bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using CFD in a GLUE framework to model the flow and dispersion characteristics of a natural fluvial dead zone
Authors: Hankin B. G. , Hardy R. , Kettle H. , Beven K. J. 
Published: August 2002

AbstractMonte Carlo simulations of a two‐dimensional depth‐averaged distributed bed‐roughness flow model, TELEMAC‐2D, are used to model a detailed tracer dispersion test in a complex reach of the River Severn in the Generalized Likelihood Uncertainty Estimation (GLUE) framework. A time efficient, zero equation, spatially distributed eddy viscosity model is derived from physical reasoning and used to close the flow equations. It is shown to have the property of low numerical diffusion, avoiding recourse to a globally large value of the eddy viscosity. For models of complex river flows, there are typically so many degrees of freedom in the specification of distributed parameters owing to the limitations of field data collection, that the identification of a unique model structure is unlikely. The data used here to constrain the model structure come from a continuous tracer injection experiment, comprising six spatially distributed time series of concentration measurements. Several hundred Monte‐Carlo simulations of different model structures were investigated and it was found that multiple model structures produced feasible simulations of the tracer mixing, giving rise to the phenomenon of equifinality. Rather than optimizing the model structure on the basis of the constraining data, we derive relative possibility measures that express our relative degree of belief in each model structure. These measures can then be used as weights for assessing predictive uncertainty when using a range of model structures, to estimate the flow distribution under varying stages, or for providing maps indicating fully distributed confidence limits in the risk assessments process. Such an approach is used here, and helps to identify the circumstances under which two‐dimensional modelling can be useful. The framework is not limited to the model structures that are developed herein, and more advanced process representation techniques can be included as computational efficiency increases. Copyright © 2001 John Wiley & Sons, Ltd.
A cellular model of Holocene upland river basin and alluvial fan evolution
Authors: Coulthard T. J. , Macklin M. G. , Kirkby M. J. 
Published: August 2002

AbstractThe CAESAR (Cellular Automaton Evolutionary Slope And River) model is used to simulate the Holocene development of a small upland catchment (4·2 km2) and the alluvial fan at its base. The model operates at a 3 m grid scale and simulates every flood over the last 9200 years, using a rainfall record reconstructed from peat bog wetness indices and land cover history derived from palynological sources.Model results show that the simulated catchment sediment discharge above the alluvial fan closely follows the climate signal, but with an increase in the amplitude of response after deforestation. The important effects of sediment storage and remobilization are shown, and findings suggest that soil creep rates may be an important control on long term (>1000 years) temperate catchment sediment yield. The simulated alluvial fan shows a complex and episodic behaviour, with frequent avulsions across the fan surface. However, there appears to be no clear link between fan response and climate or land use changes suggesting that Holocene alluvial fan dynamics may be the result of phases of sediment storage and remobilization, or instabilities and thresholds within the fan itself. Copyright © 2002 John Wiley & Sons, Ltd.
Rapid determination of bacteria in drinking water using an ATP assay
Authors: Deininger Rolf A. , Lee JiYoung 
Published: August 2002

AbstractThe presently used heterotrophic plate count (HPC) for the evaluation of the total number of bacteria in a sample of drinking water takes 7 days of incubation. When the results are known, the water has been consumed and is ineffective for the protection of the health of the consumers. Operators of water treatment systems need to know the bacterial water quality in near real time. Contamination of the system, whether it is intentional, accidental, or due to an inadequate disinfectant residual needs to be discovered much sooner because intervention can then take place in the form of flushing low quality water and/or raising the disinfectant residual. The purpose of this study was therefore to determine if a rapid ATP assay can estimate the HPC in minutes. Two additional methods were used for some samples. The first method was the acridine orange direct count (AODC) that enumerates both viable and nonviable bacteria. The second method was the direct viable count (DVC) that enumerates only viable bacteria. Water samples were obtained from local, national, and international locations. The sample selection criteria were based on proximity to the laboratory, cooperating water utilities, and the travel of the authors. The results of the study show that the rapid ATP assay is highly correlated with the conventional plate count method and the DVC method. The significance of the ATP assay is that it can determine the bacterial quality of the drinking water in less than 5 min. © 2001 John Wiley & Sons, Inc. Field Analyt Chem Technol 5: 185–189, 2001
Compression mechanical properties of wood at temperatures simulating fire conditions
Authors: Young S. A. , Clancy P. 
Published: August 2002

AbstractCompression mechanical properties of wood at temperatures simulating fire conditions have been obtained for use in structural response models to aid the design of light‐timber framed walls as fire barriers in accordance with recent performance‐based fire codes. The properties that have been measured are elastic modulus and strength. The properties were obtained from samples that had a number of similarities to studs in walls. The effects of knots, however, have been excluded from this study. The elastic modulus greatly reduces as temperatures approach the vaporization point of moisture. The properties were significantly lower compared with properties given in the literature. Input of the measured properties into a structural fire model for walls led to good comparisons with results of experiments on walls with low load ratios (that is, the ratio of the applied load to the collapse load capacity at ambient conditions). Such walls are typically used in building construction. However, the elastic moduli presented in this paper and in other literature do not lead to good model predictions for slender walls with high load ratios. Further research into creep is required. Copyright © 2001 John Wiley & Sons, Ltd.
Essential oil composition of Syzygium aromaticum leaf from Little Andaman, India
Authors: Raina V. K. , Srivastava S. K. , Aggarwal K. K. , Syamasundar K. V. , Kumar Sushil 
Published: August 2002

AbstractThe cloves are grown as plantation crops in the agroclimatic conditions of the Indian island of Little Andaman. The dried leaves, on hydrodistillation, gave 4.8% of the oil. GC and GC–MS analysis of the oil resulted in the identification of 16 compounds. The major compound was eugenol (94.4%) followed by β‐caryophyllene (2.9%). The clove oil from Little Andaman was found to be comparable with the best oil produced in south India in terms of its eugenol content. It is suggested that clove can be grown as an economically viable crop in the Andaman, Nicobar and Lakshdeep islands. Copyright © 2001 John Wiley & Sons, Ltd.
Constituents of stem and flower oils of Helichrysum litoreum Guss.
Authors: Ruberto Giuseppe , Biondi Daniela M. , Barbagallo Claudia , Meli Rosa , Savoca Francesca 
Published: August 2002

AbstractThe essential oils from flowers and stems of Helichrysum litoreum collected in the Aeolian archipelago were examined by GC and GC–MS. β‐Caryophyllene (24.4%), α‐pinene (23.2%), γ‐curcumene (5.6%) and rosifoliol (3.1%) were the predominant components of flower essential oil. The stem essential oil was almost totally characterized by monoterpene hydrocarbons (ca. 89%), limonene (74.6%) and α‐pinene (12.9%) being the main compounds. Copyright © 2001 John Wiley & Sons, Ltd.
Identification of green note compounds in malt whisky using multidimensional gas chromatography
Authors: Wanikawa Akira , Hosoi Kenji , Kato Taro , Nakagawa Kei‐ichi 
Published: August 2002

AbstractWe studied green note compounds in malt whisky using multidimensional GC–MS–olfactometry (MDGC–MS–O). Two aldehydes and three alcohols were shown to contribute to the green note: E,Z‐2,6‐nonenal and E‐2‐nonenal, and 1‐octen‐3‐ol, 4‐hepten‐1‐ol and nonan‐2‐ol, respectively. Malt whiskies with high green note scores organoleptically contained more of the aldehydes and nonan‐2‐ol than those with low scores. This is the first time that E,Z‐2,6‐nonadienal, 1‐octen‐3‐ol, and 4‐hepten‐1‐ol have been identified in malt whisky. These compounds are related to lipid oxidation and degradation, and formation may be due to the action of lipoxygenase. In addition, MDGC–MS–O was effective in examining small amounts of compounds in malt whisky, which contains many volatiles, since this method enables the volatiles in a complicated matrix to be highly resolved without the influence of large amounts of volatiles. Copyright © 2002 John Wiley & Sons, Ltd.
Chemical composition of the volatiles of Hemidesmus indicus R. Br.
Authors: Nagarajan S. , Jagan Mohan Rao L. , Gurudutt K. N. 
Published: August 2002

AbstractThe fragrant roots of Hemidesmus indicus (Indian sarsaparilla) is used in Indian native medicine and herbal tea preparations. The volatiles obtained by steam distillation (yield, 0.25%) contained 2‐hydroxy‐4‐methoxybenzaldehyde (91%) and (−) ledol (4.5%), which are isolable in pure form, as the major constituents. The GC–MS analysis of the residual oil showed the presence of over 40 minor constituents. Among them, nerolidol (1.2%), borneol (0.3%), linalyl acetate (0.2%), dihydrocarvyl acetate (0.1%), salicylaldehyde (0.1%), isocaryophyllene (0.1%), α‐terpinyl acetate (traces) and 1,8‐cineol (traces) are important as aromatic and bio‐active principles. Copyright © 2001 John Wiley & Sons, Ltd.
Incompressible flows with combustion simulated by a preconditioning method using multigrid acceleration and MUSCL reconstruction
Authors: Bellucci V. , Bruno C. 
Published: August 2002

AbstractA numerical algorithm for the steady state solution of three‐dimensional incompressible flows is presented. A preconditioned time marching scheme is applied to the conservative form of the governing equations. The preconditioning matrix multiplies the time derivatives of the system and circumvents the eigenvalue‐caused stiffness at low speed. The formulation is suitable for constant density flows and for flows where the density depends on non‐passive scalars, such as in low‐speed combustion applications. The k–ε model accounts for turbulent transport effects. A cell‐centred finite volume formulation with a Runge–Kutta time stepping scheme for the primitive variables is used. Second‐order spatial accuracy is achieved by developing for the preconditioned system an approximate Riemann solver with MUSCL reconstruction. A multi‐grid technique coupled with local time stepping and implicit residual smoothing is used to accelerate the convergence to the steady state solution. The convergence behaviour and the validation of the predicted solutions are examined for laminar and turbulent constant density flows and for a turbulent non‐premixed flame simulated by a presumed probability density function (PDF) model. Copyright © 2001 John Wiley & Sons, Ltd.
Aberrations of the hSNF5/INI1 gene are restricted to malignant rhabdoid tumors or atypical teratoid/rhabdoid tumors in pediatric solid tumors
Authors: Uno Kaoru , Takita Junko , Yokomori Kinji , Tanaka Yukichi , Ohta Shigeru , Shimada Hiroyuki , Gilles Floyd H. , Sugita Kanji , Abe Satoshi , Sako Masahiro , Hashizume Kohei , Hayashi Yasuhide 
Published: August 2002

AbstractThe hSNF5/INI1 gene, which encodes a subunit of the SWI/SNF family of chromatin‐remodeling complexes and is located at 22q11.2, has been reported as a tumor suppressor gene inactivated in malignant rhabdoid tumors (MRTs). We analyzed this gene in varieties of pediatric solid tumors including MRTs, using the reverse transcription‐polymerase chain reaction (PCR) and PCR‐single strand conformation polymorphism method. We found 5 homozygous deletions, 2 truncated mutations, one missense mutation, and one silent mutation of the hSNF5/INI1 gene in 7 MRT cell lines, and one homozygous deletion, one microdeletion, one splicing acceptor site mutation, and one absence of expression in 7 fresh tumor tissues of MRT and atypical teratoid (AT)/rhabdoid tumors (RTs). Homozygous deletions were also found in one (KYM‐1) of 8 rhabdomyosarcoma (RMS) cell lines. To investigate characteristics of the KYM‐1 cell line, we have established KYM‐1 tumors in nude mice into which KYM‐1 cells were transplanted. Notably, we found that MyoD1, known as a marker for RMS, was not expressed in the KYM‐1 cell line as well as MRT cell lines and fresh tumors. Histopathologic, cytogenetic, and molecular studies of the KYM‐1 cell line and KYM‐1 tumors in nude mice have revealed that this RMS cell line should be MRT rather than RMS. RMS‐carrying aberrations of the hSNF5/INI1 gene should be reevaluated. No aberrations of this gene were found in the other 34 cell lines or 80 fresh tumor specimens except the single nucleotide polymorphisms in the 3′ noncoding region. These results suggest that alterations of the hSNF5/INI1 gene were restricted to MRTs or AT/RTs in pediatric solid tumors. © 2002 Wiley‐Liss, Inc.
Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression
Authors: Huang Qiang , Yu Guo Pei , McCormick Steven A. , Mo Juan , Datta Bhakti , Mahimkar Manoj , Lazarus Philip , Schäffer Alejandro A. , Desper Richard , Schantz Stimson P. 
Published: August 2002

AbstractFor a better understanding of genetic alterations in head and neck squamous cell carcinoma (HNSCC), we applied comparative genomic hybridization (CGH) in the analysis of 75 HNSCCs, comprised of 18 pharyngeal squamous cell carcinomas (PSCCs), 23 laryngeal squamous cell carcinomas (LSCCs), and 34 oral squamous cell carcinomas (OSCCs). The three subgroups of HNSCC showed significant differences in genetic alteration patterns. Overall, PSCC and LSCC had more copy number aberrations (CNAs) per tumor than did OSCC. Apparent differing patterns of high‐level amplification were also observed. The smallest recurrent chromosomal regions of high‐level amplification (≥15% of cases) were 7q22, 8q24.1, and 11q12–13 in PSCC and 3q26.1–29 in OSCC. According to single frequency and combined frequencies of CNAs, we concluded that the most important chromosomal events for progression of head and neck cancer were +3q, +5p, +8q, and −3p for all subgroups of HNSCC; additionally, +7q, +17q, −9p, and −13q for PSCC; +7p, +9q, +11q12–13, +14q, and +17q for LSCC; and +1p and +11q12–13 for OSCC. To identify further important genetic alterations and the relationships among the alterations, we constructed oncogenetic tree models for tumor progression of HNSCC from CGH data using branching and distance‐based tree models. The tree models predicted that: (1) +3q21–29 was the most important early chromosomal event, and −3p, which occurred after +3q21–29, was also an important chromosomal event for all subsites of HNSCC; (2) +8q is the second most important early chromosomal event; (3) there may be at least three subgroups of HNSCC: one characterized by −3p, −9p, +7p, and −13q; another by +5p, +9qter, and +17p; and the other by +8q and +18p. These results suggest that different chromosomal aberrations may play a role in the initiation and/or progression of different subgroups of HNSCC. © 2002 Wiley‐Liss, Inc.
Identification of four new translocations involving FGFR1 in myeloid disorders
Authors: Sohal Jastinder , Chase Andrew , Mould Sarah , Corcoran Martin , Oscier David , Iqbal Sameena , Parker Sally , Welborn Jeanna , Harris Richard I. , Martinelli Giovanni , Montefusco Vittorio , Sinclair Paul , Wilkins Bridget S. , van den Berg Henk , Vanstraelen Danny , Goldman John M. , Cross Nicholas C.P. 
Published: August 2002

AbstractThe 8p11 myeloproliferative syndrome (EMS) is associated with three translocations, t(8;13)(p11;q12), t(8;9)(p11;q33), and t(6;8)(q27;p11), that fuse unrelated genes (ZNF198, CEP110, and FOP, respectively) to the entire tyrosine kinase domain of FGFR1. In all cases thus far examined (n = 10), the t(8;13) results in an identical mRNA fusion between ZNF198 exon 17 and FGFR1 exon 9. To determine if consistent fusions are also seen in the variant translocations, we performed RT‐PCR on four cases and sequenced the products. For two patients with a t(8;9), we found that CEP110 exon 15 was fused to FGFR1 exon 9. For two patients with a t(6;8), we found that FOP exon 5 (n = 1) or exon 7 (n = 1) was fused to FGFR1 exon 9. To determine if FGFR1 might be involved in other myeloid disorders with translocations of 8p, we developed a two‐color FISH assay using two differentially labeled PAC clones that flank FGFR1. Disruption of this gene was indicated in a patient with a t(8;17)(p11;q25) and Ph‐negative chronic myeloid leukemia in association with systemic malignant mast cell disease, a patient with acute myeloid leukemia with a t(8;11)(p11;p15), and two cases with T‐cell lymphoma, myeloproliferative disorder, and marrow eosinophilia with a t(8;12)(p11;q15) and ins(12;8)(p11;p11p21), respectively. For the patient with the t(8;11), the chromosome 11 breakpoint was determined to be in the vicinity of NUP98. We conclude that 1) all mRNA fusions in EMS result in splicing to FGFR1 exon 9 but breakpoints in FOP are variable, 2) two‐color FISH can identify patients with EMS, and 3) the t(8;17)(p11;q25), t(8;11)(p11;p15), t(8;12)(p11;q15), and ins(12;8)(p11;p11p21) are novel karyotypic changes that most likely involve FGFR1. © 2001 Wiley‐Liss, Inc.
Expression of Thyroid transcription factor‐1 (TTF‐1) gene in the ventral forebrain and endostyle of the agnathan vertebrate, Lampetra japonica
Authors: Ogasawara Michio , Shigetani Yasuyo , Suzuki Shintaro , Kuratani Shigeru , Satoh Nori 
Published: August 2002

AbstractSummary: The Thyroid transcription factor‐1 (TTF‐1) gene belongs to the Nkx‐2.1 subfamily and encodes a transcription factor containing an NK‐2‐type homeodomain. In our study, we isolated and characterized cDNA clones for the TTF‐1/Nkx‐2.1 orthologue (LjTTF‐1) from the agnathan vertebrate Lampetra japonica. Spatial and temporal expression patterns assessed by in situ hybridization revealed the expression of LjTTF‐1 in the anterior nerve cord and anteroventral region of the pharynx. The neural expression was subsequently restricted to the ventral diencephalon. The pharyngeal expression, on the other hand, extended posteriorly to the fourth pharyngeal‐pouch level and was finally localized in the endostyle anlage. In the differentiated endostyle of ammocoete larvae, the expression of LjTTF‐1 was chiefly detected in type 2a, 2b, and 2c cells, which develop adjacent to glandular cells. These expression patterns of LjTTF‐1 support the idea that this gene family plays an important role in the development of the rostral brain and endostyle equivalent organs. Furthermore, histological comparisons between TTF‐1/Nkx‐2.1 expression in the endostyles of ammocoetes and ascidians suggested the possibility that the organogenetic architecture of the endostyle is conserved among chordates. genesis 30:51–58, 2001. © 2001 Wiley‐Liss, Inc.
Association and aggregation analysis using kin‐cohort designs with applications to genotype and family history data from the Washington Ashkenazi Study
Authors: Chatterjee Nilanjan , Shih Joanna , Hartge Patricia , Brody Lawrence , Tucker Margaret , Wacholder Sholom 
Published: August 2002

AbstractWhen a rare inherited mutation in a disease gene, such as BRCA1, is found through extensive study of high‐risk families, it is critical to estimate not only age‐specific penetrance of the disease associated with the mutation, but also the residual effect of family history once the mutation is taken into account. The kin‐cohort design, a cross‐sectional survey of a suitable population that collects DNA and family history data, provides an efficient alternative to cohort or case‐control designs for estimating age‐specific penetrance in a population not selected because of high familial risk. In this report, we develop a method for analyzing kin‐cohort data that simultaneously estimate the age‐specific cumulative risk of the disease among the carriers and non‐carriers of the mutations and the gene‐adjusted residual familial aggregation or correlation of the disease. We employ a semiparametric modeling approach, where the marginal cumulative risks corresponding to the carriers and non‐carriers are treated non‐parametrically and the residual familial aggregation is described parametrically by a class of bivariate failure time models known as copula models. A simple and robust two‐stage method is developed for estimation. We apply the method to data from the Washington Ashkenazi Study [Struewing et al., 1997, N Engl J Med 336:1401–1408] to study the residual effect of family history on the risk of breast cancer among non‐carriers and carriers of specific BRCA1/BRCA2 germline mutations. We find that positive history of a single first‐degree relative significantly increases risk of the non‐carriers (RR = 2.0, 95% CI = 1.6–2.6) but has little or no effect on the carriers. Genet. Epidemiol. 21:123–138, 2001. © 2001 Wiley‐Liss, Inc.
Association studies for quantitative traits in structured populations
Authors: Bacanu Silviu‐Alin , Devlin B. , Roeder Kathryn 
Published: August 2002

AbstractAssociation between disease and genetic polymorphisms often contributes critical information in our search for the genetic components of common diseases. Devlin and Roeder [1999: Biometrics 55:997–1004] introduced genomic control, a statistical method that overcomes a drawback to the use of population‐based samples for tests of association, namely spurious associations induced by population structure. In essence, genomic control (GC) uses markers throughout the genome to adjust for any inflation in test statistics due to substructure. To date, genomic control (GC) has been developed for binary traits and bi‐ or multiallelic markers. Tests of association using GC have been limited to single genes. In this report, we generalize GC to quantitative traits (QT) and multilocus models. Using statistical analysis and simulations, we show that GC controls spurious associations in reasonable settings of population substructure for QT models, including gene‐gene interaction. Through simulations, we explore GC power for both random and selected samples, assuming the QT locus tested is causal and its specific heritability is 2.5–5%. We find that GC, combined with either random or selected samples, has good power in this setting, and that more complex models induce smaller GC corrections. The latter suggests greater power can be achieved by specifying more complex genetic models, but this observation only follows when such models are largely correct and specified a priori. Genet. Epidemiol. 22:78–93, 2002. © 2002 Wiley‐Liss, Inc.