bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of BIATECH‐54 standard mixtures for assessment of protein identification and relative expression
Authors: Kolker Eugene , Hogan Jason M. , Higdon Roger , Kolker Natali , Landorf Elizabeth , Yakunin Alexander F. , Collart Frank R. , van Belle Gerald 
Published: September 2007

AbstractMixtures of known proteins have been very useful in the assessment and validation of methods for high‐throughput (HTP) MS (MS/MS) proteomics experiments. However, these test mixtures have generally consisted of few proteins at near equal concentration or of a single protein at varied concentrations. Such mixtures are too simple to effectively assess the validity of error rates for protein identification and differential expression in HTP MS/MS studies. This work aimed at overcoming these limitations and simulating studies of complex biological samples. We introduced a pair of 54‐protein standard mixtures of variable concentrations with up to a 1000‐fold dynamic range in concentration and up to ten‐fold expression ratios with additional negative controls (infinite expression ratios). These test mixtures comprised 16 off‐the‐shelf Sigma–Aldrich proteins and 38 Shewanella oneidensis proteins produced in‐house. The standard proteins were systematically distributed into three main concentration groups (high, medium, and low) and then the concentrations were varied differently for each mixture within the groups to generate different expression ratios. The mixtures were analyzed with both low mass accuracy LCQ and high mass accuracy FT‐LTQ instruments. In addition, these 54 standard proteins closely follow the molecular weight distributions of both bacterial and human proteomes. As a result, these new standard mixtures allow for a much more realistic assessment of approaches for protein identification and label‐free differential expression than previous mixtures. Finally, methodology and experimental design developed in this work can be readily applied in future to development of more complex standard mixtures for HTP proteomics studies.
Proteome, salicylic acid, and jasmonic acid changes in cucumber plants inoculated with Trichoderma asperellum strain T34
Authors: Segarra Guillem , Casanova Eva , Bellido David , Odena Maria Antonia , Oliveira Eliandre , Trillas Isabel 
Published: September 2007

AbstractTrichoderma spp. is one of the most commonly used biological control agents against plant pathogens. This fungus produces changes in plant metabolism, thus increasing growth and enhancing resistance to biotic and abiotic stresses. However, its modes of action remain to be defined. In the first hours of interaction between cucumber plant roots and Trichoderma asperellum strain T34, salicylic and jasmonic acid levels and typical antipathogenic peroxidase activity increase in the cotyledons to different degrees depending on the applied concentration of the fungi. The use of 2‐DE protein profiling and MS analysis allowed us to identify 28 proteins whose expression was affected in cotyledons after cucumber root colonization by Trichoderma applied at high concentrations: 17 were found to be up‐regulated while 11 were down‐regulated. Proteins involved in ROS scavenging, stress response, isoprenoid and ethylene biosynthesis, and in photosynthesis, photorespiration, and carbohydrate metabolism were differentially regulated by Trichoderma. The proteome changes found in this study help to give an understanding of how Trichoderma‐treated plants become more resistant to pathogen attacks through the changes in expression of a set of defence‐oriented proteins which can directly protect the plant or switch the metabolism to a defensive, nonassimilatory state.
Why colchicine does not show mutarotation. With M05‐2X density functional in the realm of tricky natural products
Authors: Pietra Francesco 
Published: September 2007

AbstractIt is shown here that density functional theory (DFT) calculations with the recent M05‐2X hybrid functional correctly reproduced the conformation of, and energy difference between, (Ra,7S)‐ and (Sa,7S)‐type atropisomers of isocolchicine. Interconversion of these 1H NMR‐observable atropisomers accounts for mutarotation with this compound. In contrast, the classical B3LYP hybrid functional failed to simulate satisfactorily both the geometries and the energies involved. This extends the use of M05‐2X to natural products that embody aromatic and flexible pseudoaromatic and saturated rings, as well as cis/trans amide chains, which bring on subtle conformational problems. DFT calculations with M05‐2X also shed new light on a long‐date conundrum in organic chemistry and pharmacology, i.e., why mutarotation was never observed with colchicine. This is now best attributed to a larger energy gap between the (Ra,7S) atropisomer and the elusive (Sa,7S) atropisomer with this compound. These results solicit a rethinking of the interactions between colchicinoids and proteins. Copyright © 2007 John Wiley & Sons, Ltd.
Focused ion beam micromachining and computation of polymeric photonic band gap
Authors: Pialat E. , Trigaud T. , Moliton J. P. , Thévenot M. 
Published: September 2007

AbstractThis article introduces a new approach to the achievement of low cost devices for optical telecommunications. For this purpose, the implementation of polymer components and of the WDM method show several advantages. A polymeric photonic band gap lattice can effectively assume demultiplexing at the wavelength of 1.55 μm without energy dissipation. First, the computation of the geometrical parameters designing a polymer photonic crystal by means of the finite‐difference‐time‐domain method, implemented with Bloch functions, is presented here. Second, the achievement of 2D polymer lattices by a dry process, the focused ion beam milling, is exposed. The experimental conditions for the achievement of a master are discussed on the basis of the milling performances and of the polymers physical properties. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2993–3002, 2007
Cure temperature influence on natural rubber—A small angle X‐ray scattering study
Authors: Salgueiro W. , Somoza A. , Torriani I. L. , Marzocca A. J. 
Published: September 2007

AbstractTo analyze the natural rubber behavior during vulcanization under different cure treatments, an experimental investigation using small angle X‐ray scattering was performed. To achieve this, a set of samples were prepared using sulfur and N‐t‐butyl‐2‐benzothiazole sulfenamide as accelerator and then cured at temperatures between 403 and 463 K reaching their optimum mechanical properties considering rheometer tests. The crosslink density of the samples was evaluated by means of the swelling technique in solvent. In the usual Lorentz corrected representation of the X‐ray scattered intensity, a maximum was observed in the plots corresponding to the cured samples, revealing a highly correlated structure. This maximum shifted toward higher values of the scattering vector when the cure temperature of the samples increased. This behavior is discussed in terms of the crosslinks type present in the vulcanized rubber network at different cure temperatures. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2966–2971, 2007
Plasma Processing of Propane at Hyper‐Atmospheric Pressure: Experiment and Modelling
Authors: Hill Sarah L. , Whitehead J. Christopher , Zhang Kui 
Published: September 2007

AbstractA dielectric packed‐bed plasma reactor was used for the destruction of propane in air and was successfully created and maintained at higher than atmospheric pressure (3 bar). The effects of pressure, REF and SED on propane removal and NOx production are discussed. An increase in SED enhances propane destruction and increases NOx production. Increasing the pressure to 3 bar produces a more efficient removal process with an energy of 877 and 600 eV per molecule at 1 and 3 bar, respectively. The pressure increase also altered the ratio of NO2 to NO produced from ≈1 to >3, showing that substantially more NO2 than NO is produced in a 3 bar air discharge.
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Early intervention in CF: How to monitor the effect
Authors: Weiser Giora , Kerem Eitan 
Published: September 2007

AbstractEarly and aggressive therapy already at the stage when no apparent signs of significant lung disease are detectable, may delay the development and progression of cystic fibrosis (CF). Identification of markers for early pulmonary disease in CF is crucial to monitor adherence to preventive therapy and determine its success. Currently several surrogate markers are available that are used in both the decision making and evaluation of the timing and success of early intervention namely, pulmonary function tests (PFT), microbial cultures, imaging techniques, inflammatory markers, serological markers, and several general signs such as exacerbation rate and nutritional status. This review will present the current status and discuss the significance of their application as well as their limitations for patients with CF and no apparent pulmonary disease. 2007;42:1002–1007. © 2007 Wiley‐Liss, Inc.
Reliability of antibodies to Candida methionine synthase for diagnosis, prognosis and risk stratification in systemic candidiasis: A generic strategy for the prototype development phase of proteomic markers
Authors: Pitarch Aida , Nombela César , Gil Concha 
Published: September 2007

AbstractTo be able to diagnose systemic candidiasis (SC) and to predict outcomes in SC patients are still challenging tasks for physicians. Previous proteomic studies suggest that anti‐Candida methionine synthase (Met6p) IgG antibodies may be a candidate marker for SC. To evaluate their reliability for diagnosis, prognosis and risk stratification in SC, we developed a generic prototype strategy for their measurement in SC. Receiver‐operating‐characteristic curve analyses revealed a high diagnostic accuracy for this prototype format, which was slightly better to that for the widely used Western blot assays. Multivariate logistic‐regression models showed a positive association between serum anti‐Met6p IgG antibody levels and SC risk that was independent from established SC risk factors and other baseline variables. After adjusting for and stratifying according to known prognostic factors, a significant trend toward a lower two‐month mortality risk with increasing levels was evidenced in SC patients at presentation. We conclude that these antibodies may be useful in discriminating SC from non‐SC patients and determining risk stratification in SC. These may also confer protection against SC and be valuable for the design of future immunotherapies. Furthermore, our prototype format has the potential to make impact on other infectious diseases, cancers, allergies or autoimmune disorders.
Imidacloprid mobility and longevity in soil columns at a termiticidal application rate
Authors: Peterson Chris J 
Published: September 2007

AbstractThe mobility, longevity and termiticidal activity of imidacloprid (Premise® 2 termiticide; Bayer Environmental Sciences) at the termiticidal labeled rate for perimeter treatment were tested in vegetated and non‐vegetated soil columns in two tests: in cone plots and in polyvinyl chloride (PVC) pipes. Imidacloprid content in the cone plot eluate peaked at 1 month, declined rapidly by the second month and then entered a lagging phase. The concentration of imidacloprid in the cone plot soil declined from 84.5 µg g−1 initially to 7.5 µg g−1 (non‐vegetated plots) and 8.1 µg g−1 (vegetated plots) 6 months later. Neither eluate concentration nor soil concentration was affected by the presence of vegetation in the cone plots. In the PVC pipes, the top 15 cm of which was treated with Premise® 2 at the perimeter labeled rate, imidacloprid half‐life was estimated at 6–9 months for vegetated and non‐vegetated soil. Extractable imidacloprid declined more rapidly in the first 15 months than afterwards. Mobility of imidacloprid into lower, untreated soil depths was higher in non‐vegetated pipes, and was likely due to the effect of vegetation on soil moisture. The presence of vegetation had little effect on the termiticidal activity of treated soil in the PVC pipes. Published in 2007 by John Wiley & Sons, Ltd.
The potential environmental impact of pesticides removed from sprayers during cleaning
Authors: Ramwell Carmel T , Leak Jennifer , Cooper Simon E , Taylor William A 
Published: September 2007

AbstractBACKGROUND: There is concern that pesticide residues on the external surfaces of sprayers could have an adverse impact on the environment if they are washed off, yet there is a need to remove these residues for health reasons. The aim of this study was to quantify pesticide residues contained in washings from cleaning discrete parts of a sprayer and to assess their likely environmental impact.RESULTS: The boom/rear of the sprayer and the spray tank accounted for 80% of the total pesticide load in the washings. Predicted environmental pesticide concentrations from sprayer washings were lower than predictions from the FOCUS surface water model for pesticides used under normal agricultural conditions, although for tebuconazole this difference was smaller than for the other compounds investigated. The field area over which the residues may need to be uniformly deposited to avoid overdosing during infield cleaning was typically less than 0.5 m2, with a maximum value of 4 m2.CONCLUSIONS: It is unlikely that infield cleaning will lead to overdosing. External residues are not insignificant, so any adverse impact on the environment must be mitigated. Appropriate measures include cleaning in the field away from surface waters and other sensitive areas, and cleaning machines over bunded areas or similar. © Crown copyright 2007. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Glycosylated foldamers: synthesis of carbohydrate‐modified β3hSer and incorporation into β‐peptides
Authors: Norgren Anna S. , Norberg Thomas , Arvidsson Per I. 
Published: September 2007

AbstractFmoc‐protected β3hserine (β3hSer) was prepared and O‐linked to suitably protected N‐acetylgalactosamine (GalNAc) and N‐acetylglucosamine (GlcNAc) derivatives. Glycosylation of β3hSer was made by two independent routes: either by direct glycosyl linkage to the β3hSer, or linkage to natural L‐Ser and then utilizing the carbohydrate moiety as a protecting group in an Arndt–Eistert homologation. Both procedures gave the novel glycosylated β3‐amino acids Fmoc‐β3hSer(α‐D‐GalNAc(Ac)3)‐OH (1a), its β‐anomer (1b), and Fmoc‐β3hSer(β‐D‐GlcNAc(Ac)3)‐OH (2), which were utilized in the solid‐phase peptide synthesis of four glycosylated dipeptides (3a–d) and two heptapeptides (4a–b). The preparation of β‐amino acids bearing common post‐translational modifiers represents an important step towards functionalized foldamers with broad applications in biomedical research. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Validation of a solid‐phase‐bound steroid scaffold for the synthesis of novel cyclic peptidosteroids
Authors: Bodé Catherine A. , Muller Claude P. , Madder Annemieke 
Published: September 2007

AbstractThe current article reports on the synthesis of a new type of cyclic peptidosteroid, in which a bile‐acid‐based scaffold was used for the conformational restriction of a loop‐like peptide. Convergent coupling of two tetrapeptides to the non‐peptidic steroidal entity was carried out once in the classical C‐to‐N and once in the non‐classical N‐to‐C direction. Peptide backbone cyclisation was then carried out, giving rise to a ring size equivalent to approximately 12 amino acids. This type of construct will be used in the development of a peptide vaccine against measles. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Robert Robinson and penicillin: an unnoticed document in the saga of its structure
Authors: Curtis Rachel , Jones John 
Published: September 2007

AbstractA description and commentary is given for an unnoticed sheet of formulae and arguments in the hand of Robert Robinson concerning the structure of penicillin. In this undated document, probably of Autumn 1944, he set out his arguments for favouring a thiazolidine‐oxazolone structure over the actual β‐lactam structure. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Hepta and octapeptide agonists of protease‐activated receptor 2
Authors: Devlin Mark G. , Pfeiffer Bernhard , Flanagan Bernadine , Beyer Renée l. , Cocks Thomas M. , Fairlie David P. 
Published: September 2007

AbstractProtease‐activated receptor 2 (PAR2) is a G protein‐coupled cell surface receptor for trypsin‐like enzymes. Proteolytic cleavage at a specific site in the extracellular N‐terminus exposes a receptor‐activating sequence, the ‘tethered ligand’, which binds intramolecularly to initiate receptor signalling. Peptide or small molecule agonists for PAR2, devoid of the non‐specific and proteolytic effects of enzyme activators, may be promising therapeutic agents for proliferative and inflammatory diseases reportedly mediated by PAR2. Synthetic hexapeptides that correspond to the native tethered ligand of human or rodent PAR2 (SLIGKV and SLIGRL, respectively) can activate the receptor independently of proteolytic cleavage; however, known peptide agonists have much lower potency compared to protease‐mediated activation. Here, we investigated the agonist activity of 94 hepta and octapeptide derivatives of the human and rodent PAR2‐tethered ligand sequences in human airway epithelial (A549) cells which endogenously express PAR2. Thirty synthetic peptides were found to be as potent as or more potent than SLIGRL on the basis of intracellular Ca2+ responses. The more active peptide agonists were also examined for agonist cross‐reactivity at PAR1 in Chinese Hamster Ovary (CHO) cells that endogenously express functional PAR1 but not PAR2. Two potent and PAR2‐selective agonists were further examined for their capacity to relax phenylephrine‐contracted rat aortic rings. Our findings reveal an important role for carboxyl extensions to native PAR2 activating peptides in potentiating agonist activity. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Plant signalling peptides: some recent developments
Authors: Bahyrycz Agata , Konopińska Danuta 
Published: September 2007

AbstractThe subject of this review is plant signalling peptides, peptides of a new generation which regulate growth, differentiation, and other plant physiological functions. These peptides include systemin, the phytosulfokines (PSKs), ENOD40, CLAVATA3, Locus‐S, POLARIS, IDA, and ROT4. On the basis of literature data and our own results we discuss their structure, biological properties, and structure/biological function relationship, especially for the more studied systemin and PSK‐α. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Numerical modelling of lasing in microstructures
Authors: Zhukovsky Sergei V. , Chigrin Dmitry N. 
Published: September 2007

AbstractTwo methods suitable for numerical modelling of microlasers (including photonic crystal, microcavity, and random lasers) are presented. Finite‐difference time‐domain (FDTD) method and a generalized coupled mode theory are discussed in the context of microstructured resonators. The cases of one mode and two modes with near‐identical properties but different frequencies are investigated in detail. The predictions of the coupled mode model are compared to FDTD simulations of a microcavity laser based on a single defect and twin coupled defects in a photonic crystal lattice. Different regimes of the mode competition (simultaneous and bistable lasing) are analyzed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Diameter sorting of carbon nanotubes by gradient centrifugation: role of endohedral water
Authors: Hennrich F. , Arnold K. , Lebedkin S. , Quintillá A. , Wenzel Wolfgang , Kappes Manfred M. 
Published: September 2007

AbstractWe demonstrate that water filling has a significant, tube‐diameter dependent effect on the effective mass density of individual single‐walled carbon nanotubes suspended in aqueous suspension. On the basis of extensive molecular dynamics simulations of water‐filled carbon nanotubes we have estimated the number density and properties of water molecules inside different types of nanotubes. As the tube diameter becomes comparable with the size of a water molecule, the number density of water molecules jumps discontinously. For tube diameters just above this threshold the water molecules organize into a single file. Shell‐like arrangements are found for even larger radii. Buoyant densities are predicted to change accordingly. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of the combustible agents on the synthesis of Fe–Mo/MgO catalysts for the production of carbon nanotubes
Authors: Dias Lima Márcio , Jung de Andrade Mônica , Locatteli Andrei , Balzaretti Naira , Nobre Felipe , Perez Bergmann Carlos , Roth Siegmar 
Published: September 2007

AbstractThe production of Fe–Mo/MgO by Solution Combustion Synthesis (SCS) for use as catalysts in single‐walled carbon nanotube (SWNT) synthesis was evaluated. Glycine, urea, citric acid and polyethylene glycol 200 and 400 were tested as combustible agents (CA). Iron and magnesium nitrates and ammonium molybdate were used as catalyst precursors. Four different proportion ratios of combustible/metals salts were tested. The addition of CA greatly effects the morphology and density of the produced catalyst. Carbon nanotubes were evaluated using thermogravimetric analysis, Raman spectroscopy, scanning and transmission electron microscopes and by measuring the electrical conductivity of the carbon nanotubes dispersed in chloroform. The highest absolute carbon yield was obtained with the urea, but carbon nanotubes with higher G/D ratios were produced with glycine as the CA. However, the higher yield of carbon per volume of catalyst was produced using polyethylene glycol. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Solubilization of single‐wall carbon nanotubes in aqueous solutions of calixarenes
Authors: Lobach A. S. , Ryzhkina I. S. , Spitsina N. G. , Obraztsova E. D. 
Published: September 2007

AbstractThe present work reports the studies of the solubilization of single‐wall carbon nanotubes in aqueous solutions of calix[4]resorcinarene derivatives and p‐sulfonato‐calix[n ]arenes (n = 4, 6) modified by alkyl (butyl and dodecyl) substituents. The highest dispersion ability is demonstrated by calix[4]resocinarene, which bears aminomethyl groups on the upper rim and phosphorus‐bearing alkyl fragments on the lower rim of calixarene. Optical absorption spectroscopy justifies the formation of stable suspensions of SWNT in aqueous solutions of calixarenes. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical approach to Rayleigh and absorption spectra of semiconducting carbon nanotubes
Authors: Malić Ermin , Hirtschulz Matthias , Milde Frank , Wu Yang , Maultzsch Janina , Heinz Tony F. , Knorr Andreas , Reich Stephanie 
Published: September 2007

AbstractA microscopic calculation of the Rayleigh scattering cross section and the absorption coefficient for arbitrary single‐walled carbon nanotubes is presented. The approach is based on the density matrix formalism combined with the tight‐binding band structure. Both Rayleigh and absorption spectra show a characteristic intensity ratio behavior, which can be explained by an interplay of the optical matrix element and the joint density of states. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)