bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in protein distribution between human plasma preparations, EDTA‐plasma and heparin‐plasma, analyzed by non‐denaturing micro‐2‐DE and MALDI‐MS PMF
Authors: Jin Ya , Manabe Takashi 
Published: March 2009

AbstractThe effects of plasma preparation methods on the status of human plasma proteins were analyzed by non‐denaturing micro‐2‐DE followed with polypeptide assignment with MALDI‐TOF MS and PMF. In order to facilitate the separation of high‐molecular‐mass plasma proteins (up to ca. 2×103 kDa) in short separation time, agarose micro‐IEF gels were employed. The comparisons of the 2‐DE patterns between EDTA‐plasma (1.0 mg EDTA/mL blood) and heparin‐plasma (0.025 mg heparin/mL blood) revealed the differences in protein distribution around pI 5.4–6.5 and apparent molecular mass of ca. 1×103 kDa, which were mainly attributed to the presence of the complexes of complement C4b and C4b‐binding protein in heparin‐plasma and their absence in EDTA‐plasma. The distribution of several spots around pI 5.0–5.6 and apparent molecular mass 1.2–1.5×102 kDa was also found to be different; the fragments of complement C3 and C4 were detected in heparin‐plasma but not in EDTA‐plasma. The 2‐DE pattern of high‐heparin‐plasma (0.50 mg heparin/mL blood) showed pI changes of three plasma proteins, fibronectin, complement factor B, and pre‐alpha‐inhibitor when compared with that of heparin‐plasma, suggesting the interactions between heparin and the proteins. These results demonstrated that subtle changes in plasma proteins, caused by the different plasma preparation procedures, can be analyzed by non‐denaturing agarose‐IEF/micro‐2‐DE followed by MALDI‐MS and PMF.
Growth and solvent production by Clostridium pasteurianum ATCC® 6013™ utilizing biodiesel‐derived crude glycerol as the sole carbon source
Authors: Taconi Katherine A. , Venkataramanan Keerthi P. , Johnson Duane T. 
Published: March 2009

AbstractThe rapidly expanding market for biodiesel is dramatically altering the cost and availability of glycerol, as typical biodiesel production processes generate about 10 wt % glycerol. Biodiesel producers have little financial incentive to purify the crude glycerol, and because it contains methanol, crude glycerol is considered a hazardous waste. Therefore, it is critical that new and innovative processes for managing and utilizing the glycerol co‐product be developed. In the longer term, as supplies continue to increase, glycerol will become a versatile building block chemical for the production of high value compounds within an integrated biorefinery.This research investigated the value‐added conversion of crude glycerol generated during biodiesel production using anaerobic fermentation. Pure cultures of Clostridium pasteurianum have been shown to produce significant amounts of butanol and 1,3‐propanediol when utilizing purified glycerol as the sole substrate. Butanol is of particular interest as a renewable biofuel, as it has a higher heating value, higher octane number, lower vapor pressure, and higher miscibility than ethanol, making butanol preferable to ethanol for blending with petroleum fuels.Preliminary experiments compared growth and product formation of C. pasteurianum (ATCC®6013™) utilizing both purified and biodiesel‐derived crude glycerol as the sole carbon source in batch culture. Cultures utilizing crude glycerol demonstrated significant growth and production of butanol, 1,3‐PDO, and ethanol at concentrations up to 25 g/L crude glycerol. This work is significant in that it is the first report of butanol production from crude glycerol using this organism. The maximum yield of butanol produced from pure glycerol was 0.36 g/g, while the maximum butanol yield produced from crude glycerol was 0.30 g/g. These yields are substantially higher than the 0.15–0.20 g/g butanol yield typically achieved during the fermentation of glucose using C. acetobutylicum. These results indicate that biodiesel‐derived crude glycerol is a promising, low‐cost, renewable feedstock for butanol production. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Rapid incision of the Colorado River in Glen Canyon – insights from channel profiles, local incision rates, and modeling of lithologic controls
Authors: Cook Kristen L. , Whipple Kelin X. , Heimsath Arjun M. , Hanks Thomas C. 
Published: March 2009

AbstractThe Colorado River system in southern Utah and northern Arizona is continuing to adjust to the baselevel fall responsible for the carving of the Grand Canyon. Estimates of bedrock incision rates in this area vary widely, hinting at the transient state of the Colorado and its tributaries. In conjunction with these data, we use longitudinal profiles of the Colorado and tributaries between Marble Canyon and Cataract Canyon to investigate the incision history of the Colorado in this region. We find that almost all of the tributaries in this region steepen as they enter the Colorado River. The consistent presence of oversteepened reaches with similar elevation drops in the lower section of these channels, and their coincidence within a corridor of high local relief along the Colorado, suggest that the tributaries are steepening in response to an episode of increased incision rate on the mainstem. This analysis makes testable predictions about spatial variations in incision rates; these predictions are consistent with existing rate estimates and can be used to guide further studies. We also present cosmogenic nuclide data from the Henry Mountains of southern Utah. We measured in situ 10Be concentrations on four gravel‐covered strath surfaces elevated from 1 m to 110 m above Trachyte Creek. The surfaces yield exposure ages that range from approximately 2·5 ka to 267 ka and suggest incision rates that vary between 350 and 600 m/my. These incision rates are similar to other rates determined within the high‐relief corridor. Available data thus support the interpretation that tributaries of the Colorado River upstream of the Grand Canyon are responding to a recent pulse of rapid incision on the Colorado. Numerical modeling of detachment‐limited bedrock incision suggests that this incision pulse is likely related to the upstream‐dipping lithologic boundary at the northern edge of the Kaibab upwarp. Copyright © 2009 John Wiley & Sons, Ltd.
Short‐term forecasting of GDP using large datasets: a pseudo real‐time forecast evaluation exercise
Authors: Rünstler G. , Barhoumi K. , Benk S. , Cristadoro R. , Den Reijer A. , Jakaitiene A. , Jelonek P. , Rua A. , Ruth K. , Van Nieuwenhuyze C. 
Published: March 2009

AbstractThis paper performs a large‐scale forecast evaluation exercise to assess the performance of different models for the short‐term forecasting of GDP, resorting to large datasets from ten European countries. Several versions of factor models are considered and cross‐country evidence is provided. The forecasting exercise is performed in a simulated real‐time context, which takes account of publication lags in the individual series. In general, we find that factor models perform best and models that exploit monthly information outperform models that use purely quarterly data. However, the improvement over the simpler, quarterly models remains contained. Copyright © 2009 John Wiley & Sons, Ltd.
Expression of a novel marker, Ubc9, in squamous cell carcinoma of the head and neck
Authors: Ronen Ohad , Malone James P. , Kay Paul , Bivens Christopher , Hall Kelly , Paruchuri Lakshmi P. , Mo Yin‐Yuan , Robbins K. Thomas , Ran Sophia 
Published: March 2009

AbstractBackground.Ubiquitin‐conjugating enzyme (Ubc9) is a novel enzyme involved in posttranslational modification of cellular proteins. The objective of this study was to determine the expression of Ubc9 in squamous cell carcinoma of the head and neck (SCCHN).Methods.SCCHN specimens were stained with anti‐Ubc9 antibodies, scored using a semiquantitative method, and statistically analyzed.Results.Forty‐six tumors were stained, 26 of which included adjacent mucosa. Ubc9 was significantly upregulated in the malignant and peritumoral tissues compared with mucosa from normal individuals. In peritumoral tissues, Ubc9 expression was detected in the basal and suprabasal epithelial layers. No Ubc9 was detected in epithelial cells in normal mucosa. These differences in Ubc9 expression were statistically significant (p < .0001). Tumor Ubc9 expression significantly correlated with clinical and pathologic stage.Conclusions.Ubc9 is significantly overexpressed in the primary SCCHN tumors and peritumoral mucosa compared with normal epithelial cells. These findings suggest that Ubc9 may play an important role in tumorigenesis and tumor progression of SCCHN. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Fluorescence in situ hybridization gene amplification analysis of EGFR and HER2 in patients with malignant salivary gland tumors treated with lapatinib
Authors: Vidal Laura , Tsao Ming S. , Pond Gregory R. , Cohen Ezra E. W. , Cohen Roger B. , Chen Eric X. , Agulnik Mark , Hotte Sebastien , Winquist Eric , Laurie Scott , Neil Hayes D. , Ho James , Dancey Janet , Siu Lillian L. 
Published: March 2009

AbstractBackground.Gene amplification status of the epidermal growth factor receptor (EGFR) and the human epidermal growth factor receptor 2 (HER2) were analyzed and correlated with clinical outcome in patients with progressive malignant salivary glands tumors (MSGT) treated with the dual EGFR/Her2 tyrosine kinase inhibitor lapatinib.Methods.Fluorescence in situ hybridization (FISH) analysis for both EGFR and HER2 gene amplification was performed successfully in the archival tumor specimens of 20 patients with adenoid cystic carcinomas (ACC) and 17 patients with non‐ACC, all treated with lapatinib.Results.For ACC, no EGFR or HER2 amplifications were detected. For non‐ACC, no EGFR gene amplifications were detected but 3 patients (18%) were HER2 amplified and all had stained 3+ for both EGFR and HER2 by immunohistochemistry (IHC) in their archival specimens. Two of these patients had time‐to‐progression (TTP) durations of 8.3 months and 18.4 months, respectively. Interestingly, patients with low and high HER2/chromosome‐specific centromeric enumeration probe (CEP) 17 ratio had a prolonged TTP than those with moderate ratios for both ACC and non‐AAC subtypes.Conclusions.HER2 to CEP17 FISH ratio may predict which patients with MSGT have an increased likelihood to benefit from lapatinib. The finding of HER2:CEP17 ratio as a predictive marker of efficacy to lapatinib warrants further investigation. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Polarized diffuse reflectance measurements on cancerous and noncancerous tissues
Authors: Manhas Sandeep , Swami Mahesh K. , Patel Hari S. , Uppal Abha , Ghosh Nirmalya , Gupta Pradeep K. 
Published: March 2009

AbstractWe report the measurement of polarization parameters (linear retardance, diattenuation and depolarization) of normal and malignant tissue from human oral cavity and breast over the spectral range 390 nm to 550 nm. These parameters were determined using the 3 × 3 Mueller matrix, the elements of which could be determined using linear polarization measurements only. The significant differences observed in the polarization parameters of the normal and malignant tissues appear to arise because of the changes in the collagen matrix in the two tissue types. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Location, location, (ChIP‐)location! Mapping chromatin landscapes one immunoprecipitation at a time
Authors: Berman Benjamin P. , Frenkel Baruch , Coetzee Gerhard A. 
Published: March 2009

AbstractA small fraction of the typical animal genome (<5% in humans) codes for the organism's collection of proteins, yet the study of protein coding sequences dominated the early years of genomics research. In the decade since the sequencing of complete eukaryotic genomes, however, genomic techniques have shed a great deal of light on the non‐coding DNA making up the remainder. A single molecular technique, Chromatin Immuno‐Precipitation (ChIP) location analysis, has had a profound impact and has made possible the study of an incredible range of biology. This issue of The Journal of Cellular Biochemistry aims to put into context advancements made possible by the ChIP‐location revolution, while at the same time highlighting some of the most important technical aspects and challenges along with some of the work yet to come. J. Cell. Biochem. 107: 1–5, 2009. © 2009 Wiley‐Liss, Inc.
Functional p53 in cells contributes to the anticancer effect of the cyclin‐dependent kinase inhibitor roscovitine
Authors: Paprskářová Martina , Kryštof Vladimír , Jorda Radek , Džubák Petr , Hajdúch Marián , Węsierska‐Gądek Józefa , Strnad Miroslav 
Published: March 2009

AbstractInhibitors of cyclin‐dependent kinases (CDKs) undergoing clinical trials as anticancer agents usually target several CDKs in cells. Some of them are also able to increase cellular levels of p53 protein and to activate p53‐regulated transcription. To define the role of p53 in the anticancer effect of selective CDK inhibitors, two related compounds roscovitine and olomoucine II were studied. Roscovitine differs functionally from its congener olomoucine II only in the selectivity towards transcriptional CDK9. Action of both compounds on proliferation, cell‐cycle progression, and apoptosis was examined in RPMI‐8226 cells expressing the temperature‐sensitive mutant of p53 and in MCF‐7 cells with wild‐type p53. Both compounds blocked proliferation, decreased phosphorylation of RNA polymerase II, downregulated antiapoptotic protein Mcl‐1 in both cell lines in a dose‐dependent manner, and also activated p53 in MCF‐7 cells. Moreover, we showed that the anticancer efficiency of CDK inhibitors was enhanced by active p53 in RPMI‐8226 cells kept at permissive temperature, where downregulation of Mcl‐1, fragmentation of PARP‐1, and increased caspase‐3 activity was detected with lower doses of the compounds. The results confirm that functional p53 protein may enhance the anticancer activity of roscovitine that could be beneficial for anticancer therapy. J. Cell. Biochem. 107: 428–437, 2009. © 2009 Wiley‐Liss, Inc.
Should transition zone biopsies be added to 12‐core systematic biopsies of the prostate?
Authors: Hwang Sung Il , Lee Hak Jong , Cho Jeong Yeon , Kim Seung Hyup , Lee Sang Eun , Byun Seok‐Soo , Hong Sung Kyu , Choe Ghee Young 
Published: March 2009

AbstractPurposeTo investigate the value of additional transition zone (TZ) biopsies following 12‐core biopsies in the detection and staging of prostate cancer.MethodsFrom October 2006 to March 2007, 199 transrectal sonographic (TRUS)‐guided prostate biopsies (group 1) in 12 peripheral zones (PZ) were performed. Another 199 consecutive patients (group 2) underwent two TZ biopsies in addition to twelve PZ biopsies from March 2007 to July 2007. Mean prostate‐specific antigen (PSA) level, prostate volume, Gleason score, and cancer detection rate of each group were compared. The anatomic distribution of prostate cancer in group 2 was also analyzed.ResultsProstate cancer was detected in 76 of 199 patients (38.2%) in group 1 and 71 out of 199 patients (35.3%) in group 2. The cancer detection rate, mean PSA level, prostate volume, and Gleason score were not statistically different in the 2 groups. Cancer was detected by additional TZ biopsies alone in just one out of 71 patients (1.4%).ConclusionRoutine TZ biopsies following 12‐core systematic biopsies are not warranted for the detection of TZ cancer because of their low additional yield. © 2009 Wiley Periodicals, Inc. J Clin Ultrasound, 2009
Multipartite Ramsey numbers for odd cycles
Authors: Gyárfás András , Sárközy Gábor N. , Schelp Richard H. 
Published: March 2009

AbstractIn this paper we study multipartite Ramsey numbers for odd cycles. We formulate the following conjecture: Let n≥5 be an arbitrary positive odd integer; then, in any two‐coloring of the edges of the complete 5‐partite graph K((n−1)/2, (n−1)/2, (n−1)/2, (n−1)/2, 1) there is a monochromatic Cn, a cycle of length n. This roughly says that the Ramsey number for Cn (i.e. 2n−1 ) will not change (somewhat surprisingly) if four large “holes” are allowed. Note that this would be best possible as the statement is not true if we delete from K2n−1 the edges within a set of size (n+ 1)/2. We prove an approximate version of the above conjecture. © 2009 Wiley Periodicals, Inc. J Graph Theory 61:12‐21, 2009
Fair reception and Vizing's conjecture
Authors: Brešar Boštjan , Rall Douglas F. 
Published: March 2009

AbstractIn this paper we introduce the concept of fair reception of a graph which is related to its domination number. We prove that all graphs G with a fair reception of size γ(G) satisfy Vizing's conjecture on the domination number of Cartesian product graphs, by which we extend the well‐known result of Barcalkin and German concerning decomposable graphs. Combining our concept with a result of Aharoni, Berger and Ziv, we obtain an alternative proof of the theorem of Aharoni and Szabó that chordal graphs satisfy Vizing's conjecture. A new infinite family of graphs that satisfy Vizing's conjecture is also presented. © 2009 Wiley Periodicals, Inc. J Graph Theory 61: 45‐54, 2009
Synthesis of substituted N‐[4(5‐methyl/phenyl‐1,3,4‐oxadiazol‐2‐yl)‐3,6‐dihydropyridin‐1(2H)‐yl]benzamide/benzene sulfonamides as anti‐inflammatory and anti‐cancer agents
Authors: Gangapuram Madhavi , Redda Kinfe K. 
Published: March 2009

Abstract
magnified imageFourteen novel substituted N‐[4(5‐methyl/phenyl‐1,3,4‐oxadiazol‐2‐yl)‐3,6‐dihydropyridin‐1(2H)‐yl] benzamide/benzene sulfonamides (11a, 11b, 11c, 11d, 11e, 11f, 11g, 11h, 11i, 11j, 11k, 11l, 11m, 11n) were synthesized in fair to good yields via sodium borohydride reduction of the corresponding substituted N‐(benzoylimino)‐4‐(5‐methyl/5‐phenyl‐1,3,4‐oxadiazol‐2yl) pyridinium ylide 10a, 10b, 10c, 10d, 10e, 10f, 10g, 10h, 10i, 10j, 10k, 10m, 10n in absolute ethanol. J. Heterocyclic Chem., (2009)
Interpreting variability in global SST data using independent component analysis and principal component analysis
Authors: Westra Seth , Brown Casey , Lall Upmanu , Koch Inge , Sharma Ashish 
Published: March 2009

AbstractComponent extraction techniques are used widely in the analysis and interpretation of high‐dimensional climate datasets such as global sea surface temperatures (SSTs). Principal component analysis (PCA), a frequently used component extraction technique, provides an orthogonal representation of the multivariate dataset and maximizes the variance explained by successive components. A disadvantage of PCA, however, is that the interpretability of the second and higher components may be limited. For this reason, a Varimax rotation is often applied to the PCA solution to enhance the interpretability of the components by maximizing a simple structure. An alternative rotational approach is known as independent component analysis (ICA), which finds a set of underlying ‘source signals’ which drive the multivariate ‘mixed’ dataset.Here we compare the capacity of PCA, the Varimax rotation and ICA in explaining climate variability present in globally distributed SST anomaly (SSTA) data. We find that phenomena which are global in extent, such as the global warming trend and the El Niño‐Southern Oscillation (ENSO), are well represented using PCA. In contrast, the Varimax rotation provides distinct advantages in interpreting more localized phenomena such as variability in the tropical Atlantic. Finally, our analysis suggests that the interpretability of independent components (ICs) appears to be low. This does not diminish the statistical advantages of deriving components that are mutually independent, with potential applications ranging from synthetically generating multivariate datasets, developing statistical forecasts, and reconstructing spatial datasets from patchy observations at multiple point locations. Copyright © 2009 Royal Meteorological Society
Laser precision engineering: from microfabrication to nanoprocessing
Authors: Chong T.C. , Hong M.H. , Shi L.P. 
Published: March 2009

AbstractLaser precision engineering is being extensively applied in industries for device microfabrication due to its unique advantages of being a dry and noncontact process, coupled with the availability of reliable light sources and affordable system cost. To further reduce the feature size to the nanometer scale, the optical diffraction limit has to be overcome. With the combination of advanced processing tools such as SPM, NSOM, transparent and metallic particles, feature sizes as small as 20 nm have been achieved by near‐field laser irradiation, which has extended the application scope of laser precision engineering significantly. Meanwhile, parallel laser processing has been actively pursued to realize large‐area and high‐throughput nanofabrication by the use of microlens arrays (MLA). Laser thermal lithography using a DVD optical storage process has also been developed to achieve low‐cost and high‐speed nanofabrication. Laser interference lithography, another large area nanofabrication technique, is also capable of fabricating sub‐100 nm periodic structures. To further reduce the feature size to the atomic scale, atomic lithography using laser cooling to localize atoms is being developed, bringing laser‐processing technology to a new era of atomic engineering.
Transverse optical patterns for ultra‐low‐light‐level all‐optical switching
Authors: Dawes A.M.C. , Gauthier D.J. , Schumacher S. , Kwong N.H. , Binder R. , Smirl A.L. 
Published: March 2009

AbstractWe review recent theoretical and experimental efforts toward developing an all‐optical switch based on transverse optical patterns. Transverse optical patterns are formed when counterpropagating laser beams interact with a nonlinear medium. A perturbation, in the form of a weak switch beam injected into the nonlinear medium, controls the orientation of the generated patterns. Each state of the pattern orientation is associated with a state of the switch. That is, information is stored in the orientation state. A realization of this switch using a warm rubidium vapor shows that it can be actuated by as few as 600 ± 40 photons with a response time of 5 µs. Models of nonlinear optical interactions in semiconductor quantum wells and microresonators suggest these systems are also suitable for use as fast all‐optical switches using this same conceptual design, albeit at higher switching powers.
Modelling properties of micro‐ and nanocomposites with brush‐like reinforcement
Authors: Guz I.A. , Guz A.N. , Rushchitsky J.J. 
Published: March 2009

AbstractThis paper presents a new four‐component model for predicting the mechanical properties of micro‐ and nanocomposites reinforced either by whiskerizing the microfibres or by bristlizing the nanowires. The model is a generalization of the existing three‐component model. Instead of the thin shell model for the fibre coating, two different components are distinguished: the solid coating surrounding the fibre and the bristled coating surrounding the solid coating. The mathematical formulation of the model is based on using the Muskhelishvili complex potentials for each domain occupied by a separate component. The effective elastic constants are computed for fibrous composites with four different densities of wiskerisation. It is shown that the increase in the number of bristles per unit surface of the fibres gives a very strong rise to the value of Young’s modulus. However, the shear modulus, being the driving parameter for the strength estimation of the entire composition, is less sensitive to this factor.