Multi-dimensional schemes for scalar advection

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77204/1/AIAA-1991-1532-834.pd

Lower Willamette River Model: Boundary Conditions and Model Setup

Water Environment Services of Clackamas County is in the process of planning upgrades on several of its sewage treatment plants which discharge into the Lower Willamette River. The goals of the modeling effort are to: • Gather data to construct a computer simulation model of the Lower Willamette River system including part of the Lower Columbia River and the Willamette River above the Oregon City Falls; Because of the tidal influence in the Lower Willamette River, portions of the Columbia River that might affect the Lower Willamette River water quality were also modeled. Also, a section of the Willamette River above the head of tide, the Oregon City Falls, was modeled because of the lack of good boundary condition data at the Falls. • Ensure that the model accurately represents the system physics and chemistry (flow, temperature, dissolved oxygen and nutrient dynamics); • Use the model to evaluate how to meet various future discharge scenarios for the sewage district. A hydrodynamic and water quality model, CE-QUAL-W2 Version 3 (Wells, 1997), is being applied to model the Willamette-Columbia system. CE-QUAL-W2 is a two dimensional (longitudinal-vertical), laterally averaged, hydrodynamic and water quality model that has been under development by the Corps of Engineers Waterways Experiments Station (Cole and Wells, 2000). In order to model the system, the following data were required: • Willamette and Columbia River flow, water level and water quality data • Tributary inflows and water quality • Meteorological conditions • Bathymetry of the Columbia and Willamette Rivers and several side channels • Point source inflows and water quality characteristics Many local, state and federal agencies have been collecting data in the Lower Willamette and Columbia Rivers. This report summarizes data used in the modeling effort

Progress on multidimensional upwind Euler solvers for unstructured grids

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76503/1/AIAA-1991-1550-511.pd

Structural role of the tyrosine residues of cytochrome c

The tertiary structures of horse, tuna, Neurospora crassa, horse [Hse65,Leu67]- and horse [Hse65,Leu74]-cytochromes c were studied with high-resolution 1H n.m.r. spectroscopy. The amino acid sequences of these proteins differ at position 46, which is occupied by phenylalanine in the horse proteins but by tyrosine in the remaining two, and at positions 67, 74 and 97, which are all occupied by tyrosine residues in horse and tuna cytochrome c but in the other proteins are substituted by phenylalanine or leucine, though there is only one such substitution per protein. The various aromatic-amino-acid substitutions do not seriously affect the protein structure

Silencing of the XAF1 gene by promoter hypermethylation in cancer cells and reactivation to TRAIL-sensitization by IFN-β

BACKGROUND: XIAP-associated factor 1 (XAF1) is a putative tumor suppressor that exerts its proapoptotic effects through both caspase-dependent and – independent means. Loss of XAF1 expression through promoter methylation has been implicated in the process of tumorigenesis in a variety of cancers. In this report, we investigated the role of basal xaf1 promoter methylation in xaf1 expression and assessed the responsiveness of cancer cell lines to XAF1 induction by IFN-β. METHODS: We used the conventional bisulfite DNA modification and sequencing method to determine the methylation status in the CpG sites of xaf1 promoter in glioblastoma (SF539, SF295), neuroblastoma (SK-N-AS) and cervical carcinoma (HeLa) cells. We analysed the status and incidence of basal xaf1 promoter methylation in xaf1 expression in non-treated cells as well as under a short or long exposure to IFN-β. Stable XAF1 glioblastoma knock-down cell lines were established to characterize the direct implication of XAF1 in IFN-β-mediated sensitization to TRAIL-induced cell death. RESULTS: We found a strong variability in xaf1 promoter methylation profile and responsiveness to IFN-β across the four cancer cell lines studied. At the basal level, aberrant promoter methylation was linked to xaf1 gene silencing. After a short exposure, the IFN-β-mediated reactivation of xaf1 gene expression was related to the degree of basal promoter methylation. However, in spite of continued promoter hypermethylation, we find that IFN-β induced a transient xaf1 expression, that in turn, was followed by promoter demethylation upon a prolonged exposure. Importantly, we demonstrated for the first time that IFN-β-mediated reactivation of endogenous XAF1 plays a critical role in TRAIL-induced cell death since XAF1 knock-down cell lines completely lost their IFN-β-mediated TRAIL sensitivity. CONCLUSION: Together, these results suggest that promoter demethylation is not the sole factor determining xaf1 gene induction under IFN-β treatment. Furthermore, our study provides evidence that XAF1 is a crucial interferon-stimulated gene (ISG) mediator of IFN-induced sensitization to TRAIL in cancer

Studying Functions of All Yeast Genes Simultaneously

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain

The effect of three-dimensional visualisation on performance in endoscopic sinus surgery:A clinical training study using surgical navigation for movement analysis in a randomised crossover design

Objectives: Endoscopic imaging techniques and endoscopic endonasal surgery (EES) expertise have evolved rapidly. Only few studies have assessed the effect of three-dimensional (3D) endoscopy on endoscopic sinus surgery (ESS). The present study aimed to objectively and subjectively assess the additional value of 3D high-definition (HD) endoscopy in ESS. Design: A randomized crossover study of endoscopic surgery performance, using five ESS tasks of varying complexity, performed on Thiel embalmed human specimens. Setting: Simulated surgical environment. Participants: Thirty participants, inexperienced in ESS. Main outcome measures: Performance was assessed using video imaging, surgical navigation and questionnaires. Main outcome measures were as follows: efficiency (defined by time to task completion), distance covered inside the nose, average velocity towards target, accuracy (measured by error rate), and subjective assessment of endoscope characteristics. Results: During ESS tasks, both efficiency and accuracy did not differ significantly between 2D HD and 3D HD endoscopy. Subjectively, imaging characteristics of the 3D HD endoscope were rated significantly better. Conclusions: ESS performance of inexperienced participants was not significantly improved by the use of 3D HD endoscopy during ESS tasks, although imaging characteristics of the 3D HD endoscope were rated significantly better. Surgical field characteristics and surgical techniques are likely to influence any additional value of 3D HD endoscopy

The Chandra Multi-Wavelength Project: Optical Spectroscopy and the Broadband Spectral Energy Distributions of X-ray Selected AGN

From optical spectroscopy of X-ray sources observed as part of ChaMP, we present redshifts and classifications for a total of 1569 Chandra sources from our targeted spectroscopic follow up using the FLWO, SAAO, WIYN, CTIO, KPNO, Magellan, MMT and Gemini telescopes, and from archival SDSS spectroscopy. We classify the optical counterparts as 50% BLAGN, 16% NELG, 14% ALG, and 20% stars. We detect QSOs out to z~5.5 and galaxies out to z~3. We have compiled extensive photometry from X-ray to radio bands. Together with our spectroscopic information, this enables us to derive detailed SEDs for our extragalactic sources. We fit a variety of templates to determine bolometric luminosities, and to constrain AGN and starburst components where both are present. While ~58% of X-ray Seyferts require a starburst event to fit observed photometry only 26% of the X-ray QSO population appear to have some kind of star formation contribution. This is significantly lower than for the Seyferts, especially if we take into account torus contamination at z>1 where the majority of our X-ray QSOs lie. In addition, we observe a rapid drop of the percentage of starburst contribution as X-ray luminosity increases. This is consistent with the quenching of star formation by powerful QSOs, as predicted by the merger model, or with a time lag between the peak of star formation and QSO activity. We have tested the hypothesis that there should be a strong connection between X-ray obscuration and star-formation but we do not find any association between X-ray column density and star formation rate both in the general population or the star-forming X-ray Seyferts. Our large compilation also allows us to report here the identification of 81 XBONG, 78 z>3 X-ray sources and 8 Type-2 QSO candidates. Also we have identified the highest redshift (z=5.4135) X-ray selected QSO with optical spectroscopy.Comment: 17 pages, 16 figures, accepted for publication in ApJS. Full data table and README file can be found online at http://hea-www.harvard.edu/~pgreen/Papers.htm