bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo uniform 15N‐isotope labelling of plants: Using the greenhouse for structural proteomics
Authors: Ippel Johannes H. , Pouvreau Laurice , Kroef Toos , Gruppen Harry , Versteeg Geurt , van den Putten Peter , Struik Paul C. , van Mierlo Carlo P. M.
Published: January 2004

Isotope labelling of proteins is important for progress in the field of structural proteomics. It enables the utilisation of the power of nuclear magnetic resonance spectroscopy (NMR) for the characterisation of the three‐dimensional structures and corresponding dynamical features of proteins. The usual approach to obtain isotopically labelled protein molecules is by expressing the corresponding gene in bacterial or yeast host organisms, which grow on isotope‐enriched media. This method has several drawbacks. Here, we demonstrate that it is possible to fully label a plant with 15N‐isotopes. The advantage of in vivo labelling of higher organisms is that all constituting proteins are labelled and become available as functional, post‐translationally modified, correctly folded proteins. A hydroponics set‐up was used to create the first example of a uniformly 15N‐labelled (> 98%) plant species, the potato plant (Solanum tuberosum L., cv. Elkana). Two plants were grown at low costs using potassium‐[15N]‐nitrate as the sole nitrogen source. At harvest time, a total of 3.6 kg of potato tubers and 1.6 kg of foliage, stolons and roots were collected, all of which were fully 15N‐labelled. Gram quantities of soluble 15N‐labelled proteins (composed mainly of the glycoprotein patatin and Kunitz‐type protease inhibitors) were isolated from the tubers. NMR results on the complete proteome of potato sap and on an isolated protease inhibitor illustrate the success of the labelling procedure. The presented method of isotope labelling is easily modified to label other plants. Its envisioned impact in the field of structural proteomics of plants is discussed.
C‐Terminal sequencing method for peptides and proteins by the reaction with a vapor of perfluoric acid in acetic anhydride
Authors: Miyazaki Kenji , Tsugita Akira
Published: January 2004

A successive C‐terminal amino acid truncation reaction of peptides and proteins with a vapor generated from a low‐concentrated perfluoric acid in acetic anhydride is presented. The reaction products were analyzed with matrix‐assisted laser desorption/ionization‐time of flight mass‐spectrometry giving molecular mass ions of the C‐terminal truncated peptides or proteins from which the C‐terminal sequence information can be deduced. Acetylation reaction preceded the truncation reaction in order to protect the amino groups and other reactive groups in peptides and proteins, and after the truncation reaction, hydration reaction was carried out to afford cleaner mass spectra.
Proteome characterization of human T helper 1 and 2 cells
Authors: Rautajoki Kirsi , Nyman Tuula A. , Lahesmaa Riitta
Published: January 2004

T helper (Th) cells can be polarized into two different main subtypes, Th1 and Th2 cells. Their activation is linked to the eradication of different pathogens and to dissimilar immunological dysfunctions, which implies differences also in their protein expression patterns. To identify these differences, CD4+ T cells were isolated from human cord blood, polarized in vitro to Th1 and Th2 and activated via CD3 and CD28. Cells were lysed, soluble proteins were separated with two‐dimensional electrophoresis and differing protein spots were identified with peptide mass fingerprinting. The expression of 14 proteins differed in Th1 and Th2 cells after both 7 and 14 days of polarization. Twelve of the proteins could be identified, most of which are new in this context. Two proteins were differentially modified in the two cell types. Especially, N‐terminal acetylation of cyclophilin A was stronger in Th1 than in Th2 cells. To compare the RNA and the protein levels of the identified genes, mRNA expression was measured with Affymetrix oligonucleotide microarrays (HG‐U133A). The mRNA and protein expression level correlated only in six cases out of eleven, which highlights the complementary roles that proteomics and transcriptomics have in the elucidation of biological phenomena.
Proteogenomic mapping as a complementary method to perform genome annotation
Authors: Jaffe Jacob D. , Berg Howard C. , Church George M.
Published: January 2004

The accelerated rate of genomic sequencing has led to an abundance of completely sequenced genomes. Annotation of the open reading frames (ORFs) (i.e., gene prediction) in these genomes is an important task and is most often performed computationally based on features in the nucleic acid sequence. Using recent advances in proteomics, we set out to predict the set of ORFs for an organism based principally on expressed protein‐based evidence. Using a novel search strategy, we mapped peptides detected in a whole‐cell lysate of Mycoplasma pneumoniae onto a genomic scaffold and extended these “hits” into ORFs bound by traditional genetic signals to generate a “proteogenomic map”. We were able to generate an ORF model for M. pneumoniae strain FH using proteomic data with a high correlation to models based on sequence features. Ultimately, we detected over 81% of the genomically predicted ORFs in M. pneumoniae strain M129 (the originally sequenced strain). We were also able to detect several new ORFs not originally predicted by genomic methods, various N‐terminal extensions, and some evidence that would suggest that certain predicted ORFs are bogus. Some of these differences may be a result of the strain analyzed but demonstrate the robustness of protein analysis across closely related genomes. This technique is a cost‐effective means to add value to genome annotation, and a prerequisite for proteome quantitation and in vivo interaction measures.
Global changes in gene expression observed at the transition from growth to stationary phase in Listeria monocytogenes ScottA batch culture
Authors: Weeks Mark E. , James David C. , Robinson Gary K. , Smales C. Mark
Published: January 2004

Listeria monocytogenes is a food‐borne Gram‐positive bacterium that is responsible for a variety of infections (worldwide) annually. The organism is able to survive a variety of environmental conditions and stresses, however, the mechanisms by which L. monocytogenes adapts to environmental change are yet to be fully elucidated. An understanding of the mechanism(s) by which L. monocytogenes survives unfavourable environmental conditions will aid in developing new food processing methods to control the organism in foodstuffs. We have utilized a proteomic approach to investigate the response of L. monocytogenes batch cultures to the transition from exponential to stationary growth phase. Proteomic analysis showed that batch cultures of L. monocytogenes perceived stress and began preparations for stationary phase much earlier (approximately A600 = 0.75, mid‐exponential) than predicted by growth characteristics alone. Global analysis of the proteome revealed that the expression levels of more than 50% of all proteins observed changed significantly over a 7–9 h period during this transition phase. We have highlighted ten proteins in particular whose expression levels appear to be important in the early onset of the stationary phase. The significance of these findings in terms of functionality and the mechanistic picture are discussed.
Comparison of gene expression between left atria and left ventricles from non‐diseased humans
Authors: Tsubakihara Masako , Williams Neal K. , Keogh Anne , dos Remedios Cristobal G.
Published: January 2004

We examine the reliability and accuracy of gene array technology in analyzing differences in gene expression between human non‐diseased left atrium and left ventricle. We have used cDNA gene arrays and validated those data by carefully designed quantitative real‐time polymerase chain reaction (PCR). We have identified pitfalls using cDNA gene array technology based on comparisons with other gene array studies and with changes reported for the levels of expression of the genes corresponding to these cDNAs. The high error rate reported here underscores the cautionary comments reported by others in this field.
Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: The case of a virus‐resistant tomato
Authors: Corpillo Davide , Gardini Giulia , Vaira Anna Maria , Basso Manuela , Aime Silvio , Accotto Gian Paolo , Fasano Mauro
Published: January 2004

At present, the so‐called “substantial equivalence” is the only widely accepted criterion for deciding whether or not a transgenic food is, from an alimentary point of view, to be considered totally correspondent to the “traditional” one from which it derives. Although never exactly defined, it deals with a comparison between the chemical composition of the two foods. A more in‐depth analysis can be performed by one of the most suitable methods that allows for the simultaneous screening of many components without prior identification, the analysis of the proteome. As a model for testing this kind of approach, we compared protein expression of two types of tomato plants, having the same genetic background, except for a virus resistance trait introduced by genetic engineering. When proteins extracted from seedlings of the two types were analyzed by two‐dimensional electrophoresis, no significant differences, either qualitative or quantitative, were detected, indicating that in this case the expression of major proteins was unmodified by the genetic manipulation. Fifteen proteins were identified by peptide mass fingerprinting.
A detergent‐ and cyanogen bromide‐free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome
Authors: Blonder Josip , Conrads Thomas P. , Yu Li‐Rong , Terunuma Atsushi , Janini George M. , Issaq Haleem J. , Vogel Jonathan C. , Veenstra Timothy D.
Published: January 2004

A simple and rapid method for characterizing hydrophobic integral membrane proteins and its utility for membrane proteomics using microcapillary liquid chromatography coupled on‐line with tandem mass spectrometry (μLC‐MS/MS) is described. The present technique does not rely on the use of detergents, strong organic acids or cyanogen bromide‐mediated proteolysis. A buffered solution of 60% methanol was used to extract, solubilize, and tryptically digest proteins within a preparation of Halobacterium (H.) halobium purple membranes. Analysis of the digested purple membrane proteins by μLC‐MS/MS resulted in the identification of all the predicted tryptic peptides of bacteriorhodopsin, including those that are known to be post‐translationally modified. In addition, 40 proteins from the purple membrane preparation were also identified, of which 80% are predicted to contain between 1 and 16 transmembrane domains. To evaluate the general applicability of the method, the same extraction, solubilization, and digestion conditions were applied to a plasma membrane fraction prepared from human epidermal sheets. A total of 117 proteins was identified in a single μLC‐MS/MS analysis, of which 55% are known to be integral or associated with the plasma membrane. Due to its simplicity, efficiency, and absence of MS interfering compounds, this technique can be used for the characterization of other integral membrane proteins and may be concomitantly applied for the analysis of membrane protein complexes or large‐scale proteomic studies of different membrane samples.
Nonreducing two‐dimensional gel electrophoresis for the detection of Bence Jones proteins in serum and urine
Authors: Miller Ingrid , Teinfalt Monika , Leschnik Michael , Wait Robin , Gemeiner Manfred
Published: January 2004

Nonreducing two‐dimensional gel electrophoresis (2‐DE) is described for the study of immunoglobulin disorders with asynchronous production of single chains. Unlike classical reducing 2‐DE, this method can distinguish between complex intact molecules and their free single chains (with different degrees of polymerization) and will thus be helpful for diagnosis of this type of disease. Examples are taken from canine patients, but the method may also be applied to both urine and serum specimens from other species. Nonreducing 2‐DE thus represents a useful tool complementary to classical 2‐DE, when further information about the appearance of free subunits or modifications of proteins are required, even in the presence of intact molecules.
Use of two‐dimensional gel electrophoresis proteome reference maps of dinoflagellates for species recognition of causative agents of harmful algal blooms
Authors: Chan Leo Lai , Hodgkiss Ivor John , Lu Songhui , Lo Samuel Chun‐Lap
Published: January 2004

The sample preparation procedures established for Prorocentrum triestinum were adapted to cover both thecate and athecate dinoflagellates. Further, whether trichloroacetic acid (TCA) precipitation can be used to fix and preserve the harmful or nuisance species from local waters that they infest was tested. Optimized technical procedures developed were used to generate proteome reference maps for eight other local causative species of harmful algal blooms (HABs): Prorocentrum micans, Prorocentrum minimum, Prorocentrum sigmoides, Prorocentrum dentatum, Scrippsiella trochoidea, Karenia longicanalis, Karenia digitata and Karenia mikimotoi; together with one American species Karenia brevis (Florida, USA). These proteome maps were used to test their ability for species recognition in a mixed culture of dinoflagellates and whether such investigations will provide a comparative view at a global level. Comparisons of proteome profiles were made (i) between closely related species within the same family; (ii) between distantly related species belonging to different types, i.e., gymnodinioids, prorocentroids or peridinioids, or (iii) between different groups, i.e., thecate (armored) dinoflagellate cells against athecate (naked or unarmored) dinoflagellate cells. Species‐specific two‐dimensional electrophoresis (2‐DE) protein profiles were observed in all ten species and it was possible to distinguish between even closely related species within the same family. To demonstrate the extent of reproducibility and usefulness of these 2‐DE reference maps, 2‐DE has been used to analyze three geographically distinct isolates of Prorocentrum dentatum, and to distinguish species composition in a mixed culture. Application of 2‐D PAGE analysis to differentiate between taxonomically confused strains of a single species could be a powerful taxonomic tool.
Immunostaining with dissociable antibody microarrays
Authors: Wang Yingjian
Published: January 2004

The availability of a large number of biological materials such as cDNA, antibodies, recombinant proteins, and tissues has promoted the development of microarray technologies that make use of these materials in high‐throughput screening assays. However, because microarray technologies have been less successful in examining proteins than DNA and mRNA , there is a need for improved protein microarray systems. To address this need, we developed an antibody microarray‐based immunostaining method that can analyze the properties of a large number of proteins simultaneously. In this method, antibodies are arrayed and immobilized on a solid support and cells bearing antigens of interest are attached to a second support. Apposition of the two supports allows the antibodies to dissociate from the array support and bind to the cellular antigens. After separation of the supports, antigen‐bound antibodies can be detected by standard secondary antibody techniques. These “dissociable” antibody arrays were used to detect both the expression and subcellular localization of a large number of specific proteins in various cultured cell types.
Identification of tumor‐associated proteins in oral tongue squamous cell carcinoma by proteomics
Authors: He Qing‐Yu , Chen Jia , Kung Hsiang‐Fu , Yuen Anthony Po‐Wing , Chiu Jen‐Fu
Published: January 2004

Oral tongue carcinoma is an aggressive tumor that particularly affects chronic smokers, drinkers and betel squid chewers. Patients often present symptoms at a late stage, and there is a high recurrence rate after treatment. In this article, we report the first proteomic analysis of oral tongue carcinoma to globally search for tumor related proteins. Apart from helping us to understand the molecular pathogenesis of the carcinoma, these proteins may also have potential clinical applications as biomarkers, enabling the tumor to be identified at an early stage in high risk individuals, treatment response to be predicted, and residual or recurrent carcinoma to be detected sooner after treatment. The protein expression profiles of ten oral tongue squamous cell carcinomas and their matched normal mucosal resection margins were examined by two‐dimensional gel electrophoresis and matrix‐assisted laser desorption/ionization‐time of flight mass spectroscopy. A number of tumor‐associated proteins including heat shock protein (HSP)60, HSP27, α B‐crystalline, ATP synthase β, calgranulin B, myosin, tropomyosin and galectin 1 were consistently found to be significantly altered in their expression levels in tongue carcinoma tissues, compared with their paired normal mucosae. The expression profile portrays a global protein alteration that appears specific to oral tongue cancer. The potential of utilizing these tumor related proteins for screening cancer and monitoring recurrence warrants further investigation.
Global analysis of the Ralstonia metallidurans proteome: Prelude for the large‐scale study of heavy metal response
Authors: Noël‐Georis Isabelle , Vallaeys Tatiana , Chauvaux Renaud , Monchy Sébastien , Falmagne Paul , Mergeay Max , Wattiez Ruddy
Published: January 2004

A proteome map of Ralstonia metallidurans strain CH34 was constructed using two‐dimensional (2‐D) gel electrophoresis in combination with automated Edman degradation and mass spectrometry (MS). R. metallidurans CH34 is the type‐strain of a family of highly related strains characterized by their multiple resistance to millimolar amounts of heavy metals, conferred by two large plasmids. The protein content of this bacterium grown in minimal medium was separated by 2‐D gel electrophoresis using various pH gradients. Protein identification was carried out via N‐terminal amino acid sequencing, matrix assisted laser desorption/ionisation‐time of flight‐mass spectrometry (MALDI‐TOF‐MS) and tandem MS. So far, 224 different proteins were characterized from 352 protein spots. Although the proteome map is still not complete, one could appraise the importance of proteomics for genome analyses through (i) the identification of previously undetected open reading frames, (ii) the identification of proteins not encoded by the already sequenced genome fragments, (iii) the characterization of protein‐encoding genes spanning two different contigs, enabling their merging, and (iv) the precise delineation of the N‐terminus of several proteins. Finally, this map will prove a useful tool in the identification of proteins differentially expressed in the presence of different heavy metals.
Proteome comparative analysis of gynogenetic haploid and diploid embryos of goldfish (Carassius auratus)
Authors: Huang Lingyun , Li Bingxia , Luo Chen , Xie Jinyun , Chen Ping , Liang Songping
Published: January 2004

Recently, it was found that in the gynogenetic haploid and diploid embryos of goldfish, which have exactly the same genome, the haploid condition results in obstruction of gene expression and abnormal development while the diploid embryos have normal gene expression and development. A diploid‐dependent regulatory apparatus was proposed to regulate gene expression. To study the difference at the protein expression level of the embryos of haploid and diploid in development, we extracted the total proteins of both the gynogenetic haploid and diploid embryos of goldfish in the same eye formation stage. Two‐dimensional polyacrylamide gel electrophoresis was used to separate proteins. The stained gel images were analyzed with the PDQUEST software. A part of protein spots that were differentially expressed in haploid and diploid embryos were identified by matrix assisted laser desorption/ionisation‐time of flight‐mass spectrometry and database analysis. Sixteen protein spots that were absolutely different (only expressed in diploid embryos but not in haploid embryos or vice versa) and 16 protein spots that were up‐ and downregulated were identified unambiguously, which include some proteins that are correlative with eyes development, nerve development, developing regulation, cell differentiation, and signal transduction. The different significantly gene expression during embryos developing between diploid and haploid is demonstrated.
Optimization of the first dimension for separation by two‐dimensional gel electrophoresis of basic proteins from human brain tissue
Authors: Pennington Kyla , McGregor Emma , Beasley Clare L. , Everall Ian , Cotter David , Dunn Michael J.
Published: January 2004

A major cause of poor resolution in the alkaline pH range of two‐dimensional electrophoresis (2‐DE) gels is unsatisfactory separation of basic proteins in the first dimension. We have compared methods for the separation of basic proteins in the isoelectric focusing dimension of human brain proteins. The combined use of anodic cup‐loading and the hydroxyethyldisulphide containing solution (DeStreak) produced better resolution in both analytical and micropreparative protein loaded 2‐DE gels than the other methods investigated.
Solvent and structure effects on rotamerization in 3,4‐alkylenedioxy‐ and 3,4‐dialkoxy‐2,5‐bis[di(tert‐butyl) hydroxymethyl]thiophenes: an NMR, IR, molecular mechanics and single‐crystal x‐ray study
Authors: Lomas John S. , Vaissermann Jacqueline
Published: January 2004

Solvent effects on the rotational equilibria of two‐rotor systems consisting of 3,4‐alkylenedioxy‐ and 3,4‐dialkoxy‐2,5‐bis[di(tert‐butyl)hydroxymethyl]thiophenes have been investigated. In these systems there are three rotational isomers: syn,syn (SS); anti,syn (AS or SA) and anti,anti (AA) (syn, [free] hydroxy group; anti, intramolecularly hydrogen‐bonded hydroxy group). In non‐hydrogen‐bonding solvents, such as chloroform and benzene, the AA rotamer is preferred for the larger bridges (three or four methylenes) and the dialkoxy derivatives, AS/SA being the minor component and SS hardly detectable. In contrast, the 3,4‐methylenedioxythiophene derivative is largely SS with AS/SA minor and just perceptible. The 3,4‐ethylenedioxythiophene (EDOT) derivative shows all three isomers in similar amounts. In hydrogen bond acceptor solvents, such as pyridine and DMSO, the two equilibria AA⇋AS/SA and AS/SA⇋SS shift in favour of the AS/SA and SS forms, respectively. The equilibrium constants, K1 and K2, show different sensitivities to solvent hydrogen bond basicity, the latter being about 25% (log/log) less sensitive than the former. Work on the BiEDOT derivative suggests that this is probably due to the proximity of the two OH groups, which inhibits solvation of the SS form. Comparison of rotation barriers (mainly in the range 20–22 kcal mol−1) with those for the monosubstituted compounds indicates that the SS→AS/SA barrier is unusually low in pyridine and DMSO. The structure of the AA isomer of the 3,4‐propylenedioxythiophene derivative has been determined by single‐crystal x‐ray diffraction. Copyright © 2004 John Wiley & Sons, Ltd.

Additional material for this paper is available in Wiley Interscience
Intermolecular interaction and thermodynamic properties of N‐methylacetamide and hydroxyacetonitrile dimers
Authors: Ju Xue‐Hai , Xie Lun‐Jia , Hua Wen‐Ting , Xiao He‐Ming
Published: January 2004

Ab initio Hartree–Fock (HF) and second‐order Møller–Plesset correlation energy correction (MP2) theories with 6–311+G* and aug‐cc‐pVDZ basis sets in combination with a counterpoise procedure for basis set superposition error (BSSE) correction were applied to the investigation of intermolecular interactions and thermodynamic properties of N‐methylacetamide and hydroxyacetonitrile (HAN) dimers. The heterodimer of N‐methylacetamide with HAN was selected as the computational model for the complex of cyclo[(S)‐His‐(S)‐Phe] (CHP) with (R)‐mandelonitrile, a chiral catalyst for the asymmetric hydrocyanation of aldehydes. Cyclic structures were identified as the most stable conformation in N‐methylacetamide dimer (I), HAN dimer (II) and their heterodimer (III). The corrected binding energies for I, II and III are −52.89, −45.83 and −49.95 kJ mol−1 at the MP2/aug‐cc‐pVDZ//HF/aug‐cc‐pVDZ level, respectively. The Gibbs free energy change (ΔG) in the process I+II → 2III was predicted to be −6.41 kJ mol−1 at 298.15 K. Dimer III can be spontaneously produced in the mixture of N‐methylacetamide and HAN, which is in agreement with the experimental fact that most cyanohydrins are capable of interacting with CHP and form non‐covalent complexes. Copyright © 2004 John Wiley & Sons, Ltd.
Configurational isomerization of push–pull thiazolidinone derivatives controlled by intermolecular and intramolecular RAHB: 1H NMR dynamic investigation of concentration and temperature effects
Authors: Marković Rade , Shirazi Ata , Džambaski Zdravko , Baranac Marija , Minić Dragica
Published: January 2004

1H NMR spectroscopy was used to investigate hydrogen bonding in the structurally related (Z)‐ and (E)‐5‐substituted‐2‐alkylidene‐4‐oxothiazolidines in polar and apolar solvents. The equilibrated mixtures of these typical push–pull alkenes consist of the intramolecularly H‐bonded E‐isomer and intermolecularly H‐bonded Z‐isomer in varying proportions which depend on the solvent polarity. For a representative of the series, (E)‐(5‐ethoxycarbonylmethyl‐4‐oxothiazolidin‐2‐ylidene)‐1‐phenylethanone (1), the lack of a concentration and temperature dependence of the large chemical NH shift (δ 12.06 ppm) in CDCl3 indicates strong intramolecular resonance‐assisted hydrogen‐bond formation (RAHB). The upfield chemical shifts of the NH proton of the (Z)‐1 isomer as a function of temperature increase and the large 1H NMR Δδ/ΔT value (−11.82 ppb°C−1, Z/E=60 : 40, or −10.33 ppb°C−1, Z/E=20 : 80) in CDCl3 are explained in terms of a decrease in intermolecular H‐bonding resulting in a greater amount of free or unassociated Z‐isomer. Copyright © 2004 John Wiley & Sons, Ltd.

Additional material for this paper is available in Wiley Interscience
Scope and limitation of the inductive effect :  importance of charged substituents
Authors: Exner Otto , Böhm Stanislav
Published: January 2004

The interaction of two relatively distant charged or dipolar groups was evaluated on 1,4‐disubstituted bicyclo[2.2.2]octane derivatives as the reaction energy of the isodesmic–homodesmotic reaction, in which this derivative is formed from two mono derivatives. Energies of the individual compounds were calculated at the B3LYP/6–311+G(d,p) level. All combinations of 12 common substituents were investigated, representing 78 reaction energies in a 12×12 data matrix. The behaviour of charged and dipolar substituents is considerably different. Interaction with a charged group is described precisely (R>0.997) by one parameter, essentially identical with the standard inductive constant σI. Interaction of two dipolar substituents depends also on σI, but requires an additional parameter, important particularly in the case of donor substituents (NH2, OH, Cl), less important to insignificant with the others. It is significantly correlated with the electronegativity of the first atom. Alternatively, it can be evaluated as a new parameter characterizing the substituent effect, say a new scale of group electronegativity different from the suggested scales. With two parameters, the interaction of polar substituents is expressed with similar high precision (R>0.99) as with charged substituents and one parameter. Copyright © 2004 John Wiley & Sons, Ltd.
Role of functional groups in linear regression analysis of molecular properties
Authors: Cortés‐Guzmán F. , Bader R. F. W.
Published: January 2004

This paper contrasts the use of functional groups, coupled with the quantum theory of atoms in molecules (QTAIM), in expressing the results of linear fittings of molecular properties, as opposed to expressing the linearity in terms of the total number of electrons. The use of QTAIM brings to the fore the additivity and transferability of group properties. Copyright © 2004 John Wiley & Sons, Ltd.
Contributions of anharmonics to the nuclear relaxation second hyperpolarizability of a push–pull polyene
Authors: Squitieri Emilio
Published: January 2004

A theoretical study of the contributions of anharmonics to the nuclear relaxation second hyperpolarizability of π‐conjugated push–pull polyenes by using an analytical evaluation of electrical properties method and a valence‐bond–charge‐transfer model was carried out. A relationship between nuclear relaxation and electronic contributions to the second hyperpolarizability is derived. It was found that the anharmonicity is essential in a numerical estimation of nuclear relaxation second hyperpolarizability. Copyright © 2004 John Wiley & Sons, Ltd.
Kinetics of the reactions between 1‐fluoro‐2,6‐dinitrobenzene and pyrrolidine and piperidine in binary solvent systems: Influence of the nucleophile structure
Authors: Mancini P. M. , Fortunato G. G. , Vottero L. R.
Published: January 2004

We studied the kinetics of the reaction between 1‐fluoro‐2,6‐dinitrobenzene and pyrrolidine or piperidine in ethyl acetate–chloroform or acetonitrile and acetonitrile–chloroform binary solvent mixtures. The kinetic response of these reactions was compared with that of the reactions with homopiperidine. The aim of this work was to evaluate the influence of the nucleophile structure and of solvent effects on those reactive systems. The amine structure has a great influence on second‐order rate constants, especially on the rate constants related to the catalyzed step. In mixtures with chloroform the amine structure is also responsible for the change in the reaction mechanism. Theoretical quantum mechanics calculations confirm that the origin of these results lies in stereoelectronic effects due to the conformational difference between the amino moieties in the intermediate σ adducts as they release the nucleofuge. Solvation effects are dominated by non‐specific interactions. The order of incidence of the molecular–microscopic solvent properties on the second‐order rate coefficient kA is dipolarity/polarizability>hydrogen‐bond donor ability (HBD)>hydrogen‐bond acceptor ability (HBA). The (HBA+HBD) and (HBA+HBA/HBD) solvent systems have similar solvation mechanisms: the critical state is preferentially solvated by the structure formed by intersolvent hydrogen‐bonded species. Mixtures of the type (HBA/HBD+HBD) manifest a particular solvation behavior. Among the reactive systems selected there is only one example in which preferential solvation is not operative. Copyright © 2004 John Wiley & Sons, Ltd.

Additional material for this paper is available in Wiley Interscience
Experimental and theoretical study of the homogeneous, unimolecular gas‐phase elimination kinetics of methyl oxalyl chloride
Authors: Cordova Tania , Rotinov Alexandra , Chuchani Gabriel
Published: January 2004

The products of the gas‐phase elimination of methyl oxalyl chloride are methyl chloroformate and carbon monoxide. The kinetics were determined in a static system over the temperature range 280.3–320.7 °C and pressure range 56–140.4 Torr. The reaction, in vessels seasoned with allyl bromide and in the presence of the free‐radical inhibitor cyclohexene, is homogeneous, unimolecular and follows a first‐order rate law. The rate coefficients are given by the Arrhenius equation: log[k1 (s−1)]=(12.73 ± 0.58)−(174.3 ± 6.3) kJ mol−1 (2.303 RT)−1. Theoretical studies of the mechanism at the semi‐empirical PM3 and MP2/6–31G* levels imply a concerted non‐synchronous process. Analysis of the three‐membered ring transition state suggests that polarization of the ClC(O) bond is rate limiting in the elimination process. The kinetics and thermodynamic parameters are in good agreement with the experimental values. Copyright © 2004 John Wiley & Sons, Ltd.
Rate enhancement of Diels–Alder reactions in aqueous solutions
Authors: Graziano Giuseppe
Published: January 2004

It is shown that the concept of internal pressure cannot be used to explain the strong rate enhancement of Diels–Alder reactions when carried out in water with respect to common organic solvents. Copyright © 2004 John Wiley & Sons, Ltd.
Density functional theory study of the Diels–Alder reactivities of [b]‐annelated cyclic five‐membered dienes
Authors: Punnagai M. , Dinadayalane T. C. , Narahari Sastry G.
Published: January 2004

B3LYP/6–31G* calculcations were performed to model the Diels–Alder reaction of cyclobutano‐, cyclobuteno‐ and benzo[b]‐ fused cyclic five‐membered ring dienes with two prototypical dienophiles, ethylene and acetylene. The cyclobuteno[b]‐fused dienes, which loose the unfavorable antiaromaticity upon cycloaddition, are the most reactive; in contrast, the benzo[b]‐fused dienes, which encounter disruption of aromaticity in the course of the reaction, are the least reactive. Synchronicity calculations based on bond order analysis indicate that the reactions of benzo[b]‐annelated dienes show significant deviations from synchronicity, indicating highly unsymmetrical transition states. Deformation energies were employed to corroborate the computed activation energies. Although there are some deviations in the quantitative results between ethylene and acetylene reactions, the trends are essentially the same with all the dienes considered, with acetylene showing a slightly higher reactivity. The comparison with the corresponding [c]‐fused dienes further strengthens the argument that product stability controls the reactivity in these reactions, as exemplified by excellent linear fits between the activation and reaction energies. Copyright © 2004 John Wiley & Sons, Ltd.

Additional material for this paper is available in Wiley Interscience
Deconstruction of Taft's σ* parameter: QSAR meets QALE
Authors: Babij Claudia , Poë Anthony J.
Published: January 2004

Taft's σ* parameter has been mostly disregarded in QSAR (quantitative structure–activity relationships) analyses because it appears to reveal only simple field‐inductive substituent effects. However, it can be shown that, when a reference reaction different from that adopted by Taft is used, the σ* values reveal considerably more subtle features. This occurs when a reference reaction parameter, pKa′, is used that is closely related to the Brønsted basicity of P‐donor molecules and that is regarded in QALE (quantitative analyses of ligand effects) analyses as measuring the purely σ‐donor properties of the phosphines. Values of Taft's σ* parameter for alkyl groups show an excellent linear correlation with pKa′ but significant deviations from the correlation increase in the order CH2Ph (0.19)<Ph (0.46)<p‐O‐i‐Pr (1.38)<OEt (1.44)<OMe (1.51)<OPh (1.82)<Cl (1.88), and the deviations for the p‐YC6H4 groups increase linearly with decreasing pKa′ as Y changes in the order Me2N (0.29)<MeO (0.32)<Me (0.39)<F (0.41)<H (0.46)<Cl (0.50)<F3C (0.60). The new substituent effects for these ‘deviant’ groups that can be derived from the linear correlations of σ* with pKa′ are different (even in sign for the p‐Me2NC6H4 group) from the original values of the Taft parameter, and they are much smaller than the additional effects detected here. These results show that σ* values contain within themselves a variety of new features that should be compared with those shown by parameters used in more recent QSAR analyses, and that might be useful in such analyses. Copyright © 2004 John Wiley & Sons, Ltd.
CC chemokine concentrations increase in respiratory distress syndrome and correlate with development of bronchopulmonary dysplasia
Authors: Baier R. John , Majid Abdul , Parupia Haroon , Loggins John , Kruger Thomas E.
Published: January 2004

Inflammation is one of the primary processes underlying respiratory distress syndrome (RDS) and its evolution into bronchopulmonary dysplasia (BPD). Recruitment and subsequent activation of macrophages in the lung are mediated by CC chemokines. The role of CC chemokines has not been extensively studied in the course of RDS. Serial tracheal aspirates (TA) were obtained from 56 mechanically ventilated infants with birth weights less than 1,500 g during intervals in the first 21 days of life. Tracheal aspirate concentrations of monocyte chemoattractant proteins‐1,2,3 (MCP‐1,2,3) and macrophage inflammatory proteins‐1α and ‐1β (MIP‐1α, MIP‐1β) were determined by enzyme‐linked immunosorbent assay (ELISA). Tracheal aspirate concentrations of MCP‐1, MCP‐2, MCP‐3, and MIP‐1β increased during the first week of life in infants with RDS, whereas MIP‐1α concentrations did not increase appreciably. Increased TA cytokine concentrations were associated with the development of BPD. Maximal TA concentrations of MCP‐1, MCP‐2, MCP‐3, MIP‐1α, and MIP‐1β were significantly higher in infants who were oxygen‐dependent at 28 postnatal days compared to infant who were not. Similarly, maximal TA MCP‐1, MCP‐2, and MCP‐3 but not MIP‐1α and MIP‐1β concentrations were significantly higher in infants who were oxygen‐dependent at 36 weeks of postconceptional age (PCA) than those who were not oxygen‐dependent at 36 weeks PCA. Histologic chorioamnionitis and isolation of Ureaplasma urealyticum from the airways were associated with higher maximal TA concentrations of MIP‐1α and MIP‐1β. Pulmonary hemorrhage was associated with increased maximal concentrations of MCP‐1, MCP‐2, and MCP‐3. These data suggest a role for CC chemokines in the development of BPD in the newborn infant. Pediatr Pulmonol. 2004; 37:137–148. © 2004 Wiley‐Liss, Inc.
Redesigned face mask improves “real life” aerosol delivery for nebuchamber
Authors: Amirav Israel , Mansour Yasser , Mandelberg Avigdor , Bar‐Ilan Igal , Newhouse Michael T.
Published: January 2004

The currently available facemask interface for the Nebuchamber (N) valved‐holding chamber (VHC) provides a very poor seal to the face, which, on average, decreases the aerosol dose and was previousely shown to increase the variability of aerosol delivery. The efficiency of a redesigned mask (RD) for the Nebuchamber with a potentially better seal was compared to the standard mask (SM) supplied with the N in a randomized real‐life crossover clinical trial. Twenty children (mean age, 26 ± 10 months) were randomized to use the Nebuchamber for 1 week with the old mask and then for another week with the newer mask, and vice versa. Filters, changed daily, inserted between the mask and the VHC, trapped the delivered drug (budesonide). The dose of budesonide was quantified by high‐performance liquid chromatography (HPLC). Use of the redesigned mask improved aerosol delivery to the filter by 30%, compared to the SM (mean 28.1 ± 7.7% of nominal dose with RD vs. 21.6 ± 9.6% with SM, P = 0.017). The relatively high within‐subject variability in aerosol delivery (36–38%) did not change, however. Facemasks are arguably the most important determinants of aerosol delivery. The newly developed RD for the Nebuchamber proved to be considereably more efficient than the SM for aerosol delivery to young children. Patient‐related factors may be more important with respect to the variability observed. Pediatr Pulmonol. 2004; 37:172–177. © 2004 Wiley‐Liss, Inc.
Design of exponential observers for nonlinear systems by embedding
Authors: Rapaport A. , Maloum A.
Published: January 2004

For nonlinear systems in ℝn which are observable but not uniformly, we study how to design explicitly exponential observers, after having the system immersed in ℝm with m>n. The central issue concerns the determination of a lipschitzian extension in ℝm of the dynamics, which is defined exclusively on a subset of empty interior. We propose some constructive tools and illustrate their utility on a biological example. Copyright © 2004 John Wiley & Sons, Ltd.
Selling system dynamics to (other) social scientists
Authors: Repenning Nelson P.
Published: January 2004

In the last decade I have tried to use system dynamics to do research that is acceptable to scholars from other social science communities. In this paper I reﬂect upon this experience and outline several errors that reduced the accessibility of my work to those outside the system dynamics community. While some of these mistakes are likely unique to me, others are more common to research that uses system dynamics. Acknowledging these errors has several implications for the future organization of the ﬁeld. Copyright © 2003 John Wiley & Sons, Ltd.
Facilitating critical systemic praxis (CSP) by means of experiential learning and conceptual tools
Authors: McIntyre Janet
Published: January 2004

The article discusses and summarizes a learning resource to facilitate praxis tools for systemic governance and creative problem solving. The conceptual tools are provided as a basis for addressing challenging and complex problems through participatory design, planning and decision‐making processes that strive to be socially and environmentally just. The paper draws on earlier work on tools for ethical thinking and caring. The participatory learning process aims to promote better transdiciplinary and cultural understanding and thus to promote sustainable praxis outcomes. The learning outcomes are to develop problem‐solving ability and better governance (in the broad sense used by Vickers and White) through appreciation of the whole system and the value positions through which it is perceived. Copyright © 2004 John Wiley & Sons, Ltd.
The last days of a systems research centre: an empirical case study
Authors: Ponce Héctor R.
Published: January 2004

This paper presents an empirical case study in which the object of research was constituted by a small systems research centre within an English university. This research coincides with the [last days] of this centre and it may help to understand why other systems centres have also declined. A series of observations were collected through participant observation and later analysed through examining the underlying linguistic structures that characterized the conversational interactions among members of the centre. As a result of such analysis, some research strategies are proposed on how the researcher could have supported the development of the centre by making precise interventions on its communication structure. It is also indicated how individual and collective emergence was prevented. Copyright © 2004 John Wiley & Sons, Ltd.
The role of stressful life events in the development of depressive symptoms in adolescence—a longitudinal community study
Authors: Waaktaar Trine , Borge Anne Inger Helmen , Fundingsrud Hans Petter , Christie Helen Johnsen , Torgersen Svenn
Published: January 2004

Depressive symptoms were measured in a cohort of community‐based adolescents (n=163) at two time‐points, with 1 year intervening. At Time 2, participants also answered a scale about past‐year stressful life events. Depressive symptoms increased from Time 1 to Time 2, the effect being stronger for girls than for boys. Depressive symptoms were significantly correlated with concurrent measures of recent stressful life events, but this relationship disappeared after controlling for previous depressive symptoms. Rather, previous level of depressive symptoms predicted stressful life events. This demonstrates that a unidirectional model of stressful life events as the cause of depressive symptoms in adolescents is too simplistic.
Carbon Dioxide Laser Salvage Surgery after Radiotherapy Failure in T1 and T2 Glottic Carcinoma
Authors: Puxeddu Roberto , Piazza Cesare , Mensi Maria C. , Ledda Gian Peppino , Argiolas Federico , Peretti Giorgio
Published: January 2004

OBJECTIVES

Recurrent glottic carcinoma after radiotherapy (RT) may be managed by open neck or endoscopic surgery. The impact of endoscopic treatment with CO2 laser for recurrent glottic carcinoma after RT is reported.

METHODS

We present the oncologic and vocal outcomes of a retrospective study based on a series of 16 patients with rT1 and rT2 glottic carcinoma who were endoscopically managed between February 1995 and December 1999 after RT failure. All patients were males with a mean age of 68.7 years (range, 50 to 87 years). Before RT, the lesions had been staged as T1 N0 in 11 patients and T2 N0 in 5, and after RT as rT1 N0 in 12 and rT2 N0 in 4. According to the European Laryngological Society classification, a total of 9 transmuscular, 3 total, and 4 extended cordectomies were performed. Mean follow‐up was 45 months (range, 9 to 79 months).

RESULTS

Endoscopic salvage surgery was successful in 14 patients. One of them developed a second recurrence and was definitively cured with an additional endoscopic procedure. Two of the 16 patients had recurrent disease after salvage laser surgery and died due to progression of disease. Ultimate local control with laser alone at 3 years was 87.1%, according to the Kaplan‐Meier method. Laryngeal preservation was obtained in all survivors after endoscopic rescue surgery. Voice analysis showed a clear correlation between the amount of vocal cord tissue resected and decrease of the vocal outcome.

CONCLUSIONS

The present series indicates that selected recurrences after primary RT for T1 and T2 glottic carcinoma are eligible for endoscopic salvage surgery with oncologic results comparable to those with open neck procedures but with a lower complication rate and a favorable functional outcome.
Cellular Changes of Reissner's Membrane in Meniere's Disease: Human Temporal Bone Study
Authors: Cureoglu Sebahattin , Schachern Patricia A. , Paul Saurav , Paparella Michael M. , Singh Rajesh K.
Published: January 2004

Objective

To study the cellular characteristics of Relssner's membrane (RM) in temporal bones (TBs) from patients with endolymphatic hydrops with symptoms of Menlere's disease (EH/+MD) and TBs with endolymphatic hydrops without symptoms of Meniere's disease (EH/‐MD) in an effort to understand the role of endolymphatic hydrops in MD symptoms.

Study Design

Comparative study of human TB histopathology.

Methods and Materials

Epithelial and mesothelial cellularity of RM from control TBs, TBs from patients with EH/+MD, and TBs from patients with EH/‐MD were compared. The cellularity of epithelial and mesothelial cell nuclel (defined as number of cells/ 100 μm width of RM) were counted along the width of RM. The width of RM was measured from the vestibular crest of the spiral ligament to the limbus spiralis.

Results

The cellular densities of epithelial cells in the basal and middle turns of RM were significantly higher in the EH/+MD and EH/‐MD groups compared with “controls.” There was no difference in epithelial cellularity between EH/+MD and EH/‐MD. There was a decrease in the number of mesothelial cells of RM in the basal turn in EH/+MD and EH/‐MD groups (statistically significant only in EH/+MD group) when compared with controls. The number of mesothelial cells of RM in the middle turn in EH/+MD and EH/‐MD groups were significantly decreased compared with normals.

Discussion

Similar findings in cellularity of RM in temporal bones with EH/+MD and EH/‐MD suggest that pathophysiologic mechanisms other than hydrops may be responsible for symptoms in Meniere's disease.
Sale of monopoly information and behavior of rivaling clients: A theoretical perspective
Authors: Chang Chun‐Hao , Prakash Arun J. , Yeh Shu
Published: January 2004

This paper studies a three‐stage Bayesian–Cournot game where rivaling firms sign contracts with an information monopoly to purchase proprietary information. The rivaling firms use the external information to create competitive advantage over one another. Knowing the rivalry among its clients, the information monopoly can exploit them by playing one client against another. The information‐selling strategy depends on the clients' in‐house information technology, the uncertainty of the economic environment, and the number of potential clients. The existence of an information market makes rivaling producers worse off and consumers better off. It is possible that the service of the information monopoly is a private good but a social bad.