bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNP genotyping using microsphere‐linked PNA and flow cytometric detection
Authors: Rockenbauer Eszter , Petersen Kenneth , Vogel Ulla , Bolund Lars , Kølvraa Steen , Nielsen Kirsten Vang , Nexø Bjørn A. 
Published: February 2005

AbstractBackgroundSingle nucleotide polymorphisms (SNPs) represent the most frequent form of genetic variations. Some of the most sensitive methods for SNP genotyping employ synthetic oligonucleotides, such as the peptide nucleic acid (PNA). We introduce a new method combining allele‐specific hybridization, PNA technology, and flow cytometric detection. We tested the design by genotyping a Danish basal cell carcinoma cohort of 80 individuals for an A/C SNP in exon 6 of the XPD gene.MethodsGenomic DNA was amplified by a two‐step polymerase chain reaction (PCR) in the presence of fluorescein‐dyed primers and fluorescein‐12‐dUTP. The allele‐specific PNA molecules were covalently coupled to carboxylated microspheres with and without rhodamine. Allele‐specific hybridization between PCR products and immobilized PNA was carried out at 60°C followed by flow cytometric detection.ResultsWe present a fully functional two‐bead genotyping system based on PNA capture and flow cytometric detection used for the correct and fast regenotyping of a Danish basal cell carcinoma cohort.ConclusionsThis new assay presents a simple, rapid, and robust method for SNP genotyping for laboratories equipped with a standard flow cytometer. Moreover, this system offers potential for multiplexing and will be operational for middle‐scale genotyping. © 2005 Wiley‐Liss, Inc.
Semaphorin/neuropilin signaling influences the positioning of migratory neural crest cells within the hindbrain region of the chick
Authors: Osborne Nicola J. , Begbie Jo , Chilton John K. , Schmidt Hannes , Eickholt Britta J. 
Published: February 2005

AbstractWithin the hindbrain region, neural crest cell migration is organized into three streams that follow the segmentation of the neuroepithelium into distinct rhombomeric compartments. Although the streaming of neural crest cells is known to involve signals derived from the neuroepithelium, the molecular properties underlying this process are poorly understood. Here, we have mapped the expression of the signaling component of two secreted class III Semaphorins, Semaphorin (Sema) 3A and Sema 3F, at time points that correspond to neural crest cell migration within the hindbrain region of the chick. Both Semaphorins are expressed within rhombomeres at levels adjacent to crest‐free mesenchyme and expression of the receptor components essential for Semaphorin activity by neural crest cells suggests a function in restricting neural crest cell migration. By using bead implantation and electroporation in ovo, we define a role for both Semaphorins in the maintenance of neural crest cell streams in proximity to the neural tube. Attenuation of Semaphorin signaling by expression of soluble Neuropilin‐Fc resulted in neural crest cells invading adjacent mesenchymal territories that are normally crest‐free. The loss or misguidance of specific neural crest cell populations after changes in Semaphorin signaling also affects the integration of the cranial sensory ganglia. Thus, Sema 3A and 3F, expressed and secreted by the hindbrain neuroepithelium contributes to the appropriate positioning of neural crest cells in proximity to the neural tube, a process crucial for the subsequent establishment of neuronal connectivity within the hindbrain region. Developmental Dynamics 232:939–949, 2005. © 2005 Wiley‐Liss, Inc.
Asymmetric Synthesis of γ‐Fluorinated α‐Amino Acid Derivatives
Authors: Shendage Deepak M. , Fröhlich Roland , Bergander Klaus , Haufe Günter 
Published: February 2005

AbstractAsymmetric alkylation of (S)‐Boc‐BMI (1a, BMI = 2‐tert‐butyl‐3‐methylimidazolidin‐4‐one) and its α‐methyl derivative 1b with 2‐fluoroallyl tosylate, subsequent mild acidic deprotection of the products 2a and 2b, and basic hydrolysis of the thus formed N‐methylamides 4a and 4b gave (S)‐2‐amino‐4‐fluoropent‐4‐enoic acid (5a) and (S)‐2‐amino‐4‐fluoro‐2‐methylpent‐4‐enoic acid (5b). Basic hydrolysis of compound 4a was accompanied by partial racemization, which was overcome by applying a new stereoconservative deamidation procedure. The alkylated cis‐configured product 2a formed under kinetic control epimerized on refluxing with 2 n NaOH to give the thermodynamically more stable trans isomer 9. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Overexploitation and continuous drought effects on groundwater yield and marine intrusion: considerations arising from the modelling of Mamora coastal aquifer, Morocco
Authors: Ben Kabbour Brahim , Zouhri Lahcen , Mania Jacky 
Published: February 2005

AbstractThis paper studies the effect of drought and pumping discharge on groundwater supplies and marine intrusion. The investigation concerns the Mamora coastal aquifer, northwest of Morocco. A large‐scale groundwater model was established to model (a) the amount of freshwater discharge towards the ocean and the sea water volumes flowing inland as a consequence of the inverse hydraulic gradient, (b) the impact of drought and pumping discharge on the water table level and, as a consequence, on marine water intrusion. In fact, the simulated submarine groundwater discharge (SGWD) would decrease from 864 m3/d/km in 1987 to 425 m3/d/km in 2000. The simulated volumes of sea water intruding the aquifer as a result of inverse hydraulic gradient would increase from 0·25 Mm3/y in 1987 to 0·3 Mm3/y in 2000. As a consequence of a negative rainfall gradient of −5 mm/y, the simulated SGWD would decline to 9 m3/d/km and the sea water intrusion (SWI) would increase to 0·35 Mm3/y since the year 2010. Due to insufficient data on the trend of pumping discharge, a hypothetical increase of this latter from 38·3 Mm3/y to 53·2 Mm3/y is simulated to induce an increase of marine water intrusion from 0·25 Mm3/y to 0·9 Mm3/y. Consequently, to optimally exploit this seemingly fragile coastal aquifer, a plan of future actions to implement is proposed. Copyright © 2005 John Wiley & Sons, Ltd.
Assessment of flooding in urbanized ungauged basins: a case study in the Upper Tiber area, Italy
Authors: Moramarco T. , Melone F. , Singh V. P. 
Published: February 2005

AbstractThe reliability of a procedure for investigation of flooding into an ungauged river reach close to an urban area is investigated. The approach is based on the application of a semi‐distributed rainfall–runoff model for a gauged basin, including the flood‐prone area, and that furnishes the inlet flow conditions for a two‐dimensional hydraulic model, whose computational domain is the urban area. The flood event, which occurred in October 1998 in the Upper Tiber river basin and caused significant damage in the town of Pieve S. Stefano, was used to test the approach. The built‐up area, often inundated, is included in the gauged basin of the Montedoglio dam (275 km2), for which the rainfall–runoff model was adapted and calibrated through three flood events without over‐bank flow. With the selected set of parameters, the hydrological model was found reasonably accurate in simulating the discharge hydrograph of the three events, whereas the flood event of October 1998 was simulated poorly, with an error in peak discharge and time to peak of −58% and 20%, respectively. This discrepancy was ascribed to the combined effect of the rainfall spatial variability and a partial obstruction of the bridge located in Pieve S. Stefano. In fact, taking account of the last hypothesis, the hydraulic model reproduced with a fair accuracy the observed flooded urban area. Moreover, incorporating into the hydrological model the flow resulting from a sudden cleaning of the obstruction, which was simulated by a ‘shock‐capturing’ one‐dimensional hydraulic model, the discharge hydrograph at the basin outlet was well represented if the rainfall was supposed to have occurred in the region near the main channel. This was simulated by reducing considerably the dynamic parameter, the lag time, of the instantaneous unit hydrograph for each homogeneous element into which the basin is divided. The error in peak discharge and time to peak decreased by a few percent. A sensitivity analysis of both the flooding volume involved in the shock wave and the lag time showed that this latter parameter requires a careful evaluation. Moreover, the analysis of the hydrograph peak prediction due to error in rainfall input showed that the error in peak discharge was lower than that of the same input error quantity. Therefore, the obtained results allowed us to support the hypothesis on the causes which triggered the complex event occurring in October 1998, and pointed out that the proposed procedure can be conveniently adopted for flood risk evaluation in ungauged river basins where a built‐up area is located. The need for a more detailed analysis regarding the processes of runoff generation and flood routing is also highlighted. Copyright © 2005 John Wiley & Sons, Ltd.
Time series forecasting by combining the radial basis function network and the self‐organizing map
Authors: Lin Gwo‐Fong , Chen Lu‐Hsien 
Published: February 2005

AbstractBased on a combination of a radial basis function network (RBFN) and a self‐organizing map (SOM), a time‐series forecasting model is proposed. Traditionally, the positioning of the radial basis centres is a crucial problem for the RBFN. In the proposed model, an SOM is used to construct the two‐dimensional feature map from which the number of clusters (i.e. the number of hidden units in the RBFN) can be figured out directly by eye, and then the radial basis centres can be determined easily. The proposed model is examined using simulated time series data. The results demonstrate that the proposed RBFN is more competent in modelling and forecasting time series than an autoregressive integrated moving average (ARIMA) model. Finally, the proposed model is applied to actual groundwater head data. It is found that the proposed model can forecast more precisely than the ARIMA model. For time series forecasting, the proposed model is recommended as an alternative to the existing method, because it has a simple structure and can produce reasonable forecasts. Copyright © 2005 John Wiley & Sons, Ltd.
Transcriptional activation of survivin through the NF‐κB pathway by human T‐cell leukemia virus type I tax
Authors: Kawakami Hirochika , Tomita Mariko , Matsuda Takehiro , Ohta Takao , Tanaka Yuetsu , Fujii Masahiro , Hatano Masahiko , Tokuhisa Takeshi , Mori Naoki 
Published: February 2005

AbstractSurvivin, a unique member of the inhibitor of apoptosis protein family, is overexpressed in many cancers and considered to play an important role in oncogenesis. We previously reported the survivin expression profile in ATL, a CD4‐positive T‐cell malignancy caused by HTLV‐I. HTLV‐I Tax is thought to play an important role in immortalization of T cells. We have shown also that the expression of Tax protected the mouse T‐cell line CTLL‐2 against apoptosis induced by deprivation of IL‐2 and converted its growth from being IL‐2 dependent to being IL‐2 independent through the NF‐κB pathway. In our study, we demonstrate that constitutive expression of survivin was associated with resistance to apoptosis after IL‐2 deprivation in Tax‐expressing CTLL‐2 cells. Transient transfection assays showed that survivin promoter was transactivated by Tax, via the activation of NF‐κB. Pharmacological NF‐κB inhibition resulted in suppression of survivin expression and caused apoptosis of Tax‐expressing CTLL‐2 cells. Our findings suggest that activated NF‐κB signaling contributes directly to malignant progression of ATL by preventing apoptosis, acting through the prosurvival protein survivin. © 2005 Wiley‐Liss, Inc.
Effect of differences in cancer cells and tumor growth sites on recruiting bone marrow‐derived endothelial cells and myofibroblasts in cancer‐induced stroma
Authors: Sangai Takafumi , Ishii Genichiro , Kodama Keiji , Miyamoto Shin'ichi , Aoyagi Yasuyuki , Ito Takashi , Magae Junji , Sasaki Hiroki , Nagashima Takeshi , Miyazaki Masaru , Ochiai Atsushi 
Published: February 2005

AbstractCancer‐stromal interaction is well known to play important roles during cancer progression. Recently we have demonstrated that bone marrow‐derived vascular endothelial cells (BMD‐VE) and myofibroblasts (BMD‐MF) are recruited into the human pancreatic cancer cell line Capan‐1 induced stroma. To assess the effect of the difference in cancer cell types on the recruitment of BMD‐VE and BMD‐MF, 10 kinds of human cancer cell line were implanted into the subctaneous tissue of the immunodeficient mice transplanted with bone marrow of double‐mutant mice (RAG‐1−/− β‐gal Tg or RAG‐1−/− GFP Tg). The recruitment frequency of BMD‐VE (%BMD‐VE) and BMD‐MF (%BMD‐MF), and tumor‐associated parameters [tumor volume (TV), microvessel density (MVD) and stromal proportion (%St)] were measured. The correlation among them was analyzed. Although %BMD‐VE and %BMD‐MF varied (from 0 to 21.6%, 0 to 29.6%, respectively), depending on the cancer cell line, both parameters were significantly correlated with %St (p < 0.005). Furthermore %BMD‐VE and %BMD‐MF also significantly correlated (p < 0.005). In order to assess the effect of tumor growth sites on the recruitment of the cells of interest, a human pancreatic cancer cell line, Capan‐1, was transplanted into 5 different sites: subcutaneous tissue, peritoneum, liver, spleen and lung. Tumors in the subcutaneous tissue and peritoneum induced desmoplastic stroma (%St = 22.7%, 19.5%, respectively) and contained BMD‐VE (%BMD‐VE = 21.6%, 16.5% respectively) and BMD‐MF (%BMD‐MF = 29.6%, 24.5%, respectively), but weak stromal induction without recruitment of BMD‐VE or ‐MF was observed in the tumors at of the liver, spleen and lung (%St = 9.7%, 9.1%, 5.4%, respectively). cDNA microarray analysis identified the 29 genes that expression was especially up‐ or down‐regulated in the cell line that induced an abundant stromal reaction. However they did not encoded the molecules that were directly involved in stromal cell recruitment (chemokines), differentiation (cytokines) or proliferation (growth factors). These results indicate that the recruitment of BMD‐VE and ‐MF is required for stromal formation during cancer progression and that the cancer microenvironment is important in stromal reaction and the recruitment of BMD‐VE and ‐MF. © 2005 Wiley‐Liss, Inc.
Fitting complex potential energy surfaces to simple model potentials: Application of the simplex‐annealing method
Authors: Bustos Marún Raúl A. , Coronado Eduardo A. , Ferrero Juan C. 
Published: February 2005

AbstractA stochastic method of optimization, which combines simulated annealing with simplex, is implemented to fit the parameters of a simple model potential. The main characteristic of the method is that it explores the whole space of the parameters of the model potential, and therefore it is very efficient in locating the global minimum of the cost function, in addition to being independent of the initial guess of the parameters. The method is employed to fit the complex intermolecular potential energy surface of the dimer of water, using as a reference the spectroscopic quality anisotropic site–site potential of Feller et al. The simple model potential chosen for its reparameterization is the MCY model potential of Clementi et al. The quality of the fit is assessed by comparing the geometry of the minimum, the harmonic frequencies, and the second virial coefficients of the parameterized potential with the reference one. Finally, to prove more rigorously the robustness of this method, it is compared with standard nonstochastic methods of optimization. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 523–531, 2005
Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH
Authors: González‐García Núria , González‐Lafont Àngels , Lluch José M. 
Published: February 2005

AbstractIn the present work the potential energy surface (PES) corresponding to the different initiation routes of the oxidation mechanism of DMS by hydroxyl radical in the absence of O2 has been studied, and connections among the different stationary points have been established. Single‐point high level electronic structure calculations at lower level optimized geometries have been shown to be necessary to assure convergence of energy barriers and reaction energies. Our results demonstrate that the oxidation of DMS by OH turns out to be initiated via three channels: a hydrogen abstraction channel that through a saddle point structure finally leads to CH3SCH2 + H2O, an addition‐elimination channel that firstly leads to an adduct complex (AD) and then via an elimination saddle point structure finally gives CH3SOH and CH3 products, and a third channel that through a concerted pathway leads to CH3OH and CH3S. The H‐abstraction and the addition‐elimination channels initiate by a common pathway that goes through the same reactant complex (RC). Our theoretical results agree quite well with the branching ratios experimentally assigned to the formation of the different products. Finally, the calculated equilibrium constants of the formation of the complex AD and the hexadeuterated complex AD from the corresponding reactants, as a function of the temperature, are in good accordance with the experimental values. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 569–583, 2005
Double proton transfer and one‐electron oxidation behavior in double H‐bonded glycinamide–glycine complex in the gas phase
Authors: Li Ping , Bu Yuxiang 
Published: February 2005

AbstractThe behaviors of double proton transfer (DPT) occurring in a representative glycinamide–glycine complex have been investigated employing the B3LYP/6‐311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator‐assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and −1.83 kcal/mol with further inclusion of zero‐point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H‐bonded glycinamide–glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one‐electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H‐bond. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 552–560, 2005
Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation
Authors: Cummins Peter L. , Gready Jill E. 
Published: February 2005

AbstractWe describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree–Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 561–568, 2005
Multiple acute effects on the membrane potential of PC12 cells produced by nerve growth factor (NGF)
Authors: Shimazu Kazuhiro , Takeda Kazuyo , Yu Zu‐Xi , Jiang Hao , Liu Xu‐Wen , Nelson Phillip G. , Guroff Gordon 
Published: February 2005

AbstractWe studied whether nerve growth factor (NGF) can affect the membrane potential and conductance of PC12 cells. We demonstrate that NGF depolarizes the membrane of PC12 cells within a minute and by using transfected NIH 3T3‐Trk and ‐p75 cells we show that both the high affinity NGF receptor p140trk and the low affinity NGF receptor or p75NGF may be involved in the depolarization. Tyrosine kinase inhibitor, K252a, partially inhibited the depolarization, but two agents affecting intracellular calcium movements, Xestospongin C (XeC) and thapsigargin, did not. The early depolarization was eliminated in Na+ free solutions and under this condition, a ‘prolonged’ (>2 min) hyperpolarization was observed in PC12 cells in response to NGF. This hyperpolarization was also induced in PC12 cells by epidermal growth factor (EGF). Voltage clamp experiments showed that NGF produced a late (>2 min) increase in membrane conductance. The Ca2+‐dependent BK‐type channel blocker, iberiotoxin, and the general Ca2+‐dependent K+ channel blocker, TEA, attenuated or eliminated the hyperpolarization produced by NGF in sodium free media. Under pretreatment with the non‐selective cation channel blockers La3+ and Gd3+, NGF hyperpolarized the membrane of PC12 cells. These results suggest that three different currents are implicated in rapid NGF‐induced membrane voltage changes, namely an acutely activated Na+ current, Ca2+‐dependent potassium currents and non‐selective cation currents. Published 2005 Wiley‐Liss, Inc.