bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast Transport Simulation with an Adaptive Grid Refinement
Authors: Haefner Frieder , Boy Siegrun 
Published: December 2005

AbstractOne of the main difficulties in transport modeling and calibration is the extraordinarily long computing times necessary for simulation runs. Improved execution time is a prerequisite for calibration in transport modeling. In this paper we investigate the problem of code acceleration using an adaptive grid refinement, neglecting subdomains, and devising a method by which the Courant condition can be ignored while maintaining accurate solutions. Grid refinement is based on dividing selected cells into regular subcells and including the balance equations of subcells in the equation system. The connection of coarse and refined cells satisfies the mass balance with an interpolation scheme that is implicitly included in the equation system. The refined subdomain can move with the average transport velocity of the subdomain. Very small time steps are required on a fine or a refined grid, because of the combined effect of the Courant and Peclet conditions. Therefore, we have developed a special upwind technique in small grid cells with high velocities (velocity suppression). We have neglected grid subdomains with very small concentration gradients (zero suppression). The resulting software, MODCALIF, is a three‐dimensional, modularly constructed FORTRAN code. For convenience, the package names used by the well‐known MODFLOW and MT3D computer programs are adopted, and the same input file structure and format is used, but the program presented here is separate and independent. Also, MODCALIF includes algorithms for variable density modeling and model calibration. The method is tested by comparison with an analytical solution, and illustrated by means of a two‐dimensional theoretical example and three‐dimensional simulations of the variable‐density Cape Cod and SALTPOOL experiments. Crossing from fine to coarse grid produces numerical dispersion when the whole subdomain of interest is refined; however, we show that accurate solutions can be obtained using a fraction of the execution time required by uniformly fine‐grid solutions.
Analytical Model for Computing Residence Times Near a Pumping Well
Authors: Simpson Matthew J. , Clement T. Prabhakar , Yeomans Francis E. 
Published: December 2005

AbstractAn analytical solution for calculating the residence time of fluid flowing toward a pumping well in an unconfined aquifer has been developed. The analytical solution was derived based on a radial, steady‐state, Dupuit‐Forchheimer flow model. The resulting integral expression involved computing the imaginary error function, for which a simple series expansion is proposed. The validity of the analytical expression is demonstrated by testing its results against numerical results for an example problem. The analytical solution compared favorably with the numerical approximation.
Estimating Ground Water Discharge by Hydrograph Separation
Authors: Hannula Steven R. , Esposito Kenneth J. , Chermak John A. , Runnells Donald D. , Keith David C. , Hall Larry E. 
Published: December 2005

AbstractIron Mountain is located in the West Shasta Mining District in California. An investigation of the generation of acid rock drainage and metals loading to Boulder Creek at Iron Mountain was conducted. As part of that investigation, a hydrograph separation technique was used to determine the contribution of ground water to total flow in Boulder Creek.During high‐flow storm events in the winter months, peak flow in Boulder Creek can exceed 22.7 m3/sec, and comprises surface runoff, interflow, and ground water discharge. A hydrograph separation technique was used to estimate ground water discharge into Boulder Creek during high‐flow conditions. Total ground water discharge to the creek approaches 0.31 m3/sec during the high‐flow season. The hydrograph separation technique combined with an extensive field data set provided reasonable estimates of ground water discharge. These estimates are useful for other investigations, such as determining a corresponding metals load from the metal‐rich ground water found at Iron Mountain and thus contributing to remedial alternatives.
Revisit of Well Function Approximation and An Easy Graphical Curve Matching Technique for Theis' Solution
Authors: Giao Pham Huy 
Published: December 2005

AbstractSome approximations of Theis' solution are reviewed and compared with the numerical evaluation of the exponential integral by means of a short FORTRAN code. A graphical technique of Theis' curve matching is proposed to make this procedure as easy as plotting a graph.
The Journey from Safe Yield to Sustainability
Authors: Alley William M. , Leake Stanley A. 
Published: December 2005

AbstractSafe‐yield concepts historically focused attention on the economic and legal aspects of ground water development. Sustainability concerns have brought environmental aspects more to the forefront and have resulted in a more integrated outlook. Water resources sustainability is not a purely scientific concept, but rather a perspective that can frame scientific analysis. The evolving concept of sustainability presents a challenge to hydrologists to translate complex, and sometimes vague, socioeconomic and political questions into technical questions that can be quantified systematically. Hydrologists can contribute to sustainable water resources management by presenting the longer‐term implications of ground water development as an integral part of their analyses.
Influence of Calibration Methodology on Ground Water Flow Predictions
Authors: Saiers James E. , Genereux David P. , Bolster Carl H. 
Published: December 2005

AbstractWe constructed a numerical model of transient ground water flow and solute transport for a portion of the Biscayne Aquifer in Florida, and calibrated the model with three different combinations of data from a 193‐day period: head (h) data alone, data on h and ground water discharge to a canal (q), and data on h, q, and ground water chloride concentration (C). We used each of the three calibrated models to predict h and q during a 182‐day test period separate from the calibration period. All three calibrated models predicted h equally well during the test period (r= 0.95, where r= 1 indicates perfect agreement between measured and simulated values), though the model calibrated on h alone had significantly different parameter values than the other two models. Predictions of q during the test period depended on calibration methodology; models calibrated with multiple targets simulated q more accurately than the model calibrated on h alone (r = 0.79 compared to r = 0.49). Based on the results of these simulations, we conclude: (1) Post‐calibration prediction is important in assessing the value of different data types in automated calibration; (2) inverse‐solution uniqueness is not a requirement for accurate h predictions; (3) relatively simple models can predict with reasonable accuracy transient ground water flow in a complex aquifer, and parameters governing this prediction can be estimated by nonlinear regression methods that incorporate both h and q data; (4) addition of C data to the calibration did not improve model predictive capacity because the information in the C data was similar to that in the q data, from the perspective of model calibration (the subsurface chemical signal in question was controlled mainly by seepage of high‐chloride canal water into the low‐chloride ground water system).
South China Karst Aquifer Storm‐Scale Hydrochemistry
Authors: Liu Zaihua , Groves Chris , Yuan Daoxian , Meiman Joe 
Published: December 2005

AbstractThe peak cluster and peak forest karst regions of Southeast Asia form one of the earth's most extensive karst regions. Although there exists a rich, descriptive tradition of geomorphic work performed there, little quantitative study has been made of carbonate hydrochemistry and related aquifer/landscape behavior and evolution. In this paper, high‐resolution measurements of ground water carbonate chemistry and flow were made and analyzed at two adjacent locations within the subtropical peak cluster karst of the Guilin Karst Experimental Site in Guangxi Province, China. While waters from a large, perennial spring represent the exit for the 2 km2 catchment's conduit flow, a nearby well (within 5 m) measures water in the conduit‐adjacent, fractured media. Results indicate that within peak cluster karst aquifer flow systems, spatially heterogeneous flow conditions can exist with respect to timing, magnitude, and, in some cases, direction of responses, as different controls can operate in the different flow system components. Storm‐scale chemical responses are controlled by dilution from rapid infiltration of rain water, CO2 gas sources and sinks, and water‐carbonate rock interactions. At this particular location, there is also an influence from high pH recharge, apparently buffered by atmospheric limestone dust. An example of the varying controls on storm‐scale responses within the flow system is that within the fractured medium, variations in the ground water calcite saturation index, a key parameter influencing rates of aquifer/landscape evolution, are small and controlled by CO2 gas, while in the conduit they are more significant and dominated instead by dilution with rain water.
Numerical Implementation of a Backward Probabilistic Model of Ground Water Contamination
Authors: Neupauer Roseanna M. , Wilson John L. 
Published: December 2005

AbstractBackward location and travel time probabilities can be used to characterize known and unknown sources or prior positions of ground water contamination. Backward location probability describes the position of the observed contamination at some time in the past; backward travel time probability describes the amount of time prior to observation that the contamination was released from its source or was at a particular upgradient location. The governing equation for backward probabilities is the adjoint of the governing equation for contaminant transport, but with new load terms. Numerical codes that have been written to solve the forward equations of contaminant transport, e.g., the advection‐dispersion equation, can also be used to solve the adjoint equation for location and travel time probabilities; however, the interpretation of the results is different and some new approximations must be made for the load terms. We present the governing equations for backward location and travel time probabilities, and provide appropriate numerical approximations for these load terms using the cell‐centered finite difference method, one of the most popular numerical methods in ground water hydrology. We discuss some additional numerical considerations for the backward model including boundary conditions, reversal of the flow field, and interpretation of the results. We illustrate the implementation of the backward probability model using hypothetical examples in one‐ and two‐dimensional domains. We also present a three‐dimensional application of a pump‐and‐treat remediation capture zone delineation at the Massachusetts Military Reservation. The illustrations are performed using MODFLOW—96 for flow simulations and MT3DMS for transport simulations.
Effects of Rate‐Limited Mass Transfer on Water Sampling with Partially Penetrating Wells
Authors: Cosier Douglas J. 
Published: December 2005

AbstractNonequilibrium concentration type curves are numerically developed and sensitivity analyses are performed to examine the relationships between effluent concentrations in partially penetrating monitoring/extraction wells, the vertical plume shape, and the mass transfer characteristics of the aquifer. The governing two‐dimensional, axisym‐metric nonequilibrium solute transport equation is solved in three stages using an operator‐splitting approach. In the first two stages, the advection and dispersion terms are solved with the Eulerian‐Lagrangian method, based on the backward method of characteristics for advection and the standard implicit Galerkin finite element method for dispersion. In the third step, the first‐order, immobile‐mobile domain mass transfer term is computed analytically for both two‐site and lognormally distributed, multirate models. Effluent concentration variations with time and contour plots of the pore water concentration distribution in the aquifer are compared for a wide range of field‐ and laboratory ‐measured mass transfer rates, various plume shapes, and relevant physical/chemical parameter values, including pumping rate, vertical anisotropy ratio, retardation factor, and porosity. The simulation results show that rate‐limited mass transfer can have a significant impact on sample and aquifer pore water concentrations during three‐dimensional transport to a partially penetrating well. An alternative dimensionless form of the nonequilibrium solute transport equation is derived to illustrate the key parameter groupings that quantify rate‐limited sorption effects and show the relative importance of individual parameters. A hypothetical field application example demonstrates the fitting of dimensional type curves to discrete‐interval sampling data in order to evaluate the mass transfer characteristics of an aquifer and shows how type curve superposition can be used to model complex plume shapes.
Push‐Pull Tests for Assessing In Situ Aerobic Cometabolism
Authors: Kim Young , Istok Jonathan D. , Semprini Lewis 
Published: December 2005

AbstractThree types of single‐well push‐pull tests were developed for use in assessing the feasibility of in situ aerobic cometabolism of chlorinated aliphatic hydrocarbons (CAHs). These included transport tests, biostimulation tests, and activity tests. Transport tests are conducted to evaluate the mobility of solutes used in subsequent tests. These included bromide or chloride (conservative tracers), propane (growth substrate), ethylene, propylene (CAH surrogates), dissolved oxygen (electron acceptor), and nitrate (a minor nutrient). Tests were conducted at an experimental wellfield of Oregon State University. At this site, extraction phase breakthrough curves for all solutes were similar, indicating apparent conservative transport of the dissolved gases and nitrate prior to biostimulation. Biostimulation tests were conducted to stimulate propane‐utilizing activity of indigenous microorganisms and consisted of sequential injections of site ground water containing dissolved propane and oxygen. Biostimulation was detected by the increase in rates of propane and oxygen utilization after each injection. Activity tests were conducted to quantify rates of substrate utilization and to confirm that CAH‐transforming activity had likely been stimulated. In particular, the transformation of injected CAH surrogates ethylene and propylene to the cometabolic byproducts ethylene oxide and propylene oxide provided evidence that activity of the monooxygenase enzyme system, responsible for aerobic cometabolic transformations of CAHs, had likely also been stimulated. Estimated zero‐order transformation rates decreased in the order propane > ethylene > propylene. The series of push‐pull tests developed and field tested in this study should prove useful for conducting rapid, low‐cost feasibility assessments for in situ aerobic cometabolism of CAHs.
Strontium Isotopic Identification of Water‐Rock Interaction and Ground Water Mixing
Authors: Frost Carol D. , Toner Rachel N. 
Published: December 2005

Abstract 87Sr/86Sr ratios of ground waters in the Bighorn and Laramie basins' carbonate and carbonate‐cemented aquifer systems, Wyoming, United States, reflect the distinctive strontium isotope signatures of the minerals in their respective aquifers. Well water samples from the Madison Aquifer (Bighorn Basin) have strontium isotopic ratios that match their carbonate host rocks. Casper Aquifer ground waters (Laramie Basin) have strontium isotopic ratios that differ from the bulk host rock; however, stepwise leaching of Casper Sandstone indicates that most of the strontium in Casper Aquifer ground waters is acquired from preferential dissolution of carbonate cement. Strontium isotope data from both Bighorn and Laramie basins, along with dye tracing experiments in the Bighorn Basin and tritium data from the Laramie Basin, suggest that waters in carbonate or carbonate‐cemented aquifers acquire their strontium isotope composition very quickly—on the order of decades.Strontium isotopes were also used successfully to verify previously identified mixed Redbeds‐Casper ground waters in the Laramie Basin. The strontium isotopic compositions of ground waters near Precambrian outcrops also suggest previously unrecognized mixing between Casper and Precambrian aquifers. These results demonstrate the utility of strontium isotopic ratio data in identifying ground water sources and aquifer interactions.
Identification of thesyr-sypBox in the Promoter Regions of Genes Dedicated to Syringomycin and Syringopeptin Production byPseudomonas syringaepv. syringae B301D
Authors: Wang Nian , Lu Shi-En , Yang Qingwu , Sze Sing-Hoi , Gross Dennis C. 
Published: December 2005

ABSTRACTThe phytotoxins syringopeptin and syringomycin are synthesized by nonribosomal peptide synthetases which are encoded by the syringomycin (syr) and syringopeptin (syp) genomic island ofPseudomonas syringaepv. syringae. Previous studies demonstrated that expression of thesyr-sypgenes was controlled by thesalA-syrFregulatory pathway, which in turn was induced by plant signal molecules. In this study, the 132-kbsyr-sypgenomic island was found to be organized into five polycistronic operons along with eight individual genes based on reverse transcriptional PCR and bioinformatic analysis. The transcriptional start sites of thesalAgene and operons III and IV were located 63, 75, and 104 bp upstream of the start codons ofsalA,syrP, andsyrB1, respectively, using primer extension analysis. The predicted −10/−35 promoter region of operon IV was confirmed based on deletion and site-directed mutagenesis analyses of thesyrB1::uidAreporter with β-glucuronidase assays. A 20-bp conserved sequence (TGtCccgN6cggGaCA, termed thesyr-sypbox) with dyad symmetry around the −35 region was identified via computer analysis for thesyr-sypgenes/operons responsible for biosynthesis and secretion of syringomycin and syringopeptin. Expression of thesyrB1::uidAfusion was decreased 59% when 6 bp was deleted from the 5′ end of thesyr-sypbox in the promoter region of operon IV. These results demonstrate that the conserved promoter sequences of thesyr-sypgenes contribute to the coregulation of syringomycin and syringopeptin production.
Evidence for Clonal Evolution among Highly Polymorphic Genes in Methicillin-Resistant
Staphylococcus aureus
Authors: Kuhn G. , Francioli P. , Blanc D. S. 
Published: December 2005

ABSTRACT

The evolution of
Staphylococcus aureus
has been described as predominantly clonal, based on evidence from seven housekeeping genes. We aimed to test if this was also true for more polymorphic genes. In a collection of 60 isolates including major European epidemic methicillin-resistant
S. aureus
(MRSA) and sporadic MRSA strains, we compared the partial gene sequences of seven housekeeping genes (
arcC
,
aroE
,
glpF
,
gmk
,
pta
,
tpi
, and
yqiL
), six core adhesion genes (present in all strains) (
clfA
,
clfB
,
fnbA
,
map
,
sdrC
, and
spa
), and four accessory adhesion genes (not present in all strains) (
ebpS
,
fnbB
,
sdrD
, and
sdrE
). Nucleotide diversity of adhesion genes was 2- to 10-fold higher than genes used for multilocus sequence typing. All genes showed evidence for purifying selection with a weakly reduced level among accessory adhesion genes. Among these highly variable genes, there was no evidence for a difference in molecular evolution between epidemic and sporadic strains. Gene trees constructed from concatenated sequences of housekeeping, core adhesion, and accessory adhesion genes were highly congruent, indicating clonality, despite some evidence for homologous exchange. Further evidence for clonality was found with an overall positive correlation of allelic and nucleotidic divergence for both seven housekeeping genes and six core adhesion genes. However, for small allelic differences that fit the demarcations of clonal complexes (CCs) there was no such correlation, suggesting that recombination occurred. Therefore, despite an overall clonal population structure, recombination between related isolates within CCs might have contributed to
S. aureus
evolution.
The
Pseudomonas aeruginosa
Lipid A Deacylase: Selection for Expression and Loss within the Cystic Fibrosis Airway
Authors: Ernst Robert K. , Adams Kristin N. , Moskowitz Samuel M. , Kraig Gretchen M. , Kawasaki Kiyoshi , Stead Christopher M. , Trent M. Stephen , Miller Samuel I. 
Published: December 2005

ABSTRACT

Lipopolysaccharide (LPS) is the major surface component of gram-negative bacteria, and a component of LPS, lipid A, is recognized by the innate immune system through the Toll-like receptor 4/MD-2 complex.
Pseudomonas aeruginosa
, an environmental gram-negative bacterium that opportunistically infects the respiratory tracts of patients with cystic fibrosis (CF), can synthesize various structures of lipid A. Lipid A from
P. aeruginosa
strains isolated from infants with CF has a specific structure that includes the removal of the 3 position 3-OH C10 fatty acid. Here we demonstrate increased expression of the
P. aeruginosa
lipid A 3-
O
-deacylase (PagL) in isolates from CF infants compared to that in environmental isolates. PagL activity was increased in environmental isolates by growth in medium limited for magnesium and decreased by growth at low temperature in laboratory-adapted strains of
P. aeruginosa. P. aeruginosa
PagL was shown to be an outer membrane protein by isopycnic density gradient centrifugation. Heterologous expression of
P. aeruginosa pagL
in
Salmonella enterica
serovar Typhimurium and
Escherichia coli
resulted in removal of the 3-OH C14 fatty acid from lipid A, indicating that
P. aeruginosa
PagL recognizes either 3-OH C10 or 3-OH C14. Finally, deacylated lipid A species were not observed in some clinical
P. aeruginosa
isolates from patients with severe pulmonary disease, suggesting that loss of PagL function can occur during long-term adaptation to the CF airway.
Gene-Specific Random Mutagenesis of
Escherichia coli
In Vivo: Isolation of Temperature-Sensitive Mutations in the Acyl Carrier Protein of Fatty Acid Synthesis
Authors: De Lay Nicholas R. , Cronan John E. 
Published: December 2005

ABSTRACT

Acyl carrier proteins (ACPs) are very small acidic proteins that play a key role in fatty acid and complex lipid synthesis. Moreover, recent data indicate that the acyl carrier protein of
Escherichia coli
has a large protein interaction network that extends beyond lipid synthesis. Despite extensive efforts over many years, no temperature-sensitive mutants with mutations in the structural gene (
acpP
) that encodes ACP have been isolated. We report the isolation of three such mutants by a new approach that utilizes error-prone PCR mutagenesis, overlap extension PCR, and phage λ Red-mediated homologous recombination and that should be generally applicable. These mutants plus other experiments demonstrate that ACP function is essential for the growth of
E. coli
. Each of the mutants was efficiently modified with the phosphopantetheinyl moiety essential for the function of ACP in lipid synthesis, and thus lack of function at the nonpermissive temperature cannot be attributed to a lack of prosthetic group attachment. All of the mutant proteins were largely stable at the nonpermissive temperature except the A68T/N73D mutant protein. Fatty acid synthesis in strains that carried the D38V or A68T/N73D mutations was inhibited upon a shift to the nonpermissive temperature and in the latter case declined to a small percentage of the rate of the wild-type strain.