bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Sorption Assumptions on Aquifer Remediation Designs
Authors: Aksoy Aysegul , Culver Teresa B. 
Published: August 2005

AbstractGenetic algorithm optimization of pump‐and‐treat ground water remediation is used to explore the extent of bias introduced into remediation designs and costs by sorption assumptions. Remediation problems with equilibrium sorption and two‐site kinetic sorption with different mass transfer rates are addressed. Under the time‐scales and flow conditions of contamination, all of these sorption assumptions created similar initial plumes. Thus, calibration of sorption parameters to the initial plume may be insufficient information to differentiate between sorption rates. Two optimization formulations were considered for each sorption assumption. In one formulation, the final water quality goal is with respect to the aqueous concentration; in the other, the goal is with respect to the total concentration (aqueous and sorbed). While remediation designs could be found with the aqueous concentration formulation, the total mass of contaminant remaining within the aquifer increases with decreasing mass transfer rates, creating the potential for concentration rebound after the pumping period ends. The designs found with the total concentration formulation avoid this difficulty, although it may not always be possible to find feasible remediation schemes within the specified remediation period. If an optimal design based on the assumption of equilibrium sorption is applied to an aquifer with mass transfer limitations, the water quality goals may not be met within the specified remediation period. The length of time required to meet the water quality goals with this suboptimal design may increase exponentially as the mass transfer rate decreases, although aquifer heterogeneity reduces the scale of this effect.
Prediction of the Quality and Quantity of Maramec Spring Water
Authors: Wicks Carol M. , Hoke John A. 
Published: August 2005

AbstractOur ability to predict the response of large karstic basins to contaminant pulses and recharge events is limited due to an inability to model flow through these highly hetereogeneous and anisotropic basins. The linear systems technique is useful for simulating hydrologic processes occurring in karstic basins because detailed knowledge about the internal structure of the basin is not required. The objectives of this study were to predict changes in the quantity and quality of spring water in a large karstic basin using the linear systems approach. Using a dimensionless unit hydrograph, the change in quantity of spring water was predicted and the correlation coefficient, r, between predicted and observed discharges was 0.94. A nonpoint source kernel was used to predict the change in the specific conductance of the spring water (r = 0.97). A point‐source kernel derived from a quantitative dye trace was used to predict the first arrival and dispersion of a contaminant at the spring (r = 0.11). Even though the correlation coefficient is low, the prediction matched the first and last appearances of the contaminant. Quantitative dye traces can be used to predict the movement of aqueous contaminants through karstic aquifers using the linear systems approach. Given the findings of this research, the linear systems approach is a useful predictive tool that would enable better management of ground water resources in karstic basins.
Impact of Biomass‐Decay Terms on the Simulation of Pulsed Bioremediation
Authors: Cirpka Olaf A. , Kitanidis Peter K. 
Published: August 2005

AbstractA numerical model is used for simulating the stimulation of biomass growth by injection of alternating pulses of a primary substrate and oxygen. We consider that the substrate sorbs, whereas oxygen does not undergo mass transfer, and mixing of the reacting compounds is dominated by the chromatographic effect. Different mathematical formulations for biomass growth and decay are compared. In models considering biomass decay, a minimal time of joint exposure to both reactants can be determined. This leads to a multimodal distribution of the biomass after multiple injection cycles. In multidimensional heterogeneous domains, the location of the biomass peaks is determined by the advective arrival time. The biomass is much more homogeneously distributed when biomass decay is neglected, because under this condition there is no constraint by a minimal joint exposure time. For the case of oxygen‐dependent biomass decay, an injection scheme using shorter pulses of higher oxygen concentrations is shown to be superior to a scheme with equally long pulses of oxygen and the substrate.
Age of Irrigation Water in Ground Water from the Eastern Snake River Plain Aquifer, South‐Central Idaho
Authors: Plummer L.N. , Rupert M.G. , Busenberg E. , Schlosser P. 
Published: August 2005

AbstractStable isotope data (2H and 18O) were used in conjunction with chlorofluorocarbon (CFC) and tritium/helium‐3 (3H/3He) data to determine the fraction and age of irrigation water in ground water mixtures from farmed parts of the Eastern Snake River Plain (ESRP) Aquifer in south‐central Idaho. Two groups of waters were recognized: (1) regional background water, unaffected by irrigation and fertilizer application, and (2) mixtures of irrigation water from the Snake River with regional background water. New data are presented comparing CFC and 3H/3He dating of water recharged through deep fractured basalt, and dating of young fractions in ground water mixtures. The 3H/3He ages of irrigation water in most mixtures ranged from about zero to eight years. The CFC ages of irrigation water in mixtures ranged from values near those based on 3H/3He dating to values biased older than the 3H/3He ages by as much as eight to 10 years. Unsaturated zone air had CFC‐12 and CFC‐113 concentrations that were 60% to 95%, and 50% to 90%, respectively, of modern air concentrations and were consistently contaminated with CFC‐11. Irrigation water diverted from the Snake River was contaminated with CFC‐11 but near solubility equilibrium with CFC‐12 and CFC‐113. The dating indicates ground water velocities of 5 to 8 m/d for water along the top of the ESRP Aquifer near the southwestern boundary of the Idaho National Engineering and Environmental Laboratory (INEEL). Many of the regional background waters contain excess terrigenic helium with a 3He/4He isotope ratio of 7 × 10−6 to 11 × 10−6 (R/Ra= 5 to 8) and could not be dated. Ratios of CFC data indicate that some rangeland water may contain as much as 5% to 30% young water (ages of less than or equal to two to 11.5 years) mixed with old regional background water. The relatively low residence times of ground water in irrigated parts of the ESRP Aquifer and the dilution with low‐NO3 irrigation water from the Snake River lower the potential for NO3 contamination in agricultural areas.
Estimation of Vertical Concentration Profiles from Existing Wells
Authors: Sukop Michael C. 
Published: August 2005

AbstractA method of computing the vertical distributions of solute concentrations in aquifer strata penetrated by an existing well or borehole can be developed from a simple solute mass/water balance approach. This approach allows refinement of site characterization without the cost of drilling additional wells or using other site characterization methods. This method also allows pre‐diction of the water quality impacts of different well construction and screening options when the vertical distribution of flows from an aquifer and the aquifer water concentrations are known or can be estimated. Data requirements and methods of data collection for use of the technique are reviewed. Flowmeter or spinner logging surveys indicate the flow contribution of each portion of the well. When depth‐specific samples are collected under the same pumping conditions as the spinner logging, a solute mass/water balance approach allows vertical concentration distributions in the aquifer to be estimated. Application to a well containing arsenic concentrations that approach the maximum contaminant level (MCL) of 50 μ/L indicates that water with arsenic concentrations of nearly 100 μ/L enters the well from a particular stratum.
Transient Flow to a Horizontal Water Well
Authors: Kawecki M.W. 
Published: August 2005

AbstractEquations that approximately relate the transient head in a horizontal well to a constant well discharge are selected from the petroleum literature and converted from the notation and eclectic system of units used in the oil industry to ground water notation with consistent units. A homogeneous but not necessarily isotropic aquifer is assumed. Depending on the time since the start of discharge, the equations are basically the same in form as for flow to either a fully penetrating channel or to a vertical well, but they contain an additional term accounting for vertical flow. A modification is introduced to make the equations, which were derived for confined flow, approximately applicable to unconfined ground water conditions. The simple form of the equations makes their use practical.
Chlorine‐36 in Ground Water Containing Low Chloride Concentrations
Authors: Davis Stanley N. , Fabryka‐Martin June , Wolfsberg Laura , Moysey Stephen , Shaver Robert , Alexander E. Calvin , Krothe Noel 
Published: August 2005

AbstractAnalyses of ground water from wells and springs in the United States indicate a broad regional trend in preanthropogenic (36Cl/total Cl) ×1015 ratios in potable water. Coastal areas influenced by marine chloride have ratios less than 100. These ratios increase inland and reach a maximum of about 1400 in the central and northern Rocky Mountains. However, the magnitude of these regional variations is greatly exceeded at a local level if water samples are considered regardless of age or origin. Most local departures from regional trends can be attributed to mixing of ground water recharge with either 36Cl from nuclear fusion tests to produce higher ratios or mixing with sources of old chloride such as from evaporite minerals to produce lower ratios. A useful interpretation of 36Cl data is difficult unless the origin of the chloride is understood. The interpretation is an unusually difficult problem for water having low chloride concentrations. The assumption that low concentrations originate primarily from wet and dry atmospheric deposition can be questioned even for some dilute waters with less than 2.0 mg/L chloride. Chloride/bromide ratios in ground water can help decipher the origin of the chloride. The presence of nonatmospheric chloride can be identified in part by its association with chloride/bromide mass ratios greater than about 200 in coastal areas and 100 in inland areas. Accurate chloride and bromide analyses are recommended for virtually all studies of 36Cl in natural waters, and particularly those with low concentrations of chloride.
Ineffective Natural Attenuation of Degradable Organic Compounds in a Phenol‐Contaminated Aquifer
Authors: Lerner David N. , Thornton Steven F. , Spence Michael J. , Banwart Steven A. , Bottrell Simon H. , Higgo Jenny J. , Mallinson Helen E. H. , Pickup Roger W. , Williams Geoffrey M. 
Published: August 2005

AbstractTwo detailed vertical profiles through a complex plume of phenolic contaminants in a Triassic sandstone aquifer show that natural attenuation by biodegradation and dispersion is active but very slow. The plume has a microbially active aerobic and NO3 reducing fringe that is less than 2 m thick at both 150 and 350 m downstream of the source. The anaerobic core has evidence of active bacterial populations and degradation at total organic carbon (TOC) concentrations up to at least 1400 mg/L (1800 mg/L total phenolics), although gross half‐lives are more than 50 years. There is evidence from the same locations of Mn, Fe, and SO4 reduction, with the latter inhibited by the pollutant matrix and not significant at concentrations more than 1000 mg/L TOC. Degradation of these contaminants in this aquifer is influenced by a range of environmental factors, including the chemical toxicity and pH of the contaminant matrix, and inputs of electron acceptors into the plume by dispersion. The results show that the plume is likely to grow under the present conditions, despite the biodegradable nature of the organic pollutants and availability of suitable electron acceptors. Vertical profiles have proved a cost‐effective method of understanding the evolution of the plume.
Evaluation of Ground‐Penetrating Radar to Detect Free‐Phase Hydrocarbons in Fractured Rocks—Results of Numerical Modeling and Physical Experiments
Authors: Lane J.W. , Buursink M.L. , Haeni F.P. , Versteeg R.J. 
Published: August 2005

AbstractThe suitability of common‐offset ground‐penetrating radar (GPR) to detect free‐phase hydrocarbons in bedrock fractures was evaluated using numerical modeling and physical experiments. The results of one‐ and two‐dimensional numerical modeling at 100 megahertz indicate that GPR reflection amplitudes are relatively insensitive to fracture apertures ranging from 1 to 4 mm. The numerical modeling and physical experiments indicate that differences in the fluids that fill fractures significantly affect the amplitude and the polarity of electromagnetic waves reflected by subhorizontal fractures. Air‐filled and hydrocarbon‐filled fractures generate low‐amplitude reflections that are in‐phase with the transmitted pulse. Water‐filled fractures create reflections with greater amplitude and opposite polarity than those reflections created by air‐filled or hydrocarbon‐filled fractures.The results from the numerical modeling and physical experiments demonstrate it is possible to distinguish water‐filled fracture reflections from air‐ or hydrocarbon‐filled fracture reflections, nevertheless subsurface heterogeneity, antenna coupling changes, and other sources of noise will likely make it difficult to observe these changes in GPR field data. This indicates that the routine application of common‐offset GPR reflection methods for detection of hydrocarbon‐filled fractures will be problematic. Ideal cases will require appropriately processed, high‐quality GPR data, ground‐truth information, and detailed knowledge of subsurface physical properties.Conversely, the sensitivity of GPR methods to changes in subsurface physical properties as demonstrated by the numerical and experimental results suggests the potential of using GPR methods as a monitoring tool. GPR methods may be suited for monitoring pumping and tracer tests, changes in site hydrologic conditions, and remediation activities.
Real-Time Quantitative PCR for Determining the Burden ofPlasmodium falciparumParasites during Pregnancy and Infancy
Authors: Malhotra Indu , Dent Arlene , Mungai Peter , Muchiri Eric , King Christopher L. 
Published: August 2005

ABSTRACTReal-time quantitative PCR (RTQ-PCR) provides a quick, accurate, and reproducible quantification of parasites. However, the value of RTQ-PCR for predicting clinical outcomes of malaria is unknown. Here, we compared RTQ-PCR to microscopy of blood smears, nested PCR (nPCR), and parasite circulating-antigen (CAg) assays for detection ofPlasmodium falciparumin pregnant Kenyan women and their infants and related these findings to parity and birth weights in their newborns (n= 554). nPCR was the most sensitive assay for detection of malaria in pregnancy, followed in decreasing order of sensitivity by RTQ-PCR, CAg assays, and blood smears. RTQ-PCR detected a higher frequency of malaria infection (46%) in maternal peripheral blood in primiparous than in multiparous women (35%;P< 0.001), with a >12-fold difference in parasite burden (geometric mean = 25,870 versus 2,143 amplicons/μl blood;P< 0.0001). Similarly, the presence of placental malaria determined by RTQ-PCR was approximately twofold higher in primiparous versus multiparous women (21% versus 13%;P< 0.01). The presence and intensity of malaria infection in pregnant women estimated by RTQ-PCR strongly correlated with low-birth-weight babies, especially in those with high amplicon numbers. RTQ-PCR identified malaria-infected women, missed by blood smear, who were at risk for having underweight offspring. By contrast, malaria detected by nPCR and CAg assay showed a much weaker association with parity or low birth weight. Thus, RTQ-PCR provides an estimate of parasite burden that is more sensitive than blood smear and is predictive of clinical outcomes of malaria infection in pregnant women and newborns.
Molecular Model for Studying the Uncultivated Fungal Pathogen
Lacazia loboi
Authors: Vilela Raquel , Mendoza Leonel , Rosa Patricia S. , Belone Andréa Faria Fernandes , Madeira Suzana , Opromolla Diltor Vladimir Araújo , de Resende Maria Aparecida 
Published: August 2005

ABSTRACT

Lacazia loboi
is an uncultivated fungal pathogen of humans and dolphins that causes cutaneous and subcutaneous infections only in the tropical areas of the Americas. It was recently found by phylogenetic analysis that this unusual pathogen is closely related to
Paracoccidioides brasiliensis
and to the other fungal dimorphic members of the order
Onygenales
. That original phylogenetic study used universal primers to amplify well-known genes. However, this approach cannot be applied to the study of other proteins. We have developed a strategy for studying the gene encoding the gp43 homologous protein of
P. brasiliensis
in
L. loboi
. The gp43 protein was selected because it has been found that this
P. brasiliensis
antigen strongly reacts when it is used to test sera from patients with lacaziosis. The principle behind this idea was to obtain the gp43 amino acid sequence of
P. brasiliensis
and other homologous fungal sequences from GenBank and design primers from their aligned conserved regions. These sets of primers were used to amplify the selected regions with genomic DNA extracted from the yeast-like cells of
L. loboi
from experimentally infected mice. Using this approach, we amplified 483 bp of the
L. loboi
gp43-like gene. These sequences had 85% identity at the nucleotide level and 75% identity with the deduced amino acid sequences of the
P. brasiliensis
gp43 protein. The identity of the 483-bp DNA fragment was confirmed by phylogenetic analysis. This analysis revealed that the
L. loboi
gp43-like deduced amino acid sequence formed a strongly supported (100%) sister group with several
P. brasiliensis
gp43 sequences and that this taxon in turn was linked to the other fungal sequences used in this analysis. This study shows that the use of a molecular model for investigation of the genes encoding important proteins in
L. loboi
is feasible.
Strain Variation among
Bordetella pertussis
Isolates in Finland, Where the Whole-Cell Pertussis Vaccine Has Been Used for 50 Years
Authors: Elomaa Annika , Advani Abdolreza , Donnelly Declan , Antila Mia , Mertsola Jussi , Hallander Hans , He Qiushui 
Published: August 2005

ABSTRACT

Pertussis is an infectious disease of the respiratory tract caused by
Bordetella pertussis
. Despite the introduction of mass vaccination against pertussis in Finland in 1952, pertussis has remained an endemic disease with regular epidemics. To monitor changes in the Finnish
B. pertussis
population, 101 isolates selected from 1991 to 2003 and 21 isolates selected from 1953 to 1982 were studied together with two Finnish vaccine strains. The analyses included serotyping of fimbriae (Fim), genotyping of the pertussis toxin S1 subunit (
ptxA
) and pertactin (
prn
), and pulsed-field gel electrophoresis (PFGE) after digestion of
B. pertussis
genomic DNA with XbaI restriction enzyme. Strains isolated before 1977 were found to harbor the same
ptxA
as the strains used in the Finnish whole-cell pertussis vaccine, and strains isolated before 1982 harbored the same
prn
as the strains used in the Finnish whole-cell pertussis vaccine. All recent isolates, however, represented genotypes distinct from those of the two vaccine strains. A marked shift of predominant serotype from Fim serotype 2 (Fim2) to Fim3 has been observed since the late 1990s. Temporal changes were seen in the genome of
B. pertussis
by PFGE analysis. Three PFGE profiles (BpSR1, BpSR11, and BpSR147) were distinguished by their prevalence between 1991 and 2003. The yearly emergence of the three profiles was distributed periodically. Our study stresses the importance of the continuous monitoring of emerging strains of
B. pertussis
and the need to obtain a better understanding of the relationship of the evolution of
B. pertussis
in vaccinated populations.
DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected
Salmonella enterica
Serotypes
Authors: Sukhnanand Sharinne , Alcaine Sam , Warnick Lorin D. , Su Wan-Lin , Hof Jessica , Craver Mary Pat J. , McDonough Patrick , Boor Kathryn J. , Wiedmann Martin 
Published: August 2005

ABSTRACT

While serotyping and phage typing have been used widely to characterize
Salmonella
isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining
Salmonella
transmission, ecology, and evolution. A set of 25
Salmonella enterica
isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for
Salmonella
targeting seven housekeeping and virulence genes (
panB
,
fimA
,
aceK
,
mdh
,
icdA
,
manB
, and
spaN
). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and
Salmonella
serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since
manB
,
fimA
, and
mdh
allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41
Salmonella
isolates representing a larger diversity of serotypes. This “three-gene sequence typing scheme” allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of
Salmonella
. Three-gene sequence typing also supports the notion that
Salmonella
serotypes represent both monophyletic and polyphyletic lineages.
Use of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in
Mycobacterium tuberculosis
Complex Isolates
Authors: Hillemann Doris , Weizenegger Michael , Kubica Tanja , Richter Elvira , Niemann Stefan 
Published: August 2005

ABSTRACT

A commercially available DNA strip assay (Genotype MTBDR; Hain Lifescience, Nehren, Germany) was evaluated for its ability to detect mutations conferring resistance to rifampin (RMP) and isoniazid (INH) in clinical
Mycobacterium tuberculosis
complex isolates. A total of 103 multidrug-resistant (MDR; i.e., at least resistant to RMP and INH) and 40 fully susceptible strains isolated in Germany in 2001 in which resistance mutations have been previously defined by DNA sequencing and real-time PCR analysis were investigated. The Genotype MTBDR assay identified 102 of the 103 MDR strains with mutations in the
rpoB
gene (99%) and 91 strains (88.4%) with mutations in codon 315 of
katG
. All 40 susceptible strains showed a wild-type MTBDR hybridization pattern. The concordance between the MTBDR assay and the DNA sequencing results was 100%. Compared to conventional drug susceptibility testing, the sensitivity and specificity were 99 and 100% for RMP resistance and 88.4 and 100% for INH resistance, respectively. In conclusion, the MTBDR assay is a rapid and easy-to-perform test for the detection of the most common mutations found in MDR
M. tuberculosis
strains that can readily be included in a routine laboratory work flow.