bluuebunny/crossref_metadata_2025 huggingface dataset:
Serine phosphorylation by casein kinase II controls endocytic L1 trafficking and axon growth
Authors: Nakata Asuka , Kamiguchi Hiroyuki
Published: January 2007

The cell adhesion molecule L1 plays crucial roles in axon tract development. In vitro, L1 presented as a culture substrate stimulates axon elongation by binding to L1 expressed on the growth cone. In migrating growth cones, L1 is endocytosed via the AP‐2/clathrin‐mediated pathway at the central domain, followed by anterograde vesicular transport and recycling to the plasma membrane of the leading front. It has previously been shown that this endocytic trafficking of L1 is critical for axon elongation (Kamiguchi and Yoshihara [2001] J. Neurosci. 21:9194–9203). Adjacent to the AP‐2 recognition site, the L1 cytoplasmic domain has a cluster of acidic amino acids containing Ser1181 that can be phosphorylated by casein kinase II (CKII; Wong et al. [1996a] J. Neurochem. 66:779–786). In this paper, we demonstrate that Ser1181 phosphorylation by CKII is implicated in both normal endocytic trafficking of L1 and L1‐stimulated axon growth. Whereas L1 is sorted into transferrin‐positive endosomes after endocytosis, pharmacological inhibition of CKII caused some population of L1 to be internalized into transferrin‐negative compartments. Single‐amino‐acid mutations at Ser1181, which either prevent or mimic phosphorylation by CKII, caused similar missorting of internalized L1. Furthermore, dorsal root ganglion neurons that had been treated with a CKII inhibitor or transfected with the L1 mutants showed impaired ability to extend axons on an L1 substrate but not on other control substrates. These results demonstrate the novel role of CKII in L1‐mediated axon elongation and stress the importance of functional linkage between L1 phosphorylation and L1 trafficking in migrating growth cones. © 2007 Wiley‐Liss, Inc.
Glutamate decarboxylase protects neurons against excitotoxic injury
Authors: Matthews Christopher C. , Zielke H. Ronald , Fishman Paul S. , Remington Mary P. , Bowen Thomas G.
Published: January 2007

Although the majority of agents with antiexcitotoxic action act as glutamate receptor antagonists, enzymatic degradation of glutamate can also be neuroprotective. The very low specific activity of the mammalian form of glutamate decarboxylase (GAD), the enzyme that catalyzes the formation of γ‐aminobutyric acid (GABA) from glutamate in neurons, is likely to limit its utility as an antiglutamate neuroprotectant. In contrast, the bacterial form of GAD can be isolated with relatively high specific activity and is most active in acidic environments. We have expressed and purified GAD from Escherichia coli (bGAD) and tested the ability of the enzyme to protect against glutamate excitotoxicity. Incubation of rat hipppocampal slices with the potassium channel antagonist tetraethyl ammonium (TEA) resulted in widespread excitotoxic death of pyramidal and granule cell neurons. bGAD alone showed no significant neurotoxicity and significantly reduced excitotoxicity induced by TEA. We hypothesize that bGAD may be internalized into the synaptic vesicle compartment by nonspecific endocytosis, where both the appropriate pH and high glutamate concentrations are present. Targeting of this enzyme to the interior of synaptic vesicles may enhance its potency as a neuroprotectant against excitotoxicity. © 2007 Wiley‐Liss, Inc.
Kinetic study and UV–Vis spectra of 1:2 complexation of free base para‐substituted meso‐tetraphenylporphyrins with trimethylsilyl chloride
Authors: Safavi Afsaneh , Movahedi Zarangiz , Mohajer Daryoush , Abdollahi Hamid
Published: January 2007

The UV–Vis spectra for 1:2 complexation of four different para‐substituted meso‐tetraphenylporphyrin (H2t(4‐X)pp) and meso‐tetraphenylporphyrins (H2tpp) with trimethylsilyl chloride (TMSC) displayed large and different redshifts (28–32.4 nm) of Soret and (15–41.7 nm) Q(0‐0) bands, whereas 1:2 complexation of the less flexible tetramesitylporphyrin (H2tmp) with TMSC led to rather small redshift (24.8 nm) of the Soret band and blueshift (−7.4 nm) of the Q(0‐0) band. The varying spectral behavior for the porphyrins complexation seems to essentially reflect the different extent of π‐interactions between the meso‐aryl groups and the presumably saddled porphyrin macrocycle, through their relative coplanarity. The observed order of the rate constants for the complexation of various para‐substituted porphyrins, H2t(4‐OCH3)pp (9.27 ± 0.03) × 10−3 > H2t(4‐CH3)pp (6.68 ± 0.05) × 10−3 > H2tpp (3.2 ± 0.05) × 10−3 > H2t(4‐Cl)pp (8.36 ± 0.06) × 10−4, clearly demonstrated a higher reaction rate for the porphyrins containing para‐substituents with stronger electron donor ability. The calculated order for porphyrins (0.9 ± 0.1) and for TMSC (1.0 ± 0.1) suggests rate = K[Por][TMSC] for the complexation. Attempts were made to explain the absence of spectral evidence for the presence of an intermediate 1:1 (TMSC) Por adduct in terms of its high reactivity and/or relative instability. © 2007 Wiley Periodicals, Inc. 39: 231–235, 2007
Reduction of large detailed chemical kinetic mechanisms for autoignition using joint analyses of reaction rates and sensitivities
Authors: Saylam A. , Ribaucour M. , Pitz W. J. , Minetti R.
Published: January 2007

This study describes a new technique of reduction of detailed mechanisms for autoignition. It is based on two analysis methods. An analysis of reaction rates is coupled to an analysis of reaction sensitivity for the detection of redundant reactions. Thresholds associated with the two analyses have a great influence on the size and efficiency of the reduced mechanism. Rules of selection of the thresholds are defined. The reduction technique has been successfully applied to detailed autoignition mechanisms of two reference hydrocarbons: n‐heptane and isooctane. The efficiency of the technique and the ability of the reduced mechanisms to reproduce well the results generated by the full mechanism are discussed. A speedup of calculations by a factor of 5.9 for n‐heptane mechanism and by a factor of 16.7 for isooctane mechanism is obtained without losing accuracy of the prediction of autoignition delay times and concentrations of intermediate species. © 2007 Wiley Periodicals, Inc. 39: 181–196, 2007
Oxidation of vanillin by diperiodatocuprate(III) in aqueous alkaline medium: A kinetic and mechanistic study by stopped flow technique
Authors: Hiremath D. C. , Kiran T. S. , Nandibewoor S. T.
Published: January 2007

The kinetics of oxidation of vanillin (VAN) by diperiodatocuprate(III) (DPC) in alkaline medium at a constant ionic strength of 0.50 mol dm−3 was studied spectrophotometrically. The reaction between DPC and vanillin in alkaline medium exhibits 1:2 stoichiometry (vanillin: DPC). The reaction is of first order in [DPC] and has less than unit order in both [VAN] and [alkali]. Intervention of free radicals was observed in the reaction. Increase in periodate concentration decreases the rate. The oxidation reaction in alkaline medium has been shown to proceed via a monoperiodatocuprate(III)–vanillin complex, which decomposes slowly in a rate‐determining step followed by other fast steps to give the products. The main products were identified by spot test, IR, and MS studies. The reaction constants involved in the different steps of the mechanism are calculated. The activation parameters with respect to slow step of the mechanism are computed and discussed, and thermodynamic quantities are also determined. © 2007 Wiley Periodicals, Inc. 39: 236–244, 2007
Equine zona protein synthesis and ZP structure during folliculogenesis, oocyte maturation, and embryogenesis
Authors: Kölle Sabine , Dubois Clotilde S. , Caillaud Maud , Lahuec Cécile , Sinowatz Fred , Goudet Ghylène
Published: January 2007

In the equine, the zona pellucida (ZP) is the major barrier to successful in vitro fertilization. Therefore the aim of our studies was to analyze species‐specific features of the equine ZP in regard to structure and glycoprotein ZPB and ZPC expression sites during oocyte development and embryogenesis. The equine ZP revealed high immunological cross‐reactivity to porcine ZPB and ZPC. In the ovary, the distribution of ZPB and ZPC was co‐localized and correlated with the developmental stage of the follicle. ZPB and ZPC expression started in the oocyte of the late primordial and primary follicle. In the secondary follicle, both the oocyte and the cumulus cells contributed to ZPB and ZPC synthesis. After in vivo maturation the oocyte stopped ZPB and ZPC production whereas the cumulus cells continued synthesis. Contrary, in vitro matured (IVM) cumulus‐oocyte‐complexes (COCs) revealed a reverse expression pattern. This was correlated to alterations in the distribution, number, and size of pores in the ZP. In the zona, N‐acetylglucosamine residues were co‐localized with ZPC. The acellular glycoprotein capsule surrounding early equine embryos was negative for ZPB and ZPC. Our results imply that in the horse ZPB and ZPC glycoprotein expression is differentially regulated during folliculogenesis, oocyte maturation, and embryogenesis. Contrary to the bovine and porcine, zona protein synthesis during in vivo maturation is completely overtaken by the cumulus cells implying that in the horse these cells are crucial for zona integrity. During IVM, the cumulus cells lose their ability to synthesize glycoproteins leading to alterations in the zona structure. Mol. Reprod. Dev. 74: 851–859, 2007. © 2007 Wiley‐Liss, Inc.
Variable‐node elements for non‐matching meshes by means of MLS (moving least‐square) scheme
Authors: Lim Jae Hyuk , Im Seyoung , Cho Young‐Sam
Published: January 2007

A new class of finite elements is described for dealing with non‐matching meshes, for which the existing finite elements are hardly efficient. The approach is to employ the moving least‐square (MLS) scheme to devise a class of elements with an arbitrary number of nodal points on the parental domain. This approach generally leads to elements with the rational shape functions, which significantly extends the function space of the conventional finite element method. With a special choice of the nodal points and the base functions, the method results in useful elements with the polynomial shape functions for which the C1 continuity breaks down across the boundaries between the subdomains comprising one element. The present scheme possesses an extremely high potential for applications which deal with various problems with discontinuities, such as material inhomogeneity, crack propagation, phase transition and contact mechanics. The effectiveness of the new elements for handling the discontinuities due to non‐matching interfaces is demonstrated using appropriate examples. Copyright © 2007 John Wiley & Sons, Ltd.
Outcomes in childhood AML in the absence of transplantation in first remission—Children's Cancer Group (CCG) studies 2891 and CCG 213
Authors: Castellino Sharon M. , Alonzo Todd A. , Buxton Allen , Gold Stuart , Lange Beverly J. , Woods William G.
Published: January 2007

Background

The majority of childhood acute myeloid leukemia (AML) patients lack a matched‐related bone marrow transplant (BMT) donor in first remission.

Procedure

Disease‐free survival (DFS), overall survival (OS), relapse‐free survival (RFS), and post‐relapse outcome were evaluated for children with de novo AML on CCG 213 and the standard timing (ST) and intensive timing (IT) induction arms of CCG 2891 who were randomized to (intent‐to‐treat, ITT) or who received (as‐treated, AT) only chemotherapy intensification.

Results

Outcomes at 8 years post‐induction in ITT analysis of chemotherapy intensification were as follows: 31% DFS, 43% OS on CCG 213; 34% DFS, 51% OS on CCG 2891 ST; 48% DFS, 56% OS on CCG 2891 IT. All toxic deaths during and following Capizzi II chemotherapy intensification on both protocols were in patients >3 years of age (P ≤ 0.001). Black race was a significant poor prognostic factor for OS (P = 0.008, hazard ratio: 1.74, 95% CI: 1.15–2.61). Overall 48% of patients on both trials relapsed and 19.1% of patients who relapsed on these trials survived. CR1 >12 months portends a much better OS for patients who relapse. Post‐relapse treatment included BMT in 47% of patients.

Conclusions

OS on CCG 2891 was superior to CCG 213 but equivalent between ST and IT arms due to better salvage rates post‐relapse in ST patients. Overall survival for childhood AML in the absence of BMT in CR1 is influenced by duration of CR1 and by race. Pediatr Blood Cancer 2008;50:9–16. © 2007 Wiley‐Liss, Inc.
Analysis of ethylene oxide gas house explosion
Authors: Woodward John L. , Wesevich James W. , Thomas J. Kelly , Baker Quentin A.
Published: January 2007

An explosion destroyed a small “Gas House” in which aerosol cans were being filled with ethylene oxide on June 24, 1997. At issue was whether the ignition occurred in the Gas House or from a remote catalytic converter. Our investigation of the pattern of blast damage supports ignition at the catalytic converter that generated a burn‐back through the ducting. A strong jet ignition reached a flammable atmosphere in the Gas House and ignited an explosion that well exceeded the yield strength of the prefabricated metal Gas House in spite of the vent panels and access doors being released and discharging of the fire suppression system. One of the doors from the Gas House flew off of the building as hazardous debris, which impacted and catastrophically failed a second door located in an adjoining occupied building. This resulted in the only fatality associated with this event. This study illustrates the damage patterns that indicate the direction of the initial explosion wave. © 2007 American Institute of Chemical Engineers Process Saf Prog, 2007.
Improvement methods in U.K. and Mexican construction industries: a comparison
Authors: Hernandez David Joaquin Delgado , Aspinwall Elaine
Published: January 2007

The application of improvement methods in the manufacturing industry has proven to be a valuable feature of continuous improvement activities. To establish whether the same is true in the construction sector, a survey was conducted to assess the current level of use and the perceived importance of such methods in both the U.K. and in Mexico. Following a broad review of the literature, various improvement tools, techniques and methods were recognized and grouped using affinity diagrams. A questionnaire was designed to collect the information and served as a basis for comparison. The results of the survey showed that, in terms of use, computer networks, laws and regulations, teams and teamwork, inspection and planning software were common practice in the U.K. while computer networks, customer satisfaction surveys, design software, Gantt charts and laws and regulations were commonly used in Mexico. A similar set of methods were perceived as highly important except that inspection and planning software were replaced by customer satisfaction surveys and customer complaints, respectively, in the case of the U.K. companies and Gantt charts by inspection in the case of Mexico. When comparing the mean use and the mean perceived importance for each method in both countries, significant differences were found mainly in the use of those for gathering and organizing customer needs, those aimed at planning and controlling quality and those for technology. Copyright © 2007 John Wiley & Sons, Ltd.
An ion‐pairing liquid chromatography/tandem mass spectrometric method for the determination of cytarabine in mouse plasma
Authors: Hsieh Yunsheng , Duncan Christine J. G.
Published: January 2007

An ion‐pairing high‐performance liquid chromatographic (IP‐HPLC) system interfaced with an atmospheric pressure chemical ionization (APCI) source and a tandem mass spectrometer (MS/MS) with minimal sample preparation was developed for the determination of cytarabine (ara‐C), a very hydrophilic anticancer drug, in mouse plasma. A conventional reversed‐phase chromatographic column in combination with two ion‐pairing reagents was adapted for retention and separation of ara‐C from the endogenous interferences in mouse plasma. The effects of the experimental conditions such as the fraction of ion‐pairing reagents and organic solvents in the mobile phase on the chromatographic performance and the ionization efficiency of ara‐C were investigated. The potential of ionization suppression resulting from the endogenous biological materials on the IP‐HPLC/MS/MS method was evaluated using the post‐column infusion technique. Furthermore, the feasibility of the proposed IP‐HPLC/MS/MS procedure for analysis of ara‐C in the mouse plasma was demonstrated by comparison with those obtained by the porous graphite carbon column (PGC) HPLC/MS/MS method. Copyright © 2007 John Wiley & Sons, Ltd.
Microbial diversity of topographical gradient profiles in Fushan forest soils of Taiwan
Authors: Tsai Shu‐Hsien , Selvam Ammaiyappan , Yang Shang‐Shyng
Published: January 2007

To evaluate the microbial diversity of Fushan forest soils, the variation of soil properties, microbial populations, and soil DNA with soil depth in three sites of different altitude were analyzed. Microbial population, moisture content, total organic carbon (Corg), and total nitrogen (Ntot) decreased with increasing soil depth. The valley site had the lowest microbial populations among the three tested sites due to the low organic matter content. Bacterial population was the highest among the microbial populations. The ratios of cellulolytic microbes to the total bacteria in organic layers were high, implying their roles in the carbon cycle. The microbial biomass carbon (Cmic) and nitrogen (Nmic) contents ranged from 130.5 to 564.1 μg g−1and from 16.7 to 95.4 μg g−1, respectively. The valley had the lowest Cmicand Nmic. The organic layer had the highest Cmicand Nmicand decreased with soil depth. Analysis using denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplicons of 16S rDNA showed that the bacterial diversity of the three sites were very similar to each other in the major bands, and the variation was in the minor bands. However, the patterns in PCR‐DGGE profile through gradient horizons were different, indicating the prevalence of specific microbes at different horizons. These results suggest that the microbial diversity in the deeper horizons is not simply the diluted analogs of the surface soils and that some microbes dominate only in the deeper horizons. Topography influenced the quantity and diversity of microbial populations.
Tunable self-assembly of one-dimensional nanostructures with orthogonal directions
Authors: Allan Milan P. , Berner Simon , Corso Martina , Greber Thomas , Osterwalder Jürg
Published: January 2007

High-temperature exposure of a Mo(110) surface to borazine (HBNH)3leads to the formation of two distinctly different self-assembling nanostructures. Depending on the substrate temperature during preparation, either well-aligned, ultra-thin boron nanowires or a single-layer stripe structure of hexagonal boron nitride forms. Both structures show one-dimensional (1D) characteristics, but in directions perpendicular to each other. It is also possible to grow the two phases in coexistence. The relative weights are controlled by the sample temperature during preparation.
Increased circulating concentrations and augmented myocardial extraction of osteoprotegerin in heart failure due to left ventricular pressure overload
Authors: Helske Satu , Kovanen Petri T. , Lindstedt Ken A. , Salmela Kaija , Lommi Jyri , Turto Heikki , Werkkala Kalervo , Kupari Markku
Published: January 2007

Background

Osteoprotegerin (OPG) and the receptor activator of nuclear factor‐kB ligand (RANKL), two cytokines regulating bone remodeling, have recently been raised as potential pathogenetic factors in cardiovascular diseases. We have studied circulating and myocardial OPG and RANKL in patients having severe aortic stenosis (AS) with or without heart failure (HF).

Methods

We studied 131 adults with AS. Blood was sampled from the aortic root, coronary sinus, and femoral vein at cardiac catheterization. LV myocardial biopsies were taken at surgery. Plasma OPG and soluble (s)RANKL were analyzed by ELISA, and myocardial OPG and RANKL by RT‐PCR and immunohistochemistry.

Results

Circulating OPG was elevated in AS patients with HF, the association being independent of age, sex, and presence of coronary artery disease (β=0.17, p=0.033). Elevated plasma OPG decreased after valve replacement in patients with preoperative HF (p=0.0005). Relative to its concentration in the aortic root, plasma OPG was reduced in the coronary sinus (p<0.05) and in the femoral vein (p<0.001), these arteriovenous gradients being accentuated in HF (p=0.003).

Conclusions

HF due to LV pressure overload in AS increases circulating OPG and augments OPG extraction by the heart and peripheral tissues. OPG may be involved in the pathogenesis of HF and could serve as a useful biomarker in HF due to LV pressure overload.
Metabolic profiling using combined GC–MS and LC–MS provides a systems understanding of aristolochic acid‐induced nephrotoxicity in rat
Authors: Ni Yan , Su Mingming , Qiu Yunping , Chen Minjun , Liu Yuming , Zhao Aihua , Jia Wei
Published: January 2007

We present here a combined GC–MS and LC–MS metabolic profiling approach to unraveling the pathological outcomes of aristolochic acid (AA)‐induced nephrotoxicity. Urine samples were analyzed by GC–MS and LC–MS in combination with pattern recognition techniques, e.g. principal component analysis (PCA), orthogonal projection to latent structure‐discriminant analysis. The work indicates that AA‐induced acute renal toxicity as evidenced by histopathological examinations could be characterized by systemic disturbance of metabolic network involving free fatty acids generation, energy and amino acids metabolism, and alteration in the structure of gut microbiota. Therefore, this method is potentially applicable to the toxicological study, providing a comprehensive understanding of systems response to xenobiotic intervention.
STURM–LIOUVILLE PROBLEMS WITH REDUCIBLE BOUNDARY CONDITIONS
Authors: Binding Paul A. , Browne Patrick J. , Watson Bruce A.
Published: January 2007

The regular Sturm–Liouville problem

$$ \tau y:=-y''+qy=\lambda y\quad\text{on }[0,1],\ \lambda\in\CC, $$

is studied subject to boundary conditions

$$ P_j(\lambda)y'(j)=Q_j(\lambda)y(j),\quad j=0,1, $$

where $q\in L^1(0,1)$ and $P_j$ and $Q_j$ are polynomials with real coefficients. A comparison is made between this problem and the corresponding ‘reduced’ one where all common factors are removed from the boundary conditions. Topics treated include Jordan chain structure, eigenvalue asymptotics and eigenfunction oscillation.
‘Bones of contention’: a donor register for temporal bone donation?
Authors: Leong A C , Aldren C
Published: January 2007

Introduction: Temporal bone dissection is essential training for otological surgery. Organ retention scandals have made it difficult to obtain consent for cadaveric temporal bone removal. The current literature does not address the means of acquiring a steady supply of cadaveric temporal bones for medical education and training. The US national temporal bone registry has established a temporal bone donor bank for medical education and research. Could a similar programme in the UK be an answer to the paucity of temporal bones?

Objectives: (1) To ascertain the degree of interest amongst our regional patient population in a ‘living will’ pledge for temporal bone donation for medical education and research. (2) To delineate a demographic profile of potential temporal bone donors.

Design, setting and participants: One thousand questionnaires were distributed to patients and relatives attending out-patient clinics; 920 people responded.

Results: Seventy per cent of respondents supported temporal bone donation for medical education and research. Potential temporal bone donors tended to be ENT clinic attenders, to suffer from hearing difficulties or to have had previous ear surgery (p<0.001). Strong support also came from non-ENT clinic attenders.

Conclusions: There was strong support amongst our regional patient population for a ‘living will’ pledge for temporal bone donation for medical education and research. Based on our donor profile, we propose a temporal bone donor programme, starting on a regional basis with possible expansion nationwide. This programme would recruit donors from amongst patients attending ENT out-patient clinics, as a long term solution to improve the supply of temporal bones.
Recurrent blockage of the sucker during otological surgery: a simple solution
Authors: Badran K , Karkos P
Published: January 2007

We present a unique device for unblocking the sucker during otological surgery. This device can be made cheaply, from parts already available in most hospitals, and is reliable and effective.
Editorial
Authors: Cairns Alan
Published: January 2007

After some 12 years as Editor of the Journal I have decided that it is time to move on and I will relinquish this position at the end of 2006. From the beginning of 2007 Padma Shukla will be the sole Editor and papers should be submitted to him or to any of the Associate Editors. The web address jpp@st-andrews.ac.uk will cease to be operative from this time. I would like to thank all those authors who have contributed to the Journal during my editorship and hope that they will continue to give it their support. I have every confidence that it will flourish under Padma's able guidance.
Peter's death in Rome? Back to front and upside down
Authors: Bockmuehl Markus
Published: January 2007

Contrary to periodic challenges from a viewpoint of historical scepticism or relativism, Jerome's late fourth-century description of Simon Peter may be said to represent a critical and consensual account of the Apostle's demise in Rome as this was reflected in early Christian memory of the first two centuries, both in the East and in the West. Three centuries earlier, the much-debated passage in 1 Clement 5 represents (for all its ambiguities) an integral strand of such living memory – citing the founding apostles' death for their faith according to local Roman tradition while discreetly airbrushing the specific circumstances of their demise. It is significant, finally, that local memory of Peter's martyrdom remained confined to Rome and was never subject to competing claims elsewhere.
Video‐based observations of nearshore sand ripples and ripple migration
Authors: Becker J. M. , Firing Y. L. , Aucan J. , Holman R. , Merrifield M. , Pawlak G.
Published: January 2007

Observations of O(1 m) length and O(0.1 m) height sand ripples at Waimea Bay, a steep (slope ∼ 0.05) pocket beach on the north shore of Oahu, Hawaii, are presented. Time series of ripple patterns over a 900 m2 section of the nearshore in depths of 1–2 m are obtained using time‐averaged video images from an Argus station overlooking the bay. Ripples are detected during weak wave conditions in the summer or between winter swell events. The ripple field exhibits narrow‐band wave number structure, with ripple crests oriented parallel to the shoreline. The ripple wavelengths vary with wave orbital displacements, but they are shorter than predicted by orbital vortex ripple scaling relationships. A new suspension‐limited model (Smith and Wiberg, 2006; Traykovski, 2006) in which the suborbital ripple wavelengths vary with wave period appears to describe well the observed ripple wavelength scaling. Lagged correlations between sequential Argus images reveal area‐average ripple migration rates ranging from −3.3 m day−1 (offshore) to 4.5 m day−1. The corresponding estimated sediment transport ranges from −0.3 m3 m−1 day−1 to 0.5 m3 m−1 day−1, similar to previous estimates of cross‐shore transport based on observed volume changes at the subaerial beach. This suggests that the recovery of beach sand following major swell‐driven erosion events may be accomplished in part by the shoreward migration of seabed ripples.
Photolabelling the urotensin II receptor reveals distinct agonist- and partial-agonist-binding sites
Authors: Holleran Brian J. , Beaulieu Marie-Eve , Proulx Christophe D. , Lavigne Pierre , Escher Emanuel , Leduc Richard
Published: January 2007

The mechanism by which GPCRs (G-protein-coupled receptors) undergo activation is believed to involve conformational changes following agonist binding. We have used photoaffinity labelling to identify domains within GPCRs that make contact with various photoreactive ligands in order to better understand the activation mechanism. Here, a series of four agonist {[Bpa1]U-II (Bpa is p-benzoyl-L-phenylalanine), [Bpa2]U-II, [Bpa3]U-II and [Bpa4]U-II} and three partial agonist {[Bpa1Pen5D-Trp7Orn8]U-II (Pen is penicillamine), [Bpa2Pen5D-Trp7Orn8]U-II and [Pen5Bpa6D-Trp7Orn8]U-II} photoreactive urotensin II (U-II) analogues were used to identify ligand-binding sites on the UT receptor (U-II receptor). All peptides bound the UT receptor expressed in COS-7 cells with high affinity (Kd of 0.3–17.7 nM). Proteolytic mapping and mutational analysis led to the identification of Met288 of the third extracellular loop of the UT receptor as a binding site for all four agonist peptides. Both partial agonists containing the photoreactive group in positions 1 and 2 also cross-linked to Met288. We found that photolabelling with the partial agonist containing the photoreactive group in position 6 led to the detection of transmembrane domain 5 as a binding site for that ligand. Interestingly, this differs from Met184/Met185 of the fourth transmembrane domain that had been identified previously as a contact site for the full agonist [Bpa6]U-II. These results enable us to better map the binding pocket of the UT receptor. Moreover, the data also suggest that, although structurally related agonists or partial agonists may dock in the same general binding pocket, conformational changes induced by various states of activation may result in slight differences in spatial proximity within the cyclic portion of U-II analogues.
Influence of intramolecular cross-links on the molecular, structural and functional properties of PEGylated haemoglobin
Authors: Hu Tao , Manjula Belur N. , Li Dongxia , Brenowitz Michael , Acharya Seetharama A.
Published: January 2007

The influence of intramolecular cross-links on the molecular, structural and functional properties of PEGylated {PEG [poly(ethylene glycol)]-conjugated} haemoglobin has been investigated. The sites and the extent of PEGylation of haemoglobin by reductive alkylation are not influenced by the presence of an αα-fumaryl cross-link at Lys-99(α). The propylated hexaPEGylated cross-linked haemoglobin, (propyl-PEG5K)6-αα-Hb, exhibits a larger molecular radius and lower colloidal osmotic pressure than propylated hexaPEGylated non-cross-linked haemoglobin, (propyl-PEG5K)6-Hb. Perturbation of the haem microenvironment and the α1β2 interface by PEGylation of haemoglobin is reduced by intramolecular cross-linking. Sedimentation velocity analysis established that PEGylation destabilizes the tetrameric structure of haemoglobin. (Propyl-PEG5K)6-Hb and (propyl-PEG5K)6-αα-Hb sediment as stable dimeric and tetrameric molecules, respectively. The ββ-succinimidophenyl PEG-2000 cross-link at Cys-93(β) outside the central cavity also influences the molecular properties of haemoglobin, comparable to that by the αα-fumaryl cross-link within the central cavity. However, the influence of the two cross-links on the oxygen affinity of PEGylated haemoglobin are very distinct, indicating that the high oxygen affinity of PEGylated haemoglobin is not a direct consequence of the dissociation of the haemoglobin tetramers into dimers. αα-Fumaryl cross-linking is preferred to modulate both oxygen affinity and molecular properties of PEGylated haemoglobin, and cross-linking outside the central cavity could only modulate molecular properties of PEGylated haemoglobin. It is suggested that PEGylation induces a hydrodynamic drag on haemoglobin and this plays a role in the microcirculatory properties of PEGylated haemoglobin.
Self-aligned and stray-field-free electrodes for spintronics: An application to a spin field effect transistor
Authors: Gallo P. , Arnoult A. , Camps T. , Havard E. , Fontaine C. , Lombez L. , Amand T. , Marie X. , Bournel A.
Published: January 2007

We present a ringlike design for spin field effect transistor electrodes. This configuration solves the local Hall effect drawback as these electrodes do not generate any stray magnetic fields. The shape and size of the electrodes are adjusted in order to match the physical constraints. The gate configuration and channel length are discussed for the [110] growth direction; the GaInAs channel length for the spins to fully switch is calculated to be of the order of 0.15μm for a gate electric field of 150–300kV∕cm.
Effect of common noise on phase synchronization in coupled chaotic oscillators
Authors: Park Kwangho , Lai Ying-Cheng , Krishnamoorthy Satish , Kandangath Anil
Published: January 2007

We report a general phenomenon concerning the effect of noise on phase synchronization in coupled chaotic oscillators: the average phase-synchronization time exhibits a nonmonotonic behavior with the noise amplitude. In particular, we find that the time exhibits a local minimum for relatively small noise amplitude but a local maximum for stronger noise. We provide numerical results, experimental evidence from coupled chaotic circuits, and a heuristic argument to establish the generality of this phenomenon.
Quantum similarity study of atomic density functions: Insights from information theory and the role of relativistic effects
Authors: Borgoo A. , Godefroid M. , Indelicato P. , De Proft F. , Geerlings P.
Published: January 2007

A novel quantum similarity measure (QSM) is constructed based on concepts from information theory. In an application of QSM to atoms, the new QSM and its corresponding quantum similarity index (QSI) are evaluated throughout the periodic table, using the atomic electron densities and shape functions calculated in the Hartree-Fock approximation. The periodicity of Mendeleev’s table is regained for the first time through the evaluation of a QSM. Evaluation of the information theory based QSI demonstrates, however, that the patterns of periodicity are lost due to the renormalization of the QSM, yielding chemically less appealing results for the QSI. A comparison of the information content of a given atom on top of a group with the information content of the elements in the subsequent rows reveals another periodicity pattern. Relativistic effects on the electronic density functions of atoms are investigated. Their importance is quantified in a QSI study by comparing for each atom, the density functions evaluated in the Hartree-Fock and Dirac-Fock approximations. The smooth decreasing of the relevant QSI along the periodic table illustrates in a quantitative way the increase of relativistic corrections with the nuclear charge.
Electron beam-plasma interaction: Linear theory and Vlasov-Poisson simulations
Authors: Silin I. , Sydora R. , Sauer K.
Published: January 2007

The problem of a weak (nb∕ne∼10−3) electron beam interaction with plasma is investigated by means of linear dispersion theory and electrostatic Vlasov simulations. In the case of a warm electron beam only Langmuir-type modes in a finite wavelength band are excited. Cold beams undergo rapid heating, after which the long-wavelength Langmuir and electron-acoustic modes are damped. As the waves decelerate and heat the beam, new modes with larger wave numbers and smaller phase velocities are excited, while the fastest-growing modes saturate at a finite level. The superposition of these modes with frequencies near electron plasma frequency ωpe and broad k spectrum results in long quasiregular wave packets. The wave packets propagate slowly with group velocities typically 30 times smaller than the phase velocities and are weakly damped by the background electrons.
Static polarizability and second hyperpolarizability of closed- and open-shell π-conjugated polymers
Authors: Hu Weifeng , Ma Haibo , Liu Chungen , Jiang Yuansheng
Published: January 2007

The static longitudinal linear polarizability (α) and second order hyperpolarizability (γ) for neutral and charged, closed- and open-shell trans-polyacetylene (PA) chains C2nH2n+2, C2n−1H2n+1, C2n−1H2n+1+, C2nH2n+2+, and C2nH2n+22+ are systematically investigated and compared. The polarizabilities are calculated within the Pariser-Parr-Pople model, and the electron correlation effect is included through density matrix renormalization group. It turns out that for both α, and γ, two neutral PA chains C2nH2n+2 and C2n−1H2n+1 give similar values, while both singly charged and doubly charged systems present significantly larger magnitude of α and γ values than the two neutral chains. The two singly charged PA chains C2n−1H2n+1+ and C2nH2n+2+ give more apparent nonlinear optical responses than doubly charged case C2nH2n+22+ and both present negative second order hyperpolarizabilities for short to medium sized oligomers. The sign inversion of γ values in singly charged PA molecules is anticipated to take place at the much longer length than ever observed due to the significant effects of electron correlation and geometry.
Low energy ion assisted deposition of Ta∕Cu films
Authors: Quan J. J. , Zhou X. W. , He L. , Hull R. , Wadley H. N. G.
Published: January 2007

A combination of molecular dynamics simulations and experiments has been used to investigate the use of various low energy ion assisted vapor deposition approaches for controlling the interfacial structures of a model copper∕tantalum multilayer system. Films were grown using argon ion beam assistance with either a fixed or modulated ion energy during metal deposition. The effect of sequential ion assistance (after layer’s deposition) was also investigated. The argon ion energy was varied between 0 and 50eV and the effect on the atomic scale structure of Ta∕Cu film interfaces and the film electrical resistivity were studied. The use of simultaneous argon ion assistance with an ion energy of ∼10eV and an ion∕metal atom flux ratio of ∼6 resulted in atomically sharp interfaces with little intermixing, consistent with simulation predictions. Ion impacts in this range activated surface atom jumping and promoted a step flow film growth mode. Higher energies were also successful at interface flattening, but they caused significant intermixing between the layers and increased film’s resistivity. This could be reduced using modulated ion energy and sequential ion beam assistance. This was again consistent with atomic scale simulations, which indicated that metal layers deposited over an interface before ion assistance was initiated impeded atom exchange across interfaces and therefore intermixing.
Bifurcation of surface pattern in epitaxial thin films under anisotropic stresses
Authors: Pang Yaoyu , Huang Rui
Published: January 2007

Surface instability of epitaxial thin films leads to a variety of surface patterns. Anisotropy in surface and bulk properties has profound effects on the dynamics of pattern formation. In this paper, we theoretically predict that under anisotropic mismatch stresses, a bifurcation of surface pattern occurs in addition to generic symmetry breaking from isotropic systems. Numerical simulations based on a nonlinear evolution equation demonstrate pattern selection at an early stage and nontrivial patterns for long-time evolution.
Dissipative transport dynamics in coupled quantum dots
Authors: Batistuta M. V. , Stella M. F. , de Biagi H. C. , da Costa J. C.
Published: January 2007

A linear one-dimensional dissipative model is proposed and applied in obtaining numerical simulation results for coupled double quantum dot cells, for single-electron transport dynamics on each cell. Field coupling between cells is modeled simply from a matrix of mutual capacitances. Bistability with only one excess electron on each cell, in a pair of coupled double-dot cells, is demonstrated. Behavior prediction and performance evaluation, for applications such as computational system implementation, are made possible. It is understood from the simulations that balanced dissipation rates are essential for the implementation of optimized single-electron devices, with short settling times.
Thermal lens spectroscopy through phase transition in neodymium doped strontium barium niobate laser crystals
Authors: Jacinto C. , Catunda T. , Jaque D. , García Solé J. , Kaminskii A. A.
Published: January 2007

In this work the anisotropic thermal lens (TL) effect was studied in Nd3+ doped SrxBa1−xNb2O6 crystals with two different stoichiometries (x=0.47 and 0.61). TL measurements were carried out as a function of temperature from 30 up to 140°C so that the effect of phase transition was investigated. A strong enhancement in the TL effect during the ferro-to-paraelectric phase transition has been observed. Additionally, we have found an inversion of the TL signal with the crystal stoichiometry. This fact is explained in terms of a different thermal expansion along the c axis for both crystals, as measured by x-ray diffraction experiments. The obtained results open the possibility to tailor a crystal stoichiometry that minimizes the TL effects.
Analytic findings in the electroluminescence characterization of crystalline silicon solar cells
Authors: Fuyuki Takashi , Kondo Hayato , Kaji Yasue , Ogane Akiyoshi , Takahashi Yu
Published: January 2007

The electroluminescence intensity from Si cells under the forward bias was found to have one to one quantitative agreement with the minority carrier diffusion length. Based on the diffusion equation and simple p-n diode model, the electroluminescence intensity was analyzed relative to the cell performance. Electroluminescence intensity is proportional to the product of the injected minority carrier density and the effective diffusion length. The diode ideality factor n can be deduced by measuring the electroluminescence intensity as a function of the forward injection current. Among various crystalline silicon cells including single and polycrystalline types, the measured electroluminescence intensity at a fixed forward current has a tight relationship with the open circuit voltage of each cell, which gives a very convenient way to evaluate cell performance.
Laser-induced fluorescence and pure rotational spectroscopy of the CH2CHS (vinylthio) radical
Authors: Nakajima Masakazu , Miyoshi Akira , Sumiyoshi Yoshihiro , Endo Yasuki
Published: January 2007

Laser-induced fluorescence (LIF) excitation spectra of the B̃–X̃A″2 electronic transition of the CH2CHS radical, which is the sulfur analog of the vinoxy (CH2CHO) radical, were observed under room temperature and jet-cooled conditions. The LIF excitation spectra show very poor vibronic structures, since the fluorescence quantum yields of the upper vibronic levels are too small to detect fluorescence, except for the vibrationless level in the B̃ state. A dispersed fluorescence spectrum of jet-cooled CH2CHS from the vibrationless level of the B̃ state was also observed, and vibrational frequencies in the X̃ state were determined. Precise rotational and spin-rotation constants in the ground vibronic level of the radical were determined from pure rotational spectroscopy using a Fourier-transform microwave (FTMW) spectrometer and a FTMW-millimeter wave double-resonance technique [Y. Sumiyoshi et al., J. Chem. Phys. 123, 054324 (2005)]. The rotationally resolved LIF excitation spectrum for the vibronic origin band of the jet-cooled CH2CHS radical was analyzed using the ground state molecular constants determined from pure rotational spectroscopy. Determined molecular constants for the upper and lower electronic states agree well with results of ab initio calculations.
Phase retrieval in x-ray coherent Fresnel projection-geometry diffraction
Authors: De Caro Liberato , Giannini Cinzia , Cedola Alessia , Pelliccia Daniele , Lagomarsino Stefano , Jark Werner
Published: January 2007

Coherent x-ray diffraction experiments were performed in Fresnel regime, within a line-projection geometry. A planar x-ray waveguide was used to focus coherent cylindrical waves onto a 7.2μm Kevlar fiber, which acts as a phase object for hard x rays. The phase was retrieved, by using a Fourier-based iterative phasing algorithm, consistent with measured diffraction data and known constraints in real space, with a submicrometer spatial resolution.
Optical properties of PbSe nanocrystal quantum dots under pressure
Authors: Zhuravlev Kirill K. , Pietryga Jeffrey M. , Sander Robert K. , Schaller Richard D.
Published: January 2007

The optical properties of PbSe nanocrystal quantum dots (NQDs) were studied as a function of applied hydrostatic pressure over the range from ambient to 5.4GPa. PbSe NQDs exhibit an energy gap that is dominated by quantum confinement. Despite such strong confinement, the authors find that the energy gaps of 3, 5, and 7nm diameter PbSe NQDs change monotonically with pressure with a dependence that is almost entirely determined by the bulk deformation potential. The sizable dependence of the NQD energy gap with pressure invites applications in the areas of high speed pressure sensing and tunable IR lasers.
Strong interaction of a turbulent spot with a shock-induced separation bubble
Authors: Krishnan L. , Sandham N. D.
Published: January 2007

Direct numerical simulations have been conducted to study the passage of a turbulent spot through a shock-induced separation bubble. Localized blowing is used to trip the boundary layer well upstream of the shock impingement, leading to mature turbulent spots at impingement, with a length comparable to the length of the separation zone. Interactions are simulated at free stream Mach numbers of two and four, for isothermal (hot) wall boundary conditions. The core of the spot is seen to tunnel through the separation bubble, leading to a transient reattachment of the flow. Recovery times are long due to the influence of the calmed region behind the spot. The propagation speed of the trailing interface of the spot decreases during the interaction and a substantial increase in the lateral spreading of the spot was observed. A conceptual model based on the growth of the lateral shear layer near the wingtips of the spot is used to explain the change in lateral growth rate.
Two-dimensional analysis for emitter ledge thickness of InGaP∕GaAs heterojunction bipolar transistors
Authors: Cheng Shiou-Ying , Chu Kuei-Yi , Chen Li-Yang , Chen Lu-Ann , Chen Chun-You
Published: January 2007

In this letter, the influence of various emitter ledge thicknesses on the performances of InGaP∕GaAs heterojunction bipolar transistors is investigated based on the simulation and experimental data. The undesired surface channel phenomenon at the exposed base surface between base contact and emitter ledge is comprehensively analyzed. Moreover, improper thickness of emitter ledge passivations would cause serious surface recombination at the edge of emitter ledge. Therefore, the thickness of emitter ledge is a critical and should be carefully considered. From simulated and experimental results, the optimum emitter ledge thickness of InGaP∕GaAs heterojunction bipolar transistor is 100–200Å.
Room temperature epitaxial growth of m-plane GaN on lattice-matched ZnO substrates
Authors: Kobayashi Atsushi , Kawano Satoshi , Kawaguchi Yuji , Ohta Jitsuo , Fujioka Hiroshi
Published: January 2007

The authors have grown high-quality m-plane GaN (11¯00) films on ZnO (11¯00) substrates using pulsed laser deposition. They have found that annealing in a box made of ceramic ZnO improves the surface morphology of m-plane ZnO substrates and have succeeded in the layer-by-layer growth of m-plane GaN on the annealed ZnO substrates even at room temperature (RT). X-ray diffraction reveals that high crystalline quality m-plane GaN grows on the RT buffer layer at 700°C. The 300-nm-thick m-plane GaN film grown on the ZnO substrate contains the residual strains because the lattice mismatches between them are quite small. The relationship of in-plane and out-of-plane strains is consistent with the calculation using the elastic constants.