bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural requirements of the mRNA for intracistronic translation initiation of the enterobacterial infB gene
Authors: Laursen Brian Søgaard , De A. Steffensen Søren A. , Hedegaard Jakob , Moreno Juan Manuel Palacios , Mortensen Kim Kusk , Sperling‐Petersen Hans Uffe
Published: March 2003

Background: The gene infB encodes the prokaryotic translation initiation factor IF2, a central macromolecular component in the formation of the ribosomal 70S initiation complex. In Escherichia coli, infB encodes three forms of IF2: IF2α, IF2β and IF2γ. The expression of IF2β and IF2γ is a tandem translation from intact infB mRNA and not merely a translation of post‐transcriptionally truncated mRNA. The molecular mechanism responsible for the ribosomal recognition of the two intracistronic translation initiation sites in E. coli infB is not well characterized.

Results: We found three different forms of IF2 in Enterobacter cloacae, Klebsiella oxytoca, Salmonella enterica, Salmonella typhimurium, and two different forms in Proteus vulgaris. We identified the intracistronic translation initiation sites of the mRNA by isolation and N‐terminal sequencing of the shorter isoforms of IF2 in S. enterica and S. typhimurium. A further search in the readily available public sequence databases revealed that infB from Yersinia pestis also contains an intracistronic in‐frame initiation site used for the translation of IF2β. The base composition in a part of the 5′ end of the DNA coding strand of the enterobacterial infB gene shows a strong preference for adenine (A) over thymine (T) with a maximum ratio of A‐to‐T around the intracistronic initiation sites. We demonstrate that the mRNA has an open structure around the ribosomal binding region.

Conclusion: Efficient intracistronic translation initiation of the infB gene is suggested to require an mRNA with this special base composition that results in an open, single‐stranded structure at the ribosomal binding region.

Schematic view of the translation process of infB mRNA. The 5′‐end of the infB mRNA preceding the intracistronic translation initiation codon(s) has a number of rare codons. This stalls the translation in this region of the mRNA, providing space for the ribosomes to initiate at the intracistronic initiation site(s). The region around the intracistronic sites(s) has a high content of adenine and a low content of uracil. This leads to an open single‐stranded structure of the mRNA in the region, which is a necessity for the intracistronic translation initiation of the infB gene.

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Physical interaction between proliferating cell nuclear antigen and replication factor C fromPyrococcus furiosus
Authors: Matsumiya Shigeki , Ishino Sonoko , Ishino Yoshizumi , Morikawa Kosuke
Published: March 2003

Background: Proliferating cell nuclear antigen (PCNA), which is recognized as a DNA polymerase processivity factor, has direct interactions with various proteins involved in the important genetic information processes in Eukarya. We determined the crystal structure of PCNA from the hyperthermophilic archaeon,Pyrococcus furiosus(PfuPCNA) at 2.1 Å resolution, and found that the toroidal ring‐shaped structure, which consists of homotrimeric molecules, is highly conserved between the Eukarya and Archaea. This allowed us to examine its interaction with the loading factor at the atomic level.

Results:The replication factor C (RFC) is known as the loading factor of PCNA on to the DNA strand.P. furiosusRFC (PfuRFC) has a PCNA binding motif (PIP‐box) at the C‐terminus of the large subunit (RFCL). An 11 residue‐peptide containing a PIP‐box sequence of RFCL inhibited the PCNA‐dependent primer extension ability ofP. furiosus PolI in a concentration‐dependent manner. To understand the molecular interaction mechanism of PCNA with PCNA binding proteins, we solved the crystal structure ofPfuPCNA complexed with the PIP‐box peptide. The interaction mode of the two molecules is remarkably similar to that of human PCNA and a peptide containing the PIP‐box of p21WAF1/CIP1. Moreover, the PIP‐box binding may have some effect on the stability of the ring structure ofPfuPCNA by some domain shift.

Conclusions:Our structural analysis onPfuPCNA suggests that the interaction mode of the PIP‐box with PCNA is generally conserved among the PCNA interacting proteins and that the functional meaning of the interaction via the PIP‐box possibly depends on each protein. A movement of the C‐terminal region of the PCNA monomer by PIP‐box binding may cause the PCNA ring to be more rigid, suitable for its functions.
Artificial recruitment of certain Mediator components affects requirement of basal transcription factor IIE
Authors: Sakurai Hiroshi , Fukasawa Toshio
Published: March 2003

Background: Basal transcription factors are essential for RNA polymerase II (RNAPII)‐catalysed transcription of many but not all the mRNA‐encoding genes in vivo as well as in vitro. For example, copper‐inducible transcription of the copper metallothionein gene CUP1 occurs independently of basal factor TFIIE in budding yeast. To gain insight into the mechanism by which the requirement for TFIIE is bypassed, we artificially recruited certain constituents of Mediator, a large protein complex transmitting signals from various activators to the RNAPII machinery, to the CUP1 promoter by protein fusions with Ace1, the copper‐inducible activator.

Results: Fusions with Med2 or Pgd1 activated CUP1 independently of TFIIE. Surprisingly, fusions with neither Srb5 nor Med9 circumvented TFIIE requirement for the CUP1 activation. Components of TFIID were similarly recruited to the CUP1 promoter without activation. By using a chromatin immunoprecipitation technique, we found that TFIIE is necessary for stable binding of TFIIH and RNAPII to the ADH1 promoter, whose activation requires TFIIE. However, binding of TFIIH and RNAPII to CUP1 upon its activation did not require TFIIE.

Conclusions: Our results strongly suggest that the TFIIE requirement of a gene is determined by a target(s) in Mediator through which the signal of the cognate activator is transmitted.
Cordaites tree‐trunks in the British Coal Measures
Authors: Johnson G. A. L.
Published: March 2003

Carboniferous cordaitean tree‐trunks have been discovered in Britain for the first time.
The travertine dams of Slade Brook, Gloucestershire: their formation and conservation
Authors: Pentecost Allan , Peterken George F. , Viles Heather C.
Published: March 2003

Travertine dams along the Slade Brook, Gloucestershire, occur over a 700‐m length of stream, making this the largest active site of its kind so far recorded in the British Isles. The dams have considerable conservation value owing to their unusual geomorphology and influence on water flow (ponding and cascades) and their specialized flora and fauna.
Living with volcanoes
Authors: Rymer Hazel
Published: March 2003

The 1990s were designated the International Decade of Natural Disaster Reduction (IDNDR) by the United Nations and considerable research effort has gone into achieving a better understanding of volcanic processes and public understanding of volcanic phenomena. Some eruptions have been predicted successfully and thousands of lives have been saved through evacuation and well co‐ordinated aid programmes.
Optimum expression for computation of the gravity field of a polyhedral body with linearly increasing density
Authors: Pohánka V.
Published: March 2003

The formula for the computation of the gravity field of a polyhedral body whose density is linearly dependent on some coordinate is derived and transformed into the optimum form for numerical calculation.
Calibration shifts in a LaCoste‐and‐Romberg gravimeter: comparison with a Scintrex CG‐3M
Authors: Carbone Daniele , Rymer Hazel
Published: March 2003

The reliability and ruggedness of LaCoste‐and‐Romberg gravity meters has meant that their use has extended over recent years from gravity mapping to the investigation of small gravity changes (> 10 μGal) with time. When using the instrument at the limit of its capability, limitations become apparent. Some instruments drift more than others and some are prone to excessive tares. However, with regular servicing these problems are minimized. Here we demonstrate clear evidence for calibration changes of the order of 1000 ppm for LaCoste‐and‐Romberg meter G513, which, for gravity differences of over 50 mGal, represents a highly significant induced error of over 50 μGal. Data collected over 15 years using nearly 4000 mGal of the 7000 mGal range of the instrument illustrates that long periods of stability may be interspersed with periods lasting several months while the calibration changes by up to 0.1%. This is comparable with the calibration drift of a new Scintrex CG‐3M instrument, although the process causing the change may not be the same.
The problem of velocity inversion in refraction seismics: some observations from modelling results
Authors: Krishna  , Rao  , Sarkar
Published: March 2003

The applicability of seismic refraction profiling for the detection of velocity inversion, which is also known as a low‐velocity layer (LVL), is investigated with the aid of synthetic seismogram computations for a range of models. Our computational models focus on the inherent ambiguities in the interpretation of first‐arrival time delays or ‘skips’ in terms of LVL model parameters. The present modelling results reveal that neither the measure nor even the existence of a shadow zone and/or a time shift (skip) in first arrivals is necessarily indicative of an LVL. Besides attenuation effects, the cap‐layer velocity gradient is a critical parameter, determining the termination point of the cap‐layer diving wave and thus the time skip.

We suggest that shallow LVLs can be delineated more reliably by traveltime and amplitude modelling of coherent phases reflected from their top and bottom boundaries, often clearly observed in the pre‐ and near‐critical ranges in seismogram sections of refraction profiling experiments with a close receiver spacing. We demonstrate the applicability of this approach for a field data set of a refraction profile in the West Bengal Basin, India. The inferred LVL corresponds to the Gondwana sediments underlying the higher‐velocity layer of the Rajmahal Traps. This interpretation is consistent with the data from a nearby well in the region.
Modelling the poroelasticity of rocks and ice
Authors: Keller Thomas , Motschmann Uwe , Engelhard Ludwig
Published: March 2003

For many geophysical and astrophysical applications the relationship between physical bulk properties and porosity is needed. As part of the preparation for the ‘Rosetta’ comet rendezvous mission, a simple model for the porosity dependence of the elastic properties of granular media, i.e. the elastic moduli and the propagation velocities of elastic waves, has been developed based on textural properties and the contact stiffness of the constituent particles. It is shown that the derived relationships fit very well with sandstone data. The model is also consistent with data for snow and ice and is in agreement with the transformation mechanisms from snow to ice. A short review shows the relevance to another physical bulk property, the thermal conductivity.
Mise‐à‐la‐masse interpretation using a perfect conductor in a piecewise uniform earth
Authors: Furness Peter
Published: March 2003

A useful analysis of the mise‐à‐la‐masse problem can be made by considering a perfectly conducting orebody in a piecewise uniform conducting earth. While the use of a perfect conductor is clearly an idealization of the true geological conditions it provides several advantages for the present purpose.

The electric field associated with the above model can be expressed in terms of a surface integral of the normal potential gradient over the boundary of the conductor, where the normal gradient satisfies a well‐posed Fredholm integral equation of the first kind. This integral equation formulation remains unchanged when the conductor is arbitrarily located in the conducting earth, including the important case when it crosses surfaces of conductivity discontinuity. Moreover, it is readily specialized to the important case of a thin, perfectly conductive lamina.

Consideration of the boundary value problem relevant to a conductive body fed by a stationary current source suggests that under certain circumstances, equivalent mise‐à‐la‐masse responses will result from any perfect conductor confined by the equipotential surfaces of the original problem. This type of equivalence can only be reduced by extending the potential measurements into or on to the conductor itself.

This ambiguity in the interpretation of mise‐à‐la‐masse surveys suggests a simple if approximate integral solution to the mise‐à‐la‐masse problem. The solution is suitable for modelling the responses of perfect conductors and could possibly be used as the basis of a direct inversion scheme for mise‐à‐la‐masse data.
Source/receiver array directivity effects on marine seismic attenuation measurements
Authors: Hustedt Bernhard , Clark Roger A.
Published: March 2003

Attenuation of seismic waves, quantified by the seismic quality factor Q, holds important information for seismic interpretation, due to its sensitivity to rock and fluid properties. A recently published study of Q, based on surface seismic reflection data, used a modified spectral ratio approach (QVO), but both source and receiver responses were treated as isotropic, based on simple raypath arguments. Here, this assumption has been tested by computing apparent attenuation generated by frequency‐dependent directivity of typical marine source and receiver arrays and acquisition geometries. Synthetic wavelet spectra were computed for reflected rays, summed over the first Fresnel zone, from the base of a single interval, 50–3000 m thick and velocity 2000 m/s, overlying a 2200 m/s half‐space, and for offsets of 71–2071 m. The source and receiver geometry were those of an actual survey.

The modelled spectra are clearly affected by directivity, most strongly because of surface ghosts. In general, the strong high‐frequency component, produced by the array design, leads to apparently negative attenuation in individual reflection events, though this is dependent on offset and target depth. For shallow targets (less than 400–500 ms two‐way traveltime (TWT) depth), apparent Q‐values as extreme as −50 to −100 were obtained. For deeper target depths, the directivity effect is far smaller. The implications of the model study were tested on real data. QVO was applied to 20 true‐spectrum‐processed CMPs, in a shallow (405–730 ms TWT) and a deeper (1000–1300 ms TWT) interval, firstly using a measured far‐field source signature (effectively isotropic), and secondly using computed directivity effects instead. Mean interval Q−1‐values for the deeper interval, 0.029 ± 0.011 and 0.027 ± 0.018 for conventional and directional processing, respectively, suggested no directivity influence on attenuation estimation. For the shallow interval (despite poor spectral signal‐to‐noise ratios and hence scattered attenuation estimates), directional processing removed directivity‐generated irregularities from the spectral ratios, resulting in an improvement from Q−1int = −0.036 ± 0.130 to a realistic Q−1int = 0.012 ± 0.030: different at 94% confidence level. Equivalent Q‐values are: for the deeper interval, 35 and 37 for conventional and directional processing, respectively, and −28 and 86 for the shallow interval.

These results support the conclusions of the model studies, i.e. that source/receiver directivity has a negligible effect except for shallow targets (e.g. TWT depth ≤ 500 ms) imaged with conventional acquisition geometry. In such cases directivity corrections to spectra are strongly recommended.
Green's function interpolations for prestack imaging
Authors: Mendes Manuela
Published: March 2003

A new interpolation method is presented to estimate the Green's function values, taking into account the migration/inversion accuracy requirements and the trade‐off between resolution and computing costs. The fundamental tool used for this technique is the Dix hyperbolic equation (DHE). The procedure, when applied to evaluate the Green's function for a real source position, uses the DHE to derive the root‐mean‐square velocity, vRMS, from the precomputed traveltimes for the nearest virtual sources, and by linear interpolation generates vRMS for the real source. Then, by applying the DHE again, the required traveltimes and geometrical spreading can be estimated.

The inversion of synthetic data demonstrates that the new interpolation yields excellent results which give a better qualitative and quantitative resolution of the imaging sections, compared with those carried out by conventional linear interpolation. Furthermore, the application to synthetic and real data demonstrates the ability of the technique to interpolate Green's functions from widely spaced virtual sources. Thus the proposed interpolation, besides improving the imaging results, also reduces the overall CPU time and the hard disk space required, hence decreasing the computational effort of the imaging algorithms.
1D complete calculation for electrostatic soundings interpretation
Authors: Tabbagh Alain , Panissod Cédric
Published: March 2003

Soundings achieved with the electrostatic method cannot be interpreted correctly with 1D electrical programs if the extension of the array or the conductivity of the ground are too large. A complete calculation taking into account the induction effect due to the frequency must be performed. This paper presents the solutions for overcoming the difficulties encountered in this calculation: the iterative processes which make it possible to determine the kernel functions of the Hankel transforms and the analytic integration of the terms of the electric field. Application to practical cases first illustrates the distortion of the electrostatic curves by reference to DC sounding curves. The limitation in depth of investigation is then emphasized: in practice, the investigation is limited by the skin depth corresponding to the frequency used. The examples of the soundings obtained in the city of Alexandria (Egypt) demonstrate the importance of using the complete calculation for very conductive grounds.
A first attempt at monitoring underground gas storage by means of time‐lapse multichannel transient electromagnetics
Authors: Hördt  , Andrieux  , Neubauer  , Rüter  , Vozoff
Published: March 2003

Two successive transient electromagnetic surveys were carried out over an underground gas storage site in France. The idea was to monitor changes in the gas bubble from the differences in the data. If successful, the new methodology could help to reduce the number of monitoring wells and finally reduce costs. Preliminary 3D modelling indicated that the resistivity changes caused by movements of the gas/water contact should be detectable in the electric field transients provided that the signal‐to‐noise ratio is at least 100:1. The surveys were performed with the TEAMEX multichannel acquisition system, adapted from a seismics system. The highly redundant data were analysed by calculating the relative differences in the electric field transients. The differences were common‐midpoint‐sorted and spatially stacked. Another approach was the calculation of electric field time derivatives in a log–log domain, to eliminate static shift effects which are present in the data. Even though the data quality is excellent from a classical point of view, neither of the two approaches reveals changes in the data which might be caused by changes in the gas reservoir. In future applications to monitoring, transmitters and receivers should be installed permanently, and the transmitter input waveform should be monitored continuously, to avoid some of the problems encountered here. Moreover, the signal‐to‐noise ratio will have to be further increased by at least one order of magnitude.
A generalized Biot–Gassmann model for the acoustic properties of shaley sandstones1
Authors: Carcione José M. , Gurevich Boris , Cavallini Fabio
Published: March 2003

We obtain the wave velocities of clay‐bearing sandstones as a function of clay content, porosity and frequency. Unlike previous theories, based simply on slowness and/or moduli averaging or two‐phase models, we use a Biot‐type three‐phase theory that considers the existence of two solids (sand grains and clay particles) and a fluid. The theory, which is consistent with the critical porosity concept, uses three free parameters that determine the dependence of the dry‐rock moduli of the sand and clay matrices as a function of porosity and clay content.

Testing of the model with laboratory data shows good agreement between predictions and measurements. In addition to a rock physics model that can be useful for petrophysical interpretation of wave velocities obtained from well logs and surface seismic data, the model provides the differential equation for computing synthetic seismograms in inhomogeneous media, from the seismic to the ultrasonic frequency bands.
Automatic cross‐well tomography: an application of the differential semblance optimization to two real examples
Authors: Plessix René‐Edouard
Published: March 2003

An automatic tomography algorithm, based on differential semblance optimization (DSO), has been used to invert real cross‐well seismic data for the background velocity. The method relies on the first‐arrival transmitted waves. Given a background velocity model, the traveltimes between the sources and the receivers are computed, then semblance panels are created by back‐propagating the data traces. If the velocity model is correct all the first‐arrival transmitted waves will be aligned in the semblance panels. The DSO method consists of finding the background velocity by minimizing the L2‐norm of the difference between adjacent back‐propagated traces. Thanks to the good behaviour of this DSO cost function about the solution, a local (gradient) optimization can be performed. This provides a relatively fast algorithm when ray tracing and analytic computation of the gradient are used.

Unfortunately the method fails in the presence of caustics in the data. However, this difficulty can be circumvented by applying suitable masks to the data. This approach is first applied to a synthetic example then to two real data sets: the McElroy data set recorded in West Texas and the NIMR data set recorded in Oman. The results are quite encouraging and similar to those obtained with classical tomography.
The effect of clay distribution on the elastic properties of sandstones
Authors: Sams Mark S. , Andrea Martijn
Published: March 2003

The shape and location of clay within sandstones have a large impact on the P‐wave and S‐wave velocities of the rock. They also have a large effect on reservoir properties and the interpretation of those properties from seismic data and well logs. Numerical models of different distributions of clay – structural, laminar and dispersed clay – can lead to an understanding of these effects. Clay which is located between quartz grains, structural clay, will reduce the P‐wave and S‐wave velocities of the rock. If the clay particles become aligned or form layers, the velocities perpendicular to the alignment will be reduced further. S‐wave velocities decrease more rapidly than P‐wave velocities with increasing clay content, and therefore Poisson's ratios will increase as the velocities decrease. These effects are more pronounced for compacted sandstones. Small amounts of clay that are located in the pore space will have little effect on the P‐wave velocity due to the competing influence of the density effect and pore‐fluid stiffening. The S‐wave velocity will decrease due to the density effect and thus the Poisson's ratio will increase. When there is sufficient clay to bridge the gaps between the quartz grains, P‐wave and S‐wave velocities rise rapidly and the Poisson's ratios decrease. These effects are more pronounced for under‐compacted sandstones. These general results are only slightly modified when the intrinsic anisotropy of the clay material is taken into account. Numerical models indicate that there is a strong, nearly linear relationship between P‐wave and S‐wave velocity which is almost independent of clay distribution. S‐wave velocities can be predicted reasonably accurately from P‐wave velocities based on empirical relationships. However, this does not provide any connection between the elastic and petrophysical properties of the rocks. Numerical modelling offers this connection but requires the inclusion of clay distribution and anisotropy to provide a model that is consistent with both the elastic and petrophysical properties. If clay distribution is ignored, predicting porosities from P‐wave or S‐wave data, for example, can result in large errors. Estimation of the clay distribution from P‐wave and S‐wave velocities requires good estimates of the porosity and clay volume and verification from petrographic analyses of core or cuttings. For a real data example, numerical models of the elastic properties suggest the predominance of dispersed clay in a fluvial sand from matching P‐wave and S‐wave velocity well log data using log‐based estimates of the clay volume and porosity. This is consistent with an interpretation of other log data.
3D resistivity inversion using 2D measurements of the electric field
Authors: Jackson P.D. , Earl S.J. , Reece G.J.
Published: March 2003

Field and ‘noisy’ synthetic measurements of electric‐field components have been inverted into 3D resistivities by smoothness‐constrained inversion. Values of electrical field can incorporate changes in polarity of the measured potential differences seen when 2D electrode arrays are used with heterogeneous ‘geology’, without utilizing negative apparent resistivities or singular geometrical factors. Using both the X‐ and Y‐components of the electric field as measurements resulted in faster convergence of the smoothness‐constrained inversion compared with using one component alone. Geological structure and resistivity were reconstructed as well as, or better than, comparable published examples based on traditional measurement types. A 2D electrode grid (20 × 10), incorporating 12 current‐source electrodes, was used for both the practical and numerical experiments; this resulted in 366 measurements being made for each current‐electrode configuration. Consequently, when using this array for practical field surveys, 366 measurements could be acquired simultaneously, making the upper limit on the speed of acquisition an order of magnitude faster than a comparable conventional pole–dipole survey. Other practical advantages accrue from the closely spaced potential dipoles being insensitive to common‐mode noise (e.g. telluric) and only 7% of the electrodes (i.e. those used as current sources) being susceptible to recently reported electrode charge‐up effects.
Interval velocity and thickness estimate from wide‐angle reflection data
Authors: De Franco Roberto
Published: March 2003

A method to estimate interval velocities and thickness in a horizontal isotropic layered medium from wide‐angle reflection traveltime curves is presented. The method is based on a relationship between the squared reflection traveltime differences and the squared offset differences relative to two adjacent reflectors. The envelope of the squared‐time versus offset‐difference curves, for rays with the same ray parameter, is a straight line, whose slope is the inverse of the square of the interval velocity and whose intercept is the square of the interval time. The method yields velocity and thickness estimates without any knowledge of the overlying stratification. It can be applied to wide‐angle reflection data when either information on the upper crust and/or refraction control on the velocity is not available. Application to synthetic and real data shows that the method, used together with other methods, allows us to define a reliable 1D starting model for estimating a depth profile using either ray tracing or another technique.
Numerical simulation of 2D wave propagation on unstructured grids using explicit differential operators
Authors: Käser Martin , Igel Heiner
Published: March 2003

We present a numerical method of simulating seismic wave propagation on unstructured 2D grids. The algorithm is based on the velocity–stress formulation of the elastic wave equation and therefore uses a staggered grid approach. Unlike finite‐element or spectral‐element methods, which can also handle flexible unstructured grids, we use explicit differential operators for the calculation of spatial derivatives in each time step. As shown in previous work, three types of these operators are used, and their particular performance is analysed and compared with standard explicit finite‐difference operators on regular quadratic and hexagonal grids. Our investigations are especially focused on the influence of grid irregularity, sampling rate (i.e. gridpoints per wavelength) and numerical anisotropy on the accuracy of numerical seismograms. The results obtained from the various methods are therefore compared with analytical solutions. The algorithm is then applied to a number of models that are difficult to handle using (quasi‐)regular grid methods. Such alternative techniques may be useful in modelling the full wavefield of bodies with complex geometries (e.g. cylindrical bore‐hole samples, 2D earth models) and, because of their local character, they are well suited for parallelization.
ADI plus interpolation: accurate finite‐difference solution to 3D paraxial wave equation
Authors: Wang Yanghua
Published: March 2003

An accurate finite‐difference solution is developed for the paraxial wave equation in 3D seismic migration. The conventional alternating‐direction‐implicit (ADI) scheme used in migration causes errors, because the variables in the migration problem are complex‐valued, not real‐valued, and the imaginary part of the higher‐order spatial derivatives cannot be ignored. The accuracy of the 3D paraxial extrapolator is preserved by (i) retaining these higher‐order terms so that it does not produce the apparent azimuthal anisotropy in conventional migration, and (ii) filtering the non‐physical evanescent waves during the downward extrapolation. The implementation of the accurate solution consists of two steps: firstly, the application of ADI to solve two tridiagonal systems sequentially, and secondly, an interpolation between the extrapolated wavefields of successive extrapolation levels. The method is computationally efficient as it uses the ADI scheme and, in addition, couples the correction for azimuthal anisotropy and the suppression of evanescent waves into a single operation, the interpolation step.
Stress‐dependent elastic anisotropy of sandstones
Authors: Sayers Colin M.
Published: March 2003

Elastic wave velocities in sandstones vary with stress due to the presence of discontinuities such as grain boundaries and microcracks within the rock. In the presence of non‐hydrostatic stress fields the elastic wave velocities in sandstones often show significant stress‐induced anisotropy. The elastic anisotropy due to any discontinuities within the rock can be written in terms of a second‐rank and a fourth‐rank tensor which quantify the effect on the elastic wave velocities of the orientation distribution and normal and shear compliances of the discontinuities. This allows elastic wave velocity measurements to be inverted to obtain the components of these tensors. Application of the method to ultrasonic velocity measurements made in a triaxial loading frame shows that a simple theory using only the second‐rank tensor allows the P‐wave stress‐induced anisotropy to be predicted to reasonable accuracy from the S‐wave anisotropy and vice versa, thus confirming the correctness of the underlying model. Deviations between the measurements and the predictions of this simplified theory are used to determine the ratio of the normal to shear compliance of the discontinuities. The discontinuities are found to be more compliant in shear than in compression.
The Buffon's needle problem and the design of a geophysical survey
Authors: Sambuelli Luigi , Strobbia Claudio
Published: March 2003

A logical procedure for designing a geophysical survey when sampling an area with a regular grid can be summarized as follows: model the expected anomaly, estimate the expected noise level, estimate the area of the anomaly above the noise level, choose the spacing, in both the x‐ and y‐directions, of the measurement grid. This last step can be approached according to two main strategies: either when applying the sampling theorem to the shortest dimension of the anomaly or when using a coarser grid, leaving a more complete definition of the anomaly to a later fitting. When following this second option, it can be constructive to estimate the probability of intercepting a given anomaly with a specific segment of profile and a given profile spacing. This latter procedure is analysed by considering a rectangle approximating the plane projection of the anomaly shape and taking into account various ratios between the grid spacing and the rectangle sides. The formulae for estimating the probability of intersecting a given anomaly with a given segment of a given profile spacing are calculated. To demonstrate the accuracy of the results, a Monte‐Carlo simulation on a synthetic magnetic map was performed, obtaining, for different ratios between the sides, segment length and profile interval, an agreement better than 0.1% with the analytical formulae.
Velocity/interface model building in a thrust belt by tomographic inversion of global offset seismic data
Authors: Dell'Aversana P. , Colombo D. , Buia M. , Morandi S.
Published: March 2003

Between September and November 1999, two test seismic lines were recorded in the southern Apennine region of southern Italy using the global offset technique, which involves the acquisition of a wide offset range using two simultaneously active seismic spreads. One consisted of a symmetrical spread moving along the line, with geophone arrays every 30 m and a maximum offset of 3.6 km. The other one consisted of fixed geophone arrays every 90 m with a maximum offset of 18 km. This experimental acquisition project was carried out as part of the enhanced seismic in thrust belt (ESIT) research project, funded by the European Union, Enterprise Oil and Eni‐Agip. An iterative and interactive tomographic inversion of refraction/reflection arrivals was carried out on the data from line ESIT700 to produce a velocity/interface model in depth, which used all the available offsets. The tomographic models allowed the reconstruction of layer interface geometries and interval velocities for the target carbonate platform (Apula) and the overburden sequence. The value of this technique is highlighted by the fact that the standard approach, based on near‐vertical reflection seismic and a conventional processing flow, produced poor seismic images in both stack and migrated sections.
Effects of an anisotropic overburden on azimuthal amplitude analysis in horizontal transverse isotropic media
Authors: Maultzsch Sonja , Horne Steve , Archer Stewart , Burkhardt Hans
Published: March 2003

Azimuthal amplitude variation in fractured media, commonly used to characterize fracture systems, is a function not only of reflection at the target but also of transmission through the overburden. This study investigates the sensitivity of amplitudes to various anisotropic overburden effects in horizontal transverse isotropic (HTI) media. Issues considered here are geometric spreading, transmission coefficients and attenuation due to fluid flow. Their influence on the azimuthal amplitude variation is evaluated quantitatively over a wide model space.

Only the variation of transmission coefficients with azimuth proves to be negligible. Geometric spreading alters the amplitude signature significantly over a relatively narrow range of models, and its influence increases with layer thickness. The most severe effect of an anisotropic fractured overburden is attenuation due to fluid flow between the cracks or the cracks and pores in the surrounding matrix. The relative changes in amplitudes between the symmetry directions due to anisotropic absorption are of the same order of magnitude as the changes in the reflection coefficient. The effect is significant over a very wide range of petrophysical parameters. Thus it leads to considerable problems in the amplitude analysis for almost any case of an overburden that contains cracks and pores. A correct amplitude analysis at the target will not be possible unless the effect of attenuation is removed.
Interannual and interdecadal variation in California Current zooplankton: Calanus in the late 1950s and early 1990s
Authors: Mullin Michael M.
Published: March 2003

Samples from the southern California sector of the California Current System were examined to test for interannual changes in winter–spring abundance of the planktonic copepod, Calanus pacificus, coincident with the 1992–93 and 1958–59 El Niños, each evaluated relative to immediately preceding years, and for interdecadal change (the early 1990s relative to the late 1950s). Calanus was anomalously rare in both of the El Niño periods, as was macrozooplankton, but (unlike macrozooplanktonic biomass) was not rarer in the early 1990s than in the late 1950s. The El Niño anomalies in Calanus’s abundance and macrozooplanktonic biomass were not spatially correlated on the mesoscale, implying that different proximate ecological causes may dominate at this scale.
Organic matter, heterotrophic activity, and NO· consumption in soils
Authors: Dunfield Peter F. , Knowles Roger
Published: March 2003

When the effect of water content was minimized, soil CO2 evolution and soil organic matter content were good predictors of aerobic NO. uptake rate constants across a wide range of soil types. Field manure application to a Gleysol stimulated NO. uptake rate constants and lowered NO. compensation points compared to unfertilized or NH4NO3‐fertilized soil. This effect lasted for months after manure application. In a laboratory experiment, addition of manure reduced the NO. efflux associated with nitrification of NH4 Cl fertilizer, and manured soils had a greater capacity to remove NO. from polluted air. Evidence is presented that these observations result from NO. oxidation during heterotrophic microbial activity in soil.
Influence of O2availability on NO and N2O release by nitrification and denitrification in soils
Authors: Bollmann Annette , Conrad Ralf
Published: March 2003

The availability of O2is believed to be one of the main factors regulating nitrification and denitrification and the release of NO and N2O. The availability of O2in soil is controlled by the O2partial pressure in the gas phase and by the moisture content in the soil. Therefore, we investigated the influence of O2partial pressures and soil moisture contents on the NO and N2O release in a sandy and a loamy silt and differentiated between nitrification and denitrification by selective inhibition of nitrification with 10 Pa acetylene. At 60% whc (maximum water holding capacity) NO and N2O release by denitrification increased with decreasing O2partial pressure and reached a maximum under anoxic conditions. Under anoxic conditions NO and N2O were only released by denitrification. NO and N2O release by nitrification also increased with decreasing O2partial pressure, but reached a maximum at 0.1–0.5% O2and then decreased again. Nitrification was the main source of NO and N2O at O2partial pressures higher than 0.1–0.5% O2. At lower O2partial pressures denitrification was the main source of NO and N2O. With decreasing O2partial pressure N2O release increased more than NO release, indicating that the N2O release was more sensitive against O2than the NO release. At ambient O2partial pressure (20.5% O2) NO and N2O release by denitrification increased with increasing soil moisture content. The maximum NO and N2O release was observed at soil moisture contents of 65–80% whc and 100% whc, respectively. NO and N2O release by nitrification also increased with increasing soil moisture content with a maximum at 45–55% whc and 90% whc, respectively. Nitrification was the main source of NO and N2O at soil moisture contents lower than 90% whc and 80% whc, respectively. Higher soil moisture contents favoured NO and N2O release by denitrification. Soil texture had also an effect on the release of NO and N2O. The coarse‐textured sandy silt released more NO than N2O compared with the fine‐textured loamy silt. At high soil moisture contents (80–100% whc) the fine‐textured soil showed a higher N2O release by denitrification than the coarse‐textured soil. We assume that the fine‐textured soil became anoxic at a lower soil moisture content than the coarse‐textured soil. In conclusion, the effects of O2partial pressure, soil moisture and soil texture were consistent with the theory that denitrification increasingly contributes to the release of NO and in particular N2O when conditions for soil microorganisms become increasingly anoxic.
Soil biota and global change at the ecosystem level: describing soil biota in mathematical models
Authors: SMITH PETE. , ANDRÉN OLOF. , BRUSSAARD LIJBERT , DANGERFIELD MARK. , EKSCHMITT KLEMENS , LAVELLE PATRICK , TATE KEVIN
Published: March 2003

All current mathematical models of the soil system are underpinned by a wealth of research into soil biology and new research continues to improve the description of the real world by mathematical models. In this review we examine the various approaches for describing soil biology in mathematical models and discuss the use of each type of model in global change research. The approaches represented among models participating in the Global Change and Terrestrial Ecosystems (GCTE) Soil Organic Matter Network (SOMNET) are described. We examine the relative advantages and constraints of each modelling approach and, using these, suggest appropriate uses of each. We show that for predictive purposes at ecosystem scale and higher, process‐orientated models (which have only an implicit description of soil organisms) are most commonly used. As a research tool at the ecosystem level, both process‐orientated and organism‐orientated models (in which functional or taxonomic groups of soil organisms are explicitly described) are commonly used. Because of uncertainties introduced in internal model parameter estimation and system feedbacks, the predictive use of organism‐orientated models at the ecosystem scale and larger is currently less feasible than is the use of process‐orientated models. In some specific circumstances, however, an explicit description of some functional groups of soil organisms within models may be required to adequately describe the effects of global change. No existing models can adequately predict the feedback between global change, a change in soil community function, and the response of the changed system to future global change. To find out if these feedbacks exist and to what extent they affect future global change, more research is urgently required into the response of soil community function to global change and its potential ecosystem‐level effects.
Elevated CO2 and temperature impacts on different components of soil CO2 efflux in Douglas‐fir terracosms
Authors: Lin Guanghui , Ehleringer James R. , Rygiewicz PauL. T. , Johnson Mark G. , Tingey David T.
Published: March 2003

Although numerous studies indicate that increasing atmospheric CO2 or temperature stimulate soil CO2 efflux, few data are available on the responses of three major components of soil respiration [i.e. rhizosphere respiration (root and root exudates), litter decomposition, and oxidation of soil organic matter] to different CO2 and temperature conditions. In this study, we applied a dual stable isotope approach to investigate the impact of elevated CO2 and elevated temperature on these components of soil CO2 efflux in Douglas‐fir terracosms. We measured both soil CO2 efflux rates and the 13C and 18O isotopic compositions of soil CO2 efflux in 12 sun‐lit and environmentally controlled terracosms with 4‐year‐old Douglas fir seedlings and reconstructed forest soils under two CO2 concentrations (ambient and 200 ppmv above ambient) and two air temperature regimes (ambient and 4 °C above ambient). The stable isotope data were used to estimate the relative contributions of different components to the overall soil CO2 efflux. In most cases, litter decomposition was the dominant component of soil CO2 efflux in this system, followed by rhizosphere respiration and soil organic matter oxidation. Both elevated atmospheric CO2 concentration and elevated temperature stimulated rhizosphere respiration and litter decomposition. The oxidation of soil organic matter was stimulated only by increasing temperature. Release of newly fixed carbon as root respiration was the most responsive to elevated CO2, while soil organic matter decomposition was most responsive to increasing temperature. Although some assumptions associated with this new method need to be further validated, application of this dual‐isotope approach can provide new insights into the responses of soil carbon dynamics in forest ecosystems to future climate changes.
The effects of chamber pressurization on soil‐surface CO2 flux and the implications for NEE measurements under elevated CO2
Authors: Lund C. P. , Riley W. J. , Pierce L. L. , Field C. B.
Published: March 2003

Soil and ecosystem trace gas fluxes are commonly measured using the dynamic chamber technique. Although the chamber pressure anomalies associated with this method are known to be a source of error, their effects have not been fully characterized. In this study, we use results from soil gas‐exchange experiments and a soil CO2 transport model to characterize the effects of chamber pressure on soil CO2 efflux in an annual California grassland. For greater than ambient chamber pressures, experimental data show that soil‐surface CO2 flux decreases as a nonlinear function of increasing chamber pressure; this decrease is larger for drier soils. In dry soil, a gauge pressure of 0.5 Pa reduced the measured soil CO2 efflux by roughly 70% relative to the control measurement at ambient pressure. Results from the soil CO2 transport model show that pressurizing the flux chamber above ambient pressure effectively flushes CO2 from the soil by generating a downward flow of air through the soil air‐filled pore space. This advective flow of air reduces the CO2 concentration gradient across the soil–atmosphere interface, resulting in a smaller diffusive flux into the chamber head space. Simulations also show that the reduction in diffusive flux is a function of chamber pressure, soil moisture, soil texture, the depth distribution of soil CO2 generation, and chamber diameter. These results highlight the need for caution in the interpretation of dynamic chamber trace gas flux measurements. A portion of the frequently observed increase in net ecosystem carbon uptake under elevated CO2 may be an artifact resulting from the impact of chamber pressurization on soil CO2 efflux.