bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the interactive interface and phylogenic conservation of the Nrf2‐Keap1 system
Authors: Kobayashi Makoto , Itoh Ken , Suzuki Takafumi , Osanai Hitoshi , Nishikawa Keizo , Katoh Yasutake , Takagi Yaeko , Yamamoto Masayuki 
Published: March 2003

AbstractBackground:  The transcription factor Nrf2 and its negative regulator Keap1 play important roles in transcriptional induction of a set of detoxifying and anti‐oxidant enzymes. To gain an insight into our present enigma as to how cells receive oxidative and electrophilic signals and transduce them to Nrf2, we have developed a zebrafish model system for molecular toxicological studies.Results: We systematically cloned zebrafish cytoprotective enzyme cDNAs and found their expression to be efficiently induced by electrophilic agents. We consequently identified the presence of Nrf2 and Keap1 in zebrafish. Both loss‐ and gain‐of‐function analyses demonstrated that Nrf2 is the primary regulator of a subset of cytoprotective enzyme genes, while Keap1 suppresses Nrf2 activity in zebrafish. An ETGE motif, critical for the Nrf2–Keap1 interaction, was identified in the Neh2 domain of Nrf2 by reverse two‐hybrid screening and found to be indispensable for the regulation of Nrf2 activity in zebrafish.Conclusion: Taken together, these results indicate that the Nrf2‐Keap1 system is highly conserved among vertebrates and that the interface between Nrf2 and Keap1 forms an important molecular basis of this regulatory system.
PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA
Authors: Iida Tetsuo , Suetake Isao , Tajima Shoji , Morioka Hiroshi , Ohta Satoshi , Obuse Chikashi , Tsurimoto Toshiki 
Published: March 2003

AbstractBackground: Proliferating cell nuclear antigen (PCNA) is a ring‐shaped protein known as a processivity factor of DNA polymerase δ. In addition to this role, PCNA interacts with a number of other proteins to increase their local concentration at replicated DNA sites. DNA cytosine methyltransferase 1 (Dnmt1), which preserves epigenetic signals by completing the methylation of hemimethylated DNA after DNA replication, has been indicated as one of these PCNA binding proteins by a previous work. However, the molecular mechanisms and functional significance of their association have not yet been studied.Results: Dnmt1 can be readily isolated from nuclear extracts by PCNA affinity chromatography. Studies of the interactions between the two proteins demonstrate that the N‐terminal region of Dnmt1, which contains a typical PCNA binding motif, has core PCNA binding activity, and that the remaining portion of the protein exerts a negative influence on the interaction of Dnmt1 with PCNA. The affinity of Dnmt1 for DNA is much higher for DNA bound by PCNA than for free DNA. Furthermore, DNA methylation assays with hemimethylated DNA as a substrate revealed that PCNA clamp‐bound DNA is methylated more efficiently by Dnmt1 than is free DNA.Conclusion: These results provide the first biochemical evidence that physical interactions between PCNA and Dnmt1 facilitate the methylation of newly neplicated DNA, on which PCNA remains associated as a functional clamp.
Parsimonious Bayesian Markov chain Monte Carlo inversion in a nonlinear geophysical problem
Authors: Malinverno Alberto 
Published: March 2003

SummaryA key element in the solution of a geophysical inverse problem is the quantification of non-uniqueness, that is, how much parameters of an inferred earth model can vary while fitting a set of measurements. A widely used approach is that of Bayesian inference, where Bayes' rule is used to determine the uncertainty of the earth model parameters a posteriori given the data. I describe here, a natural extension of Bayesian parameter estimation that accounts for the posterior probability of how complex an earth model is (specifically, how many layers it contains). This approach has a built-in parsimony criterion: among all earth models that fit the data, those with fewer parameters (fewer layers) have higher posterior probabilities.To implement this approach in practice, I use a Markov chain Monte Carlo (MCMC) algorithm applied to the nonlinear problem of inverting DC resistivity sounding data to infer characteristics of a 1-D earth model. The earth model is parametrized as a layered medium, where the number of layers and their resistivities and thicknesses are poorly known a priori. The algorithm obtains a sample of layered media from the posterior distribution; this sample measures non-uniqueness in terms of how many layers are effectively resolved by the data and of the range of layer thicknesses and resistivities consistent with the data.Because the complexity of the model is effectively determined by the data, the solution does not need to be regularized. This is a desirable feature, because requiring the solution to be smooth beyond what is implied by prior information can lead to underestimating posterior uncertainty. Letting the number of layers be a free parameter, as done here, broadens the space of earth models possible a priori and makes the determination of posterior uncertainty less dependent on the parametrization.
Automated 1D interpretation of resistivity soundings by simultaneous use of the direct and iterative methods*
Authors: Başokur Ahmet T. 
Published: March 2003

Noise contamination of measured data greatly affects the final results of inversion. Three types of noise source — random and systematic errors and the uncertainties due to the inadequacy of the mathematical model in representing the actual physical conditions — are discussed in the framework of resistivity sounding data. Two methods are proposed for describing these uncertainties. The first possibility is to smooth the measured data by a combination of simple fitting functions that satisfies the ‘1D smoothness’ criteria and consequently simulates the behaviour of a 1D Schlumberger apparent resistivity curve. The second method is to derive weight coefficients from the differences between the measured and the smoothed data sets. Both methods are carried out under the control of the interpreter.The relative merits and drawbacks of the direct and iterative interpretation methods used for the estimation of the parameters of the layered earth model are summarized. Two variants of the combination of these methods are presented to obtain more powerful and automatic interpretation schemes. In the sequential interpretation, an initial guess supplied by the direct method is improved by the iterative method to obtain a reasonable fit between the measured data and the model response. In the simultaneous interpretation, the successive application of the direct and iterative methods is carried out, starting from the first branch of the apparent resistivity curve. The operation is then shifted to subsequent branches that represent the deeper parts of the geoelectric section. This is similar to the data acquisition applied in direct current sounding in which the depth penetration is increased by expanding the current electrode spacings. The proposed sequential and simultaneous interpretation algorithms require minimum aids and efforts of the interpreter.
Diffraction problems of 3D seismic imaging
Authors: Zavalishin B.R. 
Published: March 2003

Migration is essential to seismic imaging. It is carried out by backward extrapolation of the wavefield registered on the observation surface. The quality of images depends on the accuracy of the wavefield reconstruction at interior subsurface points. From the theory based on the exact solution of the scalar wave equation it is known that, for accurate wave extrapolation, data must be obtained from an infinite observation surface. Limiting of migration apertures, which is inevitable in practice, leads to artefacts in extrapolated fields. The distortion they cause in 2D and 3D imaging is different. In 2D migration, the artefacts known as truncation effects are much weaker than the signals being extrapolated and for this reason attract no special attention. In 3D migration, diffractions caused by an aperture edge are stronger and may create serious problems. For a circular aperture, their amplitudes are comparable to the amplitudes of the signals themselves. The study of aperture diffractions is intended to help in the search for ways of either suppressing them efficiently or deliberately utilizing them in order to improve imaging.In optics, diffractions by an aperture play a constructive role in image making. This research shows that the same may take place in seismic imaging.
Anisotropic inversion of refracted waves in vertical cable data in the presence of dip
Authors: Wang Hejie , Li Xiang‐Yang 
Published: March 2003

ABSTRACTRefracted arrivals are analysed to estimate the near‐surface anisotropy of marine sediments using a vertical‐cable (VC) configuration. In the presence of dip, the horizontal and vertical ray‐slownesses are obtained from the observed apparent slownesses in the up‐ and downdip directions using a sum or difference at each azimuth. The multiple azimuths generated by a VC geometry permit the ray‐slowness distribution of the marine sediments to be determined.An inversion procedure is developed to provide dip and anisotropy parameters for refractive layers from the measured refraction traveltimes in multilayered azimuthally isotropic and anisotropic media. Two sets of transversely isotropic models are used to analyse the azimuthal variations of apparent and ray slownesses. In the first set, we fix the anisotropic parameters of the models but vary the dip (0°, 5° and 10°) to test the effects of the presence of dip. In the second set, we vary the P‐wave anisotropy strength (5.2%, 10.3%, 15.8% and 22.0%) to examine the sensitivity and accuracy of ray‐slowness approximations which are independent of dip. We test this inversion procedure on synthetic P‐wave VC data calculated for six different models by a finite‐difference method. The results of applications to real VC data acquired from the North Sea are also presented.
Out‐of‐plane geometrical spreading in anisotropic media
Authors: Ettrich Norman , Sollid Anders , Ursin Bjørn 
Published: March 2003

Two‐dimensional seismic processing is successful in media with little structural and velocity variation in the direction perpendicular to the plane defined by the acquisition direction and the vertical axis. If the subsurface is anisotropic, an additional limitation is that this plane is a plane of symmetry. Kinematic ray propagation can be considered as a two‐dimensional process in this type of medium. However, two‐dimensional processing in a true‐amplitude sense requires out‐of‐plane amplitude corrections in addition to compensation for in‐plane amplitude variation. We provide formulae for the out‐of‐plane geometrical spreading for P‐ and S‐waves in transversely isotropic and orthorhombic media. These are extensions of well‐known isotropic formulae.For isotropic and transversely isotropic media, the ray propagation is independent of the azimuthal angle. The azimuthal direction is defined with respect to a possibly tilted axis of symmetry. The out‐of‐plane spreading correction can then be calculated by integrating quantities which describe in‐plane kinematics along in‐plane rays. If, in addition, the medium varies only along the vertical direction and has a vertical axis of symmetry, no ray tracing need be carried out. All quantities affecting the out‐of‐plane geometrical spreading can be derived from traveltime information available at the observation surface.Orthorhombic media possess no rotational symmetry and the out‐of‐plane geometrical spreading includes parameters which, even in principle, are not invertible from in‐plane experiments. The exact and approximate formulae derived for P‐ and S‐waves are nevertheless useful for modelling purposes.
3D description and inversion of reflection moveout of PS‐waves in anisotropic media
Authors: Tsvankin Ilya , Grechka Vladimir 
Published: March 2003

Common‐midpoint moveout of converted waves is generally asymmetric with respect to zero offset and cannot be described by the traveltime series t2(x2) conventionally used for pure modes. Here, we present concise parametric expressions for both common‐midpoint (CMP) and common‐conversion‐point (CCP) gathers of PS‐waves for arbitrary anisotropic, horizontally layered media above a plane dipping reflector. This analytic representation can be used to model 3D (multi‐azimuth) CMP gathers without time‐consuming two‐point ray tracing and to compute attributes of PS moveout such as the slope of the traveltime surface at zero offset and the coordinates of the moveout minimum.In addition to providing an efficient tool for forward modelling, our formalism helps to carry out joint inversion of P and PS data for transverse isotropy with a vertical symmetry axis (VTI media). If the medium above the reflector is laterally homogeneous, P‐wave reflection moveout cannot constrain the depth scale of the model needed for depth migration. Extending our previous results for a single VTI layer, we show that the interval vertical velocities of the P‐ and S‐waves (VP0 and VS0) and the Thomsen parameters ε and δ can be found from surface data alone by combining P‐wave moveout with the traveltimes of the converted PS(PSV)‐wave.If the data are acquired only on the dip line (i.e. in 2D), stable parameter estimation requires including the moveout of P‐ and PS‐waves from both a horizontal and a dipping interface. At the first stage of the velocity‐analysis procedure, we build an initial anisotropic model by applying a layer‐stripping algorithm to CMP moveout of P‐ and PS‐waves. To overcome the distorting influence of conversion‐point dispersal on CMP gathers, the interval VTI parameters are refined by collecting the PS data into CCP gathers and repeating the inversion.For 3D surveys with a sufficiently wide range of source–receiver azimuths, it is possible to estimate all four relevant parameters (VP0, VS0, ε and δ) using reflections from a single mildly dipping interface. In this case, the P‐wave NMO ellipse determined by 3D (azimuthal) velocity analysis is combined with azimuthally dependent traveltimes of the PS‐wave. On the whole, the joint inversion of P and PS data yields a VTI model suitable for depth migration of P‐waves, as well as processing (e.g. transformation to zero offset) of converted waves.
Fast modelling of marine surface multiples
Authors: Taylor David B. 
Published: March 2003

ABSTRACTIn the development and testing of water‐surface multiple‐removal algorithms, it is valuable to have accurate synthetic seismograms which exhibit multiples, for which the multiple‐free solution is known. A method is presented for constructing 2D and 3D solutions of the acoustic wave equation in water, by combining the solution from a primary source with other scaled solutions of secondary sources, which simulate diffractors. The computation involves function evaluation rather than numerical solution of differential equations and is consequently accurate and comparatively fast. The analytic formulae on which the method is based give insights into methods for multiple removal. Generalized reflection coefficients, defined on a horizontal plane above the diffractors, are derived and used to construct the integral equations which are the basis for many multiple‐removal schemes.
Wavelet correlation filter for wide‐angle seismic data
Authors: Carrozzo M.T. , De Franco R. , De Luca L. , Luzio D. , Primiceri R. , Quarta T. , Vitale M. 
Published: March 2003

ABSTRACTA new filtering technique for single‐fold wide‐angle reflection/refraction seismic data is presented. The technique is based on the wavelet decomposition of a set of adjacent traces followed by coherence analysis. The filtering procedure consists of three steps. In the first, a wavelet decomposition of traces into different detail levels is performed. In the second, the coherence attributes for each level are evaluated by calculating cross‐correlation functions of detail portions contained in a space–time moving window. Finally, the filtered traces are obtained as a weighted reconstruction of the trace details. Each weight is obtained from the coherence‐attributes distribution estimated in a proper interval. A sequence of tests is then conducted in order to select possible optimum or unsuitable wavelet bases. The efficiency of the filter proposed was assessed by calculating some properly designed parameters in order to compare it with other standard de‐noising techniques. The proposed method produced a clear signal enhancement in high‐density wide‐angle seismic data, thus proving that it is a useful processing tool for a reliable correlation of seismic phases.
Elevated CO2reduces the nitrogen concentration of plant tissues
Authors: Cotrufo M. Francesca , Ineson Phil , Scott AndY. 
Published: March 2003

AbstractWe summarize the impacts of elevated CO2on the N concentration of plant tissues and present data to support the hypothesis that reductions in the quality of plant tissue commonly occur when plants are grown under elevated CO2. Synthesis of existing data showed an average 14% reduction of N concentrations in plant tissue generated under elevated CO2regimes. However, elevated CO2appeared to have different effects on the N concentrations of different plant types, as the reported reductions in N have been larger in C3 plants than in C4 plants and N2‐fixers. Under elevated CO2plants changed their allocation of N between above‐ and below‐ground components: root N concentrations were reduced by an average of 9% compared to a 14% average reduction for above‐ground tissues. Although the concentration of CO2treatments represented a significant source of variance for plant N concentration, no consistent trends were observed between them.
Soil water content and temperature as independent or confounded factors controlling soil respiration in a temperate mixed hardwood forest
Authors: Davidson EriC. A. , Belk Elizabeth , Boone Richard D. 
Published: March 2003

AbstractVariation in soil temperature can account for most of the seasonal and diel variation in soil CO2 efflux, but the temperature effect is not always consistent, and other factors such as soil water content are known to influence soil respiration. The objectives of this research were to study the spatial and temporal variation in soil respiration in a temperate forested landscape and to evaluate temperature and soil water functions as predictors of soil respiration. Soil CO2 fluxes were measured with chambers throughout an annual cycle in six study areas at the Harvard Forest in central Massachusetts that include soil drainage classes from well drained to very poorly drained. The mean annual estimate of soil CO2 efflux was 7.2 Mg ha–1, but ranged from 5.3 in the swamp site to 8.5 in a well‐drained site, indicating that landscape heterogeneity is related to soil drainage class. An exponential function relating CO2 fluxes to soil temperature accounted for 80% of the seasonal variation in fluxes across all sites (Q10 = 3.9), but the Q10 ranged from 3.4 to 5.6 for the individual study sites. A significant drought in 1995 caused rapid declines in soil respiration rates in August and September in five of the six sites (a swamp site was the exception). This decline in CO2 fluxes correlated exponentially with decreasing soil matric potential, indicating a mechanistic effect of drought stress. At moderate to high water contents, however, soil water content was negatively correlated with soil temperature, which precluded distinguishing between the effects of these two confounded factors on CO2 flux. Occurrence of high Q10 values and variation in Q10 values among sites may be related to: (i) confounding effects of high soil water content; (ii) seasonal and diel patterns in root respiration and turnover of fine roots that are linked to above ground phenology and metabolism; and (iii) variation in the depth where CO2 is produced. The Q10 function can yield reasonably good predictions of annual fluxes of CO2, but it is a simplification that masks responses of root and microbial processes to variation in temperature and water content throughout the soil.
Effects of elevated CO2 on the chrysanthemum leaf‐miner, Chromatomyia syngenesiae: a greenhouse study
Authors: Smith P. H. D. , Jones T. H. 
Published: March 2003

AbstractAlthough feeding behaviour of Chromatomyia syngenesiae on plants grown in elevated CO2 (ambient + 200ppm) was unaffected, leaf‐miner development was slower in elevated compared to ambient CO2 atmospheres. Pupal weight was lower at high CO2 and correlated with the area of leaf mined; no such correlation existed in ambient CO2. There appears to be no compensatory feeding by the leaf‐miner for the reduced food quality of plants growing in elevated CO2. The implications of these findings are discussed.
Impact of global warming on the distribution and survival of the gelada baboon: a modelling approach
Authors: Dunbar R. I. M. 
Published: March 2003

AbstractThe gelada baboon is a graminivorous primate whose ecology is unusually sensitive to ambient temperature. A systems model of the socio‐ecology of the gelada is used to predict the impact of global warming on the species’ altitudinal distribution. The species’ lower altitudinal limit will rise by ≈ 500 m for every 2 °C increase in global mean temperature. A 7 °C rise in temperature would be sufficient to result in the species being confined to a small number of isolated mountain peaks, where its chances of survival will be greatly reduced. Changes in local climate are also likely to have significant effects on agricultural practice on the Ethiopian highlands, and this in turn is likely to have repercussions for the distribution patterns of the gelada by further constraining the habitat available to them.
Long‐term measurements of boreal forest carbon balance reveal large temperature sensitivity
Authors: Lindroth Anders , Grelle Achim , Morén Ann‐Sofie 
Published: March 2003

AbstractWe present results from two years’ net ecosystem flux measurements above a boreal forest in central Sweden. Fluxes were measured with an eddy correlation system based on a sonic anemometer and a closed path CO2 and H2O gas analyser. The measurements show that the forest acted as a source during this period, and that the annual balance is highly sensitive to changes in temperature. The accumulated flux of carbon dioxide during the full two‐year period was in the range 480–1600 g CO2 m–2. The broad range is caused by uncertainty regarding assessment of the night‐time fluxes. Although annual mean temperature remained close to normal, the results are partly explained by higher than normal respiration, due to abnormal temperature distribution and reduced soil moisture during one growing season. The finding that a closed forest can be a source of carbon over such a long period as two years contrasts sharply with the common belief that forests are always carbon sinks.