bluuebunny/crossref_metadata_2025 huggingface dataset:
A critical assessment of the use of compliance constants as bond strength descriptors for weak interatomic interactions
Authors: Baker Jon
Published: July 2006

Inverse compliance constants (inverse diagonal elements of the inverse Hessian matrix) have frequently been proposed as replacements for regular internal coordinate force constants, as the former are invariant to the choice of internal coordinates while the latter are not. Recently, Grunenberg and co-workers have proposed using compliance constants as descriptors of bond strength, primarily based on their invariance properties. This article critically assesses the use of compliance constants as bond strength descriptors, highlighting reasons why their use for this purpose is considered inappropriate, particularly for weak bonding interactions.
Impact of molecular structure on the lubricant squeeze-out between curved surfaces with long range elasticity
Authors: Tartaglino U. , Sivebaek I. M. , Persson B. N. J. , Tosatti E.
Published: July 2006

The properties of butane (C4H10) lubricants confined between two approaching solids are investigated by a model that accounts for the curvature and elastic properties of the solid surfaces. We consider the linear n-butane and the branched isobutane. For the linear molecule, well defined molecular layers develop in the lubricant film when the width is of the order of a few atomic diameters. The branched isobutane forms more disordered structures which permit it to stay liquidlike at smaller surface separations. During squeezing the solvation forces show oscillations corresponding to the width of a molecule. At low speeds (<0.1m∕s) the last layers of isobutane are squeezed out before those of n-butane. Since the (interfacial) squeezing velocity in most practical applications is very low when the lubricant layer has molecular thickness, one expects n-butane to be a better boundary lubricant than isobutane. With n-butane possessing a slightly lower viscosity at high pressures, our result refutes the view that squeeze-out should be harder for higher viscosities; on the other hand our results are consistent with wear experiments in which n-butane were shown to protect steel surfaces better than isobutane.
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
Authors: Janosi Lorant , Kosztin Ioan , Damjanović Ana
Published: July 2006

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations, and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 bacteriochlorophylls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.
Total absorption of electromagnetic radiation in overdense plasma
Authors: Wang Yan , Cao Jin-Xiang , Wang Ge , Wang Liang , Zhu Ying , Niu Tian-Ye
Published: July 2006

The energy transformation from electromagnetic wave to plasmas polaritons in overdense plasma is investigated by using the theory of hydrodynamics in the thin cylinder limit and surface wave resonator. The grating experiment certifies the excitation of the surface wave. Through studying the role of the magnetic field in excitation of the surface wave and analyzing the frequency domain spectrum of the reflected wave, the time series of reflection, transmission and plasma density are diagnosed when the electromagnetic wave transforms into the surface wave. The experimental scheme of Bliokh [Phys. Rev. Lett. 95, 165003 (2005)] is improved. A steady overdense plasma in a cylindrical cavity is obtained by dc high voltage discharging and measurement is taken in series. The diffraction grating is fixed in optimum position after the distance from it to the chamber is adjusted. The reflection ratios of plasma and a piece of tinfoil are compared to avoid the effect of the standing wave. The effect of incident polarization is discussed and a measurement result is obtained with a 70Gauss magnetic field. Further research on scanning measurement reveals that the collision rate is the only determinant element of the half absorption width. Numerical simulation is given, based on the theory of surface plasmons (SPs). The experimental data agree with the numerical simulation well near the resonance frequency f=5GHz, while on the trailing edge, the curve is obviously expanded. The mechanism of these phenomena is very complex and other conceivable factors must exist during the excitation of SPs, which should be studied in the further research.
Hydrogen kinetics in magnesium hydride: On different catalytic effects of niobium
Authors: Bazzanella N. , Checchetto R. , Miotello A. , Sada C. , Mazzoldi P. , Mengucci P.
Published: July 2006

The hydrogen desorption kinetics from pure and Nb-doped MgH2 samples was studied as function of the Nb concentration (6×10−4<[Nb∕Mg]<5×10−2). Structural and kinetics analyses indicate that Nb acts as catalyst both when Nb atoms aggregate forming NbH clusters dispersed in the MgH2 and also when Nb is contained as atomic impurity. It is suggested that the local atomic environment around the Nb atom acts as seed for h-Mg phase nucleation which constitutes the rate limiting step for the hydrogen kinetics while, when the Nb concentration exceeds about 1at.%, the rate limiting step is hydrogen diffusion.
Charge photogeneration effect on the exciplex emission from thin organic films
Authors: Kalinowski J. , Cocchi M. , Virgili D. , Sabatini C.
Published: July 2006

The photoexcited singlet and triplet exciplex emission of thin photocondcuctive films containing an amine derivative N,N′-diphenyl-N,N′-bis(3-methylphenyl)-1,1′-biphenyl-4,4′diamine (TPD) electron donor and the bathophenathroline (BPT) electron acceptor drops largely with electric fields, falling down to about 20% of its zero-field value at high fields. This strong electric-field-induced exciplex emission quenching is interpreted in terms of the charge-imposed decay of singlet molecular excitons of TPD acting as precursors of the exciplexes and charge photogenerated on the TPD:BPT contacting sites. The favorable interrelation between the ionization potential of the donor and electron affinity of the acceptor leads there to an efficient field-enhanced exciton dissociation. The electrons trapped on acceptor molecules act in turn as charged exciton quenching centers.
High efficiency red organic light-emitting devices using tetraphenyldibenzoperiflanthene-doped rubrene as an emitting layer
Authors: Okumoto Kenji , Kanno Hiroshi , Hamada Yuji , Takahashi Hisakazu , Shibata Kenichi
Published: July 2006

Red organic light-emitting devices (OLEDs) have been developed employing a novel fluorescent emitting layer, tetraphenyldibenzoperiflanthene-doped rubrene. The devices are characterized by low driving voltage below 4V at a current density of 20mA∕cm2 and high color purity with Commission Internationale de l’Eclairage coordinates of (0.66, 0.34). The OLED using the novel emitting layer in combination with the electron-transporting layer consisting of 9,10-bis[4-(6-methylbenzothiazol-2-yl)phenyl]anthracene exhibits a high power efficiency of 5.3lm∕W at a current density of 20mA∕cm2. The half-luminance lifetime of the red OLED is 223h at a current density of 80mA∕cm2 (initial luminance of 3570cd∕m2). Both the driving voltage and current efficiency of the device are significantly improved compared to a device using tris(8-quinolinolato)aluminum as an electron-transporting layer. The studies on charge transport for the host materials indicate that the high efficiency is attributed to the improved charge injection and balance in the device.
Annealing-time dependence in interfacial reaction between poly-Si electrode and HfO2∕Si gate stack studied by synchrotron radiation photoemission and x-ray absorption spectroscopy
Authors: Takahashi H. , Okabayashi J. , Toyoda S. , Kumigashira H. , Oshima M. , Ikeda K. , Liu G. L. , Liu Z. , Usuda K.
Published: July 2006

We have investigated annealing-time dependence in interfacial reactions between polycrystalline-Si (poly-Si) electrodes and HfO2∕Si gate stacks using synchrotron radiation photoemission and x-ray absorption spectroscopy. From photoemission core-level spectra, we found that silicidation started at the upper interface between poly-Si electrodes and HfO2 gate dielectrics under the conditions of 700°C and 3min in ultrahigh vacuum. Before silicidation, we observed nonstoichiometric silicon oxide at the upper interface, suggesting the formation of oxygen vacancies which may cause Fermi level pinning. The interface layer between HfO2 gate dielectrics and Si substrates was changed into silicide by further annealing. In addition, from valence-band photoemission and O K-edge absorption spectra, we have found that the crystallization of HfO2 gate dielectrics is independent of silicidation.
Carrier capture times of the localized states in an InGaN thin film with indium-rich nanocluster structures
Authors: Wang Hsiang-Chen , Lu Yen-Cheng , Chen Cheng-Yen , Yang C. C.
Published: July 2006

A femtosecond nondegenerate pump-probe technique of using two beta barium borate crystals for frequency doubling a 7fs Ti:sapphire laser is used for studying the ultrafast carrier dynamics in an InGaN thin film, in which nanoscale indium-rich clusters have been observed. The carrier capture time of the localized states (the cluster states) from the free-carrier states (the states of the background compound) is calibrated. The initial rise times of the differential transmission of the probe intensity are calibrated to give the time constant of about 300fs for the degenerate cases over the whole photoluminescence spectral range and for the nondegenerate cases, in which both pump and probe wavelengths correspond to the free-carrier states. However, when the carriers are excited in the free-carrier states and probed in the localized states, the rise time increases to the range of 590–715fs, which represents the carrier capture time of the localized states from the free-carrier states.
Polypyrrole thin-film field-effect transistor
Authors: Bof Bufon C. C. , Heinzel T.
Published: July 2006

The operation of a polypyrrole thin-film field-effect transistor at room temperature is reported. The polymer film is prepared by a technique based on chemical polymerization, which is capable of forming thin films with low roughness. The technique is compatible with conventional silicon processing and allows a lithographic definition of the polymer film geometry. Transport measurements indicate that the device works as Schottky barrier-type field-effect transistor. We further demonstrate that the polymer film is sensitive to oxygen exposure.
Carrier dynamics in submonolayer InGaAs∕GaAs quantum dots
Authors: Xu Zhangcheng , Zhang Yating , Hvam Jørn M. , Xu Jingjun , Chen Xiaoshuang , Lu Wei
Published: July 2006

Carrier dynamics of submonolayer InGaAs∕GaAs quantum dots (QDs) were studied by microphotoluminecence (MPL), selectively excited photoluminescence (SEPL), and time-resolved photoluminescence (TRPL). MPL and SEPL show the coexistence of localized and delocalized states, and different local phonon modes. TRPL reveals shorter recombination lifetimes and longer capture times for the QDs with higher emission energy. This suggests that the smallest SML QDs are formed by perfectly vertically correlated two-dimensional InAs islands, having the highest In content and the lowest emission energy, while a slight deviation from the perfectly vertical correlation produces larger QDs with lower In content and higher emission energy.
Detecting potential labeling errors in microarrays by data perturbation
Authors: Malossini Andrea , Blanzieri Enrico , Ng Raymond T.
Published: July 2006

Motivation: Classification is widely used in medical applications. However, the quality of the classifier depends critically on the accurate labeling of the training data. But for many medical applications, labeling a sample or grading a biopsy can be subjective. Existing studies confirm this phenomenon and show that even a very small number of mislabeled samples could deeply degrade the performance of the obtained classifier, particularly when the sample size is small. The problem we address in this paper is to develop a method for automatically detecting samples that are possibly mislabeled.

Results: We propose two algorithms, a classification-stability algorithm and a leave-one-out-error-sensitivity algorithm for detecting possibly mislabeled samples. For both algorithms, the key structure is the computation of the leave-one-out perturbation matrix. The classification-stability algorithm is based on measuring the stability of the label of a sample with respect to label changes of other samples and the version of this algorithm based on the support vector machine appears to be quite accurate for three real datasets. The suspect list produced by the version is of high quality. Furthermore, when human intervention is not available, the correction heuristic appears to be beneficial.

Contact:  malossin@dit.unitn.it
Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
Authors: Li Shao , Wu Lijiang , Zhang Zhongqi
Published: July 2006

Motivation: Network reconstruction of biological entities is very important for understanding biological processes and the organizational principles of biological systems. This work focuses on integrating both the literatures and microarray gene-expression data, and a combined literature mining and microarray analysis (LMMA) approach is developed to construct gene networks of a specific biological system.

Results: In the LMMA approach, a global network is first constructed using the literature-based co-occurrence method. It is then refined using microarray data through a multivariate selection procedure. An application of LMMA to the angiogenesis is presented. Our result shows that the LMMA-based network is more reliable than the co-occurrence-based network in dealing with multiple levels of KEGG gene, KEGG Orthology and pathway.

Availability: The LMMA program is available upon request.

Contact:  shaoli@mail.tsinghua.edu.cn

Supplementary Information: Supplementary data are available at Bioinformatics online.
Regulatory T Cells, a Potent Immunoregulatory Target for CAM Researchers: Modulating Tumor Immunity, Autoimmunity and Alloreactive Immunity (III)
Authors: Vojdani Aristo , Erde Jonathan
Published: July 2006

Regulatory T (Treg) cells are the major arbiter of immune responses, mediating actions through the suppression of inflammatory and destructive immune reactions. Inappropriate Treg cell frequency or functionality potentiates the pathogenesis of myriad diseases with ranging magnitudes of severity. Lack of suppressive capability hinders restraint on immune responses involved in autoimmunity and alloreactivity, while excessive suppressive capacity effectively blocks processes necessary for tumor destruction. Although the etiology of dysfunctional Treg cell populations is under debate, the ramifications, and their mechanisms, are increasingly brought to light in the medical community. Methods that compensate for aberrant immune regulation may not address the underlying complications; however, they hold promise for the alleviation of debilitating immune system‐related disorders. The dominant immunoregulatory nature of Treg cells, coupled with recent mechanistic knowledge of natural immunomodulatory compounds, highlights the importance of Treg cells to practitioners and researchers of complementary and alternative medicine (CAM).
Botulinum Toxin A for Neuropathic Pain After Neck Dissection: A Dose‐Finding Study
Authors: Wittekindt Claus , Liu Wei‐Chi , Preuss Simon F. , Guntinas‐Lichius Orlando
Published: July 2006

Objectives: Botulinum toxin type A (BtxA) has been reported to be feasible in chronic neuropathic pain after neck dissection. The impact of the dose on the outcome has not been investigated yet.

Study Design: Twenty‐three patients with neuropathic pain after neck dissection were selected for an open and prospective phase II trial.

Methods: In the low‐dose group (n = 13), a concentration of 10 mouse units (MU)/0.1 mL saline and in the high‐dose‐group (n = 10), a concentration of 20 MU/0.1 mL saline were injected subcutaneously. Pain and quality of life were assessed at day 0 and day 28, respectively, by visual analog scales (VAS) and European Organization for Research and Treatment of Cancer (EORTC) quality‐of‐life core and EORTC quality‐of‐life head and neck module questionnaires.

Results: Patients in the low‐dose group showed a significant pain reduction (VAS) from 4.3 at day 0 to 3.0 at day 28 (P < .05). The mean pain VAS values in the high‐dose group did not improve significantly. No serious adverse events were observed. There were trends toward improvement in quality of life in the low‐dose group.

Conclusions: BtxA in a low concentration seems to be a useful therapeutic option in chronic neuropathic pain of the neck and shoulder after neck dissection.
Contact Endoscopic Comparison of Morphology of Human Fungiform Papillae of Healthy Subjects and Patients with Transected Chorda Tympani Nerve
Authors: Just Tino , Pau Hans Wilhelm , Witt Martin , Hummel Thomas
Published: July 2006

Background: The chorda tympani nerve (CTN) carries gustatory fibers from taste buds of fungiform papillae (fPap) of the anterior portion of the tongue. Accordingly, middle ear surgery with transection of the CTN may result in gustatory impairment. With use of contact endoscopy, the present study aimed to compare number and shape of fPap and subepithelial vessel formation in patients after CTN transection with that of healthy controls.

Material and Methods: The number of fPap per square centimeter was obtained in addition to measures of gustatory sensitivity using electrogustometry and intensity ratings of natural taste stimuli. Data from 32 healthy subjects (mean age 40 yr; 16 female, 16 male) were compared with those from 14 patients whose CTN had been cut and partly resected during middle ear surgery because of cholesteatoma (mean age 38 yr; 7 female, 7 male). Middle ear surgery was performed by two of the authors.

Results: In healthy subjects, a higher fPap density was found on the tongue's tip compared with its edge; younger subjects had higher densities than older subjects. No sex‐related differences were observed. Patients with transected CTN exhibited a significant decrease of taste function as measured with both natural and electric stimuli. In patients, we found significantly fewer and flatter fPap on the side of the tongue where surgery had been performed in comparison with the contralateral side. In addition, fPap density at the ipsilateral side was significantly lower compared with fPap density on the respective side in healthy controls.

Conclusion: As established through contact endoscopy, the number of fPap decreases in relation to deafferentation and also in relation to the subjects' age, both of which are accompanied by a decreased gustatory sensitivity.
Cross‐cultural Adaptation and Validation of the Chinese Voice Handicap Index‐10
Authors: Lam Paul K. Y. , Chan Karen M , Ho WK , Kwong Elaine , Yiu Edwin M , Wei William I
Published: July 2006

Objectives/Hypothesis: Recent developments in voice assessment propose the use of quality of life measurements. The Voice Handicap Index (VHI) is one of the most psychometrically robust and well‐studied instruments among the various instruments for measuring quality of life. Two versions of VHI (VHI‐30 and VHI‐10) have been shown to be valid instruments for distinguishing dysphonic from nondysphonic individuals and also for documenting treatment effect for dysphonic patients. The VHI has been used worldwide; however, the psychometric properties of the Chinese version of VHI remains untested. This study aimed to investigate such properties of the Chinese VHI‐30 and VHI‐10 in the Hong Kong Chinese population.

Study Design: Psychometric analysis of the Chinese VHI‐30 and VHI‐10 in dysphonic patients and control subjects.

Methods: The original VHI‐30 was translated into Chinese and was completed by 131 dysphonic patients and 54 nondysphonic individuals. The dysphonic patients also self‐rated their dysphonic severity.

Results: Results showed high test‐retest reliability and high item‐total correlation for both Chinese VHI‐30 and VHI‐10. Both Chinese versions could be used to distinguish different dysphonic groups and between dysphonic and nondysphonic groups. Significant correlation was found between the VHI scores and the patients' self‐rated dysphonic severity.

Conclusion: The present study supported the original three‐factorial structures of the VHI‐30 and the use of the VHI for the Chinese population. It is shown that the Chinese VHI‐10 is a strong representation of VHI‐30 and is recommended for use in clinics because of its validity and ease of use by patients.
Viscoelastic and Histologic Properties in Scarred Rabbit Vocal Folds After Mesenchymal Stem Cell Injection
Authors: Hertegård S , Cedervall J , Svensson B , Forsberg K , Maurer F H. J. , Vidovska D , Olivius P , Ährlund‐Richter L , Le Blanc K
Published: July 2006

Objective/Hypothesis: The aim of this study was to analyze the short‐term viscoelastic and histologic properties of scarred rabbit vocal folds after injection of human mesenchymal stem cells (MSC) as well as the degree of MSC survival. Because MSCs are antiinflammatory and regenerate mesenchymal tissues, can MSC injection reduce vocal fold scarring after injury?

Study Design: Twelve vocal folds from 10 New Zealand rabbits were scarred by a localized resection and injected with human MSC or saline. Eight vocal folds were left as controls.

Material and Methods: After 4 weeks, 10 larynges were stained for histology and evaluation of the lamina propria thickness. Collagen type I content was analyzed from six rabbits. MSC survival was analyzed by fluorescent in situ hybridization staining from three rabbits. Viscoelasticity for 10 vocal folds was analyzed in a parallel‐plate rheometer.

Results: The rheometry on fresh‐frozen samples showed decreased dynamic viscosity and lower elastic modulus (P < .01) in the scarred samples injected with MSC as compared with the untreated scarred group. Normal controls had lower dynamic viscosity and elastic modulus as compared with the scarred untreated and treated vocal folds (P < .01). Histologic analysis showed a higher content of collagen type 1 in the scarred samples as compared with the normal vocal folds and with the scarred folds treated with MSC. MSCs remained in all samples analyzed.

Conclusions: The treated scarred vocal folds showed persistent MSC. Injection of scarred rabbit vocal folds with MSC rendered improved viscoelastic parameters and less signs of scarring expressed as collagen content in comparison to the untreated scarred vocal folds.
Sex Differences in Outcomes of Sinus Surgery
Authors: Mendolia‐Loffredo Sabrina , Laud Purushottam W. , Sparapani Rodney , Loehrl Todd A. , Smith Timothy L.
Published: July 2006

Purpose: Sex has been demonstrated to affect outcome in many diseases. Our current aim is to investigate the relationship between sex and outcomes of endoscopic sinus surgery (ESS) in patients with chronic rhinosinusitis (CRS).

Methods: Forty‐four males and 73 females undergoing ESS for CRS with a mean follow‐up of 1.4 years were evaluated prospectively. Computed tomography (CT), endoscopy, and quality of life (QOL) assessment was performed. Univariate analyses were performed to evaluate whether sex was predictive of outcome. Multiple logistic regression analysis was performed to evaluate sex association with patient factors predictive of outcome.

Results: Although no sex differences in CT and endoscopy were observed (CT, P = .107 and endoscopy, P > .1), females consistently scored worse than males on disease‐specific QOL pre‐ and postoperatively. Importantly, there was no effect of sex on improvement/change scores for the QOL instruments.

Predictive Models and Multiple Logistic Regression Analysis: Sex was not found to be predictive of QOL or endoscopic outcome. Female sex was, however, associated with acetylsalicylic acid (ASA) intolerance and depression, both factors that have been associated with poorer outcome.

Conclusion: Despite similarities in objective disease measures, females report significantly worse QOL scores pre‐ and postoperatively. Postoperative improvement did not differ by sex, nor was sex predictive of postoperative outcome. Sex differences in QOL reflect sex differences in ASA intolerance and depression, both more prevalent in females.
Management of Contralateral N0 Neck in Pyriform Sinus Carcinoma
Authors: Koo Bon Seok , Lim Young Chang , Lee Jin Seok , Kim Young‐Ho , Kim Se‐Heon , Choi Eun Chang
Published: July 2006

Objective: The hypopharynx has a rich lymphatic network that places patients with tumors of the hypopharynx at high risk for early dissemination of the disease into the cervical lymphatics. Therefore, ipsilateral elective neck dissection of clinically N0 neck in lateralized lesions of hypopharyngeal squamous cell carcinomas (SCCs) is widely accepted as a standard treatment. However, the management of the contralateral N0 neck is still controversial. The aim of this study was to evaluate the incidence and predictive factors of contralateral occult lymph node metastasis in pyriform sinus SCC.

Materials and Methods: We performed a retrospective analysis of 43 patients with N0 to 3 pyriform sinus SCC with contralateral clinically node‐negative necks who had also received contralateral elective neck dissections from 1994 to 2003. Surgical treatment was followed by postoperative radiotherapy in 41 patients. The follow‐up period ranged from 4 to 135 months (mean, 40 months). The Kaplan‐Meier method and log‐rank test were used to calculate the disease‐specific survival rates and prognostic significance of contralateral occult lymph node metastasis.

Results: Contralateral occult lymph node metastases occurred in 16% (seven of 43) of the subjects. Twenty‐six percent of the 27 subjects with clinically node‐positive ipsilateral neck developed contralateral occult lymph node metastases, whereas 0% of the 16 subjects with N0 ipsilateral necks (P = .035) developed the disease. Moreover, in cases with primary site extension across the midline, the rate of contralateral occult neck metastasis was significantly higher (P = .010). However, there were no statistically significant differences in age, sex, early versus advanced T stage, number of ipsilateral positive nodes, lymph nodes with extracapsular spread, primary subsite of medial versus lateral pyriform sinus, pyriform sinus apex involvement, and growth type. Patients with no evidence of contralateral nodal cancer had significantly improved disease‐specific survival over patients with any pathologically positive nodes (5‐year disease‐specific survival rate, 66% vs. 33%, P < .05).

Conclusion: The patients with pyriform sinus SCC with clinically ipsilateral N+ neck and/or extension across the midline are at greater risk for contralateral occult neck metastases. Furthermore, patients who present with a contralateral metastatic neck have a worse prognosis than those staged as N0. Therefore, we advocate bilateral neck treatment in patients with pyriform sinus SCC with clinically ipsilateral node metastases and/or extension across the midline.
Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India
Authors: Tripathi Anil K. , Verma Subhash C. , Chowdhury Soumitra Paul , Lebuhn Michael , Gattinger Andreas , Schloter Michael
Published: July 2006

A non-pigmented, motile, Gram-negative bacterium designated MTCC 4195T was isolated from surface-sterilized seeds and plant tissue from deep-water rice (Oryza sativa) cultivated in Suraha Tal Lake in northern India. This isolate was shown to reinfect and colonize deep-water rice endophytically. The highest level of 16S rRNA sequence similarity (96.8 %) to strain MTCC 4195T was shown by Ochrobactrum gallinifaecis DSM 15295T. Strain MTCC 4195T utilized γ-hydroxybutyric acid, adonitol, d-glucosaminic acid and arabinose as carbon sources, but failed to use gentiobiose or citrate. The cell-wall fatty acids of strain MTCC 4195T were characterized by the presence of a relatively large proportion of C18 : 1
ω7c and a relative small proportion of C16 : 0 in comparison with Ochrobactrum species. DNA–DNA relatedness studies showed less than 52 % binding with the DNAs of type strains of other species of the genus Ochrobactrum. On the basis of phenotypic and genotypic characteristics and the results of 16S rRNA gene sequence analysis, the novel species Ochrobactrum oryzae sp. nov. is proposed, with MTCC 4195T (=DSM 17471T) as the type strain.
Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis
Authors: Gatson Joshua W. , Benz Bruce F. , Chandrasekaran Chitra , Satomi Masataka , Venkateswaran Kasthuri , Hart Mark E.
Published: July 2006

A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate asBacillus subtilis. DNA isolated from the tomb isolate, strain 10bT, and closely related species was used to amplify aBacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodAint). Trees derived from maximum-likelihood methods applied to thesodAintsequences yielded non-zero branch lengths between strain 10bTand its closest relative, whereas a comparison of aBacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity withB. subtilis. Although the 16S rRNA gene sequences of strain 10bTandB. subtiliswere 99 % similar, PFGE ofNotI-digested DNA of strain 10bTrevealed a restriction profile that was considerably different from those ofB. subtilisand other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10bTand each of the other closely relatedBacillusspecies examined. In addition, DNA–DNA hybridization studies demonstrated that strain 10bThad a relatedness value of less than 70 % withB. subtilisand other closely related species. Evidence from thesodAintsequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA–DNA hybridization studies, justify the classification of strain 10bTas representing a distinct species, for which the nameBacillus tequilensissp. nov. is proposed. The type strain is 10bT(=ATCC BAA-819T=NCTC 13306T).
Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces
Authors: Osawa Ro , Fujisawa Tomohiko , Pukall Rüdiger
Published: July 2006

A Gram-positive, rod-shaped, non-endospore-forming bacterium, strain ASB1T, able to degrade tannin, was isolated from faeces of the Japanese large wood mouse, Apodemus speciosus. Comparative analysis of the 16S rRNA gene sequence revealed that the strain could be assigned as a member of the genus Lactobacillus. The nearest phylogenetic neighbours were determined as Lactobacillus animalis DSM 20602T (98.9 % 16S rRNA gene sequence similarity) and Lactobacillus murinus ASF 361 (98.9 %). Subsequent polyphasic analysis, including automated ribotyping and DNA–DNA hybridization experiments, confirmed that the isolate represents a novel species, for which the name Lactobacillus apodemi sp. nov. is proposed. The DNA G+C content of the novel strain is 38.5 mol%. The cell-wall peptidoglycan is of type A4α
l-lys–d-Asp. The type strain is ASB1T (=DSM 16634T=CIP 108913T).
‘Candidatus Phytoplasma americanum’, a phytoplasma associated with a potato purple top wilt disease complex
Authors: Lee Ing-Ming , Bottner Kristi D. , Secor Gary , Rivera-Varas Viviana
Published: July 2006

Potato purple top wilt (PPT) is a devastating disease that occurs in various regions of North America and Mexico. At least three distinct phytoplasma strains belonging to three different phytoplasma groups (16SrI, 16SrII and 16SrVI) have been associated with this disease. A new disease with symptoms similar to PPT was recently observed in Texas and Nebraska, USA. Two distinct phytoplasma strain clusters were identified. One belongs to the 16SrI phytoplasma group, subgroup A, and the other is a novel phytoplasma that is most closely related to, and shares 96.6 % 16S rRNA gene sequence similarity with, a member of group 16SrXII. Phylogenetic analysis of 16S rRNA gene sequences of the novel PPT-associated phytoplasma strains, previously described ‘Candidatus Phytoplasma’ organisms and other distinct unnamed phytoplasmas indicated that the novel phytoplasma, termed American potato purple top wilt (APPTW) phytoplasma, represents a distinct lineage and shares a common ancestor with stolbur phytoplasma, ‘Candidatus Phytoplasma australiense’, ‘Candidatus Phytoplasma japonicum’, ‘Candidatus Phytoplasma fragariae’, bindweed yellows phytoplasma (IBS), ‘Candidatus Phytoplasma caricae’ and ‘Candidatus Phytoplasma graminis’. On the basis of unique 16S rRNA gene sequences and biological properties, it is proposed that the APPTW phytoplasma represents ‘Candidatus Phytoplasma americanum’, with APPTW12-NE as the reference strain.
Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase
Authors: Sibille Nathalie , Favier Adrien , Azuaga Ana I. , Ganshaw Grant , Bott Richard , Bonvin Alexandre M.J.J. , Boelens Rolf , van Nuland Nico A.J.
Published: July 2006

In this work we compare the dynamics and conformational stability of Pseudomonas mendocina lipase enzyme and its F180P/S205G mutant that shows higher activity and stability for use in washing powders. Our NMR analyses indicate virtually identical structures but reveal remarkable differences in local dynamics, with striking correspondence between experimental data (i.e., 15N relaxation and H/D exchange rates) and data from Molecular Dynamics simulations. While overall the cores of both proteins are very rigid on the pico‐ to nanosecond timescale and are largely protected from H/D exchange, the two point mutations stabilize helices α1, α4, and α5 and locally destabilize the H‐bond network of the β‐sheet (β7–β9). In particular, it emerges that helix α5, undergoing some fast destabilizing motions (on the pico‐ to nanosecond timescale) in wild‐type lipase, is substantially rigidified by the mutation of Phe180 for a proline at its N terminus. This observation could be explained by the release of some penalizing strain, as proline does not require any “N‐capping” hydrogen bond acceptor in the i+3 position. The combined experimental and simulated data thus indicate that reduced molecular flexibility of the F180P/S205G mutant lipase underlies its increased stability, and thus reveals a correlation between microscopic dynamics and macroscopic thermodynamic properties. This could contribute to the observed altered enzyme activity, as may be inferred from recent studies linking enzyme kinetics to their local molecular dynamics.
Crystal structures of saposins A and C
Authors: Ahn Victoria E. , Leyko Paul , Alattia Jean‐René , Chen Lu , Privé Gilbert G.
Published: July 2006

Saposins A and C are sphingolipid activator proteins required for the lysosomal breakdown of galactosylceramide and glucosylceramide, respectively. The saposins interact with lipids, leading to an enhanced accessibility of the lipid headgroups to their cognate hydrolases. We have determined the crystal structures of human saposins A and C to 2.0 Å and 2.4 Å, respectively, and both reveal the compact, monomeric saposin fold. We confirmed that these two proteins were monomeric in solution at pH 7.0 by analytical centrifugation. However, at pH 4.8, in the presence of the detergent C8E5, saposin A assembled into dimers, while saposin C formed trimers. Saposin B was dimeric under all conditions tested. The self‐association of the saposins is likely to be relevant to how these small proteins interact with lipids, membranes, and hydrolase enzymes.
Characterization of the native and fibrillar conformation of the human Nα‐acetyltransferase ARD1
Authors: Sánchez‐Puig Nuria , Fersht Alan R.
Published: July 2006

ARD1 (arrest‐defective protein 1), together with NAT1 (N‐acetyltransferase protein 1), is part of the major Nα‐acetyltransferase complex in eukaryotes responsible for α‐acetylation of proteins and peptides. Protein acetylation has been implicated in gene expression regulation and protein–protein interaction. We characterized the native folded and misfolded conformation of hARD1. Structural characterization of native hARD1 using size exclusion chromatography, circular dichroism, and fluorescence spectroscopy shows the protein consists of a compact globular region comprising two thirds of the protein and a flexible unstructured C terminus. In addition, hARD1 forms protofilaments under physiological conditions of pH and temperature, as judged by electron microscopy and staining with the dyes Congo red and thioflavin T. The process is accelerated by thermal denaturation and high protein concentrations. Limited proteolysis of aggregated hARD1 revealed a resistant fragment whose sequence matched a region contained within the acetyl transferase domain.
Circular dichroism spectroscopy of tertiary and quaternary conformations of human hemoglobin entrapped in wet silica gels
Authors: Ronda Luca , Bruno Stefano , Viappiani Cristiano , Abbruzzetti Stefania , Mozzarelli Andrea , Lowe Kenneth C. , Bettati Stefano
Published: July 2006

The relative contributions to changes in visible and near UV circular dichroism spectra of hemoglobin of heme ligation and tertiary and quaternary conformational transitions were separated by exploiting the slowing down of structural relaxations for proteins encapsulated in wet, nanoporous silica gels. Spectral signatures, previously assumed to be characteristic of T and R quaternary states, were demonstrated to be specific to different tertiary conformations. The results support the view that ligation and allosteric effectors can modulate the structural and functional properties of hemoglobin by regulating the equilibrium between the same tertiary species within both quaternary states.
Structure of the angiogenesis inhibitor ovalicin bound to its noncognate target, human Type 1 methionine aminopeptidase
Authors: Addlagatta Anthony , Matthews Brian W.
Published: July 2006

Methionine aminopeptidases (MetAPs) remove the initiator methionine during protein biosynthesis. They exist in two isoforms, MetAP1 and MetAP2. The anti‐angiogenic compound fumagillin binds tightly to the Type 2 MetAPs but only weakly to Type 1. High‐affinity complexes of fumagillin and its relative ovalicin with Type 2 human MetAP have been reported. Here we describe the crystallographic structure of the low‐affinity complex between ovalicin and Type 1 human MetAP at 1.1 Å resolution. This provides the first opportunity to compare the structures of ovalicin or fumagillin bound to a Type 1 and a Type 2 MetAP. For both Type 1 and Type 2 human MetAPs the inhibitor makes a covalent adduct with a corresponding histidine. At the same time there are significant differences in the alignment of the inhibitors within the respective active sites. It has been argued that the lower affinity of ovalicin and fumagillin for the Type 1 MetAPs is due to the smaller size of their active sites relative to the Type 2 enzymes. Comparison with the uncomplexed structure of human Type 1 MetAP indicates that there is some truth to this. Several active site residues have to move “outward” by 0.5 Å or so to accommodate the inhibitor. Other residues move “inward.” There are, however, other factors that come into play. In particular, the side chain of His310 rotates by 134° into a different position where (together with Glu128 and Tyr195) it coordinates a metal ion not seen at this site in the native enzyme.
Characterization of SEZ6L2 cell‐surface protein as a novel prognostic marker for lung cancer
Authors: Ishikawa Nobuhisa , Daigo Yataro , Takano Atsushi , Taniwaki Masaya , Kato Tatsuya , Tanaka Sonosuke , Yasui Wataru , Takeshima Yukio , Inai Kouki , Nishimura Hitoshi , Tsuchiya Eiju , Kohno Nobuoki , Nakamura Yusuke
Published: July 2006

To identify molecules that might serve as biomarkers or targets for development of novel molecular therapies, we have been screening genes encoding transmembrane/secretory proteins that are up‐regulated in lung cancers, using cDNA microarrays coupled with purification of tumor cells by laser microdissection. A gene encoding seizure‐related 6 homolog (mouse)‐like 2 (SEZ6L2) protein, was chosen as a candidate for such molecule. Semi‐quantitative RT‐PCR and western‐blot analyses documented increased expression of SEZ6L2 in the majority of primary lung cancers and lung‐cancer cell lines examined. SEZ6L2 protein was proven to be present on the surface of lung‐cancer cells by flow cytometrical analysis using anti‐SEZ6L2 antibody. Immunohistochemical staining for tumor tissue microarray consisting of 440 archived lung‐cancer specimens detected positive SEZ6L2 staining in 327 (78%) of 420 non‐small cell lung cancers (NSCLCs) and 13 (65%) of 20 small‐cell lung cancers (SCLCs) examined. Moreover, NSCLC patients whose tumors revealed a higher level of SEZ6L2 expression suffered shorter tumor‐specific survival compared to those with no SEZ6L2 expression. These results indicate that SEZ6L2 should be a useful prognostic marker of lung cancers. (Cancer Sci 2006; 97: 737–745)
Food web structure and mercury transfer in two contrasting Ugandan highland crater lakes (East Africa)
Authors: Campbell L. , Hecky R. E. , Dixon D. G. , Chapman L. J.
Published: July 2006

Volcanic crater lakes scattered throughout western Uganda are important local sources of water and fish. Two representative but contrasting crater lakes near the Kibale National Park were sampled in 2000; the hyper‐eutrophic Lake Saka, which is highly affected by agricultural practices, and the mesotrophic Lake Nkuruba that is still surrounded by intact forest. The food web structures in these two lakes were assessed using stable nitrogen (δ15N) and carbon (δ13C) isotope analyses, and the mercury (THg) transfer patterns were quantified. The δ15N results indicate that food webs in both lakes are abbreviated, with only one to two trophic levels from primary consumers. The Lake Saka biota had distinctively enriched δ13C values compared with those in Lake Nkuruba, which may be due to 12C‐limited phytoplankton blooms in this lake. In Lake Nkuruba, two introduced tilapiine species and the introduced guppy Poecilia reticulata fed predominantly upon invertebrates and decomposed terrestrial plant material. In Lake Saka, the introduced Nile perch Lates niloticus appeared to occupy the top trophic position, but stable isotope values of the endemic haplochromine cichlids exclude those as Nile perch prey items. THg was found to biomagnify through the food web, reaching highest concentrations in P. reticulata in Nkuruba, which tended to be higher than for L. niloticus in Saka, suggesting increased bioavailability of THg in Nkuruba. Maximum THg concentrations in fish never approached WHO recommended guidelines (200 ng g−1) designed to protect at‐risk groups.
Interaction risk with proton pump inhibitors in general practice: significant disagreement between different drug‐related information sources
Authors: Trifirò Gianluca , Corrao Salvatore , Alacqua Marianna , Moretti Salvatore , Tari Michele ,   UVEC group,, Caputi Achille P. , Arcoraci Vincenzo
Published: July 2006

Aims

To compare information on drug–drug interactions (DDIs) reported on two standard drug‐related information sources (Summary of Product Characteristics and Drugdex system by Micromedex), by assessing the prevalence and predictors of potential DDI with proton pump inhibitors (PPIs) in general practice.

Methods

From the ‘Caserta‐1’ Local Health‐Service database, 156 general practitioners (GPs) were recruited. From more than 180 000 individuals registered on their lists, we selected patients receiving co‐prescription of PPI and medications at interaction risk, according to the Italian Summary of Product Characteristics (SPC) of PPI and Drugdex information, during the year 2003. Thereafter, we carried out a regression analysis to identify the predictors of co‐prescription at interaction risk with PPI, on the basis of the two information sources. A number of analyses were performed to evaluate agreement on DDI information between the SPC of PPI and Drugdex.

Results

According to SPC and Drugdex, 324 (3.0%) and 958 (9.0%) patients, respectively, received co‐prescriptions of PPI and potentially interacting medications during the study period. PPI users’ age, type of medication and number of other drug prescriptions per month were independent predictors of receiving co‐prescriptions at interaction risk, when considering only Drugdex. With regard to potential DDIs with PPI, a significant disagreement (P < 0.0001) between the two drug‐related information sources, was shown through agreement analyses.

Conclusions

Potential DDIs with PPI are a common health issue in general practice. Estimates of prevalence and predictors of potential DDIs with PPI significantly changes according to the drug information source being used.
Developing a global approach to the theory and practice of young people leaving state care
Authors: Pinkerton John
Published: July 2006

This paper argues that globalization, although needing to be recognized as a highly complex phenomenon and a contested concept, should become part of the debate about improving the life chances of young people leaving care. Understanding globalization is essential to developing the effective strategies of engagement and resistance needed to address the social exclusion of these young people. Consideration is given to the considerable difficulties faced in moving from that general recognition to a sufficiently nuanced view of the impact of globalization on care leaving required as the basis for action. Existing approaches to promoting international exchange and understanding are discussed and a conceptual model presented as the means to start the work of identifying how the needs of care leavers are assessed and met in different national contexts. It is suggested that by identifying patterns of cross‐national similarities and differences, it will become possible to understand and to engage with the processes and institutions of globalization. An international theoretical and practice agenda are proposed appropriate to the present early stage in ensuring that globalization works for and not against the interests of care leavers.
Research Review: Young people leaving care
Authors: Stein Mike
Published: July 2006

This paper reviews the international research on young people leaving care. Set in the context of a social exclusion framework, it explores young people’s accelerated and compressed transitions to adulthood, and discusses the development and classification of leaving care services in responding to their needs. It then considers the evidence from outcome studies and argues that adopting a resilience framework suggests that young people leaving care may fall into three groups: young people ‘moving on’, ‘survivors’ and ‘victims’. In concluding, it argues that these three pathways are associated with the quality of care young people receive, their transitions from care and the support they receive after care.