bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum
Authors: Paper Janet M. , Scott‐Craig John S. , Adhikari Neil D. , Cuomo Christina A. , Walton Jonathan D.
Published: August 2007

High‐throughput MS/MS was used to identify proteins secreted by Fusarium graminearum (Gibberella zeae) during growth on 13 media in vitro and in planta during infection of wheat heads. In vitro secreted proteins were collected from the culture filtrates, and in planta proteins were collected by vacuum infiltration. A total of 289 proteins (229 in vitro and 120 in planta) were identified with high statistical confidence. Forty‐nine of the in planta proteins were not found in any of the in vitro conditions. The majority (91–100%) of the in vitro proteins had predicted signal peptides, but only 56% of the in planta proteins. At least 13 of the nonsecreted proteins found only in planta were single‐copy housekeeping enzymes, including enolase, triose phosphate isomerase, phosphoglucomutase, calmodulin, aconitase, and malate dehydrogenase. The presence of these proteins in the in planta but not in vitro secretome might indicate that significant fungal lysis occurs during pathogenesis. On the other hand, several of the proteins lacking signal peptides that were found in planta have been reported to be potent immunogens secreted by animal pathogenic fungi, and therefore could be important in the interaction between F. graminearum and its host plants.
Well‐controlled polymerization of 2‐azidoethyl methacrylate at near room temperature and click functionalization
Authors: Li Yu , Yang Junwei , Benicewicz Brian C.
Published: August 2007

A functional monomer with a pendant azide moiety, 2‐azidoethyl methacrylate (AzMA), was polymerized via reversible addition‐fragmentation chain transfer (RAFT) polymerization with excellent control over the molecular weight distribution (PDI = 1.05–1.15). The subsequent copper‐catalyzed Huisgen 1,3‐dipolar cycloadditions of phenyl acetylene with polyAzMA was achieved at room temperature with high conversion. The resulting functional polymer exhibited identical 1H NMR and IR spectra with the polymer of the same molecular structure but prepared by a prefunctionalization approach, confirming the retention of the azide side chains during the RAFT polymerization of AzMA. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4300–4308, 2007
Synthesis and characterization of 6‐ and 12‐arm star polymers by nitroxide‐mediated radical polymerization of St and MA from dendritic TIPNO‐based hexafunctional and dodecafunctional macroinitiators
Authors: Miura Yozo , Dairoku Masamichi
Published: August 2007

Dendritic multifunctional macroinitiators having six and 12 TIPNO‐based alkoxyamines, TIPNO‐6 and TIPNO‐12, were synthesized and used in the living radical polymerization of styrene (St), methyl acrylate (MA), N,N‐dimethylacrylamide (DMAAm), and isoprene (IP). The polymerizations of St initiated with TIPNO‐6 gave 6‐arm star polymers with narrow polydispersities of 1.14–1.18. In the polymerizations of MA initiated with TIPNO‐6 and TIPNO‐12, the influences of added TIPNO on the polydispersity indexes (PDIs) of the resulting star polymers were first investigated, and this led to the successful formation of poly(MA) star polymers with narrow polydispersities (1.10–1.18). Moreover, the polymerizations of DMAAm and IP from TIPNO‐6 in the presence or absence of TIPNO were briefly investigated. The benzyl ether bonds of the poly(St) and poly(MA) star polymers were cleaved by treating with Me3SiI or Pd/C, and the resulting arm's parts were analyzed with SEC. The PDIs of the resulting arm parts were low (1.19–1.23), and the Mns agreed with the Mn,theor, indicating that the poly(St) and poly(MA) star polymers had well‐controlled arms. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4364–4376, 2007
Unmet needs of gynaecological cancer survivors: implications for developing community support services
Authors: Beesley Vanessa , Eakin Elizabeth , Steginga Suzanne , Aitken Joanne , Dunn Jeff , Battistutta Diana
Published: August 2007

After treatment completion, gynaecological cancer survivors may face long‐term challenges and late effects, specific to this disease. Available research on supportive care needs of women with gynaecological cancer is limited. This study aimed to determine the prevalence and correlates of unmet needs within a population of gynaecological cancer survivors. Eight hundred and two women participated in a population‐based mail survey in 2004 (56% response rate). The questionnaire included a validated instrument to assess 45 need items across multiple supportive care domains, and a range of measures to evaluate related correlates consistent with a social–ecological perspective. Forty‐three per cent of respondents reported having at least one moderate‐ or high‐level unmet need. The five highest included needing help with fear about the cancer spreading (17%), concerns about the worries of those close to them (15%), uncertainty about the future (14%), lack of energy/tiredness (14%), and not being able to do things they used to do (14%). Subgroups of women with higher odds of reporting ‘some’ unmet needs across multiple supportive care domains include those who, are not in remission, live with lymphoedema or are unable to work due to illness. Odds were also higher for women who had undergone more recent treatment, and who lived in rural or remote locations. Further assistance with the top specific concerns of gynaecological cancer survivors is recommended. Identified subgroups with higher needs are important targets for support. Copyright © 2007 John Wiley & Sons, Ltd.
Diagnostics of SiOx‐Containing Layers Deposited on Powder Particles by Dielectric Barrier Discharge
Authors: Hähnel Marcel , Brüser Volker , Kersten Holger
Published: August 2007

We report on the analysis of the composition and internal structure of SiOx layers deposited on powder particles by using HMDSO as monomer, different oxygen admixtures in argon, and a dielectric barrier surface discharge under atmospheric pressure. Composition and structure of the deposited layers with special regard to silicon, carbon, and hydrocarbon bonding were studied by FTIR and XPS measurements and compared with previous investigations from the literature. For correlation of the layer composition and the plasma gas phase we used mass spectrometric analysis of the exhaust gas. The stoichiometric ratios of the deposited layers are remarkably influenced by the Ar/O2 ratio and the discharge conditions.

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Polymorphic variants in α‐methylacyl‐CoA racemase and prostate cancer
Authors: Daugherty Sarah E. , Shugart Yin Yao , Platz Elizabeth A. , Fallin M. Daniele , Isaacs William B. , Pfeiffer Ruth M. , Welch Robert , Huang Wen‐Yi , Reding Douglas , Hayes Richard B.
Published: August 2007

BACKGROUND

Alpha‐methylacyl‐CoA racemase (AMACR), which prepares branched chain fatty acids to be metabolized for energy and is implicated in the activation of the COX‐inhibiting form of ibuprofen, is overexpressed in prostate cancer and its precursor lesions. Significant differences in AMACR allele frequencies have been reported for hereditary prostate cancer (HPC), but the relevance of AMACR in the context of its substrates have not been studied.

METHODS

We conducted a nested case‐control study of 1,318 prostate cancer cases and 1,842 controls from the screening arm of the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Five non‐synonymous (nsSNP) and two intronic AMACR polymorphisms were genotyped. Conditional logistic regression models were used to evaluate the associations between the genetic variants and prostate cancer.

RESULTS

Overall, prostate cancer was not related to AMACR gene variants; however, risks for prostate cancer were significantly reduced among regular ibuprofen users who carried allele variants at four nsSNP loci (M9V, D175G, S201L, and K277E; all Ptrend < 0.05) or carried the TGTGCG haplotype (OR = 0.65; 95% CI 0.44–0.97). No AMACR‐related associations were noted among nonregular ibuprofen users (all Pinteraction > 0.33).

CONCLUSION

AMACR gene variants were unrelated to prostate cancer overall in this study. The protective associations observed among ibuprofen users suggest that AMACR gene variants may enhance the chemopreventive effects of ibuprofen on prostate cancer risk. Prostate 67: 1487–1497, 2007. © 2007 Wiley‐Liss, Inc.
Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
Authors: Kondrashov Dmitry A. , Zhang Wei , Aranda Roman , Stec Boguslaw , Phillips George N.
Published: August 2007

Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6122 and two structures in space groups P212121 and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P21. While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Cα rmsd of 0.54–0.79 Å) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Cα rmsd values of 0.28–0.37 Å). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure. Proteins 2008. © 2007 Wiley‐Liss, Inc.
What is the relationship between the global structures of apo and holo proteins?
Authors: Brylinski Michal , Skolnick Jeffrey
Published: August 2007

It is well known that ligand binding and release may induce a wide range of structural changes in a receptor protein, varying from small movements of loops or side chains in the binding pocket to large‐scale domain hinge‐bending and shear motions or even partial unfolding that facilitates the capture and release of a ligand. An interesting question is what in general are the conformational changes triggered by ligand binding? The aim of this work is analyze the magnitude of structural changes in a protein resulting from ligand binding to assess if the state of ligand binding needs to be included in template‐based protein structure prediction algorithms. To address this issue, a nonredundant dataset of 521 paired protein structures in the ligand‐free and ligand‐bound form was created and used to estimate the degree of both local and global structure similarity between the apo and holo forms. In most cases, the proteins undergo relatively small conformational rearrangements of their tertiary structure upon ligand binding/release (most root‐mean‐square‐deviations from native, RMSD, are <1 Å). However, a clear difference was observed between single‐ and multiple‐domain proteins. For the latter, RMSD changes greater than 1 Å and sometimes larger were found for almost 1/3 of the cases; these are mainly associated with large‐scale hinge‐bending movements of entire domains. The changes in the mutual orientation of individual domains in multiple‐domain proteins upon ligand binding were investigated using a mechanistic model based on mass‐weighted principal axes as well as interface buried surface calculations. Some preferences toward the anticipated mechanism of protein domain movements are predictable based on the examination of just the ligand‐free structural form. These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Biological implications of SNPs in signal peptide domains of human proteins
Authors: Jarjanazi Hamdi , Savas Sevtap , Pabalan Noel , Dennis James W. , Ozcelik Hilmi
Published: August 2007

Proteins destined for secretion or membrane compartments possess signal peptides for insertion into the membrane. The signal peptide is therefore critical for localization and function of cell surface receptors and ligands that mediate cell–cell communication. About 4% of all human proteins listed in UniProt database have signal peptide domains in their N terminals. A comprehensive literature survey was performed to retrieve functional and disease associated genetic variants in the signal peptide domains of human proteins. In 21 human proteins we have identified 26 disease associated mutations within their signal peptide domains, 14 mutations of which have been experimentally shown to impair the signal peptide function and thus influence protein transportation. We took advantage of SignalP 3.0 predictions to characterize the signal peptide prediction score differences between the mutant and the wild‐type alleles of each mutation, as well as 189 previously uncharacterized single nucleotide polymorphisms (SNPs) found to be located in the signal peptide domains of 165 human proteins. Comparisons of signal peptide prediction outcomes of mutations and SNPs, have implicated SNPs potentially impacting the signal peptide function, and thus the cellular localization of the human proteins. The majority of the top candidate proteins represented membrane and secreted proteins that are associated with molecular transport, cell signaling and cell to cell interaction processes of the cell. This is the first study that systematically characterizes genetic variation occurring in the signal peptides of all human proteins. This study represents a useful strategy for prioritization of SNPs occurring within the signal peptide domains of human proteins. Functional evaluation of candidates identified herein may reveal effects on major cellular processes including immune cell function, cell recognition and adhesion, and signal transduction. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Prediction of kinase‐specific phosphorylation sites with sequence features by a log‐odds ratio approach
Authors: Li Tingting , Li Fei , Zhang Xuegong
Published: August 2007

Protein phosphorylation plays important roles in a variety of cellular processes. Detecting possible phosphorylation sites and their corresponding protein kinases is crucial for studying the function of many proteins. This article presents a new prediction system, called PhoScan, to predict phosphorylation sites in a kinase‐family‐specific way. Common phosphorylation features and kinase‐specific features are extracted from substrate sequences of different protein kinases based on the analysis of published experiments, and a scoring system is developed for evaluating the possibility that a peptide can be phosphorylated by the protein kinase at the specific site in its sequence context. PhoScan can achieve a specificity of above 90% with sensitivity around 90% at kinase‐family level on the data experimented. The system is applied on a set of human proteins collected from Swiss‐Prot and sets of putative phosphorylation sites are predicted for protein kinase A, cyclin‐dependent kinase, and casein kinase 2 families. PhoScan is available at http://bioinfo.au.tsinghua.edu.cn/phoscan/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structure of biosynthetic N‐acetylornithine aminotransferase from Salmonella typhimurium: Studies on substrate specificity and inhibitor binding
Authors: Rajaram V. , Ratna Prasuna P. , Savithri H. S. , Murthy M. R. N.
Published: August 2007

Acetylornithine aminotransferase (AcOAT) is one of the key enzymes involved in arginine metabolism and catalyzes the conversion of N‐acetylglutamate semialdehyde to N‐acetylornithine (AcOrn) in the presence of L‐glutamate. It belongs to the Type I subgroup II family of pyridoxal 5′‐phosphate (PLP) dependent enzymes. E. coli biosynthetic AcOAT (eAcOAT) also catalyzes the conversion of N‐succinyl‐L‐2‐amino‐6‐oxopimelate to N‐succinyl‐L,L‐diaminopimelate, one of the steps in lysine biosynthesis. In view of the critical role of AcOAT in lysine and arginine biosynthesis, structural studies were initiated on the enzyme from S. typhimurium (sAcOAT). The Km and kcat/Km values determined with the purified sAcOAT suggested that the enzyme had much higher affinity for AcOrn than for ornithine (Orn) and was more efficient than eAcOAT. sAcOAT was inhibited by gabaculine (Gcn) with an inhibition constant (Ki) of 7 μM and a second‐order rate constant (k2) of 0.16 mM−1 s−1. sAcOAT, crystallized in the unliganded form and in the presence of Gcn or L‐glutamate, diffracted to a maximum resolution of 1.90 Å and contained a dimer in the asymmetric unit. The structure of unliganded sAcOAT showed significant electron density for PLP in only one of the subunits (subunit A). The asymmetry in PLP binding could be attributed to the ordering of the loop Lαk‐βm in only one subunit (subunit B; the loop from subunit B comes close to the phosphate group of PLP in subunit A). Structural and spectral studies of sAcOAT with Gcn suggested that the enzyme might have a low affinity for PLP‐Gcn complex. Comparison of sAcOAT with T. thermophilus AcOAT and human ornithine aminotransferase suggested that the higher specificity of sAcOAT towards AcOrn may not be due to specific changes in the active site residues but could result from minor conformational changes in some of them. This is the first structural report of AcOAT from a mesophilic organism and could serve as a basis for drug design as the enzyme is important for bacterial cell wall biosynthesis. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: Implications for barnase catalysis
Authors: Roca Maite , De Maria Leonardo , Wodak Shoshana J. , Moliner Vicente , Tuñón Iñaki , Giraldo Jesús
Published: August 2007

To examine the possible relationship of guanine‐dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 ′. Similar energetic profiles featuring two minima corresponding to the anti and syn Gχ regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of ∼4 kcal/mol were obtained for the anti → syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gχ angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 ′P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2′. The simulations revealed that the O2 ′ attack along the syn Gχ was more favorable than that along the anti Gχ: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the OP bond formation; structurally, a lesser O2 ′P initial distance, and a better suited orientation for an in‐line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase–ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ′ proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure and mechanism. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A model study of protein nascent chain and cotranslational folding using hydrophobic‐polar residues
Authors: Lu Hsiao‐Mei , Liang Jie
Published: August 2007

To study protein nascent chain folding during biosynthesis, we investigate the folding behavior of models of hydrophobic and polar (HP) chains at growing length using both two‐dimensional square lattice model and an optimized three‐dimensional 4‐state discrete off‐lattice model. After enumerating all possible sequences and conformations of HP heteropolymers up to length N = 18 and N = 15 in two and three‐dimensional space, respectively, we examine changes in adopted structure, stability, and tolerance to single point mutation as the nascent chain grows. In both models, we find that stable model proteins have fewer folded nascent chains during growth, and often will only fold after reaching full length. For the few occasions where partial chains of stable proteins fold, these partial conformations on average are very similar to the corresponding parts of the final conformations at full length. Conversely, we find that sequences with fewer stable nascent chains and sequences with native‐like folded nascent chains are more stable. In addition, these stable sequences in general can have many more point mutations and still fold into the same conformation as the wild type sequence. Our results suggest that stable proteins are less likely to be trapped in metastable conformations during biosynthesis, and are more resistant to point‐mutations. Our results also imply that less stable proteins will require the assistance of chaperone and other factors during nascent chain folding. Taken together with other reported studies, it seems that cotranslational folding may not be a general mechanism of in vivo protein folding for small proteins, and in vitro folding studies are still relevant for understanding how proteins fold biologically. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Kinetically driven refolding of the hyperstable EBNA1 origin DNA‐binding dimeric β‐barrel domain into amyloid‐like spherical oligomers
Authors: Freire Eleonora , Oddo Cristian , Frappier Lori , de Prat‐Gay Gonzalo
Published: August 2007

The Epstein‐Barr nuclear antigen 1 (EBNA1) is essential for DNA replication and episome segregation of the viral genome, and participates in other gene regulatory processes of the Epstein‐Barr virus in benign and malignant diseases related to this virus. Despite the participation of other regions of the protein in evading immune response, its DNA binding, dimeric β‐barrel domain (residues 452–641) is necessary and sufficient for the main functions. This domain has an unusual topology only shared by another viral origin binding protein (OBP), the E2 DNA binding domain of papillomaviruses. Both the amino acid and DNA target sequences are completely different for these two proteins, indicating a link between fold conservation and function. In this work we investigated the folding and stability of the DNA binding domain of EBNA1 OBP and found it is extremely resistant to chemical, temperature, and pH denaturation. The thiocyanate salt of guanidine is required for obtaining a complete transition to a monomeric unfolded state. The unfolding reaction is extremely slow and shows a marked uncoupling between tertiary and secondary structure, indicating the presence of intermediate species. The Gdm.SCN unfolded protein refolds to fully soluble and spherical oligomeric species of 1.2 MDa molecular weight, with identical fluorescence centre of spectral mass but different intensity and different secondary structure. The refolded spherical oligomers are substantially less stable than the native recombinant dimer. In keeping with the substantial structural rearrangement in the oligomers, the spherical oligomers do not bind DNA, indicating that the DNA binding site is either disrupted or participates in the oligomerization interface. The puzzling extreme stability of a dimeric DNA binding domain from a protein from a human infecting virus in addition to a remarkable kinetically driven folding where all molecules do not return to the most stable original species suggests a co‐translational and directional folding of EBNA1in vivo, possibly assisted by folding accessory proteins. Finally, the oligomers bind Congo red and thioflavin‐T, both characteristic of repetitive β‐sheet elements of structure found in amyloids and their soluble precursors. The stable nature of the “kinetically trapped” oligomers suggest their value as models for understanding amyloid intermediates, their toxic nature, and the progress to amyloid fibers in misfolding diseases. The possible role of the EBNA1 spherical oligomers in the virus biology is discussed. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Modelling suppressed and active convection. Comparing a numerical weather prediction, cloud‐resolving and single‐column model
Authors: Petch J. C. , Willett M. , Wong R. Y. , Woolnough S. J.
Published: August 2007

This paper describes the design of and basic results from a case study to compare simulations of convection over the Tropical West Pacific. Simulations are carried out using a cloud‐resolving model (CRM), a global numerical weather prediction (NWP) model and a single‐column version of the NWP model (SCM). The experimental design for each model type is discussed and then results are compared. The periods simulated each include a regime with strong convective activity, a much more suppressed regime with far less convection, as well as the transition between these regimes. The description of the design and basic results from this study are given in some detail, as a study including all these model types is relatively new. Comparing the local forcing due to the dynamics in the NWP model with the observed forcing used to drive the CRM and SCM it is found that there is good agreement for one period chosen but significant differences for another. This is also seen in fields such as rain rate and top‐of‐atmosphere radiation. Using the period with good agreement we are able to identify examples of biases in the NWP model that are also reproduced in the SCM. Also discussed are examples of biases in the NWP simulation that are not reproduced in the SCM. It is suggested that understanding which biases in the SCM are consistent with the full NWP model can help focus the use of an SCM in this framework. © Crown Copyright 2007. Reproduced with the permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd
The idempotent Dirac density matrix as a functional of the diagonal ground‐state electron density obtained from diffraction experiments
Authors: March N. H.
Published: August 2007

The idempotent Dirac single‐particle (s) density matrix γs(r,r′) as a functional of a given one‐body potential V(r) was constructed to all orders in perturbation theory by March and Murray, some four and a half decades ago. While the subsequent theorems of DFT ensure that V is a functional of the ground‐state density ρ, only recently has V been written explicitly as a functional of the Dirac density matrix γs. In the present study, both functionals γs[ρ] and γs[V] are studied; first for some model potentials V and somewhat then more generally in terms of partial differential equations. This later procedure should open up a route to treat numerically molecules of biophysical interest, provided the ground‐state electron density ρ(r) is initially determined from diffraction experiments. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study of ignition reactions of linear symmetrical monoethers as potential diesel fuel additives: DFT calculations
Authors: Marrouni Karim El , Abou‐Rachid Hakima , Kaliaguine Serge
Published: August 2007

This work investigates the chemical reactivity of four linear symmetrical monoethers with molecular oxygen. Such oxygenated compounds may be considered as potential diesel fuel additives in order to reduce the ignition delay in diesel fuel engines. For this purpose, a kinetic study is proposed to clarify the relation between the molecular structure of the fuel molecule and its ignition properties. To this end, DFT calculations were performed for these reactions using B3LYP/6‐311G(d,p) and BH&HLYP/6‐311G(d,p) to determine structures, energies, and vibrational frequencies of stationary points as well as activated complexes involved in each gas‐phase combustion initiation reaction of the monoethers CH3OCH3, C2H5OC2H5, C3H7OC3H7, or C4H9OC4H9 with molecular oxygen. This theoretical kinetic study was carried out using electronic structure results and the transition state theory, to assess the rate constants for all studied combustion reactions. As it has been shown in our previous work [Abou‐Rachid et al., J Mol Struct (Theochem) 2003, 621, 293], the cetane number (CN) of a pure organic molecule depends on the initiation rate of its homogeneous gas‐phase reaction with molecular oxygen. Indeed, the calculated initiation rate constants of the H‐abstraction process of linear monoethers with O2 show a very good correlation with experimental CN data of these pure compounds at T = 1,000 K. This temperature is representative of the operating conditions of a diesel fuel engine. © 2007 Wiley Periodicals, Inc. Int Quantum Chem, 2008
Possible properties of positron states in physics and chemistry of a surface and in semiconductor nanotechnologies
Authors: Grafutin V. I. , Svetlov‐Prokop'Ev E. P. , Timoshenkov S. P. , Kalugin V. V. , Artemov E. I.
Published: August 2007

The possibilities of positron beam annihilation spectroscopy for research quantum dots, quantum wells, quantum wires in chemistry and physics of surface and semiconductor nanotechnologies are discussed. The relations between the basic characteristics of positron annihilation this states and parameters of these structures were obtained.
High‐order harmonic generation of heteronuclear diatomic molecules in intense ultrashort laser fields: An all‐electron TDDFT study
Authors: Heslar John , Carrera Juan , Telnov Dmitry , Chu Shih‐I
Published: August 2007

We present a time‐dependent density functional theory (TDDFT), with proper asymptotic long‐range potential, for nonperturbative treatment of multiphoton processes of homonuclear and heteronuclear diatomic molecules in intense ultrashort laser fields. A time‐dependent two‐center generalized pseudospectral method is presented for accurate and efficient treatment of the TDDFT equations in space and time. The procedure allows nonuniform and optimal spatial grid discretization of the Hamiltonian in prolate spheroidal coordinates and a split‐operator scheme in the energy representation is used for the time propagation of the individual molecular spin‐orbital. The theory is applied to a detailed all‐electron study of multiphoton ionization (MPI) and high‐order harmonic generation (HHG) processes of N2 and CO molecules in intense laser pulses. The results reveal intriguing and substantially different nonlinear optical response behaviors for N2 and CO, despite the fact that CO has only a very small permanent dipole moment. In particular, we found that the MPI rate for CO is higher than that of N2. Furthermore, while laser excitation of the homonuclear N2 molecule can generate only odd harmonics, both even and odd harmonics can be produced from the heteronuclear CO molecule. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Screening method for the addition of bovine blood‐based binding agents to food using liquid chromatography triple quadrupole mass spectrometry
Authors: Grundy Helen H. , Reece Paul , Sykes Mark D. , Clough Julie A. , Audsley Neil , Stones Robert
Published: August 2007

We report the development of a qualitative method to detect the addition of blood‐based binding agents to food products. The method is based on the detection of species‐specific marker peptides, fibrinopeptides, released from the blood protein fibrinogen during gelling of the blood protein by thrombin. The fibrinopeptides were isolated from foods spiked with commercial bovine binding agent by acid precipitation followed by enrichment using solid‐phase extraction and analysed by liquid chromatography electrospray ionisation triple quadrupole mass spectrometry. Fibrinopeptide A was found to be an effective marker in fresh, processed and cooked food matrices spiked with 5% (v/w) bovine binding agent. © Crown copyright 2007. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Quantitative determination of acetylcholine in microdialysis samples using liquid chromatography/atmospheric pressure spray ionization mass spectrometry
Authors: Keski‐Rahkonen Pekka , Lehtonen Marko , Ihalainen Jouni , Sarajärvi Timo , Auriola Seppo
Published: August 2007

A fast, simple and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) method was developed for the determination of acetylcholine in rat brain microdialysis samples. The chromatographic separation was achieved in 3 min on a reversed‐phase column with isocratic conditions using a mobile phase containing 2% (v/v) of acetonitrile and 0.05% (v/v) of trifluoroacetic acid (TFA). A stable isotope‐labeled internal standard was included in the analysis and detection was carried out with a linear ion trap mass spectrometer using selected reaction monitoring (SRM). Analyte ionization was performed with an atmospheric pressure chemical ionization (APCI) source without applying discharge current (atmospheric pressure spray ionization). This special ionization technique offered significant advantages over electrospray ionization for the analysis of acetylcholine with reversed‐phase ion‐pairing chromatography. The lower limit of quantification was 0.15 nM (1.5 fmol on‐column) and linearity was maintained over the range of 0.15–73 nM, providing a concentration range that is significantly wider than that of the existing LC/MS methods. Good accuracy and precision were obtained for concentrations within the standard curve range. The method was validated and has been used extensively for the determination of acetylcholine in rat brain microdialysis samples. Copyright © 2007 John Wiley & Sons, Ltd.
Simultaneous determination of atracurium and its metabolite laudanosine in post‐mortem fluids by liquid chromatography/multiple‐stage mass spectrometry on an ion trap
Authors: Ferrara Santo Davide , Nalesso Alessandro , Castagna Franca , Montisci Massimo , Vogliardi Susanna , Favretto Donata
Published: August 2007

A method was developed to accurately quantify atracurium (a non‐depolarizing skeletal muscle relaxant) and its metabolite laudanosine in post‐mortem specimens. Analytes were isolated from blood and tissues by liquid/liquid extraction after adding vecuronium as an internal standard. Chromatographic separation was accomplished by gradient elution in a Synergy Max RP 150 × 2.1 mm column. Positive ion electrospray ionization and mass spectrometric analyses were carried out in an ion trap mass spectrometer under collision‐induced dissociation conditions. The method proved selective and sensitive, and was validated in post‐mortem blood, heart, lung and liver in the range of 1–2000 ng/mL (blood) and 5–5000 ng/g (tissues); the limits of quantification obtained were 1 ng/mL in blood and 5 ng/g in tissues. Copyright © 2007 John Wiley & Sons, Ltd.
A modified Girard derivatizing reagent for universal profiling and trace analysis of aldehydes and ketones by electrospray ionization tandem mass spectrometry
Authors: Johnson David W.
Published: August 2007

4‐Hydrazino‐N,N,N‐trimethyl‐4‐oxobutanaminium iodide (HTMOB) is a modified Girard derivatizing reagent synthesized to improve the sensitivity of analysis of aldehydes and ketones with electrospray ionization tandem mass spectrometry. Compared with Girard T reagent the measured signal intensity increase is between 3.3 times (succinylacetone) and 7.0 times (17‐hydroxyprogesterone). HTMOB is a universal profiling reagent for aldehydes and ketones. A neutral loss of 59 Da scan detects all aldehydes and ketones from acetone to corticosteroids. Applications described include the profiling of ketones, ketoacids and ketodiacids in the urine of children with ketosis and the profiling of long‐chain aldehydes incorporated in plasma plasmalogens. Copyright © 2007 John Wiley & Sons, Ltd.
Quality Improvement of Environmental Secondary Electron Detector Signal Using Helium Gas in Variable Pressure Scanning Electron Microscopy
Authors: Oho Eisaku , Suzuki Kazuhiko , Yamazaki Sadao
Published: August 2007

The quality of the image signal obtained from the environmental secondary electron detector (ESED) employed in a variable pressure (VP) SEM can be dramatically improved by using helium gas. The signal‐to‐noise ratio (SNR) increases gradually in the range of the pressures that can be used in our modified SEM. This method is especially useful in low‐voltage VP SEM as well as in a variety of SEM operating conditions, because helium gas can more or less maintain the amount of unscattered primary electrons. In order to measure the SNR precisely, a digital scan generator system for obtaining two images with identical views is employed as a precondition. SCANNING 29: 225‐229, 2007. © 2007 Wiley Periodicals, Inc.
Managing development in the hillsides of Trinidad and Tobago using geoinformatics
Authors: Baban Serwan M. J. , Thomas Deborah , Canisius Francis , Sant Kamal J.
Published: August 2007

An increase in the unmanaged development of hillsides is causing environmental, social and economic problems in Trinidad and Tobago. Improved environmental awareness and deepening environmental concerns in recent years have focused attention on the need to move towards a more sustainable pattern of development. Scientific criteria for managing hillside development do not seem to exist and attempts in this regard are seriously compromised amongst other things by the lack of effective and reliable information base for decision making, i.e. information poverty. This paper advances a geoinformatics based methodology for determining suitability for built development on hillsides and to develop and implement a simple scientific criterion strategy for managing hillside development in Trinidad and Tobago whilst enduring information poverty. Additionally, a case study is presented to highlight the applicability of the concept to Tobago. The results showed all potential areas suitable for hillside development in Tobago and also identified areas not suitable and the reason(s) for disqualifying these areas. The proposed approach is adaptable, scientifically justifiable and open to scrutiny, and will lend itself to public acceptance. Copyright © 2007 John Wiley & Sons, Ltd and ERP Environment.
An application of mixture distributions in modelization of length of hospital stay
Authors: Atienza N. , García‐Heras J. , Muñoz‐Pichardo J. M. , Villa R.
Published: August 2007

Length of hospital stay (LOS) is an important indicator of the hospital activity and management of health care. The skewness exhibited by this variable poses problems in statistical modeling. The aim of this work is to model the variable LOS within diagnosis‐related groups (DRG) through finite mixtures of distributions. A mixture of the union of Gamma, Weibull and Lognormal families is used in the model, instead of a mixture of a unique distribution family. Some theoretical questions regarding the model, such as the identifiability and study of asymptotic properties of ML estimators, are analyzed. The EM algorithm is proposed for performing these estimators. Finally, this new proposed model is illustrated by using data from different DRGs. Copyright © 2007 John Wiley & Sons, Ltd.
Does workload cause work‐home interference or is it the other way around?
Authors: Dikkers Josje S. E. , Geurts Sabine A. E. , Kompier Michiel A. J. , Taris Toon W. , Houtman Irene L. D. , van den Heuvel Floor
Published: August 2007

The present study was designed to investigate the causal relationships between work‐home interference (WHI) and one of its strongest correlates, quantitative workload. Two‐phase longitudinal data (with a 1‐year time lag) were gathered from 828 Dutch police officers. Drawing on the effort‐recovery model, and in line with the current WHI literature, we hypothesized that relatively high workload precedes increased levels of WHI 1 year later (‘normal’ causation). In addition, we tested the alternative hypothesis that relatively high levels of WHI predict increased workload 1 year later (‘reversed’ causation). Results of hierarchical regression analyses showed that workload and WHI have causal and reversed causal relationships across time, supporting both hypotheses (although effect sizes are limited). Accordingly, these findings suggest that workload is not merely an antecedent of WHI but is also a potential consequence. Copyright © 2007 John Wiley & Sons, Ltd.
Thematic continuities: Talking and thinking about adaptation in a socially complex classroom
Authors: Ash Doris
Published: August 2007

In this study I rely on sociocultural views of learning and teaching to describe how fifth–sixth‐grade students in a Fostering a Community of Learners (FCL) classroom gradually adopted scientific ideas and language in a socially complex classroom. Students practiced talking science together, using everyday, scientific, and hybrid discourses as they studied endangered species. Students' overarching content themes, or “thematic continuities,” acted as generative scaffolds for developing complex lines of inquiry, leading ultimately to the appropriation of aspects of the biological principle of adaptation. Thematic continuities provided an organizing framework for thinking and talking about previously disconnected science facts, and set the stage for the adaptationist stance. Mixed method data analyses relied on written assessments, in‐depth guided clinical interviews, video and audiotaping of small and large group participant structures, in‐class student work, and ethnographic notes. Data analysis included two discrete levels, the macro (whole and half class) and the intermediate (case study of one small group) to capture both holistic and detailed aspects of dialogue. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 45: 1–30, 2008
Free‐choice worksheets increase students' exposure to curriculum during museum visits
Authors: Mortensen Marianne F. , Smart Kimberly
Published: August 2007

The museum visit is an important part of elementary school science teaching. However, a divide exists between teachers, who require curricular accountability, and museums, who emphasize free‐choice exploration. Can a carefully constructed worksheet bridge this divide by providing free‐choice exploration of curricular topics during the museum visit? In the present study, a theoretical framework was constructed to inform the design of worksheets as free‐choice learning devices. This framework was used to analyze the design of an existing museum worksheet. Subsequently, curriculum‐related conversations among school groups visiting a museum were monitored in groups supplied with the worksheet and in control groups without. Overall, the worksheet complied well with design criteria synthesized from the free‐choice learning literature. Furthermore, the use of the worksheet increased the number and diversity of curriculum‐related conversations among school groups during the visit. This study documents that the use of carefully designed worksheets may increase students' exposure to curriculum during a museum visit, and thus may help build better bridges between teacher needs and museum free‐choice identities. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 44: 1389–1414, 2007
Classification of chemical reactions: Stages of expertise
Authors: Stains Marilyne , Talanquer Vicente
Published: August 2007

In this study we explore the strategies that undergraduate and graduate chemistry students use when engaged in classification tasks involving symbolic and microscopic (particulate) representations of different chemical reactions. We were specifically interested in characterizing the basic features to which students pay attention when classifying chemical reactions at the symbolic and microscopic levels. We identified the categories that students create when classifying chemical reactions, and compared the performance in simple classification tasks of students with different levels of preparation in the discipline. Our results suggest that advanced levels of expertise in chemical classification do not necessarily evolve in a linear and continuous way with academic training; a significant proportion of undergraduate students, regardless of their level of preparation in chemistry, based their classification schemes on the identification of surface features and failed to create chemically meaningful classes. Students' ability to identify chemically meaningful groups was strongly influenced by their recent learning experiences and their graduate work in chemistry. The level of expertise and the type of chemical representation influenced the number and types of categories created, the nature of the features used to build a class, and the role that these features played during the classification process. Although all of the participants in our study expressed similar levels of unfamiliarity with the microscopic images of chemical reactions, advanced students were more adept at using the available representational features to build chemical meaning. © 2007 Wiley Periodicals, Inc. J Res Sci Teach 45: 771–793, 2008
Behavioral and physiologic responses to environmental enrichment in the maned wolf (Chrysocyon brachyurus)
Authors: Cummings Dawn , Brown Janine L. , Rodden Melissa D. , Songsasen Nucharin
Published: August 2007

The ex situ population of maned wolves is not self‐sustaining due to poor reproduction, caused primarily by parental incompetence. Studies have shown that environmental enrichment can promote natural parental behaviors in zoo animals. The objective of this study was to determine the effects of environmental enrichment on behavioral and physiological responses of maned wolves. During an 8‐week experimental period, daily behavior observations and fecal sample collection were conducted on four adult wolves (2.2) individually housed in environments without enrichment. After 2 weeks, the wolves were chronologically provided with 2‐week intervals of hiding dead mice around the exhibit, no enrichment, and introduction of boomer balls. Responses of the wolves to enrichment were assessed based on activity levels and exploratory rates, as well as the level of corticoid metabolites in fecal samples collected daily throughout the study period. Providing wolves with environmental enrichment significantly increased exploratory behaviors (P<0.05), especially when mice were hidden in the enclosure. Fecal corticoid concentrations were increased during periods of enrichment in males (P<0.05), but not in females. Overall, there were no correlations between behavioral responses to enrichment and fecal corticoid levels. Behavioral results suggest that environmental enrichment elicits positive effects on the behavior of captive maned wolves. There is evidence suggesting that providing animals with ability to forage for food is a more effective enrichment strategy than introducing objects. There is need for a longer term study to determine the impact of environmental enrichment in this species. Zoo Biol 26:331–343, 2007. © 2007 Wiley‐Liss, Inc.