bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Decision Support Model to Assess Vulnerability to Salt Water Intrusion in the Great Bend Prairie Aquifer of Kansas
Authors: Sophocleous Marios , Ma Tainshing 
Published: January 2006

AbstractA relatively simple ground water decision support system (DSS) was developed to assist in identifying salt‐water vulnerable areas and in developing management policies to prevent salt‐water intrusion in central Kansas. The DSS is based on a combination of numerical modeling sensitivity analyses, multiple regression analyses, and classification procedures derived from our knowledge of the area. Six ground water salinity models are proposed to evaluate irrigation well permit applications. The choice of model depends on the availability of site‐specific data. The DSS takes advantage of GIS database management procedures, and is applied to an actual salt‐water intrusion problem site in south‐central Kansas. This approach can help local ground water management districts make better decisions on protecting ground water use in salt water vulnerable areas.
Preferential Flow and Transport of Nitrate and Bromide in Clay pan Soil
Authors: Kelly Brian P. , Pomes Michael L. 
Published: January 2006

AbstractThe in situ measurement of water flow and chemical transport through clay pan soils is crucial to understanding potential water contamination from agricultural sources. It is important due to the large areal extent of these soils in agricultural regions of the midwestern United States and because of preferential flow paths caused by desiccation cracks, worms burrowing, and root development. A study plot at the Missouri Management Systems Evaluation Area near Centralia, Missouri, was instrumented to determine the rate of preferential flow of water and transport of NO3−1 fertilizer in the unsaturated zone through a claypan soil using 15N‐NO3−1 and Br‐1 tracers. The areal distribution of preferential flow paths was between 2 and 20% in the topsoil. Gravity lysimeter flow caused by preferential flow through the claypan was as much as 150 times greater than the estimated average rate of vertical recharge. As much as 2.4% of the volume of the soil below the clay pan may be occupied by preferential flow paths.The 15N‐NO3−1 concentrations in ground water indicate that substantial quantities of fertilizer‐derived NO3−1 were transported to ground water through the claypan during the first recharge event following fertilizer application even though that event occurred six months after application. Hydraulic conductivity, measured at three scales, ranged from 6.2 × 10−8 to 7.5 × 10−3 cm/s. The observed increase of calculated hydraulic conductivity with each increase in scale was attributed to the inclusion of more and larger preferential flow paths within the volume over which the measurement was made, indicating hydraulic conductivity measured at one scale may not describe flow and transport at another scale.
Field Evaluation of Interfacial and Partitioning Tracers for Characterization of Effective NAPL‐Water Contact Areas
Authors: Annable M.D. , Jawitz J.W. , Rao P.S.C. , Dai D.P. , Kim H. , Wood A.L. 
Published: January 2006

AbstractThe use of surface‐active tracers for measuring the interfacial area between no aqueous phase liquids (NAPLs) and water was evaluated in a hydraulically isolated test cell installed in a surficial aquifer located at Hill Air Force Base (AFB), Utah. Interfacial tracers were developed at the University of Florida for quantifying immiscible fluid‐fluid interfaces (air‐water or NAPL‐water) in porous media. Sodium dodecyl benzene sulfonate (SDBS) was used as the interfacial tracer to measure the effective NAPL‐water interfacial area (aNw), while 2,2‐dimethyl‐3‐pentanol (DMP) was used as the partitioning tracer to estimate the NAPL saturation (SN). The observed retardation of SDBS and DMP when compared to a nonreactive tracer (bromide or methanol) at eight multilevel sampling locations and one extraction well, was used to quantify the aNw and SN values averaged over the interval between the injection wells and each monitoring point. The NAPL morphology index, defined here as HN= aNw/φSN (φ= porosity), varied significantly within the test cell. In locations where the magnitude of HN was large, the NAPL was assumed to be more or less uniformly spread, providing good contact with the mobile fluid. In contrast, regions with low HN values were assumed to have NAPL that was more heterogeneously distributed as isolated patches providing poor contact with the mobile fluid. The index HN, provided by the combined use of interfacial and partitioning tracers, has important implications for NAPL source region remediation employing in situ flushing technologies.
Effects of Sea Water Canals on Fresh Water Resources: An Example from Big Pine Key, Florida
Authors: Langevin C.D. , Stewart M.T. , Beaudoin C.M. 
Published: January 2006

AbstractManagement of the limited fresh water resources on small oceanic islands has become critical with increasing population and development in coastal areas. Canals, dredged for waterfront property and boat access, penetrate water‐bearing material and accelerate the natural discharge from fresh water lenses. Big Pine Key, located in the southern portion of the Florida Keys, is a heterogeneous, two‐layer island with several canal networks. The island is approximately 3 km wide and 10 km long. The upper hydros‐tratigraphic unit (Miami Oolite Limestone) has a hydraulic conductivity of 100 meters per day (m/day). The lower unit (Key Largo Limestone) has a hydraulic conductivity of 1200 m/day.To quantify the effects of canals on the fresh water lens of Big Pine Key, a numerical model was developed using the Dupuit and Ghyben‐Herzberg assumptions. The thickness of the fresh water lens is sensitive to the location of the boundary between the upper and lower hydros‐tratigraphic layers. A simulation of present‐day Big Pine Key, including canals, compared with predevel‐opment conditions shows that the total volume of the lens has decreased by 20% in response to the dredging of canals. As dredging of canals will certainly continue in the future, the numerical model was also used to investigate the types of canals that are most detrimental to a fresh water lens. For an island 3 km wide and 10 km long, a canal that penetrates 2 km lengthwise into the island reduces the volume of the fresh water lens by 6.5%. For the same island dimensions, a canal that penetrates 2 km through the mid‐section of the island reduces the volume of the fresh water lens by 7.1 %. Several short canals, with a combined total length of 2 km decrease the volume of the fresh water lens by 4.0 %. The deeper the penetration of the canal into the lens, the greater the influence of the canal. Therefore, several short canals are preferred over one long canal because shorter canals have less of an effect on the total volume of the fresh water lens. Canals also focus ground water discharge. The three configurations of 2000 m long canals each discharge 13 to 15% of the total recharge to the island.
Semi analytical Evaluation of Three‐Dimensional Velocity Near a Partially Penetrating Well in an Unconfined Aquifer
Authors: Zlotnik Vitaly , Chen Xunhong , Sun Bei 
Published: January 2006

AbstractThis paper presents an effective semi analytical method for computation of ground water velocities near a partially penetrating well in an unconfined aquifer. The Neuman solution (1974) is presented as the sum of the Hantush solution (1964) and a correction term for water table conditions. Hydraulic gradients are directly evaluated from the Hantush solution, whereas the gradients for the Neuman correction are calculated using a numerical inversion of the Laplace transform. The method presented here is verified by comparing it with the results of a finite‐difference approximation of hydraulic gradients. Calculations of velocities near a pumping well in an unconfined aquifer indicate that, after an initial increase, the vertical velocity decreases before reaching steady state. The method provides a useful tool for the study of well hydraulics and contaminant transport to a pumping well in an unconfined aquifer.
A Controlled Experiment in Ground Water Flow Model Calibration
Authors: Hill Mary C. , Cooley Richard L. , Pollock David W. 
Published: January 2006

AbstractNonlinear regression was introduced to ground water modeling in the 1970s, but has been used very little to calibrate numerical models of complicated ground water systems. Apparently, nonlinear regression is thought by many to be incapable of addressing such complex problems. With what we believe to be the most complicated synthetic test case used for such a study, this work investigates using nonlinear regression in ground water model calibration. Results of the study fall into two categories. First, the study demonstrates how systematic use of a well designed nonlinear regression method can indicate the importance of different types of data and can lead to successive improvement of models and their parameterizations. Our method differs from previous methods presented in the ground water literature in that (1) weighting is more closely related to expected data errors than is usually the case; (2) defined diagnostic statistics allow for more effective evaluation of the available data, the model, and their interaction; and (3) prior information is used more cautiously. Second, our results challenge some commonly held beliefs about model calibration. For the test case considered, we show that (1) field measured values of hydraulic conductivity are not as directly applicable to models as their use in some geostatistical methods imply; (2) a unique model does not necessarily need to be identified to obtain accurate predictions; and (3) in the absence of obvious model bias, model error was normally distributed. The complexity of the test case involved implies that the methods used and conclusions drawn are likely to be powerful in practice.
A Method to Infer In Situ Reaction Rates from Push‐Pull Experiments
Authors: Snodgrass Mark F. , Kitanidis Peter K. 
Published: January 2006

AbstractA method to evaluate first‐order and zero‐order in situ reaction rates from a push‐pull test is presented. A single‐well push‐pull test starts with the rapid injection of a well‐mixed slug containing a known quantity of a conservative tracer and a reactive solute into the saturated zone. The slug is then periodically extracted and sampled from the same well. For zero‐ or first‐order reactions, in the absence of sorption and assuming negligible background concentrations, these measurements can be used to evaluate reaction rate coefficients directly. The method does not involve computer‐based solute transport models and requires no knowledge of regional ground water flow or hydraulic parameters. The method performs well when the dominate processes are advection, dispersion, and zero‐ or first‐order irreversible reactions. Regional flow velocities must be sufficiently low such that the slug stays within the area of the well during the sampling phase. In the case of zero‐order reactions, results using the method proposed here are compared with those obtained through the traditional method of calibrating a computer‐based transport model. The two methods give similar estimates of the reaction rate coefficient. The method is general enough to work with a broad range of push‐pull experiment designs and sampling techniques.
Modeling a Complex Multi‐Aquifer System: The Waterloo Moraine
Authors: Martin P.J. , Frind E.G. 
Published: January 2006

AbstractThe Regional Municipality of Waterloo in Ontario, Canada (population 250,000) depends on ground water for most of its water supply. The ground water is extracted from the Waterloo Moraine, an extensive and complex glacial aquifer system extending over a 400 km2 area. A methodology is being developed to inventory the ground water resource, to define its susceptibility to contamination, and to create the basis for optimal management and protection strategies. A key component of this methodology is a three‐dimensional conceptual hydrogeologic model based on the geologic characteristics of the multiple‐aquifer Moraine system. The steps in the development of the model include screening of the large database, interpretation and interpolation of the data to define the variable hydrostatigraphy and to generate consistent hydraulic conductivity functions, and model calibration. The numerical basis is a fully three‐dimensional finite element model that provides flexibility and adaptability in representing the natural boundaries, the highly irregular stratigraphy, and the numerous wellfields. The model has the capability to automatically find the location of the water table consistent with given recharge and pumping conditions, and to direct recharge from low‐permeability areas to higher‐permeability areas. Capture zones generated by the model are found to be highly sensitive with respect to the geologic structure, in particular the presence or absence of windows in the aquitard units. Professional judgment is found to be an essential component of the modeling process.
Cytokine Response and Survival of Mice Immunized with an Adenovirus Expressing
Bacillus anthracis
Protective Antigen Domain 4
Authors: McConnell Michael J. , Hanna Philip C. , Imperiale Michael J. 
Published: January 2006

ABSTRACT

Adenovirus vectors are promising for use in vaccinating against potential agents of bioterrorism and emerging infections because of their proven safety in humans and their ability to elicit rapid immune responses. Here, we describe the construction and evaluation of an adenovirus vaccine expressing domain 4 of
Bacillus anthracis
protective antigen, Ad.D4. Ad.D4 elicited antibodies to protective antigen 14 days after a single intramuscular injection, which were further increased upon boosting. Furthermore, two doses of Ad.D4 4 weeks apart were sufficient to protect 67% of mice from toxin challenge. Additionally, we have characterized the release of inflammatory cytokines from vaccinated mice after lethal-toxin challenge. We demonstrate that interleukin 1β (IL-1β) levels in mice that survive lethal toxin challenge are similar to levels in nonsurvivors and that IL-6 levels are higher in survivors than in nonsurvivors. These findings suggest that lethal-toxin-mediated death may not be a direct result of inflammatory-cytokine release.
Correlation of Molecular Characteristics, Isotype, and In Vitro Functional Activity of Human Antipneumococcal Monoclonal Antibodies
Authors: Baxendale H. E. , Goldblatt D. 
Published: January 2006

ABSTRACTStructure-function correlations of pneumococcal antibodies are important in predicting how changes in the pneumococcus (Pnc)-specific B-cell repertoire will influence humoral immunity against invasive Pnc disease. Using a unique panel of human hybridomas derived from memory B cells after pneumococcal conjugate vaccination, we analyzed the structure-function relationship of nine monoclonal antibodies (MAbs) reactive to Pnc polysaccharides. The avidities of the antibodies correlated with the avidity of donor immune serum (R, 0.7;P< 0.025), and this relationship was particularly strong for immunoglobulin A clones (R, 1;P< 0.0005), suggesting that the MAbs may represent important clones contributing to serological memory. Common heavy-light chain combinations and amino acid replacement mutations were seen for clones with the same serospecificity from different individuals. The two highest-avidity MAbs used Vh3-48, and two MAbs with the same serospecificity, using the same V gene pairings (Vh3-7 and Vk2A17), had similar avidities, suggesting that canonical V gene use makes an important contribution to avidity. Although all clones had mutation levels consistent with their being derived from memory B cells, low levels of replacement mutation were associated with high avidities. This relationship was strongest for Vh genes (R, 0.8;P< 0.01). Opsonophagocytosis was demonstrated for all clones, and there was a trend toward clones using canonical genes with low levels of mutation having high opsonophagocytic activities (R, 0.5). These data suggest that the use of canonical genes in the Pnc antibody response is associated with highly functional antibodies and that most somatic mutations seen in these genes are not antigen selected.
Cre Reporter System To Monitor the Translocation of Type III Secreted Proteins into Host Cells
Authors: Briones Gabriel , Hofreuter Dirk , Galán Jorge E. 
Published: January 2006

ABSTRACT

Central to the study of type III secretion systems is the availability of reporter systems to monitor bacterial protein translocation into host cells. We report here the development of a bacteriophage P1 Cre recombinase-based system to monitor the translocation of bacterial proteins into mammalian cells. Bacteriophage P1 Cre recombinase fused to the secretion and translocation signals of
Salmonella enterica
serovar Typhimurium of the type III secreted protein SopE was secreted in a type III secretion system-dependent fashion. More importantly, the SopE-Cre chimera was translocated into host cells via the type III secretion system and activated the expression of luciferase and green fluorescent protein reporters of Cre recombinase activity.
Virulence of
Staphylococcus aureus
Small Colony Variants in the
Caenorhabditis elegans
Infection Model
Authors: Sifri Costi D. , Baresch-Bernal Andrea , Calderwood Stephen B. , von Eiff Christof 
Published: January 2006

ABSTRACT

Small colony variants (SCVs) of
Staphylococcus aureus
are slow-growing morphological variants that have been implicated in persistent, relapsing, and antibiotic-resistant infections. The altered phenotype of SCVs in most strains has been attributed to defects in electron transport due to mutations in hemin or menadione biosynthesis. The pathogenic capacity of SCVs compared to phenotypically normal strains is variable depending on the attribute examined, with some studies showing reduced virulence of SCVs and others demonstrating normal or heightened virulence. Recently, the nematode
Caenorhabditis elegans
has been successfully employed as an alternative host to investigate virulence mechanisms of a variety of bacterial pathogens, including
S. aureus
. In this study, we show that clinical SCVs as well as
hemB
- and
menD
-deficient mutants of
S. aureus
are greatly reduced in virulence in the
C. elegans
infection model.
TheHelicobacter pyloriUrease B Subunit Binds to CD74 on Gastric Epithelial Cells and Induces NF-κB Activation and Interleukin-8 Production
Authors: Beswick Ellen J. , Pinchuk Irina V. , Minch Kyle , Suarez Giovanni , Sierra Johanna C. , Yamaoka Yoshio , Reyes Victor E. 
Published: January 2006

ABSTRACTThe pathogenesis associated withHelicobacter pyloriinfection is the result of both bacterial factors and the host response. We have previously shown thatH. pyloribinds to CD74 on gastric epithelial cells. In this study, we sought to identify the bacterial protein responsible for this interaction.H. pyloriurease from a pool of bacterial surface proteins was found to coprecipitate with CD74. To determine how urease binds to CD74, we used recombinant urease A and B subunits. Recombinant urease B was found to bind directly to CD74 in immunoprecipitation and flow cytometry studies. By utilizing both recombinant urease subunits and urease B knockout bacteria, the urease B-CD74 interaction was shown to induce NF-κB activation and interleukin-8 (IL-8) production. This response was decreased by blocking CD74 with monoclonal antibodies. Further confirmation of the interaction of urease B with CD74 was obtained using a fibroblast cell line transfected with CD74 that also responded with NF-κB activation and IL-8 production. The binding of theH. pyloriurease B subunit to CD74 expressed on gastric epithelial cells presents a novel insight into a previously unrecognizedH. pyloriinteraction that may contribute to the proinflammatory immune response seen during infection.
Unique Transcriptome Signature of
Mycobacterium tuberculosis
in Pulmonary Tuberculosis
Authors: Rachman Helmy , Strong Michael , Ulrichs Timo , Grode Leander , Schuchhardt Johannes , Mollenkopf Hans , Kosmiadi George A. , Eisenberg David , Kaufmann Stefan H. E. 
Published: January 2006

ABSTRACT

Although tuberculosis remains a substantial global threat, the mechanisms that enable mycobacterial persistence and replication within the human host are ill defined. This study represents the first genome-wide expression analysis of
Mycobacterium tuberculosis
from clinical lung samples, which has enabled the identification of
M. tuberculosis
genes actively expressed during pulmonary tuberculosis. To obtain optimal information from our DNA array analyses, we analyzed the differentially expressed genes within the context of computationally inferred protein networks. Protein networks were constructed using functional linkages established by the Rosetta stone, phylogenetic profile, conserved gene neighbor, and operon computational methods. This combined approach revealed that during pulmonary tuberculosis,
M. tuberculosis
actively transcribes a number of genes involved in active fortification and evasion from host defense systems. These genes may provide targets for novel intervention strategies.
The Established Intimin Receptor Tir and the Putative Eucaryotic Intimin Receptors Nucleolin and β1 Integrin Localize at or near the Site of Enterohemorrhagic
Escherichia coli
O157:H7 Adherence to Enterocytes In Vivo
Authors: Sinclair James F. , Dean-Nystrom Evelyn A. , O'Brien Alison D. 
Published: January 2006

ABSTRACT

For enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 to adhere tightly to the intestinal epithelium and produce
a
ttach and
e
fface (A/E) lesions, the organism must express the adhesin intimin and insert the bacterially encoded
t
ranslocated
i
ntimin
r
eceptor Tir into the plasma membrane of the host enterocyte. Additionally, some reports based on tissue culture experiments indicate that intimin has affinity for the eucaryotic proteins nucleolin and β1 integrin. To address the potential biological relevance of these eucaryotic proteins in the infection process in vivo, we sought to compare the proximity of Tir, nucleolin, and β1 integrin to regions of EHEC O157:H7 attachment in intestinal sections from three different inoculated animals: piglets, neonatal calves, and mice. Piglets and neonatal calves were chosen because intimin-mediated adherence of EHEC O157:H7 and subsequent A/E lesion formation occur at high levels in these animals. Mice were selected because of their ease of manipulation but only after we first demonstrated that in competition with the normal mouse gut flora, an EHEC O157:H7 strain with a nonpolar deletion in the intimin gene was cleared faster than strains that produced wild-type or hybrid intimin. In all three animal species, we noted immunostained Tir beneath and stained nucleolin closely associated with adherent bacteria in intestinal sections. We also observed immunostained β1 integrin clustered at locations of bacterial adherence in porcine and bovine tissue. These findings indicate that nucleolin and β1 integrin are present on the luminal surface of intestinal epithelia and are potentially accessible as receptors for intimin during EHEC O157:H7 infection.