bluuebunny/crossref_metadata_2025_split huggingface dataset:
The experimental rearing of large salmonid eggs in Petri dishes
Authors: Wedekind C. , Müller R. 
Published: December 2004

Summary

Studies on the genetics or the ecology of fish eggs are typically based on inferential statistics, which require the separate rearing of many batches.
Salmonid eggs are believed to require a constant water flow to develop safely. Therefore, the technical requirements that have been used to rear individual batches of salmonid eggs significantly limit experimental studies.
We describe a technique that allows, for the first time, the large eggs of Arctic Charr (Salvelinus alpinus) to be reared under experimental conditions in Petri dishes.
It was found that the proportion of well‐developed eggs on day 64 did not significantly correlate with egg density in the Petri dish, but that fry hatch earlier under more crowded conditions.
Oxygen concentration measured shortly before hatching appeared to be above critical values.
Allometric and phylogenetic variation in insect phosphorus content
Authors: Woods H. A. , Fagan W. F. , Elser J. J. , Harrison J. F. 
Published: December 2004

Summary

Phosphorus content was measured in adult insects and arachnids from 170 species collected in the Sonoran Desert.
Across insect body sizes spanning four orders of magnitude, phosphorus content was inversely related to body mass. The largest species (∼1 g dry) had phosphorus contents that were only about 60% (0·62% P absolute) as high as phosphorus contents of the smallest species (∼0·0001 g dry; 0·97% P). Negative phosphorus allometry was observed within each of seven insect orders and within arachnids.
Phosphorus contents of insect predators and herbivores were statistically indistinguishable.
More recently derived orders tended to have lower phosphorus contents – with the exception of the most recently derived group (Panorpida = Diptera + Lepidoptera), which had high phosphorus contents.
Prion domain interaction responsible for species discrimination in yeast [PSI+] transmission
Authors: Hara Hideyuki , Nakayashiki Toru , Crist Colin G. , Nakamura Yoshikazu 
Published: December 2004

AbstractBackground:  The yeast [PSI+] factor is transmitted by a prion mechanism involving self‐propagating Sup35 aggregates. As with mammalian prions, a species barrier prevents prion transmission between yeast species. The N‐terminal of Sup35 of Saccharomyces cerevisiae, necessary for [PSI+], contains two species‐signature elements—a Gln/Asn‐rich region (residues 1–41; designated NQ) that is followed by oligopeptide repeats (designated NR).Results:  In this study, we show that S. cerevisiae[PSI+] is transmissible through plasmid shuffling and cytoplasmic transfer to heterotypic Sup35s whose NQ is replaced with the S. cerevisiae NQ. In addition to homology, the N‐terminal location is essential for NQ mediated susceptibility to [PSI+] transmission amongst heterotypic Sup35s. In vitro, a swap of NQ of S. cerevisiae Sup35 led to cross seeding of amyloid formation.Conclusions:  These findings suggest that NQ discriminates self from non‐self, and is sufficient to initiate [PSI+] transmission irrespective of whether NR is heterotypic. NR as well as NQ alone coalesces into existing [PSI+] aggregates, showing their independent potentials to interact with the identical sequence in the [PSI+] conformer. The role of NQ and NR in [PSI+] prion formation is discussed.
Involvement of Cdc42 and Rac small G proteins in invadopodia formation of RPMI7951 cells
Authors: Nakahara Hirokazu , Otani Tomohiro , Sasaki Takuya , Miura Yasuhiro , Takai Yoshimi , Kogo Mikihiko 
Published: December 2004

AbstractBackground:  Invadopodia are membrane protrusions into the extracellular matrix by aggressive tumour cells. These structures are associated with sites of matrix degradation and invasiveness of malignant tumour cells in an in vitro fibronectin degradation/invasion assay. The Rho family small G proteins, consisting of the Rho, Rac and Cdc42 subfamilies, are implicated in various cell functions, such as cell shape change, adhesion, and motility, through reorganization of the actin cytoskeleton. We studied the roles of the Rho family small G proteins in invadopodia formation.Results:  We first demonstrated that invadopodia of RPMI7951 human melanoma cells extended into the matrix substratum on a vertical view using a laser scanning confocal microscope system. We confirmed that invadopodia were rich in actin filaments (F‐actin) and visualized clearly with F‐actin staining on a vertical view as well as on a horizontal view. We then studied the roles of Rho, Rac, and Cdc42 in invasiveness of the same cell line. In the in vitro fibronectin degradation/invasion assay, a dominant active mutant of Cdc42 enhanced dot‐like degradation, whereas a dominant active mutant of Rac enhanced diffuse‐type degradation. Furthermore, frabin, a GDP/GTP exchange protein for Cdc42 with F‐actin‐binding activity, enhanced both dot‐like and diffuse‐type degradation. However, a dominant active mutant of Rho did not affect the fibronectin degradation. Moreover, inhibition of phosphatidylinositol‐3 kinase (PI3K) disrupted the Rac and Cdc42‐dependent actin structures and blocked the fibronectin degradation.Conclusion:  These results suggest that Cdc42 and Rac play important roles in fibronectin degradation and invasiveness in a coordinate manner through the frabin‐Cdc42/Rac‐PI3K signalling pathway.
Effective elastic properties of randomly fractured soils: 3D numerical experiments
Authors: Saenger Erik H. , Krüger Oliver S. , Shapiro Serge A. 
Published: December 2004

ABSTRACTThis paper is concerned with numerical tests of several rock physical relationships. The focus is on effective velocities and scattering attenuation in 3D fractured media. We apply the so‐called rotated staggered finite‐difference grid (RSG) technique for numerical experiments. Using this modified grid, it is possible to simulate the propagation of elastic waves in a 3D medium containing cracks, pores or free surfaces without applying explicit boundary conditions and without averaging the elastic moduli. We simulate the propagation of plane waves through a set of randomly cracked 3D media. In these numerical experiments we vary the number and the distribution of cracks. The synthetic results are compared with several (most popular) theories predicting the effective elastic properties of fractured materials. We find that, for randomly distributed and randomly orientated non‐intersecting thin penny‐shaped dry cracks, the numerical simulations of P‐ and S‐wave velocities are in good agreement with the predictions of the self‐consistent approximation. We observe similar results for fluid‐filled cracks. The standard Gassmann equation cannot be applied to our 3D fractured media, although we have very low porosity in our models. This is explained by the absence of a connected porosity. There is only a slight difference in effective velocities between the cases of intersecting and non‐intersecting cracks. This can be clearly demonstrated up to a crack density that is close to the connectivity percolation threshold. For crack densities beyond this threshold, we observe that the differential effective‐medium (DEM) theory gives the best fit with numerical results for intersecting cracks. Additionally, it is shown that the scattering attenuation coefficient (of the mean field) predicted by the classical Hudson approach is in excellent agreement with our numerical results.
Euler deconvolution of the analytic signal and its application to magnetic interpretation
Authors: Keating P. , Pilkington M. 
Published: December 2004

ABSTRACTEuler deconvolution and the analytic signal are both used for semi‐automatic interpretation of magnetic data. They are used mostly to delineate contacts and obtain rapid source depth estimates. For Euler deconvolution, the quality of the depth estimation depends mainly on the choice of the proper structural index, which is a function of the geometry of the causative bodies. Euler deconvolution applies only to functions that are homogeneous. This is the case for the magnetic field due to contacts, thin dikes and poles. Fortunately, many complex geological structures can be approximated by these simple geometries. In practice, the Euler equation is also solved for a background regional field. For the analytic signal, the model used is generally a contact, although other models, such as a thin dike, can be considered. It can be shown that if a function is homogeneous, its analytic signal is also homogeneous. Deconvolution of the analytic signal is then equivalent to Euler deconvolution of the magnetic field with a background field. However, computation of the analytic signal effectively removes the background field from the data. Consequently, it is possible to solve for both the source location and structural index. Once these parameters are determined, the local dip and the susceptibility contrast can be determined from relationships between the analytic signal and the orthogonal gradients of the magnetic field. The major advantage of this technique is that it allows the automatic identification of the type of source. Implementation of this approach is demonstrated for recent high‐resolution survey data from an Archean granite‐greenstone terrane in northern Ontario, Canada.
Δx≠Δy in 3D depth migration via McClellan transformations
Authors: Levin Stewart A. 
Published: December 2004

ABSTRACTAn intuitive method is presented for extending Hale–McClellan migration operators to handle surveys binned and stacked with in‐line and cross‐line spacings unequal. This avoids re‐interpolating the input to 3D migration, either externally or internally. The algorithm does not require an integer or rational ratio between the in‐line and cross‐line spacings in order to be applied nor does it deliberately introduce artificial aliasing by interleaving subsampled grids along the more finely sampled axis. Examples of its impulse response and application to the SEG–EAGE salt model are shown.
An accurate and robust multigrid algorithm for 2D forward resistivity modelling
Authors: Moucha Robert , Bailey Richard C. 
Published: December 2004

ABSTRACTWe present an adaptation of the full multigrid algorithm in DC resistivity modelling in an effort to increase its accuracy. There is a great difficulty with conventional multigrid solvers in representing the physics of an arbitrary distribution of electrical conductivity on a very coarse grid. In general, conventional rectangular finite‐difference or 5‐point approximations of Poisson's equation cannot represent, at a coarse grid level, the effective anisotropy on a coarse scale which results from fine structure in the model. An exception to this generalization occurs when the principal axes of structural anisotropy are aligned with the coordinate axis. Additional and similarly generated problems arise when a coarse cell is obliged to represent fine structure containing very high conductivity contrasts. We have developed an adaptation of the usual resistive‐network representation of the continuum, which avoids some of these problems, and have compared it with the traditional resistive network currently used. The network adaptation consists of replacing the usual 5‐point Laplacian operator stencil used on the finite‐difference grid with a 9‐point stencil, and the conductivity scalar with a 6‐parameter conductivity parametrization. This parametrization permits representation of arbitrarily orientated anisotropy as well as more complex behaviour related to high conductivity contrasts. The importance of multigrid solvers does not lie in their speed at forward modelling (which is comparable with other methods), but rather in their potential for inverse modelling. Inverse solvers which proceed by refinement of an initially very coarse solution can, in principle, take time only linearly proportional to the number of gridpoints in the final desired model.
Adjustment of regularization in ill‐posed linear inverse problems by the empirical Bayes approach
Authors: Mitsuhata Yuji 
Published: December 2004

ABSTRACTRegularization is the most popular technique to overcome the null space of model parameters in geophysical inverse problems, and is implemented by including a constraint term as well as the data‐misfit term in the objective function being minimized. The weighting of the constraint term relative to the data‐fitting term is controlled by a regularization parameter, and its adjustment to obtain the best model has received much attention. The empirical Bayes approach discussed in this paper determines the optimum value of the regularization parameter from a given data set. The regularization term can be regarded as representing a priori information about the model parameters. The empirical Bayes approach and its more practical variant, Akaike's Bayesian Information Criterion, adjust the regularization parameter automatically in response to the level of data noise and to the suitability of the assumed a priori model information for the given data. When the noise level is high, the regularization parameter is made large, which means that the a priori information is emphasized. If the assumed a priori information is not suitable for the given data, the regularization parameter is made small. Both these behaviours are desirable characteristics for the regularized solutions of practical inverse problems. Four simple examples are presented to illustrate these characteristics for an underdetermined problem, a problem adopting an improper prior constraint and a problem having an unknown data variance, all frequently encountered geophysical inverse problems. Numerical experiments using Akaike's Bayesian Information Criterion for synthetic data provide results consistent with these characteristics. In addition, concerning the selection of an appropriate type of a priori model information, a comparison between four types of difference‐operator model – the zeroth‐, first‐, second‐ and third‐order difference‐operator models – suggests that the automatic determination of the optimum regularization parameter becomes more difficult with increasing order of the difference operators. Accordingly, taking the effect of data noise into account, it is better to employ the lower‐order difference‐operator models for inversions of noisy data.
Interpretation of magnetic data using analytic signal derivatives
Authors: Salem Ahmed 
Published: December 2004

ABSTRACTThis paper develops an automatic method for interpretation of magnetic data using derivatives of the analytic signal. A linear equation is derived to provide source location parameters of a 2D magnetic body without a priori information about the nature of the source. Then using the source location parameters, the nature of the source can be ascertained. The method has been tested using theoretical simulations with random noise for two 2D magnetic models placed at different depths with respect to the observation height. In both cases, the method gave a good estimate for the location and shape of the sources. Good results were obtained on two field data sets.
Dense 3D residual moveout analysis as a tool for HTI parameter estimation
Authors: Kozlov Evgenii A. , Varivoda Dmitry Y. 
Published: December 2004

ABSTRACTThree‐dimensional residual moveout analysis is the basic step in velocity model refinement. The analysis is generally carried out using horizontal and/or vertical semblances defined on a sparse set of in‐lines or cross‐lines with densely sampled source–receiver offsets. An alternative approach, which we call dense residual moveout analysis (DRMA), is to use all the bins of a three‐dimensional survey but sparsely sampled offsets. The proposed technique is very fast and provides unbiased and statistically efficient estimates of the residual moveout. Indeed, for the sparsest possible offset distribution, when only near‐ and far‐angle stacks are used, the variance of the residual moveout estimate is only 1.4 times larger than the variance of the least‐squares estimate obtained using all offsets.The high performance of DRMA makes it a useful tool for many applications, of which azimuthal velocity analysis is considered here. For a horizontal transverse isotropy (HTI) model, a deterministic procedure is proposed to define, at every point of residual moveout estimation, the azimuthal angle of the HTI axis of symmetry, the Thomsen anisotropy coefficients, and the interval (or root‐mean‐square) velocities in both the HTI isotropy and symmetry planes. The procedure is not restricted by DRMA assumptions; for example, it is also applicable to semblance‐based residual moveout estimates.The high resolution of the technique is illustrated by azimuthal velocity analysis over an oilfield in West Siberia.
Effects of elevated atmospheric CO2 on net ecosystem CO2 exchange of a scrub–oak ecosystem
Authors: Hymus Graham J. , Johnson David P. , Dore Sabina , Anderson Hans P. , Ross Hinkle C. , Drake Bert G. 
Published: December 2004

AbstractWe report the results of a 2‐year study of effects of the elevated (current ambient plus 350 μmol CO2 mol−1) atmospheric CO2 concentration (Ca) on net ecosystem CO2 exchange (NEE) of a scrub–oak ecosystem. The measurements were made in open‐top chambers (OTCs) modified to function as open gas‐exchange systems. The OTCs enclosed samples of the ecosystem (ca. 10 m2 surface area) that had regenerated after a fire, 5 years before, in either current ambient or elevated Ca. Throughout the study, elevated Ca increased maximum NEE (NEEmax) and the apparent quantum yield of the NEE (φNEE) during the photoperiod. The magnitude of the stimulation of NEEmax, expressed per unit ground area, was seasonal, rising from 50% in the winter to 180% in the summer. The key to this stimulation was effects of elevated Ca, and their interaction with the seasonal changes in the environment, on ecosystem leaf area index, photosynthesis and respiration. The separation of these factors was difficult. When expressed per unit leaf area the stimulation of the NEEmax ranged from 7% to 60%, with the increase being dependent on increasing soil water content (Wsoil). At night, the CO2 effluxes from the ecosystem (NEEnight) were on an average 39% higher in elevated Ca. However, the increase varied between 6% and 64%, and had no clear seasonality. The partitioning of NEEnight into its belowground (Rbelow) and aboveground (Rabove) components was carried out in the winter only. A 35% and 27% stimulation of NEEnight in December 1999 and 2000, respectively, was largely due to a 26% and 28% stimulation of Rbelow in the respective periods, because Rbelow constituted ca. 87% of NEEnight. The 37% and 42% stimulation of Rabove in December 1999 and 2000, respectively, was less than the 65% and 80% stimulation of the aboveground biomass by elevated Ca at these times. An increase in the relative amount of the aboveground biomass in woody tissue, combined with a decrease in the specific rate of stem respiration of the dominant species Quercus myrtifolia in elevated Ca, was responsible for this effect. Throughout this study, elevated Ca had a greater effect on carbon uptake than on carbon loss, in terms of both the absolute flux and relative stimulation. Consequently, for this scrub–oak ecosystem carbon sequestration was greater in the elevated Ca during this 2‐year study period.
Photosynthetic and gas exchange characteristics of dominant woody plants on a moisture gradient in an African savanna
Authors: Midgley Guy Franklin , Aranibar Julieta Nelida , Mantlana Khanyisa Brian , Macko Stephen 
Published: December 2004

AbstractWe determined key photosynthetic gas exchange parameters, and their temperature dependence, in dominant woody plants at four savanna sites on a moisture gradient in Botswana, southern Africa. Leaf stable carbon and nitrogen (N) isotope and morphological measures were made concurrently. Sampling of these predominantly non‐N‐fixing species took place during an exceptional rainfall season, representing near‐optimum conditions for primary production at these sites. The mean specific leaf area and leaf size were positively related to mean annual rainfall (MAR); species with larger leaves of lower density were more abundant in wetter sites. Almost all species at all sites showed high net light‐saturated photosynthetic rates (Amax≫10 μmol CO2 m−2 s−1) due both to high CO2 carboxylation (Vc,max) and RubP‐regeneration capacity (Jmax). These high rates were associated with high values of leaf [N]. Across all sites, the temperature response of Amax showed no clear optimum, and a gradual drop from 25°C to 35°C, without notable temperature limitation at leaf temperatures in excess of 35°C. Dark respiration rate (Rday) across all species and sites increased exponentially with increasing leaf temperature. Species sampled at selected sites revealed a negative relationship between leaf δ13C (stable carbon isotope ratio) and MAR, suggesting higher leaf‐level water‐use efficiency at drier sites when integrated over the life of the leaf. At wetter sites, specific leaf [N] was lower and photosynthetic nitrogen‐use efficiency increased, a pattern reflected at the ecosystem level by less 15N enrichment of leaves at these sites. Taken together, the results suggest a switch from water‐use to nitrogen‐use efficiency constraints with increasing moisture availability. These constraints impact leaf form and function significantly, and may emerge at the ecosystem level in aspects of water and N cycling.
Nitrogen cycling in the soil–plant system along a precipitation gradient in the Kalahari sands
Authors: Aranibar Julieta N. , Otter Luanne , Macko Stephen A. , Feral Chris J. W. , Epstein Howard E. , Dowty Peter R. , Eckardt Frank , Shugart Herman H. , Swap Robert J. 
Published: December 2004

AbstractNitrogen (N) cycling was analyzed in the Kalahari region of southern Africa, where a strong precipitation gradient (from 978 to 230 mm mean annual precipitation) is the main variable affecting vegetation. The region is underlain by a homogeneous soil substrate, the Kalahari sands, and provides the opportunity to analyze climate effects on nutrient cycling. Soil and plant N pools, 15N natural abundance (δ15N), and soil NO emissions were measured to indicate patterns of N cycling along a precipitation gradient. The importance of biogenic N2 fixation associated with vascular plants was estimated with foliar δ15N and the basal area of leguminous plants. Soil and plant N was more 15N enriched in arid than in humid areas, and the relation was steeper in samples collected during wet than during dry years. This indicates a strong effect of annual precipitation variability on N cycling. Soil organic carbon and C/N decreased with aridity, and soil N was influenced by plant functional types. Biogenic N2 fixation associated with vascular plants was more important in humid areas. Nitrogen fixation associated with trees and shrubs was almost absent in arid areas, even though Mimosoideae species dominate. Soil NO emissions increased with temperature and moisture and were therefore estimated to be lower in drier areas. The isotopic pattern observed in the Kalahari (15N enrichment with aridity) agrees with the lower soil organic matter, soil C/N, and N2 fixation found in arid areas. However, the estimated NO emissions would cause an opposite pattern in δ15N, suggesting that other processes, such as internal recycling and ammonia volatilization, may also affect isotopic signatures. This study indicates that spatial, and mainly temporal, variability of precipitation play a key role on N cycling and isotopic signatures in the soil–plant system.