bluuebunny/crossref_metadata_2025 huggingface dataset:
A rapid microassay to evaluate enzymatic hydrolysis of lignocellulosic substrates
Authors: Berlin Alex , Maximenko Vera , Bura Renata , Kang Kyu‐Young , Gilkes Neil , Saddler Jack
Published: December 2005

Current attempts to produce ethanol from lignocellulosic biomass are focused on the optimization of pretreatment to reduce substrate recalcitrance and the improvement of enzymes for hydrolysis of the cellulose and hemicellulose components to produce fermentable sugars. Research aimed at optimizing both aspects of the bioconversion process involves assessment of the effects of multiple variables on enzyme efficiency, resulting in large factorial experiments with intensive assay requirements. A rapid assay for lignocellulose hydrolysis has been developed to address this need. Pretreated lignocellulose is formed into handsheets, which are then used to prepare small disks that are easily dispensed into microtiter plates. The hydrolysis of cellulose to glucose is estimated using an enzyme‐coupled spectrophotometric assay. Using disks prepared from ethanol organosolv pretreated yellow poplar, it is shown that the assay generates data comparable with those produced by hydrolysis of pretreated yellow poplar pulp in Erlenmeyer flasks, followed by HPLC analysis of glucose. The assay shows considerable time and cost benefits over the standard assay protocol and is applicable to a broad range of lignocellulosic substrates. © 2005 Wiley Periodicals, Inc.
A critical assessment of the impact of mixing on dilution refolding
Authors: Mannall Gareth J. , Titchener‐Hooker Nigel J. , Chase Howard A. , Dalby Paul A.
Published: December 2005

Refolding often presents a bottleneck in the generation of recombinant protein expressed as inclusion bodies. Few studies have looked at the effect of physical factors on the yield from refolding steps. Refold reactors typically operate in fed‐batch mode with a slow injection rate. This paper characterizes mixing in a novel reactor, and seeks to relate the conditions of mixing to native lysozyme yields after refolding. A novel twin‐impeller system incorporating a mini‐paddle impeller located in the vicinity of the injection point was used to increase the local levels of energy dissipation experienced by the injected material, and to improve refolding yields. Mixing only affected yields during and immediately after denatured protein addition. Analysis of lysozyme refolding yield, under a variety of conditions, revealed that dispersive mixing affected the yield. The beneficial effect of the mini‐paddle impeller in providing a source of localized energy dissipation was limited to conditions where the bulk impeller intensity was low. The effects appeared to become more significant when injection times were longer, because of increased exposure of the injected material to the energy dissipation of the mini‐impeller. The results suggest that for fed‐batch protein refolding systems, where mixing has been shown to be a critical factor, the local energy dissipation experienced in the vicinity of the injection point is critical to the refolding yields. © 2005 Wiley Periodicals, Inc.
Influence of substrate concentration on the stability and yield of continuous biohydrogen production
Authors: Kyazze G. , Martinez‐Perez N. , Dinsdale R. , Premier G.C. , Hawkes F.R. , Guwy A.J. , Hawkes D.L.
Published: December 2005

The effect of substrate concentration (sucrose) on the stability and yield of a continuous fermentative process producing hydrogen was studied. High substrate concentrations are attractive from an energy standpoint as they would minimise the energy required for heating. The reactor was a CSTR; temperature was maintained at 35°C; pH was controlled between 5.2 and 5.3, and the hydraulic retention time (HRT) was 12 h. Online measurements were taken for ORP, pH, temperature, %CO2, gas output and %H2, and data logged using a MatLAB® data acquisition toolbox. Steady‐state operation was obtained at 10, 20 and 40 g/L of sucrose in the influent, but a subsequent step change to 50 g/L was unsustainable. The hydrogen content ranged between 50% and 60%. The yield of hydrogen decreased as the substrate concentration increased from 1.7 ± 0.2 mol/mol hexose added at 10 g/L, to 0.8 ± 0.1 mol/mol at 50 g/L. Sparging with nitrogen improved the hydrogen yield by at least 35% at 40 g/L and at least 33% at 50 g/L sucrose. Sparging also enabled steady‐state operation at 50 g/L sucrose. Addition of an extra 4 g/L of n‐butyric acid to the reactor operating at 40 g/L sucrose increased the butyrate concentration from 9,830 to 18,900 mg/L, immediately stopping gas production and initiating the production of propionate, whilst the addition of 2 g/L taking the butyrate concentration to 12,200 mg/L did not do so. It was shown that operation at 50 g/L sucrose in a CSTR in butyrate fermentation is possible. © 2005 Wiley Periodicals, Inc.
Influence of Serine O‐Glycosylation or O‐Phoshorylation Close to the vJun Nuclear Localisation Sequence on Nuclear Import
Authors: Schlummer Stefanie , Vetter Robin , Kuder Norman , Henkel Andreas , Chen Yong‐Xiang , Li Yan‐Mei , Kuhlmann Jürgen , Waldmann Herbert
Published: December 2005

Nuclear import triggered by the nuclear‐localisation sequence (NLS) of the viral Jun (vJun) protein is mediated by phosphorylation of a serine close to the NLS. Since phosphorylation and glycosylation of serine residues are often in a reciprocal “yin–yang” relationship, we investigated whether glycosylation of this serine with O‐linked N‐acetylglucosamine (O‐GlcNAc) would also regulate nuclear import via the vJun NLS. Peptides containing the vJun NLS with an adjacent O‐phosphorylated, O‐GlcNAc‐functionalised or unmodified serine, and equipped with an N‐terminal biotin or a 7‐nitrobenz‐2‐oxa‐1,3‐diazolyl (NBD) fluorescent label, were synthesised on the solid phase by means of an Fmoc/Boc strategy and a Pd0‐sensitive HYCRON linker. Fluorescence‐polarisation measurements on the NBD‐labelled peptides indicated that modification with phosphate or O‐GlcNAc leads to a decrease in affinity to the import‐mediating adapter protein, importin α, of about one order of magnitude compared to the unmodified NLS. Microinjection of biotinylated NLS peptide conjugated with fluorescently labelled avidin into NIH/3T3 and MDCK cells, revealed that avidin–unmodified‐NLS peptide was rapidly imported into the nucleus. However, either phosphate or O‐GlcNAc next to the NLS caused almost complete exclusion of the protein conjugate from nuclear import. These findings indicate that nuclear import by the vJun NLS might not be regulated by a “yin–yang” modification of an adjacent serine with phosphate or O‐GlcNAc. Rather, negative regulation of binding between the polybasic NLS and importin by a negatively charged or a bulky, uncharged residue appears likely.
Intra‐atrial tissue plasminogen activator infusion for prosthetic valve thrombosis
Authors: Seltzer Sharon M. , Reed Michael D. , Siwik Ernest S.
Published: December 2005

Thrombosis is a well‐known and life‐threatening complication of prosthetic mechanical valves. Therapy typically requires medical thrombolysis or surgical thrombectomy/valve replacement. We report the case of a thrombosed atrioventricular valve in a young boy with complex congenital heart disease, which was successfully treated with direct intra‐atrial infusion of recombinant tissue plasminogen activator after failed attempts at systemic therapy. We present this treatment as an alternative to conventional medical therapy. © 2005 Wiley‐Liss, Inc.
Framework for regression‐based missing data imputation methods in on‐line MSPC
Authors: Arteaga Francisco , Ferrer Alberto
Published: December 2005

Missing data are a critical issue in on‐line multivariate statistical process control (MSPC). Among the different scores estimation methods for future multivariate incomplete observations from an existing principal component analysis (PCA) model, the most statistical efficient ones are those that estimate the scores for the new incomplete observation as the prediction from a regression model. We have called them regression‐based methods. Several approximations have been proposed in the literature to overcome the singularity or ill‐conditioning problems that some of the mentioned methods can suffer due to missing data. This is particularly acute in on‐line batch process monitoring. In order to ease the comparison of the statistical performance of these methods and to improve the understanding of their relationships, in this paper we propose a framework that allows to write these regression‐based methods by an unique expression, function of a key matrix. From this framework a statistical performance index (PRESV) is introduced as a way to compare the statistical efficiency of the different framework members and to predict the impact of specific missing data combinations on scores estimation without requiring real data. The results are illustrated by application to several continuous and batch industrial data sets. Copyright © 2005 John Wiley & Sons, Ltd.
Characterization of Electroplated Copper Film Using a Mixture of CuSO4 and CuSiF6 as the Electrolyte.
Authors: Wu You‐Lin , Yeh Juin‐Tsun , Cheng Chao‐Shen , Hwang Huey‐Liang
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
A Polar Oxide with a Large Magnetization Synthesized at Ambient Pressure.
Authors: Hughes Helen , Allix Mathieu M. B. , Bridges Craig A. , Claridge John B. , Kuang Xiaojun , Niu Hongjun , Taylor Stephen , Song Wenhai , Rosseinsky Matthew J.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Unusual Gold(I)‐Catalyzed Isomerization of 3‐Hydroxylated 1,5‐Enynes: Highly Substrate‐Dependent Reaction Manifolds.
Authors: Gagosz Fabien
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Polystyrene‐Supported N‐Methylthiourea: A Convenient New Reagent for the Hydrogenolysis of Bicyclic Endoperoxides.
Authors: Spivey Alan C. , Manas Carles Giro , Mann Inderjit
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Nitrogen Ligands: The Transition Metal Catalyzed Reaction of Aryl Halides with Olefins (Mizoroki—Heck), Phenylboronic Acid (Suzuki Coupling) and Buchwald—Hartwig Amination, New Catalysts and Effect of Cocatalysts—Aryl Halide Activation. Part 1.
Authors: Iyer Suresh , Kulkarni Girish M. , Ramesh C. , Sattar Aruna K.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Use of Lithium Hexafluoroisopropoxide as a Mild Base for Horner—Wadsworth—Emmons Olefination of Epimerizable Aldehydes.
Authors: Blasdel Landy K. , Myers Andrew G.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Functionalized Cyclobutenes via Multicomponent Thermal [2 + 2] Cycloaddition Reactions.
Authors: Sheldrake Helen M. , Wallace Timothy W. , Wilson Craig P.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Rate Enhancement of Lipase‐Catalyzed Reaction in Supercritical Carbon Dioxide.
Authors: Matsuda Tomoko , Tsuji Kazuhiko , Kamitanaka Takashi , Harada Tadao , Nakamura Kaoru , Ikariya Takao
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Chemoselective Heck Arylation of Acrolein Diethyl Acetal Catalyzed by an Oxime‐Derived Palladacycle.
Authors: Najera Carmen , Botella Luis
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Stereoselective Synthesis of 1,2‐Diamino‐1,2‐diarylethane Derivatives.
Authors: Bessonov I. V. , Lozinskaya N. A. , Katashova V. R. , Proskurnina M. V. , Zefirov N. S.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
A Simple Catalyst System for the Palladium‐Catalyzed Coupling of Aryl Halides with Terminal Alkynes.
Authors: Shirakawa Eiji , Kitabata Takaaki , Otsuka Hidehito , Tsuchimoto Teruhisa
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Synthesis and Characterization of Some Novel Indeno[1,2‐c]pyrazoles.
Authors: Singh Karan , Sharma Pawan K. , Dhawan S. N. , Singh Shiv P.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Synthesis of Some Isatin‐Based Novel Spiroheterocycles and Their Biological Activity Studies.
Authors: Mashelkar Uday C. , Rane Deepak M.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
A Mild and Efficient aza‐Diels—Alder Reaction of N‐Benzhydryl Imines with trans‐1‐Methoxy‐2‐methyl‐3‐trimethylsiloxybuta‐1,3‐diene Catalyzed by Yb(OTf)3.
Authors: Cheng Ke , Lin Lili , Chen Shikui , Feng Xiaoming
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Successive Substitution of Halogen Atoms in 4,6‐Dihaloquinolines in Palladium‐Catalyzed Reactions with Amines and Arylboronic Acids.
Authors: Beletskaya I. P. , Tsvetkov A. V. , Tsvetkov P. V. , Latyshev G. V. , Lukashev N. V.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Reaction of Enamines of the 1,2,3,4‐Tetrahydrobenzo[f]isoquinoline Series with 2,3‐Dichloro‐1,4‐naphthoquinone.
Authors: Polygalova N. N. , Mikhailovskii A. G. , Gein V. L. , Vakhrin M. I.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Regioselective Synthesis of Quinolone‐Annulated Sulfur Heterocycles by Aryl Radical Cyclization.
Authors: Majumdar K. C. , Mukhopadhyay P. P. , Biswas A.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
New Mesoionic Systems of Azolopyridine Series. Part 2. Synthesis, Structures, and Biological Activity of 2‐Aminothiazolo[3,2‐a]pyridinium Salts and Thiazolo[3,2‐a]pyridinium 2‐Imidates.
Authors: Babaev E. V. , Bush A. A. , Orlova I. A. , Rybakov V. B. , Iwataki I.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Synthesis and Antitumor Activity of 2‐Aryl‐7‐fluoro‐6‐(4‐methyl‐1‐piperazinyl)‐4(3H)‐quinazolinones.
Authors: Abdel‐Jalil Raid J. , Aldoqum Hani M. , Ayoub Mikdad T. , Voelter Wolfgang
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
A Novel Method for the Synthesis of Imidazo[5,1‐f][1,2,4]triazin‐4(3H)‐ones.
Authors: Heim‐Riether Alexander , Healy Jason
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Synthesis and Biological Activity of Macrocyclic Inhibitors of Hepatitis C Virus (HCV) NS3 Protease.
Authors: Chen Kevin X. , Njoroge F. George , Prongay Andrew , Pichardo John , Madison Vincent , Girijavallabhan Viyyoor
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
The Single‐Phase Multiferroic Oxides: From Bulk to Thin Film
Authors: Prellier W. , Singh M. P. , Murugavel P.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Heterogeneous Catalysis on Chitosan‐Based Materials
Authors: Guibal E.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Single‐Site Heterogeneous Catalysts
Authors: Thomas John Meurig , Raja Robert , Lewis Dewi W.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Developments into the Enantioselective Protonation of Prostereogenic Enol Derivatives under Kinetic Control
Authors: Coumbarides G. S. , Eames J. , Ghilagaber S. , Weerasooriya N. , Yohannes Y.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Synthesis of Heterocycles by Using Thiones and Selones
Authors: Okuma Kentaro
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Supramolecular Gels: Functions and Uses
Authors: Sangeetha Neralagatta M. , Maitra Uday
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
One‐Pot Synthesis of Fused Aromatics Possessing Helical Chirality and Assignment of Absolute Configuration Assisted by Theoretical Circular Dichroism
Authors: Tanaka Yasutaka , Watanabe Masashi , Ishida Toshimasa
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Applications of Catalysts on Soluble Supports
Authors: Bergbreiter David E. , Li Jun
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Asymmetric Epoxidations of Poor‐Electron Olefins
Authors: Vidal Alberto , Monroig Juan Jose , Rodriguez Santiago , Gonzalez Florenci
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
New Catalytic Methods for the Synthesis of Selectively Substituted Aromatics Through Palladacycles
Authors: Catellani Marta , Motti Elena , Faccini Fiorenza , Ferraccioli Raffaella
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Proanthocyanidin Biosynthesis — Still More Questions than Answers?
Authors: Xie De‐Yu , Dixon Richard A.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Neurotoxins and Medicinals for the Treatment of Parkinson′s Disease. Part 1. Neurotoxins, Levodopa and Drugs Influencing Dopamine Metabolism
Authors: Kadieva M. G. , Oganesyan E. T. , Mutsueva S. Kh.
Published: December 2005

For Abstract see ChemInform Abstract in Full Text.
Clinical trial accrual among new cancer patients at a community‐based cancer center
Authors: Go Ronald S. , Frisby Kathleen A. , Lee Jennifer A. , Mathiason Michelle A. , Meyer Christine M. , Ostern Jodi L. , Walther Sara M. , Schroeder Jonean E. , Meyer Lori A. , Umberger Kathryn E.
Published: December 2005

BACKGROUND

To the authors' knowledge, only limited data are available regarding clinical trial accrual patterns and the barriers encountered among newly diagnosed patients seen at community‐based cancer centers.

METHODS

In the current study, the authors prospectively collected clinical and sociodemographic data from all adult patients seen at a community‐based cancer center who had new cancers diagnosed between 2003–2004. Clinical trial enrollment decisions were noted and factors that prevented accrual were identified.

RESULTS

There was a total of 1012 new cancer patients. In 587 patients (58%), clinical trials appropriate for the diagnosis and stage of disease were not available. Among those patients for whom trials were available, 19.8% did not meet eligibility criteria, and only 9.9% of patients were enrolled. Although more trials were found to be available for women compared with men (51% vs. 32%; P < 0.01), the accrual rates were equal (11.2% vs. 7.6%; P = 0.24). Elderly patients comprised approximately 59.4% of those patients with available trials, but they were less likely to be enrolled (5.1% vs. 16.8%; P < 0.01). The major barriers to nonparticipation can be grouped into protocol limitations (68.1%), physician triage (16%), and patient decisions (15.9%). The overall accrual rate when all patients were included was 4% (42 of 1012 patients).

CONCLUSIONS

At the study institution, participation in clinical trials is reported to be low. The unavailability of appropriate clinical trials represents the most significant barrier. Continuing efforts to encourage physicians and to educate patients remain necessary. If the current study findings are found to be applicable to other community‐based cancer centers, making a larger variety of clinical trials available to the community may help to improve the accrual of patients to national cancer clinical trials. Cancer 2006. © 2005 American Cancer Society.
American founder mutation for Lynch syndrome
Authors: Lynch Henry T. , de la Chapelle Albert , Hampel Heather , Wagner Anja , Fodde Riccardo , Lynch Jane F. , Okimoto Ross , Clark Mary Beth , Coronel Stephanie , Trowonou Abdon , Fu Yun‐Xin , Haynatzki Gleb R. , Gong Gordon
Published: December 2005

BACKGROUND

Recently, a new founder mutation, an exon 1–6 deletion in a mismatch repair gene (MMR), MSH2, in nine kindreds with Lynch syndrome was reported. In 3 of the kindreds this mutation was traced by genealogy through 11–12 generations to a common founder, and thus termed the American Founder Mutation (AFM). Since then, 13 additional ‘unrelated’ kindreds with AFM were detected by a recently designed single polymerase chain reaction. This test might serve as first‐line screening for Lynch syndrome mutations, provided AFM was prevalent, which is assessed in the current study.

METHODS

The number of current AFM carriers and the incidence of Lynch syndrome caused by AFM were estimated based on population growth of mutation carriers derived from genealogy data. For cross‐checking, its annual incidence was also estimated based on published epidemiology data.

RESULTS

There are 18,981 (5th and 95th percentiles, 6038 and 34,466, respectively) expected current AFM carriers, or 160 (range 51–290) Lynch syndrome cases diagnosed per year due to AFM estimated based on genealogy data. The incidence estimate closely overlaps with that based on published epidemiology data, which is 114–400 cases per year.

CONCLUSIONS

A large number of AFM carriers are likely to exist in the U.S., which harbors significant implications for cancer control. Given the ease of detection, testing for AFM not only among members of the existing AFM families, but also among all patients with Lynch syndrome in the U.S. is proposed. Cancer 2006. © 2005 American Cancer Society.
Epithelioid sarcoma in children and adolescents
Authors: Casanova Michela , Ferrari Andrea , Collini Paola , Bisogno Gianni , Alaggio Rita , Cecchetto Giovanni , Gronchi Alessandro , Meazza Cristina , Garaventa Alberto , Di Cataldo Andrea , Carli Modesto
Published: December 2005

BACKGROUND

Epithelioid sarcoma (ES) is an uncommon malignant soft tissue tumor. To the authors' knowledge, little information is available to date concerning its clinical features and management in children and adolescents, particularly with regard to the recently described proximal‐type variant. The current study concerns 30 patients age < 18 years who were enrolled in the Italian Soft Tissue Sarcoma Committee protocols.

METHODS

Histopathologic specimens, clinical data, and treatment modalities were reviewed for the current analysis. Nineteen patients had classic ES and 11 had proximal‐type ES. Surgery was the mainstay of treatment; radiotherapy was given to six patients considered to be at risk of local disease recurrence due to incomplete resection, and chemotherapy was administered to eight patients.

RESULTS

With a median follow‐up of 66 months, the 5‐year event‐free survival (EFS) and overall survival (OS) rates were 61.7% and 92.4%, respectively, but the OS rate dropped to 86.9% and 72.4%, respectively, at 10 years and 15 years. Local disease recurrence was the major cause of treatment failure. The most significant finding influencing both EFS and OS was tumor site, with a tumor location in the extremities predicting a favorable outcome. Initially unfavorable clinical findings and a worse outcome were associated with the proximal‐type variant of ES. A response to chemotherapy was noted in three of the seven patients with measurable disease.

CONCLUSIONS

The current study confirms some typical features of ES (i.e., the peculiar superficial distal location [i.e., the hand, fingers], indolent growth, and a tendency to recur locally). The current study data do not clearly confirm the strong tendency for the lymph node involvement described in adult ES patients. Further studies are needed to better define the clinical behavior and biology of the proximal‐type variant of ES. Cancer 2006. © 2005 American Cancer Society.
Axial symmetric stationary thermoelastic analysis by triple‐reciprocity BEM
Authors: Ochiai Yoshihiro , Sladek Vladimir , Sladek Jan
Published: December 2005

The paper deals with the boundary integral formulation for solution of 3‐D axial symmetric problems of stationary thermo‐elasticity with including the domain heat sources. The domain integral of heat sources is converted into boundary integrals of a new field variable and another summation term involving the function values of another field variable at isolated interior points. Making use of the triple‐reciprocity method, the unknown boundary densities as well as the interior point unknowns are computed by solving the integral equations without the need to use domain cells in discretization. The integral kernels involved in the developed boundary integral formulation for axial symmetric problems are received by angular integration of 3‐D kernels with using cylindrical co‐ordinates. The explicit expressions of the kernels are collected in appendix and two numerical examples are considered for illustration of the accuracy and efficiency of the proposed approach. Copyright © 2005 John Wiley & Sons, Ltd.
Newton‐like iteration methods for solving non‐linear equations
Authors: Chun Changbum , Ham YoonMee
Published: December 2005

In this paper, Newton‐like iteration methods for solving non‐linear equations or improving the existing iteration methods are proposed. The iteration formulae are obtained by applying the homotopy perturbation method which contains the well‐known Newton iteration formula in logic, so those improving the Newton method. The orders of convergence of some of those iteration formulae are derived analytically and by applying symbolic computation of Maple. Some numerical illustrations are given. Copyright © 2005 John Wiley & Sons, Ltd.
Enriched finite element methods for unsteady reaction–diffusion problems
Authors: Franca L. P. , Ramalho J. V. A. , Valentin F.
Published: December 2005

We develop enriched finite element methods for parabolic singularly perturbed problems. A Petrov–Galerkin strategy is employed, where the test and the trial spaces are enriched with ‘bubble’ and multiscale functions, respectively. We examine two semi‐discrete formulations for the unsteady reaction–diffusion equation, namely the method of lines and a variation of it inspired by the Rothe method. Numerical tests validate the approaches. Copyright © 2005 John Wiley & Sons, Ltd.
Automatic Grid workflow based on imperative programming languages
Authors: Sirvent Raül , Pérez Josep M. , Badia Rosa M. , Labarta Jesús
Published: December 2005

GRID superscalar is a Grid programming environment that enables one to parallelize the execution of sequential applications in computational Grids. The run‐time library automatically builds a task data‐dependence graph of the application and it can be seen as an implicit workflow system. The current interface supports C/C++ and Perl applications. The run‐time library is based on Globus Toolkit 2.x using GRAM and GSIFTP services. In this document we describe the GRID superscalar basics emphasizing those aspects related to Grid workflow, in particular the flexibility of using an imperative language to describe the application. Copyright © 2005 John Wiley & Sons, Ltd.
Contextual constraint modeling in Grid application workflows
Authors: Graham Greg , Afaq Anzar , Evans David , Guglielmo Gerald , Wicklund Eric , Love Peter
Published: December 2005

This paper introduces a new mechanism for specifying constraints in distributed workflows. By introducing constraints in a contextual form, it is shown how different people and groups within collaborative communities can cooperatively constrain workflows. A comparison with existing state‐of‐the‐art workflow systems is made. These ideas are explored in practice with an illustrative example from High‐Energy Physics. Copyright © 2005 John Wiley & Sons, Ltd.
Does Silica Surface Catalyse Peptide Bond Formation? New Insights from First‐Principles Calculations
Authors: Rimola Albert , Tosoni Sergio , Sodupe Mariona , Ugliengo Piero
Published: December 2005

The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6‐31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen‐bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride SisurfOC(O)R, which has been suggested in the literature to activate the CO bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6‐31+G(d,p) calculations show that formation of the surface mixed anhydride SisurfOC(O)R is disfavoured (ΔrG298≈6 kcal mol−1), and that the surface bond only moderately lowers the free‐energy barrier of the nucleophilic attack responsible for peptide bond formation (ΔG${{{{\ne}\hfill \atop 298\hfill}}}$≈48 kcal mol−1) in comparison with the uncatalysed reaction (ΔG${{{{\ne}\hfill \atop 298\hfill}}}$≈52 kcal mol−1). A further decrease of the free‐energy barrier of peptide bond formation (ΔG${{{{\ne}\hfill \atop 298\hfill}}}$≈41 kcal mol−1) is achieved by a single water molecule close to the reaction centre acting as a proton‐transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride SisurfOC(O)R has also been addressed.
Linear Extended ArcJet‐CVD – a New PECVD Approach for Continuous Wide Area Coating Under Atmospheric Pressure
Authors: Hopfe V. , Rogler D. , Maeder G. , Dani I. , Landes K. , Theophile E. , Dzulko M. , Rohrer C. , Reichhold C.
Published: December 2005

A new type of DC‐powered plasma source (LARGE) was developed and evaluated for continuous plasma‐enhanced (PE) CVD under atmospheric pressure. The linear extended emanating plasma sheet was scaled‐up to various working widths with the result that a half meter range has already been achieved. A CVD reactor was designed for continuous deposition of non‐oxide materials. The reactor operates in a remote atmospheric pressure (AP) PECVD configuration with typical deposition rates of 5–50 nm s–1 (static) and 0.1–1.0 nm m s–1 (dynamic).

The potential application range of the ArcJet‐CVD technology was evaluated by screening studies with various substrates, (stainless steel, glass, silicon wafers) and coating materials (silica, carbon, silicon nitride). In‐situ process characterization has been provided by both optical emission and Fourier transform infrared (FTIR) spectroscopy. A range of atomic and molecular intermediates, precursor fragments, and reaction products were identified, leading to the conclusion that a complete conversion of the element‐organic precursors into an inorganic layer takes place.
Neuropeptide Y receptors as therapeutic targets in anxiety and depression
Authors: Sajdyk Tammy J.
Published: December 2005

This brief overview is focused on the role of neuropeptide Y (NPY) receptors and their involvement in stress behaviors, particularly as they relate to stress‐induced psychiatric disorders. Also discussed is the potential for each of the receptors in the development of novel therapeutic treatments in the field of psychiatry. To date, there are four known human receptor subtypes: Y1, Y2, Y4, and Y5. NPY receptor subtypes Y1, Y2, and Y5 are implicated in anxiety and depression, whereas the Y4 receptor appears to be involved in feeding and endocrine regulation. Clinical evidence suggests that deficiencies in NPY levels within the cerebrospinal fluid correlate with reported anxiety or depression. Likewise, the preclinical studies have shown that anxiety and/or depressive‐like behaviors in animals also correlate with NPY activity. Specifically, the animal data show that central administration of Y1 and Y5 receptor agonists will decrease anxiety‐like responses, whereas a Y2 antagonist is necessary for a similar effect. Given the detrimental effects of chronic stress in the development of psychiatric illness, and the limitations of some of the current treatments, NPY receptors are a promising new therapeutic target for mood and affective disorders. Drug Dev. Res. 65:301–308, 2005. © 2005 Wiley‐Liss, Inc.
X‐ray Crystal Structure and Characterization in Aqueous Solution of{N,N′‐Ethylenebis(pyridoxylaminato)}zinc(II)
Authors: Correia Isabel , Dornyei Agnes , Avecilla Fernando , Kiss Tamás , Costa Pessoa João
Published: December 2005

The complexation of ZnII with H2Rpyr2en [H2Rpyr2en = N,N′‐ethylenebis(pyridoxylaminato)] in aqueous solution has been studied by pH potentiometry and 1H NMR spectroscopy. Complex formation constants are determined and binding modes proposed. Complex formation starts at around pH 4, and several species with a 1:1 ligand‐to‐metal ratio with different protonation states form up to pH 12. Only above pH 10 does a hydrolytic species [ZnLH–1]– become important. The crystal and molecular structures of [ZnCl(H2Rpyr2en)]+Cl–·1.5H2O (1) have been determined by X‐ray diffraction. The coordination of the H2Rpyr2en ligand involves the two phenolate‐O and two amine‐N atoms in a distorted square‐pyramidal geometry. The two pyridine‐N atoms are protonated, and a Cl– atom completes the coordination sphere. Upon coordination, both N‐amine atoms of H2Rpyr2en become stereogenic centres, and in both molecules of the unit cell of 1 one of the N‐amine donors has an (R)‐configuration, and the other an (S)‐configuration. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
An Investigation of the Reactivity of [(diimine)(dithiolato)M] Complexes Using the Fukui Functions Concept
Authors: Makedonas Christodoulos , Mitsopoulou Christiana A.
Published: December 2005

Fukui functions are widely used when investigating the reactivity of organic molecules, but rarely with metal complexes. Here, we investigate the reactivity of [(diimine)(dithiolato)M] complexes with different types of reagents and upon oxidation employing this concept. Mixed‐ligand complexes of this type have a peculiar electronic description due to the mixed‐metal‐ligand‐to‐ligand charge‐transfer band, which is why they are considered as very promising candidates for non‐linear optical (NLO) materials and molecular photochemical devices (MPD). As a result, their reactivity is of crucial importance for their potential applications. The obtained results of f+ and f– for the neutral [(diimine)(dithiolato)M] complexes (M = Pd, Ni and Pt) not only predict that the sulfur atom is the preferable active site for electrophilic attack but also reveal the different tunability of these complexes when they are subjected to an oxidation process, in agreement with experimental results. Under the framework of the Fukui indices we also provide an alternative explanation for crystal packing that could find widespread application. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Synthesis of Carrier‐Transporting Dendrimers with Perylenebis(dicarboximide)s as a Luminescent Core
Authors: Pan Jianfeng , Zhu Weihong , Li Shangfeng , Xu Jun , Tian He
Published: December 2005

Well‐defined, modular dendrimers enable processing techniques and electronic properties to be tuned independently. Moreover, the dendritic topology can isolate the core chromophore, thus reducing or eliminating strong intermolecular interactions. This paper presents the synthesis of three series of flexible, dendron‐functionalized dendrimers as red‐light‐emitting materials by a convergent approach: (1) carbazole (CZ) or oxadiazole (OXZ) terminated imide‐type dendrimers, (2) cascade energy‐transferring imide‐type dendrimers, and (3) CZ‐terminated perylene bay‐type dendrimers. They all consist of the luminescent core of perylenebis(dicarboximide)s with specific functional groups of CZ or OXZ at the periphery and are constructed from flexible Fréchet‐type poly(aryl ether) dendrons. The chemical structures of the dendrons and dendrimers were determined by standard spectroscopic techniques including 1H and 13C NMR spectroscopy and low/high‐resolution mass spectrometry (ESI or MALDI‐TOF). The dendrimers are designed on the basis of the following considerations: (1) dendron functionalization to incorporate CZ or OXZ units to realize the carrier‐injection adjustment, (2) tuning or improving solubility, functionality, glass‐transition temperature (Tg) with well‐defined dendrons, and (3) avoiding luminescence quenching with the help of high site‐isolation of dendrons to enhance core luminescence. DSC results indicate that the incorporation of Fréchet‐type poly(aryl ether) dendrons can improve the amorphous properties and increase Tg. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Preparation of New, Optically Active 1,2‐Ferrocenyldiamine Ligands and Their Application to Ruthenium‐Catalyzed Asymmetric Transfer Hydrogenation of Ketones
Authors: Fukuzawa Shin‐ichi , Suzuki Takashi
Published: December 2005

The treatment of (R,R)‐1,2‐bis(1‐acetoxy‐1‐phenylmethyl)ferrocene (1) with azidotrimethylsilane in CH2Cl2 in the presence of a catalytic amount of a Lewis acid such as Cu(OTf)2 or Sc(OTf)3, at –40 °C for 24 h, gives a mixture of two diastereomeric ferrocenyl diazides 4 and 5 in an 80:20 ratio. The major isomer (R,R)‐4 is formed with retention of configuration at both benzylic chiral centers whereas the minor isomer meso‐(R,S)‐5 is formed with inversion of configuration at one of the two chiral centers. After a shorter reaction time (12 h), the (R,R)‐ferrocenylazido acetate 6 was isolated as a single diastereomer, which gave 4 and 5 under the same conditions with almost the same ratio as with the longer reaction time. These results show that the first step of the reaction is the substitution, with retention of configuration, of the exo acetate of 1 by means of an iron‐assisted ionization, i.e., neighboring‐group participation, then the endo acetate is replaced by the azide ion with retention or inversion of configuration to give 4 or 5, respectively. The optically active complex 4 could be converted into the corresponding ferrocenyldiamine 2 by reduction with LiAlH4, and its ditosylamide 8a and diacetamide 8b were isolated as stable compounds. The ferrocenyldiamine and both diamides were used as ligands in the ruthenium‐catalyzed asymmetric transfer hydrogenation of aryl ketones, and the complex with 2 gave 1‐arylethanols in good yields with up to 75 % ee.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Chromogenic Meroterpenoids from the Mushrooms Russula ochroleuca and R. viscida
Authors: Sontag Bernd , Rüth Matthias , Spiteller Peter , Arnold Norbert , Steglich Wolfgang , Reichert Matthias , Bringmann Gerhard
Published: December 2005

The spirodioxolactone ochroleucin A1 (1) is responsible for the red colour produced when the stalk base of Russula ochroleuca and R. viscida is treated with aqueous KOH. The labile chromogen rearranges easily into the isomeric dilactoneochroleucin A2 (2). Ochroleucin A1 is accompanied by the biosynthetically related hemiacetal ochroleucin B (5). The new compounds, whose structures were established by MS and NMR methods, appear to be derived biosynthetically by oxidative condensation of two monomeric units. One of them, 2,5‐dihydroxy‐4‐(3‐methylbut‐3‐en‐1‐ynyl)benzaldehyde (6), was detected in the crude toadstool extract by GC/MS comparison with a synthetic sample. The absolute configurations of the ochroleucins A1 and B have been determined by quantum chemical calculation of their CD spectra. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Heterocyclic Chemistry of Sulfur Chlorides – Fast Ways to Complex Heterocycles
Authors: García‐Valverde María , Torroba Tomás
Published: December 2005

This microreview highlights the most important advances in the synthetic applications of sulfur dichloride and disulfur dichloride for the preparation of heterocycles. Sulfur chlorides can be considered some of the best sulfur‐transfer reagents for the synthesis of heterocyclic systems. Their high reactivity towards nucleophilic organic compounds such as alkenes, alkynes, amines, nitriles, oximes, and their both chlorinating and sulfurating character explain the extensive use of these reagents. In many cases, the initial reactions give rise to reactive intermediates that can be trapped by nucleophiles in a tandem fashion, expanding the possibilities of the reactions. In this way, several new heterocyclic systems can be obtained by a careful selection of the appropriate combination of reagents. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Ion‐pair association and acid–base equilibria in nonaqueous capillary electrophoresis of weakly basic compounds
Authors: Carabias‐Martínez Rita , Rodríguez‐Gonzalo Encarnación , Hernández‐Méndez Jesús , Cruz Edith Miranda , Domínguez‐Álvarez Javier
Published: December 2005

CE in nonaqueous media was used to study the migrating behavior of two weakly basic s‐triazine pesticides and one of their metabolites. The target pesticides were selected to be representative for each of the two main groups: propazine and deethylatrazine for the chloro‐s‐triazines group and ametryn for the methylthio‐s‐triazines group. To elucidate the phenomena involved, systematic studies were carried out in the different organic media studied. Absolute mobilities were determined in 50% v/v methanol (MeOH)/ACN by extrapolation of the effective mobilities to zero ionic strength in the presence of different concentrations of perchloric acid. Conductivity measurements performed in MeOH and 50 and 20% v/v methanol/ACN permitted the evaluation of the associations of the components of the BGE. The effects of ionic strength on the actual mobilities of the compounds were determined in the presence of perchloric acid and SDS in different organic media. Two different ion‐pair equilibria were considered: one due to the presence of perchlorate anions present in the BGE and second that from the added dodecyl sulfate anions. Bearing in mind that these weakly basic compounds can exhibit ion‐pair and acid–base equilibria, the acid–base and ion‐pair parasite reaction coefficients were determined. Finally, the effects of ionic strength, ion‐pair interactions and acid–base properties on the effective electrophoretic mobilities of the analytes are discussed.
An inexpensive microslab gel DNA electrophoresis system with real‐time fluorescence detection
Authors: Chen Xiaojia , Ugaz Victor M.
Published: December 2005

In this paper, we describe the construction of a simple yet powerful gel electrophoresis apparatus that can be used to perform size‐selective separations of DNA fragments in virtually any laboratory. This system employs a microslab gel format with a novel gel casting technique that eliminates the need for delicate combs to define sample loading wells. The compact size of the microslab gel format allows rapid separations to be performed at low voltages using submicroliter sample volumes. Real time fluorescence detection of the migrating DNA fragments is accomplished using an inexpensive digital microscope that directly connects to any PC with a USB interface. The microscope is readily adaptable for this application by replacing its white light source with a blue light‐emitting diode (LED) and adding an appropriate emission filter. Both polyacrylamide and agarose gels can be used as separation matrices. Separation performance was characterized using standard dsDNA ladders, and correct sizing of a 191 bp PCR product was achieved in 15 min. The low cost and simplicity of this system makes it ideally suited for use in a variety of laboratory and educational settings.
Ionizing radiation and leukaemia: more questions than answers
Authors: Wright Eric G
Published: December 2005

The mechanisms underlying the unequivocal association between ionizing radiation and the development of leukaemia remain unknown. Recent progress in defining sub‐cellular events has contributed to our understanding of the production of genetic lesions in irradiated cells but the importance of tissue effects in response to radiation damage has attracted much less attention. Thus, genetic lesions induced by radiation are considered to result from the deposition of energy in the cell nucleus and the initiating lesion for radiation‐induced transformation has been similarly attributed to direct DNA damage. Recently, however, there have been many reports of radiation effects, characteristically associated with the consequences of energy deposition in the cell nucleus, arising in non‐irradiated cells as a consequence of communication with irradiated cells. These, so‐called, non‐targeted radiation effects pose major challenges to current views of the mechanisms of radiation‐induced DNA damage and the mechanisms underlying radiogenic malignancies. Considered together with data obtained from laboratory model systems, a rather complex picture of radiation leukaemogenesis is emerging in which, additional to any damage induced directly in target stem cells, the haemopoietic microenvironment can be a source of damaging signals and cellular interactions make important genotype‐dependent contributions to determining overall outcome after radiation exposures. Copyright © 2005 John Wiley & Sons, Ltd.
Detection rates of high‐grade prostate cancer during subsequent screening visits. Results of the European Randomized Screening Study for Prostate Cancer
Authors: van der Kwast Theodorus H. , Ciatto Stefano , Martikainen Paula M. , Hoedemaeker Robert , Laurila Marita , Pihl Carl‐Gustaph , Hugosson Jonas , Neetens Ingrid , Nelen Vera , Di Lollo Simonetta , Roobol Monique J. , Määtänen Liisa , Santonja Carlos , Moss Sue , Schröder Fritz H.
Published: December 2005

Screening for prostate cancer using prostate‐specific antigen (PSA) tests has led to a stage and grade shift as compared to the pre‐PSA era. Effectiveness of screening for prostate cancer should be manifested by a reduction in detection rate of aggressive cancers during subsequent screening. In 6 centers of the European Randomized Screening study for Prostate Cancer, a total of 58,710 men were tested for prostate cancer. Screening centers differed with regard to age‐range, screening interval and biopsy indications. During the 2nd visit, the proportion of Gleason score 6 cancers increased from 62.5 to 75%, mainly at the expense of Gleason score 7 cancers. High‐grade (Gleason score 8–10) cancer detection rates varied per screening center during the 1st visit from 5.1 to 41.1, and during the 2nd visit from 6.4 to 29.3/10,000 men. The overall detection rate of high‐grade cancers showed a reduction during the 2nd visit from 26 to 12/10,000 men, an effect mainly attributable to the screening center with the highest cancer detection rate (i.e. 507/10,000 men). Variations in detection rates among screening centers related among others to biopsy compliance and age range. © 2005 Wiley‐Liss, Inc.
Frequent EGFR mutations in noninvasive bronchioloalveolar carcinoma
Authors: Matsumoto Shingo , Iwakawa Reika , Kohno Takashi , Suzuki Kenji , Matsuno Yoshihiro , Yamamoto Seiichiro , Noguchi Masayuki , Shimizu Eiji , Yokota Jun
Published: December 2005

Mutations of the epidermal growth factor receptor gene (EGFR) have been reported to be present in a considerable fraction of lung adenocarcinomas showing dramatic response to EGFR tyrosine kinase inhibitors. To clarify pathogenic significance of the mutations for the development of lung adenocarcinoma, we investigated stage I lung adenocarcinomas for the mutations. First, 107 cases of macrodissected stage I adenocarcinomas were examined for mutations in exons 18–21 of the EGFR gene. EGFR mutations were detected in 36 of the 107 cases (34%). In particular, among the stage I cases, the mutations were detected in 17 of 42 small‐sized adenocarcinomas (≤2 cm in diameter) (40%), including 7 of 11 noninvasive bronchioloalveolar carcinomas (BACs) (64%) and 7 of 25 invasive adenocarcinomas with BAC components (28%). Second, 26 cases of laser capture microdissected small‐sized adenocarcinomas, including 9 cases in the first analysis, were examined for the mutations. Reanalysis of microdissected materials in the 9 cases identified the mutations in 2 more adenocarcinomas with BAC components. Moreover, in the analysis of the other 17 microdissected materials, EGFR mutations were detected in 7 of 12 BACs (58%) and in 3 of 5 adenocarcinomas with BAC components (60%). EGFR mutations are present frequently in BACs, and are thus likely to be a critical genetic alteration for the formation of noninvasive lung adenocarcinoma. © 2005 Wiley‐Liss, Inc.