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Search Results: 1 - 10 of 22022 matches for " James West "
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Interactive Java Tools for Exploring High-dimensional Data
James W. Bradley,R. Webster West
Journal of Statistical Software , 2001,
Rolling Release Siege Engines: Teaching an Old Machine a New Trick
Joseph West,Seth Ross,James Flesher
Physics , 2010,
Abstract: The analysis of a new "rolling release" mechanism is presented for three different "siege engine" designs. The range obtained with the rolling release is compared to the ranges obtained using the simpler "cup" and the proven "sling" release mechanisms. It is found that the rolling release is a significant improvement over the cup release, but the range of the rolling release is still well short of that attained with the sling release. It is also noted that the familiar "spoon" projectile holder used on many siege engines operates in a rolling release manner, contrary to appearances and to some previous published studies. Instead, the release mechanism used in ancient engines and in modern kit-purchased replicas is the rolling release.
EGR1 is essential for transcriptional regulation of BMPR2  [PDF]
Radhika Gaddipati, James D. West, James E. Loyd, Thomas Blackwell, Kirsten A. Lane, Nicole M. Lane, Kirk B. Lane
American Journal of Molecular Biology (AJMB) , 2011, DOI: 10.4236/ajmb.2011.13014
Abstract: In this study, RLM-RACE was used to identify the transcriptional start site 387 bp upstream of the translational start. Evolutionarily conserved transcription factor binding sites were identified, and a series of luciferase reporter constructs driven by BMPR2 promoter elements used to determine their functional relevance. We found the promoter area from 983 bp to 90 bp upstream of the transcriptional start gave maximal activity, greater than longer constructs, with an area between 570 bp and 290 bp upstream of the transcriptional start containing an important repressor element. To characterize this repressor, we used a combination of EMSA, mutation of the EGR1 binding site, transfection with EGR1 and NAB1 constructs, and mutation of the NAB1 binding site within the EGR1 protein. From this we conclude that EGR1 is essential to BMPR2 transcription, but that NAB1 binding to EGR1 causes it to act as a repressor.
A Simplified GIS Approach to Modeling Global Leaf Water Isoscapes
Jason B. West, Adam Sobek, James R. Ehleringer
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002447
Abstract: The stable hydrogen (δ2H) and oxygen (δ18O) isotope ratios of organic and inorganic materials record biological and physical processes through the effects of substrate isotopic composition and fractionations that occur as reactions proceed. At large scales, these processes can exhibit spatial predictability because of the effects of coherent climatic patterns over the Earth's surface. Attempts to model spatial variation in the stable isotope ratios of water have been made for decades. Leaf water has a particular importance for some applications, including plant organic materials that record spatial and temporal climate variability and that may be a source of food for migrating animals. It is also an important source of the variability in the isotopic composition of atmospheric gases. Although efforts to model global-scale leaf water isotope ratio spatial variation have been made (especially of δ18O), significant uncertainty remains in models and their execution across spatial domains. We introduce here a Geographic Information System (GIS) approach to the generation of global, spatially-explicit isotope landscapes ( = isoscapes) of “climate normal” leaf water isotope ratios. We evaluate the approach and the resulting products by comparison with simulation model outputs and point measurements, where obtainable, over the Earth's surface. The isoscapes were generated using biophysical models of isotope fractionation and spatially continuous precipitation isotope and climate layers as input model drivers. Leaf water δ18O isoscapes produced here generally agreed with latitudinal averages from GCM/biophysical model products, as well as mean values from point measurements. These results show global-scale spatial coherence in leaf water isotope ratios, similar to that observed for precipitation and validate the GIS approach to modeling leaf water isotopes. These results demonstrate that relatively simple models of leaf water enrichment combined with spatially continuous precipitation isotope ratio and climate data layers yield accurate global leaf water estimates applicable to important questions in ecology and atmospheric science.
Gene expression in lungs of mice lacking the 5-hydroxytryptamine transporter gene
Daniel Crona, Julie Harral, Serge Adnot, Saadia Eddahibi, James West
BMC Pulmonary Medicine , 2009, DOI: 10.1186/1471-2466-9-19
Abstract: Eight week old normoxic mice with a 5-HTT knock-out (5HTT-/-) and their heterozygote(5HTT+/-) or wild-type(5HTT+/+) littermates had right ventricular systolic pressure(RVSP) assessed, lungs collected for RNA, pooled, and used in duplicate in Affymetrix array analysis. Representative genes were confirmed by quantitative RT-PCR and western blot.RVSP was normal in all groups. Only 124 genes were reliably changed between 5HTT-/- and 5HTT+/+ mice. More than half of these were either involved in inflammatory response or muscle function and organization; in addition, some matrix, heme oxygenase, developmental, and energy metabolism genes showed altered expression. Quantitative RT-PCR for examples from each major group confirmed changes seen by array, with an intermediate level in 5HTT +/- mice.These results for the first time show the in vivo effects of 5HTT knockout in lungs, and show that many of the downstream mechanisms suggested by cell culture and ex vivo experiments are also operational in vivo. This suggests that the effect of 5HTT on pulmonary vascular function arises from its impact on several systems, including vasoreactivity, proliferation, and immune function.Idiopathic pulmonary arterial hypertension (IPAH) is a disease characterized by pulmonary vasoconstriction, inflammation, and vascular remodeling, whose early events and molecular etiology are still obscure. Defects in serotonin (5-HT) signaling have long been associated with idiopathic pulmonary arterial hypertension. From 1965 to 1972, the first appetite depressant-induced epidemic of pulmonary hypertension occurred in Europe following the release of aminorex[1]. During the 1990's, French researchers reported increased incidence of pulmonary hypertension among a patient population that was administered derivatives of the medication fenfluramine[2]. Dexfenfluramine, which is the active enantiomer of fenfluramine and used to treat obesity in patients, was considered to be the chief culprit behind the incr
EphrinA1-targeted nanoshells for photothermal ablation of prostate cancer cells
Andre M Gobin,James J Moon,Jennifer L West
International Journal of Nanomedicine , 2008,
Abstract: Andre M Gobin, James J Moon, Jennifer L WestDepartment of Bioengineering, Rice University, Houston, TX, USAAbstract: Gold-coated silica nanoshells are a class of nanoparticles that can be designed to possess strong absorption of light in the near infrared (NIR) wavelength region. When injected intravenously, these nanoshells have been shown to accumulate in tumors and subsequently mediate photothermal treatment, leading to tumor regression. In this work, we sought to improve their specificity by targeting them to prostate tumor cells. We report selective targeting of PC-3 cells with nanoshells conjugated to ephrinA1, a ligand for EphA2 receptor that is overexpressed on PC-3 cells. We demonstrate selective photo-thermal destruction of these cells upon application of the NIR laser.Keywords: nanoshell, near infrared, photothermal treatment, prostate cancer
Closing in on Asymmetric Dark Matter I: Model independent limits for interactions with quarks
John March-Russell,James Unwin,Stephen M. West
Physics , 2012, DOI: 10.1007/JHEP08(2012)029
Abstract: It is argued that experimental constraints on theories of asymmetric dark matter (ADM) almost certainly require that the DM be part of a richer hidden sector of interacting states of comparable mass or lighter. A general requisite of models of ADM is that the vast majority of the symmetric component of the DM number density must be removed in order to explain the observed relationship $\Omega_B\sim\Omega_{DM}$ via the DM asymmetry. Demanding the efficient annihilation of the symmetric component leads to a tension with experimental limits if the annihilation is directly to Standard Model (SM) degrees of freedom. A comprehensive effective operator analysis of the model independent constraints on ADM from direct detection experiments and LHC monojet searches is presented. Notably, the limits obtained essentially exclude models of ADM with mass 1GeV$\lesssim m_{DM} \lesssim$ 100GeV annihilating to SM quarks via heavy mediator states. This motivates the study of portal interactions between the dark and SM sectors mediated by light states. Resonances and threshold effects involving the new light states are shown to be important for determining the exclusion limits.
Approximate entropy of network parameters
James West,Lucas Lacasa,Simone Severini,Andrew Teschendorff
Physics , 2011, DOI: 10.1103/PhysRevE.85.046111
Abstract: We study the notion of approximate entropy within the framework of network theory. Approximate entropy is an uncertainty measure originally proposed in the context of dynamical systems and time series. We firstly define a purely structural entropy obtained by computing the approximate entropy of the so called slide sequence. This is a surrogate of the degree sequence and it is suggested by the frequency partition of a graph. We examine this quantity for standard scale-free and Erd\H{o}s-R\'enyi networks. By using classical results of Pincus, we show that our entropy measure converges with network size to a certain binary Shannon entropy. On a second step, with specific attention to networks generated by dynamical processes, we investigate approximate entropy of horizontal visibility graphs. Visibility graphs permit to naturally associate to a network the notion of temporal correlations, therefore providing the measure a dynamical garment. We show that approximate entropy distinguishes visibility graphs generated by processes with different complexity. The result probes to a greater extent these networks for the study of dynamical systems. Applications to certain biological data arising in cancer genomics are finally considered in the light of both approaches.
Perfect matchings for the three-term Gale-Robinson sequences
Mireille Bousquet-Mélou,James Propp,Julian West
Mathematics , 2009,
Abstract: In 1991, David Gale and Raphael Robinson, building on explorations carried out by Michael Somos in the 1980s, introduced a three-parameter family of rational recurrence relations, each of which (with suitable initial conditions) appeared to give rise to a sequence of integers, even though a priori the recurrence might produce non-integral rational numbers. Throughout the '90s, proofs of integrality were known only for individual special cases. In the early '00s, Sergey Fomin and Andrei Zelevinsky proved Gale and Robinson's integrality conjecture. They actually proved much more, and in particular, that certain bivariate rational functions that generalize Gale-Robinson numbers are actually polynomials with integer coefficients. However, their proof did not offer any enumerative interpretation of the Gale-Robinson numbers/polynomials. Here we provide such an interpretation in the setting of perfect matchings of graphs, which makes integrality/polynomiality obvious. Moreover, this interpretation implies that the coefficients of the Gale-Robinson polynomials are positive, as Fomin and Zelevinsky conjectured.
Equivalence Classes of Permutations under Various Relations Generated by Constrained Transpositions
Steven Linton,James Propp,Tom Roby,Julian West
Mathematics , 2011,
Abstract: We consider a large family of equivalence relations on permutations in Sn that generalise those discovered by Knuth in his study of the Robinson-Schensted correspondence. In our most general setting, two permutations are equivalent if one can be obtained from the other by a sequence of pattern-replacing moves of prescribed form; however, we limit our focus to patterns where two elements are transposed, subject to the constraint that a third element of a suitable type be in a suitable position. For various instances of the problem, we compute the number of equivalence classes, determine how many n-permutations are equivalent to the identity permutation, or characterise this equivalence class. Although our results feature familiar integer sequences (e.g., Catalan, Fibonacci, and Tribonacci numbers) and special classes of permutations (layered, connected, and 123-avoiding), some of the sequences that arise appear to be new.
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