bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus epidermidis is cleared from biomaterial implants but persists in peri‐implant tissue in mice despite rifampicin/vancomycin treatment
Authors: Broekhuizen Corine A.N. , de Boer Leonie , Schipper Kim , Jones Christopher D. , Quadir Shan , Vandenbroucke‐Grauls Christina M.J.E. , Zaat Sebastian A.J. 
Published: August 2007

AbstractInfections associated with implanted biomedical devices (BAI) are predominantly caused by Staphylococcus epidermidis. We previously observed in murine experimental BAI that S. epidermidis persists in peri‐implant tissue rather than on the implanted biomaterial itself (Boelens et al., J Infect Dis 2000;181:1337–1349; Broekhuizen et al., Infect Immun 2007;75:1129–1136). To investigate the efficacy of rifampicin/vancomycin to clear S. epidermidis from implants and peri‐implant tissues, mice with two implants were challenged with 107 cfu S. epidermidis per implant and received daily injections of rifampicin (25 mg/kg) and vancomycin (50 mg/kg). On the day of termination, implants and peri‐implant tissue were collected and processed for culture and histology. After 1 and 8 days, implants of control mice were culture positive in 14/18 and 5/16 cases, respectively, and tissue biopsies were all culture positive. In the antibiotic‐treated mice, bacteria were recovered from only 1/18 and 1/16 implants after 1 and 8 days, respectively, whereas the tissues were culture positive in 14/18 and 7/16 biopsies, respectively. In microscopy, bacteria were seen in the tissue at a distance of several cell layers from the tissue‐implant interface, colocalized with host cells. Thus, although a regimen of rifampicin/vancomycin sterilized the implants, S. epidermidis persisted in peri‐implant tissue, which might be an as yet unrecognized reservoir in the pathogenesis of BAI. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2008
Effects of confinement on the mechanical properties of self‐assembled articular cartilage constructs in the direction orthogonal to the confinement surface
Authors: Elder Benjamin D. , Athanasiou Kyriacos A. 
Published: August 2007

AbstractThis study examined the effects of radial confinement and passive axial compression‐induced vertical confinement, on the biomechanical, biochemical, and histological properties of self‐assembled chondrocyte constructs. The self‐assembled constructs, engineered without the use of an exogenous scaffold, exhibited significant increases in stiffness in the direction orthogonal to that of the confinement surface. With radial confinement, the significantly increased aggregate modulus was accompanied by increased collagen organization in the direction perpendicular to the articular surface, with no change in collagen or glycosaminoglycan (GAG) content. Additionally, radial confinement was most beneficial when applied before 2 weeks. With passive axial compression, the significantly increased Young's modulus and ultimate tensile strength were accompanied by a significant increase in collagen production. This study is the first to demonstrate the beneficial effects of confinement on tissue engineered constructs in the direction orthogonal to that of the confinement surface. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:238–246, 2008
Visitor and non‐visitor images of Central and Eastern Europe: a qualitative analysis
Authors: Hughes Howard L. , Allen Danielle 
Published: August 2007

AbstractThis study examines the image of Central and Eastern Europe (CEE) as a holiday destination. The countries are linked by having had communist governments and being inaccessible to tourists from outside the communist bloc. Currently, they seek new tourist markets and this study examines the views of a number of UK residents about destination image of CEE. The study examines, through semi‐structured interviews, images held by people who have and who have not visited CEE. The data is analysed qualitatively. Few significant differences were found between views of visitors and non‐visitors; most views were positive and associated favourably with ‘culture’. Negative images were usually associated with the eastern part of the area especially ex‐Yugoslavia. Copyright © 2007 John Wiley & Sons, Ltd.
Explaining hump‐shaped inflation responses to monetary policy shocks
Authors: Yetman James 
Published: August 2007

AbstractAccording to conventional wisdom, the output effects of a monetary policy shock commence within months of the shock, while most inflationary effects lag significantly. We demonstrate a simple model that can explain the conventional wisdom and is consistent with profit maximizing price setting decisions by firms, based on the assumption that renegotiating existing contracts is costly. Thus, firms jointly choose both their price and the expected length of time for which that price will hold each time they re‐contract. We show that such a ‘sticky contracting’ assumption, combined with menu costs, generates a hump‐shaped inflation response to monetary policy shocks. Copyright © 2007 John Wiley & Sons, Ltd.
Production, inventory and waiting time
Authors: Epstein Gil S. 
Published: August 2007

AbstractIn this paper, I introduce the idea of adjusting waiting time as an alternative to price adjustment in order to study the relationship between waiting time, demand, profits and inventories. In the model, demand depends on both price and waiting time. Consumers are willing to pay more if they do not have to wait long. I derive the conditions under which a monopoly may profit from utilizing the option of holding inventory by changing the waiting time facing the consumers. Copyright © 2007 John Wiley & Sons, Ltd.
The frequency and costs of individual price adjustment
Authors: Wolman Alexander L. 
Published: August 2007

AbstractHow often do the nominal prices of individual goods change? What is the nature of costs of price adjustment? How big are these costs? Answering these questions may be important for constructing macroeconomic models that are useful for monetary policy analysis. The empirical literature reveals that many prices do change infrequently, in part because of physical costs of price adjustment. However, infrequent price adjustment also seems to be related to costs of decision making, to relationships between buyers and sellers, and to strategic behavior among sellers, all in ways that are not yet well understood. Copyright © 2007 John Wiley & Sons, Ltd.
Limited stability in cell culture medium and hydrogen peroxide formation affect the growth inhibitory properties of delphinidin and its degradation product gallic acid
Authors: Kern Melanie , Fridrich Diana , Reichert Julia , Skrbek Susanne , Nussher Anja , Hofem Sabine , Vatter Sandra , Pahlke Gudrun , Rüfer Corinna , Marko Doris 
Published: August 2007

AbstractIn the present study we investigated the stability of anthocyanidins under cell culture conditions and addressed the question whether degradation products might contribute to the cellular effects assigned to the parent compounds. Substantial degradation was found already after 30 min, measured by HPLC/DAD. However, the decrease of detectable anthocyanidins exceeded by far the formation of the respective phenolic acids. From the formed phenolic acids only gallic acid (GA) exhibited growth inhibitory properties. However, also GA was found to be degraded rapidly. Furthermore, the incubation with delphinidin (DEL) or GA resulted in a substantial formation of hydrogen peroxide. The suppression of hydrogen peroxide accumulation by catalase modified significantly the growth inhibitory effects of DEL and GA, indicating that hydrogen peroxide formation might generate experimental artefacts. In summary, the results show that the phenolic acids formed by the degradation of cyanidin (CY), pelargonidin (PG), peonidin (PN) and malvidin (MV) do not contribute to the growth inhibitory effect of the parent compound. The degradation of DEL generates a phenolic acid with substantial growth inhibitory properties (GA). However, taken into account the small proportion of generated GA and its lacking stability, the contribution of GA to the growth inhibitory properties of DEL might be limited.
New molecular and field evidences for the implication of mycotoxins but not aristolochic acid in human nephropathy and urinary tract tumor
Authors: Pfohl‐Leszkowicz Annie , Tozlovanu Mariana , Manderville Richard , Peraica Maja , Castegnaro Marcel , Stefanovic Vladislav 
Published: August 2007

AbstractTo find out whether ochratoxin A (OTA), citrinin (CIT), aristolochic acids (AA) are etiologic agents of Balkan endemic nephropathy (BEN) or Chinese herbal nephrotoxicity, and associated urinary tract tumor (UTT), we have compared (i) in human kidney cell culture, the DNA adduct formation and persistence of OTA/CIT and AA adducts (ii) analyzed DNA adduct in several tumors from human kidney suspected to be exposed to either OTA and CIT, or AAs (iii) analyzed OTA, CIT, and AA in food. In kidney cell cultures, formation of specific OTA‐DNA adduct and AA‐DNA adduct were detected in the same range (around 10 adducts/109nucleotides) and were time‐ and dose‐dependent. After 2 days all disappeared. DNA adduct related to OTA and CIT are found in human kidney tissues from Balkans, France, and Belgium whereas no DNA adducts related to AA could be found in any tumors of BEN patients from Croatia, Bulgaria, or Serbia. No DNA adduct was found in kidney biopsy or necropsy of the French women suspected to be exposed to AA. OTA and CIT are more frequently found in rural area. AA was never detected. All these plead for implication of mycotoxins, especially OTA, in BEN and UTT.
Comparison of various density functional methods for distinguishing stereoisomers based on computed 1H or 13C NMR chemical shifts using diastereomeric penam β‐lactams as a test set
Authors: Wiitala Keith W. , Cramer Christopher J. , Hoye Thomas R. 
Published: August 2007

AbstractFull 1H and 13C NMR chemical shift assignments were made for two sets of penam β‐lactams: namely, the diastereomeric (2S, 5S, 6S)‐, (2S, 5R, 6R)‐, (2S, 5S, 6R)‐, and (2S, 5R, 6S)‐methyl 6‐(1,3‐dioxoisoindolin‐2‐yl)‐3,3‐dimethyl‐7‐oxo‐4‐thia‐1‐aza‐bicyclo[3.2.0]heptane‐2‐carboxylates (1–4) and (2S, 5R, 6R)‐, (2S, 5S, 6R)‐, and (2S, 5R, 6S)‐6‐(1,3‐dioxoisoindolin‐2‐yl)‐3,3‐dimethyl‐7‐oxo‐4‐thia‐1‐aza‐bicyclo[3.2.0]heptane‐2‐carboxylic acids (6–8). Each penam was then modeled as a family of conformers obtained from Monte Carlo searches using the AMBER* force field followed by IEFPCM/B3LYP/6‐31G(d) geometry optimization of each conformer using chloroform solvation. 1H and 13C chemical shifts for each conformer were computed at the WP04, WC04, B3LYP, and PBE1 density functional levels as Boltzmann averages of IEFPCM/B3LYP/6‐311 + G(2d,p) energies over each family. Comparisons between experimental and theoretical chemical shift data were made using the total absolute error (|Δδ | T) criterion. For the 1H shift data, all methods were sufficiently accurate to identify the proper stereoisomers. Computed 13C shifts were not always successful in identifying the correct stereoisomer, regardless of which DFT method was used. The relative ability of each theoretical approach to discriminate among stereoisomers on the basis of proton shifts was also evaluated. Copyright © 2007 John Wiley & Sons, Ltd.
Coupled hydrogen‐bonding interactions between β‐carboline derivatives and acetic acid
Authors: Reyman D. , Hallwass F. , da Cruz Gonçalves Simone M. , Camacho J. J. 
Published: August 2007

AbstractIn this work, we have analysed the tendency of two β‐carboline derivatives, harmane and norharmane, in the formation of hydrogen bonds. We obtained the 1H and 13C NMR spectra of different mixtures of these derivatives with acetic acid (AcOH) in CDCl3. A cyclic 1:3 complex is proposed between harmane and AcOH, while a 1:2 complex is proposed for norharmane.Chemical shifts at temperatures between 233 and 323 K were measured: lowering the temperature produces the same effect as increasing the amount of AcOH in solution.The 13C data confirm a delocalisation of the π electron density towards the pyridinic ring that occurs when AcOH is added. Copyright © 2007 John Wiley & Sons, Ltd.
A predictive tool for assessing 13C NMR chemical shifts of flavonoids
Authors: Burns Darcy C. , Ellis David A. , March Raymond E. 
Published: August 2007

AbstractHerein are presented the 1H and 13C NMR data for seven monohydroxyflavones (3‐, 5‐, 6‐, 7‐, 2′‐, 3′‐, and 4′‐hydroxyflavone), five dihydroxyflavones (3,2′‐, 3,3′‐, 3,4′‐, 3,6‐, 2′,3′‐dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4′‐trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3′,4′‐tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin‐6C‐β‐D‐glucoside, homoorientin; luteolin‐8C‐β‐D‐glucoside, vitexin; apigenin‐8C‐β‐D‐glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid 13C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone 13C chemical shifts, is demonstrated. The tool can be used to accurately predict 13C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid 13C NMR spectra and for assigning substitution patterns in newly isolated flavonoids. Copyright © 2007 John Wiley & Sons, Ltd.
Application of unsymmetrical indirect covariance NMR methods to the computation of the 13C↔15N HSQC‐IMPEACH and 13C↔15N HMBC‐IMPEACH correlation spectra
Authors: Martin Gary E. , Hilton Bruce D. , Irish Patrick A. , Blinov Kirill A. , Williams Antony J. 
Published: August 2007

AbstractUtilization of long‐range 1H15N heteronuclear chemical shift correlation has continually grown in importance since the first applications were reported in 1995. More recently, indirect covariance NMR methods have been introduced followed by the development of unsymmetrical indirect covariance processing methods. The latter technique has been shown to allow the calculation of hyphenated 2D NMR data matrices from more readily acquired nonhyphenated 2D NMR spectra. We recently reported the use of unsymmetrical indirect covariance processing to combine 1H13C GHSQC and 1H15N GHMBC long‐range spectra to yield a 13C15N HSQC‐HMBC chemical shift correlation spectrum that could not be acquired in a reasonable period of time without resorting to 15N‐labeled molecules. We now report the unsymmetrical indirect covariance processing of 1H13C GHMBC and 1H15N IMPEACH spectra to afford a 13C15N HMBC‐IMPEACH spectrum that has the potential to span as many as six to eight bonds. Correlations for carbon resonances long‐range coupled to a protonated carbon in the 1H13C HMBC spectrum are transferred via the long‐range 1H15N coupling pathway in the 1H15N IMPEACH spectrum to afford a much broader range of correlation possibilities in the 13C15N HMBC‐IMPEACH correlation spectrum. The indole alkaloid vincamine is used as a model compound to illustrate the application of the method. Copyright © 2007 John Wiley & Sons, Ltd.
Baseline mannose binding lectin levels may not predict infection among children with leukemia
Authors: Rubnitz Jeffrey E. , Howard Scott C. , Willis Jennifer , Pui Ching‐Hon , Pounds Stanley , Hayden Randall T. 
Published: August 2007

AbstractWe measured baseline serum mannose binding lectin (MBL) levels in 91 patients with childhood leukemia to determine their predictive value for the development of febrile neutropenia or specific infections. Median MBL levels did not differ significantly between patients who developed febrile neutropenia, bacterial infection, or disseminated fungal infection and those who did not. In addition, low MBL levels were not associated with an increased cumulative incidence of infection or with a shorter time to first infection. This preliminary study suggests that baseline MBL levels may not be clinically useful to identify pediatric leukemia patients who are at increased risk of infection. Additional studies are required to determine whether serial MBL measurements may be valuable for this purpose. Pediatr Blood Cancer 2008;50:866–868. © 2007 Wiley‐Liss, Inc.
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV‐1 protease
Authors: Altman Michael D. , Nalivaika Ellen A. , Prabu‐Jeyabalan Moses , Schiffer Celia A. , Tidor Bruce 
Published: August 2007

AbstractDrug resistance in HIV‐1 protease, a barrier to effective treatment, is generally caused by mutations in the enzyme that disrupt inhibitor binding but still allow for substrate processing. Structural studies with mutant, inactive enzyme, have provided detailed information regarding how the substrates bind to the protease yet avoid resistance mutations; insights obtained inform the development of next generation therapeutics. Although structures have been obtained of complexes between substrate peptide and inactivated (D25N) protease, thermodynamic studies of peptide binding have been challenging due to low affinity. Peptides that bind tighter to the inactivated protease than the natural substrates would be valuable for thermodynamic studies as well as to explore whether the structural envelope observed for substrate peptides is a function of weak binding. Here, two computational methods—namely, charge optimization and protein design—were applied to identify peptide sequences predicted to have higher binding affinity to the inactivated protease, starting from an RT–RH derived substrate peptide. Of the candidate designed peptides, three were tested for binding with isothermal titration calorimetry, with one, containing a single threonine to valine substitution, measured to have more than a 10‐fold improvement over the tightest binding natural substrate. Crystal structures were also obtained for the same three designed peptide complexes; they show good agreement with computational prediction. Thermodynamic studies show that binding is entropically driven, more so for designed affinity enhanced variants than for the starting substrate. Structural studies show strong similarities between natural and tighter‐binding designed peptide complexes, which may have implications in understanding the molecular mechanisms of drug resistance in HIV‐1 protease. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods
Authors: Otyepka Michal , Banáš Pavel , Magistrato Alessandra , Carloni Paolo , Damborský Jiří 
Published: August 2007

AbstractMechanistic studies on the hydrolytic dehalogenation catalyzed by haloalkane dehalogenases are of importance for environmental and industrial applications. Here, Car‐Parrinello (CP) and ONIOM hybrid quantum‐mechanical/molecular mechanics (QM/MM) are used investigate the second reaction step of the catalytic cycle, which comprises a general base‐catalyzed hydrolysis of an ester intermediate (EI) to alcohol and free enzyme. We focus on the enzyme LinB from Sphingomonas paucimobilis UT26, for which the X‐ray structure at atomic resolution is available. In agreement with previous proposals, our calculations suggest that a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the EI. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP‐QM/MM calculations is equal to 19.5 ± 2 kcal · mol−1. The lowering of the energy barrier of catalyzed reaction with respect to the water reaction is caused by strong stabilization of the reaction intermediate and transition state and their preorganization by electrostatic field of the enzyme. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain
Authors: Del Vecchio Pompea , Carullo Paola , Barone Guido , Pagano Bruno , Graziano Giuseppe , Iannetti Alessio , Acquaviva Renato , Leonardi Antonio , Formisano Silvestro 
Published: August 2007

AbstractThe conformational stability of the rat thyroid transcription factor 1 homeodomain, TTF‐1HD, has been investigated by means of circular dichroism (CD) and differential scanning calorimetry (DSC) measurements at pH 5.0 as a function of KCl concentration. Thermal unfolding of TTF‐1HD is a reversible two‐state transition. The protein is not stable against temperature, showing a denaturation temperature of 32°C in the absence of salt and 50°C at 75 mMKCl. The binding energetics of TTF‐1HD to its target DNA sequence has been characterized by means of isothermal titration calorimetry (ITC) measurements, complemented with CD data. At 25°C, pH 5.0 and 75 mMKCl, the binding constant amounts to 1.5 × 108M−1and the binding enthalpy change amounts to −41 kJ mol−1. The process is enthalpy driven, but also the entropy change is favorable to complex formation. To gain a molecular level understanding of the interactions determining the association of TTF‐1HD to the target DNA sequence structural information would be requested, but it is not yet available. Therefore, structural models of two complexes, TTF‐1HD with the target DNA sequence and TTF‐1HD with a modified DNA sequence, have been constructed by using as a template the NMR structure of the complex between NK‐2 HD and its target DNA, and by performing molecular dynamics simulations 3.5 ns long. Analysis of these models allows one to shed light on the origin of the DNA binding specificity characteristic of TTF‐1HD. Proteins 2008. © 2007 Wiley‐Liss, Inc.
The noncatalytic triad of α‐amylases: A novel structural motif involved in conformational stability
Authors: Marx Jean‐Claude , Poncin Johan , Simorre Jean‐Pierre , Ramteke Pramod W. , Feller Georges 
Published: August 2007

AbstractChloride‐activated α‐amylases contain a noncatalytic triad, independent of the glycosidic active site, perfectly mimicking the catalytic triad of serine‐proteases and of other active serine hydrolytic enzymes. Mutagenesis of Glu, His, and Ser residues in various α‐amylases shows that this pattern is a structural determinant of the enzyme conformation that cannot be altered without losing the intrinsic stability of the protein. 1H‐15N NMR spectra of a bacterial α‐amylase reveal proton signals that are identical with the NMR signature of catalytic triads and especially a deshielded proton involving a protonated histidine and displaying properties similar to that of a low barrier hydrogen bond. It is proposed that the H‐bond between His and Glu of the noncatalytic triad is an unusually strong interaction, responsible for the observed NMR signal and for the weak stability of the triad mutants. Furthermore, a stringent template‐based search of the Protein Data Bank demonstrated that this motif is not restricted to α‐amylases, but is also found in 80 structures from 33 different proteins, amongst which SH2 domain‐containing proteins are the best representatives. Proteins 2008. © 2007 Wiley‐Liss, Inc.