bluuebunny/crossref_metadata_2025 huggingface dataset:
The p38 mitogen‐activated protein kinase regulates effector functions of primary human CD4 T cells
Authors: Dodeller Francis , Skapenko Alla , Kalden Joachim R. , Lipsky Peter E. , Schulze‐Koops Hendrik
Published: October 2005

The role of p38 mitogen‐activated protein kinase in primary human T cells is incompletely understood. We analyzed in detail the role of p38 in the regulation of effector functions and differentiation of human CD4 T cells by using a p38‐specific inhibitor and a dominant‐negative mutant of p38. p38 was found to mediate expression of IL‐10 and the Th2 cytokines IL‐4, IL‐5, and IL‐13 in both, primary naive and memory T cells. In contrast, inhibition of p38 activity did not affect expression of the Th1 cytokines IFN‐γ and TNF induced by TCR‐stimulation, but decreased IL‐12‐mediated IFN‐γ expression. Cytokine expression from established Th2 effector cells was also regulated by p38, however, the role of p38 was less pronounced compared to primary CD4 T cells. p38 MAPK regulated cytokine gene expression at both, the transcriptional level by activating gene transcription and the post‐transcriptional level by stabilizing cytokine mRNA. As a result of the effect of p38 on IL‐4 expression, p38 activity modulated differentiation of naive precursor T cells by inducing a shift of the Th1/Th2 balance toward the immuno‐modulatory Th2 direction. Together, the data suggest that p38 plays a key role in human Th2 cell immune responses.
The multigenic structure of the MHC locus contributes to positive selection efficiency: A role for MHC class II gene‐specific restriction
Authors: Monteiro Miguel Caetano , Couceiro Sofia , Penha‐Gonçalves Carlos
Published: October 2005

The study of T cell positive selection in the thymus has long been focused on the specificity of the MHC‐TCR interactions, making use of genetically manipulated mice that display TCR specificities or selecting peptides of limited diversity. However, little is known on the role of the MHC molecules irrespective of the peptide specificity and the implications of MHC multigenic structure in thymic positive selection have not been addressed. Here, we investigated the effect of MHC class II genetic configuration on the positive selection efficiency of naturally generated pre‐selection repertoires in the mouse thymus. Analysis of positively selected thymocyte populations in MHC‐congenic and ‐transgenic mice revealed that expression of I‐E molecule in the thymic cortex increases positive selection efficiency of CD4 cells by approximately 50%. We show that increments in positive selection attributable to either the I‐A and I‐E genes are not due to increased MHC class II expression in the thymic cortex and are not affected by the number of MHC alleles. Collectively, our findings imply that MHC class II gene‐restricted TCR specificities significantly contribute to positive selection efficiency, introducing the notion that multigenic structure of the MHC locus serves to increase selection of non‐overlapping TCR repertoires.
π‐Strain‐Induced Electrophilicity in Small Cycloalkynes: A DFT Analysis of the Polar Cycloaddition of Cyclopentyne towards Enol Ethers
Authors: Domingo Luis R. , Pérez Patricia , Contreras Renato
Published: October 2005

Small cycloalkynes possess a π‐strain‐induced electrophilicity related to the bending of the C–Csp–Csp bond angle. For cyclopentyne and benzyne, the electrophilicity index defined in the context of density functional theory gives a coherent rationale for the reactivity of these cycloalkynes, which may act as electrophiles in polar cycloaddition reactions toward enol ethers. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
The Expedient and Regioselective Metalation of Unprotected Biphenyl‐2‐, ‐3‐, and ‐4‐carboxylic Acids
Authors: Tilly David , Samanta Subhendu S. , Castanet Anne‐Sophie , De Asish , Mortier Jacques
Published: October 2005

Unprotected biphenyl‐2‐carboxylic acid can be cleanly metalated with sec‐butyllithium at the position adjacent to the carboxylate and can then be subjected to site‐selective electrophilic substitution. The remote C2′‐position is attacked by the superbasic mixture of n‐butyllithium and potassium tert‐butoxide (LICKOR, 3.5 equiv.) in THF or benzene at 20–60 °C. The resulting dianion cyclizes to give the fluorenone skeleton. The metalation reactions of biphenyl‐3‐ and ‐4‐carboxylic acids are also described. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Towards the Synthesis of Highly Functionalized Chiral α‐Amino Nitriles by Aminative Cyanation and Their Synthetic Applications
Authors: Bernardi Luca , Bonini Bianca F. , Capitò Elena , Comes‐Franchini Mauro , Dessole Gabriella , Fini Francesco , Fochi Mariafrancesca , Herrera Raquel P. , Ricci Alfredo
Published: October 2005

The cyanobis(dibenzylamino)borane‐mediated transformation of chiral aldehydes into the corresponding α‐amino nitriles is described. Starting from these compounds short synthetic routes can be envisaged for obtaining diastereomerically pure functionalized 1,2‐diamines and hydroxylated α‐amino acids that are of interest as core key units of biologically active substances or as potential ligands for asymmetric catalysis. The stereochemical outcome of the aminative cyanation reaction is discussed. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Ring Contracting Rearrangements of 3‐Amino‐4‐(arylamino)‐1H‐isochromen‐1‐ones
Authors: Opatz Till , Ferenc Dorota
Published: October 2005

Two new ring contracting rearrangements of 3‐amino‐4‐(arylamino)‐1H‐isochromen‐1‐ones, leading to 1‐(arylamino)‐3‐oxo‐1,3‐dihydroisobenzofuran‐1‐carboxamides and2‐aryl‐3‐oxo‐2,3‐dihydro‐1H‐isoindole‐1‐carboxamides, are described. Both conversions proceed in high yield and no further purification of the products is necessary. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Age‐related naturally occurring depression of hippocampal neurogenesis does not affect trace fear conditioning
Authors: Cuppini Riccardo , Bucherelli Corrado , Ambrogini Patrizia , Ciuffoli Stefano , Orsini Laura , Ferri Paola , Baldi Elisabetta
Published: October 2005

New neuron production throughout adulthood in granule cell layer (GCL) of rat hippocampus is a well‐known phenomenon. A role of new neurons in hippocampal learning has been proposed, but the question is still open. A reduction of neural precursor proliferation in GCL of 2‐month‐old rats to about 20%, induced by the cytostatic agent methylazoxymethanol, was found to cause impairment in trace conditioning, suggesting a role of immature neurons in this kind of hippocampus‐dependent learning (Shors et al., Hippocampus 2002;12:578–584). Neurogenesis decreases with increasing age. In this study, neural precursor proliferation and newborn cell survival were evaluated in GCL of adult rats within a range of ages following development and preceding old age. In 5‐month‐old rats, neural precursor proliferation was reduced to 57% and newborn cell survival was reduced to 40% in comparison to rats of 2 months of age; in 12‐month‐old rats, the decrease was to 5 and 4%, respectively. Consistently, the density of immature neurons decreased to 41 and 13% in 5‐ and 12‐month‐old rats, respectively. The role of neurogenesis in trace fear conditioning was studied in this natural model of neurogenesis depression. No impairment in trace fear conditioning was found both in 5‐ and 12‐month‐old rats in comparison to 2‐month‐old rats, notwithstanding the decrease of neurogenesis that is marked in 12‐month‐old rats. This finding shows that a lower rate of neurogenesis is sufficient for learning in 12‐month‐old rats in comparison to young rats. © 2005 Wiley‐Liss, Inc.
Isotopic time‐series partitioning of streamflow components in wetland‐dominated catchments, lower Liard River basin, Northwest Territories, Canada
Authors: St Amour Natalie A. , Gibson John J. , Edwards Thomas W. D. , Prowse Terry D. , Pietroniro Alain
Published: October 2005

The distribution of stable water isotopes provides valuable insight into runoff generation processes in subarctic wetland regions of the Mackenzie River basin, a major freshwater contributor to the Arctic Ocean and the focus of intensive hydrological research as part of Canada's contribution to the Global Energy and Water Cycle Experiment (GEWEX). This article describes a streamflow hydrograph separation analysis carried out over three complete annual cycles (1997–1999) for five subarctic catchments ranging in size from 202 to 2050 km2 situated near the confluence of the Liard and Mackenzie rivers. This heterogeneous landscape, characterized by extensive wetlands (fen and bog), shallow lakes and widespread discontinuous permafrost, is representative of vast flow‐contributing areas of the upper Mackenzie Valley, and is suspected to be highly sensitive to climate variability and change. We document seasonal patterns and interannual variability in the isotopic composition of local streamflow, attributable to mixing of three distinctly labelled flow sources, namely groundwater, surface water plus rain, and direct snowmelt, and apply these isotopic signals to partition sources and their temporal variability. Although groundwater input is the dominant and most persistent streamflow source in all five catchments throughout the year, direct snowmelt runoff via surface and shallow subsurface pathways (during spring freshet) and surface waters from lakes and wetlands situated in low‐lying areas of the basins (during summer and fall) are also significant seasonal contributors. Catchment‐specific differences are also apparent, particularly in the generation of snowmelt runoff, which is more attenuated in fen‐dominated than in bog‐dominated catchments. The data set additionally reveals notable interannual variability in snow isotope signatures and snow water equivalent, apparently enhanced by the 1998 El Niño event. Copyright © 2005 John Wiley & Sons, Ltd.
High school completion and future youth unemployment: new evidence from High School and Beyond
Authors: Li Mingliang
Published: October 2005

In this paper, I provide new evidence from High School and Beyond (HSB) on the effects of compulsory attendance on high school completion and future youth unemployment. I develop Bayesian estimation approaches to the simultaneous equation model with ordered probit and two‐limit censored regression and the bivariate duration model, accounting for the heterogeneity in returns to education and the nonlinearity in the effects of compulsory attendance. I find substantial variability in returns to education across schools and evidence of diminishing marginal effects of compulsory attendance on high school completion. The simulation results suggest that increasing the compulsory attendance age raises the probability of completing high school and reduces the proportion of time the individuals are unemployed. These effects are much more pronounced for disadvantaged students but less pronounced for advantaged students, suggesting the potential effects of compulsory attendance on reducing the inequality in education and employment. Copyright © 2005 John Wiley & Sons, Ltd.
What role do surfaces play in GB models? A new‐generation of surface‐generalized born model based on a novel gaussian surface for biomolecules
Authors: Yu Zhiyun , Jacobson Matthew P. , Friesner Richard A.
Published: October 2005

We have developed a version of our surface generalized Born (SGB) model that employs a Gaussian surface, as opposed to the van der Waals surface used previously. The Gaussian surface is smooth and its properties are analytically differentiable with respect to the positions of atoms. A significant advantage of a solvent model based on this analytically differentiable surface is the availability of analytical gradients of the surface and solvation forces. An efficient and robust algorithm is designed to construct and triangulate the Gaussian surface for large biomolecules with arbitrary shapes, and to compute the various terms required for energy gradients. The Gaussian surface is shown to better mimic the boundary between the solute and solvent by properly addressing solvent accessibility, as is demonstrated by comparisons with standard Poisson–Boltzmann calculations for proteins of different sizes. These results also demonstrate that surface definition is a dominant contribution to differences between GB and PB calculations, especially if the system is large. Application of the new surface to prediction of long loop regions is presented, and significant improvement in the energetics is seen compared with results obtained using the van der Waals surface, even in the absence of optimized empirical correction terms that were used in the latter calculations. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 72–89, 2006
Molecular structure study of dimethoxyphenyl‐substituted phosphonodipeptides by infrared, Raman, and surface enhanced Raman spectroscopies
Authors: Podstawka Edyta , Kozłowski Henryk , Proniewicz Leonard M.
Published: October 2005

In this study, Fourier‐transform Raman (FT‐RS) and infrared (FT‐IR) absorption spectroscopies were employed to characterize the molecular structures ofL‐Ala‐(3,4‐dimethoxy)‐L‐Phe‐PO3H2(A) andL‐Ala‐(3,4‐dimethoxy)‐(des‐CH2)‐L‐Phe‐PO3H2(B) phosphonodipeptides, whereL‐Phe denotesL‐phenylalanine andL‐Ala,L‐alanine. The vibrational band assignments have been proposed. In order to determine the structures of these dimethoxyphenyl‐substituted phosphonodipeptides adsorbed on a colloidal silver surface, surface enhanced Raman spectra (SERS) were measured. The analysis of SERS band intensities showed that these dimethoxyphenyl‐substituted phosphonodipeptides directly interacted with the silver surface through the aromatic ring of Phe that adopted an orientation almost perpendicular to the silver surface. We also showed that intense enhancement of the νas(NH2), δas(PO32−), and ν(PO) modes ofL‐Ala‐(3,4‐dimethoxy)‐L‐Phe‐PO3H2suggested that these groups were mainly involved in the interaction with the silver colloid. Additionally, we proved that in the SERS spectrum ofL‐Ala‐(3,4‐dimethoxy)‐(des‐CH2)‐L‐Phe‐PO3H2, several vibrations of the CH3group were enhanced, indicating a flattened orientation of the peptide backbone on the silver surface. Copyright © 2005 John Wiley & Sons, Ltd.
Multidimensional Chromatographic and Hyphenated Techniques for Hydrophilic Copolymers, 1
Authors: Adler Martina , Rittig Frank , Becker Stefan , Pasch Harald
Published: October 2005

Summary: The chromatographic analysis of hydrophilic copolymers is complicated due to the fact that in most cases aqueous eluents must be used. In aqueous eluents different polar and ionic effects may disturb the selective interactions between the macromolecules and the stationary phase making it impossible to separate such copolymers with regard to chemical composition. Therefore, 2D chromatography combining a separation according to composition with a separation according to molar mass has been applied mostly to polymers that are soluble in organic solvents. The present contribution describes experimental approaches to analyze such hydrophilic copolymers by 2D‐chromatography. For a model polymer system resulting from the copolymerization of methacrylic acid and a poly(ethylene glycol) macromonomer, it is shown that different analytical techniques including SEC, LC‐CC, MALDI‐TOF MS and 2D chromatography can be used to analyze the different parameters of molecular heterogeneity of such copolymers.

2D separation of poly(MPEG‐MM 2), 1st dimension: LC‐CC, 2nd dimension: SEC.

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2D separation of poly(MPEG‐MM 2), 1st dimension: LC‐CC, 2nd dimension: SEC.
1H and 13C NMR spectral data for a tricyclic derivative of a Diels–Alder adduct
Authors: Pedersoli Susimaire , Constantino Mauricio Gomes , José da Silva Gil Valdo
Published: October 2005

A complete NMR analysis with full assignment for 1H and 13C NMR spectral data for 5‐(acetyloxy)‐3‐hydroxy‐9,10‐dimethoxy‐6‐oxo‐11‐oxatricyclo[6.2.1.02,7]undec‐2‐yl acetate (8) is described. This compound was prepared by rapid hydrogenation of the unstable Diels–Alder adduct obtained from the reaction between 3,4‐dimethoxyfuran (4) and 2,5‐diacetoxy‐1,4‐benzoquinone (5). Full homonuclear hydrogen coupling constants measurements and molecular mechanics calculations were performed for the determination of the relative stereochemistry. Copyright © 2005 John Wiley & Sons, Ltd.
29Si NMR in LC–NMR analysis of silicones
Authors: Blechta Vratislav , Sýkora Jan , Hetflejš Jiří , Šabata Stanislav , Schraml Jan
Published: October 2005

It is demonstrated using a practical example that indirect detection of 29Si NMR signals is sufficiently sensitive in LC–NMR stop‐flow arrangement to analyze mixtures of siloxane polymers. New cryogenic probes with better signal‐to‐noise ratio will turn this version of LC–NMR into a routine method for analysis of siloxane polymers. Copyright © 2005 John Wiley & Sons, Ltd.
Assignment of absolute configuration of cyclic secondary amines by NMR techniques using Mosher's method: a general procedure exemplified with (−)‐isoanabasine
Authors: Kang Chuan‐Qing , Guo Hai‐Quan , Qiu Xue‐Peng , Bai Xiao‐Li , Yao Hai‐Bo , Gao Lian‐Xun
Published: October 2005

A general procedure to determine the absolute configuration of cyclic secondary amines with Mosher's NMR method is demonstrated, with assignment of absolute configuration of isoanabasine as an example. Each Mosher amide can adopt two stable conformations (named rotamers) caused by hindered rotation around amide CN bond. Via a three‐step structural analysis of four rotamers, the absolute configuration of (−)‐isoanabasine is deduced to be (R) on the basis of Newman projections, which makes it easy to understand and clarify the application of Mosher's method to cyclic secondary amines. Furthermore, it was observed that there was an unexpected ratio of rotamers of Mosher amide derived from (R)‐isoanabasine and (R)‐Mosher acid. This phenomenon implied that it is necessary to distinguish the predominant rotamer from the minor one prior to determining the absolute configuration while using this technique. Copyright © 2005 John Wiley & Sons, Ltd.
Changes in androgen‐producing cell size and circulating 11‐ketotestosterone level during female–male sex change of honeycomb grouper Epinephelus merra
Authors: Alam Mohammad Ashraful , Bhandari Ramji Kumar , Kobayashi Yasuhisa , Nakamura Shigeo , Soyano Kiyoshi , Nakamura Masaru
Published: October 2005

11‐ketotestosterone (11‐KT), a potent male‐specific androgen in fish, has important roles on spermatogenesis, male behavior, and nuptial coloration. The site of 11‐KT synthesis and its role on male germ cell development during protogynous sex change is not clearly understood. We examined the dynamics of steroidogenic enzymes immunolocalization, viz cholesterol side‐chain cleavage (P450scc), biomarker of steroids and cytochrome P45011β‐hydroxylase (P45011β), downstream to 11‐KT production, throughout the process of sex change in honeycomb grouper (Epinephelus merra). In female, P450scc immunoreactivity (‐ir) was observed in the theca layer and tunica near blood vessels (BV). During the onset of sex change, P450scc reactive cells were observed in the remaining follicle layer of degenerated oocyte of the ovo‐testis in early transitional (ET) and late transitional (LT). In male, P450scc‐ir was localized in the interstitial Legdig cells of testis. P45011β reactive cells were observed in the tunica near BV in female but not in theca layer. In ET and LT phases gonads, P45011β localized in remaining follicle layer of degenerated oocyte and tunica near BV. On the other hand, in male, both interstices and tunica near BV showed strong signals against P45011β. Moreover, in vivo and in vitro levels of 11‐KT related with the changes in the nuclei diameter of P45011β‐positive cells in both tunica near BV and remaining follicle layer of degenerated oocyte to interstices during the progress of sex change. The present results suggest that 11‐KT produced in the tunica near BV may provide the stimulus for female to degenerate oocytes and initiate sex change. However, 11‐KT produced both in tunica near BV and remaining follicle layer of degenerated oocyte possibly plays critical role during testicular differentiation as well as gonadal restructuring at mid to late phases (ET to LT) of sex change in honeycomb grouper. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Differential expression of transcriptional repressor snail gene at implantation site in mouse uterus
Authors: Ma Xing‐Hong , Hu Shi‐Jun , Yu Hao , Xu Li‐Bin , Yang Zeng‐Ming
Published: October 2005

The snail superfamily of zinc‐finger transcription factors is involved in pronounced cell movements during both embryonic development and tumor progression. This study was to examine snail expression in mouse uterus during early pregnancy and its regulation under pseudopregnancy, delayed implantation, steroid hormone treatment, and artificial decidualization by in situ hybridization and immunohistochemistry. There was a low level of snail mRNA signal and immunostaining in mouse uteri on day 1–4 of pregnancy. When embryo implanted on day 5, both snail mRNA signal and immunostaining were strongly detected in the subluminal stroma immediately surrounding the implanting blastocyst, but not detected in the inter‐implantation sites. Under delayed implantation, there was no detectable snail expression. After delayed implantation was terminated by estrogen treatment and embryo implanted, there was a strong level of snail mRNA and immunostaining in the subluminal stroma surrounding the implanting blastocyst, which was similar to that on day 5 of pregnancy. Furthermore, there was no detectable snail expression in mouse uterus on day 5 of pseudopregnancy. From day 6–8 of pregnancy, both snail mRNA signal and immunostaining were detected in the decidua. Our data suggest that snail may play an important role during mouse embryo implantation. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Recurrent ependymoma treated with high‐dose tamoxifen in a peripubertal female: Impact on tumor and the pituitary–ovarian axis
Authors: Yoffe Rona , Khakoo Yasmin , Dunkel Ira J. , Souweidane Mark , Lis Eric , Sklar Charles
Published: October 2005

Due to high rates of recurrence, the prognosis of childhood ependymoma remains guarded. Anecdotal evidence suggests that tamoxifen may have a role in the treatment of these tumors. We present a case of a child with recurrent ependymoma treated with tamoxifen who showed tumor regression on two separate occasions. However, treatment with tamoxifen resulted in the development of large ovarian cysts associated with supraphysiological plasma concentrations of estradiol. Pediatr Blood Cancer 2007;49:758–760. © 2005 Wiley‐Liss, Inc.
Health‐related quality of life in children and emotional reactions of parents following completion of cancer treatment
Authors: Stam Heleen , Grootenhuis Martha A. , Brons Paul P.T. , Caron Huib N. , Last Bob F.
Published: October 2005

Background

Completing therapy is one of the major transitions in care in the practice of pediatric oncology and, therefore, deserves special consideration. The purpose of the study was to investigate health‐related quality of life (HRQOL) of pediatric patients, and emotional reactions of their parents, shortly after the end of successful treatment.

Methods

HRQOL of 126 patients, aged 1–15 years, on average 2 months after the end of successful treatment, was assessed with the TNO‐AZL Pre‐school Quality of life Questionnaire and the TNO‐AZL Children's Quality of life Questionnaire. Emotional adjustment of 124 mothers and 111 fathers was assessed with the General Health Questionnaire and the Situation Specific Emotional Reaction Questionnaire. The outcomes of the patients and parents were compared with norm data by means of one sample t‐tests, one sample sign‐tests or binomial tests.

Results

All age groups, except patients aged 8–11 years, experienced worse HRQOL than the norm with respect to motor functioning. In addition, pre‐school patients were rated worse on sleeping, appetite, stomach, skin, problem behavior, anxiety, and liveliness, and patients aged 6–7 years on autonomy and cognitive functioning. Parents reported more psychological distress than the norm. Compared to parents whose children were 1–5 years after cancer treatment, they suffered more from feelings of loneliness, helplessness, and uncertainty.

Conclusions

A few months after the end of successful cancer treatment, both patients and parents appeared to experience worse well‐being than the norm to a clinically relevant extent. Supporting patients and parents should not stop when treatment ends. Pediatr Blood Cancer 2006;47:312–319. © 2005 Wiley‐Liss, Inc.
Gelation mechanism and microstructure of organogels formed with various types of gelators
Authors: Okabe Satoshi , Hanabusa Kenji , Shibayama Mitsuhiro
Published: October 2005

The small‐angle neutron scattering (SANS) and dynamic light scattering (DLS) investigation were carried out for organogels in toluene, formed by organogelators, to elucidate the relationship between the chemical structure and the gelation mechanism as well as the physical properties of the gels. Three different organogelators, that is cyclo(L‐β‐3,7‐dimethyloctylasparaginyl‐L‐phenylalanyl) (CPA), trans‐(1R,2R)‐bis(undecylcarbonylamino)cyclohexane (TCH), and Nε‐lauroyl‐Nα‐stearylaminocarbonyl‐L‐lysine ethyl ester (LEE), were chosen for comparison. The SANS intensity functions of toluene solutions of these gelators could be reduced with the concentration and were described with a scattering function for thin rods. This indicates that the gels consist of noncorrelated, rod‐like elements aggregated to each other. The characteristic features of the gelation properties, such as the critical gelation concentration, Cgel, the gelation temperature, Tgel, the gel structure, and the gelation mechanism, were different from each other. CPA had the lowest Cgel and became a gel gradually as the temperature decreased, while TCH and LEE had higher Cgels and underwent a sharp sol–gel transition. We conclude that the gelation mechanisms between the CPA and TCH solutions are different. The “CPA type” gelators form a gel by a linear extension of hydrogen‐bonded plane, while the “TCH type” gelators form a twisted wire, because of its strong helicity and crystallizability. In addition, in the latter type, a next generation of fibrils easily stacks on top of the previous ones to form larger fibrils. These models well explain the DLS results and the mechanical properties. That is, the fibrillar stems in CPA gels are rather mobile and fragile, while those in TCH and LEE are frozen and brittle. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3567–3574, 2005
Rheology and microstructures formation of immiscible model polymer blends under steady state and transient flows
Authors: Das N. C. , Wang H. , Mewis J. , Moldenaers P.
Published: October 2005

Viscoelastic properties of model immiscible blend were studied here under steady state condition at different initial conditions and transient flow conditions. The flow‐induced microstructure has been studied on these model blends. For this system, the elastic properties of the blend are mainly governed by the interface. Measurement of the dynamic modulus and of the first normal stress difference, both reflecting this enhanced elasticity, have been used to prove the blend morphology. The dynamic moduli after cessation of shear flow, the mean diameter of the disperse phase as generated by the shear flow, have been calculated using the model of Palierne. A procedure based on a direct fitting of the dynamic moduli with the model is compared with the one that uses a weight relaxation spectrum. On the other hand, the steady state normal stress data have been related to the morphology of the blend by means of Doi and Ohta model. The specific interfacial area is found to be inversely proportional to the ratio of interfacial tension over shear stress for the blend. The flow behavior during transient shear flow was also discussed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3519–3533, 2005
Simulation of mefenacet concentrations in paddy fields by an improved PCPF‐1 model
Authors: Watanabe Hirozumi , Takagi Kazuhiro , Vu Son Hong
Published: October 2005

An improved simulation model (PCPF‐1) has been evaluated for the prediction of the fate of mefenacet in an experimental paddy field. This model simulates the fate and transport of pesticide in paddy water and the top 1 cm of paddy soil. Observed concentrations of mefenacet in the paddy water and the surface soil exponentially decreased from their maximum concentrations of 0.70 mg litre−1 and 11.3 mg kg−1, respectively. Predicted mefenacet concentrations both in the water and surface soil were in excellent agreement with those measured during the first 2 weeks after herbicide application, but concentrations in paddy water were appreciably overestimated thereafter. The model simulated mefenacet losses through runoff, percolation and degradation to be respectively 41.9%, 6.4% and 57.3% of applied, and the mass balance error was about −6%. The model simulation implied that drainage and seepage control, especially shortly after application when herbicide concentrations are high, is essential for preventing pesticide losses from paddy fields. In focusing on pesticide concentrations in this early period the PCPF‐1 model can be a beneficial tool for risk assessment of pesticide losses and in the evaluation of agricultural management for reducing pesticide pollution associated with paddy rice production. Copyright © 2005 Society of Chemical Industry
Impact of cypermethrin on feeding behaviour and mortality of the spider Pardosa amentata in arenas with artificial ‘vegetation’
Authors: Shaw Emma M , Waddicor Michelle , Langan A Mark
Published: October 2005

Pesticides can modify invertebrate movement and feeding behaviour which could reduce predation in agroecosystems. Previous assays have exposed the spider Pardosa amentata (Clerck) to the synthetic pyrethroid cypermethrin and monitored prey items consumed in small containers (requiring very little movement to capture prey). The current study used larger arenas containing artificial ‘vegetation’ (a plastic analogue) to encourage spiders to hunt and capture prey. The period 24 h after exposure produced greatest variability in prey item consumption between treatments and was used to examine treatment effects. At this time, cypermethrin reduced prey consumption rates but these effects did not persist. Findings did not suggest that the presence of artificial vegetation in arenas modified prey consumption rates, which was consistent for individuals treated with cypermethrin and a control group. This is despite the majority of pesticide‐treated individuals exhibiting both ataxia and paralysis of the hind legs (these effects persisting for a maximum of 3 and 6 days respectively). These findings were consistent for both sexes. Spider longevity under starvation conditions was not significantly reduced by cypermethrin exposure but overall females survived longer than males. The findings are discussed in the context of the arenas used and the ecology of this common predator. Copyright © 2005 Society of Chemical Industry
QSPR Study of Fluorescence Wavelengths (λex/λem) Based on the Heuristic Method and Radial Basis Function Neural Networks
Authors: Shi Jing , Luan Feng , Zhang Haixia , Liu Mancang , Guo Qingxiang , Hu Zhide , Fan Botao
Published: October 2005

The Quantitative Structure–Property Relationship (QSPR) method was performed to study the fluorescence excitation wavelengths (λex) and emission wavelengths (λem) of 64 fluorescent probes. The probes included the derivatives of dansyl, bimane, pyrene, benzofurazan, nonaphthalene, coumarin, anthracene and fluorescein, with the wavelength ranging from 300 nm to 600 nm. The Heuristic Method (HM) and Radial Basis Function Neural Networks (RBFNNs) were employed to construct linear and nonlinear prediction models, respectively. The proposed linear models for λex and λem contain five descriptors with the squared correlation coefficients R2 of 0.888 and 0.897, respectively. Better prediction results were obtained from RBFNN model, with the squared correlation coefficients R2 of 0.948 and 0.939 for λex and λem, respectively. The descriptors used in the models were discussed in detail too.
Estimation of Phosphate Ester Hydrolysis Rate Constants. I. Alkaline Hydrolysis
Authors: Whiteside Tad S. , Hilal S. H. , Carreira L. A.
Published: October 2005

SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to allow the calculation of alkaline hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition states of a molecule. This difference is a function of the reference rate and internal and external perturbations to the reference rate. The internal perturbations are comprised of electrostatic and resonance effects. The external perturbations quantify solute‐solvent interactions based on the dielectric constant of the solvent and the steric effect of substituent groups. These perturbation models have been tested using 225 reliably measured second order hydrolysis rate constants over a variety of temperatures. The RMS deviation of the calculated versus observed values was 0.401 log M−1s−1.
Mass spectrometry of stanozolol and its analogues using electrospray ionization and collision‐induced dissociation with quadrupole‐linear ion trap and linear ion trap‐orbitrap hybrid mass analyzers
Authors: Thevis Mario , Makarov Alexander A. , Horning Stevan , Schänzer Wilhelm
Published: October 2005

Mass spectrometric identification and characterization of growth‐promoting anabolic‐androgenic steroids in biological matrices has been a major task for doping control as well as food safety laboratories. The fragmentation behavior of stanozolol, its metabolites 17‐epistanozolol, 3′‐OH‐stanozolol, 4α‐OH‐stanozolol, 4β‐OH‐stanozolol, 17‐epi‐16α‐OH‐stanozolol, 16α‐OH‐stanozolol, 16β‐OH‐stanozolol, as well as the synthetic analogues 4‐dehydrostanozolol, 17‐ketostanozolol, and N‐methyl‐3′‐OH‐stanozolol, was investigated after positive electrospray ionization and subsequent collision‐induced dissociation utilizing a quadrupole‐linear ion trap and a novel linear ion trap‐orbitrap hybrid mass spectrometer. Stable isotope labeling, H/D‐exchange experiments, MS3 analyses and high‐resolution/high mass accuracy measurements of fragment ions were employed to allow proposals for charge‐driven as well as charge‐remote fragmentation pathways generating characteristic product ions of stanozolol at m/z 81, 91, 95, 105, 119, 135 and 297 and 4‐hydroxylated stanozolol at m/z 145. Fragment ions were generated by dissociation of the steroidal A‐ and B‐ring retaining the introduced charge within the pyrazole function of stanozolol and by elimination of A‐ and B‐ring fractions including the pyrazole residue. In addition, a charge‐remote fragmentation causing the neutral loss of methanol was observed, which was suggested to be composed by the methyl residue at C‐18 and the hydroxyl function located at C‐17. Copyright © 2005 John Wiley & Sons, Ltd.
Cu(II)‐loaded iminodiacetic acid‐silica particles for protein profiling of human serum samples using surface‐enhanced affinity capture: support porosity effects
Authors: Trojer L. , Stecher G. , Feuerstein I. , Bonn G. K.
Published: October 2005

Silica particles of different porosity were functionalised with iminodiacetic acid (IDA) and loaded with Cu(II) ions to yield Cu(II)‐IDA‐silica. These immobilised metal affinity chromatography (IMAC) materials were subjected to a comprehensive characterisation study. The Cu(II) content – determined via UV/Vis spectroscopy and atomic absorption spectroscopy (AAS) – was found to be linearly dependent on the specific surface area of the silica particles. The evaluation of protein adsorption isotherms provided information on binding properties towards biomolecules. The data fitted Langmuir's adsorption theory. Binding capacity of hen egg white lysozyme (HEWL) was highest for Cu(II)‐IDA‐silica with mean pore diameter of 120 Å, reaching nearly 350 mg/g. All derivatised materials were applied to the fractionation of human serum samples and subsequent mass spectrometric analysis (m/z: 2000–10 000) according to a surface‐enhanced affinity capture (SEAC) protocol. Pore size of the support material affected the appearance of the mass spectra to a great extent, showing that surface morphology is another parameter that has to be considered in addition to surface chemistry. Signal intensity as well as the number of detected masses were strongly dependent on the pore diameter, indicating that the carrier material has to be carefully chosen to assure best results. Copyright © 2005 John Wiley & Sons, Ltd.
Laser ablation synthesis of selenium superoxide anion SeO via selenium trioxide photolysis. Time‐of‐flight mass spectrometry and ab initio calculations
Authors: Alberti Milan , Špalt Zbyněk , Peña‐Méndez Eladia María , Ramírez‐Galicia Guillermo , Havel Josef
Published: October 2005

Laser desorption/ionisation and laser ablation of solid selenium trioxide, as well as the gas‐phase behaviour of selenium trioxide, were studied. Selenium trioxide undergoes photochemical decomposition and, from the mass spectra obtained by laser desorption/ionisation time‐of‐flight mass spectrometry (LDI‐TOF‐MS), the following species were identified: O−, O, O, SeO−, SeO, SeO, SeO, Se2O, Se3O, and Se4O. Formation of the selenium superoxide SeO anion is described in this work for the first time. In addition, low‐abundance selenium species such as Se2O8H, Se3O11H−, and Se4O15H were also detected. The stoichiometry of all ions was confirmed via isotopic pattern modeling and/or post‐source decay (PSD) analysis. Photolysis of selenium trioxide leads partly to ozone formation. It was found that the most likely mechanisms of selenium superoxide formation are oxidation of selenium trioxide with ozone and/or reactive oxygen radicals, or photolysis of selenium trioxide tetramer (SeO3)4. Therefore, ab initio calculations were performed to support the mass spectrometric evidence and to suggest probable geometries for selenium superoxide anion SeO and diselenium superoxide anion Se2O, as well as to provide insight into and/or predict possible formation pathways. It has been found that both cyclic and non‐cyclic peroxide structures of SeO and Se2O ions are possible. In addition, the SeO4 structure was also calculated guided by thermodynamic considerations using Gaussian‐2 methodology, and the inferred stability of the SeO4 neutral molecule was supported by ab initio calculations. Copyright © 2005 John Wiley & Sons, Ltd.
Determination of microbial volatile organic compounds from Staphylococcus pasteuri against Tuber borchii using solid‐phase microextraction and gas chromatography/ion trap mass spectrometry
Authors: Barbieri E. , Gioacchini A. M. , Zambonelli A. , Bertini L. , Stocchi V.
Published: October 2005

The mycelium of Tuber borchii Vittad., a commercial truffle species, is used as a model system for in vitro ectomycorrhizal synthesis, infected seedling production and biotechnological applications. Our fungal cultures were accidentally contaminated with a Staphylococcus pasteuri strain, showing a strong antifungal activity against T. borchii mycelium. In order to identify the antifungal volatile agents produced by S. pasteuri, solid‐phase microextraction (SPME) with gas chromatography and mass spectrometry (GC/MS) was used. Using this method 65 microbial volatile organic compounds (MVOCs), synthesized by this bacterium in either single or in fungal‐bacterial dual culture, were identified. SPME combined with GC/MS may be a useful method for the determination of MVOCs involved in the antifungal activity. These results showed that bacteria with unusual biological activities could be a major problem during large‐scale production of inoculum for truffle‐infected seedling. Copyright © 2005 John Wiley & Sons, Ltd.
Performance of binary‐encounter‐Bethe (BEB) theory for electron‐impact ionization cross sections of molecules containing heavy elements (Z > 10)
Authors: Scott Gregory E. , Irikura Karl K.
Published: October 2005

The binary‐encounter‐Bethe (BEB) theory developed by Kim and coworkers has been successful for computing electron‐impact ionization cross sections of many molecules. However, some recent publications have stated that BEB theory performs poorly for molecules that contain heavier elements such as chlorine and sulfur. We have found that the BEB calculations in those publications were performed incorrectly. When performed correctly, BEB predictions are as good for heavy‐element molecules as for light‐element molecules. We recommended recently that an alternative, less‐confusing procedure be used for molecules that contain heavier elements. The alternative procedure, based upon effective core potentials (ECPs), does not require explicit kinetic energy corrections. For peak cross sections of a group of 18 molecules, the root‐mean‐square difference between BEB predictions and experimental values is 13%. Results are presented for CCl3CN, C2Cl6, C2HCl5, C2Cl4, both isomers of C2H2Cl4, CCl4, TiCl4, CBr4, CHBr3, CH2Br2, GaCl, CS2, H2S, CH3I, Al(CH3)3, Ga(CH3)3, and hexamethyldisiloxane. Incorrect BEB calculations have been reported in the literature for several of these molecules. Published in 2005 John Wiley & Sons, Ltd.
A new Monte Carlo application for complex sample geometries
Authors: Ritchie Nicholas W. M.
Published: October 2005

NISTMonte is a new application for Monte Carlo simulation1, 2 of electron transport, X‐ray generation and transmission in complex sample geometries. NISTMonte uses the Mott cross section3, 4 to model elastic scattering and the Joy–Luo expression5 to model energy loss. The ionization cross section is modeled using the empirical expression of Casnati.6 The mass absorption coefficients are those of Heinrich,7 and the fluorescence yields are tabulated experimental values.8

A defining characteristic of the application is the flexibility with which complex sample geometries may be defined. The application provides a set of basic building blocks that may be combined to build complex sample shapes. Furthermore, shapes may be embedded within shapes to model inhomogeneous samples or structured samples. The application imposes no artificial limits on the number of sample regions or on the number of elements within a material.

A detailed description of the implementation and the results of various tests, including backscatter yields, will be presented to demonstrate the range of validity of the model and the implementation.

The application has been developed in Java J2SE 1.4 for platform independence. The source code will be made available on the NIST web site or by contacting the author. Published in 2005 by John Wiley & Sons, Ltd.
Summary of the panel discussion on opportunities and needs
Authors: Powell C. J.
Published: October 2005

At the NIST workshop on modeling electron transport for applications in electron and X‐ray analysis and metrology, there was a final panel discussion on the opportunities and needs in this area. A summary of the points made by some of the contributors in this session is given. Published in 2005 John Wiley & Sons, Ltd.
X‐ray microanalysis of real materials using Monte Carlo simulations
Authors: Gauvin Raynald
Published: October 2005

In this paper, new results of Monte Carlo simulations are presented in the context of X‐ray microanalysis in the scanning electron microscope and the variable pressure scanning electron microscope. For the analysis of bulk samples in the scanning electron microscope, the simulation of X rays emitted from porous materials is covered. Modeling of electron scattering in gases is also presented in the context of X‐ray microanalysis in variable pressure scanning electron microscopy. Finally, characterization of electron trajectories from the results of Monte Carlo simulations using the concepts of fractal geometry is described with their implications for quantitative X‐ray microanalysis. Copyright © 2005 John Wiley & Sons, Ltd.
A new examination of secondary electron yield data
Authors: Lin Yinghong , Joy David C.
Published: October 2005

A new and thorough examination of secondary electron (SE) yield as a function of primary energy (EPE) and atomic number Z for the 44 elements in the database1 is made. The principles of the semiempirical universal law for the SE yield are described and a template for Monte Carlo (MC) simulation is produced accordingly. Both universal curve fitting and MC simulation are made for the 44 elements. The resulted maximum SE yield δm, corresponding primary energy $E_{\rm {PE}}^{\rm {m}}$, SE excitation energy ε, and effective escape depth λ are tabulated and plotted as a function of atomic number Z. It is found that similarities exist in the profiles of ε and λ, δm and $E_{\rm {PE}}^{\rm {m}}$, and all of these parameters seem to have characteristics associated with atomic shell filling. Copyright © 2005 John Wiley & Sons, Ltd.
Use of Monte Carlo models in the development and validation of CD operators
Authors: Frase Carl Georg , Häßler‐Grohne Wolfgang
Published: October 2005

In this article, different applications of Monte Carlo simulations in scanning electron microscope (SEM) critical dimension (CD) metrology are presented. A first field of application is the analysis of image formation that leads to functional descriptions of secondary electron (SE) signal profiles. From this, algorithms are defined to evaluate the linewidth of microstructures. Monte Carlo generated images are used to validate CD operators and to estimate model‐induced contributions to the CD uncertainty budget. New challenges and new fields of application for Monte Carlo simulations in CD metrology are discussed. Copyright © 2005 John Wiley & Sons, Ltd.
A Monte Carlo model utilizing local chemical potentials for simulating segregation and diffusion. Part 1—theory
Authors: Joubert H. D. , Swart H. C. , Terblans J. J.
Published: October 2005

Bulk‐to‐surface segregation was studied with a Monte Carlo model based on the modified Darken model.1 Chemical potentials2 are used to represent the local energy of a randomly chosen atom, while the largest positive change in chemical potential directs atomic motion, complying with the conditions associated with the lowering of the Gibbs free energy. An adjustment is made to the calculations to compensate for the segregation energy associated with the surface layer.3 The current model simulates segregation in binary alloys, represented by a crystal matrix containing two constituent elements. A random selection of an atom initiates the calculation process,4 after which the energy of the selected atom, represented by the chemical potential, is calculated for an area that includes nearest and next nearest neighbours. In addition, only nearest neighbour exchanges are allowed, resulting in a maximum of four possible moves. A test move is performed to each of the four move directions, and the chemical potential for each new configuration is calculated. The change in chemical potential for all four exchanges can be calculated, and the probabilities associated with these moves can also be calculated. The exchange that represents the largest positive change in chemical potential will possess the largest probability of motion. By including the segregation energy (associated with the surface) in the calculations, the frequency of jumps from the surface to the bulk is significantly reduced. Copyright © 2005 John Wiley & Sons, Ltd.