bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary effusion lymphoma: genomic profiling revealed amplification of SELPLG and CORO1C encoding for proteins important for cell migration
Authors: Luan Shi‐Lu , Boulanger Emmanuelle , Ye Hongtao , Chanudet Estelle , Johnson Nicola , Hamoudi Rifat A , Bacon Chris M , Liu Hongxiang , Huang Yuanxue , Said Jonathan , Chu Peiguo , Clemen Christoph S , Cesarman Ethel , Chadburn Amy , Isaacson Peter G , Du Ming‐Qing 
Published: July 2010

AbstractPrimary effusion lymphoma (PEL) is associated with Kaposi sarcoma herpesvirus (KSHV) but its pathogenesis is poorly understood. Many KSHV‐associated products can deregulate cellular pathways commonly targeted in cancer. However, KSHV infection alone is insufficient for malignant transformation. PEL also lacks the chromosomal translocations seen in other lymphoma subtypes. We investigated 28 PELs and ten PEL cell lines by 1 Mb resolution array comparative genomic hybridization (CGH) and found frequent gains of 1q21–41 (47%), 4q28.3‐35 (29%), 7q (58%), 8q (63%), 11 (32%), 12 (61%), 17q (29%), 19p (34%), and 20q (34%), and losses of 4q (32%), 11q25 (29%), and 14q32 (63%). Recurrent focal amplification was seen at several regions on chromosomes 7, 8, and 12. High‐resolution chromosome‐specific tile‐path array CGH confirmed these findings, and identified selectin‐P ligand (SELPLG) and coronin‐1C (CORO1C) as the targets of a cryptic amplification at 12q24.11. Interphase FISH and quantitative PCR showed SELPLG/CORO1C amplification (>4 extra copies) and low levels of copy number gain (1–4 extra copies) in 23% of PELs, respectively. Immunohistochemistry revealed strong expression of both SELPLG and coronin‐1C in the majority of PELs, irrespective of their gene dosage. SELPLG is critical for cell migration and chemotaxis, while CORO1C regulates actin‐dependent processes, thus important for cell motility. Their overexpression in PEL is expected to play an important role in its pathogenesis. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Proteomic study of Carissa spinarum in response to combined heat and drought stress
Authors: Zhang Minhua , Li Guowei , Huang Wei , Bi Ting , Chen Genyun , Tang Zhangcheng , Su Weiai , Sun Weining 
Published: July 2010

AbstractCarissa spinarum is one of the secondary advantage plants grown in dry‐hot valleys in China, which can survive under stress conditions of high temperature and extreme low humidity. Here, we studied the physiological and proteomic changes of C. spinarum in response to 42°C heat stress treatment in combination with drought stress. Dynamic changes in the leaf proteome were analyzed at four time points during the stress treatment and recovery stages. Approximately, 650 protein spots were reproducibly detected in each gel. Forty‐nine spots changed their expression levels upon heat and drought treatment, and 30 proteins were identified by MS and 2‐D Western blot. These proteins were classified into several categories including HSP, photosynthesis‐related protein, RNA‐processing protein and proteins involved in metabolism and energy production. The potential roles of these stress‐responsive proteins are discussed.
Proteome profile of the developing maize (Zea mays L.) rachis
Authors: Pechanova Olga , Pechan Tibor , Ozkan Seval , McCarthy Fiona M. , Williams W. Paul , Luthe Dawn S. 
Published: July 2010

AbstractIn this study, we performed the first high‐throughput proteomic analysis of developing rachis (cob) from maize genotype Mp313E. Using two proteomic approaches, 2‐DE and 2‐D LC, we identified 967 proteins. A 2‐D proteome reference map was established. Functional classification of identified proteins revealed that proteins involved in various cellular metabolisms, response to stimulus and transport, were the most abundant.
Mapping protein cysteine sulfonic acid modifications with specific enrichment and mass spectrometry: An integrated approach to explore the cysteine oxidation
Authors: Chang Yuan‐Chang , Huang Chien‐Ning , Lin Chia‐Hung , Chang Huan‐Cheng , Wu Chih‐Che 
Published: July 2010

AbstractOxidation of thiol proteins, which results in conversion of cysteine residues to cysteine sulfenic, sulfinic or sulfonic acids, is an important posttranslational control of protein function in cells. To facilitate the analysis of this process with MALDI‐MS, we have developed a method for selective enrichment and identification of peptides containing cysteine sulfonic acid (sulfopeptides) in tryptic digests of proteins based on ionic affinity capture using polyarginine‐coated nanodiamonds as high‐affinity probes. The method was applied to selectively concentrate sulfopeptides from either a highly dilute solution or a complex peptide mixture in which the abundance of the sulfonated analyte is as low as 0.02%. The polyarginine‐coated probes exhibit a higher affinity for peptides containing multiple sulfonic acids than peptides containing single sulfonic acid. The limit of the detection is in the femtomole range, with the MALDI‐TOF mass spectrometer operating in the negative ion mode. The results show that the new approach has good specificity even in the presence of phosphopeptides. An application of this method for selective enrichment and structural identification of sulfopeptides is demonstrated with the tryptic digests of performic‐acid‐oxidized BSA.
Hybrid Sputtering‐Remote PECVD Deposition of Au Nanoparticles on SiO2 Layers for Surface Plasmon Resonance‐Based Colored Coatings
Authors: Beyene Haile Takele , Tichelaar Frans D. , Peeters Paul , Kolev Ivan , van de Sanden Mauritius C. M. , Creatore Mariadriana 
Published: July 2010

AbstractIn this paper, a hybrid system consisting of metal nano‐particles dispersed on the surface of a dielectric layer is presented: a remote Expanding Thermal Plasma CVD system is used for the deposition of the inorganic (i.e. SiO2) layers from hexamethyldisiloxane/oxygen mixtures in combination with an rf magnetron sputtering tool for the deposition of metallic (i.e. gold) nanoparticles on top of the SiO2 layers. The optical properties of the Au/SiO2 layers have been investigated by means of UV‐VIS‐NIR variable angle spectroscopic ellipsometry. Rutherford backscattering and transmission electron microscopy were used to determine the film density, the nanoparticle size and its distribution, respectively. The uniform distribution of gold nanoparticles on the surface of the SiO2 layers allows obtaining red‐ to blue‐ colored coatings as a consequence of the shift of the surface plasmon resonance band to higher wavelengths, caused by an increase in size of nanoparticles and metal surface coverage.magnified image
Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in‐gel tryptic digestion followed by LC‐MS/MS
Authors: Paulo Joao A. , Lee Linda S. , Wu Bechien , Repas Kathryn , Banks Peter A. , Conwell Darwin L. , Steen Hanno 
Published: July 2010

AbstractPurpose: Proteomic analysis of gastroduodenal fluid offers an alternative strategy to study diseases, such as peptic ulcer disease and gastric cancer. We use in‐gel tryptic digestion followed by LC‐MS/MS (GeLC‐MS/MS) to profile the proteome of gastroduodenal fluid collected during the endoscopic pancreatic function test (ePFT).Experimental design: Gastroduodenal fluid specimens collected during ePFT from six patients with upper abdominal pain were subjected to proteomic analysis. We extracted proteins using three chemical precipitation reagents (acetone, ethanol, and trichloroacetic acid) and analyzed each sample by SDS‐PAGE and GeLC‐MS/MS for protein identification. Cellular origin and molecular function of the identified proteins were determined via gene ontology analysis.Results: All three precipitation techniques successfully extracted protein from gastroduodenal fluid, with acetone resulting in excellent resolution and minimal protein degradation compared with the other methods. A total of 134 unique proteins were found in our GeLC‐MS/MS analysis of ePFT‐collected gastroduodenal fluid samples. Sixty‐seven proteins were identified in at least two of the three samples. Gene ontology analysis classified these proteins mainly as being peptidases and localized extracellularly.Conclusions and clinical relevance: ePFT, followed by acetone precipitation, and coupled with LC‐MS/MS, can be used to safely collect gastroduodenal fluid from the upper gastrointestinal tract for MS‐based proteomic analysis.
The pyruvate kinase model system, a cautionary tale for the use of osmolyte perturbations to support conformational equilibria in allostery
Authors: Fenton Aron W. , Johnson Troy A. , Holyoak Todd 
Published: July 2010

AbstractIn the study of rabbit muscle pyruvate kinase (M1‐PYK), proline has previously been used as an osmolyte in an attempt to determine a role for preexisting conformational equilibria in allosteric regulation. In this context, osmolytes are small molecules assumed to have no direct interaction with the protein. In contrast to proline's proposed role as an osmolyte, the structure of M1PYK‐Mn‐pyruvate‐proline complex reported herein demonstrates that proline binds specifically to the allosteric site of M1‐PYK. Therefore, this amino acid is an allosteric effector rather than a benign osmolyte. Other compounds often used as osmolytes (polyethyleneglycol and glycerol) are also present in the structure, suggesting an interaction with the protein that would, in turn, prevent the usefulness of these compounds in the study of this and most likely other proteins. These findings highlight the need to verify that compounds used as osmolytes to perturb preexisting conformational equilibrium do not directly interact with the protein, a consideration not commonly addressed in the past.
The crystal structure of the mycobacterium tuberculosis Rv3019c‐Rv3020c ESX complex reveals a domain‐swapped heterotetramer
Authors: Arbing Mark A. , Kaufmann Markus , Phan Tung , Chan Sum , Cascio Duilio , Eisenberg David 
Published: July 2010

AbstractMycobacterium tuberculosis encodes five gene clusters (ESX‐1 to ESX‐5) for Type VII protein secretion systems that are implicated in mycobacterial pathogenicity. Substrates for the secretion apparatus are encoded within the gene clusters and in additional loci that lack the components of the secretion apparatus. The best characterized substrates are the ESX complexes, 1:1 heterodimers of ESAT‐6 and CFP‐10, the prototypical member that has been shown to be essential for Mycobacterium tuberculosis pathogenesis. We have determined the structure of EsxRS, a homolog of EsxGH of the ESX‐3 gene cluster, at 1.91 Å resolution. The EsxRS structure is composed of two four‐helix bundles resulting from the 3D domain swapping of the C‐terminal domain of EsxS, the CFP‐10 homolog. The four‐helix bundles at the extremities of the complex have a similar architecture to the structure of ESAT‐6·CFP‐10 (EsxAB) of ESX‐1, but in EsxRS a hinge loop linking the α‐helical domains of EsxS undergoes a loop‐to‐helix transition that creates the domain swapped EsxRS tetramer. Based on the atomic structure of EsxRS and existing biochemical data on ESX complexes, we propose that higher order ESX oligomers may increase avidity of ESX binding to host receptor molecules or, alternatively, the conformational change that creates the domain swapped structure may be the basis of ESX complex dissociation that would free ESAT‐6 to exert a cytotoxic effect.
Enhanced repellency of binary mixtures of Zanthoxylum piperitum pericarp steam distillate or Zanthoxylum armatum seed oil constituents and Calophyllum inophyllum nut oil and their aerosols to Stomoxys calcitrans
Authors: Hieu Tran Trung , Kim Soon‐Il , Kwon Hyung Wook , Ahn Young‐Joon 
Published: July 2010

AbstractBACKGROUND: The repellency to stable fly, Stomoxys calcitrans (L.), of Zanthoxylum piperitum (L.) DC pericarp steam distillate (ZP‐SD), Zanthoxylum armatum DC seed oil (ZA‐SO) and their constituents alone or in combination with Calophyllum inophyllum L. nut oil (CI‐NO), as well as six aerosol formulations containing ZP‐SD or ZP‐SO and CI‐NO, was compared with that of a synthetic repellent, DEET, using an exposed human hand bioassay.RESULTS: At 0.20 mg cm−2, ZP‐SD treatments resulted in 91 and 68% repellency following 30 and 60 min exposure respectively, while DEET gave 100 and 84% repellency. ZA‐SO was less effective than ZP‐SD. At 0.2 mg cm−2, the most active constituents, cuminaldehyde, cuminyl alcohol, limonene and methyl cinnamate, gave 82, 74, 74 and 64% repellency at 30 min respectively, but DEET gave 100 and 87% repellency at 30 and 60 min. An increase in effectiveness and duration of repellency was produced by binary mixtures of ZP‐SD, ZA‐SO or bioactive constituents (each 0.01 mg cm−2) and CI‐NO (0.99 mg cm−2). The repellency of aerosols containing 2.5% ZP‐SD or 2.5% ZA‐SO and 2.5% CI‐NO was comparable with that of 5% DEET aerosol.CONCLUSION: Mixtures formulated from ZP‐SD, ZA‐SO or bioactive constituents and CI‐NO could be useful as potential repellents for the control of stable fly populations in light of global efforts to reduce the level of highly toxic synthetic repellents. Copyright © 2010 Society of Chemical Industry
Risk assessment for honey bees and pesticides—recent developments and ‘new issues’
Authors: Thompson Helen M 
Published: July 2010

AbstractIn 2008, major areas of discussion at the ICPBR Bee Protection Group meeting were the development of a honey bee risk assessment scheme for systemic pesticides and revision of the test guidelines for semi‐field and field studies. The risk assessment scheme for systemic pesticides is based on analysis of conditions for exposure of bees to residues. These are based on a stepwise approach, starting with simple calculations based on existing data in dossiers and progressing to higher‐tier semi‐field and field studies (the guidelines for these have been modified in line with this). The proposed scheme has been tested with data packages of high‐ and low‐risk PPPs. A future area of interest for the group may be the risks posed by guttation fluid containing systemic pesticides. A recent paper on ‘Translocation of neonicotinoid insecticides from coated seeds to seedling guttation drops: a novel way of intoxication for bees’ has focused significant interest on the possible risks posed by the presence of residues of systemic pesticides in guttation fluid to water‐collecting honey bees. The occurrence of guttation and the presence of pesticide residues in the fluid are discussed, together with remaining questions that will need to be addressed in answering whether such a route of exposure may pose a risk to honey bees. © Crown copyright 2010. Reproduced with permission of Her Majesty's Stationery Office. Published by JohnWiley & Sons, Ltd.
Effect of electric field on dielectric, ac conduction and ferroelectric behavior of flux‐grown Pb(Zn1/3 Nb2/3)0.91Ti0.09O3 single crystals
Authors: Singh B. K. , Kumar K. , Gupta M. K. , Kumar B. 
Published: July 2010

AbstractThe temperature dependence of dielectric and piezoelectric behavior of Pb(Zn1/3 Nb2/3)0.91Ti0.09O3 single crystals has been investigated for samples poled at different fields along [0 0 1] direction. An increase in rhombohedral to tetragonal phase‐transition temperature (Trt) with dc field was observed due to the polarization rotation via a monoclinic phase. At higher field, a small kink in the dielectric constant near 125 °C was observed, suggesting a field‐induced rhombohedral to monoclinic phase transition. The activation energy for conduction, below Trt, was determined as 0.17, 0.32, and 0.11 eV for the samples poled at 0, 0.5, and 1.0 kV/mm, respectively.
Cylinder‐shaped ultrasonic motors based on conventional piezoelectric ceramics and novel single crystals
Authors: Luo Laihui , Zhu Yuejin , Luo Haosu 
Published: July 2010

AbstractTwo medium‐sized ultrasonic motors using the first‐order bending vibration (B1) of a cylinder with two free–free ends have been developed in this study. The cylinder‐shaped stators are 10 mm in diameter and 25 mm in length. They are based on novel Pb(Mg1/3Nb2/3)O3–PbTiO3 (PMN–PT) single crystal and conventional Pb(Zr,Ti)O3 (PZT) ceramic. The stators of the motors were simulated by a finite element method. The main performances of the motors were measured. The results show that the PMN–PT‐crystal‐based motor with medium size overmatches the conventional PZT‐based motor with: wider exciting frequency; lower exciting voltage, and much larger mechanical output power. The largest revolution speed of the PMN–PT motor is 780 rpm and a maximum load of ∼0.008 N m.
Luminescence of F+‐type centers in undoped Lu3Al5O12 single crystals
Authors: Babin V. , Laguta V.V. , Maaroos A. , Makhov A. , Nikl M. , Zazubovich S. 
Published: July 2010

AbstractUndoped single crystals of Lu3Al5O12 annealed in the reduced atmosphere or additively colored in Al vapors were studied at 4.2–400 K by the time‐resolved spectroscopy methods. The 3.15 eV emission, excited in the 3.4, 5.3, and 6.1 eV absorption bands and having a decay time of 3.14 ns at 10 K, was ascribed to the F+‐type centers. It was suggested that these centers consist of an oxygen vacancy with one trapped electron which is perturbed by the neighboring antisite defect (Lu) or an impurity ion at the Al3+ site. The small Stokes shift and half‐width of the emission band indicate that the F+‐type centers are characterized by a weak electron–phonon interaction.
Improved design of robust exponentially weighted moving average control charts for autocorrelated processes
Authors: Lee Hyun Cheol , Apley Daniel W. 
Published: July 2010

AbstractResidual‐based control charts for autocorrelated processes are known to be sensitive to time series modeling errors, which can seriously inflate the false alarm rate. This paper presents a design approach for a residual‐based exponentially weighted moving average (EWMA) chart that mitigates this problem by modifying the control limits based on the level of model uncertainty. Using a Bayesian analysis, we derive the approximate expected variance of the EWMA statistic, where the expectation is with respect to the posterior distribution of the unknown model parameters. The result is a relatively clean expression for the expected variance as a function of the estimated parameters and their covariance matrix. We use control limits proportional to the square root of the expected variance. We compare our approach to two other approaches for designing robust residual‐based EWMA charts and argue that our approach generally results in a more appropriate widening of the control limits. Copyright © 2010 John Wiley & Sons, Ltd.
Use of stable isotope labeled probes to facilitate liquid chromatography/mass spectrometry based high‐throughput screening of time‐dependent CYP inhibitors
Authors: Dasgupta Malini , Tang Weimin , Caldwell Gary W. , Yan Zhengyin 
Published: July 2010

AbstractInhibition curve shift is a commonly used approach for screening of time‐dependent CYP inhibitors which requires parallel paired incubations to obtain two inhibition curves for comparison. For the control incubation, a test compound is co‐incubated with a probe substrate in human liver microsomes (HLM) fortified with NADPH; for the time‐dependent incubation (TDI), the test compound is pre‐incubated with NADPH‐fortified HLM followed by a secondary incubation with a probe substrate. For both incubations, enzyme activity is measured respectively by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis of the CYP‐specific metabolite, and a TDI inhibitor can be readily identified by inhibition curve shifting as a result of CYP inactivation by the test compound during the pre‐incubation. In the present study, we describe an alternative approach to facilitate TDI screening in which stable isotope labeled CYP‐specific probes are used for the TDI, and non‐labeled substrates are included in the control incubation. Because CYP‐specific metabolites produced in the TDI are stable isotope labeled, two sets of incubation samples can be combined and then simultaneously analyzed by LC/MS/MS in the same batch run to reduce the run time. This new method has been extensively validated using both a number of known competitive and TDI inhibitors specific to five most common CYPs such as 1A2, 2C9, 2C19, 2D6, and 3A4. The assay is performed in a 96‐well format and can be fully automated. Compared to the traditional method, this approach in combination with sample pooling and a short LC/MS/MS gradient significantly enhances the throughput of TDI screening and thus can be easily implemented in drug discovery to evaluate a large number of compounds without adding additional resource. Copyright © 2010 John Wiley & Sons, Ltd.
Structural characterization of poly(amino)ester dendrimers and related impurities by electrospray tandem mass spectrometry
Authors: Tintaru Aura , Monnier Valérie , Bouillon Camille , Giordanengo Rémi , Quéléver Gilles , Peng Ling , Charles Laurence 
Published: July 2010

AbstractAn acid‐terminated poly(amino)ester dendrimer was studied by electrospray ionization tandem mass spectrometry to establish its fragmentation pathways, with the aim of using them to investigate the structure of any defective molecules generated during the dendrimer synthesis. This poly(amino)ester dendrimer could be ionized in both polarities but the most structurally relevant dissociation pathways were found from the deprotonated molecule in negative ion mode. The dissociation pattern of this dendrimer is fully described and supported by accurate mass measurements. The main dissociation reactions of the negatively charged polyacidic dendrimer were shown to consist of (i) the release of carbon dioxide and ethene within a branch, which proceeds as many times as intact neutral branches are available; and (ii) the elimination of an entire dendrimer arm. Monitoring the occurrence of these reactions together with any deviation from these two main routes allowed six major dendritic impurities to be structurally characterized. Copyright © 2010 John Wiley & Sons, Ltd.
Analysis of triglycerides in food items by desorption electrospray ionization mass spectrometry
Authors: Gerbig Stefanie , Takáts Zoltán 
Published: July 2010

AbstractThe triglyceride composition and oxidation behavior of edible oil and margarine samples were analyzed by desorption electrospray ionization mass spectrometry (DESI‐MS). For the characterization of the lipids, the chain length and the degree of unsaturation of the fatty acids were determined. The measurements were carried out in positive ion mode; the triglycerides were detected as alkali metal or ammonium adducts. The DESI solvent was water/methanol 1:1 (v/v); measurements were carried out both with and without the addition, as an ionizing agent, of ammonium acetate that enhances the signal intensity of the ammonium adduct ions. The spectra were interpreted for both cases and intensities were compared. Triglyceride monomers and dimers were observed in the spectra. Tandem mass spectrometric (MS/MS) measurements were carried out to determine the structure of the triglycerides. It was demonstrated that the terminal fatty acids in the sn1‐ or sn3‐position are more likely to be cleaved than the internal fatty acid (sn2‐position). Characteristic triglyceride patterns were obtained using a simple and rapid sample preparation protocol comprising the simple deposition of samples onto a glass carrier surface. The triglyceride data was analyzed by principal component analysis (PCA). The different edible oils were clearly separated and the hydrogenated derivatives were identified by their triglyceride spectra. The oxidation of the oil samples was observed and the oxidation products were detected and identified. This method provides a fast and simple technique for the detection and analysis of triglycerides in oil‐ or fat‐containing samples ranging from food items to tissue samples. The potential application areas include nutritional studies, the food industry and cosmetics. Copyright © 2010 John Wiley & Sons, Ltd.