bluuebunny/crossref_metadata_2025_split huggingface dataset:
Array CGH analysis of pediatric medulloblastomas
Authors: Rossi Michael R. , Conroy Jeffrey , McQuaid Devin , Nowak Norma J. , Rutka James T. , Cowell John K. 
Published: November 2005

AbstractBrain tumors are the second most common childhood cancer. We used high‐resolution array comparative genomic hybridization (aCGH) to analyze losses and gains of genetic material from 24 medulloblastomas. The bacterial artificial chromosome clones were ordered on the array, allowing for an average resolution of approximately 420 kilobases. The advantage of this high resolution is that the breakpoints associated with subregional chromosome copy number aberrations can be accurately defined, which in turn allows candidate genes within these regions to be readily defined. In this analysis, we confirmed the frequent involvement of loss of 17p and gain of 17q, although we have now established the position of the breakpoint that consistently lies in the chr17:18318880–19046234 region of the chromosome. Other frequent losses were seen on 8p, 10q, 16q, and 20p, and frequent gains were seen on 2p, 4p, 7, and 19. In addition, the fine‐resolution mapping provided by aCGH made it possible to define small chromosome deletions in 1q23.3–q24.2, 2q13.12–q13.2, 6q25–qter, 8p23.1, 10q25.1, and 12q13.12–q13.2. Overall, amplification events were rare, the most common involving MYC (16%), on 8q, although isolated events were seen in 10p11 and 3q. © 2005 Wiley‐Liss, Inc.
D324N single‐nucleotide polymorphism in the FLT3 gene is associated with higher risk of myeloid leukemias
Authors: Schnittger Susanne , Kohl Tobias M. , Leopold Nina , Schoch Claudia , Wichmann H.‐Erich , Kern Wolfgang , Lohse Peter , Hiddemann Wolfgang , Haferlach Torsten , Spiekermann Karsten 
Published: November 2005

AbstractMutations within the FLT3 gene are of growing importance for classification, risk assessment, and therapeutic targeting of acute myeloid leukemia (AML). We analyzed 656 AML patients for a recently described single‐nucleotide polymorphism (SNP) in the third immunoglobulin‐like domain of the extracellular region of FLT3. The FLT3 D324N variant was present in 42 cases (6.4%), but it was not associated with a specific AML subtype and did not show an elevated leukocyte count, as do other FLT3 mutations. In remission samples, a 50% ratio of the normal to the D324N variant was detectable. Stably expressed in IL‐3 dependent Ba/F3 cells, the D324N variant did not confer receptor autophosphorylation, factor independent growth, or increased resistance to apoptotic cell death in response to varying doses of FLT3 ligand. In 400 healthy donors, the FLT3 D324N variant was detected in 6 cases (1.5%) and segregated in a family. Thus, it was shown to be a polymorphism with a lower frequency in healthy controls than in patients with AML (P < 0.001). In addition, 21 of 234 CML (9.0%) and 7 of 155 ALL (4.5%) cases carried the FLT3 D324N. Our data suggest that the FLT3 D324N variant might be associated with a predisposition to different subtypes of leukemia. © 2005 Wiley‐Liss, Inc.
Monitoring of the principal carbonyl compounds involved in malolactic fermentation of wine by solid‐phase microextraction and positive ion chemical ionization GC/MS analysis
Authors: Flamini Riccardo , Vedova Antonio Dalla , Panighel Annarita , Perchiazzi Nicola , Ongarato Stefano 
Published: November 2005

AbstractA new method has been developed to determine acetaldehyde, 2,3‐butanedione (diacetyl) and 3‐hydroxy‐2‐butanone (acetoin) in wine by solid‐phase microextraction (SPME) and positive ion chemical ionization GC/MS analysis of O‐(2,3,4,5,6‐pentafluorobenzyl)‐hydroxylamine (PFBOA) derivatives. For SPME, a 65‐µm PEG/DVB fibre was used; chemical ionization was performed with methane as reagent gas. The best analysis‐time/sensitivity compromise was to perform the PFBOA reaction at 50 °C for 20 min, followed by 5‐min SPME at the same temperature. Quantitative analysis was performed in SCAN mode using o‐chlorobenzaldehyde as internal standard (IS), on the signal of the [M + H]+ ion at m/z 240 for acetaldehyde, 266 for acetoin (corresponding to the [M + H − 18]+ ion), 282 for diacetyl (protonated mono‐derivatized compound), and 336 for IS. The accuracy and repeatability of the method were suitable for the study aims, and linearity was good in the range of concentration studied, with correlation coefficients of calibration curves 0.997, 0.998 and 0.988 for acetaldehyde, diacetyl and acetoin respectively. Due to the higher polarity of acetoin with respect to other two compounds, lower sensitivity in the detection of this compound was observed. By following the variation of the three carbonyl compounds, malolactic fermentations (MLF) were monitored in Merlot wines and this was carried out in the laboratory by two different bacteria strains. Copyright © 2005 John Wiley & Sons, Ltd.
Activity of anchored human matrix metalloproteinase‐1 catalytic domain on Au (111) surfaces monitored by ESI‐MS
Authors: Grasso Giuseppe , D'Agata Roberta , Rizzarelli Enrico , Spoto Giuseppe , D'Andrea Luca , Pedone Carlo , Picardi Andrea , Romanelli Alessandra , Fragai Marco , Yeo Kwon Joo 
Published: November 2005

AbstractMatrix metalloproteinases (MMPs) are a family of Zn‐dependent endo‐peptidases known for their ability to cleave several components of the extracellular matrix, but which can also cleave many non‐matrix proteins. There are many evidences that MMPs are involved in physiological and pathological processes, and a huge effort has been put in the development of possible inhibitors that could reduce the activity of MMPs, as it is clear that the ability to monitor and control such activity plays a pivotal role in the search for potential drugs aimed at finding a cure for several diseases such as pulmonary emphysema, rheumatoid arthritis, fibrotic disorders and cancer.A powerful method currently available to study enzyme–inhibitor interactions is based on the use of the surface plasmon resonance (SPR) technique. When MMP interactions are studied, a procedure by which inhibitors are normally anchored on sensor chips and SPR technique is used in order to study their interaction with MMPs molecules is usually followed. This is because it is currently believed that MMPs cannot be anchored on the sensor‐chip surface without losing their activity. However, this approach gives rise to problems, as the anchoring of low‐molecular‐weight inhibitors on gold surfaces easily affects their ability to interact with MMPs. For this reason, the anchoring of MMPs is highly desirable.A new experimental protocol that couples the Fourier transform‐SPR (FT‐SPR) technique with electrospray ionization‐mass spectroscopy (ESI‐MS) is described here for the evaluation of the activity of MMP‐1 catalytic domain (cdMMP‐1) anchored on gold surfaces. The cdMMP‐1 surface coverage is calculated by using FT‐SPR and the enzyme activity is estimated by ESI‐MS. The proposed method is label‐free. Copyright © 2005 John Wiley & Sons, Ltd.
MALDI‐TOF mass spectrometry of a combinatorial peptide library: effect of matrix composition on signal suppression
Authors: Schlosser Gitta , Pocsfalvi Gabriella , Huszár Emőke , Malorni Antonio , Hudecz Ferenc 
Published: November 2005

AbstractThe effect of matrix composition on signal suppression caused by a dominant compound under MALDI ionization was studied using the combinatorial TQTXT pentapeptide library as a model system. The peptide library is composed of 19 components with all proteinogenic amino acids except cysteine in position X. From these compounds, only the Arg peptide (TQTRT) was detected with sufficient intensity in the MALDI‐TOF mass spectrum under typical MALDI conditions (CCA matrix). The analysis of a set of compounds utilized as different matrix components, additives and a cationizing agent revealed that the composition of the matrix is a critical point in signal suppression. Highly improved ion yields were achieved by using a CCA/DHB mixture as a matrix. The addition of K+ as a cationizing agent to the CCA matrix resulted in MALDI‐TOF mass spectra with relative ion intensities very similar to those obtained by electrospray ionization. Copyright © 2005 John Wiley & Sons, Ltd.
Surface‐activated chemical ionization ion trap mass spectrometry in the analysis of drugs in dilute urine samples. Part II: analysis of morphine and other street drugs
Authors: Cristoni Simone , Cantu Marco , Bernardi Luigi Rossi , Gerthoux Piermario , Mocarelli Paolo , Brambilla Maura , Gonella Elisabetta , Guidugli Federico 
Published: November 2005

AbstractThe new ionization method, called surface‐activated chemical ionization (SACI), was employed for the analysis of fives drugs (morphine, codeine, 6‐monoacetylmorphine (6‐MAM), benzoylecgonine and cocaine) by ion trap mass spectrometry. The results so obtained have been compared with those achieved by using atmospheric pressure chemical ionization (APCI), no‐discharge‐APCI and electrospray ionization (ESI) clearly showing that SACI is the most sensible one mainly due to the high ionization efficiency and the lower chemical noise. The performance of SACI in terms of sensitivity and linearity was compared with the sensitivity and linearity obtained using APCI, no‐discharge‐APCI and ESI, showing that the new SACI approach gives rise to the best results. Then, SACI was used to analyze morphine, codeine, 6‐MAM, benzoylecgonine and cocaine in urine samples. After the optimization of the instrumental parameters for a mixture of the standard compounds, eight urine samples were analyzed. They were strongly diluted (1 : 20 and 1 : 100) in order to prevent the chromatographic column damage due to the matrix composition. Furthermore, the diluted urine samples were directly analyzed, without pretreatment, through LC‐MS and LC‐MS/MS, and the obtained results are reported. Copyright © 2005 John Wiley & Sons, Ltd.
Rate constant for the reaction of CH3C(O)CH2 radical with HBr and its thermochemical implication
Authors: Farkas Edit , Kovács Gergely , Szilágyi István , Dóbé Sándor , Bérces Tibor , Márta Ferenc 
Published: November 2005

AbstractThe fast flow method with laser induced fluorescence detection of CH3C(O)CH2 was employed to obtain the rate constant of k1 (298 K) = (1.83 ± 0.12 (1σ)) × 1010 cm3 mol−1 s−1 for the reaction CH3C(O)CH2 + HBr ↔ CH3C(O)CH3 + Br (1, −1). The observed reduced reactivity compared with n‐alkyl or alkoxyl radicals can be attributed to the partial resonance stabilization of the acetonyl radical. An application of k1 in a third law estimation provides ΔfH(CH3C(O)CH2) values of −24 kJ mol−1 and −28 kJ mol−1 depending on the rate constants available for reaction (‐1) from the literature. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 38: 32–37, 2006
Master equation modeling of wide range temperature and pressure dependence of CO + OH → products
Authors: Joshi Ameya V. , Wang Hai 
Published: November 2005

AbstractThe rate coefficient of CO + OH → products is analyzed with RRKM/master equation analyses and Monte Carlo simulations. The analyses are based on the recent CCSD(T)/cc‐pvTZ potential energy surface of Yu et al. Chem Phys Lett 2001, 349, 547–554). It is shown that the experimental data over the temperature range of 80–2500 K and pressure from 1 Torr to 800 bar can be satisfactorily reproduced by lowering the CCSD(T)/cc‐pvTZ energy barrier for the CO2 + H exit channel by 1 kcal/mol and more importantly, by considering an equilibrium factor in the thermal rate constant formulation. This factor accounts for the populations of rovibrationally excited trans‐ and cis‐HOCO, which are then allowed to dissociate only through specific paths that are open to them. By modeling the isothermal but pressure‐dependent rate data of Fulle et al. (J Chem Phys 1996, 105, 983–1000) over the temperature range from 98 to 819 K, we obtained an 〈Edown〉 value equal to 150 cm−1 for M = He. The 〈Edown〉 values for M = N2, Ar, CF4, and SF6 were also obtained by fitting the OH and OD data at 298 K. Based on the theoretical analyses, we recommended that the following rate expression be used for CO + OH → CO2 + H in the temperature range from 120 to 2500 K and pressure lower than P(bar) = 9 × 10−17T 5.9 exp(520/T): k1b,0(cm3 molecule−1s−1) =1.17 × 10−19 T2.053exp(139/T) + 9.56 × 10−12 T−0.664 exp(−167/T). Fall‐off parameterization is also proposed for the rate coefficient of CO + OH → CO2 + H under extremely high pressures and for CO + OH → HOCO over the temperature range from 120 to 2500 K. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 38:57–73, 2006
Polyphenolic apple juice extracts and their major constituents reduce oxidative damage in human colon cell lines
Authors: Schaefer Sandra , Baum Matthias , Eisenbrand Gerhard , Dietrich Helmut , Will Frank , Janzowski Christine 
Published: November 2005

AbstractApple juice containing high amounts of antioxidative polyphenols might protect the intestine against oxidative cell damage. We investigated the preventive effectiveness of polyphenolic juice extracts of different origins (cider and table apples) in comparison to their major constituents in human colon cell lines (Caco‐2, HT29). Parameters studied were (oxidative) DNA damage (Comet assay), glutathione level (photometric kinetic assay), cellular redox status (dichlorofluorescein assay) and antioxidant capacity. The extracts (50–250 μg/mL) modulated DNA damage and redox status in a concentration‐dependent manner at 24‐h incubation. The pomace extraction technology, applied for juice preparation, and the preferential selection of cider apple varieties influenced the polyphenolic pattern and increased the biological effectiveness of the extracts. The preventive potential of major juice constituents (1–100 μM, 24 h) strongly differed: rutin, epicatechin and caffeic acid clearly reduced (oxidative) DNA damage (Caco‐2), chlorogenic acid efficiently decreased cellular reactive oxygen species level (HT29, Caco‐2). The aglyca quercetin and phloretin exhibited the highest preventive/antioxidant capacity in all assays. The stability of the compounds inversely correlated with their preventive effectiveness and might contribute to the observed cell specific sensitivities. In conclusion, apple juice extracts distinctly reduce oxidative cell damage in human colon cell lines, an effect, which in part can be accounted for by their major constituents.
The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions
Authors: Voigt Birgit , Schweder Thomas , Sibbald Mark J. J. B. , Albrecht Dirk , Ehrenreich Armin , Bernhardt Jörg , Feesche Jörg , Maurer Karl‐Heinz , Gottschalk Gerhard , van Dijl Jan Maarten , Hecker Michael 
Published: November 2005

AbstractThe now finished genome sequence of Bacillus licheniformis DSM 13 allows the prediction of the genes involved in protein secretion into the extracellular environment as well as the prediction of the proteins which are translocated. From the sequence 296 proteins were predicted to contain an N‐terminal signal peptide directing most of them to the Sec system, the main transport system in Gram‐positive bacteria. Using 2‐DE the extracellular proteome of B. licheniformis grown in different media was studied. From the approximately 200 spots visible on the gels, 89 were identified that either contain an N‐terminal signal sequence or are known to be secreted by other mechanisms than the Sec pathway. The extracellular proteome of B. licheniformis includes proteins from different functional classes, like enzymes for the degradation of various macromolecules, proteins involved in cell wall turnover, flagellum‐ and phage‐related proteins and some proteins of yet unknown function. Protein secretion is highest during stationary growth phase. Furthermore, cells grown in complex medium secrete considerably higher protein amounts than cells grown in minimal medium. Limitation of phosphate, carbon and nitrogen sources results in the secretion of specific proteins that may be involved in counteracting the starvation.
Multi‐modality of pI distribution in whole proteome
Authors: Wu Songfeng , Wan Ping , Li Jianqi , Li Dong , Zhu Yunping , He Fuchu 
Published: November 2005

AbstractMulti‐modality of pI distribution is a common feature in different whole proteomes. Some researchers considered it relate to the proteins with different subcellular locations, indicating the result of natural selection. We explored the pI distribution of predicted proteomes (including animals, plants, bacterium, archaeans) and random proteome [random protein sequences constructed according to the special amino acid composition and molecular weight (MW) distribution of human predicted proteome]. Our results suggest that the multi‐modality is the result of discrete pKR values for different amino acids. Amino acid composition and MW distribution of a proteome also contributes to the specific pI distribution. Although protein subcellular location was related to pI value, our analyses revealed that comparing with the random proteome, neither the multi‐modality phenomenon nor the distribution bias of pI values is caused by subcellular location. It seems that the multi‐modality distribution is just a mathematical fun. The blank region near the neutral pI was caused by the absence of amino acids with neutral pKR, and suggests that the selection of amino acids with ionizable side chain might be restricted by the requirement for a special pH environment during the origin of life. From this point of view, the special distribution was the result of natural selection.
Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large‐scale organization and robustness
Authors: Li Dong , Li Jianqi , Ouyang Shuguang , Wang Jian , Wu Songfeng , Wan Ping , Zhu Yunping , Xu Xiaojie , He Fuchu 
Published: November 2005

AbstractHigh‐throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale‐free and high‐degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small‐world property with similar diameter at 4–5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of “systems biology”.
Proteome analysis of human liver carcinoma Huh7 cells harboring hepatitis C virus subgenomic replicon
Authors: Fang Caiyun , Yi Zhigang , Liu Feng , Lan Shuiyun , Wang Jiadong , Lu Haojie , Yang Pengyuan , Yuan Zhenghong 
Published: November 2005

AbstractChronic infection by hepatitis C virus (HCV) is closely correlated with serious liver diseases. Although considerable progress has been made during recent years, the mechanism of replication and pathogenesis of HCV infection are still elusive. We have applied proteomic techniques in this work to globally analyze the protein expression profiles of a human liver cell lines Huh7 in absence and presence of HCV replication, aiming at elucidating the components of HCV replication and the cellular responses to HCV replication. The protein mixtures of three subcellular fractions from Huh7 and Huh7‐HCV were separated by 2‐DE under various pH gradients. Differentially expressed spots were identified by MALDI‐TOF MS, followed by database searching. A total of 179 comparative proteins were identified unambiguously, including proteins associated with host cytoskeleton, intracellular traffic, oxidative and ER stress, proteasome degradation, translation, apoptosis, proliferation, etc. Host proteins known to interact with HCV proteins, such as HSP27, α‐actinin, nucleolin and eukaryotic initiation factor 4A‐I, were elevated in Huh7‐HCV cells. Our study provides the global information of proteomic alteration of Huh7 cells in the presence of HCV replication and the clues for further understanding of the mechanism of HCV replication and pathogenesis.
Syntheses of conductive adhesives based on epoxy resin and polyanilines by using N‐tert‐butyl‐5‐methylisoxazolium perchlorate as a thermally latent curing reagent
Authors: Hino Tetsuo , Taniguchi Shunsuke , Kuramoto Noriyuki 
Published: November 2005

AbstractConductive composites consisted of epoxy resin and polyanilines (PANIs) doped with dodecylbenzenesulfonic acid (1), dodecylsulfonic acid (2), di(2‐ethylhexyl)sulfosuccinic acid (3), and HCl were synthesized by use of N‐tert‐butyl‐5‐methylisoxazolium perchlorate (5) under various reaction conditions. It was found that the composites with PANI doped with acid 2 (PANI‐2) prepared by curing with 10 mol % of reagent 5 at 80 °C for 12 h showed high electroconductivity along with the low conducting percolation threshold (3 wt % of PANI‐2). Furthermore, the composite with even ˜10 wt % of PANI‐2 exhibited ˜10−1 S/cm of electroconductivity. The UV–vis and IR measurements indicated that the conductive emeraldine salt form of PANI‐2 in the composite was maintained after the curing reaction. The thermal stability was studied by TGA and DSC measurements, and then, the Td10 and Tg of the composite with 5 and 10 wt % of PANI‐2 were found to be similar to those with the cured epoxy resin itself. In addition, the similar investigation with an oxetane resin instead of the epoxy resin was also carried out. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 718–726, 2006
Rheological properties of ferrite nanocomposites based on nylon‐66
Authors: Chae Dong Wook , Lee Ki Hyun , Kim Byoung Chul 
Published: November 2005

AbstractEffects of ferrite nanoparticles (0.1–20 wt %) on the rheological and other physical properties of nylon‐66 were investigated. The presence of ferrite nanoparticles less than 1 wt % increased the crystallization temperature (Tc) by 4.2 °C with ferrite content, but further addition decreased Tc. The onset temperature of degradation was increased by 7.3 °C at only 0.1 wt % loading of ferrite, after which the thermal stability of nylon‐66 was decreased with ferrite content. The incorporation of ferrite nanoparticles more than 5 wt % increased the dynamic viscosity (η′) with the loading level. Further, it produced notably shear thickening behavior in the low frequency, after which high degree of shear thinning was followed with ferrite content. In the Cole–Cole plot, the nanocomposites with ferrite lower than 5 wt % presented a single master curve, while further addition gave rise to a deviation from the curve. The relaxation time (λ) was increased with ferrite content and the difference of λ between nylon‐66 and its nanocomposite was greater at lower frequency. The tensile strength was a little increased up to 1 wt % loading, after which it was decreased with increasing the loading level. In addition, the introduction of the nanoparticles increased tensile modulus and decreased the ductility with ferrite content. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 371–377, 2006