bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrent coamplification of cytoskeleton‐associated genes EMS1 and SHANK2 with CCND1 in oral squamous cell carcinoma
Authors: Freier Kolja , Sticht Carsten , Hofele Christof , Flechtenmacher Christa , Stange Daniel , Puccio Laura , Toedt Grischa , Radlwimmer Bernhard , Lichter Peter , Joos Stefan 
Published: October 2005

AbstractChromosomal band 11q13 is frequently amplified in oral squamous cell carcinoma (OSCC) and assumed to be critically involved in tumor initiation and progression by proto‐oncogene activation. Though cyclin D1 (CCND1) is supposed to be the most relevant oncogene, several additional putative candidate genes are inside this chromosomal region, for which their actual role in tumorigenesis still needs to be elucidated. To characterize the 11q13 amplicon in detail, 40 OSCCs were analyzed by comparative genomic hybridization to DNA microarrays (matrix‐CGH) containing BAC clones derived from chromosomal band 11q13. This high‐resolution approach revealed a consistent amplicon about 1.7 Mb in size including the CCND1 oncogene. Seven BAC clones covering FGF3, EMS1, and SHANK2 were shown to be frequently coamplified inside the CCND1 amplicon. Subsequent analysis of tissue microarrays by FISH revealed amplification frequencies of 36.8% (88/239) for CCND1, 34.3% (60/175) for FGF3, 37.4% (68/182) for EMS1, and 36.3% (61/168) for SHANK2. Finally, quantitative mRNA expression analysis demonstrated consistent overexpression of CCND1 in all tumors and of EMS1 and SHANK2 in a subset of specimens with 11q13 amplification, but no expression of FGF3 in any of the cases. Our study underlines the critical role of CCND1 in OSCC development and additionally points to the functionally related genes EMS1 and SHANK2, both encoding for cytoskeleton‐associated proteins, which are frequently coamplified with CCND1 and therefore could cooperatively contribute to OSCC pathogenesis. © 2005 Wiley‐Liss, Inc.
Chromosomal changes in colorectal adenomas: Relationship to gene mutations and potential for clinical utility
Authors: Leslie Amy , Stewart Arlene , Baty David U. , Mechan Dorothy , McGreavey Louise , Smith Gillian , Wolf C. Roland , Sales Mark , Pratt Norman R. , Steele Robert J. C. , Carey Francis A. 
Published: October 2005

AbstractAlthough the occurrence of both chromosomal aberrations and specific gene mutations in colorectal tumorigenesis is firmly established, the relationship between these different forms of genetic abnormality remains poorly understood. We have previously demonstrated, in colorectal adenocarcinomas, that mutations of APC, KRAS, and TP53 are each specifically associated with certain chromosomal aberrations. Using comparative genomic hybridization and mutational analysis of APC, KRAS, and TP53 to evaluate 78 colorectal adenomas, we have shown that several of the significant relationships between gene mutations and chromosomal abnormalities reported in colorectal adenocarcinomas also exist at the adenomatous stage. KRAS mutation correlated with 12p gain (P < 0.001) and TP53 mutation with both 20q gain and 18q loss (P = 0.03 for both). In addition, we have identified two chromosomal aberrations, gain of 13q and loss of 11q, that correlate with the presence of synchronous adenomas (P = 0.049 and P = 0.03, respectively) and several chromosomal changes (20p+, 20q+, 17p−, and 18q−) that are related to the onset of high‐grade dysplasia. These data strengthen our previous contention that the co‐occurrence of specific gene mutations and chromosomal changes is not random and significant relationships do exist. Our findings also raise the possibility that certain chromosomal aberrations may act as important clinical biomarkers. © 2005 Wiley‐Liss, Inc.
Concordant copy number and transcriptional activity of genes mapping to derivative chromosomes 8 during cellular immortalization in vitro
Authors: Begley Lesa , Keeney David , Beheshti Ben , Squire Jeremy A. , Kant Rajiv , Chaib Hassan , MacDonald James W. , Rhim Johng , Macoska Jill A. 
Published: October 2005

AbstractDeletion, rearrangement, or amplification of sequences mapping to chromosome 8 are frequently observed in human prostate and other tumors. However, it is not clear whether these events alter the transcriptional activity of the affected genes. To examine this question, we have utilized oligonucleotide microarray technology and compared the transcriptional patterns of normal human prostate tissues and five immortalized cell lines carrying either two normal chromosomes 8 or one normal and one derivative chromosome 8. Comparison of the transcriptional profiles of the tissues and cell lines identified 125 differentially expressed transcripts specific to chromosome 8, with 46 transcripts mapping to 8p and 79 transcripts mapping to 8q. The majority of genes mapping to 8p (44/46, 96%) were transcriptionally down‐regulated in cells hemizygous for 8p, whereas the majority of genes mapping to 8q (58/79, 73%) were up‐regulated in cells carrying three copies of 8q. Moreover, hemizygous alleles on 8p exhibited sub‐haploinsufficient transcript levels for several genes that could be induced to haploinsufficient levels under hypomethylating conditions, suggesting that epigenetic regulation is a common mechanism for gene silencing in cells deleted for one copy of 8p. The results of these studies clearly demonstrate that alterations of gene copy number and transcriptional activity are directly correlated in cell lines harboring derivative chromosomes 8, and that these events are commonly observed during cellular immortalization in vitro. © 2005 Wiley‐Liss, Inc.
Statistical dissection of genetic pathways involved in prostate carcinogenesis
Authors: Ribeiro Franclim R. , Diep Chieu B. , Jerónimo Carmen , Henrique Rui , Lopes Carlos , Eknæs Mette , Lingjærde Ole Christian , Lothe Ragnhild A. , Teixeira Manuel R. 
Published: October 2005

AbstractMolecular markers that could stratify prostate cancer patients according to risk of disease progression would allow a significant improvement in the management of this clinically heterogeneous disease. In the present study, we analyzed the genetic profile of a consecutive series of 51 clinically confined prostate carcinomas and 27 benign prostatic hyperplasias using comparative genomic hybridization (CGH). We then added our findings to the existing literature data in order to perform a meta‐analysis on a total of 294 prostate cancers with detailed CGH and clinicopathological information, using multivariate statistical methods that included principal component, hierarchical clustering, time of occurrence, and regression analyses. Whereas several genomic imbalances were shared by organ‐confined, locally invasive, and metastatic prostate cancers, 6q and 10q losses and 7q and 8q gains were significantly more frequent in patients with extra‐prostatic disease. Regression analysis indicated that 8q gain and 13q loss were the best predictors of locally invasive disease, whereas 8q gain and 6q and 10q losses were associated with metastatic disease. We propose a genetic pathway of prostate carcinogenesis with two distinct initiating events, namely, 8p and 13q losses. These primary imbalances are then preferentially followed by 8q gain and 6q, 16q, and 18q losses, which in turn are followed by a set of late events that make recurrent and metastatic prostate cancers genetically more complex. We conclude that significant differences exist in the genetic profile of organ‐confined, locally invasive, and advanced prostate cancer and that genetic features may carry prognostic information independently of Gleason grade. © 2005 Wiley‐Liss, Inc.
The Hat Yai 2000 flood: the worst flood in Thai history
Authors: Supharatid Seree 
Published: October 2005

AbstractHat Yai, the largest commercial and tourist city in southern Thailand, is subjected to regular flood events, primarily during the northeast monsoon period. Flooding in this region is recognized as a serious disaster in terms of frequency, rate of risk, and affected areas. The monsoon of 21–25 November 2000 caused extremely heavy rain in the southern part of Thailand, resulting in a great flood occupying Hat Yai. This caused significant damage. Therefore, the use of both structural and non‐structural measures is mandatory to reduce the economic losses and the risk for society. This paper investigates two modelling approaches for flood prevention and mitigation of Hat Yai city. First, a hard computing approach by a physically distributed model was applied to study the flood behaviour in a two‐dimensional floodplain flow. Second, a soft computing approach using a neuro‐genetic algorithm was used to develop a flood‐forecasting tool. It was found that the great flood of 2000 can be simulated well by the FLO‐2D model. Computed discharges and flood level in the floodplain are close to the observed data. Countermeasures using diversion canals are guaranteed to accelerate the floodwater drainage to Songkla Lake, significantly reducing the flood impact to the people. In addition, the flood forecasting technique developed in this study can give satisfactory results. This would be very useful as a flood‐warning tool for the community Copyright © 2005 John Wiley & Sons, Ltd.
Estimation of ecological high flow
Authors: Lin Jen‐Yang , Chen Yen‐Chang , Tsao Eric Hsienshao 
Published: October 2005

AbstractFloods can destroy fish habitat. During a flood a fish has to seek shelters (refuges) to survive. It is necessary to know the maximum discharge that the fish can sustain against the strong current. Ecological and hydraulic engineers can simulate the flow condition of high flow for designing the refuge when restoring and enhancing the rivers are needed. Based on the average ratio of the mean and maximum velocities invariant with time, discharge and water level, this paper tries to introduce the concept of ecological high flow. The mean‐maximum velocity ratio can be used to estimate the mean velocity of the river. If the maximum velocity of the cross section is replaced by the maximum sustained swimming speeds of fish, the mean velocity of ecological high flow can be calculated with the constant ratio. The cross‐sectional area can be estimated by the gage height. Then the ecological high flow can be estimated as the product of mean velocity of ecological high flow multiplied by the cross‐sectional area. The available data of the upstream of the Dacha River where is the habitat of the Formosan landlocked salmon were used to illustrate the estimation of the ecological high flow. Any restoration project at Sonmou that try to improve the stream habitat can use the ecological high flow to design the hydraulic structure at suitable location to offer refuges for the Formosan landlocked salmon that is an endangered species in Taiwan Copyright © 2005 John Wiley & Sons, Ltd.
Predicting storm runoff from different land‐use classes using a geographical information system‐based distributed model
Authors: Liu Y. B. , Gebremeskel S. , De Smedt F. , Hoffmann L. , Pfister L. 
Published: October 2005

AbstractA method is presented to evaluate the storm runoff contributions from different land‐use class areas within a river basin using the geographical information system‐based hydrological model WetSpa. The modelling is based on division of the catchment into a grid mesh. Each cell has a unique response function independent of the functioning of other cells. Summation of the flow responses from the cells with the same land‐use type results in the storm runoff contribution from these areas. The model was applied on the Steinsel catchment in the Alzette river basin, Grand Duchy of Luxembourg, with 52 months of meteo‐hydrological measurements. The simulation results show that the direct runoff from urban areas is dominant for a flood event compared with runoff from other land‐use areas in this catchment, and this tends to increase for small floods and for the dry‐season floods, whereas the interflow from forested, pasture and agricultural field areas contributes to recession flow. It is demonstrated that the relative contribution from urban areas decreases with flow coefficient, that cropland relative contribution is nearly constant, and that the relative contribution from grassland and woodland increases with flow coefficient with regard to their percentage of land‐use class areas within the study catchment. Copyright © 2005 John Wiley & Sons, Ltd.
Numerical assessment of a dynamical relaxation data assimilation scheme for a catchment hydrological model
Authors: Hurkmans Ruud , Paniconi Claudio , Troch Peter A. 
Published: October 2005

AbstractA dynamical relaxation scheme for assimilating observation data into a three‐dimensional Richards equation‐based numerical model was presented in Paniconi et al. (2003. Advances in Water Resources 26: 161–178). The technique, known as Newtonian relaxation or nudging, relies on a forcing term to reduce the difference between computed and observed values of a state variable such as soil moisture content. The forcing term contains data quality and nudging influence factors, and, importantly, spatio‐temporal weighting functions that determine the manner and extent of spreading of a state variable beyond its measurement points and times. In this paper, a series of numerical experiments is run for a small catchment in southern Belgium to investigate the performance of the nudging algorithm. In a first set of runs for a short (10‐day) simulation period, the model's sensitivity to influence radii and forcing strength parameters is examined. Here, we find that prediction errors decrease and numerical cost increases for increasing values of the parameters, except for the vertical radius of influence, where intermediate values produced the lowest prediction errors. Based on a compromise between numerical and physical results for this 10‐day experiment, ‘optimal’ values were selected for these parameters, and a second, much longer (8‐month) set of simulations is used to explore the effect of the observation frequency on the quality of the assimilation. Here, it is found that prediction errors are lowest at an intermediate frequency, whereas serious numerical difficulties occur at a high frequency. As could be expected, computational costs are highest when frequent observations are assimilated. However, since CPU times increase only very slowly as more observation datasets are added, we can conclude that the nudging method is computationally efficient, albeit quite sensitive in terms of numerical performance to its parameter settings, and thus requires further study to devise more robust formulations of the algorithm. Copyright © 2005 John Wiley & Sons, Ltd.
New automatic control strategies for sludge recycling and wastage for the optimum operation of predenitrification processes
Authors: Ma Yong , Peng Yongzhen , Wang Shuying 
Published: October 2005

AbstractDynamic modelling and simulation is increasingly being employed as an aid in the design and operation of wastewater treatment plants (WWTPs). In this paper a simulation model is used to investigate the control of an activated sludge process. Two different control strategies to optimise nitrogen removal in a predenitrification process are presented, which are based on the control of the sludge blanket height (SBH) or sludge age (sludge retention time, SRT) and mixed liquor suspended solids (MLSS) in the reactor, by adjusting the sludge wastage and sludge recycle flow rates, respectively. It is shown how the recycle and wastage flow rate variables can be employed to continually maintain plant operation in the presence of disturbances. The performance of the control strategies has been assessed by the COST 624 benchmark plant and a pilot plant. The results have shown the robustness of the implementation and the efficiency of the proposed control strategies, which have been operated automatically in a safe, stable and optimum operating point, improving effluent quality and reducing energy costs. Consideration is also given as to how plant operation could be optimised in the long‐term in order to meet the yearly total nitrogen standard. Copyright © 2005 Society of Chemical Industry
A transient expression vector for recombinant protein production in Chinese hamster ovary cells
Authors: Liao Mimi ML , Sunstrom Noelle‐Anne 
Published: October 2005

AbstractAn expression vector was specifically designed for use in Chinese hamster ovary (CHO) cells to enhance the level of protein production in a transient expression system. Two key components that can increase protein production transiently are the promoter used to drive recombinant gene expression and the template copy number. In this study the modified and metal‐inducible metallothionein (M2.6) promoter was shown to be superior to the human cytomegalovirus (CMV) and to the simian virus SV40 promoters. Plasmid replication was achieved using the Polyoma (Py) virus origin of replication (PyOri) and the Py Large T antigen (PyLT). An expression vector containing Py elements was shown to replicate extensively in CHO cells. The combination of the metal‐inducible M2.6 promoter and episomal replication of the expression vector, named pPyOriLT resulted in elevated levels of transgene expression following transient transfection of CHO cells Copyright © 2005 Society of Chemical Industry
Assessment of naphthalene biodegradation efficiency of Pseudomonas and Burkholderia strains tested in soil model systems
Authors: Filonov Andrei E , Puntus Irina F , Karpov Alexander V , Kosheleva Irina A , Akhmetov Lenar I , Yonge David R , Petersen James N , Boronin Alexander M 
Published: October 2005

AbstractThe kinetic parameters of the naphthalene degradation process performed by indigenous and introduced microorganisms were studied in soil model systems. The introduction of active naphthalene‐degrading strains Pseudomonas putida BS3701 and G7 in soil model systems accelerated the naphthalene destruction process by a factor of three to four. Moreover, the addition of salicylate (0.1 mg g−1 dry soil) to the systems containing the introduced microbial strains again doubled the rate of the naphthalene degradation process. To provide a quantitative assessment of the naphthalene biodegradation process, a mathematical model describing the bacterial growth, the consumption of the naphthalene, the production and subsequent consumption of naphthalene cleavage products, and the consumption of organic soil substances in soil model systems was developed. An approach for assessment of the degradation efficiency of low solubility polycyclic aromatic hydrocarbon provided by bacteria of genera Pseudomonas and Burkholderia in soil was suggested. The approach will enable comparison and selection of the most active degraders, which have the potential for application in biotechnologies for cleaning of soils contaminated by polycyclic aromatic hydrocarbons. Copyright © 2005 Society of Chemical Industry
Oligo(p‐phenyleneethynylene)‐based coil–rod–coil triblock copolymer: Synthesis and controlled self‐organization in solution
Authors: Li Kun , Guo Liang , Liang Ziqi , Thiyagarajan Pappannan , Wang Qing 
Published: October 2005

AbstractThe self‐assembling ability of block copolymers offers an attractive strategy for the organization of π‐conjugated polymers. This article reports the synthesis of a coil–rod–coil triblock copolymer consisting of oligo(p‐phenyleneethynylene) as the rodlike segment and polystyrene as the coil‐like segment. The chemical structure of the afforded triblock copolymer has been fully characterized by various spectroscopic techniques such as NMR, Raman, gel permeation chromatography, differential scanning calorimetry, ultraviolet–visible, and fluorescence spectroscopy. The small‐angle neutron scattering and photophysical measurements indicate that this triblock copolymer exhibits unique solvatochromatic behaviors through the interplay of aggregation‐induced π–π stacking and planarization of the conjugated backbone. Supramolecular gel nanostructures have been produced via the controlled assembly of the polymer into H‐aggregates. It has been demonstrated that the use of the solvent composition to influence chain conformations and thus to manipulate the packing of the conjugated polymer blocks is important for achieving control in the assembly of conducting polymers and associated optical characteristics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6007–6019, 2005
Synthesis of poly(dimethylsiloxane)‐containing diblock and triblock copolymers by the combination of anionic ring‐opening polymerization of hexamethylcyclotrisiloxane and nitroxide‐mediated radical polymerization of methyl acrylate, isoprene, and styrene
Authors: Miura Yozo , Miyake Kazuki 
Published: October 2005

AbstractPoly(dimethylsiloxane)‐containing diblock and triblock copolymers were prepared by the combination of anionic ring‐opening polymerization (AROP) of hexamethylcyclotrisiloxane (D3) and nitroxide‐mediated radical polymerization (NMRP) of methyl acrylate (MA), isoprene (IP), and styrene (St). The first step was the preparation of a TIPNO‐based alkoxyamine carrying a 4‐bromophenyl group. The alkoxyamine was then treated with Li powder in ether, and AROP of D3 was carried out using the resulting lithiophenyl alkoxyamine at room temperature, giving functional poly(D3) with Mw/Mn of 1.09–1.16. NMRPs of MA, St, and IP from the poly(D3) at 120 °C gave poly(D3‐b‐MA), poly(D3‐b‐St), and poly(D3‐b‐IP) diblock copolymers, and subsequent NMRPs of St from poly(D3‐b‐MA) and poly(D3‐b‐IP) at 120 °C gave poly(D3‐b‐MA‐b‐St) and poly(D3‐b‐IP‐b‐St) triblock copolymers. The poly(dimethylsiloxane)‐containing diblock and triblock copolymers were analyzed by 1H NMR and size exclusion chromatography. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6153–6165, 2005
Thermosensitive gel formation of novel polypeptides containing a collagen‐derived Pro‐Hyp‐Gly sequence and an elastin‐derived Val‐Pro‐Gly‐Val‐Gly sequence
Authors: Morihara Yasushi , Ogata Shin‐Ichi , Kamitakahara Masanobu , Ohtsuki Chikara , Tanihara Masao 
Published: October 2005

AbstractA triple‐helix‐forming collagen model peptide, (prolyl‐trans‐4‐hydroxyprolyl‐glycyl)10 [(Pro‐Hyp‐Gly)10], and a thermosensitive elastin‐derived pentapeptide, valyl‐prolyl‐glycyl‐valyl‐glycyl (Val‐Pro‐Gly‐Val‐Gly), were copolymerized in various mole ratios using 1‐ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide hydrochloride and 1‐hydroxybenzotriazole in dimethyl sulfoxide at 20 °C. All of the obtained polypeptides have molecular weight higher than 103 and contain a triple‐helical structure, and showed an inverse phase transition from transparent solution to turbid suspension in response to a rise in temperature. The lower critical solution temperature of the polypeptide solution decreased upon increasing the content of Val‐Pro‐Gly‐Val‐Gly. Furthermore, polypeptides containing 82–86 mol % of Val‐Pro‐Gly‐Val‐Gly in composition showed reversible gel formation, suggesting that (Pro‐Hyp‐Gly)10 acts as a hydrated unit and Val‐Pro‐Gly‐Val‐Gly acts as a thermosensitive crosslinking point. These biodegradable thermosensitive polypeptides may be useful for biomedical applications, including, as a scaffold for tissue regeneration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6048–6056, 2005