bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease proteomics reveals altered basic gene expression regulation in leukocytes of Normal‐Tension and Primary Open‐Angle glaucoma patients
Authors: Golubnitschaja Olga , Yeghiazaryan Kristina , Wunderlich Kerstin , Schild Hans H. , Flammer Josef 
Published: September 2007

AbstractGlaucomatous damage is a neurodegenerative eye disease and one of the leading causes of blindness with 67 million patients worldwide. Major currently challenging questions include early diagnosis, risk evaluation, and follow‐up. Circulating leukocytes have been demonstrated as potentially important source of disease specific markers. The relevance of expression alterations in leukocytes for glaucomatous damage needs to be clarified. Noteworthy, gene expression patterns of trabecular meshwork and Schlemm's canal, which are anatomically and functionally highly relevant for glaucoma pathology, were shown to be similar to those of circulating leukocytes. Here, we report extensive alterations in characteristic protein expression patterns of circulating leukocytes for Normal‐Tension and Primary Open‐Angle Glaucoma, as revealed by analysis of 2‐D PAGE images. Among most conservative alterations we found the protein spot identified by MALDI‐TOF as basic transcription factor activating protein‐2beta (AP‐2β). Western‐blot analysis demonstrated significantly increased protein expression rates of AP‐2β in both Normal‐Tension and Primary Open‐Angle Glaucoma versus controls. AP proteins are essential factors of the basic transcription regulation; AP‐2 proteins play a decisive role, particularly, in morphogenesis of eye. Conservative AP‐2 up‐regulation is of special importance in terms of basic transcriptional dysregulation that might be specific for glaucoma disease.
Vascular proteomics
Authors: Vivanco Fernando , Mas Sebastian , Darde Veronica M. , De la Cuesta Fernando , Alvarez‐Llamas Gloria , Barderas Maria G. 
Published: September 2007

AbstractThe characterization of patients with acute coronary syndromes (ACS) at the molecular and cellular levels provides a novel vision for understanding the pathological and clinical expression of the disease. Recent advances in proteomic technologies permit the evaluation of systematic changes in protein expression in many biological systems and have been extensively applied to cardiovascular diseases (CVD). The cardiovascular system is in permanent intimate contact with blood, making blood‐based biomarker discovery a particularly worthwhile approach. Thus, proteomics can potentially yield novel biomarkers reflecting CVD, establish earlier detection strategies, and monitor response to therapy. Here we review the different proteomic strategies used in the study of atherosclerosis and the novel proteins differentially expressed and secreted by atherosclerotic lesions which constitute novel potential biomarkers (HSP‐27, Cathepsin D). Special attention is paid to MS‐Imaging of atheroma plaque and the generation, for the first time, of 2‐D images of lipids, showing the distribution of these molecules in the different areas of the atherosclerotic lesions. In addition new potential biomarkers have been identified in plasma (amyloid A1α, transtherytin), circulating cells (protein profile in monocytes from ACS patients) and individual cells constituents of atheroma plaques (endothelial, VSMC, macrophages) which provide novel insights into vascular pathophysiology.
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins
Authors: Pereira de Araújo Antônio F. , Gomes Antonio L. C. , Bursztyn Alexandre A. , Shakhnovich Eugene I. 
Published: September 2007

AbstractWe investigate the possibility that atomic burials, as measured by their distances from the structural geometrical center, contain sufficient information to determine the tertiary structure of globular proteins. We report Monte Carlo simulated annealing results of all‐atom hard‐sphere models in continuous space for four small proteins: the all‐β WW‐domain 1E0L, the α/β protein‐G 1IGD, the all‐α engrailed homeo‐domain 1ENH, and the α + β engineered monomeric form of the Cro protein 1ORC. We used as energy function the sum over all atoms, labeled by i, of |Ri − R|, where Ri is the atomic distance from the center of coordinates, or central distance, and R is the “ideal” central distance obtained from the native structure. Hydrogen bonds were taken into consideration by the assignment of two ideal distances for backbone atoms forming hydrogen bonds in the native structure depending on the formation of a geometrically defined bond, independently of bond partner. Lowest energy final conformations turned out to be very similar to the native structure for the four proteins under investigation and a strong correlation was observed between energy and distance root mean square deviation (DRMS) from the native in the case of all‐β 1E0L and α/β 1IGD. For all α 1ENH and α + β 1ORC the overall correlation between energy and DRMS among final conformations was not as high because some trajectories resulted in high DRMS but low energy final conformations in which α‐helices adopted a non‐native mutual orientation. Comparison between central distances and actual accessible surface areas corroborated the implicit assumption of correlation between these two quantities. The Z‐score obtained with this native‐centric potential in the discrimination of native 1ORC from a set of random compact structures confirmed that it contains a much smaller amount of native information when compared to a traditional contact Go potential but indicated that simple sequence‐dependent burial potentials still need some improvement in order to attain a similar discriminability. Taken together, our results suggest that central distances, in conjunction to physically motivated hydrogen bond constraints, contain sufficient information to determine the native conformation of these small proteins and that a solution to the folding problem for globular proteins could arise from sufficiently accurate burial predictions from sequence followed by minimization of a burial‐dependent energy function. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Exploiting 3D structural templates for detection of metal‐binding sites in protein structures
Authors: Goyal Kshama , Mande Shekhar C. 
Published: September 2007

AbstractHigh throughput structural genomics efforts have been making the structures of proteins available even before their function has been fully characterized. Therefore, methods that exploit the structural knowledge to provide evidence about the functions of proteins would be useful. Such methods would beneeded to complement the sequence‐based function annotation approaches. The current study describes generation of 3D‐structural motifs for metal‐binding sites from the known metalloproteins. It then scans all the available protein structures in the PDB database for putative metal‐binding sites. Our analysis predicted more than 1000 novel metal‐binding sites in proteins using three‐residue templates, and more than 150 novel metal‐binding sites using four‐residue templates. Prediction of metal‐binding site in a yeast protein YDR533c led to the hypothesis that it might function as metal‐dependent amidopeptidase. The structural motifs identified by our method present novel metal‐binding sites that reveal newer mechanisms for a few well‐known proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands
Authors: Cheng Feng , Wang Qinghua , Chen Mingzhi , Quiocho Florante A. , Ma Jianpeng 
Published: September 2007

AbstractHuman fatty acid synthase (hFAS) thioesterase domain (TE) is an attractive drug target to treat obesity and cancer. On the basis of the recently published crystal structure of TE domain of hFAS, we performed molecular surface analysis and docking study to characterize the molecular interactions between the enzyme and its various ligands. Surface analysis identified the ligand‐binding pocket of TE domain that encompasses the catalytic triad of Ser2308, His2481, Asp2338. Docking of palmitate, the main biological product of hFAS, into this pocket revealed the ligand‐binding mode, in which the hydrophobic interactions are the dominant driving forces. The catalytic mechanism of TE domain can also be well explained based on the generated TE‐palmitate complex structure. Moreover, the comparison of the binding modes of five fatty acids with chain lengths ranging from 12 to 20 carbons confirmed that the ligand binding pocket of TE domain is a decisive factor in chain length specificity. In addition, docking of two known TE inhibitors, c75 and orlistat revealed the pharmacophore of these hFAS TE inhibitors, which will prove useful in structure‐based drug design against this important target. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Design of serine proteinase inhibitors by combinatorial chemistry using trypsin inhibitor SFTI‐1 as a starting structure
Authors: Zabłotna Ewa , Jaśkiewicz Anna , Łęgowska Anna , Miecznikowska Hanna , Lesner Adam , Rolka Krzysztof 
Published: September 2007

AbstractA small peptide library of monocyclic SFTI‐1 trypsin inhibitor from sunflower seeds modified in positions P1 and P4′ was synthesized using a portioning‐mixing method. The peptide library was deconvoluted by the iterative approach in solution. Two trypsin ([Met9]‐SFTI‐1 and [Arg5, Abu9]‐SFTI‐1), one chymotrypsin ([Phe5]‐SFTI‐1) and one human elastase ([Leu5, Trp9]‐SFTI‐1) inhibitors were selected and resynthesized. The values of their association equilibrium constants (Ka) with target enzymes indicate that they are potent inhibitors. In addition, the last two analoges belong to the most active inhibitors of this size. The results obtained show that the conserved Pro9 residue in the Bowman–Birk inhibitor (BBI)s is not essential for inhibitory activity. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Structure and thermoelectric properties of nanocomposite bismuth telluride prepared by melt spinning or by partially alloying with IV–VI compounds
Authors: Ebling Dirk G. , Jacquot A. , Jägle M. , Böttner H. , Kühn U. , Kirste L. 
Published: September 2007

AbstractBismuth telluride samples are compared with respect to the evolution of their thermoelectric material parameters like thermal and electrical conductivity. The Seebeck coefficient is discussed in dependence on the melt spinning fabrication technique. The melt spinner used is only able to produce small thin ribbon shaped specimens, some as thin as 10 μm. This limits melt spinning to mainly production of research specimens for alloys with high critical cooling rate, which are difficult to fabricate with other techniques. Additional parameters are alloying or doping of the base material by comparing the properties as prepared to different annealing conditions. The intrinsic p‐ and n‐doped material was alloyed with up to 0.5% lead telluride by rapidly cooling the bulk material to improve the thermoelectric properties analysed from RT up to about 600 K. A Seebeck coefficient of well above 200 µV/K could be obtained for p‐ and n‐type materials. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification and relative quantification of fatty acids in Escherichia coli membranes by gas chromatography/mass spectrometry
Authors: Oursel Delphine , Loutelier‐Bourhis Corinne , Orange Nicole , Chevalier Sylvie , Norris Victor , Lange Catherine M. 
Published: September 2007

AbstractThe lipids that are essential to the functioning of the bacterial membrane exist in hundreds of different forms. The reasons for this diversity are far from clear but are presumably related to the roles of these lipids in both facilitating enzymic activities and generating proteolipid domains. A full understanding of bacterial physiology therefore requires characterization of lipids in different strains in a variety of environmental conditions. This characterization then becomes the basis for lipidomics, the lipid aspect of the growing field of metabolomics. To exploit the power of derivatization chemistry and of gas chromatography/mass spectrometry (GC/MS) and tandem mass spectrometry (MS/MS) for metabolomics studies, we report here the development of various GC/MS electron ionization (EI) and negative and positive chemical ionization (CI) methods for the identification and, for the first time, the relative quantification of fatty acids present in extracts from membranes of a laboratory strain of Escherichia coli. They consist of seven saturated fatty acids (C10:0, C12:0, C14:0, C15:0, C16:0, C17:0 and C18:0) and six unsaturated fatty acids (C16:1, cyC17:0 plus two isomers of C18:1, C18:2 and cyC19:0). Copyright © 2007 John Wiley & Sons, Ltd.
Determination of 13C isotopic enrichment of glutathione and glycine by gas chromatography/combustion/isotope ratio mass spectrometry after formation of the N‐ or N,S‐ethoxycarbonyl methyl ester derivatives
Authors: Tea Illa , Ferchaud‐Roucher Véronique , Küster Alice , Darmaun Dominique , Robins Richard J. 
Published: September 2007

AbstractThe depletion of glutathione (GSH) reported in very‐low‐birth‐weight infants is implicated in several pathologies, especially if deficiency occurs during foetal development. The cause of this depletion is suggested to be modification of GSH turnover. To probe the role of GSH, a reliable non‐invasive method adapted to very‐low‐birth‐weight infants is required. In this paper, we report the preparation of the N,S‐ethoxycarbonyl methyl ester derivatives of GSH and glycine and their application to the measurement of 13C/12C ratios at natural abundance in erythrocyte samples by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). The technique allowed the determination of 13C/12C ratios at natural abundance with a precision <3% and within‐day and between‐day variabilities both <4%. The method is able to determine accurately low 13C‐enrichments in GSH (0.00241 to 0.00753 Atom Percent Excess) in erythrocyte extracts following incubation with 13C‐glycine at low specific enrichment (approx. 1.5 atom %). Excellent agreement was obtained between the calculated GSH fractional synthesis rate (FSR) in human adult blood (approx. 300% day−1) using the low‐enrichment 13C‐glycine/GC/C/IRMS protocol and that using highly enriched 13C‐glycine (99 atom %)/GC/MS with the same derivative. The GC/C/IRMS method was shown to be suitable to measure the in vitro GSH FSR (200–660% day−1) in human venous and arterial blood from the umbilical cord. This approach provides a good tool for studying the turnover of GSH in vitro in infants, allowing both the use of minimal amounts of tracer and negligible perturbation of endogenous precursor pools. Copyright © 2007 John Wiley & Sons, Ltd.
From marginality to legitimate peripherality: Understanding the essential functions of a women's program
Authors: Kahveci Ajda , Southerland Sherry A. , Gilmer Penny J. 
Published: September 2007

AbstractThe focus of this research was to understand how a program for women in science, mathematics, and engineering (SM&E) at college level in the southeastern United States functioned to influence women's decision making in terms of participation in these fields. By employing Lave and Wenger's theory of situated learning, we explored this program through two and a half academic years. We utilized a qualitative–quantitative mixed approach in our methodology. For the case study aspect, we focused on the cases of three women participating in the support program via participant observations and in‐depth interviews. For a more general description, we developed a questionnaire and augmented this with interviews with a broad spectrum of students. Our findings illustrated that the program demonstrated a great potential to aid the traditionally marginalized to move from marginality to legitimate participation in the communities of science. The program functioned successfully in four ways, each interwoven with the others. One implication of these findings is that such programs should include a multitude of events and opportunities for cognitive, social, and emotional support. Being not tall orders financially, such programs may be considered as effective interventions in both national and international settings, where women are in disadvantaged status. © 2007 Wiley Periodicals, Inc. Sci Ed 92:33–64, 2008
Ultrashallow depth profiling using SIMS and ion scattering spectroscopy
Authors: Kataoka Y. , Itani T. 
Published: September 2007

AbstractThe accuracy of ultrashallow depth profiling was studied by secondary ion mass spectrometry (SIMS) and high‐resolution Rutherford backscattering spectroscopy (HRBS) to obtain reliable depth profiles of ultrathin gate dielectrics and ultrashallow dopant profiles, and to provide important information for the modeling and process control of advanced complimentary metal‐oxide semiconductor (CMOS) design. An ultrathin Si3N4/SiO2 stacked layer (2.5 nm) and ultrashallow arsenic implantation distributions (3 keV, 1 × 1015 cm−2) were used to explore the accuracy of near‐surface depth profiles measured by low‐energy O2+ and Cs+ bombardment (0.25 and 0.5 keV) at oblique incidence. The SIMS depth profiles were compared with those by HRBS. Comparison between HRBS and SIMS nitrogen profiles in the stacked layer suggested that SIMS depth profiling with O2+ at low energy (0.25 keV) and an impact angle of 78° provides accurate profiles. For the As+‐implanted Si, the HRBS depth profiles clearly showed redistribution in the near‐surface region. In contrast, those by the conventional SIMS measurement using Cs+ primary ions at oblique incidence were distorted at depths less than 5 nm. The distortion resulted from a long transient caused by the native oxide. To reduce the transient behavior and to obtain more accurate depth profiles in the near‐surface region, the use of O2+ primary ions was found to be effective, and 0.25 keV O2+ at normal incidence provided a more reliable result than Cs+ in the near‐surface region. Copyright © 2007 John Wiley & Sons, Ltd.
Grain characterization of nanostructured TiN coatings prepared by reactive plasma spraying
Authors: Zou Dongli , Yan Dianran , Xiao Lisong , Dong Yanchun , Zhen Liang 
Published: September 2007

AbstractNanostructured TiN coatings were prepared by reactive plasma spraying, and the microstructure and the grain morphology of the coatings were analyzed by XRD, SEM and TEM. The results show that the coatings were mainly composed of TiN and Ti3O phases (other phases were not detected), and they had the typical sprayed lamellar structures with few pores being visible. In the planar view, nanoscale grains with particle diameters ranging from 60 to 120 nm were observed in the coatings, and both fine equiaxial and columnar grains were found in some zones of the coatings. But in the cross‐sectional view, the TiN coatings were mainly composed of columnar grains, with no qualities of equiaxial grains being found. Thus, it can be concluded that the TiN coatings are composed of columnar grains, and the columnar grains are nanostructural, equiaxial grains in their cross‐section. Copyright © 2007 John Wiley & Sons, Ltd.
Combined IR and XPS analysis of the native (1 0 0) surface of single‐crystalline silicon after HFaq etching
Authors: Cerofolini G. F. , Giussani A. , Carone Fabiani F. , Modelli A. , Mascolo D. , Ruggiero D. , Narducci D. , Romano E. 
Published: September 2007

AbstractA combined analysis, based on angle‐resolved X‐ray photoelectron spectroscopy and multiple‐internal‐reflection infrared spectroscopy, of the (1 0 0) silicon surface after etching in dilute aqueous solution of HF is presented. The analysis shows that the surface is mainly formed by a heterogeneous distribution of SiH, SiH2 and SiH3 terminations, but contains (in addition to sub‐stoichiometric oxidized silicon) a form of reduced silicon, not consistent with the currently accepted picture of the native HFaq‐etched surface. Copyright © 2007 John Wiley & Sons, Ltd.
Use of instrumental variables in the analysis of generalized linear models in the presence of unmeasured confounding with applications to epidemiological research
Authors: Johnston K. M. , Gustafson P. , Levy A. R. , Grootendorst P. 
Published: September 2007

AbstractA major, often unstated, concern of researchers carrying out epidemiological studies of medical therapy is the potential impact on validity if estimates of treatment are biased due to unmeasured confounders. One technique for obtaining consistent estimates of treatment effects in the presence of unmeasured confounders is instrumental variables analysis (IVA). This technique has been well developed in the econometrics literature and is being increasingly used in epidemiological studies. However, the approach to IVA that is most commonly used in such studies is based on linear models, while many epidemiological applications make use of non‐linear models, specifically generalized linear models (GLMs) such as logistic or Poisson regression. Here we present a simple method for applying IVA within the class of GLMs using the generalized method of moments approach. We explore some of the theoretical properties of the method and illustrate its use within both a simulation example and an epidemiological study where unmeasured confounding is suspected to be present. We estimate the effects of beta‐blocker therapy on one‐year all‐cause mortality after an incident hospitalization for heart failure, in the absence of data describing disease severity, which is believed to be a confounder. Copyright © 2007 John Wiley & Sons, Ltd.
Designing a resource broker for heterogeneous grids
Authors: Venugopal Srikumar , Nadiminti Krishna , Gibbins Hussein , Buyya Rajkumar 
Published: September 2007

AbstractGrids provide uniform access to aggregations of heterogeneous resources and services such as computers, networks and storage owned by multiple organizations. However, such a dynamic environment poses many challenges for application composition and deployment. In this paper, we present the design of the Gridbus Grid resource broker that allows users to create applications and specify different objectives through different interfaces without having to deal with the complexity of Grid infrastructure. We present the unique requirements that motivated our design and discuss how these provide flexibility in extending the functionality of the broker to support different low‐level middlewares and user interfaces. We evaluate the broker with different job profiles and Grid middleware and conclude with the lessons learnt from our development experience. Copyright © 2007 John Wiley & Sons, Ltd.
Influence of Citric Acid on the Properties of Glycerol‐plasticized dry Starch (DTPS) and DTPS/Poly(lactic acid) Blends
Authors: Wang Ning , Yu Jiugao , Chang Peter R. , Ma Xiaofei 
Published: September 2007

AbstractIn the presence of citric acid (CA), one‐step extrusion processing is used to prepare poly(lactic acid)/thermoplastic dry starch (PLA/DTPS) blends (50/50, %, w/w) in a single‐screw extruder. The rheological study proves that CA decreases the viscosity of both DTPS and of DTPS/PLA blends. The low viscosity increases the dispersion and decreases the interfacial tension between DTPS and PLA, as shown by scanning electron microscopy (SEM). In the presence of CA, the tensile strength of DTPS/PLA reaches 41 MPa—similar to that of pure PLA—because of improved dispersion and compatibility. At the same time, CA increases not only the degradation of starch, but also the interaction between DTPS and PLA, as detected by Fourier transform infrared (FTIR) spectroscopy. The blend containing CA has a higher thermal stability. The water absorption of DTPS and DTPS/PLA blends is also studied.