bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of an Electromagnetic Seepage Meter to Investigate Temporal Variability in Lake Seepage
Authors: Rosenberry Donald O. , Morin Roger H. 
Published: December 2005

AbstractA commercially available electromagnetic flowmeter is attached to a seepage cylinder to create an electromagnetic seepage meter (ESM) for automating measurement of fluxes across the sediment/water interface between ground water and surface water. The ESM is evaluated through its application at two lakes in New England, one where water seeps into the lake and one where water seeps out of the lake. The electromagnetic flowmeter replaces the seepage‐meter bag and provides a continuous series of measurements from which temporal seepage processes can be investigated. It provides flow measurements over a range of three orders of magnitude, and contains no protruding components or moving parts. The ESM was used to evaluate duration of seepage disturbance following meter installation and indicated natural seepage rates resumed approximately one hour following meter insertion in a sandy lakebed. Lakebed seepage also varied considerably in response to lakebed disturbances, near‐shore waves, and rainfalls, indicating hydrologic processes are occurring in shallow lakebed settings at time scales that have largely gone unobserved.
Quantifying Ground Water Recharge at Multiple Scales Using PRMS and GIS
Authors: Cherkauer Douglas S. 
Published: December 2005

AbstractManagement of ground water resources requires a method to calculate demonstrably accurate recharge rates at local to regional scales using readily available information bases. Many methods are available to calculate recharge, but most are unable to satisfy all these conditions. A distributed parameter model is shown to meet the stated needs. Such models are input intensive, however, so a procedure to define most inputs from GIS and hydrogeological sources is presented. It simplifies the PRMS calibration observed streamflow hydrographs by reducing degrees of freedom from dozens to four.For seven watersheds (60 to 500 km2), the GIS‐aided calibrations have average errors of 5% on recharge and 2% on total streamflow, verifying the accuracy of the process. Recharge is also calculated for 63 local‐scale subwater‐sheds (average size 37 km2). For the study area, calculated recharges average 11 cm/yr. Soil and rock conductivity, porosity, and depth to the water table are shown to be the physical properties which dominate the spatial variability of recharge. The model has been extended to uncalibrated watersheds where GIS and climatic information are known. It reproduces total annual discharge and recharge to within 9% and 10%, respectively, indicating the process can also be used to calculate recharge in ungauged watersheds. It has not been tested outside the study area, however.
Surface Flow Boundary Conditions in Modeling Land Subsidence Due to Fluid Withdrawal
Authors: Baú Domenico , Ferronato Massimiliano , Gambolati Giuseppe , Teatini Pietro 
Published: December 2005

AbstractLand subsidence due to subsurface fluid (water, gas, oil) withdrawal is often predicted by either finite element or finite difference numerical models based on coupled poroelastic theory, where the soil is represented as a semi‐infinite medium bounded by the traction‐free (ground) surface. One of the variables playing a most important role on the final outcome is the flow condition used on the traction‐free boundary, which may be assumed as either permeable or impermeable. Although occasionally justified, the assumption of no‐flow surface seems to be in general rather unrealistic. A permeable boundary where the fluid pressure is fixed to the external atmospheric pressure appears to be more appropriate. This paper addresses the response, in terms of land subsidence, obtained with a coupled poroelastic finite element model that simulates a distributed pumping from a horizontal aquifer confined between two relatively impervious layers, and takes either a permeable boundary surface, i.e., constant hydraulic potential, or an impermeable boundary, i.e., a zero Neumann flow condition. The analysis reveals that land subsidence is rather sensitive to the flow condition implemented on the traction‐free boundary. In general, the no‐flow condition leads to an overestimate of the predicted ground surface settlement, which could even be 1 order of magnitude larger than that obtained with the permeable boundary.
Application of a Bayesian Approach to Stochastic Delineation of Capture Zones
Authors: Feyen L. , Dessalegn A.M. , De Smedt F. , Gebremeskel S. , Batelaan O. 
Published: December 2005

AbstractThis paper presents a Bayesian Monte Carlo method for evaluating the uncertainty in the delineation of well capture zones and its application to a wellfield in a heterogeneous, multiaquifer system. In the method presented, Bayes’ rule is used to update prior distributions for the unknown parameters of the stochastic model for the hydraulic conductivity, and to calculate probability‐based weights for parameter realizations using head residuals. These weights are then assigned to the corresponding capture zones obtained using forward particle tracking. Statistical analysis of the set of weighted protection zones results in a probability distribution for the capture zones. The suitability of the Bayesian stochastic method for a multilayered system is investigated, using the wellfield Het Rot at Nieuwrode, Belgium, located in a three‐layered aquifer system, as an example. The hydraulic conductivity of the production aquifer is modeled as a spatially correlated random function with uncertain parameters. The aquitard and overlying uncon‐fined aquifer are assigned random, homogeneous conductivities. The stochastic results are compared with deterministic capture zones obtained with a calibrated model for the area. The predictions of the stochastic approach are more conservative and indicate that parameter uncertainty should be taken into account in the delineation of well capture zones.
Gas‐Partitioning Tracer Test to Quantify Trapped Gas During Recharge
Authors: Heilweil Victor M. , Kip Solomon D. , Perkins Kim S. , Ellett Kevin M. 
Published: December 2005

AbstractDissolved helium and bromide tracers were used to evaluate trapped gas during an infiltration pond experiment. Dissolved helium preferentially partitioned into trapped gas bubbles, or other pore air, because of its low solubility in water. This produced observed helium retardation factors of as much as 12 relative to bromide. Numerical simulations of helium breakthrough with both equilibrium and kinetically limited advection/dispersion/retardation did not match observed helium concentrations. However, better fits were obtained by including a decay term representing the diffusive loss of helium through interconnected, gas‐filled pores. Calculations indicate that 7% to more than 26% of the porosity beneath the pond was filled with gas. Measurements of laboratory hydraulic properties indicate that a 10% decrease in saturation would reduce the hydraulic conductivity by at least one order of magnitude in the well‐sorted sandstone, but less in the overlying soils. This is consistent with in situ measurements during the experiment, which show steeper hydraulic gradients in sandstone than in soil. Intrinsic permeability of the soil doubled during the first six months of the experiment, likely caused by a combination of dissolution and thermal contraction of trapped gas. Managers of artificial recharge basins may consider minimizing the amount of trapped gas by using wet, rather than dry, tilling to optimize infiltration rates, particularly in well‐sorted porous media in which reintroduced trapped gas may cause substantial reductions in permeability. Trapped gas may also inhibit the amount of focused infiltration that occurs naturally during ephemeral flood events along washes and playas.
Reactive Barriers: Hydraulic Performance and Design Enhancements
Authors: Painter B.D.M. 
Published: December 2005

AbstractThe remediation of contaminated ground water is a multibillion‐dollar global industry. Permeable reactive barriers (PRBs) are one of the leading technologies being developed in the search for alternatives to the pump‐and‐treat method. Improving the hydraulic performance of these PRBs is an important part of maximizing their potential to the industry.Optimization of the hydraulic performance of a PRB can be defined in terms of finding the balance between capture, residence time, and PRB longevity that produces a minimum‐cost acceptable design. Three‐dimensional particle tracking was used to estimate capture zone and residence time distributions. Volumetric flow analysis was used for estimation of flow distribution across a PRB and in the identification of flow regimes that may affect the permeability or reactivity of portions of the PRB over time. Capture zone measurements extended below the base of partially penetrating PRBs and were measured upgradient from the portion of aquifer influenced by PRB emplacement.Hydraulic performance analysis of standard PRB designs confirmed previously presented research that identified the potential for significant variation in residence time and capture zone. These variations can result in the need to oversize the PRB to ensure that downgradient contaminant concentrations do not exceed imposed standards. The most useful PRB design enhancements for controlling residence time and capture variation were found to be customized downgradient gate faces, velocity equalization walls, deeper emplacement of the funnel than the gate, and careful manipulation of the hydraulic conductivity ratio between the gate and the aquifer.
Ground Water Whirls
Authors: Hemker Kick , van den Berg Elmer , Bakker Mark 
Published: December 2005

AbstractNumerical experiments with steady‐state ground water flow models show that spiraling flow lines occur in layered aquifers that have different anisotropic horizontal hydraulic conductivities in adjacent layers. Bundles of such flow lines turning in the same direction can be referred to as ground water whirls. An anisotropic layered block in a field of uniform horizontal flow results in one or more whirls with their axes in the uniform flow direction. The number of whirls depends on the number of interfaces between layers with different anisotropic properties. For flow to a well in an aquifer consisting of two anisotropic layers, with perpendicular major principal directions, whirls are found to occur in quadrants that are bounded by the principal directions of the hydraulic conductivity. The combined effect of flow to a well and a layered anisotropy implies that a single well in a system with a single anisotropic layer within an otherwise isotropic aquifer causes eight whirls. All adjacent whirls rotate in opposite directions.
Estimation of Anaerobic Biodegradation Rate Constants at MGP Sites
Authors: Lewandowski Gordon , Mortimer Georgene 
Published: December 2005

AbstractField data at six former manufactured gas plant sites in New Jersey were used to estimate the biodegradation rate constants for the anaerobic processes naturally occurring within the ground water contaminant plumes (primarily iron and sulfate reduction). Those rate constants turned out to be about an order of magnitude smaller than values reported for the same contaminants (primarily benzene and naphthalene) at fuel sites. At four of the sites, there appeared to be sufficient electron acceptor present to eventually degrade the contaminants in the plume. However, the presence of nonaqueous phase liquids tends to offset that capacity by continuing to act as a source of contaminants that can dissolve in the ground water.
Geochemical Processes During Five Years of Aquifer Storage Recovery
Authors: Herczeg Andrew L. , Rattray Karen J. , Dillon Peter J. , Pavelic Paul , Barry Karen E. 
Published: December 2005

AbstractA key factor in the long‐term viability of aquifer storage recovery (ASR) is the extent of mineral solution interaction between two dissimilar water types and consequent impact on water quality and aquifer stability. We collected geochemical and isotopic data from three observation wells located 25, 65, and 325 m from an injection well at an experimental ASR site located in a karstic, confined carbonate aquifer in South Australia. The experiment involved five major injection cycles of a total of 2.5 × 105 m3 of storm water (total dissolved solids [TDS] ∼ 150 mg/L) into the brackish (TDS ∼2400 mg/L) aquifer. ∼60% of the mixture was pumped out during the fifth year of the experiment. The major effect on water quality within a 25 m radius of the injection well following injection of storm water was carbonate dissolution (35 ± 6 g of CaCO3 dissolved/m3 of aquifer) and sulfide mineral oxidation (50 ± 10 g as FeS2/m3 after one injection). < 0.005% of the total aquifer carbonate matrix was dissolved during each injection event, and ∼0.2% of the total reduced sulfur. Increasing amounts of ambient ground water was entrained into the injected mixture during each of the storage periods. High 14CDIC activities and slightly more negative δ13CDIC values measured immediately after injection events show that substantial CO2(aq) is produced by oxidation of organic matter associated with injectant. There were no detectable geochemical reactions while pumping during the recovery phase in the fifth year of the experiment.
Hydraulic Conductivity Prediction for Sandy Soils
Authors: Cronican Amy E. , Gribb Molly M. 
Published: December 2005

AbstractThe potential for petroleum‐contaminated soils to impact ground water is evaluated using the soil leachability model in South Carolina and Georgia. In this model, the Green and Ampt (1911) equation is used to estimate unsat‐urated flow with saturated hydraulic conductivity (Ks) values obtained using the Rawls and Brakensiek (1989) equation from inputs of percent sand‐ and clay‐sized particles. However, many soils have > 70% sand‐sized particles, which is the maximum amount for which the Rawls and Brakensiek equation is valid. Therefore, 70 sets of Ks and particle‐size data from the literature for southeastern United States sandy soils were analyzed to develop a new equation for estimating Ks. A multiple linear regression model with an adjusted R2= 0.65 (p < 0.0001) was developed from percent clay‐ and sand‐sized particle data. Eight additional sets of data were used to validate the model. The root mean square deviation and maximum squared difference, (yi‐ŷi2), values for the new model are smaller than those obtained using the Rawls and Brakensiek equation, or Rosetta, a neural network‐based model (Schaap 1999). The new model provides estimates that are within an order of magnitude for all but one of the test data sets. Rosetta predicts Ks within one order of magnitude of measured values for six test data, and predicts Ks within two orders of magnitude for the other two. The Rawls and Brakensiek predictions are within one order of magnitude for four test data, but are two or more orders of magnitude too high for the remaining four points. The new equation is recommended for estimating Ks for sandy southeastern United States soils for which inputs are limited to percent sand and clay.
SecA Dimer Cross-Linked at Its Subunit Interface Is Functional for Protein Translocation
Authors: Jilaveanu Lucia B. , Oliver Donald 
Published: December 2005

ABSTRACT
SecA facilitates protein transport across the eubacterial plasma membrane by its association with cargo proteins and the SecYEG translocon, followed by ATP-driven conformational changes that promote protein translocation in a stepwise manner. Whether SecA functions as a monomer or a dimer during this process has been the subject of considerable controversy. Here we utilize cysteine-directed mutagenesis along with the crystal structure of the SecA dimer to create a cross-linked dimer at its subunit interface, which was normally active for in vitro protein translocation.
“UnPAKing” Human Immunodeficiency Virus (HIV) Replication: Using Small Interfering RNA Screening To Identify Novel Cofactors and Elucidate the Role of Group I PAKs in HIV Infection
Authors: Nguyen Deborah G. , Wolff Karen C. , Yin Hong , Caldwell Jeremy S. , Kuhen Kelli L. 
Published: December 2005

ABSTRACTIn order to identify novel proviral host factors involved in human immunodeficiency virus (HIV) infection, we performed a screen of a small interfering RNA (siRNA) library targeting 5,000 genes with the highest potential for being targets for therapeutics. Many siRNAs in the library against known host factors, such as TSG101, furin, and CXCR4, were identified as inhibitors by the screen and thus served as internal validation. In addition, many novel factors whose knockdown inhibited infection were identified, including Pak3, a member of the serine/threonine group I PAK kinases. The HIV accessory factor Nef has been shown to associate with a PAK kinase, leading to enhanced viral production; however, the exact identity of the kinase has remained controversial. Prompted by the Pak3 screen hit, we further investigated the involvement of group I PAK kinases in HIV using siRNA. Contrary to the current literature, Pak1 depletion strongly inhibited HIV infection in multiple cell systems and decreased levels of integrated provirus, while Pak2 depletion showed no effect. Overexpression of a constitutively active Pak1 mutant also enhanced HIV infection, further supporting its role as the dominant PAK involved.
Severe Acute Respiratory Syndrome Coronavirus 3a Protein Is Released in Membranous Structures from 3a Protein-Expressing Cells and Infected Cells
Authors: Huang Cheng , Narayanan Krishna , Ito Naoto , Peters C. J. , Makino Shinji 
Published: December 2005

ABSTRACT
Severe acute respiratory syndrome coronavirus (SCoV) accessory protein 3a is a virus structural protein. We demonstrate here that 3a protein was released efficiently in membranous structures from various cell lines expressing 3a protein. A subpopulation of the released 3a protein is associated with detergent-resistant membranes. The presence of the YxxΦ and diacidic motifs, located within the cytoplasmic tail of the 3a protein, was not required for its efficient release. Analysis of supernatant from SCoV-infected cells with sucrose gradient sedimentation and virus capture assay indicated that the 3a protein was released from infected cells in two distinct populations, as a component of SCoV particles, and in membrane structures with a lower buoyant density. These data provide new insights into the biological properties of SCoV 3a protein.
Lack of Intrinsic CTLA-4 Expression Has Minimal Effect on Regulation of Antiviral T-Cell Immunity
Authors: Homann Dirk , Dummer Wolfgang , Wolfe Tom , Rodrigo Evelyn , Theofilopoulos Argyrios N. , Oldstone Michael B. A. , von Herrath Matthias G. 
Published: December 2005

ABSTRACTCTLA-4 is considered one of the most potent negative regulators of T-cell activation. To circumvent experimental limitations due to fatal lymphoproliferative disease associated with genetic ablation of CTLA-4, we have used radiation chimeras reconstituted with a mixture of CTLA-4+/+and CTLA-4−/−bone marrow that retain a normal phenotype and allow the evaluation of long-term T-cell immunity under conditions of intrinsic CTLA-4 deficiency. Following virus infection, we profiled primary, memory, and secondary CD8+and CD4+T-cell responses directed against eight different viral epitopes. Our data demonstrate unaltered antigen-driven proliferation, acquisition of effector functions, distribution of epitope hierarchies, T-cell receptor repertoire selection, functional avidities, and long-term memory maintenance in the absence of CTLA-4. Moreover, regulation of memory T-cell survival and homeostatic proliferation, as well as secondary responses, was equivalent in virus-specific CTLA4+/+and CTL-A-4−/−T-cell populations. Thus, lack of CTLA-4 expression by antigen-specific T cells can be compensated for by extrinsic factors in the presence of CTLA-4 expression by other cells. These findings have implications for the physiologic, pathological, and therapeutic regulation of costimulation.
Neither the RNA nor the Proteins of Open Reading Frames 3a and 3b of the Coronavirus Infectious Bronchitis Virus Are Essential for Replication
Authors: Hodgson Teri , Britton Paul , Cavanagh Dave 
Published: December 2005

ABSTRACT
Gene 3 of infectious bronchitis virus is tricistronic; open reading frames (ORFs) 3a and 3b encode two small nonstructural (ns) proteins, 3a and 3b, of unknown function, and a third, structural protein E, is encoded by ORF 3c. To determine if either the 3a or the 3b protein is required for replication, we first modified their translation initiation codons to prevent translation of the 3a and 3b proteins from recombinant infectious bronchitis viruses (rIBVs). Replication in primary chick kidney (CK) cells and in chicken embryos was not affected. In chicken tracheal organ cultures (TOCs), the recombinant rIBVs reached titers similar to those of the wild-type virus, but in the case of viruses lacking the 3a protein, the titer declined reproducibly earlier. Translation of the IBV E protein is believed to be initiated by internal entry of ribosomes at a structure formed by the sequences corresponding to ORFs 3a and 3b. To assess the necessity of this mechanism, we deleted most of the sequence representing 3a and 3b to produce a gene in which ORF 3c (E) was adjacent to the gene 3 transcription-associated sequence. Western blot analysis revealed that the recombinant IBV produced fivefold less E protein. Nevertheless, titers produced in CK cells, embryos, and TOCs were similar to those of the wild-type virus, although they declined earlier in TOCs, probably due to the absence of the 3a protein. Thus, neither the tricistronic arrangement of gene 3, the internal initiation of translation of E protein, nor the 3a and 3b proteins are essential for replication per se, suggesting that these proteins are accessory proteins that may have roles in vivo.
Characterization of the Vaccinia Virus A35R Protein and Its Role in Virulence
Authors: Roper Rachel L. 
Published: December 2005

ABSTRACT
The vaccinia virus A35R gene is highly conserved among poxviruses and encodes a previously uncharacterized hydrophobic acidic protein. Western blotting with anti-A35R peptide antibodies indicated that the protein is expressed early in infection and resolved as a single sharp band of ∼23 kDa, slightly higher than the 20 kDa predicted from its sequence. The protein band appeared to be the same molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, whether expressed in an in vitro transcription/translation system without microsomes or expressed in infected cells, suggesting that it was not glycosylated. A mutant virus with the A35R gene deleted (vA35Δ) formed wild-type-sized plaques on all cell lines tested (human, monkey, mouse, and rabbit); thus, A35R is not required for replication and does not appear to be a host range gene. Although the A35R protein is hydrophobic, it is unlikely to be an integral membrane protein, as it partitioned to the aqueous phase during TX-114 partitioning. The protein could not be detected in virus-infected cell supernatants. A35R localized intracellularly to the virus factories, where the first stages of morphogenesis occur. The vA35Δ mutant formed near-normal levels of the various morphogenic stages of infectious virus particles and supported normal acid-induced fusion of virus-infected cells. Despite normal growth and morphogenesis in vitro, the vA35Δ mutant virus was attenuated in intranasal challenge of mice compared to wild-type and A35R rescue virus. Thus, the intracellular A35R protein plays a role in virulence. The A35R has little homology to any protein outside of poxviruses, suggesting a novel virulence mechanism.