational stability was found.
Reaction Engineering Aspects of Microbial Mercury Removal
Authors: Leonhäuser J. , Röhricht M. , Wagner‐Döbler I. , Deckwer W.‐D.
Published: March 2006

Mercury‐resistant microorganisms are widespread in natural environments and can effectively be used to demercurize Hg(II)‐contaminated wastewaters as was already demonstrated on an industrial scale. The aim of this paper is to find the performance limits with regard to Hg(II) loadings D cHg,in (dilution rate × Hg(II) inlet concentration) and residual Hg(II) at the reactor outlet and to provide a reasonable basis for an optimal and safe process design. To this end, comprehensive studies were carried out with different single microbes (natural isolates and a genetically engineered strain) as well as microbial consortia in batch and continuous stirred reactors and fixed beds with microorganisms immobilized as films. The rate of the biotransformation (reduction of inorganically and organically bound Hg(II) to elemental Hg(0)) was found to follow a uniform mechanism with inhibition kinetics (Haldane type). Both reactor types are able to cope with high Hg(II) loadings and yield conversions up to 98 %. The stirred vessel is particularly suited for high cHg,in but restricted to low D (D < μmax), while the fixed bed can be operated at high D, say 10 h–1, but can only deal with cHg,in < 10 mg/L due to the limited Hg(II) tolerance of microorganisms. The loading limitations can be removed by appropriate recycle flows for both reactor types. However, irrespective of reactor type used, the residual Hg at the outlet cannot be reduced below the legal discharge limit (50 μg/L) mainly owing to the adsorption of Hg(II) on biomass. Therefore, a separation step following the reactor is required (sand bed, activated carbon filter). Comparing the reactor types exhibits the superiority of the fixed bed system due to its simpler construction, easier operation and higher cost effectiveness. Furthermore, the fixed bed shows better flexibility and robustness to extreme loadings. This justifies a posteriori the choice of a fixed bed reactor applied in the technical process.
Easy Access to Enantiomerically Pure Nonproteinogenic Amino Acids
Authors: Laumen K. , Ghisalba O.
Published: March 2006

The protease from Bacillus licheniformis (alcalase) shows a remarkable broad substrate tolerance and high enantioselectivity against nonproteinogenic racemic amino acid derivatives. N‐acetyl protected amino acid esters of mono‐, di‐ or tri‐substituted phenyl alanines and even tert.‐leucine were hydrolyzed with high enantioselectivity. The obtained mixtures of (S)‐N‐acetyl amino acid and (R)‐N‐acetyl amino acid ester can easily be separated. The R‐ or S‐amino acids were obtained by acidic cleavage of the optically pure derivatives or the (R)‐ester was racemized by treatment with potassium t‐butylate.
Selective Recovery of Carbohydrates from Aqueous Solution Facilitated by a Carrier
Authors: Hameister D. , Kragl K.
Published: March 2006

Carbohydrate recovery is an active area of supramolecular chemistry, motivated by the biological importance of saccharides as well as the unusual challenge presented by these complex substances. The recovery of carbohydrates from aqueous media is a difficult separation problem due to the large, irregular and multivalent structure and the low solubility of carbohydrates in organic solvents. A method for the selective recovery of mono‐ and disaccharides from aqueous media has been developed. The use of different organic solvents like butanol, methyl tertiary‐butyl ether (MTBE), n‐hexane or toluene for liquid‐liquid extraction of carbohydrates was investigated. This extraction process is facilitated by a carrier, i.e., primary amines such as cyclooctylamine. The influence of different parameters (temperature, amine concentration, extraction time) on the efficiency of the extraction was studied. Recovery rates up to 40 % are possible in a one‐stage process. Selectivities range from 1.3 up to 875.4.
Electroenzymatic Synthesis of Chiral Sulfoxides
Authors: Kohlmann C. , Lütz S.
Published: March 2006

Chloroperoxidase (CPO) from Caldariomyces fumago (E.C. 1.11.1.10) is able to enantioselectively oxidize various sulfides to the corresponding (R)‐enantiomer of the sulfoxides. For these oxidations the enzyme requires an oxidant. Most commonly, tert‐butyl hydroperoxide (TBHP) and hydrogen peroxide are used. As it is known that these oxidants inactivate the enzyme, the enzymatic reaction was combined with the electrochemical in situ generation of hydrogen peroxide. As substrates for this combination of an enzymatic and an electrochemical reaction methyl p‐tolyl sulfide, 1‐methoxy‐4‐(methylthio)benzene and N‐MOC‐L‐methionine methyl ester were used to carry out batch experiments.
Horseradish Peroxidase Combined With Oxidase Enzymes a Valuable Bioanalytical Tool: Lactate Oxidase – A Case Study
Authors: Vojinovic V. , Bertin L. , Cabral J. M. S. , Fonseca L. P.
Published: March 2006

Enzymatic biosensors have been extensively investigated for real‐time bioprocess monitoring and other online analysis. However, implementation of biosensors has been strongly hindered by their limited stability. This work reports a significant improvement of the stability of the immobilized oxidases by in situ reduction of the harmful H2O2. Thus, stabilized oxidases can serve as the basis for ethanol, glucose, and lactate sensors, with the ability to operate for long periods of time with virtually no change in activity. As an example, a lactate sensor, containing lactate oxidase aimed for bioprocess monitoring, has been described and characterized. Operational stabilities that allow up to 8 h continuous lactate conversion with virtually no activity loss have been achieved. The described system based on the in situ stabilization strategy is a promising new tool for the development of online analyses.
Comparative Study of Cyanobacteria as Biocatalysts for the Asymmetric Synthesis of Chiral Building Blocks
Authors: Havel J. , Weuster‐Botz D.
Published: March 2006

The three representative cyanobacteria, Synechococcus PCC7942, Anabaena variabilis, and Nostoc muscorum, were studied for their ability to asymmetrically reduce the prochiral ketones 2′‐3′‐4′‐5′‐6′‐pentafluoroacetophenone, ethyl 4‐chloroacetate, 4‐chloroacetophenone, and ethylbenzoylacetate to the corresponding chiral alcohols. Photosynthesis as well as respiration was applied for intracellular regeneration of the NAD(P)H cofactor. It was shown for the first time that all cyanobacteria were able to reduce the prochiral ketones asymmetrically without light for cofactor regeneration. By comparison of the cell specific product formation capacities of cyanobacteria with typical heterotrophic whole cell biocatalysts in batch processes, it is shown that comparable or, in some cases, better performances at high enantiomeric excess (ee > 99.8 %) are obtained. As a consequence of a generally strong product inhibition, in situ product removal must be applied in order to restore process efficiency when using cyanobacteria as biocatalysts.
From Enzyme Kinetics to Metabolic Network Modeling – Visualization Tool for Enhanced Kinetic Analysis of Biochemical Network Models
Authors: Oldiges M. , Noack S. , Wahl A. , Qeli E. , Freisleben B. , Wiechert W.
Published: March 2006

Model‐based analysis of enzyme kinetics allows the determination of optimal conditions for their use in biocatalysis. For biotransformations or fermentative approaches the modeling of metabolic pathways or complex metabolic networks is necessary to obtain model‐based predictions of steps which limit product formation within the network. To set up adequate kinetic models, relevant mechanistic information about enzyme properties is required and can be taken from in vitro studies with isolated enzymes or from in vivo investigations using stimulus‐response experiments which provide a lot of kinetic information about the metabolic network. But with increasing number of reaction steps and regulatory interdependencies in the network structure the amount of simulation data dramatically increases and the simulation results from the dynamic models become difficult to analyze and interpret. Demonstrated for an Escherichia coli model of the central carbon metabolism, methods for visualization and animation of simulation data were applied and extended to facilitate model analysis and biological interpretation. The dynamic metabolite pool and metabolic flux changes were visualized simultaneously by a software tool. In addition, a new quantification method for enzyme activation/inhibition was proposed, and this information was implemented in the metabolic visualization.
Evaluation of the AERMOD dispersion model as a function of atmospheric stability for an urban area
Authors: Kumar Ashok , Dixit Shobhit , Varadarajan Charanya , Vijayan Abhilash , Masuraha Anand
Published: March 2006

The AERMOD dispersion model was used to compute ambient air concentrations of SO2 for 1‐, 3‐, and 24‐h averaging periods using the emission inventory data for Lucas County, Ohio for the year 1990. The estimated concentrations were classified based on the stability parameter, Monin–Obukhov length (L), for the two monitoring stations located in the area. The data were divided into two atmospheric stability classes (stable and convective cases) as used in the AERMOD model. These categories were further grouped into five subcategories based on the value of L to learn about fine details of model performance. The model evaluation was done using several statistical parameters used in air quality studies.

AERMOD did not yield a satisfactory performance in predicting 1‐ and 3‐h average concentrations for the multisource region but showed a slightly better performance in predicting the 24‐h concentrations using urban option for the land use parameters. The model had a tendency to underpredict in both the stable and convective cases. In the 24‐h averaging period factor of two (Fa2) values suggested a better performance than fractional bias (FB). The model seemed to perform better for the Main Street station than the Collins Park station. Limited analysis using different land use parameters reported in the paper indicates that model performance may improve for certain cases. Other errors include the unavoidable scatter arising from differences between wind direction and actual transport for an averaging period, formulation of the model, and the emission inventory. The results of the study should be used cautiously because of the limited scope of the evaluation. Future work should focus on the role of land use parameters in predicting concentrations at the monitors and finding ways to quantify errors attributed to other factors. However, it is clear that more guidance is needed to apply the AERMOD model for multisource regions. Alternative schemes to divide the data should also be considered for analyzing model performance. © 2006 American Institute of Chemical Engineers Environ Prog, 2006
Evolution of channel morphology and hydrologic response in an urbanizing drainage basin
Authors: Nelson Peter A. , Smith James A. , Miller Andrew J.
Published: March 2006

The Dead Run catchment in Baltimore County, Maryland, has undergone intense urbanization since the late 1950s. Reconstruction of the channel planform from topographic maps dating back to the 1890s and aerial photographs dating back to the 1930s indicates that the channel has remained stable in planform since at least the 1930s. The relative stability of Dead Run contrasts with the alterations in channel morphology reported for other urbanizing streams in the Piedmont physiographic province of the eastern United States. Trend analyses of discharge records in Dead Run show that urban development and stormwater control measures have had significant impacts on the hydrologic response of the catchment. The flood hydraulics of the Dead Run catchment are examined for the event that occurred on 22 June 1972 in association with Hurricane Agnes. A two‐dimensional hydraulic model, TELEMAC‐2D, was used with a finite‐element mesh constructed from a combination of high‐resolution LiDAR topographic data and detailed field survey data to analyse the distribution of boundary shear stress and unit stream power along the channel and floodplain during flooding from Hurricane Agnes. The spatial and temporal distributions of these parameters, relative to channel gradient and channel/valley bottom geometry, provide valuable insights on the stability of the Dean Run channel. The stability of Dead Run's channel planform, in spite of extreme flooding and decades of urban development, is most likely linked to geological controls of channel and floodplain morphology. Copyright © 2006 John Wiley & Sons, Ltd.
River system discontinuities due to lateral inputs: generic styles and controls
Authors: Ferguson Robert I. , Cudden Judith R. , Hoey Trevor B. , Rice Stephen P.
Published: March 2006

In alluvial river systems, lateral inputs of water and/or sediment at junctions or undercut hillsides can disrupt what would otherwise be smooth downstream trends in mainstream bed elevation, channel gradient, and bed grain size. Generic styles of mainstream response to lateral inputs are investigated using a one‐dimensional sediment routing model with multiple grain size fractions. Numerical experiments isolate the effects of three para‐meters: ratio of tributary to mainstream water flux (QR), ratio of tributary to mainstream bedload flux (FR), and ratio of tributary to mainstream bedload diameter (DR). The findings are not unduly sensitive to the choice of initial conditions or to approximations made in the model. The primary distinction is between junctions that aggrade, causing local profile convexity with interrupted downstream fining, and junctions that degrade. The immediate effects of aggradation extend further upstream than downstream, whereas degradation is much more subdued and has no upstream impact. Aggradation is typical of coarse inputs (DR > 2), and degradation of fine inputs (DR < 1), but very high ratios of QR to FR also promote degradation. Both aggrading and degrading junctions can lead to a change in mainstream bed grain size well below the junction, with higher ratios of QR to FR producing a coarser distal bed. The effect of a tributary reflects the interplay between additional bed load and additional discharge to transport it. Copyright © 2006 John Wiley & Sons, Ltd.
Structure of flow over alluvial bedforms: an experiment on linking field and laboratory methods
Authors: Sukhodolov Alexander N. , Fedele Juan J. , Rhoads Bruce L.
Published: March 2006

This paper presents results of a field study designed to examine the structure of flow over mobile and fixed bedforms in a natural stream and to compare the results with findings of previous laboratory studies within the framework of double time–space averaging approach. Measurements of turbulence were obtained in a small river in Illinois, USA, over a fine spatial grid of sampling points above a mobile sandy bedform and its artificially moulded replica. Flow structure over the artificial bedform is similar to that observed in laboratory studies, but is markedly different from the flow structure over natural bedforms. These differences are most pronounced in the roughness sublayer, whereas flow in the logarithmic layer over natural and artificial sand waves is fairly similar and exhibits spatial uniformity. The double time–space averaged distributions of turbulence statistics conform to the multilayer model of flow structure over bedforms. Mean velocity distributions indicate neither classical flow recirculation nor substantial reduction of velocities in the lee of bedform crests. However, vertical patterns of turbulence statistics over depth suggest that stacked wakes similar to those observed in laboratory studies exist above the bedforms. Thus, despite the absence of flow separation, wake development seems to be induced by the systematic influence of upstream bedforms on the vertical structure of turbulence. Copyright © 2006 John Wiley & Sons, Ltd.
National science foundation perspectives on the nature of STEM program evaluation
Authors: Katzenmeyer Conrad , Lawrenz Frances
Published: March 2006

This chapter presents the historical and present perspectives on STEM educational program evaluation of the National Science Foundation (in particular, the Division of Research, Evaluation, and Communication).
Collaborative evaluation communities in urban schools: A model of evaluation capacity building for STEM education
Authors: Huffman Douglas , Lawrenz Frances , Thomas Kelli , Clarkson Lesa
Published: March 2006

This chapter describes a new model of evaluation capacity building designed to build the organizational evaluation capacity of schools while simultaneously developing the evaluation capacity of individual teachers and STEM graduate students.
Synthesis of STEM education evaluation ideas
Authors: Lawrenz Frances , Huffman Douglas , Thomas Kelli
Published: March 2006

This chapter summarizes the main points made in the preceding chapters, highlights themes running throughout the chapters, and suggests implications for the fields of STEM education evaluation and evaluation overall.
Helicobacter pylori CagA—a bacterial intruder conspiring gastric carcinogenesis
Authors: Hatakeyama Masanori
Published: March 2006

Infection with cagA‐positive Helicobacter pylori (H. pylori) is associated with the development of gastric adenocarcinoma. The cagA gene product CagA is delivered from the bacterium into the cytoplasm of the bacterium‐attached gastric epithelial cell via the type‐IV secretion system. Upon membrane localization and subsequent tyrosine phosphorylation by Src family kinases, translocated CagA functions as a scaffolding adaptor that interacts with a number of host proteins involved in cell signaling in both tyrosine phosphorylation‐dependent and ‐independent manners. Of special interest is the interaction of CagA with the SHP‐2 tyrosine phosphatase, of which gain‐of‐function mutations have recently been found in human malignancies. Through the complex formation, SHP‐2 is catalytically activated and induces morphological transformation that is associated with increased cell motility. In addition to the perturbation of intracellular signaling, CagA disrupts the apical junctional complex that regulates the cell–cell contact and maintains the integrity of the epithelial structure. These CagA activities may collectively cause cellular dysfunctions that promote accumulation of multiple genetic changes involved in malignant transformation. Further elucidation of host cell signaling targeted by CagA should provide a new paradigm for ‘bacterial carcinogenesis’ and also give insights into general understanding of inflammation‐mediated cancers. Clinically, detailed studies on the relationship between structural diversity and degree of pathogenic activity of CagA should make it possible to identify a high‐risk group for gastric carcinoma among H. pylori‐infected populations through cagA genotyping. © 2006 Wiley‐Liss, Inc.
Understanding urothelial carcinoma through cancer pathways
Authors: Schulz Wolfgang A.
Published: March 2006

Urothelial carcinoma (UC), the common histological subtype of bladder cancer, presents as a papillary tumor or as an invasive, often lethal form. To study UC molecular biology, candidate gene and genome‐wide approaches have been followed. Here, it is argued that a ‘cancer pathway’ perspective is useful to integrate findings from both approaches. According to this view, papillary cancers typically exhibit activation of the MAPK pathway, as a consequence of oncogenic mutations in FGFR3 or HRAS, with increased Cyclin D1 expression. In contrast, invasive UC are characterized by severe disturbances in proximate cell cycle regulators, e.g. RB1 and CDKN2A/p16INK4A, which decrease dependency on mitogenic signaling. In addition, these disturbances permit, promote and are in turn exacerbated by chromosomal instability, which is further enhanced by loss of TP53 function. In another vicious cycle, defective cell cycle regulation interacts with DNA methylation alterations. The transition toward invasive UC may require concomitant and interacting defects in cell cycle regulation and the control of genomic stability. Intriguingly, neither canonical WNT/β‐Catenin nor hedgehog signaling appear to play major roles in UC. This may reflect its origin from more differentiated urothelial cells possessing a high regenerative potential rather than a stem cell population. © 2006 Wiley‐Liss, Inc.
Tumor lymphangiogenesis and metastatic spread—New players begin to emerge
Authors: Achen Marc G. , Stacker Steven A.
Published: March 2006

The metastatic spread of tumor cells is the most lethal aspect of cancer and can occur via various routes, including the lymphatic vasculature. Studies of tumor models in animals and clinicopathological data have indicated that growth of lymphatic vessels (lymphangiogenesis) in the vicinity of solid tumors may contribute to lymphatic metastasis. Research over the past 5 years has identified a range of lymphangiogenic growth factors that could conceivably play a role in promoting tumor lymphangiogenesis and lymphatic metastasis. The most extensively studied signaling system that promotes lymphangiogenesis in tumors involves the secreted lymphangiogenic proteins vascular endothelial growth factor‐C (VEGF‐C) and VEGF‐D, and their cognate receptor on lymphatic endothelium VEGF receptor‐3 (VEGFR‐3). More recent studies have identified other signaling molecules that can also promote lymphangiogenesis in vivo, including hepatocyte growth factor and members of the fibroblast growth factor, angiopoietin, platelet‐derived growth factor and insulin‐like growth factor families of secreted proteins. This article provides an overview of the molecular mechanisms that control lymphangiogenic signaling, emphasizing the more recently identified lymphangiogenic growth factors and the roles they may play in cancer biology. Molecular approaches for inhibiting lymphangiogenic signaling in cancer, designed to restrict tumor metastasis, are also examined. © 2006 Wiley‐Liss, Inc.
Starting SCF calculations by superposition of atomic densities
Authors: Van Lenthe J. H. , Zwaans R. , Van Dam H. J. J. , Guest M. F.
Published: March 2006

We describe the procedure to start an SCF calculation of the general type from a sum of atomic electron densities, as implemented in GAMESS‐UK. Although the procedure is well known for closed‐shell calculations and was already suggested when the Direct SCF procedure was proposed, the general procedure is less obvious. For instance, there is no need to converge the corresponding closed‐shell Hartree–Fock calculation when dealing with an open‐shell species. We describe the various choices and illustrate them with test calculations, showing that the procedure is easier, and on average better, than starting from a converged minimal basis calculation and much better than using a bare nucleus Hamiltonian. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 926–932, 2006
Theoretical study on the isomeric structures and the stability of silylenoid (Tsi)Cl2SiLi (Tsi = C(SiMe3)3)
Authors: Xie Ju , Feng Dacheng , Feng Shengyu
Published: March 2006

The structures and isomerization of silylenoid (Tsi)Cl2SiLi (Tsi = C(SiMe3)3) were studied by density functional theory (DFT) at the B3LYP/6‐31G(d) level. Four equilibrium structures and three isomeric transition states were located. The three‐membered ring and p‐complex structures, 1 and 2, are the two most stable forms. Two other local minima, the σ‐complex 3 and tetrahedron structure 4, should rearrange to 1 with very low barriers, and then to the most stable isomer 2. To exploit further the stability of silylenoid (Tsi)Cl2SiLi, the insertion reactions of 2 and silylene (Tsi)ClSi into the HF molecule have been investigated at the B3LYP/6‐31G(d) level, respectively. The results show that the insertion of 2 into HF is very similar to that of (Tsi)ClSi into HF, but the latter is more favorable. To probe the influence of the substituent Tsi on the stability of silylenoid (Tsi)Cl2SiLi, the isomers and insertion reaction of silylenoid CH3Cl2SiLi were investigated in a similar way of those with (Tsi)Cl2SiLi. The results indicate that silylenoid containing very bulky group Tsi exhibits unusual stability because of the severe steric hindrance produced by Tsi at the center to which it is attached. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 933–940, 2006
Survivin study: An update of “What is the next wave?”
Authors: Li Fengzhi , Ling Xiang
Published: March 2006

Studies on survivin over the past 2–3 years have shown that survivin possesses multiple subcellular localizations and is a multi‐functional molecule involved in many aspects of cellular processes and/or behaviors. The subcellular localization and function of the survivin splice variants, however, have not yet been well elucidated. We have, therefore, provided additional observations on several survivin splice variants for further exploration. This review article will update the role of survivin, and its splice variants in the mitosis/cell cycle, apoptosis, tumorigenesis, chemoprevention, drug/radiation resistance, and cancer therapeutics. J. Cell. Physiol. 208: 476–486, 2006. © 2006 Wiley‐Liss, Inc.
Characterization of freshly isolated and cultured cells derived from the fatty and fluid portions of liposuction aspirates
Authors: Yoshimura Kotaro , Shigeura Tomokuni , Matsumoto Daisuke , Sato Takahiro , Takaki Yasuyuki , Aiba‐Kojima Emiko , Sato Katsujiro , Inoue Keita , Nagase Takashi , Koshima Isao , Gonda Koichi
Published: March 2006

Liposuction aspirates (primarily saline solution, blood, and adipose tissue fragments) separate into fatty and fluid portions. Cells isolated from the fatty portion are termed processed lipoaspirate (PLA) cells and contain adipose‐derived adherent stromal cells (ASCs). Here we define cells isolated from the fluid portion of liposuction aspirates as liposuction aspirate fluid (LAF) cells. Stromal vascular fractions (SVF) were isolated separately from both portions and characterized under cultured and non‐cultured conditions. A comparable number of LAF and PLA cells were freshly isolated, but fewer LAF cells were adherent. CD34+CD45− cells from fresh LAF isolates were expanded by adherent culture, suggesting that LAF cells contain ASCs. Although freshly isolated PLA and LAF cells have distinct cell surface marker profiles, adherent PLA and LAF cells have quite similar characteristics with regard to growth kinetics, morphology, capacity for differentiation, and surface marker profiles. After plating, both PLA and LAF cells showed significant increased expression of CD29, CD44, CD49d, CD73, CD90, CD105, and CD151 and decreased expression of CD31 and CD45. Multicolor FACS analysis revealed that SVF are composed of heterogeneous cell populations including blood‐derived cells (CD45+), ASCs (CD31−CD34+CD45−CD90+CD105−CD146−), endothelial (progenitor) cells (CD31+CD34+CD45−CD90+CD105lowCD146+), pericytes (CD31−CD34−CD45−CD90+CD105−CD146+), and other cells. After plating, ASCs showed a dramatic increase in CD105 expression. Although some adherent ASCs lost CD34 expression with increasing culture time, our culture method maintained CD34 expression in ASCs for at least 10–20 weeks. These results suggest that liposuction‐derived cells may be useful and valuable for cell‐based therapies. J. Cell. Physiol. © 2006 Wiley‐Liss, Inc.
Multidisciplinary international conference on gynecologic cancer, Bologna, Italy, June 8–12, 2005
Authors: Bovicelli Alessandro , D'Andrilli Giuseppina , Giordano Antonio
Published: March 2006

The first “Multidisciplinary International Conference on Gynecologic Cancer” which was held in Bologna on June 8–12, 2005, addressed some of the most crucial topics in gynecologic oncology, presented the latest achievements and, at the same time, designed the guidelines for future developments in the field. The scientific program was intended not only to share and compare views and ideas among gynecologists but also with oncologists and researchers in basic science. The scientific committee strongly believed in the “multidisciplinary approach” towards medicine and particularly towards patients. J. Cell. Physiol. © 2006 Wiley‐Liss, Inc.