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Selected AbstractsA dam problem: simulated upstream impacts for a Searsville-like watershedECOHYDROLOGY, Issue 4 2008Christopher S. Heppner Abstract The integrated hydrology model (InHM), a physics-based hydrologic-response model with sediment-transport capabilities, was used to simulate upstream impacts from dam construction/removal for a generalized approximation of the Searsville watershed in Portola Valley, California. Four 10-year simulation scenarios (pre-dam, early dam, current and post-dam) were considered. Each scenario was simulated using the same sequence of synthetically generated rainfall and evapotranspiration. For each scenario the boundary-value problem was constructed based on the available watershed information (e.g. topography, soils, geology, reservoir bathymetry and land use). The results from the simulations are presented in terms of the temporal and spatial characteristics of hydrologic response and sediment transport. The commonalities/differences between the four Searsville-like watershed scenarios are discussed. The effort demonstrates that heuristic physics-based simulation can be a useful tool for the characterization of dam-related impacts at the watershed scale. Copyright © 2008 John Wiley & Sons, Ltd. [source] STABILITY AND EVOLUTION OF OVERLAPPING GENESEVOLUTION, Issue 3 2000David C. Krakauer Abstract., When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5'end (leading gene) decays rapidly, while the gene overlapping at the 3'end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap. [source] Sequencing and characterization of a novel serine metalloprotease from Burkholderia pseudomalleiFEMS MICROBIOLOGY LETTERS, Issue 1 2000May-Ann Lee Abstract Burkholderia pseudomallei, a Gram-negative bacterium is found in the soil and water, mainly in Southeast Asia and Northern Australia. It is responsible for melioidosis in human and animals. The bacteria produce several potential virulent factors such as extracellular protease, hemolysin, lipase and lecithinase. The isolation of virulence genes and the study of their functions will contribute to our understanding of bacterial pathogenesis. Previous studies have implicated protease as a contributing virulence factor in the pathogenesis of some bacteria. Three out of 5000 clones screened from a genomic DNA library of B. pseudomallei were found to express protease activity. The clones were found to have the same sequence. The nucleotide sequence revealed an open reading frame (designated as metalloprotease A, mprA) encoding a 500-amino acid protein, MprA, with an estimated molecular mass of 50,241 Da. The predicted amino acid sequence shares homology with the subtilisin family of serine proteases. [source] Six-Month-Olds' Detection of Clauses Embedded in Continuous Speech: Effects of Prosodic Well-FormednessINFANCY, Issue 1 2000Thierry Nazzi Three experiments investigated the role of prosodic structure for infants' recognition of embedded word sequences. Six-month-olds were familiarized with 2 versions of the same sequence, 1 corresponding to a well-formed prosodic unit and the other to a prosodically ill-formed sequence (although a successive word series). Next, infants heard 2 test passages. One included the well-formed unit, and the other included the ill-formed sequence. In Experiment 1, infants listened longer to the passage containing the well-formed unit, suggesting that such units, even when they are embedded, are better recognized. Experiments 2 and 3 showed that this better recognition does not depend on an acoustic match between the familiarized sequences and their later embeddings. This suggests that the advantage of the well-formed unit is at least partially due to infants' use of prosody to parse continuous speech. [source] End-to-end response time with fixed priority scheduling: trajectory approach versus holistic approachINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 1 2005Steven Martin Abstract In this paper, we are interested in providing deterministic end-to-end guarantees to real-time flows in a distributed system. We focus on the end-to-end response time, quality of service (QoS) parameter of the utmost importance for such flows. We assume that each node uses a Fixed Priority scheduling. We determine a bound on the end-to-end response time of any real-time flow with a worst case analysis using the trajectory approach. We establish new results that we compare with those provided by the classical holistic approach for flows visiting the same sequence of nodes. These results show that the trajectory approach is less pessimistic than the holistic one. Moreover, the bound provided by our worst-case analysis is reached in various configurations, as shown in the examples presented. Copyright © 2004 John Wiley & Sons, Ltd. [source] A computational study of the carboxylic acid of phloroglucinol in vacuo and in water solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Liliana Mammino Abstract 2,4,6-Trihydroxybenzoic acid (FA) is the carboxylic acid of phloroglucinol and, in turn, the parent compound of many biologically active compounds. The biological activities of FA are "extreme" among trihydroxybenzoic acids (e.g., lowest antioxidant activity, highest toxicity toward crustaceans). A complete MP2/6-31++G(d,p) conformational study in vacuo shows that the lowest energy conformers contain two intramolecular hydrogen bonds between the COOH function and the two ortho phenolic OH, with the Z form of COOH preferred over the E form. Comparisons with conformers in which the H-bonds are removed enable fairly reliable evaluations of their energy, because of an off-plane shift of COOH on H-bond removal, decreasing the effects of lone pair repulsion. Comparisons with the other hydroxybenzoic acids (extensively calculated in vacuo at the same level of theory) suggest that FA has the strongest intramolecular H-bonds. PCM calculations of FA in water solution show the same sequence of relative stabilities as in vacuo, with narrower differences because of the greater solvent stabilization of higher energy conformers. Calculations of adducts with water molecules H-bonded to different donor,acceptor centers of FA show the preferred arrangements of water molecules around the different regions of FA and confirm that the stronger intramolecular H-bonds are not broken on competition with the possibility of formation of intermolecular H-bonds. HF/6-31++G(d,p) calculations of adducts, in which the FA molecule is completely surrounded by water molecules, show that 14,16 water molecules (depending on the FA conformer geometry) realize arrangements corresponding to a presumable first solvation layer, with all the water molecules directly H-bonded to donor,acceptor centers of FA or bridging water molecules directly H-bonded to them. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] A convenient racemic synthesis of two isomeric tetrahydropyridyl alkaloids: Isoanatabine and anatabineJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 3 2010Anne Rouchaud Anatabine is a major alkaloid in Nicotiana tabacum and its isomer, isoanatabine, was recently found in a marine worm. Reduction of 1-methylpyridinium iodide with sodium borohydride gave 1-methyl-3-piperideine, which was transformed with hydrogen peroxide into the N -oxide. Reaction of the N -oxide successively with trifluoroacetic anhydride and potassium cyanide gave 2-cyano-1-methyl-3-piperideine. Its reaction with 3-pyridylmagnesium chloride gave (±)- N- methyl-isoanatabine. This was transformed with m -chloroperbenzoic acid into the N -oxide which was N -demethylated with iron(II) sulfate, giving (±)-isoanatabine. The successive applications of literature procedures for the N -demethylation by decomposition of N -oxide contributed to the knowledge of the mechanism of this oxidative rearrangement. On the other hand, the reduction of 1-methylpyridinium iodide with sodium borohydride and with potassium cyanide present since the start of the reaction in a two layer ether-water system, gave 2-cyano-1-methyl-4-piperideine. This was transformed into (±)-anatabine by the same sequence of reactions used for the synthesis of (±)-isoanatabine. J. Heterocyclic Chem., (2010). [source] Navigator-gated three-dimensional MR angiography of the pulmonary arteries using steady-state free precession,JOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 6 2005Benjamin K. Hui AB Abstract Purpose To assess the quality of a navigator-gated, free breathing, steady-state free precession (SSFP) technique in comparison to a single breathhold for pulmonary artery imaging in normal volunteers. Materials and Methods Sagittal sections of the left pulmonary arteries of 10 volunteers were obtained with a three-dimensional SSFP sequence using both a single breathhold of 30 seconds and a navigator-gated version of the same sequence. The images were compared and rated by a blinded cardiovascular radiologist for image quality, sharpness, and artifact. Results On a scale ranging from ,2 to 2, in which positive numbers denote that the navigator method was favorable compared to the single breathhold method, image quality was rated 0.7 ± 1.4, sharpness 0.6 ± 1.5, and artifact 0.1 ± 1.4. Thus, there was no statistical difference between the two methods. Conclusion The navigator-gated SSFP sequence is able to acquire images equal in quality to the breathhold sequence. This may be of clinical importance for pulmonary imaging in patients who are unable to sustain a long breathhold. J. Magn. Reson. Imaging 2005;21:831,835. © 2005 Wiley-Liss, Inc. [source] Poster Sessions BP06: Neurogenesis, Stem Cells and ApoptosisJOURNAL OF NEUROCHEMISTRY, Issue 2002J. Qiu The NF-,B transcription factor regulates bcl-x gene expression, which may determine hypoxia-induced neuronal apoptosis. We examined hypoxia-induced NF-,B and Bcl-xL changes in rat hippocampus. We showed differential hypoxia-induced NF-,B binding to the bcl-x promoter CS4 and IgG,,B enhancer sequences by rat hippocampal nuclear extracts. The differential NF-,B binding to these two promoter sequences was also determined in a contused spinal cord injury model and in vitro studies with LPS-treated Hela cells. There was tissue-, gene promoter-specific and time-dependent regulation of bcl-x gene expression by NF-,B in support of the hypothesis that NF-,B has tissue- and gene-specific regulatory effects and that these effects may account for both the pro- and anti-apoptotic roles assigned to NF-,B in different apoptotic processes. We applied ,decoy' oligonucleotides with sequences specific to different promoters to the rat hippocampus and measured ,decoy' inhibitory effects on nuclear NF-,B binding. The IgG-,B enhancer sequence ,decoy' showed stronger inhibition on nuclear NF-,B c-Rel/p50 binding to the bcl-x gene promoter CS4 sequence when compared to NF-,B p50/p50 binding to the same sequence. This result suggests that the ,decoy' approach has the potential to selectively manipulate NF-,B regulation of gene expression in response to hypoxia. Acknowledgements:, Supported by NINDS NS-39161, Shriner Grant 8710 and a Grant from the Sealy Center on Aging to J. Qiu. [source] Deterministic and stochastic scheduling with teamwork tasksNAVAL RESEARCH LOGISTICS: AN INTERNATIONAL JOURNAL, Issue 6 2004Xiaoqiang Cai Abstract We study a class of new scheduling problems which involve types of teamwork tasks. Each teamwork task consists of several components, and requires a team of processors to complete, with each team member to process a particular component of the task. Once the processor completes its work on the task, it will be available immediately to work on the next task regardless of whether the other components of the last task have been completed or not. Thus, the processors in a team neither have to start, nor have to finish, at the same time as they process a task. A task is completed only when all of its components have been processed. The problem is to find an optimal schedule to process all tasks, under a given objective measure. We consider both deterministic and stochastic models. For the deterministic model, we find that the optimal schedule exhibits the pattern that all processors must adopt the same sequence to process the tasks, even under a general objective function GC = F(f1(C1), f2(C2), , , fn(Cn)), where fi(Ci) is a general, nondecreasing function of the completion time Ci of task i. We show that the optimal sequence to minimize the maximum cost MC = max fi(Ci) can be derived by a simple rule if there exists an order f1(t) , , , fn(t) for all t between the functions {fi(t)}. We further show that the optimal sequence to minimize the total cost TC = , fi(Ci) can be constructed by a dynamic programming algorithm. For the stochastic model, we study three optimization criteria: (A) almost sure minimization; (B) stochastic ordering; and (C) expected cost minimization. For criterion (A), we show that the results for the corresponding deterministic model can be easily generalized. However, stochastic problems with criteria (B) and (C) become quite difficult. Conditions under which the optimal solutions can be found for these two criteria are derived. © 2004 Wiley Periodicals, Inc. Naval Research Logistics, 2004 [source] Richter syndrome in B-cell chronic lymphocytic leukemiaPATHOLOGY INTERNATIONAL, Issue 4 2003Naoya Nakamura Richter syndrome (RS) is well known as a secondary high-grade lymphoma, mostly diffuse large B-cell lymphoma (DLBCL) developed in patients with B-cell chronic lymphocytic leukemia (B-CLL). In this review, we describe clinicopathological, histological, immunophenotypical and genetic findings of RS. The patients with RS, regardless of transformation of pre-existing clone or de novo malignant clone, were resistant to conventional combined chemotherapy and died within months of diagnosis. Molecular techniques can provide convincing results for the clonal relationship of RS to pre-existing B-CLL. When RS carries a same rearrangement band or a same sequence as B-CLL by Southern blotting or nucleotide sequence analyses of immunoglobulin heavy and/or light chain genes, it is suggested to that RS transforms from original B-CLL. These analyses have showed that approximately two-thirds of RS cases evolved from a B-CLL clone. How and where does the B-CLL clone evolve to RS? The genetic alteration of transforming B-CLL clone into RS has been addressed. Abnormalities of chromosomes 11 and 14 were most frequently involved in RS, but non-specific. In addition, RS does not include chromosomal translocation between Ig locus and oncogenes or rearrangements of bcl-6 gene, both of which were found in some de novo DLBCL. Several candidates, such as mutation of p53 gene and abnormalities of cyclin dependent kinase inhibitor, have been proposed to play an important role in the transformation of a part of B-CLL. However, there is still uncertainly as to how B-CLL progresses or develops into RS. [source] Wavelet analysis and the governing dynamics of a large-amplitude mesoscale gravity-wave event along the East Coast of the United StatesTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 577 2001Fuqing Zhang Abstract Detailed diagnostic analyses are performed upon a mesoscale numerical simulation of a well-observed gravity-wave event that occurred on 4 January 1994 along the East Coast of the United States. The value of using wavelet analysis to investigate the evolving gravity-wave structure and of using potential vorticity (PV) inversion to study the nature of the flow imbalance in the wave generation region is demonstrated. The cross-stream Lagrangian Rossby number, the residual in the nonlinear balance equation, and the unbalanced geopotential-height field obtained from PV inversion are each evaluated for their usefulness in diagnosing the flow imbalance. All of these fields showed clear evidence of strong imbalance associated with a middle-to-upper tropospheric jet streak, and tropopause fold upstream of the large-amplitude gravity wave several hours before the wave became apparent at the surface. Analysis indicates that a train of gravity waves was continuously generated by geostrophic adjustment in the exit region of the unbalanced upper-level jet streak as it approached the inflection axis in the height field immediately downstream of the maximum imbalance associated with the tropopause fold. A split front in the middle troposphere, characterized by the advance of the dry conveyor belt above the warm front, was overtaken by one of these propagating waves. During this merger process, a resonant interaction resulted, which promoted the rapid amplification and scale contraction of both the incipient wave (nonlinear wave development) and the split front (frontogenesis). The gravity wave and front aloft became inseparable following this merger. The situation became even more complex within a few hours as the vertical motion enhanced by this front-wave interaction acted upon a saturated, potentially unstable layer to produce elevated moist convection. An analysis of the temporal changes in the vertical profile of wave energy flux suggests that moist convective downdraughts efficiently transported the wave energy from the midlevels downward beneath the warm-front surface, where the wave became ducted. However, pure ducting was not sufficient for maintaining and amplifying the waves; rather, wave-CISK (Conditional Instability of the Second Kind) was crucial. This complex sequence of nonlinear interactions produced a long-lived, large-amplitude gravity wave that created hazardous winter weather and disrupted society over a broad and highly populated area. Although gravity waves with similar appearance to this large-amplitude wave of depression occasionally have been seen in other strong cyclogenesis cases involving a jet streak ahead of the upper-level trough axis, it is unknown whether other such events share this same sequence of interactions. [source] Comparative insect developmental genetics: phenotypes without mutantsBIOESSAYS, Issue 5 2001Rob Denell The last decade has seen a dramatic increase in interest in the extent to which morphological evolution depends on changes in regulatory pathways. Insects provide a fertile ground for study because of their diversity and our high level of understanding of the genetic regulation of development in Drosophila melanogaster. However, comparable genetic approaches are presently possible in only a small number of non-Drosophilid insects. In a recent paper, Hughes and Kaufman(1) have used a new methodology, RNA interference, in the milkweed bug, Oncopeltus fasciatus, to phenocopy the effects of mutations in Hox genes. RNA interference involves the injection of double-stranded RNA of the same sequence as the relevant mRNA resulting in a depletion of that transcript.(2) Hughes and Kaufman focused on the gnathal segments, which elaborate specialized appendages important to feeding. Their results indicate that gnathal adaptations in this bug are correlated with changes in Hox gene functions and interactions. BioEssays 23:379,382, 2001. © 2001 John Wiley & Sons, Inc. [source] Assembly of DNA Nanostructures with Branched Tris-DNACHEMISTRY - AN ASIAN JOURNAL, Issue 4 2006Takahiro Kuroda Abstract Branched tris-DNA, in which two oligonucleotides of the same sequence and one other oligonucleotide of a different sequence are connected with a rigid central linker, was prepared chemically by using a DNA synthesizer. Two branched tris-DNA molecules with complementary DNA sequences form dimer and tetramer as well as linear and spherical oligomer complexes. The complex formation was studied by UV/thermal denaturation, enzyme digestion, gel electrophoresis, and AFM imaging. [source] Steps in Theory-of-Mind Development for Children With Deafness or AutismCHILD DEVELOPMENT, Issue 2 2005Candida C. Peterson Prior research demonstrates that understanding theory of mind (ToM) is seriously and similarly delayed in late-signing deaf children and children with autism. Are these children simply delayed in timing relative to typical children, or do they demonstrate different patterns of development? The current research addressed this question by testing 145 children (ranging from 3 to 13 years) with deafness, autism, or typical development using a ToM scale. Results indicate that all groups followed the same sequence of steps, up to a point, but that children with autism showed an importantly different sequence of understandings (in the later steps of the progression) relative to all other groups. [source] Brain Apparent Water Diffusion Coefficient Magnetic Resonance Image During a Prolonged Visual AuraHEADACHE, Issue 6 2010Robert Belvís MD (Headache 2010;50:1045-1049) Background., Reversible changes in brain magnetic resonance imaging (MRI) weighted in diffusion-weighted images (DWI) and apparent water diffusion coefficient (ADC) maps have been reported in acute stroke, epilepsy, eclampsia, and hypoglycemia, but they are contradictory regarding to migraine aura. Objective., A 41-year-old woman with known basilar migraine for 5 years consulted about a persistent visual aura (visual snow phenomenon) plus bilateral paresthesias in the extremities for 4 days. The headache was treated with success with 10 mg of wafer rizatriptan and 600 mg of ibuprophen. Methods., The neurologic and ophthalmologic examination were normal. An urgent brain MRI detected no lesions in T1, T2, fluid-attenuated inversion recovery, and DWI, but an abnormal signal appeared in the left occipital lobe in ADC and (r)ADC maps. The brain MRI angiography, carotid ultrasound study, transesophageal echocardiography, 24-hour cardiac Holter monitoring, and thrombophilia study were normal. Results., A new brain MRI 8 days after did not show any previous lesion in the same sequences. Conclusions., We present a patient with migraine and transitory abnormal signals in the ADC map of an occipital region during persistent visual aura. The clinical-radiological relationship is congruent. Some similar cases have showed these MRI signals during the aura, suggesting cytotoxic edema, without ischemic lesions in the MRI controls. Theses ADC images probably appear in complex auras. 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