bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclicity analysis of precipitation regimes in the Yangtze River basin, China
Authors: Becker S. , Hartmann H. , Zhang Q. , Wu Y. , Jiang T. 
Published: July 2007

AbstractDaily precipitation data of 148 weather stations located in the Yangtze River basin (P.R. China) are analysed to detect cycles in the annual frequency of occurrence of precipitation events of 1‐, 5‐ and 10 days duration. These events were defined in terms of exceedances of some selected thresholds. The events corresponding to 10, 25 and 30 mm thresholds for 1‐, 5‐ and 10‐day precipitation totals, respectively, are analysed in detail. For the identification of cycles, basin‐wide averaged standardized time series of frequency of precipitation events are used. It is found that peaks in the smoothed time series occurred around 1974, 1982 and 1991. The Fourier, autoregressive and wavelet analyses reveal distinct cycles of 7–9 and 2–3 year periods, which dominate large parts of the time series. In addition, a shift towards a 4–5 year period in the annual frequency of precipitation events is noticed since the mid‐ to late‐nineties. Major peaks in the annual frequency of occurrence of precipitation events are expected to occur around 2012, 2015 and 2018 according to the spectrum analyses. Copyright © 2007 Royal Meteorological Society
Solamargine upregulation of Fas, downregulation of HER2, and enhancement of cytotoxicity using epirubicin in NSCLC cells
Authors: Liang Chia‐Hua , Shiu Li‐Yen , Chang Li‐Ching , Sheu Hamm‐Ming , Kuo Kou‐Wha 
Published: July 2007

AbstractNonsmall‐cell lung cancer (NSCLC) is not generally a chemosensitive tumor, and the mechanism of resistance to the relevant anticancer drugs has not been fully elucidated. Solamargine (SM), the major steroidal glycoalkaloids extracted from the Chinese herb Solanum, inhibits the growth of human tumor cells. We have previously demonstrated that SM regulates tumor necrosis factor receptors (TNFRs)‐ and mitochondria‐mediated pathways and sensitizes NSCLC cells to initiate apoptosis. Interestingly, this investigation reveals that SM up‐regulated Fas expression and down‐regulated the expression of HER2, whose overexpression is associated with resistance to drugs, and promotes chemotherapy‐induced apoptosis in NSCLC A549 and H441 cells. After treatment with SM, the expression of HER2 mRNA was correlated with the expression of topoisomerase IIα (TOP2A) mRNA. The combinatory use of low concentrations of SM with low‐toxic topoisomerase II inhibitor epirubicin accelerated apoptotic cell death. Therefore, the downregulation of the HER2 and TOP2A expression by SM with epirubicin may partially explain the SM and epirubicin cytotoxicity synergy effect in NSCLC. Results of this study suggest that SM induces Fas and TNFR‐induced NSCLC cell apoptosis and reduces HER2 expression. These findings provide the synergistic therapeutic interaction between SM and epirubicin, suggesting that such combinations may be effectively exploited in future human cancer clinical trials.
The prediction of 1H chemical shifts in amines: a semiempirical and ab initio investigation
Authors: Basso Ernani A. , Gauze Gisele F. , Abraham Raymond J. 
Published: July 2007

AbstractTwenty one conformationally fixed amines and their N,N‐dimethyl derivatives were obtained commercially or synthesized. These included cis and trans 4‐t‐butyl cyclohexylamine, 2‐exo and 2‐endo norbornylamine, 2‐adamantylamine, 4‐phenylpiperidine, 1‐napthylamine and tetrahydro‐1‐napthylamine. The 1H NMR spectra of these amines were measured in CDCl3 solution, assigned and the 1H chemical shifts given. This data was used to investigate the effect of the amino group on the 1H chemical shifts in these molecules. These effects were analyzed using the CHARGE model. This calculates the electric field and steric effects of the amino group for protons more than three bonds removed, together with functions for the calculation of two‐bond and three‐bond effects. The rotational isomerism about the CN bond of the amino group was investigated by ab initio calculations of the potential energy surface (PES) about this bond at the HF/3–21G level. The resulting conformers were then minimized at the B3LYP/6‐311 + + G (d,p) level. These geometries were then used to calculate the 1H chemical shifts in the above compounds by CHARGE and the ab initio gauge‐invariant atomic orbital (GIAO) method at the B3LYP/6–311 + + G(d,p) level and the shifts were compared with those observed. The compounds investigated gave 170 1H chemical shifts ranging from 0.60 to 8.2 ppm. The rms errors (obs.—calc.) were ca 0.1 ppm (CHARGE) and ca 0.2 ppm (GIAO). Large deviations of ca 1.0 ppm were observed for the NH protons in the GIAO calculations. The complex spectra of alkyl and aryl amines can thus be successfully predicted by both ab initio and semiempirical methods except for the NH protons, for which the ab initio calculations are not sufficiently accurate. Copyright © 2007 John Wiley & Sons, Ltd.
Microdissecting the proteome
Authors: von Eggeling Ferdinand , Melle Christian , Ernst Günther 
Published: July 2007

AbstractThe complexity of the proteome is extremely high, because every organ or even a part of it can differ considerably in its protein composition. Performing proteomic studies therefore means to separate these functional different tissue areas before analysis. Otherwise all gained results will be depending on the question whether they are incorrect or at least dubious and do they reflect the different functions of tissues at all. The separation of functional tissue areas can be achieved by laser‐based microdissection. In this review we will discuss the compatibly of microdissected formalin or cryofixed tissue with different proteomic techniques like 2‐DE, MS and protein arrays.
Piecing together the structure–function puzzle: Experiences in structure‐based functional annotation of hypothetical proteins
Authors: Adams Melanie A. , Suits Michael D. L. , Zheng Jimin , Jia Zongchao 
Published: July 2007

AbstractThe combination of genomic sequencing with structural genomics has provided a wealth of new structures for previously uncharacterized ORFs, more commonly referred to as hypothetical proteins. This rapid growth has been the direct result of high‐throughput, automated approaches in both the identification of new ORFs and the determination of high‐resolution 3‐D protein structures. A significant bottleneck is reached, however, at the stage of functional annotation in that the assignment of function is not readily automatable. It is often the case that the initial structural analysis at best indicates a functional family for a given hypothetical protein, but further identification of a relevant ligand or substrate is impeded by the diversity of function in a particular structural classification of proteins family, a highly selective and specific ligand‐binding site, or the identification of a novel protein fold. Our approach to the functional annotation of hypothetical proteins relies on the combination of structural information with additional bioinformatics evidence garnered from operon prediction, loose functional information of additional operon members, conservation of catalytic residues, as well as cocrystallization trials and virtual ligand screening. The synthesis of all available information for each protein has permitted the functional annotation of several hypothetical proteins from Escherichia coli and each assignment has been confirmed through generally accepted biochemical methods.
Applications of field‐flow fractionation in proteomics: Presence and future
Authors: Chmelik Josef 
Published: July 2007

AbstractField‐flow fractionation (FFF) represents a group of elution separation methods where external force fields act perpendicularly on analytes in a carrier liquid flows with nonuniform velocity profiles. It is an elution separation method that enables to separate analytes in relatively short times and collect fractions for further characterization or for investigation of their properties. Other advantages of FFF are small consumption of samples and gentle experimental conditions. These make FFF uniquely qualified for separation and purification of biological samples. The most promising are applications of different variants of flow FFF utilizing a cross flow through membrane channel walls to separate proteins. The separation is based on differences in protein diffusion coefficients, which allows calculating the size of macromolecules. Other FFF techniques (e.g., electrical, isoelectric, and sedimentation FFF) were also used for separation of biomolecules. FFF appears to be not only promising rapid technique for protein separation but it offers some other advantages in sample preparation, especially, focusing (hyperlayer) FFF techniques that enable preparation of homogeneous fractions of cells. Selected applications of FFF to protein analysis are described and future trends in application of FFF to proteomics are discussed.
Modulation of human cytidine deaminase by specific aminoacids involved in the intersubunit interactions
Authors: Vincenzetti S. , Quadrini B. , Mariani P. , De Sanctis G. , Cammertoni N. , Polzonetti V. , Pucciarelli S. , Natalini P. , Vita A. 
Published: July 2007

AbstractAn investigation was made of the role exerted by some residues supposed to be involved in the intersubunit interaction and also in the catalytic site of homotetrameric human cytidine deaminase (T‐CDA). Attention was focused on Y33, Y60, R68, and F137 residues that are a part of a conserved region in most T‐CDAs. Hence, a series of site‐directed mutagenesis experiments was set up obtaining seven mutants: Y60G, Y33G, Y33F Y33S, F137A, R68G, and R68Q. Each active purified mutant protein was characterized kinetically, with a series of substrates and inhibitors, and the effect of temperature on enzyme activity and stability was also investigated. Circular dichroism (CD) experiments at different temperatures and in presence of small amounts of sodium dodecyl sulphate (SDS) were performed in all the soluble mutant CDAs. The results obtained by site‐directed mutagenesis studies were compared to the crystallographic data of B. subtilis CDA and E. coli CDA and to molecular modeling studies previously performed on human CDA. The mutation of Y60 to glycine produced an enzyme with a more compact quaternary structure with respect to the wild‐type; this mutation did not have a dramatic effect on cytidine deamination, but it slightly affected the binding with the substrate. None of the mutant CDAs in Y33 showed enzymatic activity; they existed only as monomers, indicating that this residue, located at the intersubunit interface, may be responsible for the correct folding of human CDA. The insertion of an alanine instead of phenylalanine at position 137 led to a soluble but completely inactive enzyme unable to form a tetramer, suggesting that F137 residue may be important for the assembling of the tetramer and also for the arrangement of the CDA active site. Finally, R68G and R68Q mutations revealed that the presence of the amino group seems to be important for the catalytic process but not for substrate binding, as already shown in B. subtilis CDA. The quaternary structure of R68Q was not affected by the mutation, as shown by the SDS‐induced dissociation experiments and CD studies, whereas R68G dissociated very easily in presence of small amounts of SDS. These experiments indicated that in the human CDA, the side chain of arginine 68 involved in the catalytic process in one subunit active site might come from another subunit. The data obtained from these studies confirmed the presence of a complicated set of intersubunit interactions in the active site of human CDA, as shown in other T‐CDAs. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Beyond Lumry–Eyring: An unexpected pattern of operational reversibility/irreversibility in protein denaturation
Authors: Rodriguez‐Larrea David , Ibarra‐Molero Beatriz , de Maria Leonardo , Borchert Torben V. , Sanchez‐Ruiz Jose M. 
Published: July 2007

AbstractWe have found that, contrary to naïve intuition, the degree of operational reversibility in the thermal denaturation of lipase from Thermomyces lanuginosa (an important industrial enzyme) in urea solutions is maximum when the protein is heated several degrees above the end of the temperature‐induced denaturation transition. Upon cooling to room temperature, the protein seems to reach a state with enzymatic activity similar to that of the initial native state, but with higher denaturation temperature and radically different behavior in terms of susceptibility to irreversible denaturation. These results show that patterns of operational reversibility/irreversibility in protein denaturation may be more complex than the often‐taken‐for‐granted, two‐situation classification (reversible vs. irreversible). Furthermore, they are consistent with the possibility of existence of different native or native‐like states separated by high kinetic barriers under native conditions and they suggest experimental procedures to reach and study such “alternative” native states. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A model of the complex between the PfEMP1 malaria protein and the human ICAM‐1 receptor
Authors: Bertonati Claudia , Tramontano Anna 
Published: July 2007

AbstractMalaria is caused by protozoan parasites of the genus Plasmodium. Four species of Plasmodium can infect humans: P. falciparum, P. malariae, P. vivax, and P. ovale. P. falciparum is the only able to cytoadhere to the surface of postcapillary endothelial cells. A key role in cytoadherence is played by the interaction between the PfEMP1 P. falciparum protein and the human intracellular adhesion molecule (ICAM‐1) although very little is known about the molecular details of this complex. Here we propose a model for this interaction on the basis of a homology model of the functional domain of PfEMP1 and of the ICAM‐1 three dimensional structures. Our model is consistent with the results of many experimental observations, provides a rational explanation for the different binding abilities of different strains of P. falciparum and explains the reduced binding affinity of the A4 strain of P. falciparum for the ICAM‐1Kilifi polymorphism. On the basis of our model, we can also explain why the murine ICAM‐1, although sharing 70% sequence similarity with its human homologue, does not bind PfEMP1, and why the binding of fibrinogen and PfEMP1 to ICAM‐1 is mutually exclusive. The model of the complex proposed here can serve as a useful tool for the design and interpretation of biochemical and immunological experimental results. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Modeling survival data with informative cluster size
Authors: Williamson John M. , Kim Hae‐Young , Manatunga Amita , Addiss David G. 
Published: July 2007

AbstractAnalysis of clustered data focusing on inference of the marginal distribution may be problematic when the risk of the outcome is related to the cluster size, termed as informative cluster size. In the absence of censoring, Hoffmanet al.proposed a within‐cluster resampling method, which is asymptotically equivalent to a weighted generalized estimating equations score equation. We investigate the estimation of the marginal distribution for multivariate survival data with informative cluster size using cluster‐weighted Weibull and Cox proportional hazards models. The cluster‐weighted Cox model can be implemented using standard software. Simulation results demonstrate that the proposed methods produce unbiased parameter estimation in the presence of informative cluster size. To illustrate the proposed approach, we analyze survival data from a lymphatic filariasis study in Recife, Brazil. Copyright © 2007 John Wiley & Sons, Ltd.
Increased acylated plasma ghrelin, but improved lipid profiles 24-h after consumption of carob pulp preparation rich in dietary fibre and polyphenols
Authors: Gruendel Sindy , Garcia Ada L. , Otto Baerbel , Wagner Karen , Bidlingmaier Martin , Burget Lukas , Weickert Martin O. , Dongowski Gerhard , Speth Maria , Katz Norbert , Koebnick Corinna 
Published: July 2007

We have recently shown that a polyphenol-rich insoluble dietary fibre preparation from carob pulp (Ceratonia siliqua L; carob fibre) decreased postprandial acylated ghrelin, TAG and NEFA during an acute liquid meal challenge test. However, delayed effects of carob fibre consumption are unknown. Therefore, a randomized controlled crossover study in nineteen healthy volunteers consuming foods with or without 50 g carob fibre was conducted. On the subsequent day (day 2), glucose, TAG, total and acylated ghrelin as well as insulin, NEFA and leptin were assessed at baseline and at timed intervals for 300 min after ingestion of standardized bread. Consumption of carob fibre-enriched foods did not affect fasting concentrations of glucose, TAG, total ghrelin, NEFA, insulin and leptin. Fasting acylated ghrelin was increased on the day subsequent to carob fibre consumption compared with control (P = 0·046). After consumption of the standard bread on day 2, glucose response (P = 0·029) was increased, and TAG (P = 0·033) and NEFA (P < 0·001) responses were decreased compared with control. Postprandial responses of total and acylated ghrelin, insulin and leptin on day 2 were unaffected by carob fibre consumption the previous day. In conclusion, an increase in total and acylated plasma ghrelin accompanied by enhanced lipid metabolism after carob fibre consumption suggests higher lipid utilization and suppressed lipolysis on the day subsequent to carob fibre consumption. However, elevated glucose levels after carob fibre consumption need to be addressed in future studies.
Intake of heterocyclic aromatic amines from meat in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Heidelberg cohort
Authors: Rohrmann Sabine , Zoller Dorothee , Hermann Silke , Linseisen Jakob 
Published: July 2007

It was the aim of the present study to estimate the intake of heterocyclic aromatic amines (HCA) from meat, which have been associated with cancer risk in several epidemiological studies, of 21 462 subjects who participated in the European Prospective Investigation into Cancer and Nutrition (EPIC) in Heidelberg. This was accomplished by using a detailed dietary questionnaire that assessed meat consumption, cooking methods, and degree of browning of the respective food items. Median total HCA intake from meat was 31 ng/d (mean 69 ng/d), which was lower than results observed in previous studies. 2-Amino-1-methyl-6-phenylimidazo[4,5b]pyridine was the most common HCA in this cohort (median 17; mean 48 ng/d). The present study offers the opportunity of a detailed examination of the associations between meat cooking as well as HCA intake from meat and cancer risk in a prospective way.
Failure of contrast enhanced computed tomography scans to identify an orbital abscess. The benefit of magnetic resonance imaging
Authors: Mcintosh D , Mahadevan M 
Published: July 2007

AbstractIntroduction:Acute sinusitis is a relatively common condition, which usually responds to medical therapy. In most cases, there are no sequelae or complications subsequent to this infection. However, like many acute illnesses, there are well documented complications of acute sinusitis, and in particular these include peri-orbital and intracranial spread.Objective:The purpose of this paper is to highlight the importance of vigilance in peri-orbital involvement and the limitations of imaging techniques, such as computed tomography scanning. An illustrative case is presented to demonstrate this.Conclusion:Magnetic resonance imaging scanning is a valuable modality in assessing complex presentations of peri-orbital complications of acute sinusitis.
Acute mastoiditis in children: presentation and long term consequences
Authors: Glynn F , Osman L , Colreavy M , Rowley H , Dwyer T P O , Blayney A 
Published: July 2007

AbstractAcute mastoiditis, a destructive bacterial infection of the mastoid bone and air cell system, is relatively uncommon today but remains a potentially serious condition. There is a lack of information in the literature regarding the long term otological problems that children may face following an episode of this condition.Objectives:Our aim was to examine the presentation, complications and hospital course in this patient population, and to ascertain whether these patients had long term otological problems.Methods:We retrospectively reviewed the medical records of all patients presenting with acute mastoiditis between January 1990 and December 2005. Patients' parents were contacted by telephone and questioned about further otological problems.Results:Twenty-nine patients were included in the study, and 27 of these patients' parents were contactable to complete the telephone questionnaire. Sixty-nine per cent of children had no previous history of acute otitis media prior to presentation. Forty-five per cent of patients had received oral antibiotics prior to presentation. Sixty-two per cent of patients developed complications, i.e. a subperiosteal abscess or failure to respond to medical therapy, resulting in the need for surgical intervention (in the form of incision and drainage of periosteal abscess, cortical mastoidectomy, or grommet insertion). Mean follow up of patients was eight years and one month; five (17 per cent) patients had been followed up for less than one year. Two (7 per cent) patients developed a further episode of mastoiditis within six weeks of initial presentation, both of whom required cortical mastoidectomy. Three (10 per cent) patients had further problems with recurrent acute otitis media, requiring tympanostomy tube insertion. One patient required a modified radical mastoidectomy for cholesteatoma (15 years later). Twenty-two patients (91 per cent) had been followed up for longer than one year; these patients had subjectively normal hearing and were asymptomatic at the time of study.Conclusion:The majority of patients who had suffered an episode of acute mastoiditis had no adverse long term otological sequelae.
New species of the Lepraria neglecta group (Stereocaulaceae, Ascomycota) from Europe
Authors: SLAVÍKOVÁ-BAYEROVÁ Štěpánka , FEHRER Judith 
Published: July 2007

Abstract:Lepraria granulata Slavíková, a new species from Eastern and Central Europe, is described. According to its morphology, ITS sequence and ecology, it belongs to the L. neglecta core group. Lepraria granulata is characterized by producing atranorin and two, so far unidentified, fatty acids (‘granulata unknown 1 & 2’) and phylogenetic analyses show that it is clearly distinguished from previously known species. Two additional taxa, provisionally named Lepraria sp. G and Lepraria sp. BG, are also discussed. According to their morphology and ITS sequences, they also belong to the L. neglecta group. Lepraria sp. G is sister to L. granulata whereas Lepraria sp. BG is basal and well separated from all taxa so far known in the group. Their taxonomic status is not yet entirely clear.
Gyalidea fruticola, a new corticolous lichen from Europe
Authors: SVENSSON Måns , THOR Göran 
Published: July 2007

Abstract:The diminutive species Gyalidea fruticola is described from Central Sweden and northern Italy. It is typically found on decaying bark, on semi-shaded Lonicera spp. in deciduous, mixed deciduous/coniferous or coniferous forests. The species is characterized by its small and pale apothecia, its submuriform ascospores and its habitat preference.