bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rainfall‐induced consolidation and sealing effects on soil erodibility during concentrated runoff for loess‐derived topsoils
Authors: Knapen A. , Poesen J. , Baets S. De 
Published: September 2007

AbstractFlume experiments simulating concentrated runoff were carried out on remolded silt loam soil samples (0·36 × 0·09 × 0·09 m3) to measure the effect of rainfall‐induced soil consolidation and soil surface sealing on soil erosion by concentrated flow for loess‐derived soils and to establish a relationship between soil erodibility and soil bulk density. Soil consolidation and sealing were simulated by successive simulated rainfall events (0–600 mm of cumulative rainfall) alternated by periods of drying. Soil detachment measurements were repeated for four different soil moisture contents (0·04, 0·14, 0·20 and 0·31 g g−1). Whereas no effect of soil consolidation and sealing is observed for critical flow shear stress (τcr), soil erodibility (Kc) decreases exponentially with increasing cumulative rainfall depth. The erosion‐reducing effect of soil consolidation and sealing decreases with a decreasing soil moisture content prior to erosion due to slaking effects occurring during rapid wetting of the dry topsoil. After about 100 mm of rainfall, Kc attains its minimum value for all moisture conditions, corresponding to a reduction of about 70% compared with the initial Kc value for the moist soil samples and only a 10% reduction for the driest soil samples. The relationship estimating relative Kc values from soil moisture content and cumulative rainfall depth predicts Kc values measured on a gradually consolidating cropland field in the Belgian Loess Belt reasonably well (MEF = 0·54). Kc is also shown to decrease linearly with increasing soil bulk density for all moisture treatments, suggesting that the compaction of thalwegs where concentrated flow erosion often occurs might be an alternative soil erosion control measure in addition to grassed waterways and double drilling. Copyright © 2007 John Wiley & Sons, Ltd.
The chronology and long term dynamics of a low energy river system: the Kelvin Valley, central Scotland
Authors: Tipping R. , Jones A. P. , Carter S. , Holden T. , Cressey M. 
Published: September 2007

AbstractThe long term (Holocene) channel and floodplain dynamics of a low gradient, low energy, fine grained aggradational fluvial system within a formerly glaciated landscape in central Scotland, the Kelvin Valley, are described from a series of sediment stratigraphic transects and 12 14C assays in a headwater reach between Kirkintilloch and Kilsyth. The 14C assays and dated archaeological sites on the floodplain together suggest that the River Kelvin ceased to aggrade more than 2000 years ago, probably much more, so the 4–6 m of channel and floodplain deposits are almost entirely of early to mid‐Holocene age. The Kelvin Valley is characterized, despite its low flow characteristics, by a highly variable floodplain architecture, in which some transects suggest long term channel stability and strong partitioning of floodplain sedimentation and others indicate high channel mobility. This variation makes the application of general models of fluvial evolution difficult. Copyright © 2007 John Wiley & Sons, Ltd.
A new ultra‐fast contingency screening algorithm without time‐domain simulation for online transient security assessment
Authors: Nam H. K. , Kim Y. H. , Shim K. S. , Choi J. H. , Kwak N. H. 
Published: September 2007

AbstractThis paper proposes a new ultra‐fast contingency screening (CS) method for the transient security assessment (TSA). The method is based on the Single Machine Equivalent (SIME), but computes the critical clearing times (CCT) for given disturbances without the use of time‐domain simulations. All generators and loads are represented by a classical model and constant impedance model, respectively. The critical clustering is done using two stability indices, which are defined as the ratio of the accelerating power to the synchronizing power coefficient and the accelerating area to the decelerating area, respectively. Finally, the CCT is calculated using the equal‐area criterion to the equivalent one‐machine infinite‐bus system with the assumption that the rotor angles of the critical generators increase uniformly and the rotor angles of the non‐critical ones remain constant. The proposed CS method is tested on the 950‐bus, 230‐machine, 60‐Hz KEPCO system. Copyright © 2007 John Wiley & Sons, Ltd.
Optimal measurement placement for security constrained state estimation using hybrid genetic algorithm and simulated annealing
Authors: Kerdchuen T. , Ongsakul W. 
Published: September 2007

AbstractThis paper proposes a hybrid genetic algorithm and simulated annealing (HGS) for solving optimal measurement placement for power system state estimation. Even though the minimum number of measurement pairs is N considering the single measurement loss, their positions are required to make the system observable. HGS algorithm is a genetic algorithm (GA) using the acceptance criterion of simulated annealing (SA) for chromosome selection. The Pδ observable concept is used to check the network observability with and without single measurement pair loss contingency and single branch outage. Test results of 10‐bus, IEEE 14, 30, 57, and 118‐bus systems indicate that HGS is superior to tabu search (TS), GA, and SA in terms of higher frequency of the best hit and faster computational time. Copyright © 2007 John Wiley & Sons, Ltd.
Direct, adjoint and mixed approaches for the computation of Hessian in airfoil design problems
Authors: Papadimitriou D. I. , Giannakoglou K. C. 
Published: September 2007

AbstractIn this paper, four approaches to compute the Hessian matrix of an objective function used often in aerodynamic inverse design problems are presented. The computationally less expensive among them is selected and applied to the reconstruction of cascade airfoils that reproduce a prescribed pressure distribution over their walls, under inviscid and viscous flow considerations. The selected approach is based on the direct sensitivity analysis method for the computation of first derivatives, followed by the discrete adjoint method for the computation of the Hessian matrix. The applications presented in this paper show that the Newton method, based on exact Hessian matrices, outperforms other gradient‐based algorithms such as steepest descent or BFGS algorithm. Copyright © 2007 John Wiley & Sons, Ltd.
Altered expression of the urokinase receptor homologue, C4.4A, in invasive areas of human esophageal squamous cell carcinoma
Authors: Hansen Line V. , Lærum Ole D. , Illemann Martin , Nielsen Boye S. , Ploug Michael 
Published: September 2007

AbstractC4.4A is a glycolipid‐anchored membrane protein with structural homology to the urokinase‐type plasminogen activator receptor (uPAR). Although C4.4A was identified as a metastasis‐associated protein little is known about its actual expression and possible function in malignant disease. In the present study, we have therefore analyzed the expression of C4.4A in 14 esophageal squamous cell carcinomas (ESCC). Normal squamous esophageal epithelium shows a strong cell surface associated C4.4A expression in the suprabasal layers, whereas basal cells are negative. Upon transition to dysplasia and carcinoma in situ the expression of C4.4A is abruptly and coordinately weakened. Double immunofluorescence staining of normal and dysplastic tissue showed that C4.4A colocalizes with the epithelial cell surface marker E‐cadherin in the suprabasal cells and has a complementary expression pattern compared to the proliferation marker Ki‐67. A prominent, but frequently intracellular, C4.4A expression reappeared in tumor cells located at the invasive front and local lymph node metastases. Because C4.4A was reported previously to be a putative laminin‐5 (LN5) ligand, and both proteins are expressed by invasive tumor cells, we analyzed the possible coexpression of C4.4A and the γ2‐chain of LN5 (LN5‐γ2). Although these proteins are indeed expressed by either neighboring cancer cells or in a few cases even coexpressed by the same cells in the tumor front and metastases, we found no evidence for a general colocalization in the extracellular compartment by confocal microscopy. In conclusion, C4.4A is expressed during invasion and metastasis of human ESCC and may thus provide a new histological marker in this disease. © 2007 Wiley‐Liss, Inc.
Transforming growth factor‐β signaling in cancer invasion and metastasis
Authors: Leivonen Suvi‐Katri , Kähäri Veli‐Matti 
Published: September 2007

AbstractTransforming growth factor‐β (TGF‐β) family members are polypeptides with dual tumor suppressive and oncogenic effects. They signal through serine/threonine kinase receptor complexes, which phosphorylate cytoplasmic mediators, the Smads. Upon phosphorylation, Smads translocate to the nucleus and associate with transcriptional coactivators or corepressors, and regulate the transcriptional activation of various TGF‐β responsive genes. In addition, TGF‐β activates cellular mitogen‐activated protein kinase signaling pathways, which crosstalk with Smad signaling and regulate growth, survival and motility of cells. During tumorigenesis, malignantly transformed cells often lose the response to the tumor suppressive effects of TGF‐β, which, in turn, starts to act as an autocrine tumor promoting factor by enhancing cancer invasion and metastasis. In this review, we summarize current view on the role of TGF‐β signaling in tumorigenesis, with emphasis on cancer invasion and metastasis. On the basis of these recent observations, we discuss new therapeutic strategies targeting TGF‐β signaling at distinct levels as a basis for inhibiting tumor growth, angiogenesis, invasion and metastasis. © 2007 Wiley‐Liss, Inc.
The spatial order of transcription in mammalian cells
Authors: Levsky Jeffrey M. , Shenoy Shailesh M. , Chubb Jonathan R. , Hall Charles B. , Capodieci Paola , Singer Robert H. 
Published: September 2007

AbstractWe have previously developed technology for multiplexing probes for the detection of transcription of many genes simultaneously within single cells. This has allowed us to determine the spatial localization of multiple genes with respect to each other in the nucleus, and ultimately the expression profile of the cell with respect to surrounding cells in a tissue. Six parameters of transcriptional organization in individual cells from culture and tissue were used to characterize significant differences in intracellular and intercellular expression patterns while preserving cellular morphology and histological context. We found that, unlike yeast, mammalian expression is excluded from the periphery and in addition, a subtle but complex organization underlies the transcriptional activity of these cells, both intra‐ and intercellularly. The approach has sufficient spatial resolution to be applied to the detection of chromosomal translocations or the identification of cancer cells. J. Cell. Biochem. 102: 609–617, 2007. © 2007 Wiley‐Liss, Inc.
Reciprocal regulation of Notch and PI3K/Akt signalling in T‐ALL cells In Vitro
Authors: Calzavara Elisabetta , Chiaramonte Raffaella , Cesana Daniela , Basile Andrea , Sherbet Gajanan V. , Comi Paola 
Published: September 2007

AbstractNotch signalling plays an important role in hematopoiesis and in the pathogenesis of T‐ALL. Notch is known to interact with Ras and PTEN/PI3K (phosphoinositide‐3 kinase)/Akt pathways. We investigated the interaction of Notch with these pathways and the possible reciprocal regulation of these signalling systems in T‐ALL cells in vitro. Our analyses indicate that the PI3K/Akt pathway is constitutively active in the four T‐ALL cell lines tested. Akt phosphorylation was not altered by the sequestration of growth factors, that is, Akt activation seems to be less dependent on but not completely independent of growth factors, possibly being not subject to negative feedback regulation. PTEN expression was not detected in 3/4 cell lines tested, suggesting the loss of PTEN‐mediated Akt activation. Inhibition of the PI3K/Akt pathway arrests growth and enhances apoptosis, but with no modulation of expression of Bax‐α and Bcl‐2 proteins. We analysed the relationship between Notch‐1 and the PI3K/Akt signalling and show that inhibition of the Akt pathway changes Notch expression; Notch‐1 protein decreased in all the cell lines upon treatment with the inhibitor. Our studies strongly suggest that Notch signalling interacts with PI3K/Akt signalling and further that this occurs in the absence of PTEN expression. The consequences of this to the signalling outcome are yet unclear, but we have uncovered a significant inverse relationship between Notch and PI3K/Akt pathway, which leads us to postulate the operation of a reciprocal regulatory loop between Notch and Ras‐PI3K/Akt in the pathogenesis of T‐ALL. J. Cell. Biochem. 103: 1405–1412, 2008. © 2007 Wiley‐Liss, Inc.
cclib: A library for package‐independent computational chemistry algorithms
Authors: O'boyle Noel M. , Tenderholt Adam L. , Langner Karol M. 
Published: September 2007

AbstractThere are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package‐independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Rapid acid digestion and simple microplate method for milk iodine determination
Authors: Hedayati Mehdi , Ordookhani Arash , Daneshpour Maryam Sadat , Azizi Fereidoun 
Published: September 2007

AbstractIodine deficiency leads to deficiency of thyroid hormones, which causes mental retardation in infant. Laboratory confirmation is important in its diagnosis. The major problems associated with the existing methods for iodine determination in milk samples are: 1) nonsafe alkaline solution; 2) harsh thermal condition; and 3) extra time required to complete various steps. In this study, a simple and rapid colorimetric method was investigated, which used acid digestion in combination with a rapid microplate reading format method to determine the total iodine content in milk. Sample digestion was done on 50 µL milk in metavanadate/perchloric, at 230°C for 10 min. After digestion, iodine determination was based on the Sandell‐Kolthoff reaction. The reaction results were read in 96‐well microplates by an enzyme‐linked immunosorbent assay (ELISA) reader. The determination range of the assay was between 2 and 40 µg/dL. The within‐run coefficient of variation percent in three levels (3, 12, and 36 µg/dL) ranged from 6.7 to 9.3 and between‐run coefficients of variation ranged from 8.6 to 12.3%. The results obtained (n=70) by the optimized method have good correlation with the results of alkaline incineration as a reference method (n=70; r2=0.907; y=0.952x+1.77). Recovery tests for accuracy assessment in six levels from 6.2 to 34.2 µg/dL) were between 91.3 and 113%. This method has enabled us to achieve 0.12 µg/dL sensitivity. The results of this study show that a quick acid digestion combined with mild thermal and low sample volume with a quick reading of assay results were the main advantages of the acid digestion and microplate reading format. J. Clin. Lab. Anal. 21:286–292, 2007. © 2007 Wiley‐Liss, Inc.
Influence of sample matrix and storage on BNP measurement on the Bayer Advia Centaur
Authors: Lippi Giuseppe , Fortunato Antonio , Salvagno Gian Luca , Montagnana Martina , Soffiati Giuliano , Guidi Gian Cesare 
Published: September 2007

AbstractThe assessment and management of congestive heart failure relies increasingly on the measurement of B‐type natriuretic peptide (BNP). However, the effective contribution of this biochemical test in the clinical decision making is influenced by reliability of the measure, which also depends on several preanalytical issues. Since there is controversy on the influence of the matrix and the storage conditions on BNP measurement, we compared results of BNP in serum, K2 ethylene diamine tetra‐acetic acid (EDTA) plasma and lithium heparin plasma fresh samples and in matching samples stored at −20 and −80°C for 1 week. BNP measured on the Bayer Advia Centaur was systematically underestimated in heparin plasma (−47%) and serum (−62%) when compared to K2 EDTA plasma. According to the established 100 ng/L cutoff value, 25% and 37% of the fresh samples collected in heparin plasma or serum were misclassified from the reference K2 EDTA fresh specimen, respectively. When compared to the fresh specimens, the mean and interindividual bias observed for samples stored at either −20°C or −80°C was, overall, modest for K2 EDTA plasma (−2%) and heparin plasma (+6% and −4%, respectively), though it appeared clinically meaningful in serum (+47% and +28%, respectively). Although we can not rule out that other BNP assays using different antibodies may be not affected from degradation during storage to the same extent, results of our investigation demonstrate that K2 EDTA plasma is the most suitable specimens for BNP testing on fresh and frozen samples stored at either −20°C or −80°C for up to 1 week. J. Clin. Lab. Anal. 21:293–297, 2007. © 2007 Wiley‐Liss, Inc.
Transcription‐mediated amplification linked to line probe assay as a routine tool for HCV typing in clinical laboratories
Authors: Ross R.S. , Viazov S. , Kpakiwa S.S. , Roggendorf M. 
Published: September 2007

AbstractTyping of hepatitis C virus (HCV) isolates is currently a prerequisite for adequate tailoring of antiviral combination therapy. In many diagnostic laboratories, there seems to be a tendency toward convenient and time‐saving procedures utilizing amplification products, which are already available from preceding qualitative or quantitative HCV ribonucleic acid (RNA) assays. In this context, we evaluated the performance characteristics of a combination of techniques, i.e., transcription‐mediated amplification‐line probe assay (TMA‐LiPA), which links highly sensitive TMA of HCV RNA to the VERSANT HCV Genotype Assay (version 1). A total of 100 clinical samples were genotyped by TMA‐LiPA. The obtained results were compared to those recorded by the original, nested reverse transcription (RT)‐polymerase chain reaction (PCR)‐based VERSANT assay, the core‐related GEN‐ETI‐K DEIA, and phylogenetic analyses of partial sequences from the HCV core and NS5B regions. TMA‐LiPA assigned the correct genotype to all 100 HCV isolates. For subtyping of genotype 1 and 2 isolates, TMA‐LiPA only showed discriminatory powers of 82% and 53%, respectively. Thus, TMA‐LiPA in our hands turned out as a convenient and time‐saving routine procedure for HCV typing which currently provides sufficient information for clinical purposes. Like all 5′untranslated region (UTR)‐based assays, the technique is limited, however, in its potentials to resolve the complexity of existing HCV subtypes. J. Clin. Lab. Anal. 21:340–347, 2007. © 2007 Wiley‐Liss, Inc.
Short dysfunctional telomeres impair the repair of arsenite‐induced oxidative damage in mouse cells
Authors: Newman Jennifer P.A. , Banerjee Birendranath , Fang Wanru , Poonepalli Anuradha , Balakrishnan Lakshmidevi , Low Grace Kah Mun , Bhattacharjee Rabindra N. , Akira Shizuo , Jayapal Manikandan , Melendez Alirio J. , Baskar Rajamanickam , Lee Han‐Woong , Hande M. Prakash 
Published: September 2007

AbstractTelomeres and telomerase appear to participate in the repair of broken DNA ends produced by oxidative damage. Arsenite is an environmental contaminant and a potent human carcinogen, which induces oxidative stress on cells via the generation of reactive oxygen species affecting cell viability and chromosome stability. It promotes telomere attrition and reduces cell survival by apoptosis. In this study, we used mouse embryonic fibroblasts (MEFs) from mice lacking telomerase RNA component (mTERC−/− mice) with long (early passage or EP) and short (late passage or LP) telomeres to investigate the extent of oxidative damage by comparing the differences in DNA damage, chromosome instability, and cell survival at 24 and 48 h of exposure to sodium arsenite (As3+; NaAsO2). There was significantly high level of DNA damage in mTERC−/− cells with short telomeres as determined by alkaline comet assay. Consistent with elevated DNA damage, increased micronuclei (MN) induction reflecting gross genomic instability was also observed. Fluorescence in situ hybridization (FISH) analysis revealed that increasing doses of arsenite augmented the chromosome aberrations, which contributes to genomic instability leading to possibly apoptotic cell death and cell cycle arrest. Microarray analysis has revealed that As3+ treatment altered the expression of 456 genes of which 20% of them have known functions in cell cycle and DNA damage signaling and response, cell growth, and/or maintenance. Results from our studies imply that short dysfunctional telomeres impair the repair of oxidative damage caused by arsenite. The results will have implications in risk estimation as well as cancer chemotherapy. J. Cell. Physiol. 214: 796–809, 2008. © 2007 Wiley‐Liss, Inc.
Confocal imaging of chromatographic fouling under flow conditions
Authors: Siu Sun Chau , Boushaba Rihab , Liau Jonathan , Hjorth Rolf , Titchener‐Hooker Nigel J 
Published: September 2007

AbstractBACKGROUND: The fouling impact of selected fouling species was assessed by utilising confocal scanning laser microscopy (CSLM) to image a packed chromatographic bed during operation. A custom‐made flow cell was packed with Q Sepharose FF and loaded with partially clarified E. coli homogenate. Selective, multicoloured fluorescent dyes were used to label a bovine serum albumin (BSA) test protein (Cy5.5), dsDNA (PicoGreen) and host cell proteins (HCPs) (Cy3). The fouling caused by the various fluorescently labelled components was visualised as a result of the fluorescence emitted by the PicoGreen‐labelled dsDNA and the Cy3‐labelled protein in the foulant stream, and by testing the adsorptive capacity of a test protein (BSA) onto the resin prior to and post‐fouling as well as following the application of a common CIP procedure.RESULTS: Values for the effective diffusivity of BSA (De) were derived from the confocal images and the fouling impact was assessed by comparing De values obtained from different fouling scenarios. Under the most extreme conditions examined, fouling caused a 20% reduction in capacity compared to a fresh bed. BSA diffusivity did not appear to be affected by the fouling conditions studied. Sequential CIP using 15 CVs of 1 mol L−1 NaCl then 15 CVs of 1 mol L−1 NaOH was shown to be effective in removing nucleic acids and HCPs. Subsequent BSA adsorption showed that the CIP regime successfully restored the column capacity to its original value. In contrast, 15 CVs of 1 mol L−1 NaCl were ineffective in removing dsDNA but substantially removed HCPs.CONCLUSION: CSLM was demonstrated to be a useful tool for visualising fouling mechanisms. Comparing the results obtained by this technique using different modes of chromatographic operation provided insights into the fouling characteristics of finite baths versus packed beds. Copyright © 2007 Society of Chemical Industry