bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of grapefruit juice on digoxin pharmacokinetics in humans
Authors: Becquemont Laurent , Verstuyft Céline , Kerb Reinhold , Brinkmann Ulrich , Lebot Martine , Jaillon Patrice , Funck‐Brentano Christian
Published: December 2004

Objectives

Grapefruit juice is responsible for drug interactions mediated by intestinal cytochrome P4503A4 inhibition and possibly P‐glycoprotein inhibition in enterocytes. Our main objective was to determine whether grapefruit juice alters the bioavailability of digoxin, a P‐glycoprotein substrate. The secondary objective was to determine whether the magnitude of the pharmacokinetic interaction was influenced by P‐glycoprotein genetic polymorphism.

Methods

Twelve healthy volunteers participated in this open randomized crossover study comparing the effect of grapefruit juice consumption (versus water) on the pharmacokinetics of a single oral dose of digoxin (0.5 mg). The P‐glycoprotein genotype was determined according to MDR1 genetic polymorphism in exon 26 (C3435T).

Results

Grapefruit juice had no significant effect on the maximum plasma drug concentration (Cmax) of digoxin or the area under the plasma concentration‐time curve (AUC) from time zero to 48 hours. However, there was a 9% increase in the digoxin AUC from time zero to 4 hours and from time zero to 24 hours (P = .01) during grapefruit juice administration. The digoxin renal clearance remained unchanged during both periods. No relationship between MDR1 C3435T genotype and early digoxin pharmacokinetic changes could be detected.

Conclusion

The modest changes in digoxin pharmacokinetics observed during grapefruit juice ingestion do not support an important P‐glycoprotein inhibition. Under our experimental conditions, grapefruit juice‐mediated P‐glycoprotein inhibition does not appear to play a relevant role in drug interactions, at least when assessed by use of digoxin disposition kinetics.

Clinical Pharmacology & Therapeutics (2001) 70, 311–316; doi: 10.1016/S0009‐9236(01)17221‐8
Association of polymorphism in the cytochrome CYP2D6 and the efficacy and tolerability of simvastatin
Authors: Mulder André B. , van Lijf Hans J. , Bon Michelle A. M. , van den Bergh Frank A. J. T. M. , Touw Daan J. , Neef Cees , Vermes István
Published: December 2004

Objective

Because clinical data about the therapeutic consequences of polymorphic oxidation of simvastatin by CYP2D6 have not been well reported, we sought to investigate the possible link between polymorphism of CYP2D6 and the efficacy and tolerability of simvastatin treatment in a group of 88 patients with hypercholesterolemia.

Methods

TheCYP2D6 genotype was determined with use of polymerase chain reaction and restriction fragment analysis, whereas the CYP2D6 phenotype was determined by monitoring the dextromethorphan metabolism.

Results

Four of 5 patients with 2 defectiveCYP2D6 alleles discontinued the therapy at a low daily dose because of adverse events, with a significant mean decrease in the cholesterol levels of 0.23 mmol/L per milligram of simvastatin in the daily dose. In the group of 28 patients with 1 mutatedCYP2D6 gene, 13 did not tolerate the therapy, whereas a mean decrease in the cholesterol levels of 0.20 mmol/L per milligram of simvastatin was found. One patient with a multiplication of theCYP2D6 gene showed a cholesterol reduction of only 0.01 mmol/L per milligram of simvastatin, at a maximal daily dose of 40 mg. Only 9 patients of the group of 54 persons who were homozygous for the wild‐type allele discontinued the therapy because of intolerance. In that group, a mean decrease of cholesterol of 0.10 mmol/L per milligram of simvastatin was observed.

Conclusions

Our data provide evidence that the cholesterol‐lowering effect of simvastatin is influenced by CYP2D6 polymorphism. The clinical use of this knowledge may allow for more efficient individual therapies.

Clinical Pharmacology & Therapeutics (2001) 70, 546–551; doi: 10.1016/S0009‐9236(01)25429‐0
Effect of rifampin and tobacco smoking on the pharmacokinetics of ropivacaine
Authors: Jokinen Mika J. , Olkkola Klaus T. , Ahonen Jouni , Neuvonen Pertti J.
Published: December 2004

Objective

Our objective was to assess the effect or rifampin (INN, rifampicin) and tobacco smoking on the pharmacokinetics of ropivacaine.

Methods

A randomized, 2‐phase, crossover study was performed in both a group of 10 healthy nonsmokers and a group of 8 healthy smokers. In both groups each subject ingested daily for 5 days either placebo or 600 mg rifampin. On day 6 each subject received intravenously over 30 minutes a single dose of 0.6 mg/kg ropivacaine. Ropivacaine, 3‐hydroxyropivacaine (3‐OH‐ropivacaine), and (S)‐2′,6′‐pipecoloxylidide (PPX) in venous plasma and urine were measured for up to 12 hours and 24 hours, respectively. Pharmacokinetic parameters were calculated with noncompartmental methods, and t tests were used for comparisons between the phases and between the smokers and nonsmokers. The electrocardiogram was monitored for 3 hours.

Results

There were no statistically significant differences in the area under the plasma concentration‐time curve (AUC), plasma clearance (CL), or half‐life (t1/2) of ropivacaine between the smokers and nonsmokers. However, smokers excreted in urine 31% more 3‐OH‐ropivacaine and 62% less PPX than nonsmokers did. Rifampin decreased the AUC of ropivacaine in nonsmokers by 52% and in smokers by 38%. In nonsmokers rifampin increased the CL of ropivacaine by 93% and shortened its t1/2 by 25%. In smokers rifampin increased the CL of ropivacaine by 47% and shortened its t1/2 by 20%. Rifampin decreased the urinary excretion of 3‐OH‐ropivacaine in nonsmokers by 74% and in smokers by 68%, and it increased the excretion of PPX by 97% and 158%, respectively. No clinically significant differences in the QTc times were found between the groups or treatments.

Conclusions

Tobacco smoking increases the excretion of 3‐OH‐ropivacaine in urine, probably because of the increased cytochrome P450 (CYP) 1A2‐mediated metabolism of ropivacaine, and decreases the excretion of CYP3A4‐formed PPX in urine. Rifampin considerably increases the metabolism of ropivacaine to PPX and decreases the metabolism to 3‐OH‐ropivacaine in both nonsmokers and smokers.

Clinical Pharmacology & Therapeutics (2001) 70, 344–350; doi: 10.1016/S0009‐9236(01)29243‐1
Ritonavir increases loperamide plasma concentrations without evidence for P‐glycoprotein involvement
Authors: Tayrouz Yorki , Ganssmann Beate , Ding Reinhard , Klingmann Andrea , Aderjan Rolf , Burhenne Jürgen , Haefeli Walter Emil , Mikus Gerd
Published: December 2004

Background

The antidiarrheal drug loperamide is frequently used to treat ritonavir‐associated diarrhea in patients with human immunodeficiency virus. The absence of marked central opioid effects has been attributed to its low bioavailability and its poor penetration of the blood‐brain barrier, both of which might be altered by ritonavir, a potent P‐glycoprotein and cytochrome P4503A inhibitor.

Methods

A 16‐mg dose of loperamide was administered to 12 healthy male and female volunteers together with either 600 mg of ritonavir or placebo. Detailed pharmacokinetics of loperamide and its metabolites were determined over 72 hours. Central opioid effects were measured by evaluation of pupil diameter, cold pressor test, and transcutaneous PCO2 and PO2.

Results

Ritonavir caused a major pharmacokinetic interaction, increasing the area under the concentration‐time curve of loperamide from 104 ± 60 h · pmol/ml after placebo to 276 ± 68 h · pmol/ml and delayed formation of the major metabolite desmethylloperamide (time to reach maximum concentration after drug administration [tmax], 7.1 ± 2.6 hours versus 19.6 ± 9.1 hours). The urinary metabolic ratio of loperamide increased 3 times whereas the total molar amount of loperamide and metabolites excreted in urine remained unchanged. No central pharmacodynamic effects were observed after coadministration of loperamide with either ritonavir or placebo.

Conclusion

This study demonstrates a major metabolic interaction probably by cytochrome P4503A4 with no evidence of P‐glycoprotein involvement. This might explain the lack of central effects after ritonavir.

Clinical Pharmacology & Therapeutics (2001) 70, 405–414; doi: 10.1016/S0009‐9236(01)35864‐2
QTc prolongation and drugs
Authors: Henderson William , Chu Jason , Hoffman Robert
Published: December 2004

Clinical Pharmacology & Therapeutics (2001) 70, 567–568; doi: 10.1016/S0009‐9236(01)90121‐3
Phosphatidylinositol 3,4,5-trisphosphate and Ca2+/calmodulin competitively bind to the regulators of G-protein-signalling (RGS) domain of RGS4 and reciprocally regulate its action
Authors: ISHII Masaru , FUJITA Satoru , YAMADA Mitsuhiko , HOSAKA Yukio , KURACHI Yoshihisa
Published: December 2004

RGS (regulators of G-protein signalling) are a diverse group of proteins, which accelerate intrinsic GTP hydrolysis on heterotrimeric G-protein α subunits. They are involved in the control of a physiological behaviour known as ‘relaxation’ of G-protein-gated K+ channels in cardiac myocytes. The GTPase-accelerating activity of cardiac RGS proteins, such as RGS4, is inhibited by PtdIns(3,4,5)P3 (phosphatidylinositol 3,4,5-trisphosphate) and this inhibition is cancelled by Ca2+/calmodulin (CaM) formed during membrane depolarization. G-protein-gated K+ channel activity decreases on depolarization owing to the facilitation of GTPase-activating protein activity by RGS proteins and vice versa on hyperpolarization. The molecular mechanism responsible for this reciprocal control of RGS action by PtdIns(3,4,5)P3 and Ca2+/CaM, however, has not been fully elucidated. Using lipid–protein co-sedimentation assay and surface plasmon resonance measurements, we show in the present study that the control of the GTPase-accelerating activity of the RGS4 protein is achieved through the competitive binding of PtdIns(3,4,5)P3 and Ca2+/CaM within its RGS domain. Competitive binding occurs exclusively within the RGS domain and involves a cluster of positively charged residues located on the surface opposite to the Gα interaction site. In the RGS proteins conserving these residues, the reciprocal regulation by PtdIns(3,4,5)P3 and Ca2+/CaM may be important for their physiological regulation of G-protein signalling.
Tissue specificity and regulation of the N-terminal diversity of reticulon 3
Authors: DI SCALA Franck , DUPUIS Luc , GAIDDON Christian , DE TAPIA Marc , JOKIC Natasa , GONZALEZ DE AGUILAR Jose-Luis , RAUL Jean-Sébastien , LUDES Bertrand , LOEFFLER Jean-Philippe
Published: December 2004

Over the last few years, the widely distributed family of reticulons (RTNs) is receiving renewed interest because of the implication of RTN4/Nogo in neurite regeneration. Four genes were identified in mammals and are referred to as RTN1, 2, 3 and the neurite outgrowth inhibitor RTN4/Nogo. In the present paper, we describe the existence of five new isoforms of RTN3 that differ in their N-termini, and analysed their tissue distribution and expression in neurons. We redefined the structure of human and murine rtn3 genes, and identified two supplementary exons that may generate up to seven putative isoforms arising by alternative splicing or differential promoter usage. We confirmed the presence of five of these isoforms at the mRNA and protein levels, and showed their preferential expression in the central nervous system. We analysed rtn3 expression in the cerebellum further, and observed increased levels of several of the RTN3 isoforms during cerebellum development and during in vitro maturation of cerebellar granule cells. This pattern of expression paralleled that shown by RTN4/Nogo isoforms. Specifically, RTN3A1 expression was down-regulated upon cell death of cerebellar granule neurons triggered by potassium deprivation. Altogether, our results demonstrate that the rtn3 gene generates multiple isoforms varying in their N-termini, and that their expression is tightly regulated in neurons. These findings suggest that RTN3 isoforms may contribute, by as yet unknown mechanisms, to neuronal survival and plasticity.
The predominant polyphenol in the leaves of the resurrection plantMyrothamnus flabellifolius, 3,4,5 tri-O-galloylquinic acid, protects membranes against desiccation and free radical-induced oxidation
Authors: MOORE John P. , WESTALL Kim L. , RAVENSCROFT Neil , FARRANT Jill M. , LINDSEY George G. , BRANDT Wolf F.
Published: December 2004

The predominant (>90%) low-molecular-mass polyphenol was isolated from the leaves of the resurrection plant Myrothamnus flabellifolius and identified to be 3,4,5 tri-O-galloylquinic acid using 1H and 13C one- and two-dimensional NMR spectroscopy. The structure was confirmed by mass spectrometric analysis. This compound was present at high concentrations, 44% (by weight) in hydrated leaves and 74% (by weight) in dehydrated leaves. Electron microscopy of leaf material fixed with glutaraldehyde and caffeine demonstrated that the polyphenols were localized in large vacuoles in both hydrated and dehydrated leaves. 3,4,5 Tri-O-galloylquinic acid was shown to stabilize an artificial membrane system, liposomes, against desiccation if the polyphenol concentration was between 1 and 2 μg/μg phospholipid. The phase transition of these liposomes observed at 46 °C was markedly diminished by the presence of 3,4,5 tri-O-galloylquinic acid, suggesting that the presence of the polyphenol maintained the membranes in the liquid crystalline phase at physiological temperatures. 3,4,5 Tri-O-galloylquinic acid was also shown to protect linoleic acid against free radical-induced oxidation.
ADP-ribosylation of integrin α7 modulates the binding of integrin α7β1 to laminin
Authors: ZHAO Zhefeng , GRUSZCZYNSKA-BIEGALA Joanna , ZOLKIEWSKA Anna
Published: December 2004

The extracellular domain of integrin α7 is ADP-ribosylated by an arginine-specific ecto-ADP-ribosyltransferase after adding exogenous NAD+ to intact C2C12 skeletal muscle cells. The effect of ADP-ribosylation on the structure or function of integrin α7β1 has not been explored. In the present study, we show that ADP-ribosylation of integrin α7 takes place exclusively in differentiated myotubes and that this post-translational modification modulates the affinity of α7β1 dimer for its ligand, laminin. ADP-ribosylation in the 37-kDa ‘stalk’ region of α7 that takes place at micromolar NAD+ concentrations increases the binding of the α7β1 dimer to laminin. Increased in vitro binding of integrin α7β1 to laminin after ADP-ribosylation of the 37-kDa fragment of α7 requires the presence of Mn2+ and it is not observed in the presence of Mg2+. In contrast, ADP-ribosylation of the 63-kDa N-terminal region comprising the ligand-binding site of α7 that occurs at approx. 100 μM NAD+ inhibits the binding of integrin α7β1 to laminin. Furthermore, incubation of C2C12 myotubes with NAD+ increases the expression of an epitope on integrin β1 subunit recognized by monoclonal antibody 9EG7. We discuss our results based on the current models of integrin activation. We also hypothesize that ADP-ribosylation may represent a mechanism of regulation of integrin α7β1 function in myofibres in vivo when the continuity of the membrane is compromised and NAD+ is available as a substrate for ecto-ADP-ribosylation.
Conserved extracellular cysteine residues and cytoplasmic loop–loop interplay are required for functionality of the heptahelical MLO protein
Authors: ELLIOTT Candace , MÜLLER Judith , MIKLIS Marco , BHAT Riyaz A. , SCHULZE-LEFERT Paul , PANSTRUGA Ralph
Published: December 2004

We performed a structure–function analysis of the plasma membrane-localized plant-specific barley (Hordeum vulgare) MLO (powdery-mildew-resistance gene o) protein. Invariant cysteine and proline residues, located either in extracellular loops or transmembrane domains that have been conserved in MLO proteins for more than 400 million years, were found to be essential for MLO functionality and/or stability. Similarly to many metazoan G-protein-coupled receptors known to function as homo- and hetero-oligomers, FRET (fluorescence resonance energy transfer) analysis revealed evidence for in planta MLO dimerization/oligomerization. Domain-swap experiments with closely related wheat and rice as well as diverged Arabidopsis MLO isoforms demonstrated that the identity of the C-terminal cytoplasmic tail contributes to MLO activity. Likewise, analysis of a progressive deletion series revealed that integrity of the C-terminus determines both MLO accumulation and functionality. A series of domain swaps of cytoplasmic loops with the wheat (Triticum aestivum) orthologue, TaMLO-B1, provided strong evidence for co-operative loop–loop interplay either within the protein or between MLO molecules. Our data indicate extensive intramolecular co-evolution of cytoplasmic domains in the evolutionary history of the MLO protein family.
Functional interaction between p75NTR and TrkA: the endocytic trafficking of p75NTR is driven by TrkA and regulates TrkA-mediated signalling
Authors: PERRONE Lorena , PALADINO Simona , MAZZONE Marialuisa , NITSCH Lucio , GULISANO Massimo , ZURZOLO Chiara
Published: December 2004

The topology and trafficking of receptors play a key role in their signalling capability. Indeed, receptor function is related to the microenvironment inside the cell, where specific signalling molecules are compartmentalized. The response to NGF (nerve growth factor) is strongly dependent on the trafficking of its receptor, TrkA. However, information is still scarce about the role of the cellular localization of the TrkA co-receptor, p75NTR (where NTR is neurotrophin receptor), following stimulation by NGF. It has been shown that these two receptors play a key role in epithelial tissue and in epithelial-derived tumours, where the microenvironment at the plasma membrane is defined by the presence of tight junctions. Indeed, in thyroid carcinomas, rearrangements of TrkA are frequently found, which produce TrkA mutants that are localized exclusively in the cytoplasm. We used a thyroid cellular model in which it was possible to dissect the trafficking of the two NGF receptors upon neurotrophin stimulation. In FRT (Fischer rat thyroid) cells, endogenous TrkA is localized exclusively on the basolateral surface, while transfected p75NTR is selectively distributed on the apical membrane. This cellular system enabled us to selectively stimulate either p75NTR or TrkA and to analyse the role of receptor trafficking in their signalling capability. We found that, after binding to NGF, p75NTR was co-immunoprecipitated with TrkA and was transcytosed at the basolateral membrane. We showed that the TrkA–p75NTR interaction is necessary for this relocation of p75NTR to the basolateral side. Interestingly, TrkA-specific stimulation by basolateral NGF loading also induced the TrkA–p75NTR interaction and subsequent p75NTR transcytosis at the basolateral surface. Moreover, specific stimulation of p75NTR by NGF activated TrkA and the MAPK (mitogen-activated protein kinase) pathway. Our data indicate that TrkA regulates the subcellular localization of p75NTR upon stimulation with neurotrophins, thus affecting the topology of the signal transduction molecules, driving the activation of a specific signal transduction pathway.
Search for disease-specific cardiovascular reactivity patterns: developing the methodology
Authors: NASCHITZ Jochanan E. , ROZENBAUM Michael , FIELDS Madeline , ISSEROFF Hillel , ENIS Sean , BABICH Jay P. , PECK Shannon , RUBIN PECK Elisabeth , GAITINI Louis , NASCHITZ Shaul , SABO Edmond , ROSNER Itzhak
Published: December 2004

Aberrations of CVR (cardiovascular reactivity), an expression of autonomic function, lack specificity for a particular disorder. Recently, a CVR pattern particular to chronic fatigue syndrome has been observed. In the present study, we aimed to develop methodologies for assessing disease-specific CVR patterns. As a prototype, a population of 50 consecutive patients with FMF (familial Mediterranean fever) was studied and compared with control populations. A 10 min supine/30 min head-up tilt test with recording of the heart rate and blood pressure or the pulse transit time was performed. Five studies were conducted applying different methods. In each study, statistical analysis identified independent predictors of CVR in FMF. Based on regression coefficients of these predictors, a linear DS (discriminant score) was computed for every subject. Each study established an equation to assess CVR, calculate DS for FMF and determine the sensitivity and specificity of the DS cut-off. In each of the five studies, abnormal CVR was observed in FMF patients. The best accuracy (88% sensitivity and 90.1% specificity for FMF) was obtained by a method based on beat-to-beat heart rate and pulse transit time recordings. Data was processed by fractal and recurrence quantitative analysis with recordings in FMF patients compared with a mixed control population. Identification of disease-specific CVR patterns was possible with the methodologies described in the present study. In FMF, disease-specific CVR may be explained by the interplay between neuroendocrine loops specific to FMF with cardiovascular homoeostatic mechanisms. Recognition of disease-specific CVR patterns may advance the understanding of homoeostatic mechanisms and have implications in clinical practice.
Structural and electronic properties of TaSin (n=1–13) clusters: A relativistic density functional investigation
Authors: Guo Ping , Ren Zhao-Yu , Wang Fan , Bian Jiang , Han Ju-Guang , Wang Guang-Hou
Published: December 2004

The TaSin (n=1–13) clusters with doublet, quartet, and sextet spin configurations have been systematically investigated by a relativistic density functional theory with the generalized gradient approximation available in Amsterdam density functional program. The total bonding energies, equilibrium geometries, Mulliken populations as well as Hirshfeld charges of TaSin (n=1–13) clusters are calculated and presented. The emphasis on the stabilities and electronic properties is discussed. The most stable structures of the small TaSin (n=1–6) clusters and the evolutional rule of low-lying geometries of the larger TaSin (n=7–13) clusters are obtained. Theoretical results indicate that the most stable structure of TaSin (n=1–6) clusters keeps the similar framework as the most stable structure of Sin+1 clusters except for TaSi3 cluster. The Ta atom in the lowest-energy TaSin (n=1–13) isomers occupies a gradual sinking site, and the site moves from convex, to flatness, and to concave with the number of Si atom varying from 1 to 13. When n=12, the Ta atom in TaSi12 cluster completely falls into the center of the Si frame, and a cagelike TaSi12 geometry is formed. Meanwhile, the net Mulliken and Hirsheld populations of the Ta atom in the TaSin (n=1–13) clusters vary from positive to negative, manifesting that the charges in TaSin (n⩾12) clusters transfer from Si atoms to Ta atom. Additionally, the contribution of Si–Si and Si–Ta interactions to the stability of TaSin clusters is briefly discussed. Furthermore, the investigations on atomic averaged binding energies and fragmentation energies show that the TaSin (n=2,3,5,7,10,11,12) clusters have enhanced stabilities. Compared with pure silicon clusters, a universal narrowing of highest occupied molecular orbital—lowest unoccupied molecular orbital gap in TaSin clusters is found.
A search for a strong physisorption site for H2 in Li-doped porous carbons
Authors: Maresca O. , Pellenq R. J.-M. , Marinelli F. , Conard J.
Published: December 2004

The mechanism of hydrogen absorption between two coronene molecules has been studied by first principle calculations. Examination of different sites for H2 molecule confirmed the classical picture of physisorption. We have also considered molecular hydrogen adsorption in a charged carbon structure achieved by doping with lithium at a density corresponding to the intercalate compound LiC6. We have performed different types of calculations [Hartree-Fock and density functional theory (DFT)] for various atomic basis sets using CRYSTAL98, GAUSSIAN98, and DMOL3 codes. B3LYP-DFT (B3LYP—three-parameter functional of Backe, Lee, Yang and Parr) energy minimization calculations unravel that there is a stable adsorption site for molecular hydrogen in Li-doped sp2 carbon structure. These calculations also give an insight into the atomic configurations of interlayer species (H2 and Li) as the interlayer spacing increases. It can be shown that large changes occur in the positions and electronic properties of interlayer species. Hydrogen molecule does not show any tendency for dissociation and adopts a position in the interlayer void that is deeply related to that of lithium ions. We have evidenced a rather large charge transfer from lithium and capping hydrogen species on neighboring slab carbon atoms that induce the stabilization of molecular hydrogen. We have also found that rotating one carbon layer with respect to the other one (at constant interlayer distance) does not change the adsorption energy to a large extent. The best adsorption site is about five times deeper than the physisorption site found in the undoped case and occurs at an interlayer separation of 5.5±0.5 Å. The corresponding atomic configuration consists in a hydrogen molecule standing (nearly) perpendicular to the plane surface surrounded by the three lithium ions in a configuration close to that of the LiC6 intercalation compound.
Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application
Authors: Schmitz Matthias , Tavan Paul
Published: December 2004

Hybrid molecular dynamics (MD) simulations, which combine density functional theory (DFT) descriptions of a molecule with a molecular mechanics (MM) modeling of its solvent environment, have opened the way towards accurate computations of solvation effects in the vibrational spectra of molecules. Recently, Wheeler et al. [ChemPhysChem 4, 382 (2002)] have suggested to compute these spectra from DFT/MM-MD trajectories by diagonalizing the covariance matrix of atomic fluctuations. This so-called principal mode analysis (PMA) allegedly can replace the well-established approaches, which are based on Fourier transform methods or on conventional normal mode analyses. By scrutinizing and revising the PMA approach we identify five conditions, which must be guaranteed if PMA is supposed to render exact vibrational frequencies. Besides specific choices of (a) coordinates and (b) coordinate systems, these conditions cover (c) a harmonic intramolecular potential, (d) a complete thermal equilibrium within the molecule, and (e) a molecular Hamiltonian independent of time. However, the PMA conditions [(c)–(d)] and [(c)–(e)] are generally violated in gas phase DFT-MD and liquid phase DFT/MM-MD trajectories, respectively. Based on a series of simple analytical model calculations and on the analysis of MD trajectories calculated for the formaldehyde molecule in the gas phase (DFT) and in liquid water (DFT/MM) we show that in both phases the violation of condition (d) can cause huge errors in PMA frequency computations, whereas the inevitable violations of conditions (c) and (e), the latter being generic to the liquid phase, imply systematic and sizable underestimates of the vibrational frequencies by PMA. We demonstrate that the huge errors, which are caused by an incomplete thermal equilibrium violating (d), can be avoided if one introduces mode-specific temperatures Tj and calculates the frequencies from a “generalized virial” (GV) expression instead from PMA. Concerning ways to additionally remove the remaining errors, which GV still shares with PMA, we refer to Paper II of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12247 (2004)].
The permanent electric dipole moments of iron monoxide, FeO
Authors: Steimle T. C. , Gengler Jamie , Hodges Philip J.
Published: December 2004

The Q(4) and R(4) branch features of the (0,0)D 5Δ4-X 5Δ4 band system and the Q(3) and R(3) branch features of the (0,0)D 5Δ3-X 5Δ3 band system of iron monoxide FeO have been studied by optical Stark spectroscopy. The Stark splittings in the high resolution laser induced fluorescence spectra were analyzed to produce values for the magnitude of the permanent electric dipole moments |μ| of 4.50±0.03, 4.29±0.05, 2.53±0.04, and 2.58±0.06 D for the X 5Δ4 (v=0), X 5Δ3 (v=0), D 5Δ4 (v=0), and D 5Δ3 (v=0) states, respectively. The results are compared to several ab initio predictions and to FeC. The qualitative trends are explained in terms of a molecular orbital correlation picture.
The numerical stability of leaping methods for stochastic simulation of chemically reacting systems
Authors: Cao Yang , Petzold Linda R. , Rathinam Muruhan , Gillespie Daniel T.
Published: December 2004

Tau-leaping methods have recently been proposed for the acceleration of discrete stochastic simulation of chemically reacting systems. This paper considers the numerical stability of these methods. The concept of stochastic absolute stability is defined, discussed, and applied to the following leaping methods: the explicit tau, implicit tau, and trapezoidal tau.
Impact of cholesterol on voids in phospholipid membranes
Authors: Falck Emma , Patra Michael , Karttunen Mikko , Hyvönen Marja T. , Vattulainen Ilpo
Published: December 2004

Free volume pockets or voids are important to many biological processes in cell membranes. Free volume fluctuations are a prerequisite for diffusion of lipids and other macromolecules in lipid bilayers. Permeation of small solutes across a membrane, as well as diffusion of solutes in the membrane interior are further examples of phenomena where voids and their properties play a central role. Cholesterol has been suggested to change the structure and function of membranes by altering their free volume properties. We study the effect of cholesterol on the properties of voids in dipalmitoylphosphatidylcholine (DPPC) bilayers by means of atomistic molecular dynamics simulations. We find that an increasing cholesterol concentration reduces the total amount of free volume in a bilayer. The effect of cholesterol on individual voids is most prominent in the region where the steroid ring structures of cholesterol molecules are located. Here a growing cholesterol content reduces the number of voids, completely removing voids of the size of a cholesterol molecule. The voids also become more elongated. The broad orientational distribution of voids observed in pure DPPC is, with a 30% molar concentration of cholesterol, replaced by a distribution where orientation along the bilayer normal is favored. Our results suggest that instead of being uniformly distributed to the whole bilayer, these effects are localized to the close vicinity of cholesterol molecules.
Exact solutions for two-dimensional steady flows of a power-law liquid on an incline
Authors: Perazzo Carlos Alberto , Gratton Julio
Published: December 2004

Under assumptions that are not too restrictive it is possible to reduce the equations that describe steady viscous gravity flows of a power-law liquid on an inclined plane to an equivalent problem consisting of an unsteady one-dimensional nonlinear diffusion process. In a paper dealing with the steady spreading flow of a Herschel–Buckley liquid, Wilson and Burgess [“The steady, spreading flow of a rivulet of mud,” J. Non-Newtonian Fluid Mech. 79, 77 (1998)] noticed a formal analogy between the steady, two-dimensional viscous gravity flows of a power-law liquid on an incline and a one-dimensional time-dependent nonlinear diffusion phenomena; however, they did not pursue the matter further. Here we develop the analogy and show how it can be used to find a large number of exact solutions representing steady two-dimensional flows of power-law liquids, based on the available knowledge concerning nonlinear diffusion. We describe flows whose widths stay constant until a certain distance from the source, which are analogous to the well-known waiting-time solutions of nonlinear diffusion. We then introduce a phase-plane formalism that allows us to find self-similar solutions and we give as examples three different currents limited laterally by a wall that ends abruptly and currents on an inclined stripe. Finally we describe the two-dimensional currents that are analogous to the traveling wave solutions of the nonlinear diffusion equation. The approximations involved in the analogy are essentially equivalent to those of the lubrication theory, so that they do not impose restrictions more severe than those usually present in problems of this type. The present theory does not include surface tension effects, which implies that the appropriate Bond number must be large.
Mechanisms of target poisoning during magnetron sputtering as investigated by real-time in situ analysis and collisional computer simulation
Authors: Güttler D. , Abendroth B. , Grötzschel R. , Möller W. , Depla D.
Published: December 2004

The evolution of reactive gas uptake at the target surface has been investigated by real-time in situ diagnostics during magnetron sputtering. Using a planar circular dc magnetron for reactive sputter deposition of TiN from a Ti target in an argon/nitrogen gas mixture, the target uptake of nitrogen was determined at varying gas flows of nitrogen using the N14(d,α)C12 nuclear reaction, directly demonstrating the target “poisoning” effect. The expected hysteresis behavior at increasing/decreasing nitrogen gas flow is confirmed. Within the precision of the measurement, the nitrogen content remains unaltered after switching off the magnetron, indicating the absence of a significant mobile fraction of nitrogen in the target. The maximum amount of retained nitrogen significantly exceeds one adsorbed monolayer, which is attributed to nitrogen ion implantation and recoil implantation of adsorbed nitrogen. This is quantitatively reproduced by TRIDYN collisional computer simulations.
Experimental and numerical investigation of terahertz transmission through strongly scattering sub-wavelength size spheres
Authors: Mujumdar S. , Chau K. J. , Elezzabi A. Y.
Published: December 2004

We report on experimental and numerical studies of terahertz propagation in strongly scattering random media. The experimental variations of the terahertz pulse group delay and scattering-induced effects such as temporal pulse distortion, spectral decay, and power attenuation as a function of sample thickness are in excellent agreement with those predicted from a Monte Carlo photon migration model. The transmitted pulses are analyzed with a classical effective medium approximation. Due to the subwavelength size of the random scatterers, it is found that the effective medium approximation underestimates the accumulated pulse phase acquired by the high frequencies during pulse propagation.
Ion-exchanged waveguides in glass doped with PbS quantum dots
Authors: Auxier Jason M. , Morrell Michael M. , West Brian R. , Honkanen Seppo , Schülzgen Axel , Peyghambarian Nasser , Sen Sabyasachi , Borrelli Nicholas F.
Published: December 2004

The lowest-loss (≲1dB∕cm) ion-exchanged waveguides in glass doped with PbS quantum dots are presented. Near-field mode profile and refractive index profile using the refracted near-field technique were measured for these waveguides. We demonstrate that the optical properties of this glass remain unchanged during the ion-exchange process.
Room temperature photoluminescence from nanostructured amorphous carbon
Authors: Henley S. J. , Carey J. D. , Silva S. R. P.
Published: December 2004

Visible room-temperature photoluminescence (PL) was observed from hydrogen-free nanostructured amorphous carbon films deposited by pulsed laser ablation in different background pressures of argon (PAr). By varying PAr from 5to340mTorr, the film morphology changed from smooth to rough and at the highest pressures, low-density filamentary growth was observed. Over the same pressure regime an increase in the ordering of sp2 bonded C content was observed using visible Raman spectroscopy. The origin of the PL is discussed in terms of improved carrier localization within an increased sp2 rich phase.
In situ measurements of the critical thickness for strain relaxation in AlGaN∕GaN heterostructures
Authors: Lee S. R. , Koleske D. D. , Cross K. C. , Floro J. A. , Waldrip K. E. , Wise A. T. , Mahajan S.
Published: December 2004

Using in situ wafer-curvature measurements of thin-film stress, we determine the critical thickness for strain relaxation in AlxGa1−xN∕GaN heterostructures with 0.14⩽x⩽1. The surface morphology of selected films is examined by atomic force microscopy. Comparison of these measurements with critical-thickness models for brittle fracture and dislocation glide suggests that the onset of strain relaxation occurs by surface fracture for all compositions. Misfit-dislocations follow initial fracture, with slip-system selection occurring under the influence of composition-dependent changes in surface morphology.
Determination of elastic properties of a film-substrate system by using the neural networks
Authors: Xu Baiqiang , Shen Zhonghua , Ni Xiaowu , Wang Jijun , Guan Jianfei , Lu Jian
Published: December 2004

An inverse method based on artificial neural network (ANN) is presented to determine the elastic properties of films from laser-genrated surface waves. The surface displacement responses are used as the inputs for the ANN model; the outputs of the ANN are the Young’s modulus, density, Poisson’s ratio, and thickness of the film. The finite element method is used to calculate the surface displacement responses in a film-substrate system. Levenberg Marquardt algorithm is used as numerical optimization to speed up the training process for the ANN model. In this method, the materials parameters are not recovered from the dispersion curves but rather directly from the transient surface displacement. We have also found that this procedure is very efficient for determining the materials parameters of layered systems.
Hand-made cloning approach: potentials and limitations
Authors: Vajta G. , Kragh P. M. , Mtango N. R. , Callesen H.
Published: December 2004

Two major drawbacks hamper the advancement of somatic cell nuclear transfer in domestic animals. The first is a biological problem that has been studied extensively by many scientists and from many viewpoints, including the cell, molecular and developmental biology, morphology, biochemistry and tissue culture. The second is a technical problem that may be responsible for 50% or more of quantitative and/or qualitative failures of routine cloning experiments and is partially the result of the demanding and complicated procedure. However, even the relatively rare documented efforts focusing on technique are usually restricted to details and accept the principles of the micromanipulator-based approach, with its inherent limitations. Over the past decade, a small alternative group of procedures, called hand-made cloning (HMC), has emerged that has the common feature of removal of the zona pellucida prior to enucleation and fusion, resulting in a limited (or no) requirement for micromanipulators. The benefits of HMC are low equipment costs, a simple and rapid procedure and an in vitro efficiency comparable with or higher than that of traditional nuclear transfer. Embryos created by the zona-free techniques can be cryopreserved and, although data are still sparse, are capable of establishing pregnancies and resulting in the birth of calves. Hand-made cloning may also open the way to partial or full automation of somatic cell nuclear transfer. Consequently, the zona- and micromanipulator-free approach may become a useful alternative to traditional cloning, either in special situations or generally for the standardisation and widespread application of somatic cell nuclear transfer.
101 OVARIAN RESPONSE AND DEVELOPMENTAL COMPETENCE OF OOCYTES COLLECTED BY OPU IN SHEEP TREATED WITH GnRH ANTAGONIST
Authors: Berlinguer F. , Gonzalez-Bulnes A. , Succu S. , Leoni G. , Rosati I. , Veiga-Lopez A. , Garcia Garcia R.M. , Cocero M.J. , Naitana S.
Published: December 2004

The use of a single dose of GnRH antagonists during the progestagen treatment prior to superovulatory treatment protocols in sheep increases the number of smaller follicles able to grow and ovulate in response to the exogenous FSH treatment (Lopez-Alonso C et al. 2004 Reprod. Fertil. Dev. 16, 233). The aim of our study was to test if such treatment affects the in vitro developmental competence of oocytes collected by ovum pick up (OPU) from GnRH-antagonist treated sheep during an ovarian by perstimulation protocol. Adult Sarda sheep (n = 18) were synchronized by the insertion of intravaginal sponges (Day 0) which were left in situ for 12 days; on Day 7, group A (n = 10) received a single dose of 3 mg of Antarelix (Teverelix, Europeptides, France) s.c., while group B (n = 8) served as control. All animals received 96 IU of FSH (Ovagen, ICP, New Zealand) administered in 4 equal doses given i.m. every 12 h starting on Day 10. Twelve hours after the last FSH administration oocytes were collected by OPU technique. Follicular growth was monitored by transrectal ultrasonography from Day 7 to Day 11. Collected oocytes were matured, fertilized, and cultured in vitro up to blastocyst stage under standard conditions used in our laboratory (Berlinguer F et al. 2004 Theriogenology 61, 1477–1486). After IVF, uncleaved oocytes were stained with acetolacmoid to evaluate chromatin configuration, while the cleaved ones were cultured in SOF + 0.4% BSA up to the blastocyst stage. Data were analyzed by ANOVA statistical analysis after arcsine transformation of the value percentages. Ultrasonographic monitoring showed a significant increase in the number of follicles (mean ± SEM) present in the ovaries from Day 8 to Day 11 of treatment in group A compared to group B (Day 8: 19 ± 5.1 vs. 13 ± 3.4, P > 0.05; Day 9: 20.1 ± 4.6 vs. 14.1 ± 2.4, P > 0.001; Day 10: 22.5 ± 6.1 vs. 14.7 ± 2.7, P > 0.001; Day 11: 25.3 ± 5.1 vs. 20.5 ± 4.1, P > 0.05), thus confirming that GnRH antagonist administration enhances ovarian response to exogenous FSH stimulation. On the other hand, oocytes collected from untreated sheep lead to a higher blastocyst output (P = 0.014), as illustrated in the table. These results indicated that although GnRH antagonist administration caused a significant increase in the ovarian response to the hormonal treatment, the final blastocyst output was significantly lower compared to that of the control group. This finding seems to suggest an impairment in the developmental competence of treated sheep oocytes.

Table 1.
In vitro maturation, fertilization, and developmental capacity of oocytes collected from follicles of GnRH antagonist-treated (group A) and untreated (group B) sheep

This work was supported by funds from the Spanish MEC (projects SC 00-051-C3.1 and HI2002-0004) and the Italian MIUR (cofin).
106 GENOMIC IMPRINTING OF IGF2R IN TISSUES OF BOVINE FETUSES GENERATED BY ARTIFICIAL INSEMINATION OR IN VITRO FERTILIZATION
Authors: Hiendleder S. , Bebbere D. , Bauersachs S. , Stojkovic M. , Wenigerkind H. , Reichenbach H.-D. , Ledda S. , Wolf E.
Published: December 2004

The insulin-like growth factor 2 receptor gene (IGF2R) is involved in fetal growth regulation. A study in sheep associated fetal overgrowth after in vitro embryo culture with abnormal DNA methylation and expression of IGF2R (Young et al. 2001 Nat. Genet. 27, 153–154). This suggested that abnormal IGF2R imprinting is a major cause of fetal overgrowth. To test this hypothesis in bovine fetuses, we developed a microsatellite marker for IGF2R from cDNA sequence data and screened 45 Day-80 fetuses generated in vivo, by artificial insemination (AI), or in vitro, by in vitro fertilization (IVF) procedures, for parent-of-origin-specific gene expression. A total of 17 fetuses were heterozygous, but available parental DNA samples showed that only 12 (8 AI, 4 IVF) allowed unambiguous discrimination of parental alleles. Parent-of-origin-specific allelic expression patterns indicated that bovine IGF2R was expressed predominantly from the maternal allele and thus imprinted in fetal heart, kidney, liver, lung, muscle, and cotyledon tissue. However, the relative amount of expression from the paternal allele was tissue-specific and ranged from 6.4 ± 0.8% in skeletal muscle up to 27.4 ± 0.9% in cotyledon (SPSS or 11.5, ANOVA, P < 0.001). Tissues that originated from the same germ layer showed similar allelic expression ratios whereas significantly different expression ratios (P < 0.05) were observed between tissues originating from different germ layers. Contrary to expectations from sheep data, there was no evidence for gross abnormalities in IGF2R imprinting in tissues from overgrown (n = 2) or normal sized (n = 2) IVF fetuses. However, relative paternal expression levels in several tissues showed significant relationships (P < 0.05–0.001) with growth parameters and pointed to subtle changes in paternal IGF2R expression in overgrown IVF fetuses.
We thank W. Scholz and M. Weppert for excellent technical assistance.
114 PORCINE EMBRYO FRAGMENTATION, DEVELOPMENT AND APOPTOSIS: A CONFOCAL MICROSCOPY STUDY
Authors: Mateusen B. , Van Soom A. , Maes D. , de Kruif A.
Published: December 2004

The relationship between embryonic fragmentation, embryonic arrest, and apoptosis has been the subject of some controversy (Hardy K 1999 Rev. Reprod. 4, 125–134). In order to investigate possible links, in vivo-produced, in vitro-cultured porcine embryos (n = 132) were scored for developmental stage and fragmentation at 7 days post insemination (dpi) and processed for propidium iodide and annexin V labelling. After fixation, embryos were processed for terminal deoxynucleotidyl transferase mediated dUTP nick end labelling (TUNEL). Using confocal microscopy, a cell was categorized apoptotic if (i) it had a fragmented or condensed nucleus, (ii) the cell membrane was annexin V-positive, and (iii) the nucleus was TUNEL labelled. An apoptotic cell ratio (ACR) was determined as the percentage of apoptotic cells per embryo. Differences in the % of fragmented and apoptotic embryos and correlations were analyzed using chi-square. Logistic regression was used to compare the average fragmentation % and the ACR. Sixty-one embryos (46%) arrested during the culture period, with 8 embryos arresting before or at the 4-cell stage. Significantly more arrested embryos were fragmented compared to embryos that were blastocysts at 7 dpi. Also, the average fragmentation percentage was significantly higher for arrested embryos compared to blastocysts. The correlation detected between developmental arrest and fragmentation was 0.60 (P < 0.05). None of the embryos without fragmentation had cells categorized as apoptotic, whereas 50 out of 55 embryos with fragmentation possessed apoptotic cells, which led to a correlation of 0.87 (P < 0.01) between fragmentation and apoptosis. The percentage of embryos with apoptotic cells was significantly higher for embryos arrested during the 5-cell to the morula stage compared to embryos that arrested before or at the 4-cell stage and embryos with blastocyst development at 7 dpi. The average ACR of embryos arrested during the 5-cell to the morula stage was significantly higher compared to the average ACR of blastocysts at 7 dpi. The correlation detected between the developmental arrest, during the 5-cell to the morula stage period and apoptosis was 0.57 (P < 0.01). Taken together, significant correlations between fragmentation, developmental arrest and apoptosis were detected. However, the association between embryonic arrest and apoptosis could be established only for embryos arrested after embryonic genome activation.