bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationships among sexually transmitted infection, depression, and lifetime violence in a sample of predominantly African American women
Authors: Laughon Kathryn , Gielen Andrea Carlson , Campbell Jacquelyn C. , Burke Jessica , McDonnell Karen , O'Campo Patricia 
Published: July 2007

AbstractThis study was a secondary analysis of the relationships among lifetime experiences of violence, depressive symptoms, substance use, safer sex behaviors use, and past‐year sexually transmitted infection (STI) treatment among a sample of 445 low income, primarily African American women (257 HIV‐, 188 HIV+) reporting a male intimate partner within the past year. Twenty‐one percent of HIV− and 33% of HIV+ women reported past‐year STI treatment. Violence victimization increased women's odds of past‐year STI treatment, controlling for HIV status and age. Depressive symptoms increased, and use of safer sex behaviors decreased, women's odds of past‐year STI treatment. Results suggest that positive assessment for violence and/or depression indicates need for STI screening. © 2007 Wiley Periodicals, Inc. Res Nurs Health 30:413–428, 2007.
Sonocrystallization of polycarbonate melts
Authors: Yoo Youngjae , Park Changhyun , Won Jong Chan , Lee Sung‐Goo , Choi Kil‐Yeong , Lee Jae Heung 
Published: July 2007

AbstractIn this paper, we showed the simplified continuous process to crystallize the polycarbonate (PC) melts using sonocrystallization which is based on ultrasonic cavitation and ‘hot spot’ theory. High power ultrasonic wave was introduced to crystallize the PC prepolymers which is generally used for solid‐state polymerization (SSP) to obtain the ultra‐high molecular weight PCs. The structure and properties of PC treated with ultrasonic wave such as torque changes and crystallinities were studied. The experimental results showed that ultrasonic wave could improve the crystallinities of PCs and sonication time was proportional to their crystallinity. This is attributed to the decrease of the specific volume and the resulting shrinkage is compensated by a flux of a polymer melt toward the crystallization front. Torque data were collected directly from the Haake internal mixer and crystallinities were evaluated from differential scanning calorimeter (DSC). This process is an environmentally benign process so that no additional solvents or treatments are needed and will be very useful in the conventional solid‐state process which is used industrially. Copyright © 2007 John Wiley & Sons, Ltd.
Selective analysis of phenolic compounds in propolis by HPLC‐MS/MS
Authors: Medana Claudio , Carbone Francesco , Aigotti Riccardo , Appendino Giovanni , Baiocchi Claudio 
Published: July 2007

AbstractPhenolic compounds (flavonoids and phenolic acid derivatives) are major active constituents of the resinous fraction of propolis, and also represent its allergenic principles. We have developed a chromatography electrospray ionisation tandem mass spectrometry (HPLC‐ESI‐MS/MS) method to characterise the polyphenolic fraction of propolis rapidly and quali‐quantitatively. With precursor ion scanning, selective detection of caffeic esters was easily achieved, confirming the identification of prenyl caffeate, benzyl caffeate and phenylethyl caffeate by comparison with synthetic standards. The ionisation and fragmentation behaviour of the major propolis flavonoids was rationalised and applied to selected real samples. Taken together, the results of this study show that the introduction of precursor ion analysis leads to a significant improvement in the characterisation of the phenolic fraction of propolis, paving the way to the establishment of a better quality control for this important natural remedy. Copyright © 2007 John Wiley & Sons, Ltd.
Optimisation of supercritical fluid extraction of indole alkaloids from Catharanthus roseus using experimental design methodology—comparison with other extraction techniques
Authors: Verma Arvind , Hartonen Kari , Riekkola Marja‐Liisa 
Published: July 2007

AbstractResponse surface modelling, using MODDE 6 software for Design of Experiments and Optimisation, was applied to optimise supercritical fluid extraction (SFE) conditions for the extraction of indole alkaloids from the dried leaves of Catharanthus roseus. The effects of pressure (200–400 bar), temperature (40–80°C), modifier concentration (2.2–6.6 vol%) and dynamic extraction time (20–60 min) on the yield of alkaloids were evaluated. The extracts were analysed by high‐performance liquid chromatography and the analytes were identified using ion trap‐electrospray ionisation–mass spectrometry. The method was linear for alkaloid concentration in the range 0.18–31 µg/mL. The limits of detection and quantification for catharanthine, vindoline, vinblastine and vincristine were 0.2, 0.15, 0.1 and 0.08 µg/mL and 2.7, 2.0, 1.3 and 1.1 µg/g, respectively. The dry weight content of major alkaloids in the plants were compared using different extraction methods, i.e. SFE, Soxhlet extraction, solid–liquid extraction with sonication and hot water extraction at various temperatures. The extraction techniques were also compared in terms of reproducibility, selectivity and analyte recoveries. Relative standard deviations for the major alkaloids varied from 4.1 to 17.5% in different extraction methods. The best recoveries (100%) for catharanthine were obtained by SFE at 250 bar and 80°C using 6.6 vol% methanol as modifier for 40 min, for vindoline by Soxhlet extraction using dichloromethane in a reflux for 16 h, and for 3′,4′‐anhydrovinblastine by solid–liquid extraction using a solution of 0.5 m sulphuric acid and methanol (3:1 v/v) in an ultrasonic bath for 3 h. Copyright © 2007 John Wiley & Sons, Ltd.
Isoflavones in the rutaceae family: twenty selected representatives of the genera Citrus, Fortunella, Poncirus, Ruta and Severinia
Authors: Koblovská Radka , Macková Zuzana , Vítková Michaela , Kokoška Ladislav , Klejdus Bořivoj , Lapčík Oldřich 
Published: July 2007

AbstractEnzyme‐linked immunosorbent assays in combination with semi‐preparative high‐performance liquid chromatography (HPLC) and analytical HPLC with mass spectroscopy in the selective ion monitoring mode were used for the determination of selected isoflavones, daidzein, genistein, biochanin A and their homologues, in 20 representatives of the Rutaceae family. Species belonging to five genera were studied, namely Citrus, Fortunella, Poncirus, Ruta and Severinia. The enzyme immunoassays used were based on polyclonal antibodies raised against isoflavonoid conjugates with bovine serum albumin (BSA), namely biochanin A‐7‐BSA, daidzein‐7‐BSA, daidzein‐4′‐BSA, genistein‐7‐BSA and genistein‐4′‐BSA. Aglycones as well as glycosides were detected, and methoxyisoflavones appeared to be more abundant than hydoxyisoflavones. The content of individual isoflavonoids ranged from 0 to 2.6 mg/kg (dry weight); the sum of all measured substances reached up to 5.9 mg. Copyright © 2007 John Wiley & Sons, Ltd.
Plant proteome analysis: A 2006 update
Authors: Jorrín Jesús V. , Maldonado Ana M. , Castillejo Ma Angeles 
Published: July 2007

AbstractThis 2006 ‘Plant Proteomics Update’ is a continuation of the two previously published in ‘Proteomics’ by 2004 (Canovas et al., Proteomics 2004, 4, 285–298) and 2006 (Rossignol et al., Proteomics 2006, 6, 5529–5548) and it aims to bring up‐to‐date the contribution of proteomics to plant biology on the basis of the original research papers published throughout 2006, with references to those appearing last year. According to the published papers and topics addressed, we can conclude that, as observed for the three previous years, there has been a quantitative, but not qualitative leap in plant proteomics. The full potential of proteomics is far from being exploited in plant biology research, especially if compared to other organisms, mainly yeast and humans, and a number of challenges, mainly technological, remain to be tackled. The original papers published last year numbered nearly 100 and deal with the proteome of at least 26 plant species, with a high percentage for Arabidopsis thaliana (28) and rice (11). Scientific objectives ranged from proteomic analysis of organs/tissues/cell suspensions (57) or subcellular fractions (29), to the study of plant development (12), the effect of hormones and signalling molecules (8) and response to symbionts (4) and stresses (27). A small number of contributions have covered PTMs (8) and protein interactions (4). 2‐DE (specifically IEF‐SDS‐PAGE) coupled to MS still constitutes the almost unique platform utilized in plant proteome analysis. The application of gel‐free protein separation methods and ‘second generation’ proteomic techniques such as multidimensional protein identification technology (MudPIT), and those for quantitative proteomics including DIGE, isotope‐coded affinity tags (ICAT), iTRAQ and stable isotope labelling by amino acids in cell culture (SILAC) still remains anecdotal. This review is divided into seven sections: Introduction, Methodology, Subcellular proteomes, Development, Responses to biotic and abiotic stresses, PTMs and Protein interactions. Section 8 summarizes the major pitfalls and challenges of plant proteomics.
Surface energetics, dispersion, and nanotribomechanical behavior of POSS/PP hybrid nanocomposites
Authors: Misra Rahul , Fu Bruce X. , Morgan Sarah E. 
Published: July 2007

AbstractHybrid organic–inorganic polymer nanocomposites incorporating polyhedral oligomeric silsesquioxane (POSS) nanoparticles are of increasing interest for high performance materials applications. Octaisobutyl POSS/polypropylene nanocomposites were prepared at varying POSS concentrations via melt blending. The interplay of POSS molecular geometry, composition, and concentration in relation to the tribological, nanomechanical, surface energy, and bulk properties of the nanocomposites were investigated. Ultra‐low friction and enhanced hardness, modulus, and hydrophobicity were observed for the nanocomposite surfaces, with minimal changes in the bulk thermomechanical properties. Parallel AFM, SEM, TEM, and spectroscopic analyses demonstrated significant differences in POSS distribution and aggregation in the surface and the bulk, with preferential segregation of POSS to the surface. Additionally, contact angle studies reveal significant reduction in surface energy and increase in hysteresis with incorporation of POSS nanoparticles. The differences in bulk and surface properties are largely explained by the gradient concentration of POSS in the polymer matrix, driven by POSS/POSS and POSS/polymer interactions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2441–2455, 2007
Sorption and diffusion of normal alkanes through poly(ethylene‐co‐vinyl acetate) membranes
Authors: Kumar S. Anil , Kumaran M. G. , Thomas Sabu 
Published: July 2007

AbstractThe transport behavior of uncrosslinked and crosslinked poly(ethylene‐co‐vinyl acetate) membranes has been investigated using normal alkanes as probe molecules, in the temperature range of 30–60 °C. Benzoyl peroxide was used for crosslinking the matrix. It has been observed that, a critical concentration of crosslinker is necessary for maximum solvent uptake, followed by a decrease at higher concentration. The effect of free volume on liquid transport was investigated by positron annihilation lifetime spectroscopy. The mechanism of transport has been found to deviate from the regular Fickian behavior. The dependence of the transport coefficients on crosslink density, nature of penetrants, and temperature was studied. The polymer–solvent interaction parameter, enthalpy, and entropy of sorption have also been estimated from the transport data. The affine and phantom models for chemical crosslinks were used to predict the nature of crosslinks. Finally, the experimental sorption data were compared with theoretical predictions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2470–2480, 2007
High resolution oligonucleotide CGH using DNA from archived prostate tissue
Authors: Paris Pamela L. , Sridharan Shivaranjani , Scheffer Alicia , Tsalenko Anya , Bruhn Laurakay , Collins Colin 
Published: July 2007

AbstractBackgroundThe current focus on biomarker discovery is a result of an improved understanding of the biological basis for carcinogenesis and advances in technology. Biomarkers can aid in diagnosis, prognosis, treatment selection, and drug development. There is an urgent need for high‐resolution tools that perform well using archived tissue for biomarker discovery and tools that can translate into the clinic.MethodsOligonucleotide array comparative genomic hybridization (oCGH) was compared to BAC‐based aCGH using unamplified total genomic DNA from formalin fixed paraffin‐embedded (FFPE) prostate tissue.ResultsThe copy number aberrations detected with the BAC and oligonucleotide arrays were highly correlated in cases where the arrays contained probes in similar genomic locations. The oligonucleotide array platform provided more precise mapping due to the higher density of oligonucleotide probes.ConclusionsThese results demonstrate the utility of high‐resolution oligonucleotide arrays designed to use genomic DNA for CGH measurements using archived tissue samples for discovery and clinic based assays. Prostate 67: 1447–1455, 2007. © 2007 Wiley‐Liss, Inc.
Classification of conformational stability of protein mutants from 3D pseudo‐folding graph representation of protein sequences using support vector machines
Authors: Fernández Michael , Caballero Julio , Fernández Leyden , Abreu Jose Ignacio , Acosta Gianco 
Published: July 2007

AbstractThis work reports a novel 3D pseudo‐folding graph representation of protein sequences for modeling purposes. Amino acids euclidean distances matrices (EDMs) encode primary structural information. Amino Acid Pseudo‐Folding 3D Distances Count (AAp3DC) descriptors, calculated from the EDMs of a large data set of 1363 single protein mutants of 64 proteins, were tested for building a classifier for the signs of the change of thermal unfolding Gibbs free energy change (ΔΔG) upon single mutations. An optimum support vector machine (SVM) with a radial basis function (RBF) kernel well recognized stable and unstable mutants with accuracies over 70% in crossvalidation test. To the best of our knowledge, this result for stable mutant recognition is the highest ever reported for a sequence‐based predictor with more than 1000 mutants. Furthermore, the model adequately classified mutations associated to diseases of human prion protein and human transthyretin. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Amino acid pairing at the N‐ and C‐termini of helical segments in proteins
Authors: Fonseca Nuno A. , Camacho Rui , Magalhães A. L. 
Published: July 2007

AbstractA systematic survey was carried out in an unbiased sample of 815 protein chains with a maximum of 20% homology selected from the Protein Data Bank, whose structures were solved at a resolution higher than 1.6 Å and with a R‐factor lower than 25%. A set of 5556 subsequences with α‐helix or 310‐helix motifs was extracted from the protein chains considered. Global and local propensities were then calculated for all possible amino acid pairs of the type (i, i + 1), (i, i + 2), (i, i + 3), and (i, i + 4), starting at the relevant helical positions N1, N2, N3, C3, C2, C1, and N‐int (interior positions), and also at the first nonhelical positions in both termini of the helices, namely, N‐cap and C‐cap. The statistical analysis of the propensity values has shown that pairing is significantly dependent on the type of the amino acids and on the position of the pair. A few sequences of three and four amino acids were selected and their high prevalence in helices is outlined in this work. The Glu‐Lys‐Tyr‐Pro sequence shows a peculiar distribution in proteins, which may suggest a relevant structural role in α‐helices when Pro is located at the C‐cap position. A bioinformatics tool was developed, which updates automatically and periodically the results and makes them available in a web site. Proteins 2008. © 2007 Wiley‐Liss, Inc.
A potential molecular switch in an α‐helical coiled coil
Authors: Laughton Charles A. , Luisi Ben F. , Pratap J. Venkatesh , Calladine Chris R. 
Published: July 2007

AbstractThe yeast DNA‐binding protein GCN4 forms a homo‐dimer through a self‐complementary coiled‐coil interface. In this article, we describe how such coiled‐coils might be bistable and, through Molecular Dynamics computations on the GCN4 coiled coil, we show that the coiled coil can indeed switch between the two states by a pathway in which there is a progressive “flipping” of consecutive steps along the interface. We discuss the general implications of potentially bistable coiled‐coil interfaces for allosteric signal‐transmission mechanisms along homo‐dimeric coiled coils and for the packing of helices in globular proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker‐based method
Authors: Joosten Henk‐Jan , Han Ying , Niu Weiling , Vervoort Jacques , Dunaway‐Mariano Debra , Schaap Peter J. 
Published: July 2007

AbstractAspergillus niger produces oxalic acid through the hydrolysis of oxaloacetate, catalyzed by the cytoplasmic enzyme oxaloacetate acetylhydrolase (OAH). The A. niger genome encodes four additional open reading frames with strong sequence similarity to OAH yet only the oahA gene encodes OAH activity. OAH and OAH‐like proteins form subclass of the isocitrate lyase/PEP mutase enzyme superfamily, which is ubiquitous present filamentous fungi. Analysis of function‐specific residues using a superfamily‐based approach revealed an active site serine as a possible sequence marker for OAH activity. We propose that presence of this serine in family members correlates with presence of OAH activity whereas its absence correlates with absence of OAH. This hypothesis was tested by carrying out a serine mutagenesis study with the OAH from the fungal oxalic acid producer Botrytis cinerea and the OAH active plant petal death protein as test systems. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Identification and structural characterization of heme binding in a novel dye‐decolorizing peroxidase, TyrA
Authors: Zubieta Chloe , Joseph Rosanne , Sri Krishna S. , McMullan Daniel , Kapoor Mili , Axelrod Herbert L. , Miller Mitchell D. , Abdubek Polat , Acosta Claire , Astakhova Tamara , Carlton Dennis , Chiu Hsiu‐Ju , Clayton Thomas , Deller Marc C. , Duan Lian , Elias Ylva , Elsliger Marc‐André , Feuerhelm Julie , Grzechnik Slawomir K. , Hale Joanna , Han Gye Won , Jaroszewski Lukasz , Jin Kevin K. , Klock Heath E. , Knuth Mark W. , Kozbial Piotr , Kumar Abhinav , Marciano David , Morse Andrew T. , Murphy Kevin D. , Nigoghossian Edward , Okach Linda , Oommachen Silvya , Reyes Ron , Rife Christopher L. , Schimmel Paul , Trout Christina V. , van den Bedem Henry , Weekes Dana , White Aprilfawn , Xu Qingping , Hodgson Keith O. , Wooley John , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Wilson Ian A. 
Published: July 2007

AbstractTyrA is a member of the dye‐decolorizing peroxidase (DyP) family, a new family of heme‐dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 Å. TyrA is a dimer, with each monomer exhibiting a two‐domain, α/β ferredoxin‐like fold. Both domains contribute to the heme‐binding site. Co‐crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe‐His‐Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structural characterization of native high‐methoxylated pectin using nuclear magnetic resonance spectroscopy and ultraviolet matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Comparative use of 2,5‐dihydroxybenzoic acid and nor‐harmane as UV‐MALDI matrices
Authors: Monge María Eugenia , Negri R. Martín , Kolender Adriana A. , Erra‐Balsells Rosa 
Published: July 2007

AbstractThe successful analysis by ultraviolet matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (UV‐MALDI‐TOF MS) of native and hydrolyzed high‐methoxylated pectin samples is described. In order to find the optimal conditions for UV‐MALDI‐TOF MS analysis several experimental variables were studied such as: different UV‐MALDI matrices (nor‐harmane, 2,5‐dihydroxybenzoic acid), sample preparation methods (mixture, sandwich), inorganic salt addition (doping salts, NaCl, KCl, NH4Cl), ion mode (positive, negative), linear and reflectron mode, etc. nor‐Harmane has never been used as a UV‐MALDI matrix for the analysis of pectins but its use avoids pre‐treatment of the sample, such as an enzymatic digestion or an acid hydrolysis, and there is no need to add salts, making the analysis easier and faster. This study suggested an alternative way of analyzing native high‐methoxylated pectins, with UV‐MALDI‐TOF MS, by using nor‐harmane as the matrix in negative ion mode. The analysis by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy of the native and hydrolyzed pectin is also briefly described. Copyright © 2007 John Wiley & Sons, Ltd.
A liquid chromatography/atmospheric pressure ionization tandem mass spectrometry quantitation method for nevirapine and its two oxidative metabolites, 2‐hydroxynevirapine and nevirapine 4‐carboxylic acid, and pharmacokinetics in baboons
Authors: Liu Zhongfa , Fan‐Havard Patty , Xie Zhiliang , Ren Chen , Chan Kenneth K. 
Published: July 2007

AbstractA rapid highly sensitive and specific electrospray ionization (ESI) liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for quantification of nevirapine (NVP) and its two metabolites, 2‐hydroxynevirapine (2‐OHNVP) and nevirapine 4‐carboxylic acid (4‐CANVP), in baboon serum was developed and validated. Nevirapine, 2‐OHNVP, 4‐CANVP, and the internal standard, hesperetin, were extracted from baboon serum with ethyl acetate. Components in the extract were separated on a 50 × 2.1 mm Aquasil C185 µm stainless steel column by isocratic elution with 40% acetonitrile/0.1% formic acid at a flow rate of 0.2 mL/min. The liquid flow was passed through a pre‐source splitter and 5% of the eluant was introduced into the atmospheric pressure ionization (API) source. The components were analyzed in the multiple‐reaction monitoring (MRM) mode as the precursor/product ion pair ofm/z267.2/226.2 for NVP, 283.0/161.2 for 2‐OHNVP, 297.2/279.2 for 4‐CANVP, and 303.2/177.2 for hesperetin. Linear calibration curves were obtained in the range of 1–1000 ng/mL for NVP and 2‐OHNVP and 5–1000 ng/mL for 4‐CANVP, using 0.2 mL baboon serum, respectively. The within‐day and between‐day precisions were <10% for NVP and 2‐OHNVP, and <11.5% for 4‐CANVP. Due to the similar structures and fragmentation patterns of 2‐OHNVP and 3‐OHNVP, it is not expected that the LC/MS/MS can differentiate 2‐OHNVP and 3‐OHNVP and they were assayed as a composite. The method was applied to a single‐dose escalation study of NVP in non‐pregnant baboons (Papio anubis) to characterize the pharmacokinetics of NVP, 2‐OHNVP plus 3‐OHNVP, and 4‐CANVP, and to determine the appropriate dose necessary to achieve comparable peak serum concentration of NVP as reported in healthy human adults. Copyright © 2007 John Wiley & Sons, Ltd.